diff --git a/.nojekyll b/.nojekyll
new file mode 100644
index 00000000..e69de29b
diff --git a/_sources/about.rst.txt b/_sources/about.rst.txt
new file mode 100644
index 00000000..9c23887e
--- /dev/null
+++ b/_sources/about.rst.txt
@@ -0,0 +1,8 @@
+.. about credits, etc
+
+
+Credits
+=======
+
+The pilot version of this automatic documentation was constructed by Sameli Siljamo during his two-week work-life trainee period.
+
diff --git a/_sources/biot_savart.rst.txt b/_sources/biot_savart.rst.txt
new file mode 100644
index 00000000..b0829b03
--- /dev/null
+++ b/_sources/biot_savart.rst.txt
@@ -0,0 +1,5 @@
+biot_savart
+-----------
+
+.. automodule:: biot_savart
+	:members:
\ No newline at end of file
diff --git a/_sources/calculations.rst.txt b/_sources/calculations.rst.txt
new file mode 100644
index 00000000..a9ac10db
--- /dev/null
+++ b/_sources/calculations.rst.txt
@@ -0,0 +1,6 @@
+calculations
+=================================
+
+.. automodule:: pytools.calculations
+   :members:
+   :imported-members:
diff --git a/_sources/gics.rst.txt b/_sources/gics.rst.txt
new file mode 100644
index 00000000..1dcdebf1
--- /dev/null
+++ b/_sources/gics.rst.txt
@@ -0,0 +1,5 @@
+gics
+----
+
+.. automodule:: gics
+	:members:
\ No newline at end of file
diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt
new file mode 100644
index 00000000..66d760c7
--- /dev/null
+++ b/_sources/index.rst.txt
@@ -0,0 +1,40 @@
+.. analysator documentation master file, created by
+   sphinx-quickstart on Tue Oct 29 10:43:26 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+analysator documentation
+========================
+
+.. .. image:: logo_color.png
+..    :height: 37
+..    :width: 300
+..    :scale: 75
+..    :align: right
+..    :alt: Vlasiator Logo
+
+`Analysator <https://github.com/fmihpc/analysator>`_ is a set of Python tools and scripts used to read and analyze `Vlasiator <https://github.com/fmihpc/vlasiator>`_ output files (`VLSV <https://github.com/fmihpc/vlsv>`_). Vlasiator and its related tools are developed at `University of Helsinki <https://www.helsinki.fi/en/researchgroups/vlasiator>`_, and are open source. 
+
+
+This documentation is generated via Sphinx-autodoc from Analysator source. This page is a work in progress, with docstrings and the documentation layout in flux. Contributions via Analysator repo are welcome.
+
+Add your content using ``reStructuredText`` syntax. See the
+`reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
+documentation for details.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   plot
+   calculations
+   vlsvfile
+   miscellaneous
+   scripts
+   about
+
+.. automodule:: pytools 
+   :members:
+   :imported-members:
+   :undoc-members:
+
diff --git a/_sources/magnetopause2d.rst.txt b/_sources/magnetopause2d.rst.txt
new file mode 100644
index 00000000..8e1717f1
--- /dev/null
+++ b/_sources/magnetopause2d.rst.txt
@@ -0,0 +1,5 @@
+magnetopause2d
+--------------
+
+.. automodule:: magnetopause2d
+	:members:
\ No newline at end of file
diff --git a/_sources/magnetopause3d.rst.txt b/_sources/magnetopause3d.rst.txt
new file mode 100644
index 00000000..7d90752f
--- /dev/null
+++ b/_sources/magnetopause3d.rst.txt
@@ -0,0 +1,5 @@
+magnetopause3d
+--------------
+
+.. automodule:: magnetopause3d
+	:members:
\ No newline at end of file
diff --git a/_sources/miscellaneous.rst.txt b/_sources/miscellaneous.rst.txt
new file mode 100644
index 00000000..7a7e9bf8
--- /dev/null
+++ b/_sources/miscellaneous.rst.txt
@@ -0,0 +1,6 @@
+miscellaneous
+==================================
+
+.. automodule:: pytools.miscellaneous
+   :members:
+   :imported-members:
diff --git a/_sources/plot.rst.txt b/_sources/plot.rst.txt
new file mode 100644
index 00000000..f0b19c91
--- /dev/null
+++ b/_sources/plot.rst.txt
@@ -0,0 +1,8 @@
+plot
+============================
+
+.. automodule:: pytools.plot
+   :members:
+   :exclude-members: Version
+   :imported-members:
+   
diff --git a/_sources/scripts.rst.txt b/_sources/scripts.rst.txt
new file mode 100644
index 00000000..6da5198f
--- /dev/null
+++ b/_sources/scripts.rst.txt
@@ -0,0 +1,70 @@
+scripts
+=====================
+
+Scripts are not included in the main Analysator module import; instead, these are separate scripts utilising Analysator to some purpose.
+
+biot_savart
+-----------
+:doc:`biot_savart`
+
+.. automodule:: biot_savart
+    :no-index:
+
+------------
+
+gics
+----
+:doc:`gics`
+
+.. automodule:: gics
+    :no-index:
+ 
+------------
+
+magnetopause2d
+--------------
+:doc:`magnetopause2d`
+
+.. automodule:: magnetopause2d
+    :no-index:
+
+------------
+
+magnetopause3d
+--------------
+:doc:`magnetopause3d`
+
+.. automodule:: magnetopause3d
+    :no-index:
+
+------------
+
+shue
+--------------
+:doc:`shue`
+
+.. automodule:: shue
+    :no-index:
+
+------------
+
+tsyganenko
+--------------
+:doc:`tsyganenko`
+
+.. automodule:: tsyganenko
+    :no-index:
+
+------------
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Scripts:
+
+   biot_savart
+   gics
+   magnetopause2d
+   magnetopause3d
+   shue
+   tsyganenko
+
diff --git a/_sources/shue.rst.txt b/_sources/shue.rst.txt
new file mode 100644
index 00000000..362c0fa9
--- /dev/null
+++ b/_sources/shue.rst.txt
@@ -0,0 +1,5 @@
+shue
+----
+
+.. automodule:: shue
+	:members:
\ No newline at end of file
diff --git a/_sources/tsyganenko.rst.txt b/_sources/tsyganenko.rst.txt
new file mode 100644
index 00000000..7804f48c
--- /dev/null
+++ b/_sources/tsyganenko.rst.txt
@@ -0,0 +1,5 @@
+tsyganenko
+----------
+
+.. automodule:: tsyganenko
+	:members:
\ No newline at end of file
diff --git a/_sources/vlsvfile.rst.txt b/_sources/vlsvfile.rst.txt
new file mode 100644
index 00000000..6fcf3ea2
--- /dev/null
+++ b/_sources/vlsvfile.rst.txt
@@ -0,0 +1,8 @@
+vlsvfile
+============================
+
+VlsvFile is responsibe for implementing read and write functionality for the vlsv format, as well as defining data reducers and reduction pipelines. Some of this will be likely moved around to be more modular in some indefinite point in the future.
+
+.. automodule:: pytools.vlsvfile
+   :members:
+   :imported-members:
diff --git a/_static/_sphinx_javascript_frameworks_compat.js b/_static/_sphinx_javascript_frameworks_compat.js
new file mode 100644
index 00000000..81415803
--- /dev/null
+++ b/_static/_sphinx_javascript_frameworks_compat.js
@@ -0,0 +1,123 @@
+/* Compatability shim for jQuery and underscores.js.
+ *
+ * Copyright Sphinx contributors
+ * Released under the two clause BSD licence
+ */
+
+/**
+ * small helper function to urldecode strings
+ *
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
+ */
+jQuery.urldecode = function(x) {
+    if (!x) {
+        return x
+    }
+    return decodeURIComponent(x.replace(/\+/g, ' '));
+};
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+    if (typeof s === 'undefined')
+        s = document.location.search;
+    var parts = s.substr(s.indexOf('?') + 1).split('&');
+    var result = {};
+    for (var i = 0; i < parts.length; i++) {
+        var tmp = parts[i].split('=', 2);
+        var key = jQuery.urldecode(tmp[0]);
+        var value = jQuery.urldecode(tmp[1]);
+        if (key in result)
+            result[key].push(value);
+        else
+            result[key] = [value];
+    }
+    return result;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+    function highlight(node, addItems) {
+        if (node.nodeType === 3) {
+            var val = node.nodeValue;
+            var pos = val.toLowerCase().indexOf(text);
+            if (pos >= 0 &&
+                !jQuery(node.parentNode).hasClass(className) &&
+                !jQuery(node.parentNode).hasClass("nohighlight")) {
+                var span;
+                var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
+                if (isInSVG) {
+                    span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+                } else {
+                    span = document.createElement("span");
+                    span.className = className;
+                }
+                span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+                node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+                    document.createTextNode(val.substr(pos + text.length)),
+                    node.nextSibling));
+                node.nodeValue = val.substr(0, pos);
+                if (isInSVG) {
+                    var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
+                    var bbox = node.parentElement.getBBox();
+                    rect.x.baseVal.value = bbox.x;
+                    rect.y.baseVal.value = bbox.y;
+                    rect.width.baseVal.value = bbox.width;
+                    rect.height.baseVal.value = bbox.height;
+                    rect.setAttribute('class', className);
+                    addItems.push({
+                        "parent": node.parentNode,
+                        "target": rect});
+                }
+            }
+        }
+        else if (!jQuery(node).is("button, select, textarea")) {
+            jQuery.each(node.childNodes, function() {
+                highlight(this, addItems);
+            });
+        }
+    }
+    var addItems = [];
+    var result = this.each(function() {
+        highlight(this, addItems);
+    });
+    for (var i = 0; i < addItems.length; ++i) {
+        jQuery(addItems[i].parent).before(addItems[i].target);
+    }
+    return result;
+};
+
+/*
+ * backward compatibility for jQuery.browser
+ * This will be supported until firefox bug is fixed.
+ */
+if (!jQuery.browser) {
+    jQuery.uaMatch = function(ua) {
+        ua = ua.toLowerCase();
+
+        var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
+            /(webkit)[ \/]([\w.]+)/.exec(ua) ||
+            /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
+            /(msie) ([\w.]+)/.exec(ua) ||
+            ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
+            [];
+
+        return {
+            browser: match[ 1 ] || "",
+            version: match[ 2 ] || "0"
+        };
+    };
+    jQuery.browser = {};
+    jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
+}
diff --git a/_static/basic.css b/_static/basic.css
new file mode 100644
index 00000000..7ebbd6d0
--- /dev/null
+++ b/_static/basic.css
@@ -0,0 +1,914 @@
+/*
+ * Sphinx stylesheet -- basic theme.
+ */
+
+/* -- main layout ----------------------------------------------------------- */
+
+div.clearer {
+    clear: both;
+}
+
+div.section::after {
+    display: block;
+    content: '';
+    clear: left;
+}
+
+/* -- relbar ---------------------------------------------------------------- */
+
+div.related {
+    width: 100%;
+    font-size: 90%;
+}
+
+div.related h3 {
+    display: none;
+}
+
+div.related ul {
+    margin: 0;
+    padding: 0 0 0 10px;
+    list-style: none;
+}
+
+div.related li {
+    display: inline;
+}
+
+div.related li.right {
+    float: right;
+    margin-right: 5px;
+}
+
+/* -- sidebar --------------------------------------------------------------- */
+
+div.sphinxsidebarwrapper {
+    padding: 10px 5px 0 10px;
+}
+
+div.sphinxsidebar {
+    float: left;
+    width: 230px;
+    margin-left: -100%;
+    font-size: 90%;
+    word-wrap: break-word;
+    overflow-wrap : break-word;
+}
+
+div.sphinxsidebar ul {
+    list-style: none;
+}
+
+div.sphinxsidebar ul ul,
+div.sphinxsidebar ul.want-points {
+    margin-left: 20px;
+    list-style: square;
+}
+
+div.sphinxsidebar ul ul {
+    margin-top: 0;
+    margin-bottom: 0;
+}
+
+div.sphinxsidebar form {
+    margin-top: 10px;
+}
+
+div.sphinxsidebar input {
+    border: 1px solid #98dbcc;
+    font-family: sans-serif;
+    font-size: 1em;
+}
+
+div.sphinxsidebar #searchbox form.search {
+    overflow: hidden;
+}
+
+div.sphinxsidebar #searchbox input[type="text"] {
+    float: left;
+    width: 80%;
+    padding: 0.25em;
+    box-sizing: border-box;
+}
+
+div.sphinxsidebar #searchbox input[type="submit"] {
+    float: left;
+    width: 20%;
+    border-left: none;
+    padding: 0.25em;
+    box-sizing: border-box;
+}
+
+
+img {
+    border: 0;
+    max-width: 100%;
+}
+
+/* -- search page ----------------------------------------------------------- */
+
+ul.search {
+    margin-top: 10px;
+}
+
+ul.search li {
+    padding: 5px 0;
+}
+
+ul.search li a {
+    font-weight: bold;
+}
+
+ul.search li p.context {
+    color: #888;
+    margin: 2px 0 0 30px;
+    text-align: left;
+}
+
+ul.keywordmatches li.goodmatch a {
+    font-weight: bold;
+}
+
+/* -- index page ------------------------------------------------------------ */
+
+table.contentstable {
+    width: 90%;
+    margin-left: auto;
+    margin-right: auto;
+}
+
+table.contentstable p.biglink {
+    line-height: 150%;
+}
+
+a.biglink {
+    font-size: 1.3em;
+}
+
+span.linkdescr {
+    font-style: italic;
+    padding-top: 5px;
+    font-size: 90%;
+}
+
+/* -- general index --------------------------------------------------------- */
+
+table.indextable {
+    width: 100%;
+}
+
+table.indextable td {
+    text-align: left;
+    vertical-align: top;
+}
+
+table.indextable ul {
+    margin-top: 0;
+    margin-bottom: 0;
+    list-style-type: none;
+}
+
+table.indextable > tbody > tr > td > ul {
+    padding-left: 0em;
+}
+
+table.indextable tr.pcap {
+    height: 10px;
+}
+
+table.indextable tr.cap {
+    margin-top: 10px;
+    background-color: #f2f2f2;
+}
+
+img.toggler {
+    margin-right: 3px;
+    margin-top: 3px;
+    cursor: pointer;
+}
+
+div.modindex-jumpbox {
+    border-top: 1px solid #ddd;
+    border-bottom: 1px solid #ddd;
+    margin: 1em 0 1em 0;
+    padding: 0.4em;
+}
+
+div.genindex-jumpbox {
+    border-top: 1px solid #ddd;
+    border-bottom: 1px solid #ddd;
+    margin: 1em 0 1em 0;
+    padding: 0.4em;
+}
+
+/* -- domain module index --------------------------------------------------- */
+
+table.modindextable td {
+    padding: 2px;
+    border-collapse: collapse;
+}
+
+/* -- general body styles --------------------------------------------------- */
+
+div.body {
+    min-width: 360px;
+    max-width: 800px;
+}
+
+div.body p, div.body dd, div.body li, div.body blockquote {
+    -moz-hyphens: auto;
+    -ms-hyphens: auto;
+    -webkit-hyphens: auto;
+    hyphens: auto;
+}
+
+a.headerlink {
+    visibility: hidden;
+}
+
+a:visited {
+    color: #551A8B;
+}
+
+h1:hover > a.headerlink,
+h2:hover > a.headerlink,
+h3:hover > a.headerlink,
+h4:hover > a.headerlink,
+h5:hover > a.headerlink,
+h6:hover > a.headerlink,
+dt:hover > a.headerlink,
+caption:hover > a.headerlink,
+p.caption:hover > a.headerlink,
+div.code-block-caption:hover > a.headerlink {
+    visibility: visible;
+}
+
+div.body p.caption {
+    text-align: inherit;
+}
+
+div.body td {
+    text-align: left;
+}
+
+.first {
+    margin-top: 0 !important;
+}
+
+p.rubric {
+    margin-top: 30px;
+    font-weight: bold;
+}
+
+img.align-left, figure.align-left, .figure.align-left, object.align-left {
+    clear: left;
+    float: left;
+    margin-right: 1em;
+}
+
+img.align-right, figure.align-right, .figure.align-right, object.align-right {
+    clear: right;
+    float: right;
+    margin-left: 1em;
+}
+
+img.align-center, figure.align-center, .figure.align-center, object.align-center {
+  display: block;
+  margin-left: auto;
+  margin-right: auto;
+}
+
+img.align-default, figure.align-default, .figure.align-default {
+  display: block;
+  margin-left: auto;
+  margin-right: auto;
+}
+
+.align-left {
+    text-align: left;
+}
+
+.align-center {
+    text-align: center;
+}
+
+.align-default {
+    text-align: center;
+}
+
+.align-right {
+    text-align: right;
+}
+
+/* -- sidebars -------------------------------------------------------------- */
+
+div.sidebar,
+aside.sidebar {
+    margin: 0 0 0.5em 1em;
+    border: 1px solid #ddb;
+    padding: 7px;
+    background-color: #ffe;
+    width: 40%;
+    float: right;
+    clear: right;
+    overflow-x: auto;
+}
+
+p.sidebar-title {
+    font-weight: bold;
+}
+
+nav.contents,
+aside.topic,
+div.admonition, div.topic, blockquote {
+    clear: left;
+}
+
+/* -- topics ---------------------------------------------------------------- */
+
+nav.contents,
+aside.topic,
+div.topic {
+    border: 1px solid #ccc;
+    padding: 7px;
+    margin: 10px 0 10px 0;
+}
+
+p.topic-title {
+    font-size: 1.1em;
+    font-weight: bold;
+    margin-top: 10px;
+}
+
+/* -- admonitions ----------------------------------------------------------- */
+
+div.admonition {
+    margin-top: 10px;
+    margin-bottom: 10px;
+    padding: 7px;
+}
+
+div.admonition dt {
+    font-weight: bold;
+}
+
+p.admonition-title {
+    margin: 0px 10px 5px 0px;
+    font-weight: bold;
+}
+
+div.body p.centered {
+    text-align: center;
+    margin-top: 25px;
+}
+
+/* -- content of sidebars/topics/admonitions -------------------------------- */
+
+div.sidebar > :last-child,
+aside.sidebar > :last-child,
+nav.contents > :last-child,
+aside.topic > :last-child,
+div.topic > :last-child,
+div.admonition > :last-child {
+    margin-bottom: 0;
+}
+
+div.sidebar::after,
+aside.sidebar::after,
+nav.contents::after,
+aside.topic::after,
+div.topic::after,
+div.admonition::after,
+blockquote::after {
+    display: block;
+    content: '';
+    clear: both;
+}
+
+/* -- tables ---------------------------------------------------------------- */
+
+table.docutils {
+    margin-top: 10px;
+    margin-bottom: 10px;
+    border: 0;
+    border-collapse: collapse;
+}
+
+table.align-center {
+    margin-left: auto;
+    margin-right: auto;
+}
+
+table.align-default {
+    margin-left: auto;
+    margin-right: auto;
+}
+
+table caption span.caption-number {
+    font-style: italic;
+}
+
+table caption span.caption-text {
+}
+
+table.docutils td, table.docutils th {
+    padding: 1px 8px 1px 5px;
+    border-top: 0;
+    border-left: 0;
+    border-right: 0;
+    border-bottom: 1px solid #aaa;
+}
+
+th {
+    text-align: left;
+    padding-right: 5px;
+}
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+table.citation {
+    border-left: solid 1px gray;
+    margin-left: 1px;
+}
+
+table.citation td {
+    border-bottom: none;
+}
+
+th > :first-child,
+td > :first-child {
+    margin-top: 0px;
+}
+
+th > :last-child,
+td > :last-child {
+    margin-bottom: 0px;
+}
+
+/* -- figures --------------------------------------------------------------- */
+
+div.figure, figure {
+    margin: 0.5em;
+    padding: 0.5em;
+}
+
+div.figure p.caption, figcaption {
+    padding: 0.3em;
+}
+
+div.figure p.caption span.caption-number,
+figcaption span.caption-number {
+    font-style: italic;
+}
+
+div.figure p.caption span.caption-text,
+figcaption span.caption-text {
+}
+
+/* -- field list styles ----------------------------------------------------- */
+
+table.field-list td, table.field-list th {
+    border: 0 !important;
+}
+
+.field-list ul {
+    margin: 0;
+    padding-left: 1em;
+}
+
+.field-list p {
+    margin: 0;
+}
+
+.field-name {
+    -moz-hyphens: manual;
+    -ms-hyphens: manual;
+    -webkit-hyphens: manual;
+    hyphens: manual;
+}
+
+/* -- hlist styles ---------------------------------------------------------- */
+
+table.hlist {
+    margin: 1em 0;
+}
+
+table.hlist td {
+    vertical-align: top;
+}
+
+/* -- object description styles --------------------------------------------- */
+
+.sig {
+	font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace;
+}
+
+.sig-name, code.descname {
+    background-color: transparent;
+    font-weight: bold;
+}
+
+.sig-name {
+	font-size: 1.1em;
+}
+
+code.descname {
+    font-size: 1.2em;
+}
+
+.sig-prename, code.descclassname {
+    background-color: transparent;
+}
+
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+}
+
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+    font-size: larger;
+}
+
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+	font-style: italic;
+}
+
+/* C++ specific styling */
+
+.sig-inline.c-texpr,
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+	font-family: unset;
+}
+
+.sig.c   .k, .sig.c   .kt,
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+	color: #0033B3;
+}
+
+.sig.c   .m,
+.sig.cpp .m {
+	color: #1750EB;
+}
+
+.sig.c   .s, .sig.c   .sc,
+.sig.cpp .s, .sig.cpp .sc {
+	color: #067D17;
+}
+
+
+/* -- other body styles ----------------------------------------------------- */
+
+ol.arabic {
+    list-style: decimal;
+}
+
+ol.loweralpha {
+    list-style: lower-alpha;
+}
+
+ol.upperalpha {
+    list-style: upper-alpha;
+}
+
+ol.lowerroman {
+    list-style: lower-roman;
+}
+
+ol.upperroman {
+    list-style: upper-roman;
+}
+
+:not(li) > ol > li:first-child > :first-child,
+:not(li) > ul > li:first-child > :first-child {
+    margin-top: 0px;
+}
+
+:not(li) > ol > li:last-child > :last-child,
+:not(li) > ul > li:last-child > :last-child {
+    margin-bottom: 0px;
+}
+
+ol.simple ol p,
+ol.simple ul p,
+ul.simple ol p,
+ul.simple ul p {
+    margin-top: 0;
+}
+
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+ul.simple > li:not(:first-child) > p {
+    margin-top: 0;
+}
+
+ol.simple p,
+ul.simple p {
+    margin-bottom: 0;
+}
+
+aside.footnote > span,
+div.citation > span {
+    float: left;
+}
+aside.footnote > span:last-of-type,
+div.citation > span:last-of-type {
+  padding-right: 0.5em;
+}
+aside.footnote > p {
+  margin-left: 2em;
+}
+div.citation > p {
+  margin-left: 4em;
+}
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+    margin-bottom: 0em;
+}
+aside.footnote > p:last-of-type:after,
+div.citation > p:last-of-type:after {
+    content: "";
+    clear: both;
+}
+
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+    display: grid;
+    grid-template-columns: fit-content(30%) auto;
+}
+
+dl.field-list > dt {
+    font-weight: bold;
+    word-break: break-word;
+    padding-left: 0.5em;
+    padding-right: 5px;
+}
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+dl.field-list > dd {
+    padding-left: 0.5em;
+    margin-top: 0em;
+    margin-left: 0em;
+    margin-bottom: 0em;
+}
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+dl {
+    margin-bottom: 15px;
+}
+
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+    margin-top: 0px;
+}
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+    margin-bottom: 10px;
+}
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+    margin-top: 3px;
+    margin-bottom: 10px;
+    margin-left: 30px;
+}
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+    margin-top: 0px;
+    margin-bottom: 0px;
+}
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+    margin-bottom: 0px;
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+}
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+}
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+    font-size: 1.1em;
+}
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+    font-style: italic;
+}
+
+.system-message {
+    background-color: #fda;
+    padding: 5px;
+    border: 3px solid red;
+}
+
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+    background-color: #ffa;
+}
+
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+    display: block;
+    margin-top: 1em;
+    margin-bottom: 1em;
+}
+
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+    margin-top: 0;
+    margin-bottom: 0;
+    margin-left: 1.5em;
+}
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+}
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+}
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+    font-style: normal;
+    margin: 0 0.5em;
+    content: ":";
+    display: inline-block;
+}
+
+abbr, acronym {
+    border-bottom: dotted 1px;
+    cursor: help;
+}
+
+.translated {
+    background-color: rgba(207, 255, 207, 0.2)
+}
+
+.untranslated {
+    background-color: rgba(255, 207, 207, 0.2)
+}
+
+/* -- code displays --------------------------------------------------------- */
+
+pre {
+    overflow: auto;
+    overflow-y: hidden;  /* fixes display issues on Chrome browsers */
+}
+
+pre, div[class*="highlight-"] {
+    clear: both;
+}
+
+span.pre {
+    -moz-hyphens: none;
+    -ms-hyphens: none;
+    -webkit-hyphens: none;
+    hyphens: none;
+    white-space: nowrap;
+}
+
+div[class*="highlight-"] {
+    margin: 1em 0;
+}
+
+td.linenos pre {
+    border: 0;
+    background-color: transparent;
+    color: #aaa;
+}
+
+table.highlighttable {
+    display: block;
+}
+
+table.highlighttable tbody {
+    display: block;
+}
+
+table.highlighttable tr {
+    display: flex;
+}
+
+table.highlighttable td {
+    margin: 0;
+    padding: 0;
+}
+
+table.highlighttable td.linenos {
+    padding-right: 0.5em;
+}
+
+table.highlighttable td.code {
+    flex: 1;
+    overflow: hidden;
+}
+
+.highlight .hll {
+    display: block;
+}
+
+div.highlight pre,
+table.highlighttable pre {
+    margin: 0;
+}
+
+div.code-block-caption + div {
+    margin-top: 0;
+}
+
+div.code-block-caption {
+    margin-top: 1em;
+    padding: 2px 5px;
+    font-size: small;
+}
+
+div.code-block-caption code {
+    background-color: transparent;
+}
+
+table.highlighttable td.linenos,
+span.linenos,
+div.highlight span.gp {  /* gp: Generic.Prompt */
+  user-select: none;
+  -webkit-user-select: text; /* Safari fallback only */
+  -webkit-user-select: none; /* Chrome/Safari */
+  -moz-user-select: none; /* Firefox */
+  -ms-user-select: none; /* IE10+ */
+}
+
+div.code-block-caption span.caption-number {
+    padding: 0.1em 0.3em;
+    font-style: italic;
+}
+
+div.code-block-caption span.caption-text {
+}
+
+div.literal-block-wrapper {
+    margin: 1em 0;
+}
+
+code.xref, a code {
+    background-color: transparent;
+    font-weight: bold;
+}
+
+h1 code, h2 code, h3 code, h4 code, h5 code, h6 code {
+    background-color: transparent;
+}
+
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+    float: right;
+}
+
+.viewcode-back {
+    float: right;
+    font-family: sans-serif;
+}
+
+div.viewcode-block:target {
+    margin: -1px -10px;
+    padding: 0 10px;
+}
+
+/* -- math display ---------------------------------------------------------- */
+
+img.math {
+    vertical-align: middle;
+}
+
+div.body div.math p {
+    text-align: center;
+}
+
+span.eqno {
+    float: right;
+}
+
+span.eqno a.headerlink {
+    position: absolute;
+    z-index: 1;
+}
+
+div.math:hover a.headerlink {
+    visibility: visible;
+}
+
+/* -- printout stylesheet --------------------------------------------------- */
+
+@media print {
+    div.document,
+    div.documentwrapper,
+    div.bodywrapper {
+        margin: 0 !important;
+        width: 100%;
+    }
+
+    div.sphinxsidebar,
+    div.related,
+    div.footer,
+    #top-link {
+        display: none;
+    }
+}
\ No newline at end of file
diff --git a/_static/css/badge_only.css b/_static/css/badge_only.css
new file mode 100644
index 00000000..88ba55b9
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new file mode 100644
index 00000000..855c845e
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diff --git a/_static/doctools.js b/_static/doctools.js
new file mode 100644
index 00000000..0398ebb9
--- /dev/null
+++ b/_static/doctools.js
@@ -0,0 +1,149 @@
+/*
+ * Base JavaScript utilities for all Sphinx HTML documentation.
+ */
+"use strict";
+
+const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([
+  "TEXTAREA",
+  "INPUT",
+  "SELECT",
+  "BUTTON",
+]);
+
+const _ready = (callback) => {
+  if (document.readyState !== "loading") {
+    callback();
+  } else {
+    document.addEventListener("DOMContentLoaded", callback);
+  }
+};
+
+/**
+ * Small JavaScript module for the documentation.
+ */
+const Documentation = {
+  init: () => {
+    Documentation.initDomainIndexTable();
+    Documentation.initOnKeyListeners();
+  },
+
+  /**
+   * i18n support
+   */
+  TRANSLATIONS: {},
+  PLURAL_EXPR: (n) => (n === 1 ? 0 : 1),
+  LOCALE: "unknown",
+
+  // gettext and ngettext don't access this so that the functions
+  // can safely bound to a different name (_ = Documentation.gettext)
+  gettext: (string) => {
+    const translated = Documentation.TRANSLATIONS[string];
+    switch (typeof translated) {
+      case "undefined":
+        return string; // no translation
+      case "string":
+        return translated; // translation exists
+      default:
+        return translated[0]; // (singular, plural) translation tuple exists
+    }
+  },
+
+  ngettext: (singular, plural, n) => {
+    const translated = Documentation.TRANSLATIONS[singular];
+    if (typeof translated !== "undefined")
+      return translated[Documentation.PLURAL_EXPR(n)];
+    return n === 1 ? singular : plural;
+  },
+
+  addTranslations: (catalog) => {
+    Object.assign(Documentation.TRANSLATIONS, catalog.messages);
+    Documentation.PLURAL_EXPR = new Function(
+      "n",
+      `return (${catalog.plural_expr})`
+    );
+    Documentation.LOCALE = catalog.locale;
+  },
+
+  /**
+   * helper function to focus on search bar
+   */
+  focusSearchBar: () => {
+    document.querySelectorAll("input[name=q]")[0]?.focus();
+  },
+
+  /**
+   * Initialise the domain index toggle buttons
+   */
+  initDomainIndexTable: () => {
+    const toggler = (el) => {
+      const idNumber = el.id.substr(7);
+      const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`);
+      if (el.src.substr(-9) === "minus.png") {
+        el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`;
+        toggledRows.forEach((el) => (el.style.display = "none"));
+      } else {
+        el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`;
+        toggledRows.forEach((el) => (el.style.display = ""));
+      }
+    };
+
+    const togglerElements = document.querySelectorAll("img.toggler");
+    togglerElements.forEach((el) =>
+      el.addEventListener("click", (event) => toggler(event.currentTarget))
+    );
+    togglerElements.forEach((el) => (el.style.display = ""));
+    if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler);
+  },
+
+  initOnKeyListeners: () => {
+    // only install a listener if it is really needed
+    if (
+      !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS &&
+      !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS
+    )
+      return;
+
+    document.addEventListener("keydown", (event) => {
+      // bail for input elements
+      if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return;
+      // bail with special keys
+      if (event.altKey || event.ctrlKey || event.metaKey) return;
+
+      if (!event.shiftKey) {
+        switch (event.key) {
+          case "ArrowLeft":
+            if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break;
+
+            const prevLink = document.querySelector('link[rel="prev"]');
+            if (prevLink && prevLink.href) {
+              window.location.href = prevLink.href;
+              event.preventDefault();
+            }
+            break;
+          case "ArrowRight":
+            if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break;
+
+            const nextLink = document.querySelector('link[rel="next"]');
+            if (nextLink && nextLink.href) {
+              window.location.href = nextLink.href;
+              event.preventDefault();
+            }
+            break;
+        }
+      }
+
+      // some keyboard layouts may need Shift to get /
+      switch (event.key) {
+        case "/":
+          if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break;
+          Documentation.focusSearchBar();
+          event.preventDefault();
+      }
+    });
+  },
+};
+
+// quick alias for translations
+const _ = Documentation.gettext;
+
+_ready(Documentation.init);
diff --git a/_static/documentation_options.js b/_static/documentation_options.js
new file mode 100644
index 00000000..87fc516a
--- /dev/null
+++ b/_static/documentation_options.js
@@ -0,0 +1,13 @@
+const DOCUMENTATION_OPTIONS = {
+    VERSION: '',
+    LANGUAGE: 'en',
+    COLLAPSE_INDEX: false,
+    BUILDER: 'dirhtml',
+    FILE_SUFFIX: '.html',
+    LINK_SUFFIX: '.html',
+    HAS_SOURCE: true,
+    SOURCELINK_SUFFIX: '.txt',
+    NAVIGATION_WITH_KEYS: false,
+    SHOW_SEARCH_SUMMARY: true,
+    ENABLE_SEARCH_SHORTCUTS: true,
+};
\ No newline at end of file
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new file mode 100644
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Binary files /dev/null and b/_static/file.png differ
diff --git a/_static/fonts/Lato/lato-bold.eot b/_static/fonts/Lato/lato-bold.eot
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diff --git a/_static/fonts/Lato/lato-bolditalic.eot b/_static/fonts/Lato/lato-bolditalic.eot
new file mode 100644
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diff --git a/_static/fonts/Lato/lato-bolditalic.ttf b/_static/fonts/Lato/lato-bolditalic.ttf
new file mode 100644
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diff --git a/_static/fonts/Lato/lato-bolditalic.woff b/_static/fonts/Lato/lato-bolditalic.woff
new file mode 100644
index 00000000..88ad05b9
Binary files /dev/null and b/_static/fonts/Lato/lato-bolditalic.woff differ
diff --git a/_static/fonts/Lato/lato-bolditalic.woff2 b/_static/fonts/Lato/lato-bolditalic.woff2
new file mode 100644
index 00000000..c4e3d804
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diff --git a/_static/fonts/Lato/lato-italic.eot b/_static/fonts/Lato/lato-italic.eot
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new file mode 100644
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diff --git a/_static/fonts/Lato/lato-italic.woff b/_static/fonts/Lato/lato-italic.woff
new file mode 100644
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diff --git a/_static/fonts/Lato/lato-italic.woff2 b/_static/fonts/Lato/lato-italic.woff2
new file mode 100644
index 00000000..3404f37e
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diff --git a/_static/fonts/Lato/lato-regular.eot b/_static/fonts/Lato/lato-regular.eot
new file mode 100644
index 00000000..11e3f2a5
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diff --git a/_static/fonts/Lato/lato-regular.ttf b/_static/fonts/Lato/lato-regular.ttf
new file mode 100644
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Binary files /dev/null and b/_static/fonts/Lato/lato-regular.ttf differ
diff --git a/_static/fonts/Lato/lato-regular.woff b/_static/fonts/Lato/lato-regular.woff
new file mode 100644
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diff --git a/_static/fonts/Lato/lato-regular.woff2 b/_static/fonts/Lato/lato-regular.woff2
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diff --git a/_static/jquery.js b/_static/jquery.js
new file mode 100644
index 00000000..c4c6022f
--- /dev/null
+++ b/_static/jquery.js
@@ -0,0 +1,2 @@
+/*! jQuery v3.6.0 | (c) OpenJS Foundation and other contributors | jquery.org/license */
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\ No newline at end of file
diff --git a/_static/js/versions.js b/_static/js/versions.js
new file mode 100644
index 00000000..4958195e
--- /dev/null
+++ b/_static/js/versions.js
@@ -0,0 +1,228 @@
+const themeFlyoutDisplay = "hidden";
+const themeVersionSelector = true;
+const themeLanguageSelector = true;
+
+if (themeFlyoutDisplay === "attached") {
+  function renderLanguages(config) {
+    if (!config.projects.translations.length) {
+      return "";
+    }
+
+    // Insert the current language to the options on the selector
+    let languages = config.projects.translations.concat(config.projects.current);
+    languages = languages.sort((a, b) => a.language.name.localeCompare(b.language.name));
+
+    const languagesHTML = `
+      <dl>
+        <dt>Languages</dt>
+        ${languages
+          .map(
+            (translation) => `
+        <dd ${translation.slug == config.projects.current.slug ? 'class="rtd-current-item"' : ""}>
+          <a href="${translation.urls.documentation}">${translation.language.code}</a>
+        </dd>
+        `,
+          )
+          .join("\n")}
+      </dl>
+    `;
+    return languagesHTML;
+  }
+
+  function renderVersions(config) {
+    if (!config.versions.active.length) {
+      return "";
+    }
+    const versionsHTML = `
+      <dl>
+        <dt>Versions</dt>
+        ${config.versions.active
+          .map(
+            (version) => `
+        <dd ${version.slug === config.versions.current.slug ? 'class="rtd-current-item"' : ""}>
+          <a href="${version.urls.documentation}">${version.slug}</a>
+        </dd>
+        `,
+          )
+          .join("\n")}
+      </dl>
+    `;
+    return versionsHTML;
+  }
+
+  function renderDownloads(config) {
+    if (!Object.keys(config.versions.current.downloads).length) {
+      return "";
+    }
+    const downloadsNameDisplay = {
+      pdf: "PDF",
+      epub: "Epub",
+      htmlzip: "HTML",
+    };
+
+    const downloadsHTML = `
+      <dl>
+        <dt>Downloads</dt>
+        ${Object.entries(config.versions.current.downloads)
+          .map(
+            ([name, url]) => `
+          <dd>
+            <a href="${url}">${downloadsNameDisplay[name]}</a>
+          </dd>
+        `,
+          )
+          .join("\n")}
+      </dl>
+    `;
+    return downloadsHTML;
+  }
+
+  document.addEventListener("readthedocs-addons-data-ready", function (event) {
+    const config = event.detail.data();
+
+    const flyout = `
+      <div class="rst-versions" data-toggle="rst-versions" role="note">
+        <span class="rst-current-version" data-toggle="rst-current-version">
+          <span class="fa fa-book"> Read the Docs</span>
+          v: ${config.versions.current.slug}
+          <span class="fa fa-caret-down"></span>
+        </span>
+        <div class="rst-other-versions">
+          <div class="injected">
+            ${renderLanguages(config)}
+            ${renderVersions(config)}
+            ${renderDownloads(config)}
+            <dl>
+              <dt>On Read the Docs</dt>
+              <dd>
+                <a href="${config.projects.current.urls.home}">Project Home</a>
+              </dd>
+              <dd>
+                <a href="${config.projects.current.urls.builds}">Builds</a>
+              </dd>
+              <dd>
+                <a href="${config.projects.current.urls.downloads}">Downloads</a>
+              </dd>
+            </dl>
+            <dl>
+              <dt>Search</dt>
+              <dd>
+                <form id="flyout-search-form">
+                  <input
+                    class="wy-form"
+                    type="text"
+                    name="q"
+                    aria-label="Search docs"
+                    placeholder="Search docs"
+                    />
+                </form>
+              </dd>
+            </dl>
+            <hr />
+            <small>
+              <span>Hosted by <a href="https://about.readthedocs.org/?utm_source=&utm_content=flyout">Read the Docs</a></span>
+            </small>
+          </div>
+        </div>
+    `;
+
+    // Inject the generated flyout into the body HTML element.
+    document.body.insertAdjacentHTML("beforeend", flyout);
+
+    // Trigger the Read the Docs Addons Search modal when clicking on the "Search docs" input from inside the flyout.
+    document
+      .querySelector("#flyout-search-form")
+      .addEventListener("focusin", () => {
+        const event = new CustomEvent("readthedocs-search-show");
+        document.dispatchEvent(event);
+      });
+  })
+}
+
+if (themeLanguageSelector || themeVersionSelector) {
+  function onSelectorSwitch(event) {
+    const option = event.target.selectedIndex;
+    const item = event.target.options[option];
+    window.location.href = item.dataset.url;
+  }
+
+  document.addEventListener("readthedocs-addons-data-ready", function (event) {
+    const config = event.detail.data();
+
+    const versionSwitch = document.querySelector(
+      "div.switch-menus > div.version-switch",
+    );
+    if (themeVersionSelector) {
+      let versions = config.versions.active;
+      if (config.versions.current.hidden || config.versions.current.type === "external") {
+        versions.unshift(config.versions.current);
+      }
+      const versionSelect = `
+    <select>
+      ${versions
+        .map(
+          (version) => `
+        <option
+  value="${version.slug}"
+  ${config.versions.current.slug === version.slug ? 'selected="selected"' : ""}
+              data-url="${version.urls.documentation}">
+              ${version.slug}
+          </option>`,
+        )
+        .join("\n")}
+    </select>
+  `;
+
+      versionSwitch.innerHTML = versionSelect;
+      versionSwitch.firstElementChild.addEventListener("change", onSelectorSwitch);
+    }
+
+    const languageSwitch = document.querySelector(
+      "div.switch-menus > div.language-switch",
+    );
+
+    if (themeLanguageSelector) {
+      if (config.projects.translations.length) {
+        // Add the current language to the options on the selector
+        let languages = config.projects.translations.concat(
+          config.projects.current,
+        );
+        languages = languages.sort((a, b) =>
+          a.language.name.localeCompare(b.language.name),
+        );
+
+        const languageSelect = `
+      <select>
+        ${languages
+          .map(
+            (language) => `
+              <option
+                  value="${language.language.code}"
+                  ${config.projects.current.slug === language.slug ? 'selected="selected"' : ""}
+                  data-url="${language.urls.documentation}">
+                  ${language.language.name}
+              </option>`,
+          )
+          .join("\n")}
+       </select>
+    `;
+
+        languageSwitch.innerHTML = languageSelect;
+        languageSwitch.firstElementChild.addEventListener("change", onSelectorSwitch);
+      }
+      else {
+        languageSwitch.remove();
+      }
+    }
+  });
+}
+
+document.addEventListener("readthedocs-addons-data-ready", function (event) {
+  // Trigger the Read the Docs Addons Search modal when clicking on "Search docs" input from the topnav.
+  document
+    .querySelector("[role='search'] input")
+    .addEventListener("focusin", () => {
+      const event = new CustomEvent("readthedocs-search-show");
+      document.dispatchEvent(event);
+    });
+});
\ No newline at end of file
diff --git a/_static/language_data.js b/_static/language_data.js
new file mode 100644
index 00000000..c7fe6c6f
--- /dev/null
+++ b/_static/language_data.js
@@ -0,0 +1,192 @@
+/*
+ * This script contains the language-specific data used by searchtools.js,
+ * namely the list of stopwords, stemmer, scorer and splitter.
+ */
+
+var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
+
+
+/* Non-minified version is copied as a separate JS file, if available */
+
+/**
+ * Porter Stemmer
+ */
+var Stemmer = function() {
+
+  var step2list = {
+    ational: 'ate',
+    tional: 'tion',
+    enci: 'ence',
+    anci: 'ance',
+    izer: 'ize',
+    bli: 'ble',
+    alli: 'al',
+    entli: 'ent',
+    eli: 'e',
+    ousli: 'ous',
+    ization: 'ize',
+    ation: 'ate',
+    ator: 'ate',
+    alism: 'al',
+    iveness: 'ive',
+    fulness: 'ful',
+    ousness: 'ous',
+    aliti: 'al',
+    iviti: 'ive',
+    biliti: 'ble',
+    logi: 'log'
+  };
+
+  var step3list = {
+    icate: 'ic',
+    ative: '',
+    alize: 'al',
+    iciti: 'ic',
+    ical: 'ic',
+    ful: '',
+    ness: ''
+  };
+
+  var c = "[^aeiou]";          // consonant
+  var v = "[aeiouy]";          // vowel
+  var C = c + "[^aeiouy]*";    // consonant sequence
+  var V = v + "[aeiou]*";      // vowel sequence
+
+  var mgr0 = "^(" + C + ")?" + V + C;                      // [C]VC... is m>0
+  var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$";    // [C]VC[V] is m=1
+  var mgr1 = "^(" + C + ")?" + V + C + V + C;              // [C]VCVC... is m>1
+  var s_v   = "^(" + C + ")?" + v;                         // vowel in stem
+
+  this.stemWord = function (w) {
+    var stem;
+    var suffix;
+    var firstch;
+    var origword = w;
+
+    if (w.length < 3)
+      return w;
+
+    var re;
+    var re2;
+    var re3;
+    var re4;
+
+    firstch = w.substr(0,1);
+    if (firstch == "y")
+      w = firstch.toUpperCase() + w.substr(1);
+
+    // Step 1a
+    re = /^(.+?)(ss|i)es$/;
+    re2 = /^(.+?)([^s])s$/;
+
+    if (re.test(w))
+      w = w.replace(re,"$1$2");
+    else if (re2.test(w))
+      w = w.replace(re2,"$1$2");
+
+    // Step 1b
+    re = /^(.+?)eed$/;
+    re2 = /^(.+?)(ed|ing)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      re = new RegExp(mgr0);
+      if (re.test(fp[1])) {
+        re = /.$/;
+        w = w.replace(re,"");
+      }
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1];
+      re2 = new RegExp(s_v);
+      if (re2.test(stem)) {
+        w = stem;
+        re2 = /(at|bl|iz)$/;
+        re3 = new RegExp("([^aeiouylsz])\\1$");
+        re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+        if (re2.test(w))
+          w = w + "e";
+        else if (re3.test(w)) {
+          re = /.$/;
+          w = w.replace(re,"");
+        }
+        else if (re4.test(w))
+          w = w + "e";
+      }
+    }
+
+    // Step 1c
+    re = /^(.+?)y$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(s_v);
+      if (re.test(stem))
+        w = stem + "i";
+    }
+
+    // Step 2
+    re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step2list[suffix];
+    }
+
+    // Step 3
+    re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step3list[suffix];
+    }
+
+    // Step 4
+    re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
+    re2 = /^(.+?)(s|t)(ion)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      if (re.test(stem))
+        w = stem;
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1] + fp[2];
+      re2 = new RegExp(mgr1);
+      if (re2.test(stem))
+        w = stem;
+    }
+
+    // Step 5
+    re = /^(.+?)e$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      re2 = new RegExp(meq1);
+      re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+      if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
+        w = stem;
+    }
+    re = /ll$/;
+    re2 = new RegExp(mgr1);
+    if (re.test(w) && re2.test(w)) {
+      re = /.$/;
+      w = w.replace(re,"");
+    }
+
+    // and turn initial Y back to y
+    if (firstch == "y")
+      w = firstch.toLowerCase() + w.substr(1);
+    return w;
+  }
+}
+
diff --git a/_static/logo_color.png b/_static/logo_color.png
new file mode 100644
index 00000000..3bd85b59
Binary files /dev/null and b/_static/logo_color.png differ
diff --git a/_static/minus.png b/_static/minus.png
new file mode 100644
index 00000000..d96755fd
Binary files /dev/null and b/_static/minus.png differ
diff --git a/_static/plus.png b/_static/plus.png
new file mode 100644
index 00000000..7107cec9
Binary files /dev/null and b/_static/plus.png differ
diff --git a/_static/pygments.css b/_static/pygments.css
new file mode 100644
index 00000000..84ab3030
--- /dev/null
+++ b/_static/pygments.css
@@ -0,0 +1,75 @@
+pre { line-height: 125%; }
+td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
+span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
+td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
+span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
+.highlight .hll { background-color: #ffffcc }
+.highlight { background: #f8f8f8; }
+.highlight .c { color: #3D7B7B; font-style: italic } /* Comment */
+.highlight .err { border: 1px solid #FF0000 } /* Error */
+.highlight .k { color: #008000; font-weight: bold } /* Keyword */
+.highlight .o { color: #666666 } /* Operator */
+.highlight .ch { color: #3D7B7B; font-style: italic } /* Comment.Hashbang */
+.highlight .cm { color: #3D7B7B; font-style: italic } /* Comment.Multiline */
+.highlight .cp { color: #9C6500 } /* Comment.Preproc */
+.highlight .cpf { color: #3D7B7B; font-style: italic } /* Comment.PreprocFile */
+.highlight .c1 { color: #3D7B7B; font-style: italic } /* Comment.Single */
+.highlight .cs { color: #3D7B7B; font-style: italic } /* Comment.Special */
+.highlight .gd { color: #A00000 } /* Generic.Deleted */
+.highlight .ge { font-style: italic } /* Generic.Emph */
+.highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */
+.highlight .gr { color: #E40000 } /* Generic.Error */
+.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
+.highlight .gi { color: #008400 } /* Generic.Inserted */
+.highlight .go { color: #717171 } /* Generic.Output */
+.highlight .gp { color: #000080; font-weight: bold } /* Generic.Prompt */
+.highlight .gs { font-weight: bold } /* Generic.Strong */
+.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
+.highlight .gt { color: #0044DD } /* Generic.Traceback */
+.highlight .kc { color: #008000; font-weight: bold } /* Keyword.Constant */
+.highlight .kd { color: #008000; font-weight: bold } /* Keyword.Declaration */
+.highlight .kn { color: #008000; font-weight: bold } /* Keyword.Namespace */
+.highlight .kp { color: #008000 } /* Keyword.Pseudo */
+.highlight .kr { color: #008000; font-weight: bold } /* Keyword.Reserved */
+.highlight .kt { color: #B00040 } /* Keyword.Type */
+.highlight .m { color: #666666 } /* Literal.Number */
+.highlight .s { color: #BA2121 } /* Literal.String */
+.highlight .na { color: #687822 } /* Name.Attribute */
+.highlight .nb { color: #008000 } /* Name.Builtin */
+.highlight .nc { color: #0000FF; font-weight: bold } /* Name.Class */
+.highlight .no { color: #880000 } /* Name.Constant */
+.highlight .nd { color: #AA22FF } /* Name.Decorator */
+.highlight .ni { color: #717171; font-weight: bold } /* Name.Entity */
+.highlight .ne { color: #CB3F38; font-weight: bold } /* Name.Exception */
+.highlight .nf { color: #0000FF } /* Name.Function */
+.highlight .nl { color: #767600 } /* Name.Label */
+.highlight .nn { color: #0000FF; font-weight: bold } /* Name.Namespace */
+.highlight .nt { color: #008000; font-weight: bold } /* Name.Tag */
+.highlight .nv { color: #19177C } /* Name.Variable */
+.highlight .ow { color: #AA22FF; font-weight: bold } /* Operator.Word */
+.highlight .w { color: #bbbbbb } /* Text.Whitespace */
+.highlight .mb { color: #666666 } /* Literal.Number.Bin */
+.highlight .mf { color: #666666 } /* Literal.Number.Float */
+.highlight .mh { color: #666666 } /* Literal.Number.Hex */
+.highlight .mi { color: #666666 } /* Literal.Number.Integer */
+.highlight .mo { color: #666666 } /* Literal.Number.Oct */
+.highlight .sa { color: #BA2121 } /* Literal.String.Affix */
+.highlight .sb { color: #BA2121 } /* Literal.String.Backtick */
+.highlight .sc { color: #BA2121 } /* Literal.String.Char */
+.highlight .dl { color: #BA2121 } /* Literal.String.Delimiter */
+.highlight .sd { color: #BA2121; font-style: italic } /* Literal.String.Doc */
+.highlight .s2 { color: #BA2121 } /* Literal.String.Double */
+.highlight .se { color: #AA5D1F; font-weight: bold } /* Literal.String.Escape */
+.highlight .sh { color: #BA2121 } /* Literal.String.Heredoc */
+.highlight .si { color: #A45A77; font-weight: bold } /* Literal.String.Interpol */
+.highlight .sx { color: #008000 } /* Literal.String.Other */
+.highlight .sr { color: #A45A77 } /* Literal.String.Regex */
+.highlight .s1 { color: #BA2121 } /* Literal.String.Single */
+.highlight .ss { color: #19177C } /* Literal.String.Symbol */
+.highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */
+.highlight .fm { color: #0000FF } /* Name.Function.Magic */
+.highlight .vc { color: #19177C } /* Name.Variable.Class */
+.highlight .vg { color: #19177C } /* Name.Variable.Global */
+.highlight .vi { color: #19177C } /* Name.Variable.Instance */
+.highlight .vm { color: #19177C } /* Name.Variable.Magic */
+.highlight .il { color: #666666 } /* Literal.Number.Integer.Long */
\ No newline at end of file
diff --git a/_static/searchtools.js b/_static/searchtools.js
new file mode 100644
index 00000000..2c774d17
--- /dev/null
+++ b/_static/searchtools.js
@@ -0,0 +1,632 @@
+/*
+ * Sphinx JavaScript utilities for the full-text search.
+ */
+"use strict";
+
+/**
+ * Simple result scoring code.
+ */
+if (typeof Scorer === "undefined") {
+  var Scorer = {
+    // Implement the following function to further tweak the score for each result
+    // The function takes a result array [docname, title, anchor, descr, score, filename]
+    // and returns the new score.
+    /*
+    score: result => {
+      const [docname, title, anchor, descr, score, filename, kind] = result
+      return score
+    },
+    */
+
+    // query matches the full name of an object
+    objNameMatch: 11,
+    // or matches in the last dotted part of the object name
+    objPartialMatch: 6,
+    // Additive scores depending on the priority of the object
+    objPrio: {
+      0: 15, // used to be importantResults
+      1: 5, // used to be objectResults
+      2: -5, // used to be unimportantResults
+    },
+    //  Used when the priority is not in the mapping.
+    objPrioDefault: 0,
+
+    // query found in title
+    title: 15,
+    partialTitle: 7,
+    // query found in terms
+    term: 5,
+    partialTerm: 2,
+  };
+}
+
+// Global search result kind enum, used by themes to style search results.
+class SearchResultKind {
+    static get index() { return  "index"; }
+    static get object() { return "object"; }
+    static get text() { return "text"; }
+    static get title() { return "title"; }
+}
+
+const _removeChildren = (element) => {
+  while (element && element.lastChild) element.removeChild(element.lastChild);
+};
+
+/**
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping
+ */
+const _escapeRegExp = (string) =>
+  string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
+
+const _displayItem = (item, searchTerms, highlightTerms) => {
+  const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
+  const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
+  const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
+  const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
+  const contentRoot = document.documentElement.dataset.content_root;
+
+  const [docName, title, anchor, descr, score, _filename, kind] = item;
+
+  let listItem = document.createElement("li");
+  // Add a class representing the item's type:
+  // can be used by a theme's CSS selector for styling
+  // See SearchResultKind for the class names.
+  listItem.classList.add(`kind-${kind}`);
+  let requestUrl;
+  let linkUrl;
+  if (docBuilder === "dirhtml") {
+    // dirhtml builder
+    let dirname = docName + "/";
+    if (dirname.match(/\/index\/$/))
+      dirname = dirname.substring(0, dirname.length - 6);
+    else if (dirname === "index/") dirname = "";
+    requestUrl = contentRoot + dirname;
+    linkUrl = requestUrl;
+  } else {
+    // normal html builders
+    requestUrl = contentRoot + docName + docFileSuffix;
+    linkUrl = docName + docLinkSuffix;
+  }
+  let linkEl = listItem.appendChild(document.createElement("a"));
+  linkEl.href = linkUrl + anchor;
+  linkEl.dataset.score = score;
+  linkEl.innerHTML = title;
+  if (descr) {
+    listItem.appendChild(document.createElement("span")).innerHTML =
+      " (" + descr + ")";
+    // highlight search terms in the description
+    if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+      highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
+  }
+  else if (showSearchSummary)
+    fetch(requestUrl)
+      .then((responseData) => responseData.text())
+      .then((data) => {
+        if (data)
+          listItem.appendChild(
+            Search.makeSearchSummary(data, searchTerms, anchor)
+          );
+        // highlight search terms in the summary
+        if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+          highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
+      });
+  Search.output.appendChild(listItem);
+};
+const _finishSearch = (resultCount) => {
+  Search.stopPulse();
+  Search.title.innerText = _("Search Results");
+  if (!resultCount)
+    Search.status.innerText = Documentation.gettext(
+      "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories."
+    );
+  else
+    Search.status.innerText = Documentation.ngettext(
+      "Search finished, found one page matching the search query.",
+      "Search finished, found ${resultCount} pages matching the search query.",
+      resultCount,
+    ).replace('${resultCount}', resultCount);
+};
+const _displayNextItem = (
+  results,
+  resultCount,
+  searchTerms,
+  highlightTerms,
+) => {
+  // results left, load the summary and display it
+  // this is intended to be dynamic (don't sub resultsCount)
+  if (results.length) {
+    _displayItem(results.pop(), searchTerms, highlightTerms);
+    setTimeout(
+      () => _displayNextItem(results, resultCount, searchTerms, highlightTerms),
+      5
+    );
+  }
+  // search finished, update title and status message
+  else _finishSearch(resultCount);
+};
+// Helper function used by query() to order search results.
+// Each input is an array of [docname, title, anchor, descr, score, filename, kind].
+// Order the results by score (in opposite order of appearance, since the
+// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically.
+const _orderResultsByScoreThenName = (a, b) => {
+  const leftScore = a[4];
+  const rightScore = b[4];
+  if (leftScore === rightScore) {
+    // same score: sort alphabetically
+    const leftTitle = a[1].toLowerCase();
+    const rightTitle = b[1].toLowerCase();
+    if (leftTitle === rightTitle) return 0;
+    return leftTitle > rightTitle ? -1 : 1; // inverted is intentional
+  }
+  return leftScore > rightScore ? 1 : -1;
+};
+
+/**
+ * Default splitQuery function. Can be overridden in ``sphinx.search`` with a
+ * custom function per language.
+ *
+ * The regular expression works by splitting the string on consecutive characters
+ * that are not Unicode letters, numbers, underscores, or emoji characters.
+ * This is the same as ``\W+`` in Python, preserving the surrogate pair area.
+ */
+if (typeof splitQuery === "undefined") {
+  var splitQuery = (query) => query
+      .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu)
+      .filter(term => term)  // remove remaining empty strings
+}
+
+/**
+ * Search Module
+ */
+const Search = {
+  _index: null,
+  _queued_query: null,
+  _pulse_status: -1,
+
+  htmlToText: (htmlString, anchor) => {
+    const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
+    for (const removalQuery of [".headerlink", "script", "style"]) {
+      htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() });
+    }
+    if (anchor) {
+      const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`);
+      if (anchorContent) return anchorContent.textContent;
+
+      console.warn(
+        `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.`
+      );
+    }
+
+    // if anchor not specified or not found, fall back to main content
+    const docContent = htmlElement.querySelector('[role="main"]');
+    if (docContent) return docContent.textContent;
+
+    console.warn(
+      "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template."
+    );
+    return "";
+  },
+
+  init: () => {
+    const query = new URLSearchParams(window.location.search).get("q");
+    document
+      .querySelectorAll('input[name="q"]')
+      .forEach((el) => (el.value = query));
+    if (query) Search.performSearch(query);
+  },
+
+  loadIndex: (url) =>
+    (document.body.appendChild(document.createElement("script")).src = url),
+
+  setIndex: (index) => {
+    Search._index = index;
+    if (Search._queued_query !== null) {
+      const query = Search._queued_query;
+      Search._queued_query = null;
+      Search.query(query);
+    }
+  },
+
+  hasIndex: () => Search._index !== null,
+
+  deferQuery: (query) => (Search._queued_query = query),
+
+  stopPulse: () => (Search._pulse_status = -1),
+
+  startPulse: () => {
+    if (Search._pulse_status >= 0) return;
+
+    const pulse = () => {
+      Search._pulse_status = (Search._pulse_status + 1) % 4;
+      Search.dots.innerText = ".".repeat(Search._pulse_status);
+      if (Search._pulse_status >= 0) window.setTimeout(pulse, 500);
+    };
+    pulse();
+  },
+
+  /**
+   * perform a search for something (or wait until index is loaded)
+   */
+  performSearch: (query) => {
+    // create the required interface elements
+    const searchText = document.createElement("h2");
+    searchText.textContent = _("Searching");
+    const searchSummary = document.createElement("p");
+    searchSummary.classList.add("search-summary");
+    searchSummary.innerText = "";
+    const searchList = document.createElement("ul");
+    searchList.setAttribute("role", "list");
+    searchList.classList.add("search");
+
+    const out = document.getElementById("search-results");
+    Search.title = out.appendChild(searchText);
+    Search.dots = Search.title.appendChild(document.createElement("span"));
+    Search.status = out.appendChild(searchSummary);
+    Search.output = out.appendChild(searchList);
+
+    const searchProgress = document.getElementById("search-progress");
+    // Some themes don't use the search progress node
+    if (searchProgress) {
+      searchProgress.innerText = _("Preparing search...");
+    }
+    Search.startPulse();
+
+    // index already loaded, the browser was quick!
+    if (Search.hasIndex()) Search.query(query);
+    else Search.deferQuery(query);
+  },
+
+  _parseQuery: (query) => {
+    // stem the search terms and add them to the correct list
+    const stemmer = new Stemmer();
+    const searchTerms = new Set();
+    const excludedTerms = new Set();
+    const highlightTerms = new Set();
+    const objectTerms = new Set(splitQuery(query.toLowerCase().trim()));
+    splitQuery(query.trim()).forEach((queryTerm) => {
+      const queryTermLower = queryTerm.toLowerCase();
+
+      // maybe skip this "word"
+      // stopwords array is from language_data.js
+      if (
+        stopwords.indexOf(queryTermLower) !== -1 ||
+        queryTerm.match(/^\d+$/)
+      )
+        return;
+
+      // stem the word
+      let word = stemmer.stemWord(queryTermLower);
+      // select the correct list
+      if (word[0] === "-") excludedTerms.add(word.substr(1));
+      else {
+        searchTerms.add(word);
+        highlightTerms.add(queryTermLower);
+      }
+    });
+
+    if (SPHINX_HIGHLIGHT_ENABLED) {  // set in sphinx_highlight.js
+      localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" "))
+    }
+
+    // console.debug("SEARCH: searching for:");
+    // console.info("required: ", [...searchTerms]);
+    // console.info("excluded: ", [...excludedTerms]);
+
+    return [query, searchTerms, excludedTerms, highlightTerms, objectTerms];
+  },
+
+  /**
+   * execute search (requires search index to be loaded)
+   */
+  _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => {
+    const filenames = Search._index.filenames;
+    const docNames = Search._index.docnames;
+    const titles = Search._index.titles;
+    const allTitles = Search._index.alltitles;
+    const indexEntries = Search._index.indexentries;
+
+    // Collect multiple result groups to be sorted separately and then ordered.
+    // Each is an array of [docname, title, anchor, descr, score, filename, kind].
+    const normalResults = [];
+    const nonMainIndexResults = [];
+
+    _removeChildren(document.getElementById("search-progress"));
+
+    const queryLower = query.toLowerCase().trim();
+    for (const [title, foundTitles] of Object.entries(allTitles)) {
+      if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) {
+        for (const [file, id] of foundTitles) {
+          const score = Math.round(Scorer.title * queryLower.length / title.length);
+          const boost = titles[file] === title ? 1 : 0;  // add a boost for document titles
+          normalResults.push([
+            docNames[file],
+            titles[file] !== title ? `${titles[file]} > ${title}` : title,
+            id !== null ? "#" + id : "",
+            null,
+            score + boost,
+            filenames[file],
+            SearchResultKind.title,
+          ]);
+        }
+      }
+    }
+
+    // search for explicit entries in index directives
+    for (const [entry, foundEntries] of Object.entries(indexEntries)) {
+      if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) {
+        for (const [file, id, isMain] of foundEntries) {
+          const score = Math.round(100 * queryLower.length / entry.length);
+          const result = [
+            docNames[file],
+            titles[file],
+            id ? "#" + id : "",
+            null,
+            score,
+            filenames[file],
+            SearchResultKind.index,
+          ];
+          if (isMain) {
+            normalResults.push(result);
+          } else {
+            nonMainIndexResults.push(result);
+          }
+        }
+      }
+    }
+
+    // lookup as object
+    objectTerms.forEach((term) =>
+      normalResults.push(...Search.performObjectSearch(term, objectTerms))
+    );
+
+    // lookup as search terms in fulltext
+    normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms));
+
+    // let the scorer override scores with a custom scoring function
+    if (Scorer.score) {
+      normalResults.forEach((item) => (item[4] = Scorer.score(item)));
+      nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item)));
+    }
+
+    // Sort each group of results by score and then alphabetically by name.
+    normalResults.sort(_orderResultsByScoreThenName);
+    nonMainIndexResults.sort(_orderResultsByScoreThenName);
+
+    // Combine the result groups in (reverse) order.
+    // Non-main index entries are typically arbitrary cross-references,
+    // so display them after other results.
+    let results = [...nonMainIndexResults, ...normalResults];
+
+    // remove duplicate search results
+    // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept
+    let seen = new Set();
+    results = results.reverse().reduce((acc, result) => {
+      let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(',');
+      if (!seen.has(resultStr)) {
+        acc.push(result);
+        seen.add(resultStr);
+      }
+      return acc;
+    }, []);
+
+    return results.reverse();
+  },
+
+  query: (query) => {
+    const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query);
+    const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms);
+
+    // for debugging
+    //Search.lastresults = results.slice();  // a copy
+    // console.info("search results:", Search.lastresults);
+
+    // print the results
+    _displayNextItem(results, results.length, searchTerms, highlightTerms);
+  },
+
+  /**
+   * search for object names
+   */
+  performObjectSearch: (object, objectTerms) => {
+    const filenames = Search._index.filenames;
+    const docNames = Search._index.docnames;
+    const objects = Search._index.objects;
+    const objNames = Search._index.objnames;
+    const titles = Search._index.titles;
+
+    const results = [];
+
+    const objectSearchCallback = (prefix, match) => {
+      const name = match[4]
+      const fullname = (prefix ? prefix + "." : "") + name;
+      const fullnameLower = fullname.toLowerCase();
+      if (fullnameLower.indexOf(object) < 0) return;
+
+      let score = 0;
+      const parts = fullnameLower.split(".");
+
+      // check for different match types: exact matches of full name or
+      // "last name" (i.e. last dotted part)
+      if (fullnameLower === object || parts.slice(-1)[0] === object)
+        score += Scorer.objNameMatch;
+      else if (parts.slice(-1)[0].indexOf(object) > -1)
+        score += Scorer.objPartialMatch; // matches in last name
+
+      const objName = objNames[match[1]][2];
+      const title = titles[match[0]];
+
+      // If more than one term searched for, we require other words to be
+      // found in the name/title/description
+      const otherTerms = new Set(objectTerms);
+      otherTerms.delete(object);
+      if (otherTerms.size > 0) {
+        const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase();
+        if (
+          [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0)
+        )
+          return;
+      }
+
+      let anchor = match[3];
+      if (anchor === "") anchor = fullname;
+      else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname;
+
+      const descr = objName + _(", in ") + title;
+
+      // add custom score for some objects according to scorer
+      if (Scorer.objPrio.hasOwnProperty(match[2]))
+        score += Scorer.objPrio[match[2]];
+      else score += Scorer.objPrioDefault;
+
+      results.push([
+        docNames[match[0]],
+        fullname,
+        "#" + anchor,
+        descr,
+        score,
+        filenames[match[0]],
+        SearchResultKind.object,
+      ]);
+    };
+    Object.keys(objects).forEach((prefix) =>
+      objects[prefix].forEach((array) =>
+        objectSearchCallback(prefix, array)
+      )
+    );
+    return results;
+  },
+
+  /**
+   * search for full-text terms in the index
+   */
+  performTermsSearch: (searchTerms, excludedTerms) => {
+    // prepare search
+    const terms = Search._index.terms;
+    const titleTerms = Search._index.titleterms;
+    const filenames = Search._index.filenames;
+    const docNames = Search._index.docnames;
+    const titles = Search._index.titles;
+
+    const scoreMap = new Map();
+    const fileMap = new Map();
+
+    // perform the search on the required terms
+    searchTerms.forEach((word) => {
+      const files = [];
+      const arr = [
+        { files: terms[word], score: Scorer.term },
+        { files: titleTerms[word], score: Scorer.title },
+      ];
+      // add support for partial matches
+      if (word.length > 2) {
+        const escapedWord = _escapeRegExp(word);
+        if (!terms.hasOwnProperty(word)) {
+          Object.keys(terms).forEach((term) => {
+            if (term.match(escapedWord))
+              arr.push({ files: terms[term], score: Scorer.partialTerm });
+          });
+        }
+        if (!titleTerms.hasOwnProperty(word)) {
+          Object.keys(titleTerms).forEach((term) => {
+            if (term.match(escapedWord))
+              arr.push({ files: titleTerms[term], score: Scorer.partialTitle });
+          });
+        }
+      }
+
+      // no match but word was a required one
+      if (arr.every((record) => record.files === undefined)) return;
+
+      // found search word in contents
+      arr.forEach((record) => {
+        if (record.files === undefined) return;
+
+        let recordFiles = record.files;
+        if (recordFiles.length === undefined) recordFiles = [recordFiles];
+        files.push(...recordFiles);
+
+        // set score for the word in each file
+        recordFiles.forEach((file) => {
+          if (!scoreMap.has(file)) scoreMap.set(file, {});
+          scoreMap.get(file)[word] = record.score;
+        });
+      });
+
+      // create the mapping
+      files.forEach((file) => {
+        if (!fileMap.has(file)) fileMap.set(file, [word]);
+        else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word);
+      });
+    });
+
+    // now check if the files don't contain excluded terms
+    const results = [];
+    for (const [file, wordList] of fileMap) {
+      // check if all requirements are matched
+
+      // as search terms with length < 3 are discarded
+      const filteredTermCount = [...searchTerms].filter(
+        (term) => term.length > 2
+      ).length;
+      if (
+        wordList.length !== searchTerms.size &&
+        wordList.length !== filteredTermCount
+      )
+        continue;
+
+      // ensure that none of the excluded terms is in the search result
+      if (
+        [...excludedTerms].some(
+          (term) =>
+            terms[term] === file ||
+            titleTerms[term] === file ||
+            (terms[term] || []).includes(file) ||
+            (titleTerms[term] || []).includes(file)
+        )
+      )
+        break;
+
+      // select one (max) score for the file.
+      const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w]));
+      // add result to the result list
+      results.push([
+        docNames[file],
+        titles[file],
+        "",
+        null,
+        score,
+        filenames[file],
+        SearchResultKind.text,
+      ]);
+    }
+    return results;
+  },
+
+  /**
+   * helper function to return a node containing the
+   * search summary for a given text. keywords is a list
+   * of stemmed words.
+   */
+  makeSearchSummary: (htmlText, keywords, anchor) => {
+    const text = Search.htmlToText(htmlText, anchor);
+    if (text === "") return null;
+
+    const textLower = text.toLowerCase();
+    const actualStartPosition = [...keywords]
+      .map((k) => textLower.indexOf(k.toLowerCase()))
+      .filter((i) => i > -1)
+      .slice(-1)[0];
+    const startWithContext = Math.max(actualStartPosition - 120, 0);
+
+    const top = startWithContext === 0 ? "" : "...";
+    const tail = startWithContext + 240 < text.length ? "..." : "";
+
+    let summary = document.createElement("p");
+    summary.classList.add("context");
+    summary.textContent = top + text.substr(startWithContext, 240).trim() + tail;
+
+    return summary;
+  },
+};
+
+_ready(Search.init);
diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js
new file mode 100644
index 00000000..8a96c69a
--- /dev/null
+++ b/_static/sphinx_highlight.js
@@ -0,0 +1,154 @@
+/* Highlighting utilities for Sphinx HTML documentation. */
+"use strict";
+
+const SPHINX_HIGHLIGHT_ENABLED = true
+
+/**
+ * highlight a given string on a node by wrapping it in
+ * span elements with the given class name.
+ */
+const _highlight = (node, addItems, text, className) => {
+  if (node.nodeType === Node.TEXT_NODE) {
+    const val = node.nodeValue;
+    const parent = node.parentNode;
+    const pos = val.toLowerCase().indexOf(text);
+    if (
+      pos >= 0 &&
+      !parent.classList.contains(className) &&
+      !parent.classList.contains("nohighlight")
+    ) {
+      let span;
+
+      const closestNode = parent.closest("body, svg, foreignObject");
+      const isInSVG = closestNode && closestNode.matches("svg");
+      if (isInSVG) {
+        span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+      } else {
+        span = document.createElement("span");
+        span.classList.add(className);
+      }
+
+      span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+      const rest = document.createTextNode(val.substr(pos + text.length));
+      parent.insertBefore(
+        span,
+        parent.insertBefore(
+          rest,
+          node.nextSibling
+        )
+      );
+      node.nodeValue = val.substr(0, pos);
+      /* There may be more occurrences of search term in this node. So call this
+       * function recursively on the remaining fragment.
+       */
+      _highlight(rest, addItems, text, className);
+
+      if (isInSVG) {
+        const rect = document.createElementNS(
+          "http://www.w3.org/2000/svg",
+          "rect"
+        );
+        const bbox = parent.getBBox();
+        rect.x.baseVal.value = bbox.x;
+        rect.y.baseVal.value = bbox.y;
+        rect.width.baseVal.value = bbox.width;
+        rect.height.baseVal.value = bbox.height;
+        rect.setAttribute("class", className);
+        addItems.push({ parent: parent, target: rect });
+      }
+    }
+  } else if (node.matches && !node.matches("button, select, textarea")) {
+    node.childNodes.forEach((el) => _highlight(el, addItems, text, className));
+  }
+};
+const _highlightText = (thisNode, text, className) => {
+  let addItems = [];
+  _highlight(thisNode, addItems, text, className);
+  addItems.forEach((obj) =>
+    obj.parent.insertAdjacentElement("beforebegin", obj.target)
+  );
+};
+
+/**
+ * Small JavaScript module for the documentation.
+ */
+const SphinxHighlight = {
+
+  /**
+   * highlight the search words provided in localstorage in the text
+   */
+  highlightSearchWords: () => {
+    if (!SPHINX_HIGHLIGHT_ENABLED) return;  // bail if no highlight
+
+    // get and clear terms from localstorage
+    const url = new URL(window.location);
+    const highlight =
+        localStorage.getItem("sphinx_highlight_terms")
+        || url.searchParams.get("highlight")
+        || "";
+    localStorage.removeItem("sphinx_highlight_terms")
+    url.searchParams.delete("highlight");
+    window.history.replaceState({}, "", url);
+
+    // get individual terms from highlight string
+    const terms = highlight.toLowerCase().split(/\s+/).filter(x => x);
+    if (terms.length === 0) return; // nothing to do
+
+    // There should never be more than one element matching "div.body"
+    const divBody = document.querySelectorAll("div.body");
+    const body = divBody.length ? divBody[0] : document.querySelector("body");
+    window.setTimeout(() => {
+      terms.forEach((term) => _highlightText(body, term, "highlighted"));
+    }, 10);
+
+    const searchBox = document.getElementById("searchbox");
+    if (searchBox === null) return;
+    searchBox.appendChild(
+      document
+        .createRange()
+        .createContextualFragment(
+          '<p class="highlight-link">' +
+            '<a href="javascript:SphinxHighlight.hideSearchWords()">' +
+            _("Hide Search Matches") +
+            "</a></p>"
+        )
+    );
+  },
+
+  /**
+   * helper function to hide the search marks again
+   */
+  hideSearchWords: () => {
+    document
+      .querySelectorAll("#searchbox .highlight-link")
+      .forEach((el) => el.remove());
+    document
+      .querySelectorAll("span.highlighted")
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+<li class="toctree-l3 current"><a class="current reference internal" href="#">biot_savart</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#biot_savart.B_ionosphere"><code class="docutils literal notranslate"><span class="pre">B_ionosphere()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#biot_savart.B_magnetosphere"><code class="docutils literal notranslate"><span class="pre">B_magnetosphere()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#biot_savart.b_dip"><code class="docutils literal notranslate"><span class="pre">b_dip()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#biot_savart.b_dip_direction"><code class="docutils literal notranslate"><span class="pre">b_dip_direction()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#biot_savart.b_dip_magnitude"><code class="docutils literal notranslate"><span class="pre">b_dip_magnitude()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#biot_savart.biot_savart"><code class="docutils literal notranslate"><span class="pre">biot_savart()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#biot_savart.cartesian_to_spherical"><code class="docutils literal notranslate"><span class="pre">cartesian_to_spherical()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#biot_savart.fac_map"><code class="docutils literal notranslate"><span class="pre">fac_map()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#biot_savart.graded_mesh"><code class="docutils literal notranslate"><span class="pre">graded_mesh()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#biot_savart.integrate_biot_savart"><code class="docutils literal notranslate"><span class="pre">integrate_biot_savart()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#biot_savart.mkdir_path"><code class="docutils literal notranslate"><span class="pre">mkdir_path()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#biot_savart.nearest_node_index"><code class="docutils literal notranslate"><span class="pre">nearest_node_index()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#biot_savart.refine_mesh"><code class="docutils literal notranslate"><span class="pre">refine_mesh()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#biot_savart.save_B_vlsv"><code class="docutils literal notranslate"><span class="pre">save_B_vlsv()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#biot_savart.spherical_to_cartesian"><code class="docutils literal notranslate"><span class="pre">spherical_to_cartesian()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#biot_savart.vec_len_2d"><code class="docutils literal notranslate"><span class="pre">vec_len_2d()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#biot_savart.vec_unit"><code class="docutils literal notranslate"><span class="pre">vec_unit()</span></code></a></li>
+</ul>
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+<li class="toctree-l3"><a class="reference internal" href="../gics/">gics</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../magnetopause2d/">magnetopause2d</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../magnetopause3d/">magnetopause3d</a></li>
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+             
+  <section id="module-biot_savart">
+<span id="biot-savart"></span><h1>biot_savart<a class="headerlink" href="#module-biot_savart" title="Link to this heading"></a></h1>
+<blockquote>
+<div><p>Follow Welling et al. (2020) calculate the magnetic field at Earth’s surface.</p>
+</div></blockquote>
+<p>Integrate Biot-Savart over:</p>
+<blockquote>
+<div><ol class="arabic simple">
+<li><p>All currents within the Vlasov domain</p></li>
+<li><p>Birkeland currents (FACs) in the “gap region” between the MHD inner boundary and the ionosphere, mapped (assuming J propto B) along the field lines connecting ionosphere radius R_IONO to coupling radius r_C</p></li>
+<li><p>Horizontal Ionospheric currents (altitude 100 km)</p></li>
+</ol>
+</div></blockquote>
+<p>The integration is a discrete summation over the 3 domains.</p>
+<p>Integrating the domain #2 will likely require this mesh to be ‘refined’ in order to resolve the FAC structures
+see the functions refine_mesh() and graded_mesh()</p>
+<p>This script has been tested with the Vlasiator runs EGL, FHA, FIA
+note that the usefulness for EGL is limited because there is no ionosphere (domain #3) for that run</p>
+<p>To run this script, require access to the data reducer/variable ‘vg_J’ in the .vlsv  file
+This may be supplied by a .vlsv file’s vlsvReader object, see keyword f_J_sidecar</p>
+<p>This script is written for the UH environment. Adapt file paths as needed.</p>
+<p>###</p>
+<p>EXAMPLE CALL (1 thread):
+python biot_savart.py -nproc 1 -task 1 -run FHA</p>
+<dl class="simple">
+<dt>Example sidecar .vlsv files,  containing ground magnetic field data, can be found at:</dt><dd><p>/wrk-vakka/group/spacephysics/vlasiator/3D/{run name}/sidecars/ig_B/</p>
+</dd>
+</dl>
+<dl class="py function">
+<dt class="sig sig-object py" id="biot_savart.B_ionosphere">
+<span class="sig-prename descclassname"><span class="pre">biot_savart.</span></span><span class="sig-name descname"><span class="pre">B_ionosphere</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">f</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coord_list</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ig_r</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'integrate'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#biot_savart.B_ionosphere" title="Link to this definition"></a></dt>
+<dd><p>Ionospheric (domain #3) current contribution to magnetic field</p>
+<p>B_ionosphere() evaluates the magnetic field produced by ionospheric currents</p>
+<dl>
+<dt>Inputs:</dt><dd><p>f: VlsvReader object</p>
+<p>keyword coord_list: locations where B-field is calculated</p>
+<p>keyword ig_r: the ionospheric mesh</p>
+<p>keyword method:</p>
+<blockquote>
+<div><p>=’integrate’ (default): integrate over the whole ionosphere using Biot-Savart law</p>
+<p>=’local’: ionosphere produces magnetic field locally, as by an infinite plane of current overhead</p>
+</div></blockquote>
+</dd>
+<dt>Outputs:</dt><dd><p>Magnetic field evaluated at coord_list</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="biot_savart.B_magnetosphere">
+<span class="sig-prename descclassname"><span class="pre">biot_savart.</span></span><span class="sig-name descname"><span class="pre">B_magnetosphere</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">f</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">f_J_sidecar</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">r_C</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">31855000.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ig_r</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#biot_savart.B_magnetosphere" title="Link to this definition"></a></dt>
+<dd><p>Inner and outer magnetospheric contributions to Biot-Savart integral (domains #1, #2)
+wrapper for biot_savart()</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="biot_savart.b_dip">
+<span class="sig-prename descclassname"><span class="pre">biot_savart.</span></span><span class="sig-name descname"><span class="pre">b_dip</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">z</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mag_mom_vector</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">array([0.e+00,</span> <span class="pre">0.e+00,</span> <span class="pre">-8.e+22])</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#biot_savart.b_dip" title="Link to this definition"></a></dt>
+<dd><dl class="simple">
+<dt>Inputs: cartesian coordinates x,y,z [m]</dt><dd><p>keyword mag_mom_vector: Earth’s vector magnetic dipole moment</p>
+</dd>
+</dl>
+<p>Outputs: dipole magnetic field</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="biot_savart.b_dip_direction">
+<span class="sig-prename descclassname"><span class="pre">biot_savart.</span></span><span class="sig-name descname"><span class="pre">b_dip_direction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">z</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mag_mom_vector</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">array([0.e+00,</span> <span class="pre">0.e+00,</span> <span class="pre">-8.e+22])</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#biot_savart.b_dip_direction" title="Link to this definition"></a></dt>
+<dd><dl class="simple">
+<dt>Inputs: cartesian coordinates x,y,z [m]</dt><dd><p>keyword mag_mom_vector: Earth’s vector magnetic dipole moment</p>
+</dd>
+</dl>
+<p>Outputs: dipole magnetic field unit vector</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="biot_savart.b_dip_magnitude">
+<span class="sig-prename descclassname"><span class="pre">biot_savart.</span></span><span class="sig-name descname"><span class="pre">b_dip_magnitude</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">theta</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">r</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mag_mom</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">8e+22</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#biot_savart.b_dip_magnitude" title="Link to this definition"></a></dt>
+<dd><p>Inputs:
+theta: colatitude [radians]
+r: radial distance [m]
+keyword mag_mom: magnetic dipole moment, default=8e22 [A / m^2], as in EGI, EGL, FIA, FHA runs</p>
+<p>Outputs: Earth’s magnetic field magnitude [Tesla]</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="biot_savart.biot_savart">
+<span class="sig-prename descclassname"><span class="pre">biot_savart.</span></span><span class="sig-name descname"><span class="pre">biot_savart</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">coord_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">f</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">f_J_sidecar</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">r_C</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">31855000.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mesh</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'graded'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#biot_savart.biot_savart" title="Link to this definition"></a></dt>
+<dd><dl class="simple">
+<dt>param coord_list:   a list of 3-element arrays of coordinates [ [x1,y1,z1], [x2,y2,z2], … ], SI units</dt><dd><p>if considering just a single starting point, the code accepts a 3-element array-like object [x1,y1,z1]</p>
+</dd>
+</dl>
+<p>f: vlsvReader object
+f_J_sidecar: vlsvReader object that contains pre-computed current ‘vg_J’</p>
+<blockquote>
+<div><p>e.g., for EGL, files at: /wrk-vakka/group/spacephysics/vlasiator/3D/EGL/visualizations_2/ballooning/*.vlsv</p>
+</div></blockquote>
+<p>runtime (FHA): overhead of about 200 sec (setup), plus 0.2 sec for each element of coord_list</p>
+<p>returns a tuple (B_inner, B_outer) 
+B_inner: the B-field [T] generated by FACs at 1 R_E &lt; r&lt; r_C
+B_outer: the B-field [T] generated by currents in simulation domain at r &gt; r_C</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="biot_savart.cartesian_to_spherical">
+<span class="sig-prename descclassname"><span class="pre">biot_savart.</span></span><span class="sig-name descname"><span class="pre">cartesian_to_spherical</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">z</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#biot_savart.cartesian_to_spherical" title="Link to this definition"></a></dt>
+<dd><p>r &gt; 0
+0 &lt; theta &lt; pi
+-pi &lt; phi &lt; pi
+all are assumed to be numpy arrays of equal dimensions</p>
+<p>returns:  r, theta, phi  [tuple]</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="biot_savart.fac_map">
+<span class="sig-prename descclassname"><span class="pre">biot_savart.</span></span><span class="sig-name descname"><span class="pre">fac_map</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">f</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vg_x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vg_y</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vg_z</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dx</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">f_J_sidecar</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">r_C</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">31855000.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mag_mom_vector</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">array([0.e+00,</span> <span class="pre">0.e+00,</span> <span class="pre">-8.e+22])</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#biot_savart.fac_map" title="Link to this definition"></a></dt>
+<dd><blockquote>
+<div><p>Map the FACs along magnetic field lines (J propto B).</p>
+<dl>
+<dt>Inputs:</dt><dd><p>f: VlsvReader object
+f_J_sidecar: vlsvReader object that contains pre-computed current ‘vg_J’</p>
+<blockquote>
+<div><dl class="simple">
+<dt><code class="docutils literal notranslate"><span class="pre">if</span> <span class="pre">f_J_sidecar</span> <span class="pre">=</span> <span class="pre">None:</span></code></dt><dd><p>here is assumed the data reducer ‘ig_fac’ exists (such as for runs FHA and FIA)
+In this case, the currents in the FAC region (domain #2) will be mapped UP from the ionosphere ‘ig_’ grid</p>
+</dd>
+<dt>otherwise (f_J_sidecar = a *.vlsv string, for a file containing the current density J in the vlasov ‘vg_’ grid)</dt><dd><p>for run EGL, see files at /wrk-vakka/group/spacephysics/vlasiator/3D/EGL/visualizations_2/ballooning/*.vlsv
+In this case, the currents in the FAC region (domain #2) will be mapped DOWN from the vg_ grid</p>
+</dd>
+</dl>
+</div></blockquote>
+<dl class="simple">
+<dt>vg_x,vg_y,vg_z position [m], 1D numpy arrays. </dt><dd><p>note: these coordinates do not have to correspond with Vlasiator’s vg_ grid,
+This is relevant when fac_map() is called by biot_savart(), with keyword mesh=’refined’ or mesh=’graded’</p>
+</dd>
+</dl>
+<p>dx is grid resolution [m], 1D numpy array, This is for the input cells which can be defined arbitrarily—not necessarily same as vg cells.</p>
+</dd>
+</dl>
+<p><strong>*  coordinates, not just coordinates on the vg_ grid *</strong></p>
+</div></blockquote>
+<dl class="simple">
+<dt>Returns:</dt><dd><p>the vector current density [A/m^2] at specified positions vg_x, vg_y, vg_z position
+output J=0 for cells that fall outside the FAC region (i.e if cell is not in region R_EARTH+dx/2 &lt; r&lt; r_C)</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="biot_savart.graded_mesh">
+<span class="sig-prename descclassname"><span class="pre">biot_savart.</span></span><span class="sig-name descname"><span class="pre">graded_mesh</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">z</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dV</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ns</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">array([8,</span> <span class="pre">4,</span> <span class="pre">2])</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Rs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">array([6371000.,</span> <span class="pre">12742000.,</span> <span class="pre">25484000.])</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#biot_savart.graded_mesh" title="Link to this definition"></a></dt>
+<dd><blockquote>
+<div><p>Iteratively refine the mesh in ‘inner’ FAC region  R_IONO &lt; r &lt; r_C,
+used to calculate FAC contribution to Biot-Savart integral</p>
+</div></blockquote>
+<p>Calls refine mesh with different refinement factors n, at specified refinement boundaries
+ns: numpy array of refinement factors (ints)
+Rs: numpy array of refinement boundary radii [R_E]
+edge case: arrays are aligned so that for r&gt;Rs[-1], use ns[-1] refinement</p>
+<p>Want the refinement level to roughly scale as r^{-3/2}. To resolve the mapped features at all radii
+This works because magnetic dipole field goes as 1/r^3, roughly, and area A goes as r^2. 
+(Need to set areas of the cell faces so B*A~constant, to resolve features mapped along field lines)</p>
+<dl class="simple">
+<dt>Example: graded_mesh(x, y, z, dV, ns = np.array([8, 4, 2]), Rs = np.array([R_EARTH, R_EARTH*2, R_EARTH*4]))</dt><dd><p>–&gt; refines 1D mesh size by factor of 8 for 1 RE&lt;r&lt;=2 RE, by factor of 4 for 2 RE&lt;r&lt;=4 RE, by factor of 2 for r&gt;4 RE</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="biot_savart.integrate_biot_savart">
+<span class="sig-prename descclassname"><span class="pre">biot_savart.</span></span><span class="sig-name descname"><span class="pre">integrate_biot_savart</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">coord_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">z</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">J</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delta</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#biot_savart.integrate_biot_savart" title="Link to this definition"></a></dt>
+<dd><p>integration of the Biot-savart law
+magnetic field is evaluated at coordinates specified in coord_list (for example, the ionospheric coordinates)</p>
+<dl>
+<dt>Inputs:</dt><dd><blockquote>
+<div><p>x,y,z (1D array, size n): Cartesian coordinates
+delta (1D array, size n): the volume or area of the element being integrated
+J (2D array, size [3, n]): current density</p>
+</div></blockquote>
+<p>all units SI</p>
+</dd>
+<dt>Outputs:</dt><dd><p>magnetic field evaluated at coord_list</p>
+</dd>
+</dl>
+<p>Note: the units of J and delta depend on the type of integral (volume or surface), but the equation form is unchanged</p>
+<dl class="simple">
+<dt>Biot-Savart (volume): B = (mu_0 / 4 * pi) int { J x r’ / |r’|^3 } dV  ([J] = A/m^2, delta == dV)</dt><dd><p>(surface): B = (mu_0 / 4 * pi) int { J x r’ / |r’|^3 } dA  ([J] = A/m, delta = dS)</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="biot_savart.mkdir_path">
+<span class="sig-prename descclassname"><span class="pre">biot_savart.</span></span><span class="sig-name descname"><span class="pre">mkdir_path</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#biot_savart.mkdir_path" title="Link to this definition"></a></dt>
+<dd><p>Make a directory from the stem of an input file name (path)</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="biot_savart.nearest_node_index">
+<span class="sig-prename descclassname"><span class="pre">biot_savart.</span></span><span class="sig-name descname"><span class="pre">nearest_node_index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">f</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">z</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">node_coords_iono</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#biot_savart.nearest_node_index" title="Link to this definition"></a></dt>
+<dd><p>helper function for finding nearest ionospheric node</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="biot_savart.refine_mesh">
+<span class="sig-prename descclassname"><span class="pre">biot_savart.</span></span><span class="sig-name descname"><span class="pre">refine_mesh</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">z</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dV</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#biot_savart.refine_mesh" title="Link to this definition"></a></dt>
+<dd><p>refine the mesh in ‘inner’ FAC region  R_IONO &lt; r &lt; r_C,
+used to calculate FAC contribution to Biot-Savart integral</p>
+<p>x, y, z: initial coordinates (1D numpy float arrays), assumed to be at the center of cubic cell
+dV: cell volume 1D array or scalar value
+dx_0: side length of initial mesh (1D numpy array or single scalar value)
+n (int): the factor by which to refine the mesh</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="biot_savart.save_B_vlsv">
+<span class="sig-prename descclassname"><span class="pre">biot_savart.</span></span><span class="sig-name descname"><span class="pre">save_B_vlsv</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_tuple</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#biot_savart.save_B_vlsv" title="Link to this definition"></a></dt>
+<dd><p>calculate magnetic field at the Earth’s surface and save in a .vslv file</p>
+<dl>
+<dt>Inputs: input tuple</dt><dd><p>input_tuple[0]: run (string)  # ‘EGL’, ‘FHA’, or ‘FIA’
+input_tuple[1]: fileIndex (int)</p>
+</dd>
+<dt>Outputs:</dt><dd><dl class="simple">
+<dt>ig_r: Cartesian ionospheric grid locations (radius R_EARTH + 100km)</dt><dd><p>note that B_iono, B_inner, B_outer are in fact evaluated at radius R_EARTH
+ig_r is a copy of the Vlasiator ionosphere mesh, to enable combination with other data reducers</p>
+</dd>
+</dl>
+<p>B_iono: Ionospheric (Domain #3) contribution to ground magnetic field (radius R_EARTH)
+B_inner: Ionospheric (Domain #2) contribution to ground magnetic field (radius R_EARTH)
+B_outer: Ionospheric (Domain #1) contribution to ground magnetic field (radius R_EARTH)</p>
+</dd>
+</dl>
+<p>Note: the input and output .vlsv file paths may need to be modified in this script for different users</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="biot_savart.spherical_to_cartesian">
+<span class="sig-prename descclassname"><span class="pre">biot_savart.</span></span><span class="sig-name descname"><span class="pre">spherical_to_cartesian</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">r</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">theta</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">phi</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#biot_savart.spherical_to_cartesian" title="Link to this definition"></a></dt>
+<dd><p>r &gt; 0
+0 &lt; theta &lt; pi
+-pi &lt; phi &lt; pi
+all are assumed to be numpy arrays of equal dimensions</p>
+<p>returns:  x, y, z   [tuple]</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="biot_savart.vec_len_2d">
+<span class="sig-prename descclassname"><span class="pre">biot_savart.</span></span><span class="sig-name descname"><span class="pre">vec_len_2d</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">arr_2d</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#biot_savart.vec_len_2d" title="Link to this definition"></a></dt>
+<dd><p>Vector length</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="biot_savart.vec_unit">
+<span class="sig-prename descclassname"><span class="pre">biot_savart.</span></span><span class="sig-name descname"><span class="pre">vec_unit</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">arr_2d</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#biot_savart.vec_unit" title="Link to this definition"></a></dt>
+<dd><p>assume arr_2d is a numpy array with shape [N, 3]. Return unit vectors with same shape</p>
+</dd></dl>
+
+</section>
+
+
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+
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>calculations &mdash; analysator  documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
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+              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="../plot/">plot</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">calculations</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.calculations.AMRInterpolator"><code class="docutils literal notranslate"><span class="pre">AMRInterpolator</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.calculations.LMN_null_lines_FOTE"><code class="docutils literal notranslate"><span class="pre">LMN_null_lines_FOTE()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.calculations.VariableInfo"><code class="docutils literal notranslate"><span class="pre">VariableInfo</span></code></a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.calculations.VariableInfo.get_scaled_units"><code class="docutils literal notranslate"><span class="pre">VariableInfo.get_scaled_units()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.calculations.VariableInfo.get_scaled_var"><code class="docutils literal notranslate"><span class="pre">VariableInfo.get_scaled_var()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.calculations.VariableInfo.get_variable"><code class="docutils literal notranslate"><span class="pre">VariableInfo.get_variable()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.calculations.cell_time_evolution"><code class="docutils literal notranslate"><span class="pre">cell_time_evolution()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.calculations.cut3d"><code class="docutils literal notranslate"><span class="pre">cut3d()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.calculations.cut_through"><code class="docutils literal notranslate"><span class="pre">cut_through()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.calculations.cut_through_curve"><code class="docutils literal notranslate"><span class="pre">cut_through_curve()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.calculations.cut_through_step"><code class="docutils literal notranslate"><span class="pre">cut_through_step()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.calculations.dynamic_field_tracer"><code class="docutils literal notranslate"><span class="pre">dynamic_field_tracer()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.calculations.epsilon_M"><code class="docutils literal notranslate"><span class="pre">epsilon_M()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.calculations.fourier"><code class="docutils literal notranslate"><span class="pre">fourier()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.calculations.gyrophase_angles_from_file"><code class="docutils literal notranslate"><span class="pre">gyrophase_angles_from_file()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.calculations.lineout"><code class="docutils literal notranslate"><span class="pre">lineout()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.calculations.pitch_angles"><code class="docutils literal notranslate"><span class="pre">pitch_angles()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.calculations.static_field_tracer"><code class="docutils literal notranslate"><span class="pre">static_field_tracer()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.calculations.static_field_tracer_3d"><code class="docutils literal notranslate"><span class="pre">static_field_tracer_3d()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.calculations.themis_observation_from_file"><code class="docutils literal notranslate"><span class="pre">themis_observation_from_file()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.calculations.themis_plot_detector"><code class="docutils literal notranslate"><span class="pre">themis_plot_detector()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.calculations.themis_plot_phasespace_contour"><code class="docutils literal notranslate"><span class="pre">themis_plot_phasespace_contour()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.calculations.themis_plot_phasespace_helistyle"><code class="docutils literal notranslate"><span class="pre">themis_plot_phasespace_helistyle()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.calculations.vlsv_intpol_file"><code class="docutils literal notranslate"><span class="pre">vlsv_intpol_file()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.calculations.vlsv_intpol_points"><code class="docutils literal notranslate"><span class="pre">vlsv_intpol_points()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../vlsvfile/">vlsvfile</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../miscellaneous/">miscellaneous</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../scripts/">scripts</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../about/">Credits</a></li>
+</ul>
+
+        </div>
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="../">analysator</a>
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+      <div class="wy-nav-content">
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+  <ul class="wy-breadcrumbs">
+      <li><a href="../" class="icon icon-home" aria-label="Home"></a></li>
+      <li class="breadcrumb-item active">calculations</li>
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+            <a href="../_sources/calculations.rst.txt" rel="nofollow"> View page source</a>
+      </li>
+  </ul>
+  <hr/>
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+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+             
+  <section id="module-pytools.calculations">
+<span id="calculations"></span><h1>calculations<a class="headerlink" href="#module-pytools.calculations" title="Link to this heading"></a></h1>
+<p>This is a module that includes most, if not all, calculations within the analysator. Please type “.” and press tab to see which functions this module includes.</p>
+<p>Example:
+import pytools as pt</p>
+<p>pt.calculations.
+#press tab</p>
+<p>#Output: list of functions</p>
+<p>pt.calculations.fourier?
+#Press Enter</p>
+<dl class="py class">
+<dt class="sig sig-object py" id="pytools.calculations.AMRInterpolator">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pytools.calculations.</span></span><span class="sig-name descname"><span class="pre">AMRInterpolator</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reader</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'linear'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cellids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">array([1,</span> <span class="pre">2,</span> <span class="pre">3,</span> <span class="pre">4,</span> <span class="pre">5])</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.AMRInterpolator" title="Link to this definition"></a></dt>
+<dd><p>Wrapper class for interpolators, esp. at refinement interfaces.
+Supported methods:</p>
+<dl class="simple">
+<dt>linear</dt><dd><ul class="simple">
+<li><p>(nearly) C0 continuous, regular-grid trilinear interpolant extended to collapsed hexahedral cells.</p></li>
+<li><p>Non-parametric</p></li>
+<li><p>Exact handling of multiply-degenerate hexahedra is missing, with the enabling hack causing errors in trilinear coordinate on the order of 1m</p></li>
+</ul>
+</dd>
+<dt>Radial Basis Functions, <cite>rbf</cite></dt><dd><ul class="simple">
+<li><p>Accurate, slow-ish, but hard to make properly continuous and number of neighbors on which to base the interpolant is not trivial to find.</p></li>
+<li><p>Not continuous with regular-grid trilinear interpolants, needs to be used in the entire interpolation domain.</p></li>
+<li><p>kword options: “neighbors” for number of neighbors (64)</p></li>
+<li><p>basis function uses SciPy default. A free parameter.</p></li>
+</ul>
+</dd>
+<dt>delaunay (not recommended)</dt><dd><ul class="simple">
+<li><p>Choice of triangulation is not unique with regular grids, including refinement interfaces.</p></li>
+<li><p>kword options as in qhull; “qhull_options” : “QJ” (breaks degeneracies)</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.calculations.LMN_null_lines_FOTE">
+<span class="sig-prename descclassname"><span class="pre">pytools.calculations.</span></span><span class="sig-name descname"><span class="pre">LMN_null_lines_FOTE</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">LMNs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">jacobs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Bs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dxs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coords</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.LMN_null_lines_FOTE" title="Link to this definition"></a></dt>
+<dd><p>Function that uses a linear approximation of B from B and its Jacobian
+in the LMN coordinates to get an approximate distance to the neutral line.
+inputs:
+* LMN basis vectors stack
+* Jacobian of B in 9-element vector stack
+* vg_b_vol</p>
+<p>return a measure for closeness to the cell center for a neutral line and other data.
+The return value is the minimum of the signed distance function between the neutral
+line</p>
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="pytools.calculations.VariableInfo">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pytools.calculations.</span></span><span class="sig-name descname"><span class="pre">VariableInfo</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data_array</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">units</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">latex</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">latexunits</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.VariableInfo" title="Link to this definition"></a></dt>
+<dd><p>A class/struct for holding variable info. This includes the variable data in array form, the name and the units.
+Variable info is in: data, name, units.</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">LIST</span> <span class="n">VARIABLES</span> <span class="n">IN</span> <span class="n">VARIBLE</span> <span class="n">INFO</span><span class="p">:</span>
+<span class="n">data</span>              <span class="n">Data</span> <span class="n">of</span> <span class="n">the</span> <span class="n">variable</span> <span class="p">(</span><span class="n">array</span> <span class="nb">list</span><span class="p">)</span>
+<span class="n">name</span>              <span class="n">Name</span> <span class="n">of</span> <span class="n">the</span> <span class="n">variable</span>
+<span class="n">units</span>             <span class="n">Units</span> <span class="n">of</span> <span class="n">the</span> <span class="n">variable</span>
+<span class="n">latex</span>             <span class="n">Name</span> <span class="n">of</span> <span class="n">the</span> <span class="n">variable</span> <span class="ow">in</span> <span class="n">LaTeX</span>
+<span class="n">latexunits</span>        <span class="n">Units</span> <span class="n">of</span> <span class="n">the</span> <span class="n">variable</span> <span class="ow">in</span> <span class="n">LaTeX</span>
+</pre></div>
+</div>
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.calculations.VariableInfo.get_scaled_units">
+<span class="sig-name descname"><span class="pre">get_scaled_units</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vscale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">env</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'EarthSpace'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manualDict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.VariableInfo.get_scaled_units" title="Link to this definition"></a></dt>
+<dd><p>Return scaling metadata</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>env</strong> – A string to choose the scaling dictionary [default: EarthSpace]</p></li>
+<li><p><strong>manualDict</strong> – a dictionary of {units : {scalingparams}}; used to update the included dictionary</p></li>
+<li><p><strong>vscale</strong> – float, factor to scale the variable with</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>(norming factor, scaledUnits, scaledLatexUnits)</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.calculations.VariableInfo.get_scaled_var">
+<span class="sig-name descname"><span class="pre">get_scaled_var</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vscale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">env</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'EarthSpace'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manualDict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.VariableInfo.get_scaled_var" title="Link to this definition"></a></dt>
+<dd><p>Automatically scales the variableinfo data and adjusts the units correspondingly with the
+default dictionaries.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>data</strong> – in case you wish to provide new data array (why, though?)</p></li>
+<li><p><strong>env</strong> – A string to choose the scaling dictionary [default: EarthSpace]</p></li>
+<li><p><strong>manualDict</strong> – a dictionary of {units : {scalingparams}}; used to update the included dictionary</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>self, with scaled units with pre-formatted units included in the varinfo.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.calculations.VariableInfo.get_variable">
+<span class="sig-name descname"><span class="pre">get_variable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">index</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.VariableInfo.get_variable" title="Link to this definition"></a></dt>
+<dd><p>Creates a new variable with identical data but only certain index is included</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>index</strong> – Vector index</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>an edited version of the variable</p>
+</dd>
+</dl>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>E.g. if the data is an array of 3d vectors, get_variable(0) would return the variable with data[:,0] as the data</p>
+</div>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.calculations.cell_time_evolution">
+<span class="sig-prename descclassname"><span class="pre">pytools.calculations.</span></span><span class="sig-name descname"><span class="pre">cell_time_evolution</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vlsvReader_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">variables</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cellids</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">units</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.cell_time_evolution" title="Link to this definition"></a></dt>
+<dd><p>Returns variable data from a time evolution of some certain cell ids</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>vlsvReader_list</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">vlsvfile.VlsvReader</span></code>) – List containing VlsvReaders with a file open</p></li>
+<li><p><strong>variables</strong> – Name of the variables</p></li>
+<li><p><strong>cellids</strong> – List of cell ids</p></li>
+<li><p><strong>units</strong> – List of units for the variables (OPTIONAL)</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>an array containing the data for the time evolution for every cell id</p>
+</dd>
+</dl>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">pytools</span> <span class="k">as</span> <span class="nn">pt</span><span class="p">;</span> <span class="kn">import</span> <span class="nn">pylab</span> <span class="k">as</span> <span class="nn">pl</span>
+<span class="c1"># Example of usage:</span>
+<span class="n">time_data</span> <span class="o">=</span> <span class="n">pt</span><span class="o">.</span><span class="n">calculations</span><span class="o">.</span><span class="n">cell_time_evolution</span><span class="p">(</span> <span class="n">vlsvReader_list</span><span class="o">=</span><span class="p">[</span><span class="n">VlsvReader</span><span class="p">(</span><span class="s2">&quot;bulk.000.vlsv&quot;</span><span class="p">),</span> <span class="n">VlsvReader</span><span class="p">(</span><span class="s2">&quot;bulk.001.vlsv&quot;</span><span class="p">),</span> <span class="n">VlsvReader</span><span class="p">(</span><span class="s2">&quot;bulk.002.vlsv&quot;</span><span class="p">)],</span> <span class="n">variables</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;rho&quot;</span><span class="p">,</span> <span class="s2">&quot;Pressure&quot;</span><span class="p">,</span> <span class="s2">&quot;B&quot;</span><span class="p">],</span> <span class="n">cellids</span><span class="o">=</span><span class="p">[</span><span class="mi">2</span><span class="p">,</span><span class="mi">4</span><span class="p">],</span> <span class="n">units</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;N&quot;</span><span class="p">,</span> <span class="s2">&quot;Pascal&quot;</span><span class="p">,</span> <span class="s2">&quot;T&quot;</span><span class="p">]</span> <span class="p">)</span>
+
+<span class="c1"># Check output</span>
+<span class="n">logging</span><span class="o">.</span><span class="n">info</span> <span class="n">time_data</span>
+
+<span class="c1"># Now plot the results:</span>
+<span class="n">time</span> <span class="o">=</span> <span class="n">time_data</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+<span class="n">rho</span> <span class="o">=</span> <span class="n">time_data</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
+<span class="n">pt</span><span class="o">.</span><span class="n">plot</span><span class="o">.</span><span class="n">plot_variables</span><span class="p">(</span><span class="n">time</span><span class="p">,</span> <span class="n">rho</span><span class="p">)</span>
+<span class="n">pl</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
+
+<span class="c1"># Do post processing:</span>
+<span class="n">rho_data</span> <span class="o">=</span> <span class="n">rho</span><span class="o">.</span><span class="n">data</span>
+<span class="n">non_existing_example_function</span><span class="p">(</span><span class="n">rho_data</span><span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.calculations.cut3d">
+<span class="sig-prename descclassname"><span class="pre">pytools.calculations.</span></span><span class="sig-name descname"><span class="pre">cut3d</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vlsvReader</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xmin</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xmax</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ymin</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ymax</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">zmin</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">zmax</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">variable</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">operator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pass'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trim_array</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.cut3d" title="Link to this definition"></a></dt>
+<dd><p>Retrieves variables for the given 3d cut</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>vlsvReader</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">vlsvfile.VlsvReader</span></code>) – Some VlsvReader with a file open</p></li>
+<li><p><strong>xmin</strong> – The minimum x coordinate of the 2d cut</p></li>
+<li><p><strong>xmax</strong> – The maximum x coordinate of the 2d cut</p></li>
+<li><p><strong>ymin</strong> – The minimum y coordinate of the 2d cut</p></li>
+<li><p><strong>ymax</strong> – The maximum y coordinate of the 2d cut</p></li>
+<li><p><strong>zmin</strong> – The minimum z coordinate of the 2d cut</p></li>
+<li><p><strong>zmax</strong> – The maximum z coordinate of the 2d cut</p></li>
+<li><p><strong>variable</strong> – Some variable to read from the vlsv file</p></li>
+<li><p><strong>operator</strong> – The variable operator</p></li>
+<li><p><strong>trim_array</strong> – If true, shapes the array into an array with minimum amount of dimensions, e.g. if the cut is zmax-zmin=0 then this will return a 2d array</p></li>
+</ul>
+</dd>
+</dl>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">Example</span><span class="p">:</span>
+<span class="kn">import</span> <span class="nn">pytools</span> <span class="k">as</span> <span class="nn">pt</span>
+<span class="n">f</span> <span class="o">=</span> <span class="n">pt</span><span class="o">.</span><span class="n">vlsvfile</span><span class="o">.</span><span class="n">VlsvReader</span><span class="p">(</span><span class="s1">&#39;example.vlsv&#39;</span><span class="p">)</span>
+<span class="n">three_cut</span> <span class="o">=</span> <span class="n">pt</span><span class="o">.</span><span class="n">calculations</span><span class="o">.</span><span class="n">cut3d</span><span class="p">(</span> <span class="n">vlsvReader</span><span class="o">=</span><span class="n">f</span><span class="p">,</span> <span class="n">xmin</span><span class="o">=</span><span class="mf">1e6</span><span class="p">,</span> <span class="n">xmax</span><span class="o">=</span><span class="mf">4e6</span><span class="p">,</span> <span class="n">ymin</span><span class="o">=</span><span class="mf">1e6</span><span class="p">,</span> <span class="n">xmax</span><span class="o">=</span><span class="mf">4e6</span><span class="p">,</span> <span class="n">zmin</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">zmax</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">variable</span><span class="o">=</span><span class="s2">&quot;rho&quot;</span> <span class="p">)</span>
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
+<span class="c1"># Now three_cut is a three-dimensional array (x,y,z), but we can transform it into a 2-d array (x,y) with:</span>
+<span class="n">dimensions</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">shape</span><span class="p">(</span> <span class="n">three_cut</span> <span class="p">)</span>
+<span class="n">two_cut</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span> <span class="n">three_cut</span><span class="p">,</span> <span class="n">dimensions</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="mi">2</span><span class="p">]</span> <span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.calculations.cut_through">
+<span class="sig-prename descclassname"><span class="pre">pytools.calculations.</span></span><span class="sig-name descname"><span class="pre">cut_through</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vlsvReader</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">point1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">point2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.cut_through" title="Link to this definition"></a></dt>
+<dd><p>Returns cell ids and distances from point 1 for every cell in a line between given point1 and point2</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>vlsvReader</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">vlsvfile.VlsvReader</span></code>) – Some open VlsvReader</p></li>
+<li><p><strong>point1</strong> – The starting point of a cut-through line</p></li>
+<li><p><strong>point2</strong> – The ending point of a cut-through line</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>an array containing cell ids, coordinates and distances in the following format: [cell ids, distances, coordinates]. NB. Last cellid is a duplicate.</p>
+</dd>
+</dl>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">Example</span><span class="p">:</span>
+<span class="n">vlsvReader</span> <span class="o">=</span> <span class="n">VlsvReader</span><span class="p">(</span><span class="s2">&quot;testfile.vlsv&quot;</span><span class="p">)</span>
+<span class="n">cut_through</span> <span class="o">=</span> <span class="n">cut_through</span><span class="p">(</span><span class="n">vlsvReader</span><span class="p">,</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">2</span><span class="p">,</span><span class="mf">5e6</span><span class="p">,</span><span class="mi">0</span><span class="p">])</span>
+<span class="n">cellids</span> <span class="o">=</span> <span class="n">cut_through</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+<span class="n">distances</span> <span class="o">=</span> <span class="n">cut_through</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+<span class="n">logging</span><span class="o">.</span><span class="n">info</span> <span class="s2">&quot;Cell ids: &quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">cellids</span><span class="p">)</span>
+<span class="n">logging</span><span class="o">.</span><span class="n">info</span> <span class="s2">&quot;Distance from point 1 for every cell: &quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">distances</span><span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.calculations.cut_through_curve">
+<span class="sig-prename descclassname"><span class="pre">pytools.calculations.</span></span><span class="sig-name descname"><span class="pre">cut_through_curve</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vlsvReader</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">curve</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.cut_through_curve" title="Link to this definition"></a></dt>
+<dd><p>Returns cell ids and distances from point 1 for every cell in a line between given point1 and point2</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>vlsvReader</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">vlsvfile.VlsvReader</span></code>) – Some open VlsvReader</p></li>
+<li><p><strong>point1</strong> – The starting point of a cut-through line</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>an array containing cell ids, edge distances, and the coordinates of edges in the following format: [cell ids, distances, coordinates]. NB. Last cellid is a duplicate.</p>
+</dd>
+</dl>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">Example</span><span class="p">:</span>
+<span class="n">vlsvReader</span> <span class="o">=</span> <span class="n">VlsvReader</span><span class="p">(</span><span class="s2">&quot;testfile.vlsv&quot;</span><span class="p">)</span>
+<span class="n">cut_through_curve</span> <span class="o">=</span> <span class="n">cut_through</span><span class="p">(</span><span class="n">vlsvReader</span><span class="p">,</span> <span class="p">[[</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">2</span><span class="p">,</span><span class="mf">5e6</span><span class="p">,</span><span class="mi">0</span><span class="p">]])</span>
+<span class="n">cellids</span> <span class="o">=</span> <span class="n">cut_through</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+<span class="n">distances</span> <span class="o">=</span> <span class="n">cut_through</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+<span class="n">logging</span><span class="o">.</span><span class="n">info</span> <span class="s2">&quot;Cell ids: &quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">cellids</span><span class="p">)</span>
+<span class="n">logging</span><span class="o">.</span><span class="n">info</span> <span class="s2">&quot;Distance from point 1 for every cell: &quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">distances</span><span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.calculations.cut_through_step">
+<span class="sig-prename descclassname"><span class="pre">pytools.calculations.</span></span><span class="sig-name descname"><span class="pre">cut_through_step</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vlsvReader</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">point1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">point2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.cut_through_step" title="Link to this definition"></a></dt>
+<dd><p>Returns cell ids and distances from point 1 to point 2, returning not every cell in a line
+but rather the amount of cells which corresponds with the largest axis-aligned component of the line.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>vlsvReader</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">vlsvfile.VlsvReader</span></code>) – Some open VlsvReader</p></li>
+<li><p><strong>point1</strong> – The starting point of a cut-through line</p></li>
+<li><p><strong>point2</strong> – The ending point of a cut-through line</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>an array containing cell ids, coordinates and distances in the following format: [cell ids, distances, coordinates]</p>
+</dd>
+</dl>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">Example</span><span class="p">:</span>
+<span class="n">vlsvReader</span> <span class="o">=</span> <span class="n">VlsvReader</span><span class="p">(</span><span class="s2">&quot;testfile.vlsv&quot;</span><span class="p">)</span>
+<span class="n">cut_through</span> <span class="o">=</span> <span class="n">cut_through_step</span><span class="p">(</span><span class="n">vlsvReader</span><span class="p">,</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">2</span><span class="p">,</span><span class="mf">5e6</span><span class="p">,</span><span class="mi">0</span><span class="p">])</span>
+<span class="n">cellids</span> <span class="o">=</span> <span class="n">cut_through</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+<span class="n">distances</span> <span class="o">=</span> <span class="n">cut_through</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+<span class="n">logging</span><span class="o">.</span><span class="n">info</span> <span class="s2">&quot;Cell ids: &quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">cellids</span><span class="p">)</span>
+<span class="n">logging</span><span class="o">.</span><span class="n">info</span> <span class="s2">&quot;Distance from point 1 for every cell: &quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">distances</span><span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.calculations.dynamic_field_tracer">
+<span class="sig-prename descclassname"><span class="pre">pytools.calculations.</span></span><span class="sig-name descname"><span class="pre">dynamic_field_tracer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vlsvReader_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">x0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_iterations</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dx</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.dynamic_field_tracer" title="Link to this definition"></a></dt>
+<dd><p>Field tracer in a dynamic time frame</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>vlsvReader_list</strong> – List of vlsv readers</p></li>
+<li><p><strong>x0</strong> – The starting point for the streamlines</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.calculations.epsilon_M">
+<span class="sig-prename descclassname"><span class="pre">pytools.calculations.</span></span><span class="sig-name descname"><span class="pre">epsilon_M</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">f</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cell</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'proton'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">m</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.67262192369e-27</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bulk</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">B</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'bimaxwellian'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">normorder</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">norm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">threshold</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dummy</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.epsilon_M" title="Link to this definition"></a></dt>
+<dd><p>Calculates the ‘non-maxwellianity’ parameter for a distribution function f_i and its corresponding Maxwellian g_M.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>f</strong> – VlsvReader containing VDF data</p></li>
+<li><p><strong>cell</strong> – CellID for the queried cell</p></li>
+</ul>
+</dd>
+<dt class="field-even">Kword pop<span class="colon">:</span></dt>
+<dd class="field-even"><p>Population to calculate the parameter for</p>
+</dd>
+<dt class="field-odd">Kword m<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Species mass (default: m_p)</p>
+</dd>
+<dt class="field-even">Kword bulk<span class="colon">:</span></dt>
+<dd class="field-even"><p>Bulk file name to use for moments (if available and needed)</p>
+</dd>
+<dt class="field-odd">Kword B<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Optional, user-given magnetic field vector for a bimaxwellian model distribution</p>
+</dd>
+<dt class="field-even">Kword model<span class="colon">:</span></dt>
+<dd class="field-even"><p>VDF model to be used. Available models “maxwellian”, “bimaxwellian” (default)</p>
+</dd>
+<dt class="field-odd">Kword normorder<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Norm used for model-data distance measure (default: 1)</p>
+</dd>
+<dt class="field-even">Kword norm<span class="colon">:</span></dt>
+<dd class="field-even"><p>Constant norm (default 2, see below)</p>
+</dd>
+<dt class="field-odd">Kword threshold<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Disregard vspace cells under this threshold [0]</p>
+</dd>
+<dt class="field-even">Kword dummy<span class="colon">:</span></dt>
+<dd class="field-even"><p>If not None, generate dummy data for e.g. integration.</p>
+</dd>
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>scalar, non-Maxwellianity parameter for given model and norm</p>
+</dd>
+</dl>
+<p>The definition is given by Graham et al. (2021):
+(1/2n) * integral(|f_i - g_M|) d^3v</p>
+<p>valued between 0 (bi-Maxwellian) and 1 (complete deviation from a bi-Maxwellian).</p>
+<p>NOTE that this is different to the definition by Greco et al. (2012):
+(1/n) * sqrt(integral((f_i - g_M)^2) d^3v)</p>
+<p>examples comparing these two definitions can be found in Settino et al. (2021).</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.calculations.fourier">
+<span class="sig-prename descclassname"><span class="pre">pytools.calculations.</span></span><span class="sig-name descname"><span class="pre">fourier</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">t</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">kaiserwindowparameter</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.fourier" title="Link to this definition"></a></dt>
+<dd><p>Function for returning fourier series and frequencies of some given arrays t and y</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>t</strong> – Time</p></li>
+<li><p><strong>y</strong> – Some variable data</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>the frequencies, new time variables and frequencies</p>
+</dd>
+</dl>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>return format: [FFT, frequencies, t, y]</p>
+</div>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>t must have a constant time stepping</p>
+</div>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">Example</span> <span class="n">usage</span><span class="p">:</span>
+<span class="n">fourier_data</span> <span class="o">=</span> <span class="n">fourier</span><span class="p">(</span> <span class="n">t</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">500</span><span class="p">,</span><span class="mf">0.5</span><span class="p">),</span> <span class="n">y</span><span class="o">=</span><span class="n">rho_data</span><span class="p">,</span> <span class="n">kaiserwindowparameter</span><span class="o">=</span><span class="mi">14</span> <span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.calculations.gyrophase_angles_from_file">
+<span class="sig-prename descclassname"><span class="pre">pytools.calculations.</span></span><span class="sig-name descname"><span class="pre">gyrophase_angles_from_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vlsvReader</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cellid</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.gyrophase_angles_from_file" title="Link to this definition"></a></dt>
+<dd><p>Calculates the gyrophase angle angle distribution for a given cell with a given file
+:param vlsvReader:        Some VlsvReader class with a file open
+:type vlsvReader:         <code class="xref py py-class docutils literal notranslate"><span class="pre">vlsvfile.VlsvReader</span></code>
+:param cellid:            The cell id whose gyrophase angle the user wants NOTE: The cell id must have a velocity distribution!
+:returns: gyrophase angles and avgs [gyro_angles, avgs]</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span>
+</pre></div>
+</div>
+<p># Example usage:
+vlsvReader = VlsvReader(“fullf.0001.vlsv”)
+result = gyrophase_angles_from_file( vlsvReader=vlsvReader, cellid=1924)
+# Plot the data
+import pylab as pl
+pl.hist(result[0].data, weights=result[1].data, bins=100, log=False)</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.calculations.lineout">
+<span class="sig-prename descclassname"><span class="pre">pytools.calculations.</span></span><span class="sig-name descname"><span class="pre">lineout</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vlsvReader</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">point1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">point2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">variable</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">operator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pass'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interpolation_order</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">points</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.lineout" title="Link to this definition"></a></dt>
+<dd><p>Returns a line cut-through from a given VLSV file for distance, coordinates and variable values. The main difference between this and cut_through is that this function interpolates a given variable.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>vlsvReader</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">vlsvfile.VlsvReader</span></code>) – Some open VlsvReader</p></li>
+<li><p><strong>point1</strong> – The starting point of a cut-through line</p></li>
+<li><p><strong>point2</strong> – The ending point of a cut-through line</p></li>
+<li><p><strong>variable</strong> – Variable to return</p></li>
+<li><p><strong>operator</strong> – The operator for the variable, for example “x” for x-component or “magnitude” for magnitude</p></li>
+<li><p><strong>interpolation_order</strong> – Order of interpolation (0 or 1), defaults to 1</p></li>
+<li><p><strong>points</strong> – Number of points to return</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A tuple with output: (distance, coordinates, variable_values)</p>
+</dd>
+</dl>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># Example:</span>
+<span class="kn">import</span> <span class="nn">pytools</span> <span class="k">as</span> <span class="nn">pt</span> <span class="c1"># import analysator</span>
+
+<span class="n">vlsvReader</span> <span class="o">=</span> <span class="n">pt</span><span class="o">.</span><span class="n">vlsvfile</span><span class="o">.</span><span class="n">VlsvReader</span><span class="p">(</span><span class="s2">&quot;testfile.vlsv&quot;</span><span class="p">)</span> <span class="c1"># Open a vlsv file</span>
+<span class="n">lineout_rho</span> <span class="o">=</span> <span class="n">pt</span><span class="o">.</span><span class="n">calculations</span><span class="o">.</span><span class="n">lineout</span><span class="p">(</span> <span class="n">vlsvReader</span><span class="o">=</span><span class="n">vlsvReader</span><span class="p">,</span> <span class="n">point1</span><span class="o">=</span><span class="p">[</span><span class="mf">1.0e5</span><span class="p">,</span> <span class="mf">1.0e6</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">point2</span><span class="o">=</span><span class="p">[</span><span class="mf">2.0e5</span><span class="p">,</span> <span class="mf">2.0e6</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">variable</span><span class="o">=</span><span class="s2">&quot;rho&quot;</span><span class="p">,</span> <span class="n">interpolation_order</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">points</span><span class="o">=</span><span class="mi">100</span> <span class="p">)</span>
+<span class="n">distance</span> <span class="o">=</span> <span class="n">lineout_rho</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+<span class="n">coordinates</span> <span class="o">=</span> <span class="n">lineout_rho</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+<span class="n">values</span> <span class="o">=</span> <span class="n">lineout_rho</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.calculations.pitch_angles">
+<span class="sig-prename descclassname"><span class="pre">pytools.calculations.</span></span><span class="sig-name descname"><span class="pre">pitch_angles</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vlsvReader</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cellid</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nbins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filedir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">step</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outputdir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outputfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cosine</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">plasmaframe</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vcut</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vcutmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'proton'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.pitch_angles" title="Link to this definition"></a></dt>
+<dd><p>Calculates the pitch angle distribution for a given cell</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>vlsvReader</strong> – Some VlsvReader class with a file open. Can be overriden by keywords.</p></li>
+<li><p><strong>cellid</strong> – The cell id whose pitch angle the user wants
+NOTE: The cell id must have a velocity distribution!</p></li>
+</ul>
+</dd>
+<dt class="field-even">Kword filename<span class="colon">:</span></dt>
+<dd class="field-even"><p>path to .vlsv file to use for input.</p>
+</dd>
+<dt class="field-odd">Kword filedir<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Optionally provide directory where files are located and use step for bulk file name</p>
+</dd>
+<dt class="field-even">Kword step<span class="colon">:</span></dt>
+<dd class="field-even"><p>output step index, used for constructing output (and possibly input) filename</p>
+</dd>
+<dt class="field-odd">Kword nbins<span class="colon">:</span></dt>
+<dd class="field-odd"><p>How many bins to use for the distribution</p>
+</dd>
+<dt class="field-even">Kword cosine<span class="colon">:</span></dt>
+<dd class="field-even"><p>True if returning the pitch angles as a cosine(alpha) plot [-1,1].
+If false, returns as pitch angle in degrees [0,180].</p>
+</dd>
+<dt class="field-odd">Kword plasmaframe<span class="colon">:</span></dt>
+<dd class="field-odd"><p>True if the user wants to get the pitch angle distribution
+in the plasma frame (for this population).
+If set to a string, will try to use the string as a variable for
+the frame to transform into.
+If set to a 3-element vector, will use that frame instead.</p>
+</dd>
+<dt class="field-even">Kword vcut<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set to True to ignore velocity cells below 2x the thermal speed.
+If set to a number, will use that velocity in m/s instead.</p>
+</dd>
+<dt class="field-odd">Kword vcutmax<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set to True to ignore velocity cells above 2x the thermal speed.
+If set to a number, will use that velocity in m/s instead.</p>
+</dd>
+<dt class="field-even">Kword outputdir<span class="colon">:</span></dt>
+<dd class="field-even"><p>Optional (recommended) method to save results to a file in the given directory.
+If directory does not exist, it will be created. Filenames within directory are
+generated automatically.</p>
+</dd>
+<dt class="field-odd">Kword outputfile<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Provide exact output file name (including complete path)</p>
+</dd>
+<dt class="field-even">Kword pop<span class="colon">:</span></dt>
+<dd class="field-even"><p>Active population, defaults to proton (avgs)</p>
+</dd>
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>pitch angles and avgs [pitch_angles, avgs]</p>
+</dd>
+</dl>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># Example usage:</span>
+<span class="n">vlsvReader</span> <span class="o">=</span> <span class="n">VlsvReader</span><span class="p">(</span><span class="s2">&quot;restart.0000798.vlsv&quot;</span><span class="p">)</span>
+<span class="n">result</span> <span class="o">=</span> <span class="n">pitch_angles</span><span class="p">(</span> <span class="n">vlsvReader</span><span class="o">=</span><span class="n">vlsvReader</span><span class="p">,</span> <span class="mi">1924</span><span class="p">,</span> <span class="n">cosine</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+                     <span class="n">plasmaframe</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">outputdir</span><span class="o">=</span><span class="s2">&quot;/wrk/username/pitchangledirectory/&quot;</span> <span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.calculations.static_field_tracer">
+<span class="sig-prename descclassname"><span class="pre">pytools.calculations.</span></span><span class="sig-name descname"><span class="pre">static_field_tracer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vlsvReader</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">x0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_iterations</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dx</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'+'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bvar</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'B'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">centering</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'default'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">boundary_inner</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-1</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.static_field_tracer" title="Link to this definition"></a></dt>
+<dd><p>Field tracer in a static frame</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>vlsvReader</strong> – An open vlsv file</p></li>
+<li><p><strong>x</strong> – Starting point for the field trace</p></li>
+<li><p><strong>max_iterations</strong> – The maximum amount of iteractions before the algorithm stops</p></li>
+<li><p><strong>dx</strong> – One iteration step length</p></li>
+<li><p><strong>direction</strong> – ‘+’ or ‘-’ or ‘+-’ Follow field in the plus direction or minus direction</p></li>
+<li><p><strong>bvar</strong> – String, variable name to trace [default ‘B’]</p></li>
+<li><p><strong>centering</strong> – String, variable centering: ‘face’, ‘volume’, ‘node’ [defaults to ‘face’]</p></li>
+<li><p><strong>boundary_inner</strong> – Float, stop propagation if closer to origin than this value [default -1]</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>List of coordinates</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.calculations.static_field_tracer_3d">
+<span class="sig-prename descclassname"><span class="pre">pytools.calculations.</span></span><span class="sig-name descname"><span class="pre">static_field_tracer_3d</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vlsvReader</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seed_coords</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_iterations</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dx</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction='+'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">grid_var='vg_b_vol'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop_condition=&lt;function</span> <span class="pre">default_stopping_condition&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">centering=None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.static_field_tracer_3d" title="Link to this definition"></a></dt>
+<dd><p>static_field_tracer_3d() integrates along the (static) field-grid vector field to calculate a final position. 
+Code uses forward Euler method to conduct the tracing.
+Based on Analysator’s static_field_tracer()
+:Inputs:</p>
+<blockquote>
+<div><p>param vlsvReader:      A vlsvReader object (~an open .vlsv file)</p>
+<dl class="simple">
+<dt>param coord_list:      a list of 3-element array-like initial coordinates [ [x1,y1,z1], [x2,y2,z2], … ] ::</dt><dd><p>if considering just a single starting point, the code accepts a 3-element array-like object [x1,y1,z1]</p>
+</dd>
+</dl>
+<p>param max_iterations:  The maximum number of iterations (int) before the algorithm stops. Total traced length is dx*max_iterations</p>
+<p>param dx:              One iteration step length [meters] (ex. dx=1e4 for typical applications)</p>
+<p>keyword direction:     ‘+’ or ‘-’ or ‘+-’ Follow field in the plus direction, minus direction, or both</p>
+<dl>
+<dt>keyword grid_var:      Variable to be traced (A string)</dt><dd><dl>
+<dt>options include:</dt><dd><dl>
+<dt>grid_var = some string</dt><dd><p>grid_var = ‘vg_b_vol’: AMR-grid B-field
+grid_var =’fg_b’: fieldsolver grid B-field, grid_var=’fg_e’: fieldsolver grid E-field
+static_field_tracer_3d() will load the appropriate variable via the vlsvReader object
+NOTE: volumetric variables, with ‘_vol’ suffix, may not work as intended. Use face-centered values: ‘fg_b’, ‘fg_e’ etc.</p>
+</dd>
+<dt>grid_var = some fieldsolver-grid (“fg”) array.          dimensions [dimx,dimy,dimz,3]</dt><dd><p>ex. fg = vlsvobj.read_variable(‘fg_b’)
+field grid data is already loaded externally using read_variable() method (see vlsvreader.py).
+If fg keyword is set this way, the input vlsvReader is only referred to for metadata (esp. grid dimensions)</p>
+<blockquote>
+<div><p>keyword stop_condition: Boolean array (seed_coords.shape[0],)</p>
+</div></blockquote>
+</dd>
+</dl>
+</dd>
+</dl>
+<p>Determine when the iteration stop, for the vg trace only
+If not specified, it will always be True for each seed points.
+eg. def my_stop(points):</p>
+<blockquote>
+<div><p>distances = np.linalg.norm(points[:,:],axis = 1)
+return (distances &lt;= lower_bound) | (distances &gt;= upper_bound)</p>
+</div></blockquote>
+</dd>
+</dl>
+</div></blockquote>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>points_traced — a 3d numpy array [len(seed_coords),max_iterations (or 2*max_iterations-1 for ‘+-‘),3]
+Non-traced sections (e.g. iterations after reaching outer boundaries) filled with np.nan</p>
+</dd>
+</dl>
+<dl class="simple">
+<dt>keyword centering:     Set to a string (‘face’ or ‘edge’) indicating whether the fg variable is face- or edge-centered</dt><dd><p>If keyword fg == ‘fg_b’, then centering = ‘face’ (overriding input)
+If keyword fg == ‘fg_e’, then centering = ‘edge’ (overriding input)</p>
+</dd>
+<dt>EXAMPLE:            vlsvobj = pytools.vlsvfile.VlsvReader(vlsvfile) </dt><dd><p>fg_b = vlsvobj.read_variable(‘fg_b’)
+traces = static_field_tracer_3d( vlsvobj, [[5e7,0,0], [0,0,5e7]], 10, 1e5, direction=’+’, fg = fg_b )</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.calculations.themis_observation_from_file">
+<span class="sig-prename descclassname"><span class="pre">pytools.calculations.</span></span><span class="sig-name descname"><span class="pre">themis_observation_from_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vlsvReader</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cellid</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">matrix</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">array([[1,</span> <span class="pre">0,</span> <span class="pre">0],</span> <span class="pre">[0,</span> <span class="pre">1,</span> <span class="pre">0],</span> <span class="pre">[0,</span> <span class="pre">0,</span> <span class="pre">1]])</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">countrates</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interpolate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">binOffset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[0.0,</span> <span class="pre">0.0]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'proton'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.themis_observation_from_file" title="Link to this definition"></a></dt>
+<dd><p>Calculates artificial THEMIS EMS observation from the given cell
+:param vlsvReader:        Some VlsvReader class with a file open
+:type vlsvReader:         <code class="xref py py-class docutils literal notranslate"><span class="pre">vlsvfile.VlsvReader</span></code>
+:param cellid:            The cell id where the distribution is supposet to be sampled NOTE: The cell id must have a velocity distribution!
+:param matrix:            Matrix to transform velocities from simulation space into detector space (use simulation_to_spacecraft_frame helper function)
+:param countrates: Transform phase space densities into count rates?
+:param interpolate: interpolate into detector bins?
+:param binOffset: offset bin allocation in (angle, energy) by this amount (used to align polar plots)
+:returns: detector bins angles, energies and counts [bin_thetas,energies,min,max,counts]</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span>
+</pre></div>
+</div>
+<p># Example usage:
+vlsvReader = VlsvReader(“fullf.0001.vlsv”)
+angles, energies, vmin, vmax, values = themis_observation_from_file( vlsvReader=self.vlsvReader, cellid=cellid)
+# plot:
+grid_r, grid_theta = np.meshgrid(energies,angles)
+fig,ax=pl.subplots(subplot_kw=dict(projection=”polar”),figsize=(12,10))
+ax.set_title(“Detector view at cell “ + str(cellid))
+cax = ax.pcolormesh(grid_theta,grid_r,values, norm=matplotlib.colors.LogNorm(vmin=vmin,vmax=vmax))
+pl.show()</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.calculations.themis_plot_detector">
+<span class="sig-prename descclassname"><span class="pre">pytools.calculations.</span></span><span class="sig-name descname"><span class="pre">themis_plot_detector</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vlsvReader</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cellID</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">detector_axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">array([0,</span> <span class="pre">1,</span> <span class="pre">0])</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'proton'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.themis_plot_detector" title="Link to this definition"></a></dt>
+<dd><p>Plots a view of the detector countrates using matplotlib
+:param vlsvReader:        Some VlsvReader class with a file open
+:type vlsvReader:         <code class="xref py py-class docutils literal notranslate"><span class="pre">vlsvfile.VlsvReader</span></code>
+:param cellid:            The cell id where the distribution is supposet to be sampled NOTE: The cell id must have a velocity distribution!
+:param detector_axis:     detector axis direction (note: this is not spacecraft spin axis!)</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.calculations.themis_plot_phasespace_contour">
+<span class="sig-prename descclassname"><span class="pre">pytools.calculations.</span></span><span class="sig-name descname"><span class="pre">themis_plot_phasespace_contour</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vlsvReader</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cellID</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">plane_x</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">array([1.,</span> <span class="pre">0.,</span> <span class="pre">0.])</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">plane_y</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">array([0.,</span> <span class="pre">0.,</span> <span class="pre">1.])</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">smooth</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xlabel</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'Vx'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ylabel</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'Vy'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'proton'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.themis_plot_phasespace_contour" title="Link to this definition"></a></dt>
+<dd><p>Plots a contour view of phasespace, as seen by a themis detector, at the given cellID
+:param vlsvReader:        Some VlsvReader class with a file open
+:type vlsvReader:         <code class="xref py py-class docutils literal notranslate"><span class="pre">vlsvfile.VlsvReader</span></code>
+:param cellid:            The cell id where the distribution is supposet to be sampled NOTE: The cell id must have a velocity distribution!
+:param plane_x and plane_y: x and y direction of the resulting plot plane</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.calculations.themis_plot_phasespace_helistyle">
+<span class="sig-prename descclassname"><span class="pre">pytools.calculations.</span></span><span class="sig-name descname"><span class="pre">themis_plot_phasespace_helistyle</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vlsvReader</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cellID</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">plane_x</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">array([1.,</span> <span class="pre">0.,</span> <span class="pre">0.])</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">plane_y</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">array([0.,</span> <span class="pre">0.,</span> <span class="pre">1.])</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">smooth</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xlabel</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'Vx'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ylabel</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'Vy'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.themis_plot_phasespace_helistyle" title="Link to this definition"></a></dt>
+<dd><p>Plots a view of phasespace, as seen by a themis detector, at the given cellID, in the style that heli likes.
+:param vlsvReader:        Some VlsvReader class with a file open
+:type vlsvReader:         <code class="xref py py-class docutils literal notranslate"><span class="pre">vlsvfile.VlsvReader</span></code>
+:param cellid:            The cell id where the distribution is supposet to be sampled NOTE: The cell id must have a velocity distribution!
+:param smooth:            Smooth re-gridded phasespace before plotting
+:param plane_x and plane_y: x and y direction of the resulting plot plane</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.calculations.vlsv_intpol_file">
+<span class="sig-prename descclassname"><span class="pre">pytools.calculations.</span></span><span class="sig-name descname"><span class="pre">vlsv_intpol_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file_vlsv</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">file_orbit</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">varlist</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">file_output</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.vlsv_intpol_file" title="Link to this definition"></a></dt>
+<dd><p>Writes interpolated values of variables in ascii file
+:param file_vlsv:             VLSV file
+:param file_orbit:            Orbit file (columns: x,y,z or t,x,y,z)
+:param varlist:               Variable list
+:param file_output:           Output ascii file (columns: x,y,z,cellid,var1,var2,var3,…)
+:returns: none</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># Example:</span>
+<span class="kn">import</span> <span class="nn">pytools</span> <span class="k">as</span> <span class="nn">pt</span>
+<span class="n">pt</span><span class="o">.</span><span class="n">calculations</span><span class="o">.</span><span class="n">vlsv_intpol_file</span><span class="p">(</span><span class="s2">&quot;state00040000.vlsv&quot;</span><span class="p">,</span><span class="s2">&quot;orbit.dat&quot;</span><span class="p">,[</span><span class="s2">&quot;cellB&quot;</span><span class="p">,</span><span class="s2">&quot;n_H+sw_ave&quot;</span><span class="p">],</span><span class="s2">&quot;output.dat&quot;</span><span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.calculations.vlsv_intpol_points">
+<span class="sig-prename descclassname"><span class="pre">pytools.calculations.</span></span><span class="sig-name descname"><span class="pre">vlsv_intpol_points</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vlsvReader</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">points</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">varlist</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">operator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pass'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interpolation_order</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.calculations.vlsv_intpol_points" title="Link to this definition"></a></dt>
+<dd><p>Returns interpolated values of variables at given points
+:param vlsvReader:            Some open VlsvReader
+:type vlsvReader:             <code class="xref py py-class docutils literal notranslate"><span class="pre">vlsvfile.VlsvReader</span></code>
+:param points:                Coordinate points
+:param varlist:               Variable list, if empty all variables are got
+:param operator:              The operator for the variable, for example “x” for x-component or “magnitude” for magnitude
+:param interpolation_order:   Order of interpolation (0 or 1), defaults to 1
+:returns: A tuple with output: (coordinates,variable_values,header_string)</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># Example:</span>
+<span class="kn">import</span> <span class="nn">pytools</span> <span class="k">as</span> <span class="nn">pt</span>
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
+<span class="n">f</span><span class="o">=</span><span class="n">pt</span><span class="o">.</span><span class="n">vlsvfile</span><span class="o">.</span><span class="n">VlsvReader</span><span class="p">(</span><span class="n">file_name</span><span class="o">=</span><span class="s2">&quot;state00040000.vlsv&quot;</span><span class="p">)</span>
+<span class="n">mesh_limits</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">get_spatial_mesh_extent</span><span class="p">()</span>
+<span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="n">mesh_limits</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span><span class="n">mesh_limits</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span><span class="mi">100</span><span class="p">)</span> <span class="c1"># points along x-axis</span>
+<span class="n">y</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">x</span><span class="p">))</span>
+<span class="n">z</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">x</span><span class="p">))</span>
+<span class="n">points</span><span class="o">=</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span><span class="p">]))</span><span class="o">.</span><span class="n">transpose</span><span class="p">()</span>
+<span class="n">varlist</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;cellB&quot;</span><span class="p">,</span><span class="s2">&quot;n_H+sw_ave&quot;</span><span class="p">]</span>
+<span class="p">[</span><span class="n">crd</span><span class="p">,</span><span class="n">cellids</span><span class="p">,</span><span class="n">params</span><span class="p">,</span><span class="n">hstr</span><span class="p">]</span><span class="o">=</span><span class="n">pt</span><span class="o">.</span><span class="n">calculations</span><span class="o">.</span><span class="n">vlsv_intpol_points</span><span class="p">(</span><span class="n">f</span><span class="p">,</span><span class="n">points</span><span class="p">,</span><span class="n">varlist</span><span class="p">)</span>
+<span class="n">x</span><span class="o">=</span><span class="n">crd</span><span class="p">[:,</span><span class="mi">0</span><span class="p">]</span>
+<span class="n">y</span><span class="o">=</span><span class="n">crd</span><span class="p">[:,</span><span class="mi">1</span><span class="p">]</span>
+<span class="n">z</span><span class="o">=</span><span class="n">crd</span><span class="p">[:,</span><span class="mi">2</span><span class="p">]</span>
+<span class="n">Bx</span><span class="o">=</span><span class="n">params</span><span class="p">[:,</span><span class="mi">0</span><span class="p">]</span>
+<span class="n">By</span><span class="o">=</span><span class="n">params</span><span class="p">[:,</span><span class="mi">1</span><span class="p">]</span>
+<span class="n">Bz</span><span class="o">=</span><span class="n">params</span><span class="p">[:,</span><span class="mi">2</span><span class="p">]</span>
+<span class="n">n</span><span class="o">=</span><span class="n">params</span><span class="p">[:,</span><span class="mi">3</span><span class="p">]</span>
+</pre></div>
+</div>
+</dd></dl>
+
+</section>
+
+
+           </div>
+          </div>
+          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
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diff --git a/genindex/index.html b/genindex/index.html
new file mode 100644
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--- /dev/null
+++ b/genindex/index.html
@@ -0,0 +1,721 @@
+
+
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../">
+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Index &mdash; analysator  documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
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+    <script src="../_static/js/theme.js"></script>
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+    <link rel="index" title="Index" href="#" />
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+</head>
+
+<body class="wy-body-for-nav"> 
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
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+          
+          
+          <a href="../" class="icon icon-home">
+            analysator
+              <img src="../_static/logo_color.png" class="logo" alt="Logo"/>
+          </a>
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="../search/" method="get">
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
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+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../plot/">plot</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../calculations/">calculations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../vlsvfile/">vlsvfile</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../miscellaneous/">miscellaneous</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../scripts/">scripts</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../about/">Credits</a></li>
+</ul>
+
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+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
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+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+             
+
+<h1 id="index">Index</h1>
+
+<div class="genindex-jumpbox">
+ <a href="#A"><strong>A</strong></a>
+ | <a href="#B"><strong>B</strong></a>
+ | <a href="#C"><strong>C</strong></a>
+ | <a href="#D"><strong>D</strong></a>
+ | <a href="#E"><strong>E</strong></a>
+ | <a href="#F"><strong>F</strong></a>
+ | <a href="#G"><strong>G</strong></a>
+ | <a href="#I"><strong>I</strong></a>
+ | <a href="#L"><strong>L</strong></a>
+ | <a href="#M"><strong>M</strong></a>
+ | <a href="#N"><strong>N</strong></a>
+ | <a href="#O"><strong>O</strong></a>
+ | <a href="#P"><strong>P</strong></a>
+ | <a href="#R"><strong>R</strong></a>
+ | <a href="#S"><strong>S</strong></a>
+ | <a href="#T"><strong>T</strong></a>
+ | <a href="#U"><strong>U</strong></a>
+ | <a href="#V"><strong>V</strong></a>
+ | <a href="#W"><strong>W</strong></a>
+ 
+</div>
+<h2 id="A">A</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../calculations/#pytools.calculations.AMRInterpolator">AMRInterpolator (class in pytools.calculations)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="B">B</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../biot_savart/#biot_savart.b_dip">b_dip() (in module biot_savart)</a>
+</li>
+      <li><a href="../biot_savart/#biot_savart.b_dip_direction">b_dip_direction() (in module biot_savart)</a>
+</li>
+      <li><a href="../biot_savart/#biot_savart.b_dip_magnitude">b_dip_magnitude() (in module biot_savart)</a>
+</li>
+      <li><a href="../biot_savart/#biot_savart.B_ionosphere">B_ionosphere() (in module biot_savart)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../biot_savart/#biot_savart.B_magnetosphere">B_magnetosphere() (in module biot_savart)</a>
+</li>
+      <li>
+    biot_savart
+
+      <ul>
+        <li><a href="../biot_savart/#module-biot_savart">module</a>
+</li>
+      </ul></li>
+      <li><a href="../biot_savart/#biot_savart.biot_savart">biot_savart() (in module biot_savart)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.build_cell_vertices">build_cell_vertices() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="C">C</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../biot_savart/#biot_savart.cartesian_to_spherical">cartesian_to_spherical() (in module biot_savart)</a>
+
+      <ul>
+        <li><a href="../gics/#gics.cartesian_to_spherical">(in module gics)</a>
+</li>
+      </ul></li>
+      <li><a href="../gics/#gics.cartesian_to_spherical_vector">cartesian_to_spherical_vector() (in module gics)</a>
+</li>
+      <li><a href="../calculations/#pytools.calculations.cell_time_evolution">cell_time_evolution() (in module pytools.calculations)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.cellid_has_vdf">cellid_has_vdf() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.check_parameter">check_parameter() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.check_population">check_population() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.check_variable">check_variable() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvWriter.clone_file">clone_file() (pytools.vlsvfile.VlsvWriter method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.construct_velocity_cell_coordinates">construct_velocity_cell_coordinates() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.construct_velocity_cell_nodes">construct_velocity_cell_nodes() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.construct_velocity_cells">construct_velocity_cells() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvWriter.copy_variables">copy_variables() (pytools.vlsvfile.VlsvWriter method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvWriter.copy_variables_list">copy_variables_list() (pytools.vlsvfile.VlsvWriter method)</a>
+</li>
+      <li><a href="../calculations/#pytools.calculations.cut3d">cut3d() (in module pytools.calculations)</a>
+</li>
+      <li><a href="../calculations/#pytools.calculations.cut_through">cut_through() (in module pytools.calculations)</a>
+</li>
+      <li><a href="../calculations/#pytools.calculations.cut_through_curve">cut_through_curve() (in module pytools.calculations)</a>
+</li>
+      <li><a href="../calculations/#pytools.calculations.cut_through_step">cut_through_step() (in module pytools.calculations)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="D">D</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.downsample_fsgrid_subarray">downsample_fsgrid_subarray() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../calculations/#pytools.calculations.dynamic_field_tracer">dynamic_field_tracer() (in module pytools.calculations)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="E">E</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../gics/#gics.E_horizontal">E_horizontal() (in module gics)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../calculations/#pytools.calculations.epsilon_M">epsilon_M() (in module pytools.calculations)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="F">F</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../shue/#shue.f_shue">f_shue() (in module shue)</a>
+</li>
+      <li><a href="../biot_savart/#biot_savart.fac_map">fac_map() (in module biot_savart)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../calculations/#pytools.calculations.fourier">fourier() (in module pytools.calculations)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.fsgrid_array_to_vg">fsgrid_array_to_vg() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="G">G</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_all_variables">get_all_variables() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_amr_level">get_amr_level() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_bbox_fsgrid_slicemap">get_bbox_fsgrid_slicemap() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_bbox_fsgrid_subarray">get_bbox_fsgrid_subarray() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_cell_bbox">get_cell_bbox() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_cell_coordinates">get_cell_coordinates() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_cell_corner_vertices">get_cell_corner_vertices() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_cell_dx">get_cell_dx() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_cell_fsgrid">get_cell_fsgrid() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_cell_fsgrid_slicemap">get_cell_fsgrid_slicemap() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_cell_fsgrid_subarray">get_cell_fsgrid_subarray() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_cell_indices">get_cell_indices() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_cell_neighbor">get_cell_neighbor() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_cellid">get_cellid() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_cellid_locations">get_cellid_locations() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_cellid_with_vdf">get_cellid_with_vdf() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_config">get_config() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_config_string">get_config_string() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_dual">get_dual() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_duals">get_duals() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_fsgrid_cell_size">get_fsgrid_cell_size() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_fsgrid_coordinates">get_fsgrid_coordinates() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_fsgrid_indices">get_fsgrid_indices() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_fsgrid_mesh_extent">get_fsgrid_mesh_extent() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_fsgrid_mesh_size">get_fsgrid_mesh_size() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_fsgrid_slice_indices">get_fsgrid_slice_indices() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_ionosphere_element_coords">get_ionosphere_element_coords() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_ionosphere_element_corners">get_ionosphere_element_corners() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_ionosphere_latlon_coords">get_ionosphere_latlon_coords() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_ionosphere_mesh_area">get_ionosphere_mesh_area() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_ionosphere_mesh_size">get_ionosphere_mesh_size() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_ionosphere_node_coords">get_ionosphere_node_coords() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_max_refinement_level">get_max_refinement_level() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_precipitation_centre_energy">get_precipitation_centre_energy() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../calculations/#pytools.calculations.VariableInfo.get_scaled_units">get_scaled_units() (pytools.calculations.VariableInfo method)</a>
+</li>
+      <li><a href="../calculations/#pytools.calculations.VariableInfo.get_scaled_var">get_scaled_var() (pytools.calculations.VariableInfo method)</a>
+</li>
+      <li><a href="../miscellaneous/#pytools.miscellaneous.get_sorted_file_names">get_sorted_file_names() (in module pytools.miscellaneous)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_spatial_block_size">get_spatial_block_size() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_spatial_mesh_extent">get_spatial_mesh_extent() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_spatial_mesh_size">get_spatial_mesh_size() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_unique_cellids">get_unique_cellids() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../calculations/#pytools.calculations.VariableInfo.get_variable">get_variable() (pytools.calculations.VariableInfo method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_velocity_block_coordinates">get_velocity_block_coordinates() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_velocity_block_indices">get_velocity_block_indices() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_velocity_block_size">get_velocity_block_size() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_velocity_blocks">get_velocity_blocks() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_velocity_cell_coordinates">get_velocity_cell_coordinates() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_velocity_cell_ids">get_velocity_cell_ids() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_velocity_mesh_dv">get_velocity_mesh_dv() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_velocity_mesh_extent">get_velocity_mesh_extent() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_velocity_mesh_size">get_velocity_mesh_size() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_vertex_coordinates_from_indices">get_vertex_coordinates_from_indices() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.get_vertex_indices">get_vertex_indices() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li>
+    gics
+
+      <ul>
+        <li><a href="../gics/#module-gics">module</a>
+</li>
+      </ul></li>
+      <li><a href="../biot_savart/#biot_savart.graded_mesh">graded_mesh() (in module biot_savart)</a>
+</li>
+      <li><a href="../calculations/#pytools.calculations.gyrophase_angles_from_file">gyrophase_angles_from_file() (in module pytools.calculations)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="I">I</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../biot_savart/#biot_savart.integrate_biot_savart">integrate_biot_savart() (in module biot_savart)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="L">L</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../calculations/#pytools.calculations.lineout">lineout() (in module pytools.calculations)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvParticles.list">list() (pytools.vlsvfile.VlsvParticles method)</a>
+
+      <ul>
+        <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.list">(pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../calculations/#pytools.calculations.LMN_null_lines_FOTE">LMN_null_lines_FOTE() (in module pytools.calculations)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="M">M</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li>
+    magnetopause2d
+
+      <ul>
+        <li><a href="../magnetopause2d/#module-magnetopause2d">module</a>
+</li>
+      </ul></li>
+      <li>
+    magnetopause3d
+
+      <ul>
+        <li><a href="../magnetopause3d/#module-magnetopause3d">module</a>
+</li>
+      </ul></li>
+      <li><a href="../magnetopause3d/#magnetopause3d.make_surface">make_surface() (in module magnetopause3d)</a>
+</li>
+      <li><a href="../biot_savart/#biot_savart.mkdir_path">mkdir_path() (in module biot_savart)</a>
+
+      <ul>
+        <li><a href="../gics/#gics.mkdir_path">(in module gics)</a>
+</li>
+      </ul></li>
+      <li>
+    module
+
+      <ul>
+        <li><a href="../biot_savart/#module-biot_savart">biot_savart</a>
+</li>
+        <li><a href="../gics/#module-gics">gics</a>
+</li>
+        <li><a href="../magnetopause2d/#module-magnetopause2d">magnetopause2d</a>
+</li>
+        <li><a href="../magnetopause3d/#module-magnetopause3d">magnetopause3d</a>
+</li>
+        <li><a href="../#module-pytools">pytools</a>
+</li>
+        <li><a href="../calculations/#module-pytools.calculations">pytools.calculations</a>
+</li>
+        <li><a href="../miscellaneous/#module-pytools.miscellaneous">pytools.miscellaneous</a>
+</li>
+        <li><a href="../plot/#module-pytools.plot">pytools.plot</a>
+</li>
+        <li><a href="../vlsvfile/#module-pytools.vlsvfile">pytools.vlsvfile</a>
+</li>
+        <li><a href="../shue/#module-shue">shue</a>
+</li>
+        <li><a href="../tsyganenko/#module-tsyganenko">tsyganenko</a>
+</li>
+      </ul></li>
+  </ul></td>
+</tr></table>
+
+<h2 id="N">N</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../biot_savart/#biot_savart.nearest_node_index">nearest_node_index() (in module biot_savart)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="O">O</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../miscellaneous/#pytools.miscellaneous.oblique_shock">oblique_shock() (in module pytools.miscellaneous)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.optimize_clear_fileindex_for_cellid">optimize_clear_fileindex_for_cellid() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.optimize_clear_fileindex_for_cellid_blocks">optimize_clear_fileindex_for_cellid_blocks() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.optimize_close_file">optimize_close_file() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.optimize_open_file">optimize_open_file() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="P">P</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../calculations/#pytools.calculations.pitch_angles">pitch_angles() (in module pytools.calculations)</a>
+</li>
+      <li><a href="../plot/#pytools.plot.plot_colormap">plot_colormap() (in module pytools.plot)</a>
+</li>
+      <li><a href="../plot/#pytools.plot.plot_colormap3dslice">plot_colormap3dslice() (in module pytools.plot)</a>
+</li>
+      <li><a href="../plot/#pytools.plot.plot_ionosphere">plot_ionosphere() (in module pytools.plot)</a>
+</li>
+      <li><a href="../plot/#pytools.plot.plot_isosurface">plot_isosurface() (in module pytools.plot)</a>
+</li>
+      <li><a href="../plot/#pytools.plot.plot_multiple_variables">plot_multiple_variables() (in module pytools.plot)</a>
+</li>
+      <li><a href="../plot/#pytools.plot.plot_neutral_sheet">plot_neutral_sheet() (in module pytools.plot)</a>
+</li>
+      <li><a href="../miscellaneous/#pytools.miscellaneous.plot_rankine">plot_rankine() (in module pytools.miscellaneous)</a>
+</li>
+      <li><a href="../plot/#pytools.plot.plot_threeslice">plot_threeslice() (in module pytools.plot)</a>
+</li>
+      <li><a href="../plot/#pytools.plot.plot_variables">plot_variables() (in module pytools.plot)</a>
+</li>
+      <li><a href="../plot/#pytools.plot.plot_vdf">plot_vdf() (in module pytools.plot)</a>
+</li>
+      <li><a href="../plot/#pytools.plot.plot_vdf_profiles">plot_vdf_profiles() (in module pytools.plot)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../plot/#pytools.plot.plot_vdfdiff">plot_vdfdiff() (in module pytools.plot)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.print_config">print_config() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.print_version">print_version() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li>
+    pytools
+
+      <ul>
+        <li><a href="../#module-pytools">module</a>
+</li>
+      </ul></li>
+      <li>
+    pytools.calculations
+
+      <ul>
+        <li><a href="../calculations/#module-pytools.calculations">module</a>
+</li>
+      </ul></li>
+      <li>
+    pytools.miscellaneous
+
+      <ul>
+        <li><a href="../miscellaneous/#module-pytools.miscellaneous">module</a>
+</li>
+      </ul></li>
+      <li>
+    pytools.plot
+
+      <ul>
+        <li><a href="../plot/#module-pytools.plot">module</a>
+</li>
+      </ul></li>
+      <li>
+    pytools.vlsvfile
+
+      <ul>
+        <li><a href="../vlsvfile/#module-pytools.vlsvfile">module</a>
+</li>
+      </ul></li>
+  </ul></td>
+</tr></table>
+
+<h2 id="R">R</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.read">read() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.read_attribute">read_attribute() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.read_blocks">read_blocks() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.read_fsgrid_variable">read_fsgrid_variable() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.read_fsgrid_variable_cellid">read_fsgrid_variable_cellid() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.read_interpolated_fsgrid_variable">read_interpolated_fsgrid_variable() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.read_interpolated_ionosphere_variable">read_interpolated_ionosphere_variable() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.read_interpolated_variable">read_interpolated_variable() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.read_interpolated_variable_irregular">read_interpolated_variable_irregular() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.read_ionosphere_node_variable_at_elements">read_ionosphere_node_variable_at_elements() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.read_ionosphere_variable">read_ionosphere_variable() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.read_metadata">read_metadata() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.read_parameter">read_parameter() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvParticles.read_particles">read_particles() (pytools.vlsvfile.VlsvParticles method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvParticles.read_particles_all">read_particles_all() (pytools.vlsvfile.VlsvParticles method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.read_variable">read_variable() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.read_variable_from_cache">read_variable_from_cache() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.read_variable_info">read_variable_info() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.read_variable_to_cache">read_variable_to_cache() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.read_velocity_cells">read_velocity_cells() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+      <li><a href="../biot_savart/#biot_savart.refine_mesh">refine_mesh() (in module biot_savart)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="S">S</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../biot_savart/#biot_savart.save_B_vlsv">save_B_vlsv() (in module biot_savart)</a>
+</li>
+      <li>
+    shue
+
+      <ul>
+        <li><a href="../shue/#module-shue">module</a>
+</li>
+      </ul></li>
+      <li><a href="../biot_savart/#biot_savart.spherical_to_cartesian">spherical_to_cartesian() (in module biot_savart)</a>
+
+      <ul>
+        <li><a href="../gics/#gics.spherical_to_cartesian">(in module gics)</a>
+</li>
+        <li><a href="../tsyganenko/#tsyganenko.spherical_to_cartesian">(in module tsyganenko)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../calculations/#pytools.calculations.static_field_tracer">static_field_tracer() (in module pytools.calculations)</a>
+</li>
+      <li><a href="../calculations/#pytools.calculations.static_field_tracer_3d">static_field_tracer_3d() (in module pytools.calculations)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="T">T</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../calculations/#pytools.calculations.themis_observation_from_file">themis_observation_from_file() (in module pytools.calculations)</a>
+</li>
+      <li><a href="../calculations/#pytools.calculations.themis_plot_detector">themis_plot_detector() (in module pytools.calculations)</a>
+</li>
+      <li><a href="../calculations/#pytools.calculations.themis_plot_phasespace_contour">themis_plot_phasespace_contour() (in module pytools.calculations)</a>
+</li>
+      <li><a href="../calculations/#pytools.calculations.themis_plot_phasespace_helistyle">themis_plot_phasespace_helistyle() (in module pytools.calculations)</a>
+</li>
+      <li>
+    tsyganenko
+
+      <ul>
+        <li><a href="../tsyganenko/#module-tsyganenko">module</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../tsyganenko/#tsyganenko.tsyganenko_b">tsyganenko_b() (in module tsyganenko)</a>
+</li>
+      <li><a href="../tsyganenko/#tsyganenko.tsyganenko_ocb">tsyganenko_ocb() (in module tsyganenko)</a>
+</li>
+      <li><a href="../tsyganenko/#tsyganenko.tsyganenko_open">tsyganenko_open() (in module tsyganenko)</a>
+</li>
+      <li><a href="../tsyganenko/#tsyganenko.tsyganenko_trace">tsyganenko_trace() (in module tsyganenko)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="U">U</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader.upsample_fsgrid_subarray">upsample_fsgrid_subarray() (pytools.vlsvfile.VlsvReader method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="V">V</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../calculations/#pytools.calculations.VariableInfo">VariableInfo (class in pytools.calculations)</a>
+</li>
+      <li><a href="../biot_savart/#biot_savart.vec_len_2d">vec_len_2d() (in module biot_savart)</a>
+</li>
+      <li><a href="../biot_savart/#biot_savart.vec_unit">vec_unit() (in module biot_savart)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlasiatorReader">VlasiatorReader (class in pytools.vlsvfile)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../calculations/#pytools.calculations.vlsv_intpol_file">vlsv_intpol_file() (in module pytools.calculations)</a>
+</li>
+      <li><a href="../calculations/#pytools.calculations.vlsv_intpol_points">vlsv_intpol_points() (in module pytools.calculations)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvParticles">VlsvParticles (class in pytools.vlsvfile)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvReader">VlsvReader (class in pytools.vlsvfile)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvWriter">VlsvWriter (class in pytools.vlsvfile)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="W">W</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvWriter.write">write() (pytools.vlsvfile.VlsvWriter method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvWriter.write_variable">write_variable() (pytools.vlsvfile.VlsvWriter method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvWriter.write_variable_info">write_variable_info() (pytools.vlsvfile.VlsvWriter method)</a>
+</li>
+      <li><a href="../vlsvfile/#pytools.vlsvfile.VlsvWriter.write_velocity_space">write_velocity_space() (pytools.vlsvfile.VlsvWriter method)</a>
+</li>
+      <li><a href="../miscellaneous/#pytools.miscellaneous.write_vtk_file">write_vtk_file() (in module pytools.miscellaneous)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+
+
+           </div>
+          </div>
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+
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+<li class="toctree-l1"><a class="reference internal" href="../plot/">plot</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../calculations/">calculations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../vlsvfile/">vlsvfile</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../miscellaneous/">miscellaneous</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="../scripts/">scripts</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../scripts/#biot-savart">biot_savart</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scripts/#gics">gics</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scripts/#magnetopause2d">magnetopause2d</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scripts/#magnetopause3d">magnetopause3d</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scripts/#shue">shue</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="../scripts/#tsyganenko">tsyganenko</a><ul class="current">
+<li class="toctree-l3"><a class="reference internal" href="../biot_savart/">biot_savart</a></li>
+<li class="toctree-l3 current"><a class="current reference internal" href="#">gics</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#gics.E_horizontal"><code class="docutils literal notranslate"><span class="pre">E_horizontal()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#gics.cartesian_to_spherical"><code class="docutils literal notranslate"><span class="pre">cartesian_to_spherical()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#gics.cartesian_to_spherical_vector"><code class="docutils literal notranslate"><span class="pre">cartesian_to_spherical_vector()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#gics.mkdir_path"><code class="docutils literal notranslate"><span class="pre">mkdir_path()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#gics.spherical_to_cartesian"><code class="docutils literal notranslate"><span class="pre">spherical_to_cartesian()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="../magnetopause2d/">magnetopause2d</a></li>
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+<li class="toctree-l3"><a class="reference internal" href="../shue/">shue</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../tsyganenko/">tsyganenko</a></li>
+</ul>
+</li>
+</ul>
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+<li class="toctree-l1"><a class="reference internal" href="../about/">Credits</a></li>
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+           <div itemprop="articleBody">
+             
+  <section id="module-gics">
+<span id="gics"></span><h1>gics<a class="headerlink" href="#module-gics" title="Link to this heading"></a></h1>
+<p>Given a batch of .vlsv files, containing ground magnetic field vector data at different times,
+calculate the north &amp; east components of induced ground electric field [V/m], and save in corresponding .vlsv files</p>
+<p>This script has been tested with the Vlasiator runs EGL, FHA, FIA
+note that the usefulness for EGL is limited because there is no ionosphere (domain #3) for that run</p>
+<p>Note that the Geomagnetically Induced Currents (GICs) can be computed immediately from the geoelectric field:
+The surface current density is J = sigma*E, where E, sigma are respectively the ground electric field and conductivity.</p>
+<p>This script is written for the UH environment. Adapt file paths as needed.</p>
+<p>###</p>
+<dl class="simple">
+<dt>EXAMPLE CALL:</dt><dd><p>python gics.py</p>
+</dd>
+<dt>Example sidecar .vlsv files,  containing ground magnetic field data (over the ionosphere mesh), can be found at:</dt><dd><p>/wrk-vakka/group/spacephysics/vlasiator/3D/FHA/bulk1_sidecars/geoelectric_field/</p>
+</dd>
+</dl>
+<dl class="py function">
+<dt class="sig sig-object py" id="gics.E_horizontal">
+<span class="sig-prename descclassname"><span class="pre">gics.</span></span><span class="sig-name descname"><span class="pre">E_horizontal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dB_dt</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pos</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">time</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sigma</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.001</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'liu'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gics.E_horizontal" title="Link to this definition"></a></dt>
+<dd><dl>
+<dt>Calculate the horizontal electric field by integrating components of dB/dt</dt><dd><p>References: Cagniard et al 1952 (eq. 12), Pulkinnen et al 2006 (eq. 19)</p>
+</dd>
+<dt>Inputs:</dt><dd><p>dB_dt: cartesian dB/dt    [T/s] array dimension [3, len(time)]
+pos: cartesian position [m] 1D 3-element array, vector position
+time: 1D array of times [s], monotonically increasing</p>
+</dd>
+<dt>Keywords:</dt><dd><p>sigma = ground conductivity (siemens/meter)
+method:</p>
+<blockquote>
+<div><dl class="simple">
+<dt>‘liu’: use integration method described in Liu et al., (2009) doi:10.1029/2008SW000439, 2009</dt><dd><p>this method is exact for piecewise linear B (i.e., piecewise constant dB/dt)</p>
+</dd>
+</dl>
+<p>‘RH-riemann’: use right-handed Riemann sum.</p>
+</div></blockquote>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="gics.cartesian_to_spherical">
+<span class="sig-prename descclassname"><span class="pre">gics.</span></span><span class="sig-name descname"><span class="pre">cartesian_to_spherical</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">z</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gics.cartesian_to_spherical" title="Link to this definition"></a></dt>
+<dd><p>r &gt; 0
+0 &lt; theta &lt; pi
+-pi &lt; phi &lt; pi
+all are assumed to be numpy arrays of equal dimensions</p>
+<p>returns:  r, theta, phi  [tuple]</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="gics.cartesian_to_spherical_vector">
+<span class="sig-prename descclassname"><span class="pre">gics.</span></span><span class="sig-name descname"><span class="pre">cartesian_to_spherical_vector</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vx</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vy</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vz</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">z</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gics.cartesian_to_spherical_vector" title="Link to this definition"></a></dt>
+<dd><p>Convert cartesian vector(s) with coordinates (vx, vy, vz)
+at the position(s) theta, phi (note: position r does not affect the vector transformation)
+to spherical coordinates (v_r, v_theta, v_phi)</p>
+<p>dimensions of vx, vy, vz, x, y, z arrays must either match or be a single number</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="gics.mkdir_path">
+<span class="sig-prename descclassname"><span class="pre">gics.</span></span><span class="sig-name descname"><span class="pre">mkdir_path</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gics.mkdir_path" title="Link to this definition"></a></dt>
+<dd><p>Make a directory from the stem of an input file name (path)</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="gics.spherical_to_cartesian">
+<span class="sig-prename descclassname"><span class="pre">gics.</span></span><span class="sig-name descname"><span class="pre">spherical_to_cartesian</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">r</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">theta</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">phi</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gics.spherical_to_cartesian" title="Link to this definition"></a></dt>
+<dd><p>r &gt; 0
+0 &lt; theta &lt; pi
+-pi &lt; phi &lt; pi
+all are assumed to be numpy arrays of equal dimensions</p>
+<p>returns:  x, y, z   [tuple]</p>
+</dd></dl>
+
+</section>
+
+
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+  <section id="analysator-documentation">
+<h1>analysator documentation<a class="headerlink" href="#analysator-documentation" title="Link to this heading"></a></h1>
+<p><a class="reference external" href="https://github.com/fmihpc/analysator">Analysator</a> is a set of Python tools and scripts used to read and analyze <a class="reference external" href="https://github.com/fmihpc/vlasiator">Vlasiator</a> output files (<a class="reference external" href="https://github.com/fmihpc/vlsv">VLSV</a>). Vlasiator and its related tools are developed at <a class="reference external" href="https://www.helsinki.fi/en/researchgroups/vlasiator">University of Helsinki</a>, and are open source.</p>
+<p>This documentation is generated via Sphinx-autodoc from Analysator source. This page is a work in progress, with docstrings and the documentation layout in flux. Contributions via Analysator repo are welcome.</p>
+<p>Add your content using <code class="docutils literal notranslate"><span class="pre">reStructuredText</span></code> syntax. See the
+<a class="reference external" href="https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html">reStructuredText</a>
+documentation for details.</p>
+<div class="toctree-wrapper compound">
+<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
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+<li class="toctree-l1"><a class="reference internal" href="plot/">plot</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="plot/#pytools.plot.plot_colormap"><code class="docutils literal notranslate"><span class="pre">plot_colormap()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="plot/#pytools.plot.plot_colormap3dslice"><code class="docutils literal notranslate"><span class="pre">plot_colormap3dslice()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="plot/#pytools.plot.plot_ionosphere"><code class="docutils literal notranslate"><span class="pre">plot_ionosphere()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="plot/#pytools.plot.plot_isosurface"><code class="docutils literal notranslate"><span class="pre">plot_isosurface()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="plot/#pytools.plot.plot_multiple_variables"><code class="docutils literal notranslate"><span class="pre">plot_multiple_variables()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="plot/#pytools.plot.plot_neutral_sheet"><code class="docutils literal notranslate"><span class="pre">plot_neutral_sheet()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="plot/#pytools.plot.plot_threeslice"><code class="docutils literal notranslate"><span class="pre">plot_threeslice()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="plot/#pytools.plot.plot_variables"><code class="docutils literal notranslate"><span class="pre">plot_variables()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="plot/#pytools.plot.plot_vdf"><code class="docutils literal notranslate"><span class="pre">plot_vdf()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="plot/#pytools.plot.plot_vdf_profiles"><code class="docutils literal notranslate"><span class="pre">plot_vdf_profiles()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="plot/#pytools.plot.plot_vdfdiff"><code class="docutils literal notranslate"><span class="pre">plot_vdfdiff()</span></code></a></li>
+</ul>
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+<li class="toctree-l1"><a class="reference internal" href="calculations/">calculations</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="calculations/#pytools.calculations.AMRInterpolator"><code class="docutils literal notranslate"><span class="pre">AMRInterpolator</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="calculations/#pytools.calculations.LMN_null_lines_FOTE"><code class="docutils literal notranslate"><span class="pre">LMN_null_lines_FOTE()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="calculations/#pytools.calculations.VariableInfo"><code class="docutils literal notranslate"><span class="pre">VariableInfo</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="calculations/#pytools.calculations.cell_time_evolution"><code class="docutils literal notranslate"><span class="pre">cell_time_evolution()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="calculations/#pytools.calculations.cut3d"><code class="docutils literal notranslate"><span class="pre">cut3d()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="calculations/#pytools.calculations.cut_through"><code class="docutils literal notranslate"><span class="pre">cut_through()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="calculations/#pytools.calculations.cut_through_curve"><code class="docutils literal notranslate"><span class="pre">cut_through_curve()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="calculations/#pytools.calculations.cut_through_step"><code class="docutils literal notranslate"><span class="pre">cut_through_step()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="calculations/#pytools.calculations.dynamic_field_tracer"><code class="docutils literal notranslate"><span class="pre">dynamic_field_tracer()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="calculations/#pytools.calculations.epsilon_M"><code class="docutils literal notranslate"><span class="pre">epsilon_M()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="calculations/#pytools.calculations.fourier"><code class="docutils literal notranslate"><span class="pre">fourier()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="calculations/#pytools.calculations.gyrophase_angles_from_file"><code class="docutils literal notranslate"><span class="pre">gyrophase_angles_from_file()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="calculations/#pytools.calculations.lineout"><code class="docutils literal notranslate"><span class="pre">lineout()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="calculations/#pytools.calculations.pitch_angles"><code class="docutils literal notranslate"><span class="pre">pitch_angles()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="calculations/#pytools.calculations.static_field_tracer"><code class="docutils literal notranslate"><span class="pre">static_field_tracer()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="calculations/#pytools.calculations.static_field_tracer_3d"><code class="docutils literal notranslate"><span class="pre">static_field_tracer_3d()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="calculations/#pytools.calculations.themis_observation_from_file"><code class="docutils literal notranslate"><span class="pre">themis_observation_from_file()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="calculations/#pytools.calculations.themis_plot_detector"><code class="docutils literal notranslate"><span class="pre">themis_plot_detector()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="calculations/#pytools.calculations.themis_plot_phasespace_contour"><code class="docutils literal notranslate"><span class="pre">themis_plot_phasespace_contour()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="calculations/#pytools.calculations.themis_plot_phasespace_helistyle"><code class="docutils literal notranslate"><span class="pre">themis_plot_phasespace_helistyle()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="calculations/#pytools.calculations.vlsv_intpol_file"><code class="docutils literal notranslate"><span class="pre">vlsv_intpol_file()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="calculations/#pytools.calculations.vlsv_intpol_points"><code class="docutils literal notranslate"><span class="pre">vlsv_intpol_points()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="vlsvfile/">vlsvfile</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="vlsvfile/#pytools.vlsvfile.VlasiatorReader"><code class="docutils literal notranslate"><span class="pre">VlasiatorReader</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="vlsvfile/#pytools.vlsvfile.VlsvParticles"><code class="docutils literal notranslate"><span class="pre">VlsvParticles</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="vlsvfile/#pytools.vlsvfile.VlsvReader"><code class="docutils literal notranslate"><span class="pre">VlsvReader</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="vlsvfile/#pytools.vlsvfile.VlsvWriter"><code class="docutils literal notranslate"><span class="pre">VlsvWriter</span></code></a></li>
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+<li class="toctree-l2"><a class="reference internal" href="miscellaneous/#pytools.miscellaneous.get_sorted_file_names"><code class="docutils literal notranslate"><span class="pre">get_sorted_file_names()</span></code></a></li>
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+  <section id="module-magnetopause2d">
+<span id="magnetopause2d"></span><h1>magnetopause2d<a class="headerlink" href="#module-magnetopause2d" title="Link to this heading"></a></h1>
+<p>Finds the magnetopause position by tracing steamines of the plasma flow for two-dimensional Vlasiator runs. Needs the yt package.</p>
+</section>
+
+
+           </div>
+          </div>
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diff --git a/magnetopause3d/index.html b/magnetopause3d/index.html
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+++ b/magnetopause3d/index.html
@@ -0,0 +1,162 @@
+
+
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../">
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+<li class="toctree-l1 current"><a class="reference internal" href="../scripts/">scripts</a><ul class="current">
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+<li class="toctree-l2"><a class="reference internal" href="../scripts/#magnetopause3d">magnetopause3d</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scripts/#shue">shue</a></li>
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+<li class="toctree-l3"><a class="reference internal" href="../gics/">gics</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../magnetopause2d/">magnetopause2d</a></li>
+<li class="toctree-l3 current"><a class="current reference internal" href="#">magnetopause3d</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#magnetopause3d.make_surface"><code class="docutils literal notranslate"><span class="pre">make_surface()</span></code></a></li>
+</ul>
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+           <div itemprop="articleBody">
+             
+  <section id="module-magnetopause3d">
+<span id="magnetopause3d"></span><h1>magnetopause3d<a class="headerlink" href="#module-magnetopause3d" title="Link to this heading"></a></h1>
+<p>Finds the magnetopause position by tracing steamines of the plasma flow for three-dimensional Vlasiator runs. Needs the yt package.</p>
+<dl class="py function">
+<dt class="sig sig-object py" id="magnetopause3d.make_surface">
+<span class="sig-prename descclassname"><span class="pre">magnetopause3d.</span></span><span class="sig-name descname"><span class="pre">make_surface</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">coords</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#magnetopause3d.make_surface" title="Link to this definition"></a></dt>
+<dd><p>Defines surface constructed of input coordinates as triangles
+Returns list of verts and vert indices of surface triangles</p>
+<p>coordinates must be in form […[c11, c21, c31, … cn1],[c12, c22, c32, … cn2],…
+where cij = [xij, yij, zij], i marks slice, j marks yz-plane (x_coord) index</p>
+<p>How it works:
+Three points make a triangle, triangles make the surface.
+For every two planes next to each other:
+- take every other point from plane1, every other from plane2 (in order!)
+- from list of points: every three points closest to each other make a surface</p>
+<p>Example:
+plane 1: [v1, v2, v3, v4]
+plane 2: [v5, v6, v7, v8]</p>
+<p>-&gt; list: [v1, v5, v2, v6, v3,…]
+-&gt; triangles:
+v1 v5 v2
+v5 v2 v6
+v2 v6 v3
+.
+.
+.</p>
+</dd></dl>
+
+</section>
+
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new file mode 100644
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@@ -0,0 +1,204 @@
+
+
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../">
+<head>
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
+
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>miscellaneous &mdash; analysator  documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
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+              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="../plot/">plot</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../calculations/">calculations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../vlsvfile/">vlsvfile</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">miscellaneous</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.miscellaneous.get_sorted_file_names"><code class="docutils literal notranslate"><span class="pre">get_sorted_file_names()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.miscellaneous.oblique_shock"><code class="docutils literal notranslate"><span class="pre">oblique_shock()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.miscellaneous.plot_rankine"><code class="docutils literal notranslate"><span class="pre">plot_rankine()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.miscellaneous.write_vtk_file"><code class="docutils literal notranslate"><span class="pre">write_vtk_file()</span></code></a></li>
+</ul>
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+           <div itemprop="articleBody">
+             
+  <section id="module-pytools.miscellaneous">
+<span id="miscellaneous"></span><h1>miscellaneous<a class="headerlink" href="#module-pytools.miscellaneous" title="Link to this heading"></a></h1>
+<p>This file module includes all the relevant functions/classes from the misc folder
+Miscellaneous functions include functions which dont fit any other category</p>
+<p># List of functions:</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">pytools</span> <span class="k">as</span> <span class="nn">pt</span>
+<span class="n">pt</span><span class="o">.</span><span class="n">miscellaneous</span><span class="o">.</span>
+<span class="c1">#press tab -&gt; get the functions</span>
+</pre></div>
+</div>
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.miscellaneous.get_sorted_file_names">
+<span class="sig-prename descclassname"><span class="pre">pytools.miscellaneous.</span></span><span class="sig-name descname"><span class="pre">get_sorted_file_names</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'*.vlsv'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.miscellaneous.get_sorted_file_names" title="Link to this definition"></a></dt>
+<dd><p>Gets the file names in the current directory and sorts them.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>name</strong> – Name of the file(s), for example <cite>“*.vlsv”</cite></p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>a list of file names in sorted order</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.miscellaneous.oblique_shock">
+<span class="sig-prename descclassname"><span class="pre">pytools.miscellaneous.</span></span><span class="sig-name descname"><span class="pre">oblique_shock</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">Vx1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Vy1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Bx1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">By1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">T1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rho1</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.miscellaneous.oblique_shock" title="Link to this definition"></a></dt>
+<dd><p>Calculates the rankine hugoniot jump conditions on the other side of the shock for given parameters</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>Vx1</strong> – Velocity component parallel to the shock normal vector on one side of the shock</p></li>
+<li><p><strong>Vy1</strong> – Velocity component perpendicular to the shock normal vector on one side of the shock</p></li>
+<li><p><strong>Bx1</strong> – Magnetic field component parallel to the shock normal vector on one side of the shock</p></li>
+<li><p><strong>By1</strong> – Magnetic field component perpendicular to the shock normal vector on one side of the shock</p></li>
+<li><p><strong>T1</strong> – Temperature on one side of the shock</p></li>
+<li><p><strong>rho1</strong> – Density on one side of the shock</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Components on the other side plus pressure P2 and compression ratio X in format [Vx2, Vy2, Bx2, By2, T2, rho2, P2, X]</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.miscellaneous.plot_rankine">
+<span class="sig-prename descclassname"><span class="pre">pytools.miscellaneous.</span></span><span class="sig-name descname"><span class="pre">plot_rankine</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vlsvReader</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">point1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">point2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.miscellaneous.plot_rankine" title="Link to this definition"></a></dt>
+<dd><p>A function that plots the theoretical rankine-hugoniot jump condition variables for two given points along with the actual values from a given vlsv file</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>vlsvReader</strong> – Some open vlsv reader file</p></li>
+<li><p><strong>point1</strong> – The first point of interest along the bow-shock</p></li>
+<li><p><strong>point2</strong> – The second point of interest along the bow-shock</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>pylab figure</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.miscellaneous.write_vtk_file">
+<span class="sig-prename descclassname"><span class="pre">pytools.miscellaneous.</span></span><span class="sig-name descname"><span class="pre">write_vtk_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">point_data</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.miscellaneous.write_vtk_file" title="Link to this definition"></a></dt>
+<dd><p>Writes a line into a VTK file with given points</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>filename</strong> – Name of the file e.g. “test.vtk”</p></li>
+<li><p><strong>points</strong> – Points in a line in array format</p></li>
+</ul>
+</dd>
+</dl>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># Example usage:</span>
+<span class="kn">import</span> <span class="nn">pytools</span> <span class="k">as</span> <span class="nn">pt</span>
+<span class="n">filename</span> <span class="o">=</span> <span class="s2">&quot;test.vtk&quot;</span>
+<span class="n">point_data</span> <span class="o">=</span> <span class="p">[[</span><span class="mf">0.</span><span class="p">,</span><span class="mf">0.</span><span class="p">,</span><span class="mf">0.</span><span class="p">],</span> <span class="p">[</span><span class="mf">1.</span><span class="p">,</span><span class="mf">1.</span><span class="p">,</span><span class="mf">1.</span><span class="p">],</span> <span class="p">[</span><span class="mf">2.</span><span class="p">,</span><span class="mf">2.</span><span class="p">,</span><span class="mf">2.</span><span class="p">],</span> <span class="p">[</span><span class="mf">3.</span><span class="p">,</span><span class="mf">3.</span><span class="p">,</span><span class="mf">3.</span><span class="p">],</span> <span class="p">[</span><span class="mf">4.</span><span class="p">,</span><span class="mf">4.</span><span class="p">,</span><span class="mf">4.</span><span class="p">]]</span>
+<span class="n">pt</span><span class="o">.</span><span class="n">miscellaneous</span><span class="o">.</span><span class="n">write_vtk_file</span><span class="p">(</span> <span class="n">filename</span><span class="o">=</span><span class="n">filename</span><span class="p">,</span> <span class="n">point_data</span><span class="o">=</span><span class="n">point_data</span> <span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+</section>
+
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+           </div>
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+            analysator
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+              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul class="current">
+<li class="toctree-l1 current"><a class="current reference internal" href="#">plot</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.plot.plot_colormap"><code class="docutils literal notranslate"><span class="pre">plot_colormap()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.plot.plot_colormap3dslice"><code class="docutils literal notranslate"><span class="pre">plot_colormap3dslice()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.plot.plot_ionosphere"><code class="docutils literal notranslate"><span class="pre">plot_ionosphere()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.plot.plot_isosurface"><code class="docutils literal notranslate"><span class="pre">plot_isosurface()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.plot.plot_multiple_variables"><code class="docutils literal notranslate"><span class="pre">plot_multiple_variables()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.plot.plot_neutral_sheet"><code class="docutils literal notranslate"><span class="pre">plot_neutral_sheet()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.plot.plot_threeslice"><code class="docutils literal notranslate"><span class="pre">plot_threeslice()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.plot.plot_variables"><code class="docutils literal notranslate"><span class="pre">plot_variables()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.plot.plot_vdf"><code class="docutils literal notranslate"><span class="pre">plot_vdf()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.plot.plot_vdf_profiles"><code class="docutils literal notranslate"><span class="pre">plot_vdf_profiles()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.plot.plot_vdfdiff"><code class="docutils literal notranslate"><span class="pre">plot_vdfdiff()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../calculations/">calculations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../vlsvfile/">vlsvfile</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../miscellaneous/">miscellaneous</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../scripts/">scripts</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../about/">Credits</a></li>
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+            <a href="../_sources/plot.rst.txt" rel="nofollow"> View page source</a>
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+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+             
+  <section id="module-pytools.plot">
+<span id="plot"></span><h1>plot<a class="headerlink" href="#module-pytools.plot" title="Link to this heading"></a></h1>
+<p>The plot module has all the functions related to plotting variables.</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># Example:</span>
+<span class="kn">import</span> <span class="nn">pytools</span> <span class="k">as</span> <span class="nn">pt</span>
+<span class="n">pt</span><span class="o">.</span><span class="n">pt</span><span class="o">.</span>
+<span class="c1">#press [tab] -&gt; get the functions</span>
+</pre></div>
+</div>
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.plot.plot_colormap">
+<span class="sig-prename descclassname"><span class="pre">pytools.plot.</span></span><span class="sig-name descname"><span class="pre">plot_colormap</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vlsvobj</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filedir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">step</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outputdir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outputfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nooverwrite</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">var</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">op</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">operator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">title</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cbtitle</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">draw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">usesci</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">symlog</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">diff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">boxm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">boxre</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">colormap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">run</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nocb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">internalcb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wmark</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wmarkb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axisunit</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">thick</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tickinterval</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">noborder</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">noxlabels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">noylabels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vmin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">external</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">expression</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vscale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">absolute</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">symmetric</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pass_vars</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pass_times</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pass_full</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fluxfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fluxdir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">flux_levels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fluxthick</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fluxlines</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fsaved</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nomask</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Earth</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">highres</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vectors</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vectordensity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vectorcolormap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'gray'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vectorsize</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">streamlines</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">streamlinedensity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">streamlinecolor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'white'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">streamlinethick</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cbaxes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">useimshow</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">imshowinterp</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'none'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.plot.plot_colormap" title="Link to this definition"></a></dt>
+<dd><p>Plots a coloured plot with axes and a colour bar.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Kword filename<span class="colon">:</span></dt>
+<dd class="field-odd"><p>path to .vlsv file to use for input. Assumes a bulk file.</p>
+</dd>
+<dt class="field-even">Kword vlsvobj<span class="colon">:</span></dt>
+<dd class="field-even"><p>Optionally provide a python vlsvfile object instead</p>
+</dd>
+<dt class="field-odd">Kword filedir<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Optionally provide directory where files are located and use step for bulk file name</p>
+</dd>
+<dt class="field-even">Kword step<span class="colon">:</span></dt>
+<dd class="field-even"><p>output step index, used for constructing output (and possibly input) filename</p>
+</dd>
+<dt class="field-odd">Kword outputdir<span class="colon">:</span></dt>
+<dd class="field-odd"><p>path to directory where output files are created (default: $HOME/Plots/ or override with PTOUTPUTDIR)
+If directory does not exist, it will be created. If the string does not end in a
+forward slash, the final part will be used as a prefix for the files.</p>
+</dd>
+<dt class="field-even">Kword outputfile<span class="colon">:</span></dt>
+<dd class="field-even"><p>Singular output file name</p>
+</dd>
+<dt class="field-odd">Kword nooverwrite<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set to only perform actions if the target output file does not yet exist</p>
+</dd>
+<dt class="field-even">Kword var<span class="colon">:</span></dt>
+<dd class="field-even"><p>variable to plot, e.g. rho, RhoBackstream, beta, Temperature, MA, Mms, va, vms,
+E, B, v, V or others. Accepts any variable known by analysator/pytools.
+Per-population variables are simply given as “proton/rho” etc</p>
+</dd>
+<dt class="field-odd">Kword operator<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Operator to apply to variable: None, x, y, or z. Vector variables return either
+the queried component, or otherwise the magnitude.</p>
+</dd>
+<dt class="field-even">Kword op<span class="colon">:</span></dt>
+<dd class="field-even"><p>duplicate of operator</p>
+</dd>
+<dt class="field-odd">Kword boxm<span class="colon">:</span></dt>
+<dd class="field-odd"><p>zoom box extents [x0,x1,y0,y1] in metres (default and truncate to: whole simulation box)</p>
+</dd>
+<dt class="field-even">Kword boxre<span class="colon">:</span></dt>
+<dd class="field-even"><p>zoom box extents [x0,x1,y0,y1] in Earth radii (default and truncate to: whole simulation box)</p>
+</dd>
+<dt class="field-odd">Kword colormap<span class="colon">:</span></dt>
+<dd class="field-odd"><p>colour scale for plot, use e.g. hot_desaturated, jet, viridis, plasma, inferno,
+magma, parula, nipy_spectral, RdBu, bwr</p>
+</dd>
+<dt class="field-even">Kword run<span class="colon">:</span></dt>
+<dd class="field-even"><p>run identifier, used for constructing output filename</p>
+</dd>
+<dt class="field-odd">Kword title<span class="colon">:</span></dt>
+<dd class="field-odd"><p>string to use as plot title instead of time.
+Special case: Set to “msec” to plot time with millisecond accuracy or “musec”
+for microsecond accuracy. “sec” is integer second accuracy.</p>
+</dd>
+<dt class="field-even">Kword cbtitle<span class="colon">:</span></dt>
+<dd class="field-even"><p>string to use as colorbar title instead of map name</p>
+</dd>
+<dt class="field-odd">Kword axisunit<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Plot axes using 10^{axisunit} m (default: Earth radius R_E)</p>
+</dd>
+<dt class="field-even">Kword tickinterval<span class="colon">:</span></dt>
+<dd class="field-even"><p>Interval at which to have ticks on axes (not colorbar)</p>
+</dd>
+<dt class="field-odd">Kwird usesci<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Use scientific notation for colorbar ticks? (default: True)</p>
+</dd>
+<dt class="field-even">Kword vmin,vmax<span class="colon">:</span></dt>
+<dd class="field-even"><p>min and max values for colour scale and colour bar. If no values are given,
+min and max values for whole plot (non-zero rho regions only) are used.</p>
+</dd>
+<dt class="field-odd">Kword symmetric<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set the absolute value of vmin and vmax to the greater of the two</p>
+</dd>
+<dt class="field-even">Kword lin<span class="colon">:</span></dt>
+<dd class="field-even"><p>Flag for using linear colour scaling instead of log. If an integer, defines number
+of colorbar ticks.</p>
+</dd>
+<dt class="field-odd">Kword symlog<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Use logarithmic scaling, but linear when abs(value) is below the value given to symlog.
+Allows symmetric quasi-logarithmic plots of e.g. transverse field components.
+A given of 0 or True translates to a threshold of max(abs(vmin),abs(vmax)) * 1.e-2, but this can
+result in the innermost tick marks overlapping. In this case, using a larger value for 
+symlog is suggested.</p>
+</dd>
+<dt class="field-even">Kword wmark<span class="colon">:</span></dt>
+<dd class="field-even"><p>If set to non-zero, will plot a Vlasiator watermark in the top left corner. If set to a text
+string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”</p>
+</dd>
+<dt class="field-odd">Kword wmarkb<span class="colon">:</span></dt>
+<dd class="field-odd"><p>As for wmark, but uses an all-black Vlasiator logo.</p>
+</dd>
+<dt class="field-even">Kword Earth<span class="colon">:</span></dt>
+<dd class="field-even"><p>If set, draws an earth at (0,0)</p>
+</dd>
+<dt class="field-odd">Kword highres<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Creates the image in high resolution, scaled up by this value (suitable for print).</p>
+</dd>
+<dt class="field-even">Kword draw<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set to anything but None or False in order to draw image on-screen instead of saving to file (requires x-windowing)</p>
+</dd>
+<dt class="field-odd">Kword noborder<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Plot figure edge-to-edge without borders (default off)</p>
+</dd>
+<dt class="field-even">Kword noxlabels<span class="colon">:</span></dt>
+<dd class="field-even"><p>Suppress x-axis labels and title</p>
+</dd>
+<dt class="field-odd">Kword noylabels<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Suppress y-axis labels and title</p>
+</dd>
+<dt class="field-even">Kword scale<span class="colon">:</span></dt>
+<dd class="field-even"><p>Scale text size (default=1.0)</p>
+</dd>
+<dt class="field-odd">Kword thick<span class="colon">:</span></dt>
+<dd class="field-odd"><p>line and axis thickness, default=1.0</p>
+</dd>
+<dt class="field-even">Kword nocb<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set to suppress drawing of colourbar</p>
+</dd>
+<dt class="field-odd">Kword internalcb<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set to draw colorbar inside plot instead of outside. If set to a text
+string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”</p>
+</dd>
+<dt class="field-even">Kword external<span class="colon">:</span></dt>
+<dd class="field-even"><p>Optional function to use for external plotting of e.g. contours. The function
+receives the following arguments: ax, XmeshXY,YmeshXY, pass_maps
+If the function accepts a fifth variable, if set to true, it is expected to 
+return a list of required variables for constructing the pass_maps dictionary.</p>
+</dd>
+<dt class="field-odd">Kword expression<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Optional function which calculates a custom expression to plot. The function
+receives the same dictionary of numpy arrays as external, as an argument pass_maps,
+the contents of which are maps of variables. Each is either of size [ysize,xsize]
+or for multi-dimensional variables (vectors, tensors) it’s [ysize,xsize,dim].
+If the function accepts a second variable, if set to true, it is expected to 
+return a list of required variables for pass_maps.</p>
+</dd>
+<dt class="field-even">Kword diff<span class="colon">:</span></dt>
+<dd class="field-even"><p>Instead of a regular plot, plot the difference between the selected plot type for
+the regular source file and the file given by this keyword. This overides external
+and expression keywords, as well as related pass_vars, pass_times, and pass_full.</p>
+</dd>
+</dl>
+<p>Important note: the dictionaries of arrays passed to external and expression are of shape [ysize,xzize], so
+for some analysis transposing them is necessary. For pre-existing functions to use and to base new functions
+on, see the plot_helpers.py file.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Kword vscale<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Scale all values with this before plotting. Useful for going from e.g. m^-3 to cm^-3
+or from tesla to nanotesla. Guesses correct units for colourbar for some known
+variables. Set to None to search for a default scaling settings.</p>
+</dd>
+<dt class="field-even">Kword absolute<span class="colon">:</span></dt>
+<dd class="field-even"><p>Plot the absolute of the evaluated variable</p>
+</dd>
+<dt class="field-odd">Kword pass_vars<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Optional list of map names to pass to the external/expression functions 
+as a dictionary of numpy arrays. Each is either of size [ysize,xsize] or 
+for multi-dimensional variables (vectors, tensors) it’s [ysize,xsize,dim].</p>
+</dd>
+<dt class="field-even">Kword pass_times<span class="colon">:</span></dt>
+<dd class="field-even"><p>Integer, how many timesteps in each direction should be passed to external/expression
+functions in pass_vars (e.g. pass_times=1 passes the values of three timesteps). If
+pass_times has two values, the first is the extent before, the second after.
+(e.g. pass_times=[2,1] passes the values of two preceding and one following timesteps
+for a total of four timesteps)
+This causes pass_vars to become a list of timesteps, with each timestep containing
+a dictionary of numpy arrays as for regular pass_vars. An additional dictionary entry is
+added as ‘dstep’ which gives the timestep offset from the master frame.
+Does not work if working from a vlsv-object.</p>
+</dd>
+<dt class="field-odd">Kword pass_full<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set to anything but None in order to pass the full arrays instead of a zoomed-in section</p>
+</dd>
+<dt class="field-even">Kword fluxfile<span class="colon">:</span></dt>
+<dd class="field-even"><p>Filename to plot fluxfunction from</p>
+</dd>
+<dt class="field-odd">Kword flux_levels<span class="colon">:</span></dt>
+<dd class="field-odd"><p>A list of flux function values to plot as the contours (default: None, a set of constant 
+intervals: np.linspace(-10,10,fluxlines*60))</p>
+</dd>
+<dt class="field-even">Kword fluxdir<span class="colon">:</span></dt>
+<dd class="field-even"><p>Directory in which fluxfunction files can be found</p>
+</dd>
+<dt class="field-odd">Kword fluxthick<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Scale fluxfunction line thickness</p>
+</dd>
+<dt class="field-even">Kword fluxlines<span class="colon">:</span></dt>
+<dd class="field-even"><p>Relative density of fluxfunction contours</p>
+</dd>
+<dt class="field-odd">Kword fsaved<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Overplot locations of fSaved. If keyword is set to a string, that will be the colour used.</p>
+</dd>
+<dt class="field-even">Kword nomask<span class="colon">:</span></dt>
+<dd class="field-even"><p>Do not mask plotting based on proton density</p>
+</dd>
+<dt class="field-odd">Kword vectors<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set to a vector variable to overplot (unit length vectors, color displays variable magnitude)</p>
+</dd>
+<dt class="field-even">Kword vectordensity<span class="colon">:</span></dt>
+<dd class="field-even"><p>Aim for how many vectors to show in plot window (default 100)</p>
+</dd>
+<dt class="field-odd">Kword vectorcolormap<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Colormap to use for overplotted vectors (default: gray)</p>
+</dd>
+<dt class="field-even">Kword vectorsize<span class="colon">:</span></dt>
+<dd class="field-even"><p>Scaling of vector sizes</p>
+</dd>
+<dt class="field-odd">Kword streamlines<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set to a vector variable to overplot as streamlines</p>
+</dd>
+<dt class="field-even">Kword streamlinedensity<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set streamline density (default 1)</p>
+</dd>
+<dt class="field-odd">Kword streamlinecolor<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set streamline color (default white)</p>
+</dd>
+<dt class="field-even">Kword streamlinethick<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set streamline thickness</p>
+</dd>
+<dt class="field-odd">Kword axes<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Provide the routine a set of axes to draw within instead of generating a new image.
+It is recommended to either also provide cbaxes or activate nocb, unless one wants a colorbar
+to be automatically added next to the panel (but this may affect the overall layout)
+Note that the aspect ratio of the colormap is made equal in any case, hence the axes
+proportions may change if the box and axes size are not designed to match by the user</p>
+</dd>
+<dt class="field-even">Kword cbaxes<span class="colon">:</span></dt>
+<dd class="field-even"><p>Provide the routine a set of axes for the colourbar.</p>
+</dd>
+<dt class="field-odd">Kword useimshow<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Use imshow for raster background instead (default: False)</p>
+</dd>
+<dt class="field-even">Kword imshowinterp<span class="colon">:</span></dt>
+<dd class="field-even"><p>Use this matplotlib interpolation for imshow (default: ‘none’)</p>
+</dd>
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Outputs an image to a file or to the screen.</p>
+</dd>
+</dl>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># Example usage:</span>
+<span class="n">plot_colormap</span><span class="p">(</span><span class="n">filename</span><span class="o">=</span><span class="n">fileLocation</span><span class="p">,</span> <span class="n">var</span><span class="o">=</span><span class="s2">&quot;MA&quot;</span><span class="p">,</span> <span class="n">run</span><span class="o">=</span><span class="s2">&quot;BCQ&quot;</span><span class="p">,</span>
+            <span class="n">colormap</span><span class="o">=</span><span class="s1">&#39;nipy_spectral&#39;</span><span class="p">,</span><span class="n">step</span><span class="o">=</span><span class="n">j</span><span class="p">,</span> <span class="n">outputdir</span><span class="o">=</span><span class="n">outputLocation</span><span class="p">,</span>
+            <span class="n">lin</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">wmark</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">vmin</span><span class="o">=</span><span class="mf">2.7</span><span class="p">,</span> <span class="n">vmax</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> 
+            <span class="n">external</span><span class="o">=</span><span class="n">cavitoncontours</span><span class="p">,</span> <span class="n">pass_vars</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;rho&#39;</span><span class="p">,</span><span class="s1">&#39;B&#39;</span><span class="p">,</span><span class="s1">&#39;beta&#39;</span><span class="p">])</span>
+<span class="c1"># Where cavitoncontours is an external function which receives the arguments</span>
+<span class="c1">#  ax, XmeshXY,YmeshXY, pass_maps</span>
+<span class="c1"># where pass_maps is a dictionary of maps for the requested variables.</span>
+
+<span class="c1"># example (simple) use of expressions:</span>
+<span class="k">def</span> <span class="nf">exprMA_cust</span><span class="p">(</span><span class="n">exprmaps</span><span class="p">,</span> <span class="n">requestvariables</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+    <span class="k">if</span> <span class="n">requestvariables</span><span class="o">==</span><span class="kc">True</span><span class="p">:</span>
+    <span class="k">return</span> <span class="p">[</span><span class="s1">&#39;va&#39;</span><span class="p">]</span>
+    <span class="n">custombulkspeed</span><span class="o">=</span><span class="mf">750000.</span> <span class="c1"># m/s</span>
+    <span class="n">va</span> <span class="o">=</span> <span class="n">exprmaps</span><span class="p">[</span><span class="s1">&#39;va&#39;</span><span class="p">][:,:]</span>
+    <span class="n">MA</span> <span class="o">=</span> <span class="n">custombulkspeed</span><span class="o">/</span><span class="n">va</span>
+    <span class="k">return</span> <span class="n">MA</span>
+<span class="n">plot_colormap</span><span class="p">(</span><span class="n">filename</span><span class="o">=</span><span class="n">fileLocation</span><span class="p">,</span> <span class="n">vmin</span><span class="o">=</span><span class="mi">1</span> <span class="n">vmax</span><span class="o">=</span><span class="mi">40</span><span class="p">,</span> <span class="n">expression</span><span class="o">=</span><span class="n">exprMA_cust</span><span class="p">,</span><span class="n">lin</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.plot.plot_colormap3dslice">
+<span class="sig-prename descclassname"><span class="pre">pytools.plot.</span></span><span class="sig-name descname"><span class="pre">plot_colormap3dslice</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vlsvobj</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filedir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">step</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">run</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outputdir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outputfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nooverwrite</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">var</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">op</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">operator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">title</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cbtitle</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">draw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">usesci</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">symlog</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">boxm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">boxre</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">colormap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nocb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">internalcb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wmark</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wmarkb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axisunit</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">thick</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tickinterval</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">noborder</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">noxlabels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">noylabels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vmin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">external</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">expression</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">diff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vscale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">absolute</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">symmetric</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pass_vars</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pass_times</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pass_full</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fsaved</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nomask</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Earth</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">highres</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vectors</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vectordensity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vectorcolormap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'gray'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vectorsize</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">streamlines</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">streamlinedensity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">streamlinecolor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'white'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">streamlinethick</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cbaxes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">normal</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'y'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutpoint</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutpointre</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">useimshow</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">imshowinterp</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'none'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.plot.plot_colormap3dslice" title="Link to this definition"></a></dt>
+<dd><p>Plots a coloured plot with axes and a colour bar.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Kword filename<span class="colon">:</span></dt>
+<dd class="field-odd"><p>path to .vlsv file to use for input. Assumes a bulk file.</p>
+</dd>
+<dt class="field-even">Kword vlsvobj<span class="colon">:</span></dt>
+<dd class="field-even"><p>Optionally provide a python vlsvfile object instead</p>
+</dd>
+<dt class="field-odd">Kword filedir<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Optionally provide directory where files are located and use step for bulk file name</p>
+</dd>
+<dt class="field-even">Kword step<span class="colon">:</span></dt>
+<dd class="field-even"><p>output step index, used for constructing output (and possibly input) filename</p>
+</dd>
+<dt class="field-odd">Kword run<span class="colon">:</span></dt>
+<dd class="field-odd"><p>run identifier, used for constructing output filename</p>
+</dd>
+<dt class="field-even">Kword outputdir<span class="colon">:</span></dt>
+<dd class="field-even"><p>path to directory where output files are created (default: $HOME/Plots/ or override with PTOUTPUTDIR)
+If directory does not exist, it will be created. If the string does not end in a
+forward slash, the final part will be used as a prefix for the files.</p>
+</dd>
+<dt class="field-odd">Kword outputfile<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Singular output file name</p>
+</dd>
+<dt class="field-even">Kword nooverwrite<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set to only perform actions if the target output file does not yet exist</p>
+</dd>
+<dt class="field-odd">Kword var<span class="colon">:</span></dt>
+<dd class="field-odd"><p>variable to plot, e.g. rho, RhoBackstream, beta, Temperature, MA, Mms, va, vms,
+E, B, v, V or others. Accepts any variable known by analysator/pytools.
+Per-population variables are simply given as “proton/rho” etc</p>
+</dd>
+<dt class="field-even">Kword operator<span class="colon">:</span></dt>
+<dd class="field-even"><p>Operator to apply to variable: None, x, y, or z. Vector variables return either
+the queried component, or otherwise the magnitude.</p>
+</dd>
+<dt class="field-odd">Kword op<span class="colon">:</span></dt>
+<dd class="field-odd"><p>duplicate of operator</p>
+</dd>
+<dt class="field-even">Kword boxm<span class="colon">:</span></dt>
+<dd class="field-even"><p>zoom box extents [x0,x1,y0,y1] in metres (default and truncate to: whole simulation box)</p>
+</dd>
+<dt class="field-odd">Kword boxre<span class="colon">:</span></dt>
+<dd class="field-odd"><p>zoom box extents [x0,x1,y0,y1] in Earth radii (default and truncate to: whole simulation box)</p>
+</dd>
+<dt class="field-even">Kword colormap<span class="colon">:</span></dt>
+<dd class="field-even"><p>colour scale for plot, use e.g. hot_desaturated, jet, viridis, plasma, inferno,
+magma, parula, nipy_spectral, RdBu, bwr</p>
+</dd>
+<dt class="field-odd">Kword title<span class="colon">:</span></dt>
+<dd class="field-odd"><p>string to use as plot title instead of time.
+Special case: Set to “msec” to plot time with millisecond accuracy or “musec”
+for microsecond accuracy. “sec” is integer second accuracy.</p>
+</dd>
+<dt class="field-even">Kword cbtitle<span class="colon">:</span></dt>
+<dd class="field-even"><p>string to use as colorbar title instead of map name</p>
+</dd>
+<dt class="field-odd">Kword axisunit<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Plot axes using 10^{axisunit} m (default: Earth radius R_E)</p>
+</dd>
+<dt class="field-even">Kword tickinterval<span class="colon">:</span></dt>
+<dd class="field-even"><p>Interval at which to have ticks on axes (not colorbar)</p>
+</dd>
+<dt class="field-odd">Kwird usesci<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Use scientific notation for colorbar ticks? (default: True)</p>
+</dd>
+<dt class="field-even">Kword vmin,vmax<span class="colon">:</span></dt>
+<dd class="field-even"><p>min and max values for colour scale and colour bar. If no values are given,
+min and max values for whole plot (non-zero rho regions only) are used.</p>
+</dd>
+<dt class="field-odd">Kword symmetric<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set the absolute value of vmin and vmax to the greater of the two</p>
+</dd>
+<dt class="field-even">Kword lin<span class="colon">:</span></dt>
+<dd class="field-even"><p>Flag for using linear colour scaling instead of log</p>
+</dd>
+<dt class="field-odd">Kword symlog<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Use logarithmic scaling, but linear when abs(value) is below the value given to symlog.
+Allows symmetric quasi-logarithmic plots of e.g. transverse field components.
+A given of 0 translates to a threshold of max(abs(vmin),abs(vmax)) * 1.e-2, but this can
+result in the innermost tick marks overlapping. In this case, using a larger value for 
+symlog is suggested.</p>
+</dd>
+<dt class="field-even">Kword wmark<span class="colon">:</span></dt>
+<dd class="field-even"><p>If set to non-zero, will plot a Vlasiator watermark in the top left corner. If set to a text
+string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”</p>
+</dd>
+<dt class="field-odd">Kword wmarkb<span class="colon">:</span></dt>
+<dd class="field-odd"><p>As for wmark, but uses an all-black Vlasiator logo.</p>
+</dd>
+<dt class="field-even">Kword Earth<span class="colon">:</span></dt>
+<dd class="field-even"><p>If set, draws an earth at (0,0)</p>
+</dd>
+<dt class="field-odd">Kword highres<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Creates the image in high resolution, scaled up by this value (suitable for print).</p>
+</dd>
+<dt class="field-even">Kword draw<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set to nonzero in order to draw image on-screen instead of saving to file (requires x-windowing)</p>
+</dd>
+<dt class="field-odd">Kword noborder<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Plot figure edge-to-edge without borders (default off)</p>
+</dd>
+<dt class="field-even">Kword noxlabels<span class="colon">:</span></dt>
+<dd class="field-even"><p>Suppress x-axis labels and title</p>
+</dd>
+<dt class="field-odd">Kword noylabels<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Suppress y-axis labels and title</p>
+</dd>
+<dt class="field-even">Kword scale<span class="colon">:</span></dt>
+<dd class="field-even"><p>Scale text size (default=1.0)</p>
+</dd>
+<dt class="field-odd">Kword thick<span class="colon">:</span></dt>
+<dd class="field-odd"><p>line and axis thickness, default=1.0</p>
+</dd>
+<dt class="field-even">Kword nocb<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set to suppress drawing of colourbar</p>
+</dd>
+<dt class="field-odd">Kword internalcb<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set to draw colorbar inside plot instead of outside. If set to a text
+string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”</p>
+</dd>
+<dt class="field-even">Kword external<span class="colon">:</span></dt>
+<dd class="field-even"><p>Optional function to use for external plotting of e.g. contours. The function
+receives the following arguments: ax, XmeshXY,YmeshXY, pass_maps
+If the function accepts a fifth variable, if set to true, it is expected to 
+return a list of required variables for constructing the pass_maps dictionary.</p>
+</dd>
+<dt class="field-odd">Kword expression<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Optional function which calculates a custom expression to plot. The function
+receives the same dictionary of numpy arrays as external, as an argument pass_maps,
+the contents of which are maps of variables. Each is either of size [ysize,xsize]
+or for multi-dimensional variables (vectors, tensors) it’s [ysize,xsize,dim].
+If the function accepts a second variable, if set to true, it is expected to 
+return a list of required variables for pass_maps.</p>
+</dd>
+</dl>
+<p>Important note: the dictionaries of arrays passed to external and expression are of shape [ysize,xzize], so
+for some analysis transposing them is necessary. For pre-existing functions to use and to base new functions
+on, see the plot_helpers.py file.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Kword vscale<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Scale all values with this before plotting. Useful for going from e.g. m^-3 to cm^-3
+or from tesla to nanotesla. Guesses correct units for colourbar for some known
+variables. Set to None to seek for a default scaling.</p>
+</dd>
+<dt class="field-even">Kword absolute<span class="colon">:</span></dt>
+<dd class="field-even"><p>Plot the absolute of the evaluated variable</p>
+</dd>
+<dt class="field-odd">Kword pass_vars<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Optional list of map names to pass to the external/expression functions 
+as a dictionary of numpy arrays. Each is either of size [ysize,xsize] or 
+for multi-dimensional variables (vectors, tensors) it’s [ysize,xsize,dim].</p>
+</dd>
+<dt class="field-even">Kword pass_times<span class="colon">:</span></dt>
+<dd class="field-even"><p>Integer, how many timesteps in each direction should be passed to external/expression
+functions in pass_vars (e.g. pass_times=1 passes the values of three timesteps). If
+pass_times has two values, the first is the extent before, the second after.
+(e.g. pass_times=[2,1] passes the values of two preceding and one following timesteps
+for a total of four timesteps)
+This causes pass_vars to become a list of timesteps, with each timestep containing
+a dictionary of numpy arrays as for regular pass_vars. An additional dictionary entry is
+added as ‘dstep’ which gives the timestep offset from the master frame.
+Does not work if working from a vlsv-object.</p>
+</dd>
+<dt class="field-odd">Kword pass_full<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set to anything but None in order to pass the full arrays instead of a zoomed-in section</p>
+</dd>
+<dt class="field-even">Kword diff<span class="colon">:</span></dt>
+<dd class="field-even"><p>Instead of a regular plot, plot the difference between the selected plot type for
+the regular source file and the file given by this keyword. This overides external
+and expression keywords, as well as related pass_vars, pass_times, and pass_full.</p>
+</dd>
+<dt class="field-odd">Kword fsaved<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Overplot locations of fSaved. If keyword is set to a string, that will be the colour used.</p>
+</dd>
+<dt class="field-even">Kword nomask<span class="colon">:</span></dt>
+<dd class="field-even"><p>Do not mask plotting based on proton density</p>
+</dd>
+<dt class="field-odd">Kword vectors<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set to a vector variable to overplot (unit length vectors, color displays variable magnitude)</p>
+</dd>
+<dt class="field-even">Kword vectordensity<span class="colon">:</span></dt>
+<dd class="field-even"><p>Aim for how many vectors to show in plot window (default 100)</p>
+</dd>
+<dt class="field-odd">Kword vectorcolormap<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Colormap to use for overplotted vectors (default: gray)</p>
+</dd>
+<dt class="field-even">Kword vectorsize<span class="colon">:</span></dt>
+<dd class="field-even"><p>Scaling of vector sizes</p>
+</dd>
+<dt class="field-odd">Kword streamlines<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set to a vector variable to overplot as streamlines</p>
+</dd>
+<dt class="field-even">Kword streamlinedensity<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set streamline density (default 1)</p>
+</dd>
+<dt class="field-odd">Kword streamlinecolor<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set streamline color (default white)</p>
+</dd>
+<dt class="field-even">Kword streamlinethick<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set streamline thickness</p>
+</dd>
+<dt class="field-odd">Kword axes<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Provide the routine a set of axes to draw within instead of generating a new image.
+It is recommended to either also provide cbaxes or activate nocb, unless one wants a colorbar
+to be automatically added next to the panel (but this may affect the overall layout)
+Note that the aspect ratio of the colormap is made equal in any case, hence the axes
+proportions may change if the box and axes size are not designed to match by the user</p>
+</dd>
+<dt class="field-even">Kword cbaxes<span class="colon">:</span></dt>
+<dd class="field-even"><p>Provide the routine a set of axes for the colourbar.</p>
+</dd>
+<dt class="field-odd">Kword normal<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Direction of the normal of the 2D cut through (‘x’, ‘y’, or ‘z’ or a vector)</p>
+</dd>
+<dt class="field-even">Kword cutpoint<span class="colon">:</span></dt>
+<dd class="field-even"><p>Coordinate (in normal direction) through which the cut must pass [m]</p>
+</dd>
+<dt class="field-odd">Kword cutpointre<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Coordinate (in normal direction) through which the cut must pass [rE]</p>
+</dd>
+<dt class="field-even">Kword useimshow<span class="colon">:</span></dt>
+<dd class="field-even"><p>Use imshow for raster background instead (default: False)</p>
+</dd>
+<dt class="field-odd">Kword imshowinterp<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Use this matplotlib interpolation for imshow (default: ‘none’)</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Outputs an image to a file or to the screen.</p>
+</dd>
+</dl>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># Example usage:</span>
+<span class="n">plot_colormap</span><span class="p">(</span><span class="n">filename</span><span class="o">=</span><span class="n">fileLocation</span><span class="p">,</span> <span class="n">var</span><span class="o">=</span><span class="s2">&quot;MA&quot;</span><span class="p">,</span> <span class="n">run</span><span class="o">=</span><span class="s2">&quot;BCQ&quot;</span><span class="p">,</span>
+            <span class="n">colormap</span><span class="o">=</span><span class="s1">&#39;nipy_spectral&#39;</span><span class="p">,</span><span class="n">step</span><span class="o">=</span><span class="n">j</span><span class="p">,</span> <span class="n">outputdir</span><span class="o">=</span><span class="n">outputLocation</span><span class="p">,</span>
+            <span class="n">lin</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">wmark</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">vmin</span><span class="o">=</span><span class="mf">2.7</span><span class="p">,</span> <span class="n">vmax</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> 
+            <span class="n">external</span><span class="o">=</span><span class="n">cavitoncontours</span><span class="p">,</span> <span class="n">pass_vars</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;rho&#39;</span><span class="p">,</span><span class="s1">&#39;B&#39;</span><span class="p">,</span><span class="s1">&#39;beta&#39;</span><span class="p">])</span>
+<span class="c1"># Where cavitoncontours is an external function which receives the arguments</span>
+<span class="c1">#  ax, XmeshXY,YmeshXY, pass_maps</span>
+<span class="c1"># where pass_maps is a dictionary of maps for the requested variables.</span>
+
+<span class="c1"># example (simple) use of expressions:</span>
+<span class="k">def</span> <span class="nf">exprMA_cust</span><span class="p">(</span><span class="n">exprmaps</span><span class="p">,</span> <span class="n">requestvariables</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+    <span class="k">if</span> <span class="n">requestvariables</span><span class="o">==</span><span class="kc">True</span><span class="p">:</span>
+    <span class="k">return</span> <span class="p">[</span><span class="s1">&#39;va&#39;</span><span class="p">]</span>
+    <span class="n">custombulkspeed</span><span class="o">=</span><span class="mf">750000.</span> <span class="c1"># m/s</span>
+    <span class="n">va</span> <span class="o">=</span> <span class="n">exprmaps</span><span class="p">[</span><span class="s1">&#39;va&#39;</span><span class="p">][:,:]</span>
+    <span class="n">MA</span> <span class="o">=</span> <span class="n">custombulkspeed</span><span class="o">/</span><span class="n">va</span>
+    <span class="k">return</span> <span class="n">MA</span>
+<span class="n">plot_colormap</span><span class="p">(</span><span class="n">filename</span><span class="o">=</span><span class="n">fileLocation</span><span class="p">,</span> <span class="n">vmin</span><span class="o">=</span><span class="mi">1</span> <span class="n">vmax</span><span class="o">=</span><span class="mi">40</span><span class="p">,</span> <span class="n">expression</span><span class="o">=</span><span class="n">exprMA_cust</span><span class="p">,</span><span class="n">lin</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.plot.plot_ionosphere">
+<span class="sig-prename descclassname"><span class="pre">pytools.plot.</span></span><span class="sig-name descname"><span class="pre">plot_ionosphere</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vlsvobj</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filedir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">step</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">run</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outputdir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outputfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nooverwrite</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">var</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">op</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">operator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">colormap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vmin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">symmetric</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">absolute</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">usesci</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">symlog</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nocb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">internalcb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">minlatitude</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">60</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cbtitle</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">title</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cbaxes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">thick</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vscale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wmark</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wmarkb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">viewdir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">draw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.plot.plot_ionosphere" title="Link to this definition"></a></dt>
+<dd><p>Plots a 2d projection of an ionosphere variable</p>
+<dl class="field-list simple">
+<dt class="field-odd">Kword filename<span class="colon">:</span></dt>
+<dd class="field-odd"><p>path to .vlsv file to use for input. Assumes a bulk file.</p>
+</dd>
+<dt class="field-even">Kword vlsvobj<span class="colon">:</span></dt>
+<dd class="field-even"><p>Optionally provide a python vlsvfile object instead</p>
+</dd>
+<dt class="field-odd">Kword filedir<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Optionally provide directory where files are located and use step for bulk file name</p>
+</dd>
+<dt class="field-even">Kword step<span class="colon">:</span></dt>
+<dd class="field-even"><p>output step index, used for constructing output (and possibly input) filename</p>
+</dd>
+<dt class="field-odd">Kword run<span class="colon">:</span></dt>
+<dd class="field-odd"><p>run identifier, used for constructing output filename</p>
+</dd>
+<dt class="field-even">Kword outputdir<span class="colon">:</span></dt>
+<dd class="field-even"><p>path to directory where output files are created (default: $HOME/Plots/ or override with PTOUTPUTDIR)
+If directory does not exist, it will be created. If the string does not end in a
+forward slash, the final part will be used as a prefix for the files.</p>
+</dd>
+<dt class="field-odd">Kword outputfile<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Singular output file name</p>
+</dd>
+<dt class="field-even">Kword nooverwrite<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set to only perform actions if the target output file does not yet exist</p>
+</dd>
+<dt class="field-odd">Kword var<span class="colon">:</span></dt>
+<dd class="field-odd"><p>variable to plot, e.g. rho, RhoBackstream, beta, Temperature, MA, Mms, va, vms,
+E, B, v, V or others. Accepts any variable known by analysator/pytools.
+Per-population variables are simply given as “proton/rho” etc</p>
+</dd>
+<dt class="field-even">Kword operator<span class="colon">:</span></dt>
+<dd class="field-even"><p>Operator to apply to variable: None, x, y, or z. Vector variables return either
+the queried component, or otherwise the magnitude.</p>
+</dd>
+<dt class="field-odd">Kword op<span class="colon">:</span></dt>
+<dd class="field-odd"><p>duplicate of operator</p>
+</dd>
+<dt class="field-even">Kword colormap<span class="colon">:</span></dt>
+<dd class="field-even"><p>colour scale for plot, use e.g. hot_desaturated, jet, viridis, plasma, inferno,
+magma, parula, nipy_spectral, RdBu, bwr</p>
+</dd>
+<dt class="field-odd">Kword vmin,vmax<span class="colon">:</span></dt>
+<dd class="field-odd"><p>min and max values for colour scale and colour bar. If no values are given,
+min and max values for whole plot (non-zero rho regions only) are used.</p>
+</dd>
+<dt class="field-even">Kword symmetric<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set the absolute value of vmin and vmax to the greater of the two</p>
+</dd>
+<dt class="field-odd">Kword absolute<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Plot the absolute of the evaluated variable</p>
+</dd>
+<dt class="field-even">Kwird usesci<span class="colon">:</span></dt>
+<dd class="field-even"><p>Use scientific notation for colorbar ticks? (default: True)</p>
+</dd>
+<dt class="field-odd">Kword lin<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Flag for using linear colour scaling instead of log</p>
+</dd>
+<dt class="field-even">Kword symlog<span class="colon">:</span></dt>
+<dd class="field-even"><p>Use logarithmic scaling, but linear when abs(value) is below the value given to symlog.
+Allows symmetric quasi-logarithmic plots of e.g. transverse field components.
+A given of 0 translates to a threshold of max(abs(vmin),abs(vmax)) * 1.e-2, but this can
+result in the innermost tick marks overlapping. In this case, using a larger value for 
+symlog is suggested.</p>
+</dd>
+<dt class="field-odd">Kword nocb<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set to suppress drawing of colourbar</p>
+</dd>
+<dt class="field-even">Kword internalcb<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set to draw colorbar inside plot instead of outside. If set to a text
+string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”</p>
+</dd>
+<dt class="field-odd">Kword minlatitude<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Minimum plot latitude (default=60 degrees)</p>
+</dd>
+<dt class="field-even">Kword title<span class="colon">:</span></dt>
+<dd class="field-even"><p>string to use as plot title instead of time.
+Special case: Set to “msec” to plot time with millisecond accuracy or “musec”
+for microsecond accuracy. “sec” is integer second accuracy.</p>
+</dd>
+<dt class="field-odd">Kword cbtitle<span class="colon">:</span></dt>
+<dd class="field-odd"><p>string to use as colorbar title instead of map name</p>
+</dd>
+<dt class="field-even">Kword viewdir<span class="colon">:</span></dt>
+<dd class="field-even"><p>view direction onto the sphere. Positive value: North pole. Negative values: South pole.</p>
+</dd>
+<dt class="field-odd">Kword scale<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Scale text size (default=1.0)</p>
+</dd>
+<dt class="field-even">Kword vscale<span class="colon">:</span></dt>
+<dd class="field-even"><p>Scale all values with this before plotting. Useful for going from e.g. m^-3 to cm^-3
+or from tesla to nanotesla. Guesses correct units for colourbar for some known
+variables.</p>
+</dd>
+<dt class="field-odd">Kword axes<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Provide the routine a set of axes to draw within instead of generating a new image.</p>
+</dd>
+<dt class="field-even">Kword cbaxes<span class="colon">:</span></dt>
+<dd class="field-even"><p>Provide the routine a set of axes for the colourbar.</p>
+</dd>
+<dt class="field-odd">Kword thick<span class="colon">:</span></dt>
+<dd class="field-odd"><p>line and axis thickness, default=1.0</p>
+</dd>
+<dt class="field-even">Kword draw<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set to anything but None or False in order to draw image on-screen instead of saving to file (requires x-windowing)</p>
+</dd>
+<dt class="field-odd">Kword wmark<span class="colon">:</span></dt>
+<dd class="field-odd"><p>If set to non-zero, will plot a Vlasiator watermark in the top left corner. If set to a text
+string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”</p>
+</dd>
+<dt class="field-even">Kword wmarkb<span class="colon">:</span></dt>
+<dd class="field-even"><p>As for wmark, but uses an all-black Vlasiator logo.</p>
+</dd>
+</dl>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.plot.plot_isosurface">
+<span class="sig-prename descclassname"><span class="pre">pytools.plot.</span></span><span class="sig-name descname"><span class="pre">plot_isosurface</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vlsvobj</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filedir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">step</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outputdir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nooverwrite</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">surf_var</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">surf_op</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">surf_level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">color_var</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">color_op</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">surf_step</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">title</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cbtitle</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">draw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">usesci</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">symmetric</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">highres</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">boxm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">boxre</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">colormap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">run</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wmark</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nocb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">unit</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">thick</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vscale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vmin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">symlog</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">angle</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[30.0,</span> <span class="pre">90.0]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">transparent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.plot.plot_isosurface" title="Link to this definition"></a></dt>
+<dd><p>Plots a coloured isosurface plot with axes and a colour bar.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Kword filename<span class="colon">:</span></dt>
+<dd class="field-odd"><p>path to .vlsv file to use for input. Assumes a bulk file.</p>
+</dd>
+<dt class="field-even">Kword vlsvobj<span class="colon">:</span></dt>
+<dd class="field-even"><p>Optionally provide a python vlsvfile object instead</p>
+</dd>
+<dt class="field-odd">Kword filedir<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Optionally provide directory where files are located and use step for bulk file name</p>
+</dd>
+<dt class="field-even">Kword step<span class="colon">:</span></dt>
+<dd class="field-even"><p>output step index, used for constructing output (and possibly input) filename</p>
+</dd>
+<dt class="field-odd">Kword outputdir<span class="colon">:</span></dt>
+<dd class="field-odd"><p>path to directory where output files are created (default: $HOME/Plots/ or override with PTOUTPUTDIR)
+If directory does not exist, it will be created. If the string does not end in a
+forward slash, the final parti will be used as a perfix for the files.</p>
+</dd>
+<dt class="field-even">Kword nooverwrite<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set to only perform actions if the target output file does not yet exist</p>
+</dd>
+<dt class="field-odd">Kword surf_var<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Variable to read for defining surface</p>
+</dd>
+<dt class="field-even">Kword surf_op<span class="colon">:</span></dt>
+<dd class="field-even"><p>Operator to use for variable to read surface</p>
+</dd>
+<dt class="field-odd">Kword surf_level<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Level at which to define surface</p>
+</dd>
+<dt class="field-even">Kword surf_step<span class="colon">:</span></dt>
+<dd class="field-even"><p>Vertex stepping for surface generation: larger value returns coarser surface</p>
+</dd>
+<dt class="field-odd">Kword color_var<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Variable to read for coloring surface</p>
+</dd>
+<dt class="field-even">Kword color_op<span class="colon">:</span></dt>
+<dd class="field-even"><p>Operator to use for variable to color surface (‘x’, ‘y’, ‘z’; if None and color_var is a vector, the magnitude is taken)</p>
+</dd>
+<dt class="field-odd">Kword boxm<span class="colon">:</span></dt>
+<dd class="field-odd"><p>zoom box extents [x0,x1,y0,y1] in metres (default and truncate to: whole simulation box)</p>
+</dd>
+<dt class="field-even">Kword boxre<span class="colon">:</span></dt>
+<dd class="field-even"><p>zoom box extents [x0,x1,y0,y1] in Earth radii (default and truncate to: whole simulation box)</p>
+</dd>
+<dt class="field-odd">Kword colormap<span class="colon">:</span></dt>
+<dd class="field-odd"><p>colour scale for plot, use e.g. hot_desaturated, jet, viridis, plasma, inferno,
+magma, parula, nipy_spectral, RdBu, bwr</p>
+</dd>
+<dt class="field-even">Kword run<span class="colon">:</span></dt>
+<dd class="field-even"><p>run identifier, used for constructing output filename</p>
+</dd>
+<dt class="field-odd">Kword title<span class="colon">:</span></dt>
+<dd class="field-odd"><p>string to use as plot title instead of time</p>
+</dd>
+<dt class="field-even">Kword cbtitle<span class="colon">:</span></dt>
+<dd class="field-even"><p>string to use as colorbar title instead of map name</p>
+</dd>
+<dt class="field-odd">Kword unit<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Plot axes using 10^{unit} m (default: Earth radius R_E)</p>
+</dd>
+<dt class="field-even">Kwird usesci<span class="colon">:</span></dt>
+<dd class="field-even"><p>Use scientific notation for colorbar ticks? (default: 1)</p>
+</dd>
+<dt class="field-odd">Kword vscale<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Scale all values with this before plotting. Useful for going from e.g. m^-3 to cm^-3
+or from tesla to nanotesla. Guesses correct units for colourbar for some known
+variables. Set to None to seek for a default scaling.</p>
+</dd>
+<dt class="field-even">Kword vmin,vmax<span class="colon">:</span></dt>
+<dd class="field-even"><p>min and max values for colour scale and colour bar. If no values are given,
+min and max values for whole plot (non-zero rho regions only) are used.</p>
+</dd>
+<dt class="field-odd">Kword symmetric<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set the absolute value of vmin and vmax to the greater of the two</p>
+</dd>
+<dt class="field-even">Kword lin<span class="colon">:</span></dt>
+<dd class="field-even"><p>Flag for using linear colour scaling instead of log</p>
+</dd>
+<dt class="field-odd">Kword symlog<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Use logarithmic scaling, but linear when abs(value) is below the value given to symlog.
+Allows symmetric quasi-logarithmic plots of e.g. transverse field components.
+A given of 0 translates to a threshold of max(abs(vmin),abs(vmax)) * 1.e-2.</p>
+</dd>
+<dt class="field-even">Kword wmark<span class="colon">:</span></dt>
+<dd class="field-even"><p>If set to non-zero, will plot a Vlasiator watermark in the top left corner.</p>
+</dd>
+<dt class="field-odd">Kword highres<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Creates the image in high resolution, scaled up by this value (suitable for logging.info).</p>
+</dd>
+<dt class="field-even">Kword draw<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set to nonzero in order to draw image on-screen instead of saving to file (requires x-windowing)</p>
+</dd>
+<dt class="field-odd">Kword transparent<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set to False in order to make the surface opaque</p>
+</dd>
+<dt class="field-even">Kword scale<span class="colon">:</span></dt>
+<dd class="field-even"><p>Scale text size (default=1.0)</p>
+</dd>
+<dt class="field-odd">Kword thick<span class="colon">:</span></dt>
+<dd class="field-odd"><p>line and axis thickness, default=1.0</p>
+</dd>
+<dt class="field-even">Kword nocb<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set to suppress drawing of colourbar</p>
+</dd>
+<dt class="field-odd">Kword angle<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Viewing elevation and azimuthal angles in degrees</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Outputs an image to a file or to the screen.</p>
+</dd>
+</dl>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span>
+</pre></div>
+</div>
+<p># Example usage:</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.plot.plot_multiple_variables">
+<span class="sig-prename descclassname"><span class="pre">pytools.plot.</span></span><span class="sig-name descname"><span class="pre">plot_multiple_variables</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">variables_x_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">variables_y_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">figure</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">clean_xticks</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.plot.plot_multiple_variables" title="Link to this definition"></a></dt>
+<dd><p>Plots multiple variables from the input with pylab</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>variables_x_list</strong> – Some list of variables to be plotted in the x-axis</p></li>
+<li><p><strong>variables_y_list</strong> – Some list of variables to be plotted in the y-axis</p></li>
+<li><p><strong>figure</strong> – If one wants to plot into an existing figure then the matplotlib figure should be passed as an argument (OPTIONAL)</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>a pylab figure with the plot</p>
+</dd>
+</dl>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1">#Example usage:</span>
+<span class="n">plot_multiple_variables</span><span class="p">(</span> <span class="p">[</span><span class="n">distances</span><span class="p">,</span> <span class="n">xcoordinates</span><span class="p">],</span> <span class="p">[</span><span class="n">rho</span><span class="p">,</span> <span class="n">B_x</span><span class="p">]</span> <span class="p">)</span>
+<span class="c1"># This would plot rho_values as a function of distance and B_x_values as a function of xcoordinates</span>
+</pre></div>
+</div>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>Multiplot expects variables to be saved in the VariableInfo class</p>
+</div>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>If for some reason some variable list (x or y) is empty, e.g. variables_x_list = [B_x, [], B_z, rho], then the variable will not be plotted. This can be used if one wants to plot only into certain subplots.</p>
+</div>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.plot.plot_neutral_sheet">
+<span class="sig-prename descclassname"><span class="pre">pytools.plot.</span></span><span class="sig-name descname"><span class="pre">plot_neutral_sheet</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vlsvobj</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filedir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">step</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">run</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outputdir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outputfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nooverwrite</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">var</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">op</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">operator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">title</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cbtitle</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">draw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">usesci</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">symlog</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">boxm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">boxre</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">colormap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nocb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">internalcb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wmark</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wmarkb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axisunit</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">thick</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tickinterval</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">noborder</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">noxlabels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">noylabels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vmin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">external</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">expression</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">diff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vscale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">absolute</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">symmetric</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pass_vars</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pass_times</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pass_full</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nomask</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Earth</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">highres</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vectors</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vectordensity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vectorcolormap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'gray'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vectorsize</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">streamlines</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">streamlinedensity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">streamlinecolor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'white'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">streamlinethick</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cbaxes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">useimshow</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">imshowinterp</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'none'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">folding_alpha</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">z_extent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[-5,</span> <span class="pre">5]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sheetlayer</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'above'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.plot.plot_neutral_sheet" title="Link to this definition"></a></dt>
+<dd><p>Plots a coloured plot along the neutral sheet with axes and a colour bar.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Kword filename<span class="colon">:</span></dt>
+<dd class="field-odd"><p>path to .vlsv file to use for input. Assumes a bulk file.</p>
+</dd>
+<dt class="field-even">Kword vlsvobj<span class="colon">:</span></dt>
+<dd class="field-even"><p>Optionally provide a python vlsvfile object instead</p>
+</dd>
+<dt class="field-odd">Kword filedir<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Optionally provide directory where files are located and use step for bulk file name</p>
+</dd>
+<dt class="field-even">Kword step<span class="colon">:</span></dt>
+<dd class="field-even"><p>output step index, used for constructing output (and possibly input) filename</p>
+</dd>
+<dt class="field-odd">Kword run<span class="colon">:</span></dt>
+<dd class="field-odd"><p>run identifier, used for constructing output filename</p>
+</dd>
+<dt class="field-even">Kword outputdir<span class="colon">:</span></dt>
+<dd class="field-even"><p>path to directory where output files are created (default: $HOME/Plots/ or override with PTOUTPUTDIR)
+If directory does not exist, it will be created. If the string does not end in a
+forward slash, the final part will be used as a prefix for the files.</p>
+</dd>
+<dt class="field-odd">Kword outputfile<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Singular output file name</p>
+</dd>
+<dt class="field-even">Kword nooverwrite<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set to only perform actions if the target output file does not yet exist</p>
+</dd>
+<dt class="field-odd">Kword var<span class="colon">:</span></dt>
+<dd class="field-odd"><p>variable to plot, e.g. rho, RhoBackstream, beta, Temperature, MA, Mms, va, vms,
+E, B, v, V or others. Accepts any variable known by analysator/pytools.
+Per-population variables are simply given as “proton/rho” etc</p>
+</dd>
+<dt class="field-even">Kword operator<span class="colon">:</span></dt>
+<dd class="field-even"><p>Operator to apply to variable: None, x, y, or z. Vector variables return either
+the queried component, or otherwise the magnitude.</p>
+</dd>
+<dt class="field-odd">Kword op<span class="colon">:</span></dt>
+<dd class="field-odd"><p>duplicate of operator</p>
+</dd>
+<dt class="field-even">Kword boxm<span class="colon">:</span></dt>
+<dd class="field-even"><p>zoom box extents [x0,x1,y0,y1] in metres (default and truncate to: whole simulation box)</p>
+</dd>
+<dt class="field-odd">Kword boxre<span class="colon">:</span></dt>
+<dd class="field-odd"><p>zoom box extents [x0,x1,y0,y1] in Earth radii (default and truncate to: whole simulation box)</p>
+</dd>
+<dt class="field-even">Kword colormap<span class="colon">:</span></dt>
+<dd class="field-even"><p>colour scale for plot, use e.g. hot_desaturated, jet, viridis, plasma, inferno,
+magma, parula, nipy_spectral, RdBu, bwr</p>
+</dd>
+<dt class="field-odd">Kword title<span class="colon">:</span></dt>
+<dd class="field-odd"><p>string to use as plot title instead of time.
+Special case: Set to “msec” to plot time with millisecond accuracy or “musec”
+for microsecond accuracy. “sec” is integer second accuracy.</p>
+</dd>
+<dt class="field-even">Kword cbtitle<span class="colon">:</span></dt>
+<dd class="field-even"><p>string to use as colorbar title instead of map name</p>
+</dd>
+<dt class="field-odd">Kword axisunit<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Plot axes using 10^{axisunit} m (default: Earth radius R_E)</p>
+</dd>
+<dt class="field-even">Kword tickinterval<span class="colon">:</span></dt>
+<dd class="field-even"><p>Interval at which to have ticks on axes (not colorbar)</p>
+</dd>
+<dt class="field-odd">Kwird usesci<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Use scientific notation for colorbar ticks? (default: True)</p>
+</dd>
+<dt class="field-even">Kword vmin,vmax<span class="colon">:</span></dt>
+<dd class="field-even"><p>min and max values for colour scale and colour bar. If no values are given,
+min and max values for whole plot (non-zero rho regions only) are used.</p>
+</dd>
+<dt class="field-odd">Kword symmetric<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set the absolute value of vmin and vmax to the greater of the two</p>
+</dd>
+<dt class="field-even">Kword lin<span class="colon">:</span></dt>
+<dd class="field-even"><p>Flag for using linear colour scaling instead of log</p>
+</dd>
+<dt class="field-odd">Kword symlog<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Use logarithmic scaling, but linear when abs(value) is below the value given to symlog.
+Allows symmetric quasi-logarithmic plots of e.g. transverse field components.
+A given of 0 translates to a threshold of max(abs(vmin),abs(vmax)) * 1.e-2, but this can
+result in the innermost tick marks overlapping. In this case, using a larger value for 
+symlog is suggested.</p>
+</dd>
+<dt class="field-even">Kword wmark<span class="colon">:</span></dt>
+<dd class="field-even"><p>If set to non-zero, will plot a Vlasiator watermark in the top left corner. If set to a text
+string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”</p>
+</dd>
+<dt class="field-odd">Kword wmarkb<span class="colon">:</span></dt>
+<dd class="field-odd"><p>As for wmark, but uses an all-black Vlasiator logo.</p>
+</dd>
+<dt class="field-even">Kword Earth<span class="colon">:</span></dt>
+<dd class="field-even"><p>If set, draws an earth at (0,0)</p>
+</dd>
+<dt class="field-odd">Kword highres<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Creates the image in high resolution, scaled up by this value (suitable for print).</p>
+</dd>
+<dt class="field-even">Kword draw<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set to nonzero in order to draw image on-screen instead of saving to file (requires x-windowing)</p>
+</dd>
+<dt class="field-odd">Kword noborder<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Plot figure edge-to-edge without borders (default off)</p>
+</dd>
+<dt class="field-even">Kword noxlabels<span class="colon">:</span></dt>
+<dd class="field-even"><p>Suppress x-axis labels and title</p>
+</dd>
+<dt class="field-odd">Kword noylabels<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Suppress y-axis labels and title</p>
+</dd>
+<dt class="field-even">Kword scale<span class="colon">:</span></dt>
+<dd class="field-even"><p>Scale text size (default=1.0)</p>
+</dd>
+<dt class="field-odd">Kword thick<span class="colon">:</span></dt>
+<dd class="field-odd"><p>line and axis thickness, default=1.0</p>
+</dd>
+<dt class="field-even">Kword nocb<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set to suppress drawing of colourbar</p>
+</dd>
+<dt class="field-odd">Kword internalcb<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set to draw colorbar inside plot instead of outside. If set to a text
+string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”</p>
+</dd>
+<dt class="field-even">Kword external<span class="colon">:</span></dt>
+<dd class="field-even"><p>Optional function to use for external plotting of e.g. contours. The function
+receives the following arguments: ax, XmeshXY,YmeshXY, pass_maps
+If the function accepts a fifth variable, if set to true, it is expected to 
+return a list of required variables for constructing the pass_maps dictionary.</p>
+</dd>
+<dt class="field-odd">Kword expression<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Optional function which calculates a custom expression to plot. The function
+receives the same dictionary of numpy arrays as external, as an argument pass_maps,
+the contents of which are maps of variables. Each is either of size [ysize,xsize]
+or for multi-dimensional variables (vectors, tensors) it’s [ysize,xsize,dim].
+If the function accepts a second variable, if set to true, it is expected to 
+return a list of required variables for pass_maps.</p>
+</dd>
+</dl>
+<p>Important note: the dictionaries of arrays passed to external and expression are of shape [ysize,xzize], so
+for some analysis transposing them is necessary. For pre-existing functions to use and to base new functions
+on, see the plot_helpers.py file.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Kword vscale<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Scale all values with this before plotting. Useful for going from e.g. m^-3 to cm^-3
+or from tesla to nanotesla. Guesses correct units for colourbar for some known
+variables. Set to None to seek for a default scaling.</p>
+</dd>
+<dt class="field-even">Kword absolute<span class="colon">:</span></dt>
+<dd class="field-even"><p>Plot the absolute of the evaluated variable</p>
+</dd>
+<dt class="field-odd">Kword pass_vars<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Optional list of map names to pass to the external/expression functions 
+as a dictionary of numpy arrays. Each is either of size [ysize,xsize] or 
+for multi-dimensional variables (vectors, tensors) it’s [ysize,xsize,dim].</p>
+</dd>
+<dt class="field-even">Kword pass_times<span class="colon">:</span></dt>
+<dd class="field-even"><p>Integer, how many timesteps in each direction should be passed to external/expression
+functions in pass_vars (e.g. pass_times=1 passes the values of three timesteps). If
+pass_times has two values, the first is the extent before, the second after.
+(e.g. pass_times=[2,1] passes the values of two preceding and one following timesteps
+for a total of four timesteps)
+This causes pass_vars to become a list of timesteps, with each timestep containing
+a dictionary of numpy arrays as for regular pass_vars. An additional dictionary entry is
+added as ‘dstep’ which gives the timestep offset from the master frame.
+Does not work if working from a vlsv-object.</p>
+</dd>
+<dt class="field-odd">Kword pass_full<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set to anything but None in order to pass the full arrays instead of a zoomed-in section</p>
+</dd>
+<dt class="field-even">Kword diff<span class="colon">:</span></dt>
+<dd class="field-even"><p>Instead of a regular plot, plot the difference between the selected plot type for
+the regular source file and the file given by this keyword. This overides external
+and expression keywords, as well as related pass_vars, pass_times, and pass_full.</p>
+</dd>
+<dt class="field-odd">Kword z_extent<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Search bracket for the neutral sheet in axisunit units</p>
+</dd>
+<dt class="field-even">Kword folding_alpha<span class="colon">:</span></dt>
+<dd class="field-even"><p>If non-zero, plots transparent dots over the regions where the sheet has multiple separate z-values. A value of 1.0 is opaque, a value of 0.0 is transparent.</p>
+</dd>
+<dt class="field-odd">Kword sheetlayer<span class="colon">:</span></dt>
+<dd class="field-odd"><p>If set to ‘above’, plots the topmost layer of the neutral sheet in case of folding. If set to anything else, 
+the downmost layer is plotted.</p>
+</dd>
+<dt class="field-even">Kword nomask<span class="colon">:</span></dt>
+<dd class="field-even"><p>Do not mask plotting based on proton density</p>
+</dd>
+<dt class="field-odd">Kword vectors<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set to a vector variable to overplot (unit length vectors, color displays variable magnitude)</p>
+</dd>
+<dt class="field-even">Kword vectordensity<span class="colon">:</span></dt>
+<dd class="field-even"><p>Aim for how many vectors to show in plot window (default 100)</p>
+</dd>
+<dt class="field-odd">Kword vectorcolormap<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Colormap to use for overplotted vectors (default: gray)</p>
+</dd>
+<dt class="field-even">Kword vectorsize<span class="colon">:</span></dt>
+<dd class="field-even"><p>Scaling of vector sizes</p>
+</dd>
+<dt class="field-odd">Kword streamlines<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set to a vector variable to overplot as streamlines</p>
+</dd>
+<dt class="field-even">Kword streamlinedensity<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set streamline density (default 1)</p>
+</dd>
+<dt class="field-odd">Kword streamlinecolor<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set streamline color (default white)</p>
+</dd>
+<dt class="field-even">Kword streamlinethick<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set streamline thickness</p>
+</dd>
+<dt class="field-odd">Kword axes<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Provide the routine a set of axes to draw within instead of generating a new image.
+It is recommended to either also provide cbaxes or activate nocb, unless one wants a colorbar
+to be automatically added next to the panel (but this may affect the overall layout)
+Note that the aspect ratio of the colormap is made equal in any case, hence the axes
+proportions may change if the box and axes size are not designed to match by the user</p>
+</dd>
+<dt class="field-even">Kword cbaxes<span class="colon">:</span></dt>
+<dd class="field-even"><p>Provide the routine a set of axes for the colourbar.</p>
+</dd>
+<dt class="field-odd">Kword normal<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Direction of the normal of the 2D cut through (‘x’, ‘y’, or ‘z’ or a vector)</p>
+</dd>
+<dt class="field-even">Kword cutpoint<span class="colon">:</span></dt>
+<dd class="field-even"><p>Coordinate (in normal direction) through which the cut must pass [m]</p>
+</dd>
+<dt class="field-odd">Kword cutpointre<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Coordinate (in normal direction) through which the cut must pass [rE]</p>
+</dd>
+<dt class="field-even">Kword useimshow<span class="colon">:</span></dt>
+<dd class="field-even"><p>Use imshow for raster background instead (default: False)</p>
+</dd>
+<dt class="field-odd">Kword imshowinterp<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Use this matplotlib interpolation for imshow (default: ‘none’)</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Outputs an image to a file or to the screen.</p>
+</dd>
+</dl>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># Example usage:</span>
+<span class="n">plot_colormap</span><span class="p">(</span><span class="n">filename</span><span class="o">=</span><span class="n">fileLocation</span><span class="p">,</span> <span class="n">var</span><span class="o">=</span><span class="s2">&quot;MA&quot;</span><span class="p">,</span> <span class="n">run</span><span class="o">=</span><span class="s2">&quot;BCQ&quot;</span><span class="p">,</span>
+            <span class="n">colormap</span><span class="o">=</span><span class="s1">&#39;nipy_spectral&#39;</span><span class="p">,</span><span class="n">step</span><span class="o">=</span><span class="n">j</span><span class="p">,</span> <span class="n">outputdir</span><span class="o">=</span><span class="n">outputLocation</span><span class="p">,</span>
+            <span class="n">lin</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">wmark</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">vmin</span><span class="o">=</span><span class="mf">2.7</span><span class="p">,</span> <span class="n">vmax</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> 
+            <span class="n">external</span><span class="o">=</span><span class="n">cavitoncontours</span><span class="p">,</span> <span class="n">pass_vars</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;rho&#39;</span><span class="p">,</span><span class="s1">&#39;B&#39;</span><span class="p">,</span><span class="s1">&#39;beta&#39;</span><span class="p">])</span>
+<span class="c1"># Where cavitoncontours is an external function which receives the arguments</span>
+<span class="c1">#  ax, XmeshXY,YmeshXY, pass_maps</span>
+<span class="c1"># where pass_maps is a dictionary of maps for the requested variables.</span>
+
+<span class="c1"># example (simple) use of expressions:</span>
+<span class="k">def</span> <span class="nf">exprMA_cust</span><span class="p">(</span><span class="n">exprmaps</span><span class="p">,</span> <span class="n">requestvariables</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+    <span class="k">if</span> <span class="n">requestvariables</span><span class="o">==</span><span class="kc">True</span><span class="p">:</span>
+    <span class="k">return</span> <span class="p">[</span><span class="s1">&#39;va&#39;</span><span class="p">]</span>
+    <span class="n">custombulkspeed</span><span class="o">=</span><span class="mf">750000.</span> <span class="c1"># m/s</span>
+    <span class="n">va</span> <span class="o">=</span> <span class="n">exprmaps</span><span class="p">[</span><span class="s1">&#39;va&#39;</span><span class="p">][:,:]</span>
+    <span class="n">MA</span> <span class="o">=</span> <span class="n">custombulkspeed</span><span class="o">/</span><span class="n">va</span>
+    <span class="k">return</span> <span class="n">MA</span>
+<span class="n">plot_colormap</span><span class="p">(</span><span class="n">filename</span><span class="o">=</span><span class="n">fileLocation</span><span class="p">,</span> <span class="n">vmin</span><span class="o">=</span><span class="mi">1</span> <span class="n">vmax</span><span class="o">=</span><span class="mi">40</span><span class="p">,</span> <span class="n">expression</span><span class="o">=</span><span class="n">exprMA_cust</span><span class="p">,</span><span class="n">lin</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.plot.plot_threeslice">
+<span class="sig-prename descclassname"><span class="pre">pytools.plot.</span></span><span class="sig-name descname"><span class="pre">plot_threeslice</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vlsvobj</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filedir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">step</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">run</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outputdir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outputfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nooverwrite</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">var</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">op</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">operator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">boxm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">boxre</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">colormap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vmin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">symmetric</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">absolute</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">symlog</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nocb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cbtitle</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">title</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">halfaxes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">usesci</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axisunit</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axiscolor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">shadings</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">draw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tickinterval</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fixedticks</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pass_full</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wmark</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wmarkb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nomask</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Earth</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">thick</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">expression</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vscale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">viewangle</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(-60.0,</span> <span class="pre">30.0)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutpointm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutpointre</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">slices</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.plot.plot_threeslice" title="Link to this definition"></a></dt>
+<dd><p>Plots a 3d plot constructed of three 2d cut throughs.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Kword filename<span class="colon">:</span></dt>
+<dd class="field-odd"><p>path to .vlsv file to use for input. Assumes a bulk file.</p>
+</dd>
+<dt class="field-even">Kword vlsvobj<span class="colon">:</span></dt>
+<dd class="field-even"><p>Optionally provide a python vlsvfile object instead</p>
+</dd>
+<dt class="field-odd">Kword filedir<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Optionally provide directory where files are located and use step for bulk file name</p>
+</dd>
+<dt class="field-even">Kword step<span class="colon">:</span></dt>
+<dd class="field-even"><p>output step index, used for constructing output (and possibly input) filename</p>
+</dd>
+<dt class="field-odd">Kword run<span class="colon">:</span></dt>
+<dd class="field-odd"><p>run identifier, used for constructing output filename</p>
+</dd>
+<dt class="field-even">Kword outputdir<span class="colon">:</span></dt>
+<dd class="field-even"><p>path to directory where output files are created (default: $HOME/Plots/ or override with PTOUTPUTDIR)
+If directory does not exist, it will be created. If the string does not end in a
+forward slash, the final part will be used as a prefix for the files.</p>
+</dd>
+<dt class="field-odd">Kword outputfile<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Singular output file name</p>
+</dd>
+<dt class="field-even">Kword draw<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set to anything but None or False in order to draw image on-screen instead of saving to file (requires x-windowing)</p>
+</dd>
+<dt class="field-odd">Kword nooverwrite<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set to only perform actions if the target output file does not yet exist</p>
+</dd>
+<dt class="field-even">Kword var<span class="colon">:</span></dt>
+<dd class="field-even"><p>variable to plot, e.g. rho, RhoBackstream, beta, Temperature, MA, Mms, va, vms,
+E, B, v, V or others. Accepts any variable known by analysator/pytools.
+Per-population variables are simply given as “proton/rho” etc</p>
+</dd>
+<dt class="field-odd">Kword operator<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Operator to apply to variable: None, x, y, or z. Vector variables return either
+the queried component, or otherwise the magnitude.</p>
+</dd>
+<dt class="field-even">Kword op<span class="colon">:</span></dt>
+<dd class="field-even"><p>duplicate of operator</p>
+</dd>
+<dt class="field-odd">Kword boxm<span class="colon">:</span></dt>
+<dd class="field-odd"><p>zoom box extents [x0,x1,y0,y1,z0,z1] in metres (default and truncate to: whole simulation box)</p>
+</dd>
+<dt class="field-even">Kword boxre<span class="colon">:</span></dt>
+<dd class="field-even"><p>zoom box extents [x0,x1,y0,y1,z0,z1] in Earth radii (default and truncate to: whole simulation box)</p>
+</dd>
+<dt class="field-odd">Kword colormap<span class="colon">:</span></dt>
+<dd class="field-odd"><p>colour scale for plot, use e.g. hot_desaturated, jet, viridis, plasma, inferno,
+magma, parula, nipy_spectral, RdBu, bwr</p>
+</dd>
+<dt class="field-even">Kword vmin,vmax<span class="colon">:</span></dt>
+<dd class="field-even"><p>min and max values for colour scale and colour bar. If no values are given,
+min and max values for whole plot (non-zero rho regions only) are used.</p>
+</dd>
+<dt class="field-odd">Kword symmetric<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set the absolute value of vmin and vmax to the greater of the two</p>
+</dd>
+<dt class="field-even">Kword absolute<span class="colon">:</span></dt>
+<dd class="field-even"><p>Plot the absolute of the evaluated variable</p>
+</dd>
+<dt class="field-odd">Kword lin<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Flag for using linear colour scaling instead of log</p>
+</dd>
+<dt class="field-even">Kword symlog<span class="colon">:</span></dt>
+<dd class="field-even"><p>Use logarithmic scaling, but linear when abs(value) is below the value given to symlog.
+Allows symmetric quasi-logarithmic plots of e.g. transverse field components.
+A given of 0 translates to a threshold of max(abs(vmin),abs(vmax)) * 1.e-2, but this can
+result in the innermost tick marks overlapping. In this case, using a larger value for 
+symlog is suggested.</p>
+</dd>
+<dt class="field-odd">Kword nocb<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set to suppress drawing of colourbar</p>
+</dd>
+<dt class="field-even">Kword title<span class="colon">:</span></dt>
+<dd class="field-even"><p>string to use as plot title instead of time.
+Special case: Set to “msec” to plot time with millisecond accuracy or “musec”
+for microsecond accuracy. “sec” is integer second accuracy.</p>
+</dd>
+<dt class="field-odd">Kword cbtitle<span class="colon">:</span></dt>
+<dd class="field-odd"><p>string to use as colorbar title instead of map name</p>
+</dd>
+<dt class="field-even">Kword halfaxes<span class="colon">:</span></dt>
+<dd class="field-even"><p>Flag to prevent plotting the hidden half of the axes, otherwise shown as dashed lines
+(default: False)</p>
+</dd>
+<dt class="field-odd">Kwird usesci<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Use scientific notation for colorbar ticks? (default: True)</p>
+</dd>
+<dt class="field-even">Kword axisunit<span class="colon">:</span></dt>
+<dd class="field-even"><p>Plot axes using 10^{axisunit} m (default: Earth radius R_E)</p>
+</dd>
+<dt class="field-odd">Kword axiscolor<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Color for drawing axes (default black)</p>
+</dd>
+<dt class="field-even">Kword shadings<span class="colon">:</span></dt>
+<dd class="field-even"><p>Dimming values for the surfaces normal to the X, Y, Z directions, respectively,
+to better distinguish the slices, e.g. “(0.6,0.8,1.0). Default using the angles between
+the surface normal directions and the viewing angle.</p>
+</dd>
+<dt class="field-odd">Kword tickinterval:Axis tick interval, expressed in 10^{axisunit} (default<span class="colon">:</span></dt>
+<dd class="field-odd"><p>10 Earth radii)</p>
+</dd>
+<dt class="field-even">Kword fixedticks<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set ticks at fixed locations instead of relative to the triple cut point (default: False)</p>
+</dd>
+<dt class="field-odd">Kword pass_full<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set to anything but None in order to pass the full arrays instead of a zoomed-in section</p>
+</dd>
+<dt class="field-even">Kword wmark<span class="colon">:</span></dt>
+<dd class="field-even"><p>If set to non-zero, will plot a Vlasiator watermark in the top left corner. If set to a text
+string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”</p>
+</dd>
+<dt class="field-odd">Kword wmarkb<span class="colon">:</span></dt>
+<dd class="field-odd"><p>As for wmark, but uses an all-black Vlasiator logo.</p>
+</dd>
+<dt class="field-even">Kword nomask<span class="colon">:</span></dt>
+<dd class="field-even"><p>Do not mask plotting based on proton density</p>
+</dd>
+<dt class="field-odd">Kword Earth<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Draw Earth at origin (default True)</p>
+</dd>
+<dt class="field-even">Kword scale<span class="colon">:</span></dt>
+<dd class="field-even"><p>Scale text size (default=1.0)</p>
+</dd>
+<dt class="field-odd">Kword thick<span class="colon">:</span></dt>
+<dd class="field-odd"><p>line and axis thickness, default=1.0</p>
+</dd>
+<dt class="field-even">Kword expression<span class="colon">:</span></dt>
+<dd class="field-even"><p>Optional function which calculates a custom expression to plot. The function
+receives the same dictionary of numpy arrays as external, as an argument pass_maps,
+the contents of which are maps of variables. Each is either of size [ysize,xsize]
+or for multi-dimensional variables (vectors, tensors) it’s [ysize,xsize,dim].
+If the function accepts a second variable, if set to true, it is expected to 
+return a list of required variables for pass_maps.</p>
+</dd>
+</dl>
+<p>Important note: the dictionaries of arrays passed to external and expression are of shape [ysize,xzize], so
+for some analysis transposing them is necessary. For pre-existing functions to use and to base new functions
+on, see the plot_helpers.py file.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Kword vscale<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Scale all values with this before plotting. Useful for going from e.g. m^-3 to cm^-3
+or from tesla to nanotesla. Guesses correct units for colourbar for some known
+variables. Set to None to search for a default scaling.</p>
+</dd>
+<dt class="field-even">Kword viewangle<span class="colon">:</span></dt>
+<dd class="field-even"><p>Azimuth and elevation angles giving the point of view on the 3D axes, in degrees.
+(default=(-60.,30.); corresponds to dayside, morningside, northern hemisphere)</p>
+</dd>
+<dt class="field-odd">Kword cutpointm<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Coordinates of the point through which all three 2D cuts must pass [m]</p>
+</dd>
+<dt class="field-even">Kword cutpointre<span class="colon">:</span></dt>
+<dd class="field-even"><p>Coordinates of the point through which all three 2D cuts must pass [rE]</p>
+</dd>
+<dt class="field-odd">Kword slices<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Normal directions of the slices to plot, default=’xyz’</p>
+</dd>
+</dl>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.plot.plot_variables">
+<span class="sig-prename descclassname"><span class="pre">pytools.plot.</span></span><span class="sig-name descname"><span class="pre">plot_variables</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">figure</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.plot.plot_variables" title="Link to this definition"></a></dt>
+<dd><p>Plots x and y variables from the input with pylab</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>x</strong> – Some variable to be plotted in the x-axis</p></li>
+<li><p><strong>y</strong> – Some variable to be plotted in the y-axis</p></li>
+<li><p><strong>figure</strong> – If one wants to plot into an existing figure then the matplotlib figure should be passed as an argument (OPTIONAL)</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>a pylab figure with the plot</p>
+</dd>
+</dl>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># Example usage:</span>
+<span class="n">plot_variables</span><span class="p">(</span> <span class="n">distances</span><span class="p">,</span> <span class="n">rho</span> <span class="p">)</span>
+<span class="c1"># This would plot rho as a function of distance</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.plot.plot_vdf">
+<span class="sig-prename descclassname"><span class="pre">pytools.plot.</span></span><span class="sig-name descname"><span class="pre">plot_vdf</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vlsvobj</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filedir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">step</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cellids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'proton'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coordinates</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coordre</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outputdir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outputfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nooverwrite</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">draw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axisunit</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axiskmps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">title</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cbtitle</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tickinterval</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">colormap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">box</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nocb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">internalcb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">run</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">thick</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wmark</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wmarkb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">slicethick</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reducer</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'integrate'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resampler</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cellsize</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xy</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xz</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">yz</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">normal</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">normalx</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bpara</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bpara1</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bperp</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coordswap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bvector</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bvectorscale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cbulk</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cpeak</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">center</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wflux</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">setThreshold</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">noborder</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale_text</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">8.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale_title</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale_cb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale_label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">12.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">biglabel</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">biglabloc</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">noxlabels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">noylabels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cbaxes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">contours</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.plot.plot_vdf" title="Link to this definition"></a></dt>
+<dd><p>Plots a coloured 2D plot of a VDF (a slice of given thickness or fully projected) with axes and a colour bar.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Kword filename<span class="colon">:</span></dt>
+<dd class="field-odd"><p>path to .vlsv file to use for input. Assumes a bulk file.</p>
+</dd>
+<dt class="field-even">Kword vlsvobj<span class="colon">:</span></dt>
+<dd class="field-even"><p>Optionally provide a python vlsvfile object instead</p>
+</dd>
+<dt class="field-odd">Kword filedir<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Optionally provide directory where files are located and use step for bulk file name</p>
+</dd>
+<dt class="field-even">Kword step<span class="colon">:</span></dt>
+<dd class="field-even"><p>output step index, used for constructing output (and possibly input) filename</p>
+</dd>
+<dt class="field-odd">Kword outputdir<span class="colon">:</span></dt>
+<dd class="field-odd"><p>path to directory where output files are created (default: $HOME/Plots/ or override with PTOUTPUTDIR)
+If directory does not exist, it will be created. If the string does not end in a
+forward slash, the final parti will be used as a perfix for the files.</p>
+</dd>
+<dt class="field-even">Kword nooverwrite<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set to only perform actions if the target output file does not yet exist</p>
+</dd>
+<dt class="field-odd">Kword cellids<span class="colon">:</span></dt>
+<dd class="field-odd"><p>LIST of cell IDs to plot VDF for</p>
+</dd>
+<dt class="field-even">Kword coordinates<span class="colon">:</span></dt>
+<dd class="field-even"><p>LIST of 3-element spatial coordinate lusts to plot VDF for (given in metres)</p>
+</dd>
+<dt class="field-odd">Kword coordre<span class="colon">:</span></dt>
+<dd class="field-odd"><p>LIST of 3-element spatial coordinate lists to plot VDF for (given in Earth radii)</p>
+</dd>
+<dt class="field-even">Kword pop<span class="colon">:</span></dt>
+<dd class="field-even"><p>Population to plot, default proton</p>
+</dd>
+<dt class="field-odd">Kword colormap<span class="colon">:</span></dt>
+<dd class="field-odd"><p>colour scale for plot, use e.g. hot_desaturated, jet, viridis, plasma, inferno,
+magma, parula, nipy_spectral, RdBu, bwr</p>
+</dd>
+<dt class="field-even">Kword run<span class="colon">:</span></dt>
+<dd class="field-even"><p>run identifier, used for constructing output filename</p>
+</dd>
+<dt class="field-odd">Kword title<span class="colon">:</span></dt>
+<dd class="field-odd"><p>string to use as plot title instead of time.
+Special case: Set to “msec” to plot time with millisecond accuracy or “musec”
+for microsecond accuracy. “sec” is integer second accuracy.</p>
+</dd>
+<dt class="field-even">Kword cbtitle<span class="colon">:</span></dt>
+<dd class="field-even"><p>string to use as colorbar title instead of phase space density of flux</p>
+</dd>
+<dt class="field-odd">Kword contours<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set to number of contours to draw</p>
+</dd>
+<dt class="field-even">Kword fmin,fmax<span class="colon">:</span></dt>
+<dd class="field-even"><p>min and max values for colour scale and colour bar. If no values are given,
+min and max values for whole plot are used.</p>
+</dd>
+<dt class="field-odd">Kword box<span class="colon">:</span></dt>
+<dd class="field-odd"><p>extents of plotted velocity grid as [x0,x1,y0,y1] (in m/s)</p>
+</dd>
+<dt class="field-even">Kword axisunit<span class="colon">:</span></dt>
+<dd class="field-even"><p>Plot v-axes using 10^{axisunit} m/s (default: km/s)</p>
+</dd>
+<dt class="field-odd">Kword axiskmps<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Plot v-axes using 10^{axiskmps} km/s (default: km/s, when the kword has a value)</p>
+</dd>
+<dt class="field-even">Kword tickinterval<span class="colon">:</span></dt>
+<dd class="field-even"><p>Interval at which to have ticks on axes</p>
+</dd>
+<dt class="field-odd">Kword xy<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Perform slice in x-y-direction</p>
+</dd>
+<dt class="field-even">Kword xz<span class="colon">:</span></dt>
+<dd class="field-even"><p>Perform slice in x-z-direction</p>
+</dd>
+<dt class="field-odd">Kword yz<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Perform slice in y-z-direction</p>
+</dd>
+<dt class="field-even">Kword normal<span class="colon">:</span></dt>
+<dd class="field-even"><p>Perform slice in plane perpendicular to given vector</p>
+</dd>
+<dt class="field-odd">Kword normalx<span class="colon">:</span></dt>
+<dd class="field-odd"><p>X-axis direction for slice in plane perpendicular to given vector</p>
+</dd>
+<dt class="field-even">Kword bpara<span class="colon">:</span></dt>
+<dd class="field-even"><p>Perform slice in B_para / B_perp2 plane</p>
+</dd>
+<dt class="field-odd">Kword bpara1<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Perform slice in B_para / B_perp1 plane</p>
+</dd>
+<dt class="field-even">Kword bperp<span class="colon">:</span></dt>
+<dd class="field-even"><p>Perform slice in B_perp1 / B_perp2 plane
+If no plane is given, default is simulation plane (for 2D simulations)</p>
+</dd>
+<dt class="field-odd">Kword coordswap<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Swap the parallel and perpendicular coordinates</p>
+</dd>
+<dt class="field-even">Kword bvector<span class="colon">:</span></dt>
+<dd class="field-even"><p>Plot a magnetic field vector projection in-plane</p>
+</dd>
+<dt class="field-odd">Kword bvectorscale<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Scale of bvector (default: 0.2 in units of axis lengths)</p>
+</dd>
+<dt class="field-even">Kword cbulk<span class="colon">:</span></dt>
+<dd class="field-even"><p>Center plot on position of total bulk velocity (or if not available,
+bulk velocity for this population)</p>
+</dd>
+<dt class="field-odd">Kword cpeak<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Center plot on velocity associated with highest (peak) phase-space density for
+this population)</p>
+</dd>
+<dt class="field-even">Kword center<span class="colon">:</span></dt>
+<dd class="field-even"><p>Center plot on provided 3-element velocity vector position (in m/s)
+If set instead to “bulk” will center on bulk velocity
+If set instead to “peak” will center on velocity with highest phase-space density</p>
+</dd>
+<dt class="field-odd">Kword wflux<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Plot flux instead of distribution function</p>
+</dd>
+<dt class="field-even">Kword slicethick<span class="colon">:</span></dt>
+<dd class="field-even"><p>Thickness of slice as multiplier of cell size (default: 1 or minimum for good coverage).
+This can be set to zero in order to project the whole VDF to a plane.</p>
+</dd>
+<dt class="field-odd">Kword reducer<span class="colon">:</span></dt>
+<dd class="field-odd"><p>How to reduce to 2D - default ‘integrate’ for LOS integration
+and reduced units, ‘average’ for old (slightly questionable) behaviour</p>
+</dd>
+<dt class="field-even">Kword resampler<span class="colon">:</span></dt>
+<dd class="field-even"><p>Resample onto a regular grid? Default: yes, use False to disable.</p>
+</dd>
+<dt class="field-odd">Kword cellsize<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Plotting grid cell size as multiplier of input cell size (default: 1 or minimum for good coverage)</p>
+</dd>
+<dt class="field-even">Kword setThreshold<span class="colon">:</span></dt>
+<dd class="field-even"><p>Use given setThreshold value instead of EffectiveSparsityThreshold or MinValue value read from file
+Useful if EffectiveSparsityThreshold wasn’t saved, or user wants to draw buffer cells
+with values below the sparsity threshold</p>
+</dd>
+<dt class="field-odd">Kword wmark<span class="colon">:</span></dt>
+<dd class="field-odd"><p>If set to non-zero, will plot a Vlasiator watermark in the top left corner. If set to a text
+string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”</p>
+</dd>
+<dt class="field-even">Kword wmarkb<span class="colon">:</span></dt>
+<dd class="field-even"><p>As for wmark, but uses an all-black Vlasiator logo.</p>
+</dd>
+<dt class="field-odd">Kword draw<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Draw image on-screen instead of saving to file (requires x-windowing)</p>
+</dd>
+<dt class="field-even">Kword nocb<span class="colon">:</span></dt>
+<dd class="field-even"><p>Suppress plotting of colourbar legend</p>
+</dd>
+<dt class="field-odd">Kword internalcb<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set to draw colorbar inside plot instead of outside. If set to a text
+string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”</p>
+</dd>
+<dt class="field-even">Kword biglabel<span class="colon">:</span></dt>
+<dd class="field-even"><p>Plot large label (in top-left corner)</p>
+</dd>
+<dt class="field-odd">Kword biglabloc<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Move large label to: 0: NW 1: NE 2: SE 3: SW corner</p>
+</dd>
+<dt class="field-even">Kword axes<span class="colon">:</span></dt>
+<dd class="field-even"><p>Provide the routine a set of axes to draw within instead of generating a new image.</p>
+</dd>
+<dt class="field-odd">Kword cbaxes<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Provide the routine a set of axes for the colourbar.</p>
+</dd>
+<dt class="field-even">Kword noborder<span class="colon">:</span></dt>
+<dd class="field-even"><p>Plot figure edge-to-edge without borders (default off)</p>
+</dd>
+<dt class="field-odd">Kword noxlabels<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Suppress x-axis labels and title</p>
+</dd>
+<dt class="field-even">Kword noylabels<span class="colon">:</span></dt>
+<dd class="field-even"><p>Suppress y-axis labels and title</p>
+</dd>
+<dt class="field-odd">Kword scale<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Scale text size everywhere (default=1.0)</p>
+</dd>
+<dt class="field-even">Kword scale_text<span class="colon">:</span></dt>
+<dd class="field-even"><p>Most text additional scale factor (default=8.0)</p>
+</dd>
+<dt class="field-odd">Kword scale_title<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Title additional scale factor (default=10.0)</p>
+</dd>
+<dt class="field-even">Kword scale_cb<span class="colon">:</span></dt>
+<dd class="field-even"><p>Colour bar text additional scale factor (default=5.0)</p>
+</dd>
+<dt class="field-odd">Kword scale_label<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Big label text additional scale factor (default=12.0)</p>
+</dd>
+<dt class="field-even">Kword thick<span class="colon">:</span></dt>
+<dd class="field-even"><p>line and axis thickness, default=1.0</p>
+</dd>
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Outputs an image to a file or to the screen.</p>
+</dd>
+</dl>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span>
+</pre></div>
+</div>
+<p># Example usage:</p>
+<dl class="simple">
+<dt>pt.plot.plot_vdf(filename=”/proj/vlasov/2D/ABC/distributions/distributions.0000100.vlsv”,</dt><dd><p>coordre=[[11.7,-1.6,0.]], cbulk=1, bpara=1,box=[-2e6,2e6,-2e6,2e6],draw=1)</p>
+</dd>
+<dt>pt.plot.plot_vdf(filename=”/proj/vlasov/2D/ABC/distributions/distributions.0000100.vlsv”,</dt><dd><p>cellids=1670561, xy=1, box=[-2e6,2e6,-2e6,2e6], slicethick=5)</p>
+</dd>
+<dt>pt.plot.plot_vdf(filename=”/proj/vlasov/2D/ABC/distributions/distributions.0000100.vlsv”,</dt><dd><p>cellids=[1670561,], xz=1, box=[-2e6,2e6,-2e6,2e6], slicethick=0)</p>
+</dd>
+</dl>
+<p>Note tilted slices: By default, the program samples the V-space with a slice where each cell is cube the
+dimensions of which are found by performing a rotation on a sample square and finding the maximum xyz-extent. This ensures
+adequate coverage and decreases sampling effects. This behaviour can be overridden with the slicethick and cellsize keywords.</p>
+<p>Setting a value of slicethick=0 will result in the whole VDF being flattened into a single plane. This may result in
+some slight sampling artefacts, but is a good measure of complex populations.</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.plot.plot_vdf_profiles">
+<span class="sig-prename descclassname"><span class="pre">pytools.plot.</span></span><span class="sig-name descname"><span class="pre">plot_vdf_profiles</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vlsvobj</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filedir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">step</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cellids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'proton'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coordinates</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coordre</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outputdir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outputfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nooverwrite</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">draw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axisunit</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">title</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tickinterval</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">run</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">thick</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wmark</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wmarkb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vmin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xy</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xz</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">yz</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">normal</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bpara</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bpara1</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bperp</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cbulk</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cpeak</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">center</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">setThreshold</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.plot.plot_vdf_profiles" title="Link to this definition"></a></dt>
+<dd><p>Plots vdf values along axis-aligned lines (see axis definitions).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Kword filename<span class="colon">:</span></dt>
+<dd class="field-odd"><p>path to .vlsv file to use for input. Assumes a bulk file.</p>
+</dd>
+<dt class="field-even">Kword vlsvobj<span class="colon">:</span></dt>
+<dd class="field-even"><p>Optionally provide a python vlsvfile object instead</p>
+</dd>
+<dt class="field-odd">Kword filedir<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Optionally provide directory where files are located and use step for bulk file name</p>
+</dd>
+<dt class="field-even">Kword step<span class="colon">:</span></dt>
+<dd class="field-even"><p>output step index, used for constructing output (and possibly input) filename</p>
+</dd>
+<dt class="field-odd">Kword outputdir<span class="colon">:</span></dt>
+<dd class="field-odd"><p>path to directory where output files are created (default: $HOME/Plots/ or override with PTOUTPUTDIR)
+If directory does not exist, it will be created. If the string does not end in a
+forward slash, the final parti will be used as a perfix for the files.</p>
+</dd>
+<dt class="field-even">Kword nooverwrite<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set to only perform actions if the target output file does not yet exist</p>
+</dd>
+<dt class="field-odd">Kword cellids<span class="colon">:</span></dt>
+<dd class="field-odd"><p>LIST of cell IDs to plot VDF for</p>
+</dd>
+<dt class="field-even">Kword coordinates<span class="colon">:</span></dt>
+<dd class="field-even"><p>LIST of 3-element spatial coordinate lusts to plot VDF for (given in metres)</p>
+</dd>
+<dt class="field-odd">Kword coordre<span class="colon">:</span></dt>
+<dd class="field-odd"><p>LIST of 3-element spatial coordinate lists to plot VDF for (given in Earth radii)</p>
+</dd>
+<dt class="field-even">Kword pop<span class="colon">:</span></dt>
+<dd class="field-even"><p>Population to plot, default proton</p>
+</dd>
+<dt class="field-odd">Kword run<span class="colon">:</span></dt>
+<dd class="field-odd"><p>run identifier, used for constructing output filename</p>
+</dd>
+<dt class="field-even">Kword title<span class="colon">:</span></dt>
+<dd class="field-even"><p>string to use as plot title instead of time.
+Special case: Set to “msec” to plot time with millisecond accuracy or “musec”
+for microsecond accuracy. “sec” is integer second accuracy.</p>
+</dd>
+<dt class="field-odd">Kword fmin,fmax<span class="colon">:</span></dt>
+<dd class="field-odd"><p>min and max values for colour scale and colour bar. If no values are given,
+min and max values for whole plot are used.</p>
+</dd>
+<dt class="field-even">Kword vmin,vmax<span class="colon">:</span></dt>
+<dd class="field-even"><p>min and max values for x-axis</p>
+</dd>
+<dt class="field-odd">Kword axisunit<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Plot v-axes using 10^{axisunit} m/s (default: km/s)</p>
+</dd>
+<dt class="field-even">Kword tickinterval<span class="colon">:</span></dt>
+<dd class="field-even"><p>Interval at which to have ticks on axes</p>
+</dd>
+<dt class="field-odd">Kword lin<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Plot using linear y-axis (default log)</p>
+</dd>
+<dt class="field-even">Kword xy<span class="colon">:</span></dt>
+<dd class="field-even"><p>Perform slice in x-y-direction</p>
+</dd>
+<dt class="field-odd">Kword xz<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Perform slice in x-z-direction</p>
+</dd>
+<dt class="field-even">Kword yz<span class="colon">:</span></dt>
+<dd class="field-even"><p>Perform slice in y-z-direction</p>
+</dd>
+<dt class="field-odd">Kword normal<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Perform slice in plane perpendicular to given vector</p>
+</dd>
+<dt class="field-even">Kword bpara<span class="colon">:</span></dt>
+<dd class="field-even"><p>Perform slice in B_para / B_perp2 plane</p>
+</dd>
+<dt class="field-odd">Kword bpara1<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Perform slice in B_para / B_perp1 plane</p>
+</dd>
+<dt class="field-even">Kword bperp<span class="colon">:</span></dt>
+<dd class="field-even"><p>Perform slice in B_perp1 / B_perp2 plane
+If no plane is given, default is simulation plane (for 2D simulations)</p>
+</dd>
+<dt class="field-odd">Kword cbulk<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Center plot on position of total bulk velocity (or if not available,
+bulk velocity for this population)</p>
+</dd>
+<dt class="field-even">Kword cpeak<span class="colon">:</span></dt>
+<dd class="field-even"><p>Center plot on velocity with highest phase-space density</p>
+</dd>
+<dt class="field-odd">Kword center<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Center plot on provided 3-element velocity vector position (in m/s)
+If set instead to “bulk” will center on bulk velocity
+If set instead to “peak” will center on velocity with highest phase-space density</p>
+</dd>
+<dt class="field-even">Kword setThreshold<span class="colon">:</span></dt>
+<dd class="field-even"><p>Use given setThreshold value instead of EffectiveSparsityThreshold or MinValue value read from file
+Useful if EffectiveSparsityThreshold wasn’t saved, or user wants to draw buffer cells
+with values below the sparsity threshold</p>
+</dd>
+<dt class="field-odd">Kword wmark<span class="colon">:</span></dt>
+<dd class="field-odd"><p>If set to non-zero, will plot a Vlasiator watermark in the top left corner. If set to a text
+string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”</p>
+</dd>
+<dt class="field-even">Kword wmarkb<span class="colon">:</span></dt>
+<dd class="field-even"><p>As for wmark, but uses an all-black Vlasiator logo.</p>
+</dd>
+<dt class="field-odd">Kword draw<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Draw image on-screen instead of saving to file (requires x-windowing)</p>
+</dd>
+<dt class="field-even">Kword axes<span class="colon">:</span></dt>
+<dd class="field-even"><p>Provide the routine a set of axes to draw within instead of generating a new image.</p>
+</dd>
+<dt class="field-odd">Kword scale<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Scale text size (default=1.0)</p>
+</dd>
+<dt class="field-even">Kword thick<span class="colon">:</span></dt>
+<dd class="field-even"><p>line and axis thickness, default=1.0</p>
+</dd>
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Outputs an image to a file or to the screen.</p>
+</dd>
+</dl>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span>
+</pre></div>
+</div>
+<p># Example usage:</p>
+<dl class="simple">
+<dt>pt.plot.plot_vdf(filename=”/proj/vlasov/2D/ABC/distributions/distributions.0000100.vlsv”,</dt><dd><p>coordre=[[11.7,-1.6,0.]], cbulk=1, bpara=1,box=[-2e6,2e6,-2e6,2e6],draw=1)</p>
+</dd>
+<dt>pt.plot.plot_vdf(filename=”/proj/vlasov/2D/ABC/distributions/distributions.0000100.vlsv”,</dt><dd><p>cellids=1670561, xy=1, box=[-2e6,2e6,-2e6,2e6], slicethick=5)</p>
+</dd>
+<dt>pt.plot.plot_vdf(filename=”/proj/vlasov/2D/ABC/distributions/distributions.0000100.vlsv”,</dt><dd><p>cellids=[1670561,], xz=1, box=[-2e6,2e6,-2e6,2e6], slicethick=0)</p>
+</dd>
+</dl>
+<p>Note tilted slices: By default, the program samples the V-space with a slice where each cell is cube the
+dimensions of which are found by performing a rotation on a sample square and finding the maximum xyz-extent. This ensures
+adequate coverage and decreases sampling effects. This behaviour can be overridden with the slicethick and cellsize keywords.</p>
+<p>Setting a value of slicethick=0 will result in the whole VDF being flattened into a single plane. This may result in
+some slight sampling artefacts, but is a good measure of complex populations.</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="pytools.plot.plot_vdfdiff">
+<span class="sig-prename descclassname"><span class="pre">pytools.plot.</span></span><span class="sig-name descname"><span class="pre">plot_vdfdiff</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename1</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename2</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vlsvobj1</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vlsvobj2</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filedir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">step</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cellids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cellids2</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'proton'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coordinates</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coordre</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outputdir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outputfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nooverwrite</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">draw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axisunit</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axiskmps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">title</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cbtitle</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tickinterval</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">colormap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">box</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nocb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">internalcb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">run</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">thick</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wmark</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wmarkb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">slicethick</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reducer</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'integrate'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resampler</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cellsize</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xy</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xz</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">yz</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">normal</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">normalx</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bpara</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bpara1</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bperp</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coordswap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bvector</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bvectorscale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cbulk</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">center</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wflux</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">setThreshold</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">noborder</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale_text</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">8.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale_title</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale_cb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale_label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">12.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">biglabel</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">biglabloc</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">noxlabels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">noylabels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cbaxes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">contours</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.plot.plot_vdfdiff" title="Link to this definition"></a></dt>
+<dd><p>Plots the difference between VDFs as a coloured 2D plot with axes and a colour bar.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Kword filename1<span class="colon">:</span></dt>
+<dd class="field-odd"><p>path to .vlsv file to use for input. Assumes a bulk file.</p>
+</dd>
+<dt class="field-even">Kword filename2<span class="colon">:</span></dt>
+<dd class="field-even"><p>path to .vlsv file to use for input. Assumes a bulk file.</p>
+</dd>
+<dt class="field-odd">Kword vlsvobj1<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Optionally provide a python vlsvfile object instead</p>
+</dd>
+<dt class="field-even">Kword vlsvobj2<span class="colon">:</span></dt>
+<dd class="field-even"><p>Optionally provide a python vlsvfile object instead</p>
+</dd>
+<dt class="field-odd">Kword filedir<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Optionally provide directory where files are located and use step for bulk file name</p>
+</dd>
+<dt class="field-even">Kword step<span class="colon">:</span></dt>
+<dd class="field-even"><p>output step index, used for constructing output (and possibly input) filename</p>
+</dd>
+<dt class="field-odd">Kword outputdir<span class="colon">:</span></dt>
+<dd class="field-odd"><p>path to directory where output files are created (default: $HOME/Plots/ or override with PTOUTPUTDIR)
+If directory does not exist, it will be created. If the string does not end in a
+forward slash, the final parti will be used as a perfix for the files.</p>
+</dd>
+<dt class="field-even">Kword nooverwrite<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set to only perform actions if the target output file does not yet exist</p>
+</dd>
+<dt class="field-odd">Kword cellids<span class="colon">:</span></dt>
+<dd class="field-odd"><p>LIST of cell IDs to plot VDF for</p>
+</dd>
+<dt class="field-even">Kword cellids2<span class="colon">:</span></dt>
+<dd class="field-even"><p>Optional: LIST of cell IDs from input file 2. Same as cellids if omitted.</p>
+</dd>
+<dt class="field-odd">Kword coordinates<span class="colon">:</span></dt>
+<dd class="field-odd"><p>LIST of 3-element spatial coordinate lusts to plot VDF for (given in metres)</p>
+</dd>
+<dt class="field-even">Kword coordre<span class="colon">:</span></dt>
+<dd class="field-even"><p>LIST of 3-element spatial coordinate lists to plot VDF for (given in Earth radii)</p>
+</dd>
+<dt class="field-odd">Kword pop<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Population to plot, default proton</p>
+</dd>
+<dt class="field-even">Kword colormap<span class="colon">:</span></dt>
+<dd class="field-even"><p>colour scale for plot, use e.g. hot_desaturated, jet, viridis, plasma, inferno,
+magma, parula, nipy_spectral, RdBu, bwr</p>
+</dd>
+<dt class="field-odd">Kword run<span class="colon">:</span></dt>
+<dd class="field-odd"><p>run identifier, used for constructing output filename</p>
+</dd>
+<dt class="field-even">Kword title<span class="colon">:</span></dt>
+<dd class="field-even"><p>string to use as plot title instead of time.
+Special case: Set to “msec” to plot time with millisecond accuracy or “musec”
+for microsecond accuracy. “sec” is integer second accuracy.</p>
+</dd>
+<dt class="field-odd">Kword cbtitle<span class="colon">:</span></dt>
+<dd class="field-odd"><p>string to use as colorbar title instead of phase space density of flux</p>
+</dd>
+<dt class="field-even">Kword contours<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set to number of contours to draw</p>
+</dd>
+<dt class="field-odd">Kword fmin,fmax<span class="colon">:</span></dt>
+<dd class="field-odd"><p>min and max values for colour scale and colour bar. If no values are given,
+min and max values for whole plot are used.</p>
+</dd>
+<dt class="field-even">Kword box<span class="colon">:</span></dt>
+<dd class="field-even"><p>extents of plotted velocity grid as [x0,x1,y0,y1] (in m/s)</p>
+</dd>
+<dt class="field-odd">Kword axisunit<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Plot v-axes using 10^{axisunit} m/s (default: km/s)</p>
+</dd>
+<dt class="field-even">Kword axiskmps<span class="colon">:</span></dt>
+<dd class="field-even"><p>Plot v-axes using 10^{axiskmps} km/s (default: km/s, when the kword has a value)</p>
+</dd>
+<dt class="field-odd">Kword tickinterval<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Interval at which to have ticks on axes</p>
+</dd>
+<dt class="field-even">Kword xy<span class="colon">:</span></dt>
+<dd class="field-even"><p>Perform slice in x-y-direction</p>
+</dd>
+<dt class="field-odd">Kword xz<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Perform slice in x-z-direction</p>
+</dd>
+<dt class="field-even">Kword yz<span class="colon">:</span></dt>
+<dd class="field-even"><p>Perform slice in y-z-direction</p>
+</dd>
+<dt class="field-odd">Kword normal<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Perform slice in plane perpendicular to given vector</p>
+</dd>
+<dt class="field-even">Kword normalx<span class="colon">:</span></dt>
+<dd class="field-even"><p>X-axis direction for slice in plane perpendicular to given vector</p>
+</dd>
+<dt class="field-odd">Kword bpara<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Perform slice in B_para / B_perp2 plane</p>
+</dd>
+<dt class="field-even">Kword bpara1<span class="colon">:</span></dt>
+<dd class="field-even"><p>Perform slice in B_para / B_perp1 plane</p>
+</dd>
+<dt class="field-odd">Kword bperp<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Perform slice in B_perp1 / B_perp2 plane
+If no plane is given, default is simulation plane (for 2D simulations)</p>
+</dd>
+<dt class="field-even">Kword coordswap<span class="colon">:</span></dt>
+<dd class="field-even"><p>Swap the parallel and perpendicular coordinates</p>
+</dd>
+<dt class="field-odd">Kword bvector<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Plot a magnetic field vector projection in-plane</p>
+</dd>
+<dt class="field-even">Kword bvectorscale<span class="colon">:</span></dt>
+<dd class="field-even"><p>Scale of bvector (default: 0.2 in units of axis lengths)</p>
+</dd>
+<dt class="field-odd">Kword cbulk<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Center plot on position of total bulk velocity (or if not available,
+bulk velocity for this population)</p>
+</dd>
+<dt class="field-even">Kword center<span class="colon">:</span></dt>
+<dd class="field-even"><p>Center plot on provided 3-element velocity vector position (in m/s)
+If set instead to “bulk” will center on bulk velocity
+If set instead to “peak” will center on velocity with highest phase-space density</p>
+</dd>
+<dt class="field-odd">Kword wflux<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Plot flux instead of distribution function</p>
+</dd>
+<dt class="field-even">Kword slicethick<span class="colon">:</span></dt>
+<dd class="field-even"><p>Thickness of slice as multiplier of cell size (default: 1 or minimum for good coverage).
+This can be set to zero in order to project the whole VDF to a plane.</p>
+</dd>
+<dt class="field-odd">Kword reducer<span class="colon">:</span></dt>
+<dd class="field-odd"><p>How to reduce to 2D - default ‘integrate’ for LOS integration
+and reduced units, ‘average’ for old (slightly questionable) behaviour</p>
+</dd>
+<dt class="field-even">Kword resampler<span class="colon">:</span></dt>
+<dd class="field-even"><p>Resample onto a regular grid? Default: yes, use False to disable.</p>
+</dd>
+<dt class="field-odd">Kword cellsize<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Plotting grid cell size as multiplier of input cell size (default: 1 or minimum for good coverage)</p>
+</dd>
+<dt class="field-even">Kword setThreshold<span class="colon">:</span></dt>
+<dd class="field-even"><p>Use given setThreshold value instead of EffectiveSparsityThreshold or MinValue value read from file
+Useful if EffectiveSparsityThreshold wasn’t saved, or user wants to draw buffer cells
+with values below the sparsity threshold</p>
+</dd>
+<dt class="field-odd">Kword wmark<span class="colon">:</span></dt>
+<dd class="field-odd"><p>If set to non-zero, will plot a Vlasiator watermark in the top left corner. If set to a text
+string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”</p>
+</dd>
+<dt class="field-even">Kword wmarkb<span class="colon">:</span></dt>
+<dd class="field-even"><p>As for wmark, but uses an all-black Vlasiator logo.</p>
+</dd>
+<dt class="field-odd">Kword draw<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Draw image on-screen instead of saving to file (requires x-windowing)</p>
+</dd>
+<dt class="field-even">Kword nocb<span class="colon">:</span></dt>
+<dd class="field-even"><p>Suppress plotting of colourbar legend</p>
+</dd>
+<dt class="field-odd">Kword internalcb<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set to draw colorbar inside plot instead of outside. If set to a text
+string, tries to use that as the location, e.g. “NW”,”NE”,”SW”,”SW”</p>
+</dd>
+<dt class="field-even">Kword biglabel<span class="colon">:</span></dt>
+<dd class="field-even"><p>Plot large label (in top-left corner)</p>
+</dd>
+<dt class="field-odd">Kword biglabloc<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Move large label to: 0: NW 1: NE 2: SE 3: SW corner</p>
+</dd>
+<dt class="field-even">Kword axes<span class="colon">:</span></dt>
+<dd class="field-even"><p>Provide the routine a set of axes to draw within instead of generating a new image.</p>
+</dd>
+<dt class="field-odd">Kword cbaxes<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Provide the routine a set of axes for the colourbar.</p>
+</dd>
+<dt class="field-even">Kword noborder<span class="colon">:</span></dt>
+<dd class="field-even"><p>Plot figure edge-to-edge without borders (default off)</p>
+</dd>
+<dt class="field-odd">Kword noxlabels<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Suppress x-axis labels and title</p>
+</dd>
+<dt class="field-even">Kword noylabels<span class="colon">:</span></dt>
+<dd class="field-even"><p>Suppress y-axis labels and title</p>
+</dd>
+<dt class="field-odd">Kword scale<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Scale text size everywhere (default=1.0)</p>
+</dd>
+<dt class="field-even">Kword scale_text<span class="colon">:</span></dt>
+<dd class="field-even"><p>Most text additional scale factor (default=8.0)</p>
+</dd>
+<dt class="field-odd">Kword scale_title<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Title additional scale factor (default=10.0)</p>
+</dd>
+<dt class="field-even">Kword scale_cb<span class="colon">:</span></dt>
+<dd class="field-even"><p>Colour bar text additional scale factor (default=5.0)</p>
+</dd>
+<dt class="field-odd">Kword scale_label<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Big label text additional scale factor (default=12.0)</p>
+</dd>
+<dt class="field-even">Kword thick<span class="colon">:</span></dt>
+<dd class="field-even"><p>line and axis thickness, default=1.0</p>
+</dd>
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Outputs an image to a file or to the screen.</p>
+</dd>
+</dl>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span>
+</pre></div>
+</div>
+<p># Example usage:</p>
+<dl class="simple">
+<dt>pt.plot.plot_vdfdiff(“bulk.0000040.vlsv”,”bulk.0000048.vlsv”,cellids=1,xy=1,slicethick=1,colormap=”seismic”,</dt><dd><p>fmin=-1e-9,fmax=1e-9,cbulk=1)</p>
+</dd>
+</dl>
+<p>See documentation of plot_vdf() for more usage information.</p>
+</dd></dl>
+
+</section>
+
+
+           </div>
+          </div>
+          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
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+<li class="toctree-l1"><a class="reference internal" href="../miscellaneous/">miscellaneous</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../scripts/">scripts</a></li>
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+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+             
+
+   <h1>Python Module Index</h1>
+
+   <div class="modindex-jumpbox">
+   <a href="#cap-b"><strong>b</strong></a> | 
+   <a href="#cap-g"><strong>g</strong></a> | 
+   <a href="#cap-m"><strong>m</strong></a> | 
+   <a href="#cap-p"><strong>p</strong></a> | 
+   <a href="#cap-s"><strong>s</strong></a> | 
+   <a href="#cap-t"><strong>t</strong></a>
+   </div>
+
+   <table class="indextable modindextable">
+     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
+     <tr class="cap" id="cap-b"><td></td><td>
+       <strong>b</strong></td><td></td></tr>
+     <tr>
+       <td></td>
+       <td>
+       <a href="../biot_savart/#module-biot_savart"><code class="xref">biot_savart</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
+     <tr class="cap" id="cap-g"><td></td><td>
+       <strong>g</strong></td><td></td></tr>
+     <tr>
+       <td></td>
+       <td>
+       <a href="../gics/#module-gics"><code class="xref">gics</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
+     <tr class="cap" id="cap-m"><td></td><td>
+       <strong>m</strong></td><td></td></tr>
+     <tr>
+       <td></td>
+       <td>
+       <a href="../magnetopause2d/#module-magnetopause2d"><code class="xref">magnetopause2d</code></a></td><td>
+       <em></em></td></tr>
+     <tr>
+       <td></td>
+       <td>
+       <a href="../magnetopause3d/#module-magnetopause3d"><code class="xref">magnetopause3d</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
+     <tr class="cap" id="cap-p"><td></td><td>
+       <strong>p</strong></td><td></td></tr>
+     <tr>
+       <td><img src="../_static/minus.png" class="toggler"
+              id="toggle-1" style="display: none" alt="-" /></td>
+       <td>
+       <a href="../#module-pytools"><code class="xref">pytools</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="../calculations/#module-pytools.calculations"><code class="xref">pytools.calculations</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="../miscellaneous/#module-pytools.miscellaneous"><code class="xref">pytools.miscellaneous</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="../plot/#module-pytools.plot"><code class="xref">pytools.plot</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="../vlsvfile/#module-pytools.vlsvfile"><code class="xref">pytools.vlsvfile</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
+     <tr class="cap" id="cap-s"><td></td><td>
+       <strong>s</strong></td><td></td></tr>
+     <tr>
+       <td></td>
+       <td>
+       <a href="../shue/#module-shue"><code class="xref">shue</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
+     <tr class="cap" id="cap-t"><td></td><td>
+       <strong>t</strong></td><td></td></tr>
+     <tr>
+       <td></td>
+       <td>
+       <a href="../tsyganenko/#module-tsyganenko"><code class="xref">tsyganenko</code></a></td><td>
+       <em></em></td></tr>
+   </table>
+
+
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+
+
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+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>scripts &mdash; analysator  documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
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+              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="../plot/">plot</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../calculations/">calculations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../vlsvfile/">vlsvfile</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../miscellaneous/">miscellaneous</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">scripts</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#biot-savart">biot_savart</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#gics">gics</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#magnetopause2d">magnetopause2d</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#magnetopause3d">magnetopause3d</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#shue">shue</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#tsyganenko">tsyganenko</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="../biot_savart/">biot_savart</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../gics/">gics</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../magnetopause2d/">magnetopause2d</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../magnetopause3d/">magnetopause3d</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../shue/">shue</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../tsyganenko/">tsyganenko</a></li>
+</ul>
+</li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../about/">Credits</a></li>
+</ul>
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+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+             
+  <section id="scripts">
+<h1>scripts<a class="headerlink" href="#scripts" title="Link to this heading"></a></h1>
+<p>Scripts are not included in the main Analysator module import; instead, these are separate scripts utilising Analysator to some purpose.</p>
+<section id="biot-savart">
+<h2>biot_savart<a class="headerlink" href="#biot-savart" title="Link to this heading"></a></h2>
+<p><a class="reference internal" href="../biot_savart/"><span class="doc">biot_savart</span></a></p>
+<blockquote>
+<div><p>Follow Welling et al. (2020) calculate the magnetic field at Earth’s surface.</p>
+</div></blockquote>
+<p>Integrate Biot-Savart over:</p>
+<blockquote>
+<div><ol class="arabic simple">
+<li><p>All currents within the Vlasov domain</p></li>
+<li><p>Birkeland currents (FACs) in the “gap region” between the MHD inner boundary and the ionosphere, mapped (assuming J propto B) along the field lines connecting ionosphere radius R_IONO to coupling radius r_C</p></li>
+<li><p>Horizontal Ionospheric currents (altitude 100 km)</p></li>
+</ol>
+</div></blockquote>
+<p>The integration is a discrete summation over the 3 domains.</p>
+<p>Integrating the domain #2 will likely require this mesh to be ‘refined’ in order to resolve the FAC structures
+see the functions refine_mesh() and graded_mesh()</p>
+<p>This script has been tested with the Vlasiator runs EGL, FHA, FIA
+note that the usefulness for EGL is limited because there is no ionosphere (domain #3) for that run</p>
+<p>To run this script, require access to the data reducer/variable ‘vg_J’ in the .vlsv  file
+This may be supplied by a .vlsv file’s vlsvReader object, see keyword f_J_sidecar</p>
+<p>This script is written for the UH environment. Adapt file paths as needed.</p>
+<p>###</p>
+<p>EXAMPLE CALL (1 thread):
+python biot_savart.py -nproc 1 -task 1 -run FHA</p>
+<dl class="simple">
+<dt>Example sidecar .vlsv files,  containing ground magnetic field data, can be found at:</dt><dd><p>/wrk-vakka/group/spacephysics/vlasiator/3D/{run name}/sidecars/ig_B/</p>
+</dd>
+</dl>
+</section>
+<hr class="docutils" />
+<section id="gics">
+<h2>gics<a class="headerlink" href="#gics" title="Link to this heading"></a></h2>
+<p><a class="reference internal" href="../gics/"><span class="doc">gics</span></a></p>
+<p>Given a batch of .vlsv files, containing ground magnetic field vector data at different times,
+calculate the north &amp; east components of induced ground electric field [V/m], and save in corresponding .vlsv files</p>
+<p>This script has been tested with the Vlasiator runs EGL, FHA, FIA
+note that the usefulness for EGL is limited because there is no ionosphere (domain #3) for that run</p>
+<p>Note that the Geomagnetically Induced Currents (GICs) can be computed immediately from the geoelectric field:
+The surface current density is J = sigma*E, where E, sigma are respectively the ground electric field and conductivity.</p>
+<p>This script is written for the UH environment. Adapt file paths as needed.</p>
+<p>###</p>
+<dl class="simple">
+<dt>EXAMPLE CALL:</dt><dd><p>python gics.py</p>
+</dd>
+<dt>Example sidecar .vlsv files,  containing ground magnetic field data (over the ionosphere mesh), can be found at:</dt><dd><p>/wrk-vakka/group/spacephysics/vlasiator/3D/FHA/bulk1_sidecars/geoelectric_field/</p>
+</dd>
+</dl>
+</section>
+<hr class="docutils" />
+<section id="magnetopause2d">
+<h2>magnetopause2d<a class="headerlink" href="#magnetopause2d" title="Link to this heading"></a></h2>
+<p><a class="reference internal" href="../magnetopause2d/"><span class="doc">magnetopause2d</span></a></p>
+<p>Finds the magnetopause position by tracing steamines of the plasma flow for two-dimensional Vlasiator runs. Needs the yt package.</p>
+</section>
+<hr class="docutils" />
+<section id="magnetopause3d">
+<h2>magnetopause3d<a class="headerlink" href="#magnetopause3d" title="Link to this heading"></a></h2>
+<p><a class="reference internal" href="../magnetopause3d/"><span class="doc">magnetopause3d</span></a></p>
+<p>Finds the magnetopause position by tracing steamines of the plasma flow for three-dimensional Vlasiator runs. Needs the yt package.</p>
+</section>
+<hr class="docutils" />
+<section id="shue">
+<h2>shue<a class="headerlink" href="#shue" title="Link to this heading"></a></h2>
+<p><a class="reference internal" href="../shue/"><span class="doc">shue</span></a></p>
+<blockquote>
+<div><p>See Shue et al. (1997): “A new functional form to study the solar wind control of the magnetopause size and shape”</p>
+<p>They describe a model where the radial magnetopause position r is treated as a function of angle wrt x-GSE axis</p>
+<blockquote>
+<div><p>r(theta) = r_0 * (2 / (1+ cos(theta)))^alpha</p>
+</div></blockquote>
+<p>r_0 is the subsolar standoff distance [in earth radii], alpha is a dimensionless parameter</p>
+<dl class="simple">
+<dt>The parameters r_0, alpha depend on the solar wind parameters:</dt><dd><p>B_z: z-component (GSE) of the magnetic field [nT]
+n_p: number density [cm^-3]
+v_sw: solar wind speed [km/sec]</p>
+</dd>
+</dl>
+<p>Different Vlasiator runs had</p>
+</div></blockquote>
+<p>Example usage (plot magnetopause for run ‘EGI’):</p>
+<blockquote>
+<div><p>import numpy as np
+import matplotlib.pyplot as plt</p>
+<p>theta = np.linspace(0,np.pi / 2, 1000)
+r, r0, alpha = f_shue(theta, run=’EGI’)
+x = r*np.cos(theta)
+y = r*np.sin(theta)
+plt.plot(x,y)</p>
+</div></blockquote>
+</section>
+<hr class="docutils" />
+<section id="tsyganenko">
+<h2>tsyganenko<a class="headerlink" href="#tsyganenko" title="Link to this heading"></a></h2>
+<p><a class="reference internal" href="../tsyganenko/"><span class="doc">tsyganenko</span></a></p>
+<hr class="docutils" />
+<div class="toctree-wrapper compound">
+<p class="caption" role="heading"><span class="caption-text">Scripts:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../biot_savart/">biot_savart</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../biot_savart/#biot_savart.B_ionosphere"><code class="docutils literal notranslate"><span class="pre">B_ionosphere()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../biot_savart/#biot_savart.B_magnetosphere"><code class="docutils literal notranslate"><span class="pre">B_magnetosphere()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../biot_savart/#biot_savart.b_dip"><code class="docutils literal notranslate"><span class="pre">b_dip()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../biot_savart/#biot_savart.b_dip_direction"><code class="docutils literal notranslate"><span class="pre">b_dip_direction()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../biot_savart/#biot_savart.b_dip_magnitude"><code class="docutils literal notranslate"><span class="pre">b_dip_magnitude()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../biot_savart/#biot_savart.biot_savart"><code class="docutils literal notranslate"><span class="pre">biot_savart()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../biot_savart/#biot_savart.cartesian_to_spherical"><code class="docutils literal notranslate"><span class="pre">cartesian_to_spherical()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../biot_savart/#biot_savart.fac_map"><code class="docutils literal notranslate"><span class="pre">fac_map()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../biot_savart/#biot_savart.graded_mesh"><code class="docutils literal notranslate"><span class="pre">graded_mesh()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../biot_savart/#biot_savart.integrate_biot_savart"><code class="docutils literal notranslate"><span class="pre">integrate_biot_savart()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../biot_savart/#biot_savart.mkdir_path"><code class="docutils literal notranslate"><span class="pre">mkdir_path()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../biot_savart/#biot_savart.nearest_node_index"><code class="docutils literal notranslate"><span class="pre">nearest_node_index()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../biot_savart/#biot_savart.refine_mesh"><code class="docutils literal notranslate"><span class="pre">refine_mesh()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../biot_savart/#biot_savart.save_B_vlsv"><code class="docutils literal notranslate"><span class="pre">save_B_vlsv()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../biot_savart/#biot_savart.spherical_to_cartesian"><code class="docutils literal notranslate"><span class="pre">spherical_to_cartesian()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../biot_savart/#biot_savart.vec_len_2d"><code class="docutils literal notranslate"><span class="pre">vec_len_2d()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../biot_savart/#biot_savart.vec_unit"><code class="docutils literal notranslate"><span class="pre">vec_unit()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../gics/">gics</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../gics/#gics.E_horizontal"><code class="docutils literal notranslate"><span class="pre">E_horizontal()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../gics/#gics.cartesian_to_spherical"><code class="docutils literal notranslate"><span class="pre">cartesian_to_spherical()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../gics/#gics.cartesian_to_spherical_vector"><code class="docutils literal notranslate"><span class="pre">cartesian_to_spherical_vector()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../gics/#gics.mkdir_path"><code class="docutils literal notranslate"><span class="pre">mkdir_path()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../gics/#gics.spherical_to_cartesian"><code class="docutils literal notranslate"><span class="pre">spherical_to_cartesian()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../magnetopause2d/">magnetopause2d</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../magnetopause3d/">magnetopause3d</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../magnetopause3d/#magnetopause3d.make_surface"><code class="docutils literal notranslate"><span class="pre">make_surface()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../shue/">shue</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../shue/#shue.f_shue"><code class="docutils literal notranslate"><span class="pre">f_shue()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../tsyganenko/">tsyganenko</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../tsyganenko/#tsyganenko.spherical_to_cartesian"><code class="docutils literal notranslate"><span class="pre">spherical_to_cartesian()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../tsyganenko/#tsyganenko.tsyganenko_b"><code class="docutils literal notranslate"><span class="pre">tsyganenko_b()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../tsyganenko/#tsyganenko.tsyganenko_ocb"><code class="docutils literal notranslate"><span class="pre">tsyganenko_ocb()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../tsyganenko/#tsyganenko.tsyganenko_open"><code class="docutils literal notranslate"><span class="pre">tsyganenko_open()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../tsyganenko/#tsyganenko.tsyganenko_trace"><code class="docutils literal notranslate"><span class="pre">tsyganenko_trace()</span></code></a></li>
+</ul>
+</li>
+</ul>
+</div>
+</section>
+</section>
+
+
+           </div>
+          </div>
+          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
+        <a href="../miscellaneous/" class="btn btn-neutral float-left" title="miscellaneous" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="../biot_savart/" class="btn btn-neutral float-right" title="biot_savart" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+    </div>
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diff --git a/search/index.html b/search/index.html
new file mode 100644
index 00000000..66077cef
--- /dev/null
+++ b/search/index.html
@@ -0,0 +1,127 @@
+
+
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../">
+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Search &mdash; analysator  documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
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+      <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
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+    <script src="../_static/language_data.js"></script>
+    <link rel="author" title="About these documents" href="../about/" />
+    <link rel="index" title="Index" href="../genindex/" />
+    <link rel="search" title="Search" href="#" /> 
+</head>
+
+<body class="wy-body-for-nav"> 
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
+
+          
+          
+          <a href="../" class="icon icon-home">
+            analysator
+              <img src="../_static/logo_color.png" class="logo" alt="Logo"/>
+          </a>
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="#" method="get">
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
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+  </form>
+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../plot/">plot</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../calculations/">calculations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../vlsvfile/">vlsvfile</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../miscellaneous/">miscellaneous</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../scripts/">scripts</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../about/">Credits</a></li>
+</ul>
+
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+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="../">analysator</a>
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+        <div class="rst-content">
+          <div role="navigation" aria-label="Page navigation">
+  <ul class="wy-breadcrumbs">
+      <li><a href="../" class="icon icon-home" aria-label="Home"></a></li>
+      <li class="breadcrumb-item active">Search</li>
+      <li class="wy-breadcrumbs-aside">
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+             
+  <noscript>
+  <div id="fallback" class="admonition warning">
+    <p class="last">
+      Please activate JavaScript to enable the search functionality.
+    </p>
+  </div>
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+  <div id="search-results">
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+           </div>
+          </div>
+          <footer>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2024, University of Helsinki.</p>
+  </div>
+
+  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
+    provided by <a href="https://readthedocs.org">Read the Docs</a>.
+   
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+</footer>
+        </div>
+      </div>
+    </section>
+  </div>
+  <script>
+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
+      });
+  </script>
+  <script>
+    jQuery(function() { Search.loadIndex("../searchindex.js"); });
+  </script>
+  
+  <script id="searchindexloader"></script>
+   
+
+
+</body>
+</html>
\ No newline at end of file
diff --git a/searchindex.js b/searchindex.js
new file mode 100644
index 00000000..4523e1e9
--- /dev/null
+++ b/searchindex.js
@@ -0,0 +1 @@
+Search.setIndex({"alltitles": {"Contents:": [[4, null]], "Credits": [[0, null]], "Scripts:": [[9, null]], "analysator documentation": [[4, null]], "biot_savart": [[1, null], [9, "biot-savart"]], "calculations": [[2, null]], "gics": [[3, null], [9, "gics"]], "magnetopause2d": [[5, null], [9, "magnetopause2d"]], "magnetopause3d": [[6, null], [9, "magnetopause3d"]], "miscellaneous": [[7, null]], "plot": [[8, null]], "scripts": [[9, null]], "shue": [[9, "shue"], [10, null]], "tsyganenko": [[9, "tsyganenko"], [11, null]], "vlsvfile": [[12, null]]}, "docnames": ["about", "biot_savart", "calculations", "gics", "index", "magnetopause2d", "magnetopause3d", "miscellaneous", "plot", "scripts", "shue", "tsyganenko", "vlsvfile"], "envversion": {"sphinx": 64, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 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pytools.calculations)": [[2, "pytools.calculations.cut_through_curve", false]], "cut_through_step() (in module pytools.calculations)": [[2, "pytools.calculations.cut_through_step", false]], "downsample_fsgrid_subarray() (pytools.vlsvfile.vlsvreader method)": [[12, "pytools.vlsvfile.VlsvReader.downsample_fsgrid_subarray", false]], "dynamic_field_tracer() (in module pytools.calculations)": [[2, "pytools.calculations.dynamic_field_tracer", false]], "e_horizontal() (in module gics)": [[3, "gics.E_horizontal", false]], "epsilon_m() (in module pytools.calculations)": [[2, "pytools.calculations.epsilon_M", false]], "f_shue() (in module shue)": [[10, "shue.f_shue", false]], "fac_map() (in module biot_savart)": [[1, "biot_savart.fac_map", false]], "fourier() (in module pytools.calculations)": [[2, "pytools.calculations.fourier", false]], "fsgrid_array_to_vg() (pytools.vlsvfile.vlsvreader method)": [[12, "pytools.vlsvfile.VlsvReader.fsgrid_array_to_vg", false]], "get_all_variables() 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+<li class="toctree-l3 current"><a class="current reference internal" href="#">shue</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#shue.f_shue"><code class="docutils literal notranslate"><span class="pre">f_shue()</span></code></a></li>
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+             
+  <section id="module-shue">
+<span id="shue"></span><h1>shue<a class="headerlink" href="#module-shue" title="Link to this heading"></a></h1>
+<blockquote>
+<div><p>See Shue et al. (1997): “A new functional form to study the solar wind control of the magnetopause size and shape”</p>
+<p>They describe a model where the radial magnetopause position r is treated as a function of angle wrt x-GSE axis</p>
+<blockquote>
+<div><p>r(theta) = r_0 * (2 / (1+ cos(theta)))^alpha</p>
+</div></blockquote>
+<p>r_0 is the subsolar standoff distance [in earth radii], alpha is a dimensionless parameter</p>
+<dl class="simple">
+<dt>The parameters r_0, alpha depend on the solar wind parameters:</dt><dd><p>B_z: z-component (GSE) of the magnetic field [nT]
+n_p: number density [cm^-3]
+v_sw: solar wind speed [km/sec]</p>
+</dd>
+</dl>
+<p>Different Vlasiator runs had</p>
+</div></blockquote>
+<p>Example usage (plot magnetopause for run ‘EGI’):</p>
+<blockquote>
+<div><p>import numpy as np
+import matplotlib.pyplot as plt</p>
+<p>theta = np.linspace(0,np.pi / 2, 1000)
+r, r0, alpha = f_shue(theta, run=’EGI’)
+x = r*np.cos(theta)
+y = r*np.sin(theta)
+plt.plot(x,y)</p>
+</div></blockquote>
+<dl class="py function">
+<dt class="sig sig-object py" id="shue.f_shue">
+<span class="sig-prename descclassname"><span class="pre">shue.</span></span><span class="sig-name descname"><span class="pre">f_shue</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">theta_polar</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">run</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">B_z</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n_p</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v_sw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#shue.f_shue" title="Link to this definition"></a></dt>
+<dd><p>Shue et al. (1997): ‘A new functional form to study the solar wind control of the magnetopause size and shape’`</p>
+<dl class="simple">
+<dt>Inputs:</dt><dd><dl class="simple">
+<dt>theta_polar: 1D numpy array [radians], angle wrt x-GSE axis</dt><dd><p>0 &lt; theta_polar &lt; 2pi</p>
+</dd>
+<dt>keyword run: string containing Vlasiator run name (e.g. ‘EGI’) </dt><dd><p>If set, look up the solar wind parameters B_z, n_p, v_sw for this run</p>
+</dd>
+</dl>
+</dd>
+<dt>Output:</dt><dd><p>magnetopause position r(theta) [R_E]</p>
+</dd>
+</dl>
+<p>TODO: instead of using _f_shue_parameters(), use VlsvReader object’s get_config() method to look up parameters.</p>
+</dd></dl>
+
+</section>
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+<li class="toctree-l3"><a class="reference internal" href="../shue/">shue</a></li>
+<li class="toctree-l3 current"><a class="current reference internal" href="#">tsyganenko</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#tsyganenko.spherical_to_cartesian"><code class="docutils literal notranslate"><span class="pre">spherical_to_cartesian()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#tsyganenko.tsyganenko_b"><code class="docutils literal notranslate"><span class="pre">tsyganenko_b()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#tsyganenko.tsyganenko_ocb"><code class="docutils literal notranslate"><span class="pre">tsyganenko_ocb()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#tsyganenko.tsyganenko_open"><code class="docutils literal notranslate"><span class="pre">tsyganenko_open()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#tsyganenko.tsyganenko_trace"><code class="docutils literal notranslate"><span class="pre">tsyganenko_trace()</span></code></a></li>
+</ul>
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+             
+  <section id="module-tsyganenko">
+<span id="tsyganenko"></span><h1>tsyganenko<a class="headerlink" href="#module-tsyganenko" title="Link to this heading"></a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="tsyganenko.spherical_to_cartesian">
+<span class="sig-prename descclassname"><span class="pre">tsyganenko.</span></span><span class="sig-name descname"><span class="pre">spherical_to_cartesian</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">r</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">theta</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">phi</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#tsyganenko.spherical_to_cartesian" title="Link to this definition"></a></dt>
+<dd><p>r &gt; 0
+0 &lt; theta &lt; pi
+-pi &lt; phi &lt; pi
+all are assumed to be numpy arrays of equal dimensions</p>
+<p>returns:  x, y, z   [tuple]</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="tsyganenko.tsyganenko_b">
+<span class="sig-prename descclassname"><span class="pre">tsyganenko.</span></span><span class="sig-name descname"><span class="pre">tsyganenko_b</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">z</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Txx</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'t01'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">InternalB</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'dipole'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Dst</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-30</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Kp</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">4</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Vx_sw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-750.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">N_sw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Bx_imf</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">By_imf</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Bz_imf</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-5.0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#tsyganenko.tsyganenko_b" title="Link to this definition"></a></dt>
+<dd><p>Wrapper for Geopack’s trace() routine, for tracing field lines along Tsyganenko model</p>
+<dl>
+<dt>Inputs:</dt><dd><p>x0: x-coordinate(s) (GSE) to evaluate the field [R_E]  (float)
+y0: y-coordinate(s) (GSE) to evaluate the field [R_E]  (float)
+z0: z-coordinate(s) (GSE) to evaluate the field [R_E]  (float)</p>
+<p>–Keywords–</p>
+<dl class="simple">
+<dt>Txx: (external) field model, by Tsyganenko publication year. options: ‘t89’, ‘t96’, ‘t01’</dt><dd><p>Need to test: does ‘t04’ work? Is geomagnetic activity estimated with Kp or Dst in that case?</p>
+</dd>
+</dl>
+<p>InternalB: internal model. options: ‘dipole’, ‘igrf’
+Dst: Dst index in nT (geomagnetic activity), used for Txx= ‘t96’, ‘t01’ (‘t04’?)
+Kp: Kp index 0-9 (geomagnetic activity), used for Txx=’T89’
+Vx_sw: solar wind x-component of velocity [km/s] (GSE), other components assumed zero
+N_sw: solar wind density [cm-3]
+Bx_imf: driving solar wind imf Bx [nT] (GSE)
+By_imf: driving solar wind GSE imf By [nT] (GSE)
+Bz_imf: driving solar wind GSE imf Bz [nT] (GSE)
+R_inner: inner radius [R_E] of the tracing, if the tracing goes r&lt;R_inner it stops
+R_outer: outer radius [R_E] of the tracing, if the tracing goes r&gt;R_outer it stops</p>
+<dl>
+<dt>dir: direction of the tracing relative to the magnetic field direction (parallel: dir= 1, anti-parallel: dir= -1)</dt><dd><p>If unspecified (dir=None), dir traces against the field when z0&gt;0 with the field when z0&lt;0</p>
+<dl class="simple">
+<dt>*** this is the opposite convention used by geopack’s trace() function?</dt><dd><p>From geopack.py docs: “dir: Direction of tracing. dir = -1 for parallel; dir = 1 for anti-parallel.”</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd>
+<dt>Returns:</dt><dd><p>3-element tuple bx,by,bz
+bx: x-component(s) of field [nT]
+by: y-component(s) of field [nT]
+bz: z-component(s) of field [nT]</p>
+<p>** All positional inputs can either be single values or numpy arrays (or lists) **
+** Depending on the inputs, the outputs bx, by, bz will either be single numbers or numpy arrays **
+** All inputs and outputs are in GSE coordinate system **</p>
+</dd>
+<dt>Example:</dt><dd><p>bx,by,bz = tsyganenko_b(0,0, 1., Txx = ‘t01’, Dst = -80, Kp = 4, Vx_sw = -750., N_sw = 4., Bx_imf = 0., By_imf = 0., Bz_imf = -10. )</p>
+<p>bx,by,bz = tsyganenko_b([0,0,0],[0,0,0], [1.,2,3], Txx = ‘t01’, Dst = -80, Kp = 4, Vx_sw = -750., N_sw = 4., Bx_imf = 0., By_imf = 0., Bz_imf = -10. )</p>
+</dd>
+</dl>
+<p>Notes:</p>
+<blockquote>
+<div><p>Earth’s dipole is assumed to point (~exactly) in the -z GSE direction</p>
+<p>Default solar wind and IMF parameters are for the EGI Vlasiator run, see Grandin et al. (2022?)</p>
+<blockquote>
+<div><p>Other runs:</p>
+<dl class="simple">
+<dt>EGL (note: pulse arrives at magnetopause at roughly t=857 sec)</dt><dd><p>(~before pulse arrival): Dst = -30 (Grandin et al. 2022), N_sw = 1, Bz_imf = -5
+(~after pulse arrival):  Dst = -80 (Horaites et al.), N_sw = 4, Bz_imf = -10</p>
+</dd>
+</dl>
+</div></blockquote>
+<p>The geopack package doesn’t allow for easy specification of the dipole tilt angle.
+Rather, a UT was found when the tilt was nearly zero (see gp.recalc() line below)
+The specified UT results in a tilt angle of theta~1e-5 radians, or 6e-4 degrees
+Technically, the solutions should be rotated back by theta, to be compared with Vlasiator’s zero-tilt runs
+But this small theta is within tolerance for most applications.</p>
+</div></blockquote>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="tsyganenko.tsyganenko_ocb">
+<span class="sig-prename descclassname"><span class="pre">tsyganenko.</span></span><span class="sig-name descname"><span class="pre">tsyganenko_ocb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">phi</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lat_range</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[0,</span> <span class="pre">90]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nsteps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#tsyganenko.tsyganenko_ocb" title="Link to this definition"></a></dt>
+<dd><p>Find the open/closed field line boundary (OCB)
+algorithm uses a binary search within a specified latitude range</p>
+<dl>
+<dt>Inputs:</dt><dd><p>phi: ~longitude, in degrees                                                     -180&lt;=phi&lt;=180
+lat_range: 2-element list or numpy array,</p>
+<blockquote>
+<div><p>containing min. and max. latidues [degrees] to search within         -90&lt;=lat&lt;=90</p>
+</div></blockquote>
+<p>kwargs are passed to tsyanenko_open()</p>
+</dd>
+</dl>
+<p>Returns:</p>
+<blockquote>
+<div><p>Estimate of the OCB latitude at the given phi, in degrees</p>
+</div></blockquote>
+<dl>
+<dt>Notes:</dt><dd><p>Algorithm assumes OBC latitude is a single-valued function of phi</p>
+<p>Theoretical accuracy of the OCB determination is ~ (lat_range[1]-lat_range[0]) / 2^nsteps</p>
+</dd>
+</dl>
+<p>Example:   # dayside (noon) cusp</p>
+<blockquote>
+<div><dl class="simple">
+<dt>tsyganenko_ocb(0, lat_range = [60,80], nsteps = 10, </dt><dd><p>Txx = ‘t01’, Dst = -80, Kp = 4, Vx_sw = -750., N_sw = 4., Bx_imf = 0., By_imf = 0., Bz_imf = -10., 
+R_inner = 1., R_outer=15., dir = None, maxloop = 10000)</p>
+</dd>
+</dl>
+</div></blockquote>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="tsyganenko.tsyganenko_open">
+<span class="sig-prename descclassname"><span class="pre">tsyganenko.</span></span><span class="sig-name descname"><span class="pre">tsyganenko_open</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">phi</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lat</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">R_inner</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">R_outer</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">15</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#tsyganenko.tsyganenko_open" title="Link to this definition"></a></dt>
+<dd><p>Checks whether the field line starting at radius ~R_inner
+will trace out to beyond R_outer. R_outer is chosen to be large, so if 
+a magnetic field line makes it out this far, it may be assumed to be open
+If the tracing crosses R_inner, the field line is closed</p>
+<dl>
+<dt>Inputs: </dt><dd><p>phi: ~longitude, in degrees                    -180&lt;=phi&lt;=180
+lat: geographic latitude, in degrees           -90&lt;=lat&lt;=90</p>
+<blockquote>
+<div><dl class="simple">
+<dt>e.g.,</dt><dd><p>(phi=0, lat = 0) corresponds with subsolar point
+(phi=anything, lat = 90) corresponds with geographic north pole</p>
+</dd>
+</dl>
+</div></blockquote>
+<p>R_inner: inner radius [R_E] of the tracing, if the tracing goes r&lt;R_inner it stops
+R_outer: outer radius [R_E] of the tracing, if the tracing goes r&gt;R_outer it stops</p>
+<p>Keywords (and kwargs) all get passed to tsyganenko_trace()</p>
+</dd>
+<dt>Returns:</dt><dd><dl class="simple">
+<dt>Boolean—</dt><dd><p>True (if open)
+False (if closed)</p>
+</dd>
+</dl>
+</dd>
+<dt>Example: </dt><dd><p>tsyganenko_open(0, 45)   # returns False
+tsyganenko_open(0, 80)   # returns True</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="tsyganenko.tsyganenko_trace">
+<span class="sig-prename descclassname"><span class="pre">tsyganenko.</span></span><span class="sig-name descname"><span class="pre">tsyganenko_trace</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">z0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Txx</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'t01'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">InternalB</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'dipole'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Dst</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-30</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Kp</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">4</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Vx_sw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-750.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">N_sw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Bx_imf</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">By_imf</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Bz_imf</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-5.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">R_inner</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.99</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">R_outer</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">4.8</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">maxloop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">20000</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#tsyganenko.tsyganenko_trace" title="Link to this definition"></a></dt>
+<dd><p>Wrapper for Geopack’s trace() routine, for tracing field lines along Tsyganenko model</p>
+<dl>
+<dt>Inputs:</dt><dd><p>x0: initial x-coordinate (GSE) of field tracing [R_E]  (float)
+y0: initial y-coordinate (GSE) of field tracing [R_E]  (float)
+z0: initial z-coordinate (GSE) of field tracing [R_E]  (float)</p>
+<p>–Keywords–</p>
+<dl class="simple">
+<dt>Txx:</dt><dd><dl class="simple">
+<dt>(external) field model, by Tsyganenko publication year. options: ‘t89’, ‘t96’, ‘t01’</dt><dd><p>Need to test: does ‘t04’ work? Is geomagnetic activity estimated with Kp or Dst in that case?</p>
+</dd>
+</dl>
+</dd>
+</dl>
+<p>InternalB: internal model. options: ‘dipole’, ‘igrf’
+Dst: Dst index in nT (geomagnetic activity), used for Txx= ‘t96’, ‘t01’ (‘t04’?)
+Kp: Kp index 0-9 (geomagnetic activity), used for Txx=’T89’
+Vx_sw: solar wind x-component of velocity [km/s] (GSE), other components assumed zero
+N_sw: solar wind density [cm-3]
+Bx_imf: driving solar wind imf Bx [nT] (GSE)
+By_imf: driving solar wind GSE imf By [nT] (GSE)
+Bz_imf: driving solar wind GSE imf Bz [nT] (GSE)
+R_inner: inner radius [R_E] of the tracing, if the tracing goes r&lt;R_inner it stops
+R_outer: outer radius [R_E] of the tracing, if the tracing goes r&gt;R_outer it stops</p>
+<dl>
+<dt>dir: direction of the tracing relative to the magnetic field direction (parallel: dir= 1, anti-parallel: dir= -1)</dt><dd><p>If unspecified (dir=None), dir traces against the field when z0&gt;0 with the field when z0&lt;0</p>
+<dl class="simple">
+<dt>*** this is the opposite convention used by geopack’s trace() function?</dt><dd><p>From geopack.py docs: “dir: Direction of tracing. dir = -1 for parallel; dir = 1 for anti-parallel.”</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd>
+<dt>Returns:</dt><dd><p>6-element tuple x,y,z,xx,yy,zz
+x: final x-coordinate(s) of field tracing [R_E]
+y: final y-coordinate(s) of field tracing [R_E]
+z: final z-coordinate(s) of field tracing [R_E]
+xx: numpy array containing the traced field line x-coordinates 
+yy: numpy array containing the traced field line y-coordinates 
+zz: numpy array containing the traced field line z-coordinates</p>
+<p>** All inputs and outputs are in GSE coordinate system **</p>
+</dd>
+<dt>Example:</dt><dd><p>x,y,z,xx,yy,zz = tsyganenko_trace(0,0, 1., Txx = ‘t01’, Dst = -80, Kp = 4, Vx_sw = -750., N_sw = 4., Bx_imf = 0., By_imf = 0., Bz_imf = -10., R_inner = 1., R_outer=5., dir = None, maxloop = 20000 )</p>
+</dd>
+</dl>
+<p>Notes:</p>
+<blockquote>
+<div><p>Earth’s dipole is assumed to point (~exactly) in the -z GSE direction</p>
+<p>Default solar wind and IMF parameters are for the EGI Vlasiator run, see Grandin et al. (2022?)</p>
+<blockquote>
+<div><p>Other runs:</p>
+<dl class="simple">
+<dt>EGL (note: pulse arrives at magnetopause at roughly t=857 sec)</dt><dd><p>(~before pulse arrival): Dst = -30 (Grandin et al. 2022), N_sw = 1, Bz_imf = -5
+(~after pulse arrival):  Dst = -80 (Horaites et al.), N_sw = 4, Bz_imf = -10</p>
+</dd>
+</dl>
+</div></blockquote>
+<p>The geopack package doesn’t allow for easy specification of the dipole tilt angle.
+Rather, a UT was found when the tilt was nearly zero (see gp.recalc() line below)
+The specified UT results in a tilt angle of theta~1e-5 radians, or 6e-4 degrees
+Technically, the solutions should be rotated back by theta, to be compared with Vlasiator’s zero-tilt runs
+But this small theta is within tolerance for most applications.</p>
+</div></blockquote>
+</dd></dl>
+
+</section>
+
+
+           </div>
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diff --git a/vlsvfile/index.html b/vlsvfile/index.html
new file mode 100644
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+              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="../plot/">plot</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../calculations/">calculations</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">vlsvfile</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.vlsvfile.VlasiatorReader"><code class="docutils literal notranslate"><span class="pre">VlasiatorReader</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.vlsvfile.VlsvParticles"><code class="docutils literal notranslate"><span class="pre">VlsvParticles</span></code></a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvParticles.list"><code class="docutils literal notranslate"><span class="pre">VlsvParticles.list()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvParticles.read_particles"><code class="docutils literal notranslate"><span class="pre">VlsvParticles.read_particles()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvParticles.read_particles_all"><code class="docutils literal notranslate"><span class="pre">VlsvParticles.read_particles_all()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader"><code class="docutils literal notranslate"><span class="pre">VlsvReader</span></code></a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.build_cell_vertices"><code class="docutils literal notranslate"><span class="pre">VlsvReader.build_cell_vertices()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.cellid_has_vdf"><code class="docutils literal notranslate"><span class="pre">VlsvReader.cellid_has_vdf()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.check_parameter"><code class="docutils literal notranslate"><span class="pre">VlsvReader.check_parameter()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.check_population"><code class="docutils literal notranslate"><span class="pre">VlsvReader.check_population()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.check_variable"><code class="docutils literal notranslate"><span class="pre">VlsvReader.check_variable()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.construct_velocity_cell_coordinates"><code class="docutils literal notranslate"><span class="pre">VlsvReader.construct_velocity_cell_coordinates()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.construct_velocity_cell_nodes"><code class="docutils literal notranslate"><span class="pre">VlsvReader.construct_velocity_cell_nodes()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.construct_velocity_cells"><code class="docutils literal notranslate"><span class="pre">VlsvReader.construct_velocity_cells()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.downsample_fsgrid_subarray"><code class="docutils literal notranslate"><span class="pre">VlsvReader.downsample_fsgrid_subarray()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.fsgrid_array_to_vg"><code class="docutils literal notranslate"><span class="pre">VlsvReader.fsgrid_array_to_vg()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_all_variables"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_all_variables()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_amr_level"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_amr_level()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_bbox_fsgrid_slicemap"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_bbox_fsgrid_slicemap()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_bbox_fsgrid_subarray"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_bbox_fsgrid_subarray()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_cell_bbox"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_cell_bbox()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_cell_coordinates"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_cell_coordinates()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_cell_corner_vertices"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_cell_corner_vertices()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_cell_dx"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_cell_dx()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_cell_fsgrid"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_cell_fsgrid()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_cell_fsgrid_slicemap"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_cell_fsgrid_slicemap()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_cell_fsgrid_subarray"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_cell_fsgrid_subarray()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_cell_indices"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_cell_indices()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_cell_neighbor"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_cell_neighbor()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_cellid"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_cellid()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_cellid_locations"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_cellid_locations()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_cellid_with_vdf"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_cellid_with_vdf()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_config"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_config()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_config_string"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_config_string()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_dual"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_dual()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_duals"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_duals()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_fsgrid_cell_size"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_fsgrid_cell_size()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_fsgrid_coordinates"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_fsgrid_coordinates()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_fsgrid_indices"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_fsgrid_indices()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_fsgrid_mesh_extent"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_fsgrid_mesh_extent()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_fsgrid_mesh_size"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_fsgrid_mesh_size()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_fsgrid_slice_indices"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_fsgrid_slice_indices()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_ionosphere_element_coords"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_ionosphere_element_coords()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_ionosphere_element_corners"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_ionosphere_element_corners()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_ionosphere_latlon_coords"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_ionosphere_latlon_coords()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_ionosphere_mesh_area"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_ionosphere_mesh_area()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_ionosphere_mesh_size"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_ionosphere_mesh_size()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_ionosphere_node_coords"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_ionosphere_node_coords()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_max_refinement_level"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_max_refinement_level()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_precipitation_centre_energy"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_precipitation_centre_energy()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_spatial_block_size"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_spatial_block_size()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_spatial_mesh_extent"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_spatial_mesh_extent()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_spatial_mesh_size"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_spatial_mesh_size()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_unique_cellids"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_unique_cellids()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_velocity_block_coordinates"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_velocity_block_coordinates()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_velocity_block_indices"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_velocity_block_indices()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_velocity_block_size"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_velocity_block_size()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_velocity_blocks"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_velocity_blocks()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_velocity_cell_coordinates"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_velocity_cell_coordinates()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_velocity_cell_ids"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_velocity_cell_ids()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_velocity_mesh_dv"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_velocity_mesh_dv()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_velocity_mesh_extent"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_velocity_mesh_extent()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_velocity_mesh_size"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_velocity_mesh_size()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_vertex_coordinates_from_indices"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_vertex_coordinates_from_indices()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_vertex_indices"><code class="docutils literal notranslate"><span class="pre">VlsvReader.get_vertex_indices()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.list"><code class="docutils literal notranslate"><span class="pre">VlsvReader.list()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.optimize_clear_fileindex_for_cellid"><code class="docutils literal notranslate"><span class="pre">VlsvReader.optimize_clear_fileindex_for_cellid()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.optimize_clear_fileindex_for_cellid_blocks"><code class="docutils literal notranslate"><span class="pre">VlsvReader.optimize_clear_fileindex_for_cellid_blocks()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.optimize_close_file"><code class="docutils literal notranslate"><span class="pre">VlsvReader.optimize_close_file()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.optimize_open_file"><code class="docutils literal notranslate"><span class="pre">VlsvReader.optimize_open_file()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.print_config"><code class="docutils literal notranslate"><span class="pre">VlsvReader.print_config()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.print_version"><code class="docutils literal notranslate"><span class="pre">VlsvReader.print_version()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read"><code class="docutils literal notranslate"><span class="pre">VlsvReader.read()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_attribute"><code class="docutils literal notranslate"><span class="pre">VlsvReader.read_attribute()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_blocks"><code class="docutils literal notranslate"><span class="pre">VlsvReader.read_blocks()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_fsgrid_variable"><code class="docutils literal notranslate"><span class="pre">VlsvReader.read_fsgrid_variable()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_fsgrid_variable_cellid"><code class="docutils literal notranslate"><span class="pre">VlsvReader.read_fsgrid_variable_cellid()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_interpolated_fsgrid_variable"><code class="docutils literal notranslate"><span class="pre">VlsvReader.read_interpolated_fsgrid_variable()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_interpolated_ionosphere_variable"><code class="docutils literal notranslate"><span class="pre">VlsvReader.read_interpolated_ionosphere_variable()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_interpolated_variable"><code class="docutils literal notranslate"><span class="pre">VlsvReader.read_interpolated_variable()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_interpolated_variable_irregular"><code class="docutils literal notranslate"><span class="pre">VlsvReader.read_interpolated_variable_irregular()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_ionosphere_node_variable_at_elements"><code class="docutils literal notranslate"><span class="pre">VlsvReader.read_ionosphere_node_variable_at_elements()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_ionosphere_variable"><code class="docutils literal notranslate"><span class="pre">VlsvReader.read_ionosphere_variable()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_metadata"><code class="docutils literal notranslate"><span class="pre">VlsvReader.read_metadata()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_parameter"><code class="docutils literal notranslate"><span class="pre">VlsvReader.read_parameter()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_variable"><code class="docutils literal notranslate"><span class="pre">VlsvReader.read_variable()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_variable_from_cache"><code class="docutils literal notranslate"><span class="pre">VlsvReader.read_variable_from_cache()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_variable_info"><code class="docutils literal notranslate"><span class="pre">VlsvReader.read_variable_info()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_variable_to_cache"><code class="docutils literal notranslate"><span class="pre">VlsvReader.read_variable_to_cache()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_velocity_cells"><code class="docutils literal notranslate"><span class="pre">VlsvReader.read_velocity_cells()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.upsample_fsgrid_subarray"><code class="docutils literal notranslate"><span class="pre">VlsvReader.upsample_fsgrid_subarray()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="#pytools.vlsvfile.VlsvWriter"><code class="docutils literal notranslate"><span class="pre">VlsvWriter</span></code></a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvWriter.clone_file"><code class="docutils literal notranslate"><span class="pre">VlsvWriter.clone_file()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvWriter.copy_variables"><code class="docutils literal notranslate"><span class="pre">VlsvWriter.copy_variables()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvWriter.copy_variables_list"><code class="docutils literal notranslate"><span class="pre">VlsvWriter.copy_variables_list()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvWriter.write"><code class="docutils literal notranslate"><span class="pre">VlsvWriter.write()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvWriter.write_variable"><code class="docutils literal notranslate"><span class="pre">VlsvWriter.write_variable()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvWriter.write_variable_info"><code class="docutils literal notranslate"><span class="pre">VlsvWriter.write_variable_info()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#pytools.vlsvfile.VlsvWriter.write_velocity_space"><code class="docutils literal notranslate"><span class="pre">VlsvWriter.write_velocity_space()</span></code></a></li>
+</ul>
+</li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../miscellaneous/">miscellaneous</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../scripts/">scripts</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../about/">Credits</a></li>
+</ul>
+
+        </div>
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="../">analysator</a>
+      </nav>
+
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="Page navigation">
+  <ul class="wy-breadcrumbs">
+      <li><a href="../" class="icon icon-home" aria-label="Home"></a></li>
+      <li class="breadcrumb-item active">vlsvfile</li>
+      <li class="wy-breadcrumbs-aside">
+            <a href="../_sources/vlsvfile.rst.txt" rel="nofollow"> View page source</a>
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+             
+  <section id="vlsvfile">
+<h1>vlsvfile<a class="headerlink" href="#vlsvfile" title="Link to this heading"></a></h1>
+<p>VlsvFile is responsibe for implementing read and write functionality for the vlsv format, as well as defining data reducers and reduction pipelines. Some of this will be likely moved around to be more modular in some indefinite point in the future.</p>
+<p id="module-pytools.vlsvfile">The vlsvfile module has all the classes related to reading and writing vlsv files</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># Example:</span>
+<span class="kn">import</span> <span class="nn">pytools</span> <span class="k">as</span> <span class="nn">pt</span>
+<span class="n">pt</span><span class="o">.</span><span class="n">vlsvfile</span><span class="o">.</span>
+<span class="c1">#press [tab] -&gt; get the functions</span>
+</pre></div>
+</div>
+<dl class="py class">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlasiatorReader">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pytools.vlsvfile.</span></span><span class="sig-name descname"><span class="pre">VlasiatorReader</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fsGridDecomposition</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlasiatorReader" title="Link to this definition"></a></dt>
+<dd><p>Class for reading VLSV files with support for Vlasiator velocity space and structures</p>
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvParticles">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pytools.vlsvfile.</span></span><span class="sig-name descname"><span class="pre">VlsvParticles</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file_name</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvParticles" title="Link to this definition"></a></dt>
+<dd><p>Class for reading VLSV files of particle pusher output</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvParticles.list">
+<span class="sig-name descname"><span class="pre">list</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvParticles.list" title="Link to this definition"></a></dt>
+<dd><p>Print out a description of the content of the file. Useful
+for interactive usage</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvParticles.read_particles">
+<span class="sig-name descname"><span class="pre">read_particles</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvParticles.read_particles" title="Link to this definition"></a></dt>
+<dd><p>Read particle pusher data from the open vlsv file. 
+This routine returns only active particles.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvParticles.read_particles_all">
+<span class="sig-name descname"><span class="pre">read_particles_all</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvParticles.read_particles_all" title="Link to this definition"></a></dt>
+<dd><p>Read particle pusher data from the open vlsv file.
+This routine returns all particles, including inactive ones.</p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pytools.vlsvfile.</span></span><span class="sig-name descname"><span class="pre">VlsvReader</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fsGridDecomposition</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader" title="Link to this definition"></a></dt>
+<dd><p>Class for reading VLSV files</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.build_cell_vertices">
+<span class="sig-name descname"><span class="pre">build_cell_vertices</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cid</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prune_unique</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.build_cell_vertices" title="Link to this definition"></a></dt>
+<dd><p>Builds, caches and returns the vertices that lie on the surfaces of CellIDs cid.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>cid</strong> – numpy array of CellIDs</p></li>
+<li><p><strong>prune_unique</strong> – bool [False], if you suspect you might be calling the function many times with the 
+same CellID in the list, it might be beneficial to enable this and not repeat the operation for duplicate entries.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Dictionary of cell c (int) : set of vertex indices (3-tuple) that touch the cell c.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.cellid_has_vdf">
+<span class="sig-name descname"><span class="pre">cellid_has_vdf</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cid</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'proton'</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">bool</span></span></span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.cellid_has_vdf" title="Link to this definition"></a></dt>
+<dd><p>Returns whether the cid in question has a vdf or not
+:param coords:    the cellid to test for
+:returns: bool</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.check_parameter">
+<span class="sig-name descname"><span class="pre">check_parameter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.check_parameter" title="Link to this definition"></a></dt>
+<dd><p>Checks if a given parameter is in the vlsv reader</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>name</strong> – Name of the parameter</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>True if the parameter is in the vlsv file, false if not</p>
+</dd>
+</dl>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>This should be used for checking if a parameter exists, e.g. for different Vlasiator versions and time output</p>
+</div>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># Example usage:</span>
+<span class="n">vlsvReader</span> <span class="o">=</span> <span class="n">pt</span><span class="o">.</span><span class="n">vlsvfile</span><span class="o">.</span><span class="n">VlsvReader</span><span class="p">(</span><span class="s2">&quot;test.vlsv&quot;</span><span class="p">)</span>
+<span class="k">if</span> <span class="n">vlsvReader</span><span class="o">.</span><span class="n">check_parameter</span><span class="p">(</span> <span class="s2">&quot;time&quot;</span> <span class="p">):</span>
+   <span class="n">time</span> <span class="o">=</span> <span class="n">vlsvReader</span><span class="o">.</span><span class="n">read_parameter</span><span class="p">(</span><span class="s2">&quot;time&quot;</span><span class="p">)</span>
+<span class="k">elif</span> <span class="n">vlsvReader</span><span class="o">.</span><span class="n">check_parameter</span><span class="p">(</span> <span class="s2">&quot;t&quot;</span> <span class="p">):</span>
+   <span class="n">time</span> <span class="o">=</span> <span class="n">vlsvReader</span><span class="o">.</span><span class="n">read_parameter</span><span class="p">(</span><span class="s2">&quot;t&quot;</span><span class="p">)</span>
+<span class="k">else</span><span class="p">:</span>
+   <span class="n">time</span> <span class="o">=</span> <span class="kc">None</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.check_population">
+<span class="sig-name descname"><span class="pre">check_population</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">popname</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.check_population" title="Link to this definition"></a></dt>
+<dd><p>Checks if a given population is in the vlsv file</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>name</strong> – Name of the population</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>True if the population is in the vlsv file, false if not</p>
+</dd>
+</dl>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># Example usage:</span>
+<span class="n">vlsvReader</span> <span class="o">=</span> <span class="n">pt</span><span class="o">.</span><span class="n">vlsvfile</span><span class="o">.</span><span class="n">VlsvReader</span><span class="p">(</span><span class="s2">&quot;test.vlsv&quot;</span><span class="p">)</span>
+<span class="k">if</span> <span class="n">vlsvReader</span><span class="o">.</span><span class="n">check_population</span><span class="p">(</span> <span class="s2">&quot;avgs&quot;</span> <span class="p">):</span>
+   <span class="n">plot_population</span><span class="p">(</span><span class="s1">&#39;avgs&#39;</span><span class="p">)</span>
+<span class="k">else</span><span class="p">:</span>
+   <span class="k">if</span> <span class="n">vlsvReader</span><span class="o">.</span><span class="n">check_population</span><span class="p">(</span> <span class="s2">&quot;proton&quot;</span> <span class="p">):</span>
+      <span class="c1"># File is newer with proton population</span>
+      <span class="n">plot_population</span><span class="p">(</span><span class="s1">&#39;proton&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.check_variable">
+<span class="sig-name descname"><span class="pre">check_variable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.check_variable" title="Link to this definition"></a></dt>
+<dd><p>Checks if a given variable is in the vlsv reader</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>name</strong> – Name of the variable</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>True if the variable is in the vlsv file, false if not</p>
+</dd>
+</dl>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>This should be used for checking if a variable exists in case a function behaves differently for ex. if B vector is in the vlsv and if not</p>
+</div>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># Example usage:</span>
+<span class="n">vlsvReader</span> <span class="o">=</span> <span class="n">pt</span><span class="o">.</span><span class="n">vlsvfile</span><span class="o">.</span><span class="n">VlsvReader</span><span class="p">(</span><span class="s2">&quot;test.vlsv&quot;</span><span class="p">)</span>
+<span class="k">if</span> <span class="n">vlsvReader</span><span class="o">.</span><span class="n">check_variable</span><span class="p">(</span> <span class="s2">&quot;B&quot;</span> <span class="p">):</span>
+   <span class="c1"># Variable can be plotted</span>
+   <span class="n">plot_B</span><span class="p">()</span>
+<span class="k">else</span><span class="p">:</span>
+   <span class="c1"># Variable not in the vlsv file</span>
+   <span class="n">plot_B_vol</span><span class="p">()</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.construct_velocity_cell_coordinates">
+<span class="sig-name descname"><span class="pre">construct_velocity_cell_coordinates</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">blocks</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.construct_velocity_cell_coordinates" title="Link to this definition"></a></dt>
+<dd><p>Returns velocity cell coordinates in given blocks</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>blocks</strong> – list of block ids</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>a numpy array containing the velocity cell ids e.g. np.array([4,2,56,44,522, ..])</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.construct_velocity_cell_nodes">
+<span class="sig-name descname"><span class="pre">construct_velocity_cell_nodes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">blocks</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'proton'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.construct_velocity_cell_nodes" title="Link to this definition"></a></dt>
+<dd><p>Returns velocity cell nodes in given blocks</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>blocks</strong> – list of block ids</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>a numpy array containing velocity cell nodes and the keys for velocity cells</p>
+</dd>
+</dl>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>This is used for constructing velocity space inside the mayavi module</p>
+</div>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><code class="xref py py-mod docutils literal notranslate"><span class="pre">grid</span></code></p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.construct_velocity_cells">
+<span class="sig-name descname"><span class="pre">construct_velocity_cells</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">blocks</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.construct_velocity_cells" title="Link to this definition"></a></dt>
+<dd><p>Returns velocity cells in given blocks</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>blocks</strong> – list of block ids</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>a numpy array containing the velocity cell ids e.g. np.array([4,2,56,44,522, ..])</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.downsample_fsgrid_subarray">
+<span class="sig-name descname"><span class="pre">downsample_fsgrid_subarray</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cellid</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">array</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.downsample_fsgrid_subarray" title="Link to this definition"></a></dt>
+<dd><p>Returns a mean value of fsgrid values underlying the SpatialGrid cellid.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.fsgrid_array_to_vg">
+<span class="sig-name descname"><span class="pre">fsgrid_array_to_vg</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">array</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.fsgrid_array_to_vg" title="Link to this definition"></a></dt>
+<dd><p>Downsample, via averaging, an fsgrid array to the Vlasov grid
+of this reader.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>array</strong> – array with first three dimensions corresponding to the
+dimensions of the fsgrid associated with this reader.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Vlasov grid data (in file order) of array averaged to Vlasov Grid.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_all_variables">
+<span class="sig-name descname"><span class="pre">get_all_variables</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_all_variables" title="Link to this definition"></a></dt>
+<dd><p>Returns all variables in the vlsv reader and the data reducer
+:returns:                List of variable is in the vlsv file
+.. code-block:: python</p>
+<blockquote>
+<div><p># Example usage:
+vlsvReader = pt.vlsvfile.VlsvReader(“test.vlsv”)
+vars = vlsvReader.get_variables()</p>
+</div></blockquote>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_amr_level">
+<span class="sig-name descname"><span class="pre">get_amr_level</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cellid</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_amr_level" title="Link to this definition"></a></dt>
+<dd><p>Returns the AMR level of a given cell defined by its cellid</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>cellid</strong> – The cell’s cellid</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>The cell’s refinement level in the AMR</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_bbox_fsgrid_slicemap">
+<span class="sig-name descname"><span class="pre">get_bbox_fsgrid_slicemap</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">low</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">up</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_bbox_fsgrid_slicemap" title="Link to this definition"></a></dt>
+<dd><p>Returns a slice tuple of fsgrid indices that are contained in the (low, up) bounding box.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_bbox_fsgrid_subarray">
+<span class="sig-name descname"><span class="pre">get_bbox_fsgrid_subarray</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">low</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">up</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">array</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_bbox_fsgrid_subarray" title="Link to this definition"></a></dt>
+<dd><p>Returns a subarray of the fsgrid array, corresponding to the (low, up) bounding box.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_cell_bbox">
+<span class="sig-name descname"><span class="pre">get_cell_bbox</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cellid</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_cell_bbox" title="Link to this definition"></a></dt>
+<dd><p>Returns the bounding box of a given cell defined by its cellid</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>cellid</strong> – The cell’s cellid</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>The cell’s bbox [xmin,ymin,zmin],[xmax,ymax,zmax]</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_cell_coordinates">
+<span class="sig-name descname"><span class="pre">get_cell_coordinates</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cellids</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_cell_coordinates" title="Link to this definition"></a></dt>
+<dd><p>Returns a given cell’s coordinates as a numpy array</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>cellids</strong> – The array of cell IDs</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>a numpy array with the coordinates</p>
+</dd>
+</dl>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_cellid" title="pytools.vlsvfile.VlsvReader.get_cellid"><code class="xref py py-func docutils literal notranslate"><span class="pre">get_cellid()</span></code></a></p>
+</div>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>The cell ids go from 1 .. max not from 0</p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_cell_corner_vertices">
+<span class="sig-name descname"><span class="pre">get_cell_corner_vertices</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cids</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_cell_corner_vertices" title="Link to this definition"></a></dt>
+<dd><p>Builds, caches and returns the vertices that lie on the corners of CellIDs cid.
+:parameter cid: numpy array of CellIDs</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Dictionary of cell c (int) : 8-tuple of vertex indices (3-tuples).</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_cell_dx">
+<span class="sig-name descname"><span class="pre">get_cell_dx</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cellid</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_cell_dx" title="Link to this definition"></a></dt>
+<dd><p>Returns the dx of a given cell defined by its cellid</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>cellid</strong> – The cell’s cellid</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>The cell’s size [dx, dy, dz]</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_cell_fsgrid">
+<span class="sig-name descname"><span class="pre">get_cell_fsgrid</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cellid</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_cell_fsgrid" title="Link to this definition"></a></dt>
+<dd><p>Returns a slice tuple of fsgrid indices that are contained in the SpatialGrid
+cell.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_cell_fsgrid_slicemap">
+<span class="sig-name descname"><span class="pre">get_cell_fsgrid_slicemap</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cellid</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_cell_fsgrid_slicemap" title="Link to this definition"></a></dt>
+<dd><p>Returns a slice tuple of fsgrid indices that are contained in the SpatialGrid
+cell.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_cell_fsgrid_subarray">
+<span class="sig-name descname"><span class="pre">get_cell_fsgrid_subarray</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cellid</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">array</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_cell_fsgrid_subarray" title="Link to this definition"></a></dt>
+<dd><p>Returns a subarray of the fsgrid array, corresponding to the fsgrid
+covered by the SpatialGrid cellid.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_cell_indices">
+<span class="sig-name descname"><span class="pre">get_cell_indices</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cellids</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reflevels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_cell_indices" title="Link to this definition"></a></dt>
+<dd><p>Returns a given cell’s indices as a numpy array</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>cellid</strong> – The cell’s ID, numpy array</p></li>
+<li><p><strong>reflevel</strong> – The cell’s refinement level in the AMR</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>a numpy array with the coordinates</p>
+</dd>
+</dl>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_cellid" title="pytools.vlsvfile.VlsvReader.get_cellid"><code class="xref py py-func docutils literal notranslate"><span class="pre">get_cellid()</span></code></a></p>
+</div>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>The cell ids go from 1 .. max not from 0</p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_cell_neighbor">
+<span class="sig-name descname"><span class="pre">get_cell_neighbor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cellidss</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">offsetss</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">periodic</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prune_uniques</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_cell_neighbor" title="Link to this definition"></a></dt>
+<dd><p>Returns a given cells neighbor at offset (in indices)</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>cellids</strong> – The cell’s ID</p></li>
+<li><p><strong>offsets</strong> – The offset to the neighbor in indices</p></li>
+<li><p><strong>periodic</strong> – For each dimension, is the system periodic</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>the cellid of the neighbor</p>
+</dd>
+</dl>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>Returns 0 if the offset is out of bounds!</p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_cellid">
+<span class="sig-name descname"><span class="pre">get_cellid</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">coords</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_cellid" title="Link to this definition"></a></dt>
+<dd><p>Returns the cell ids at given coordinates</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>coords</strong> – The cells’ coordinates</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>the cell ids</p>
+</dd>
+</dl>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>Returns 0 if the cellid is out of bounds!</p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_cellid_locations">
+<span class="sig-name descname"><span class="pre">get_cellid_locations</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_cellid_locations" title="Link to this definition"></a></dt>
+<dd><p>Returns a dictionary with cell id as the key and the index of the cell id as the value. The index is used to locate the cell id’s values in the arrays that this reader returns</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_cellid_with_vdf">
+<span class="sig-name descname"><span class="pre">get_cellid_with_vdf</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">coords</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'proton'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_cellid_with_vdf" title="Link to this definition"></a></dt>
+<dd><p>Returns the cell ids nearest to test points, that contain VDFs</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>coords</strong> – Test coordinates [meters] of N_in points in ND-dimensional space
+array with shape [N_in, ND] or [ND]</p>
+</dd>
+</dl>
+<p>Example: cellid = vlsvReader.get_cellid_with_vdf(np.array([1e8, 0, 0]))
+:returns: the cell ids</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_config">
+<span class="sig-name descname"><span class="pre">get_config</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_config" title="Link to this definition"></a></dt>
+<dd><p>Gets config information from VLSV file</p>
+<dl class="simple">
+<dt>:returns a nested dictionary of dictionaries,</dt><dd><p>where keys (str) are config file group headings (appearing in ‘[]’)
+and values are dictionaries which contain (lists of) strings</p>
+</dd>
+</dl>
+<p>If the same heading/parameter pair appears &gt;once in the config file,
+the different values are appended to the list .</p>
+<p>EXAMPLE:
+if the config contains these lines:</p>
+<blockquote>
+<div><p>[proton_precipitation]
+nChannels = 9</p>
+</div></blockquote>
+<p>then the following returns [‘9’]:
+vlsvReader.get_config()[‘proton_precipitation’][‘nChannels’]</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_config_string">
+<span class="sig-name descname"><span class="pre">get_config_string</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_config_string" title="Link to this definition"></a></dt>
+<dd><p>Gets config information from VLSV file.
+TAG is hardcoded to CONFIG</p>
+<p>:returns configuration file string if config is found otherwise returns None</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_dual">
+<span class="sig-name descname"><span class="pre">get_dual</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cellids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_dual" title="Link to this definition"></a></dt>
+<dd><p>Find the duals that contain the coordinate points pts. This will call the iterative find_ksi function
+to see if the resulting interpolation weights for the coordinate are in the range [0,1]; if not, it will iterate 
+through neighbouring duals until a dual is found.
+:parameter pts: numpy array of coordinates (N,3)</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>duals (numpy array of N 3-tuples), ksis (numpy array of interpolation weights (N, 8))</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_duals">
+<span class="sig-name descname"><span class="pre">get_duals</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cids</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_duals" title="Link to this definition"></a></dt>
+<dd><dl class="simple">
+<dt>Get the union of dual cells that cover each of CellIDs in cids.</dt><dd><p>Assumes all required duals are defined! TODO handling of missing duals, do not call separately.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Dict of vertex-indices v (3-tuple) : 8-tuple of cellids (corners of dual cells indexed by v)</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_fsgrid_cell_size">
+<span class="sig-name descname"><span class="pre">get_fsgrid_cell_size</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_fsgrid_cell_size" title="Link to this definition"></a></dt>
+<dd><p>Read fsgrid cell size</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Maximum and minimum coordinates of the mesh, [dx, dy, dz]</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_fsgrid_coordinates">
+<span class="sig-name descname"><span class="pre">get_fsgrid_coordinates</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ri</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_fsgrid_coordinates" title="Link to this definition"></a></dt>
+<dd><p>Returns real-space center coordinates of the fsgrid 3-index.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_fsgrid_indices">
+<span class="sig-name descname"><span class="pre">get_fsgrid_indices</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">coords</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_fsgrid_indices" title="Link to this definition"></a></dt>
+<dd><p>Convert spatial coordinates coords to an index array [xi, yi, zi] for fsgrid</p>
+<p>:returns 3-tuple of integers [xi, yi, zi] corresponding to fsgrid cell containing coords (low-inclusive)
+Example:
+ii = f.get_fsgrid_mesh_extent(coords)
+fsvar_at_coords = fsvar_array.item(ii)</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_fsgrid_mesh_extent">
+<span class="sig-name descname"><span class="pre">get_fsgrid_mesh_extent</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_fsgrid_mesh_extent" title="Link to this definition"></a></dt>
+<dd><p>Read fsgrid mesh extent</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Maximum and minimum coordinates of the mesh, [xmin, ymin, zmin, xmax, ymax, zmax]</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_fsgrid_mesh_size">
+<span class="sig-name descname"><span class="pre">get_fsgrid_mesh_size</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_fsgrid_mesh_size" title="Link to this definition"></a></dt>
+<dd><p>Read fsgrid mesh size</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Size of mesh in number of cells, array with three elements</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_fsgrid_slice_indices">
+<span class="sig-name descname"><span class="pre">get_fsgrid_slice_indices</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lower</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">upper</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">eps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.001</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_fsgrid_slice_indices" title="Link to this definition"></a></dt>
+<dd><p>Get indices for a subarray of an fsgrid variable, in the cuboid from lower to upper.
+This is meant for mapping a set of fsgrid cells to a given SpatialGrid cell.
+Shifts the corners (lower, upper) by dx_fsgrid*eps inward, if direct low-inclusive behaviour
+is required, set kword eps = 0.</p>
+<p>:returns two 3-tuples of integers.
+Example:
+ii = f.get_fsgrid_mesh_extent(coords)
+fsvar_at_coords = fsvar_array.item(ii)</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_ionosphere_element_coords">
+<span class="sig-name descname"><span class="pre">get_ionosphere_element_coords</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_ionosphere_element_coords" title="Link to this definition"></a></dt>
+<dd><p>Read coordinates of ionosphere elements (triangle barycenters)</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>[x, y, z] array of ionosphere element barycenter coordinates (in meters).</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_ionosphere_element_corners">
+<span class="sig-name descname"><span class="pre">get_ionosphere_element_corners</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_ionosphere_element_corners" title="Link to this definition"></a></dt>
+<dd><p>Read ionosphere mesh element corners</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>[c1,c2,c3] array of ionosphere mesh node indices (starting from 0)</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_ionosphere_latlon_coords">
+<span class="sig-name descname"><span class="pre">get_ionosphere_latlon_coords</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_ionosphere_latlon_coords" title="Link to this definition"></a></dt>
+<dd><p>Read ionosphere node coordinates (in magnetic longitude / latitude)</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>[lat,lon] array of ionosphere node coordinates</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_ionosphere_mesh_area">
+<span class="sig-name descname"><span class="pre">get_ionosphere_mesh_area</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_ionosphere_mesh_area" title="Link to this definition"></a></dt>
+<dd><p>Read areas of ionosphere elements (triangular mesh)</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>1D array, areas of the triangular elements [m^2]</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_ionosphere_mesh_size">
+<span class="sig-name descname"><span class="pre">get_ionosphere_mesh_size</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_ionosphere_mesh_size" title="Link to this definition"></a></dt>
+<dd><p>Read size of the ionosphere mesh, if there is one.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Size of the mesh in number of nodes and elements, array with two elements</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_ionosphere_node_coords">
+<span class="sig-name descname"><span class="pre">get_ionosphere_node_coords</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_ionosphere_node_coords" title="Link to this definition"></a></dt>
+<dd><p>Read ionosphere node coordinates (in cartesian GSM coordinate system).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>[x,y,z] array of ionosphere node coordinates (in meters)</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_max_refinement_level">
+<span class="sig-name descname"><span class="pre">get_max_refinement_level</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_max_refinement_level" title="Link to this definition"></a></dt>
+<dd><p>Returns the maximum refinement level of the AMR</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_precipitation_centre_energy">
+<span class="sig-name descname"><span class="pre">get_precipitation_centre_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'proton'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_precipitation_centre_energy" title="Link to this definition"></a></dt>
+<dd><p>Read precipitation energy bins</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Array of centre energies</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_spatial_block_size">
+<span class="sig-name descname"><span class="pre">get_spatial_block_size</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_spatial_block_size" title="Link to this definition"></a></dt>
+<dd><p>Read spatial mesh block size</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Size of block in number of cells, array with three elements</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_spatial_mesh_extent">
+<span class="sig-name descname"><span class="pre">get_spatial_mesh_extent</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_spatial_mesh_extent" title="Link to this definition"></a></dt>
+<dd><p>Read spatial mesh extent</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Maximum and minimum coordinates of the mesh, [xmin, ymin, zmin, xmax, ymax, zmax]</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_spatial_mesh_size">
+<span class="sig-name descname"><span class="pre">get_spatial_mesh_size</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_spatial_mesh_size" title="Link to this definition"></a></dt>
+<dd><p>Read spatial mesh size</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Size of mesh in number of blocks, array with three elements</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_unique_cellids">
+<span class="sig-name descname"><span class="pre">get_unique_cellids</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">coords</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_unique_cellids" title="Link to this definition"></a></dt>
+<dd><dl class="simple">
+<dt>Returns a list of cellids containing all the coordinates in coords,</dt><dd><p>with no duplicate cellids. Relative order of elements is conserved.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>coords</strong> – A list of coordinates</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>a list of unique cell ids</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_velocity_block_coordinates">
+<span class="sig-name descname"><span class="pre">get_velocity_block_coordinates</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">blocks</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'proton'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_velocity_block_coordinates" title="Link to this definition"></a></dt>
+<dd><p>Returns the block coordinates of the given blocks in a numpy array</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>blocks</strong> – list of block ids</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>a numpy array containing the block coordinates e.g. np.array([np.array([2,1,3]), np.array([5,6,6]), ..])</p>
+</dd>
+</dl>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_velocity_cell_coordinates" title="pytools.vlsvfile.VlsvReader.get_velocity_cell_coordinates"><code class="xref py py-func docutils literal notranslate"><span class="pre">get_velocity_cell_coordinates()</span></code></a></p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_velocity_block_indices">
+<span class="sig-name descname"><span class="pre">get_velocity_block_indices</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">blocks</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'proton'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_velocity_block_indices" title="Link to this definition"></a></dt>
+<dd><p>Returns the block indices of the given blocks in a numpy array</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>blocks</strong> – list of block ids</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>a numpy array containing the block indices e.g. np.array([np.array([2,1,3]), np.array([5,6,6]), ..])</p>
+</dd>
+</dl>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_velocity_block_coordinates" title="pytools.vlsvfile.VlsvReader.get_velocity_block_coordinates"><code class="xref py py-func docutils literal notranslate"><span class="pre">get_velocity_block_coordinates()</span></code></a></p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_velocity_block_size">
+<span class="sig-name descname"><span class="pre">get_velocity_block_size</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'proton'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_velocity_block_size" title="Link to this definition"></a></dt>
+<dd><p>Read velocity mesh block size</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Size of block in number of cells, array with three elements</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_velocity_blocks">
+<span class="sig-name descname"><span class="pre">get_velocity_blocks</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">blockCoordinates</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'proton'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_velocity_blocks" title="Link to this definition"></a></dt>
+<dd><p>Returns the block ids of the given block coordinates in a numpy array form</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>blockcoordinates</strong> – list of block coordinates e.g. np.array([np.array([2,1,3]), np.array([5,6,6]), ..])</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>a numpy array containing the block ids e.g. np.array([4,2,56,44,2, ..])</p>
+</dd>
+</dl>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_velocity_block_coordinates" title="pytools.vlsvfile.VlsvReader.get_velocity_block_coordinates"><code class="xref py py-func docutils literal notranslate"><span class="pre">get_velocity_block_coordinates()</span></code></a></p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_velocity_cell_coordinates">
+<span class="sig-name descname"><span class="pre">get_velocity_cell_coordinates</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vcellids</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'proton'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_velocity_cell_coordinates" title="Link to this definition"></a></dt>
+<dd><p>Returns a given velocity cell’s coordinates as a numpy array</p>
+<p>Arguments:
+:param vcellids:       The velocity cell’s ID
+:returns: a numpy array with the coordinates</p>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_cell_coordinates" title="pytools.vlsvfile.VlsvReader.get_cell_coordinates"><code class="xref py py-func docutils literal notranslate"><span class="pre">get_cell_coordinates()</span></code></a> <a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_velocity_block_coordinates" title="pytools.vlsvfile.VlsvReader.get_velocity_block_coordinates"><code class="xref py py-func docutils literal notranslate"><span class="pre">get_velocity_block_coordinates()</span></code></a></p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_velocity_cell_ids">
+<span class="sig-name descname"><span class="pre">get_velocity_cell_ids</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vcellcoord</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'proton'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_velocity_cell_ids" title="Link to this definition"></a></dt>
+<dd><p>Returns velocity cell ids of given coordinate</p>
+<p>Arguments:
+:param vcellcoords: One 3d coordinate
+:returns: Velocity cell id</p>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.get_velocity_cell_coordinates" title="pytools.vlsvfile.VlsvReader.get_velocity_cell_coordinates"><code class="xref py py-func docutils literal notranslate"><span class="pre">get_velocity_cell_coordinates()</span></code></a></p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_velocity_mesh_dv">
+<span class="sig-name descname"><span class="pre">get_velocity_mesh_dv</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'proton'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_velocity_mesh_dv" title="Link to this definition"></a></dt>
+<dd><p>Read velocity mesh cell size</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Velocity mesh cell size, array with three elements [dvx, dvy, dvz]</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_velocity_mesh_extent">
+<span class="sig-name descname"><span class="pre">get_velocity_mesh_extent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'proton'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_velocity_mesh_extent" title="Link to this definition"></a></dt>
+<dd><p>Read velocity mesh extent</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Maximum and minimum coordinates of the mesh, [vxmin, vymin, vzmin, vxmax, vymax, vzmax]</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_velocity_mesh_size">
+<span class="sig-name descname"><span class="pre">get_velocity_mesh_size</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'proton'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_velocity_mesh_size" title="Link to this definition"></a></dt>
+<dd><p>Read velocity mesh size</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Size of mesh in number of blocks, array with three elements</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_vertex_coordinates_from_indices">
+<span class="sig-name descname"><span class="pre">get_vertex_coordinates_from_indices</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">indices</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_vertex_coordinates_from_indices" title="Link to this definition"></a></dt>
+<dd><p>Convert vertex indices to physical coordinates.
+:param indices: numpy array of vertex indices, either (3,) or (N,3)</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>numpy array of coordinates, with matching shape to indices</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.get_vertex_indices">
+<span class="sig-name descname"><span class="pre">get_vertex_indices</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">coordinates</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.get_vertex_indices" title="Link to this definition"></a></dt>
+<dd><p>Get dual grid vertex indices for all coordinates.</p>
+<p>Works by truncation to integer indices at fsgrid resolution, for cell low-corners.
+:param coordinates: np.array of coordinates, shaped either (3,) or (N,3)</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.list">
+<span class="sig-name descname"><span class="pre">list</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parameter</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">variable</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mesh</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">datareducer</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">operator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">other</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.list" title="Link to this definition"></a></dt>
+<dd><p>Print out a description of the content of the file. Useful
+for interactive usage. Default is to list parameters and variables, query selection can be adjusted with keywords:</p>
+<p>Default and supported keywords:</p>
+<p>parameter=True 
+variable=True
+mesh=False
+datareducer=False 
+operator=False 
+other=False</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.optimize_clear_fileindex_for_cellid">
+<span class="sig-name descname"><span class="pre">optimize_clear_fileindex_for_cellid</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.optimize_clear_fileindex_for_cellid" title="Link to this definition"></a></dt>
+<dd><p>Clears a private variable containing cell ids and their locations</p>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>This should only be used for optimization purposes.</p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.optimize_clear_fileindex_for_cellid_blocks">
+<span class="sig-name descname"><span class="pre">optimize_clear_fileindex_for_cellid_blocks</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.optimize_clear_fileindex_for_cellid_blocks" title="Link to this definition"></a></dt>
+<dd><p>Clears a private variable containing number of blocks and offsets for particular cell ids</p>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>This should only be used for optimization purposes.</p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.optimize_close_file">
+<span class="sig-name descname"><span class="pre">optimize_close_file</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.optimize_close_file" title="Link to this definition"></a></dt>
+<dd><p>Closes the vlsv file
+Files are opened and closed automatically upon reading and in the case of reading multiple times it will help to keep the file open with this command</p>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>This should only be used for optimization purposes.</p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.optimize_open_file">
+<span class="sig-name descname"><span class="pre">optimize_open_file</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.optimize_open_file" title="Link to this definition"></a></dt>
+<dd><p>Opens the vlsv file for reading
+Files are opened and closed automatically upon reading and in the case of reading multiple times it will help to keep the file open with this command</p>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>This should only be used for optimization purposes.</p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.print_config">
+<span class="sig-name descname"><span class="pre">print_config</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.print_config" title="Link to this definition"></a></dt>
+<dd><p>Prints config information from VLSV file.</p>
+<p>:returns True if config is found otherwise returns False</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.print_version">
+<span class="sig-name descname"><span class="pre">print_version</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.print_version" title="Link to this definition"></a></dt>
+<dd><p>Prints version information from VLSV file.
+TAG is hardcoded to VERSION</p>
+<p>:returns True if version is found otherwise returns False</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.read">
+<span class="sig-name descname"><span class="pre">read</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tag</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mesh</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">operator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pass'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cellids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-1</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.read" title="Link to this definition"></a></dt>
+<dd><p>Read data from the open vlsv file.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> – Name of the data array</p></li>
+<li><p><strong>tag</strong> – Tag of the data array.</p></li>
+<li><p><strong>mesh</strong> – Mesh for the data array</p></li>
+<li><p><strong>operator</strong> – Datareduction operator. “pass” does no operation on data.</p></li>
+<li><p><strong>cellids</strong> – If -1 then all data is read. If nonzero then only the vector
+for the specified cell id or cellids is read</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>numpy array with the data</p>
+</dd>
+</dl>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_variable" title="pytools.vlsvfile.VlsvReader.read_variable"><code class="xref py py-func docutils literal notranslate"><span class="pre">read_variable()</span></code></a> <a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_variable_info" title="pytools.vlsvfile.VlsvReader.read_variable_info"><code class="xref py py-func docutils literal notranslate"><span class="pre">read_variable_info()</span></code></a></p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.read_attribute">
+<span class="sig-name descname"><span class="pre">read_attribute</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mesh</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attribute</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tag</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.read_attribute" title="Link to this definition"></a></dt>
+<dd><p>Read data from the open vlsv file.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> – Name of the data array</p></li>
+<li><p><strong>tag</strong> – Tag of the data array.</p></li>
+<li><p><strong>mesh</strong> – Mesh for the data array</p></li>
+<li><p><strong>operator</strong> – Datareduction operator. “pass” does no operation on data.</p></li>
+<li><p><strong>cellids</strong> – If -1 then all data is read. If nonzero then only the vector
+for the specified cell id or cellids is read</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>numpy array with the data</p>
+</dd>
+</dl>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_variable" title="pytools.vlsvfile.VlsvReader.read_variable"><code class="xref py py-func docutils literal notranslate"><span class="pre">read_variable()</span></code></a> <a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_variable_info" title="pytools.vlsvfile.VlsvReader.read_variable_info"><code class="xref py py-func docutils literal notranslate"><span class="pre">read_variable_info()</span></code></a></p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.read_blocks">
+<span class="sig-name descname"><span class="pre">read_blocks</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cellid</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'proton'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.read_blocks" title="Link to this definition"></a></dt>
+<dd><p>Read raw block data from the open file and return the data along with block ids</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>cellid</strong> – Cell ID of the cell whose velocity blocks are read</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A numpy array with block ids and data eg [array([2, 5, 6, 234, 21]), array([1.0e-8, 2.1e-8, 2.1e-8, 0, 4.0e-8])]</p>
+</dd>
+</dl>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_velocity_cells" title="pytools.vlsvfile.VlsvReader.read_velocity_cells"><code class="xref py py-func docutils literal notranslate"><span class="pre">read_velocity_cells()</span></code></a></p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.read_fsgrid_variable">
+<span class="sig-name descname"><span class="pre">read_fsgrid_variable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">operator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pass'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.read_fsgrid_variable" title="Link to this definition"></a></dt>
+<dd><p>Reads fsgrid variables from the open vlsv file.
+Arguments:
+:param name: Name of the variable
+:param operator: Datareduction operator. “pass” does no operation on data
+:returns: <em>ordered</em> numpy array with the data</p>
+<p>… seealso:: <a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_variable" title="pytools.vlsvfile.VlsvReader.read_variable"><code class="xref py py-func docutils literal notranslate"><span class="pre">read_variable()</span></code></a></p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.read_fsgrid_variable_cellid">
+<span class="sig-name descname"><span class="pre">read_fsgrid_variable_cellid</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cellids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">operator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pass'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.read_fsgrid_variable_cellid" title="Link to this definition"></a></dt>
+<dd><p>Reads fsgrid variables from the open vlsv file.
+Arguments:
+:param name:     Name of the variable
+:param cellids:  SpatialGrid cellids for which to fetch data. Default: return full fsgrid data
+:param operator: Datareduction operator. “pass” does no operation on data
+:returns: <em>ordered</em> list of numpy arrays with the data</p>
+<p>… seealso:: <a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_fsgrid_variable" title="pytools.vlsvfile.VlsvReader.read_fsgrid_variable"><code class="xref py py-func docutils literal notranslate"><span class="pre">read_fsgrid_variable()</span></code></a></p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.read_interpolated_fsgrid_variable">
+<span class="sig-name descname"><span class="pre">read_interpolated_fsgrid_variable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coordinates</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">operator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pass'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">periodic</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[True,</span> <span class="pre">True,</span> <span class="pre">True]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'linear'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.read_interpolated_fsgrid_variable" title="Link to this definition"></a></dt>
+<dd><p>Read a linearly interpolated FSgrid variable value from the open vlsv file. Feel free to vectorize!
+Note that this does not account for varying centerings of fsgrid data.
+Arguments:
+:param name: Name of the (FSgrid) variable
+:param coords: Coordinates from which to read data 
+:param periodic: Periodicity of the system. Default is periodic in all dimension
+:param operator: Datareduction operator. “pass” does no operation on data
+:returns: numpy array with the data</p>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read" title="pytools.vlsvfile.VlsvReader.read"><code class="xref py py-func docutils literal notranslate"><span class="pre">read()</span></code></a> <a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_variable_info" title="pytools.vlsvfile.VlsvReader.read_variable_info"><code class="xref py py-func docutils literal notranslate"><span class="pre">read_variable_info()</span></code></a></p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.read_interpolated_ionosphere_variable">
+<span class="sig-name descname"><span class="pre">read_interpolated_ionosphere_variable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coordinates</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">operator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pass'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'linear'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.read_interpolated_ionosphere_variable" title="Link to this definition"></a></dt>
+<dd><p>Read a linearly interpolated ionosphere variable value from the open vlsv file.
+Arguments:
+:param name: Name of the (ionosphere) variable
+:param coords: Coordinates (x,y,z) from which to read data 
+:param operator: Datareduction operator. “pass” does no operation on data
+:param method: Interpolation method. Not implemented; barycentric interp would fall under linear.
+:returns: numpy array with the data</p>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read" title="pytools.vlsvfile.VlsvReader.read"><code class="xref py py-func docutils literal notranslate"><span class="pre">read()</span></code></a> <a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_variable_info" title="pytools.vlsvfile.VlsvReader.read_variable_info"><code class="xref py py-func docutils literal notranslate"><span class="pre">read_variable_info()</span></code></a></p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.read_interpolated_variable">
+<span class="sig-name descname"><span class="pre">read_interpolated_variable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coords</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">operator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pass'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">periodic</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[True,</span> <span class="pre">True,</span> <span class="pre">True]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'linear'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.read_interpolated_variable" title="Link to this definition"></a></dt>
+<dd><p>Read a linearly interpolated variable value from the open vlsv file.
+Arguments:
+:param name: Name of the variable
+:param coords: Coordinates from which to read data 
+:param periodic: Periodicity of the system. Default is periodic in all dimension
+:param operator: Datareduction operator. “pass” does no operation on data
+:param method: Interpolation method, default “linear”, options: [“nearest”, “linear”]</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>numpy array with the data</p>
+</dd>
+</dl>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read" title="pytools.vlsvfile.VlsvReader.read"><code class="xref py py-func docutils literal notranslate"><span class="pre">read()</span></code></a> <a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_variable_info" title="pytools.vlsvfile.VlsvReader.read_variable_info"><code class="xref py py-func docutils literal notranslate"><span class="pre">read_variable_info()</span></code></a></p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.read_interpolated_variable_irregular">
+<span class="sig-name descname"><span class="pre">read_interpolated_variable_irregular</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coords</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">operator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pass'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">periodic</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[True,</span> <span class="pre">True,</span> <span class="pre">True]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'linear'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">methodargs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">{'delaunay':</span> <span class="pre">{'qhull_options':</span> <span class="pre">'QJ'},</span> <span class="pre">'rbf':</span> <span class="pre">{'neighbors':</span> <span class="pre">64}}</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.read_interpolated_variable_irregular" title="Link to this definition"></a></dt>
+<dd><p>Read a linearly interpolated variable value from the open vlsv file.
+Arguments:</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> – Name of the variable</p></li>
+<li><p><strong>coords</strong> – Coordinates from which to read data</p></li>
+<li><p><strong>periodic</strong> – Periodicity of the system. Default is periodic in all dimension</p></li>
+<li><p><strong>operator</strong> – Datareduction operator. “pass” does no operation on data</p></li>
+<li><p><strong>method</strong> – Method for interpolation, default “linear” (“nearest”, “rbf, “delaunay”)</p></li>
+<li><p><strong>methodargs</strong> – <p>Dict of dicts to pass kwargs to interpolators. Default values for “rbf”, “delaunay”;</p>
+<p>see scipy.interpolate.RBFInterpolator for rbf and scipy.interpolate.LinearNDInterpolator for delaunay</p>
+</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>numpy array with the data</p>
+</dd>
+</dl>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read" title="pytools.vlsvfile.VlsvReader.read"><code class="xref py py-func docutils literal notranslate"><span class="pre">read()</span></code></a> <a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_variable_info" title="pytools.vlsvfile.VlsvReader.read_variable_info"><code class="xref py py-func docutils literal notranslate"><span class="pre">read_variable_info()</span></code></a></p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.read_ionosphere_node_variable_at_elements">
+<span class="sig-name descname"><span class="pre">read_ionosphere_node_variable_at_elements</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">varname</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.read_ionosphere_node_variable_at_elements" title="Link to this definition"></a></dt>
+<dd><p>Interpolate an ionospheric node variavle to the element barycenters</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>varname</strong> – string, specifying variable (or data reducer) defined at ionosphere nodes</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><p>specified variable interpolated to the elements’ barycenters</p>
+<p>note: linear barycentric interpolation is just the sum of 3 corner values divided by 3!</p>
+<p>TODO: check behavior for var.ndim&gt;1</p>
+</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.read_ionosphere_variable">
+<span class="sig-name descname"><span class="pre">read_ionosphere_variable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">operator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pass'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.read_ionosphere_variable" title="Link to this definition"></a></dt>
+<dd><p>Reads fsgrid variables from the open vlsv file.
+Arguments:
+:param name: Name of the variable
+:param operator: Datareduction operator. “pass” does no operation on data
+:returns: numpy array with the data in node order</p>
+<p>… seealso:: <a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_variable" title="pytools.vlsvfile.VlsvReader.read_variable"><code class="xref py py-func docutils literal notranslate"><span class="pre">read_variable()</span></code></a></p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.read_metadata">
+<span class="sig-name descname"><span class="pre">read_metadata</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tag</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mesh</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.read_metadata" title="Link to this definition"></a></dt>
+<dd><p>Read variable metadata from the open vlsv file.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> – Name of the data array</p></li>
+<li><p><strong>tag</strong> – Tag of the data array.</p></li>
+<li><p><strong>mesh</strong> – Mesh for the data array</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>four strings:
+the unit of the variable as a regular string
+the unit of the variable as a LaTeX-formatted string
+the description of the variable as a LaTeX-formatted string
+the conversion factor to SI units as a string</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.read_parameter">
+<span class="sig-name descname"><span class="pre">read_parameter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.read_parameter" title="Link to this definition"></a></dt>
+<dd><p>Read a parameter from the vlsv file</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>name</strong> – Name of the parameter</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>The parameter value</p>
+</dd>
+</dl>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_variable" title="pytools.vlsvfile.VlsvReader.read_variable"><code class="xref py py-func docutils literal notranslate"><span class="pre">read_variable()</span></code></a> <a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_variable_info" title="pytools.vlsvfile.VlsvReader.read_variable_info"><code class="xref py py-func docutils literal notranslate"><span class="pre">read_variable_info()</span></code></a></p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.read_variable">
+<span class="sig-name descname"><span class="pre">read_variable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cellids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">operator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pass'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.read_variable" title="Link to this definition"></a></dt>
+<dd><p>Read variables from the open vlsv file. 
+Arguments:
+:param name: Name of the variable
+:param cellids: a value of -1 reads all data
+:param operator: Datareduction operator. “pass” does no operation on data
+:returns: numpy array with the data</p>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read" title="pytools.vlsvfile.VlsvReader.read"><code class="xref py py-func docutils literal notranslate"><span class="pre">read()</span></code></a> <a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_variable_info" title="pytools.vlsvfile.VlsvReader.read_variable_info"><code class="xref py py-func docutils literal notranslate"><span class="pre">read_variable_info()</span></code></a></p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.read_variable_from_cache">
+<span class="sig-name descname"><span class="pre">read_variable_from_cache</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cellids</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">operator</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.read_variable_from_cache" title="Link to this definition"></a></dt>
+<dd><p>Read variable from cache instead of the vlsv file.
+:param name: Name of the variable
+:param cellids: a value of -1 reads all data
+:param operator: Datareduction operator. “pass” does no operation on data
+:returns: numpy array with the data, same format as read_variable</p>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_variable" title="pytools.vlsvfile.VlsvReader.read_variable"><code class="xref py py-func docutils literal notranslate"><span class="pre">read_variable()</span></code></a></p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.read_variable_info">
+<span class="sig-name descname"><span class="pre">read_variable_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cellids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">operator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pass'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.read_variable_info" title="Link to this definition"></a></dt>
+<dd><p>Read variables from the open vlsv file and input the data into VariableInfo</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> – Name of the variable</p></li>
+<li><p><strong>cellids</strong> – a value of -1 reads all data</p></li>
+<li><p><strong>operator</strong> – Datareduction operator. “pass” does no operation on data</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>numpy array with the data</p>
+</dd>
+</dl>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_variable" title="pytools.vlsvfile.VlsvReader.read_variable"><code class="xref py py-func docutils literal notranslate"><span class="pre">read_variable()</span></code></a></p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.read_variable_to_cache">
+<span class="sig-name descname"><span class="pre">read_variable_to_cache</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">operator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pass'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.read_variable_to_cache" title="Link to this definition"></a></dt>
+<dd><p>Read variable from vlsv file to cache, for the whole grid and after applying
+operator.
+:param name: Name of the variable (or datareducer)
+:param operator: Datareduction operator. “pass” does no operation on data.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.read_velocity_cells">
+<span class="sig-name descname"><span class="pre">read_velocity_cells</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cellid</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'proton'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.read_velocity_cells" title="Link to this definition"></a></dt>
+<dd><p>Read velocity cells from a spatial cell</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>cellid</strong> – Cell ID of the cell whose velocity cells the function will read</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Map of velocity cell ids (unique for every velocity cell) and corresponding value</p>
+</dd>
+</dl>
+<p>#Example:</p>
+<p>example_cellid = 1111</p>
+<p>velocity_cell_map = vlsvReader.read_velocity_cells(example_cellid)
+velocity_cell_ids = velocity_cell_map.keys()
+velocity_cell_values = velocity_cell_map.values()</p>
+<p>random_index = 4 # Just some index
+random_velocity_cell_id = velocity_cell_ids[random_index]</p>
+<p>print (“Velocity cell value at velocity cell id “ + str(random_velocity_cell_id) + “: “ + str(velocity_cell_map[random_velocity_cell_id]))</p>
+<p># Getting the corresponding coordinates might be more useful than having the velocity cell id so:
+velocity_cell_coordinates = vlsvReader.get_velocity_cell_coordinates(velocity_cell_ids) # Get velocity cell coordinates corresponding to each velocity cell id</p>
+<p>random_velocity_cell_coordinates = velocity_cell_ids[random_index]
+print(“Velocity cell value at velocity cell id “ + str(random_velocity_cell_id) + “and coordinates “ + str(random_velocity_cell_coordinates) + “: “ + str(velocity_cell_map[random_velocity_cell_id]))</p>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="#pytools.vlsvfile.VlsvReader.read_blocks" title="pytools.vlsvfile.VlsvReader.read_blocks"><code class="xref py py-func docutils literal notranslate"><span class="pre">read_blocks()</span></code></a></p>
+</div>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvReader.upsample_fsgrid_subarray">
+<span class="sig-name descname"><span class="pre">upsample_fsgrid_subarray</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cellid</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">var</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">array</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvReader.upsample_fsgrid_subarray" title="Link to this definition"></a></dt>
+<dd><p>Set the elements of the fsgrid array to the value of corresponding SpatialGrid
+cellid. Mutator for array.</p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvWriter">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pytools.vlsvfile.</span></span><span class="sig-name descname"><span class="pre">VlsvWriter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vlsvReader</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">file_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">copy_meshes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">clone</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvWriter" title="Link to this definition"></a></dt>
+<dd><p>Class for reading VLSV files</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvWriter.clone_file">
+<span class="sig-name descname"><span class="pre">clone_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vlsvReader</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dst</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvWriter.clone_file" title="Link to this definition"></a></dt>
+<dd><p>Simply copies overs the file in vlsvReader to a fresh new file
+:param vlsvReader:    Some open vlsv file 
+:param dst:     Name of output file</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvWriter.copy_variables">
+<span class="sig-name descname"><span class="pre">copy_variables</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vlsvReader</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">varlist</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvWriter.copy_variables" title="Link to this definition"></a></dt>
+<dd><p>Copies variables from vlsv reader to the file.
+varlist = None: list of variables to copy; if no
+varlist is provided, copy all variables (default)</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvWriter.copy_variables_list">
+<span class="sig-name descname"><span class="pre">copy_variables_list</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vlsvReader</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vars</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvWriter.copy_variables_list" title="Link to this definition"></a></dt>
+<dd><p>Copies variables in the list vars from vlsv reader to the file</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvWriter.write">
+<span class="sig-name descname"><span class="pre">write</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tag</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mesh</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extra_attribs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">{}</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvWriter.write" title="Link to this definition"></a></dt>
+<dd><p>Writes an array into the vlsv file</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> – Name of the data array</p></li>
+<li><p><strong>tag</strong> – Tag of the data array.</p></li>
+<li><p><strong>mesh</strong> – Mesh for the data array</p></li>
+<li><p><strong>extra_attribs</strong> – Dictionary with whatever xml attributes that should be defined in the array that aren’t name, tag, or mesh</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>True if the data was written successfully</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvWriter.write_variable">
+<span class="sig-name descname"><span class="pre">write_variable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mesh</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">units</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">latex</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">latexunits</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">unitConversion</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extra_attribs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">{}</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvWriter.write_variable" title="Link to this definition"></a></dt>
+<dd><p>Writes an array into the vlsv file as a variable; requires input of metadata required by VlsvReader
+:param data: The variable data (array)
+:param name: Name of the data array
+:param mesh: Mesh for the data array
+:param latex: LaTeX string representation of the variable name
+:param units: plaintext string representation of the unit
+:param latexunits: LaTeX string representation of the unit
+:param unitConversion: string representation of the unit conversion to get to SI
+:param extra_attribs: Dictionary with whatever xml attributes that should be defined in the array that aren’t name, tag, or mesh.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>True if the data was written successfully</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvWriter.write_variable_info">
+<span class="sig-name descname"><span class="pre">write_variable_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">varinfo</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mesh</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">unitConversion</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extra_attribs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">{}</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvWriter.write_variable_info" title="Link to this definition"></a></dt>
+<dd><p>Writes an array into the vlsv file as a variable; requires input of metadata required by VlsvReader</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>varinfo</strong> – VariableInfo object containing
+-data: The variable data (array)
+-name: Name of the data array
+-latex: LaTeX string representation of the variable name
+-units: plaintext string representation of the unit
+-latexunits: LaTeX string representation of the unit</p></li>
+<li><p><strong>mesh</strong> – Mesh for the data array</p></li>
+<li><p><strong>unitConversion</strong> – string representation of the unit conversion to get to SI</p></li>
+<li><p><strong>extra_attribs</strong> – Dictionary with whatever xml attributes that should be defined in the array that aren’t name, tag, or mesh,
+or contained in varinfo. Can be used to overwrite varinfo values besids name.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>True if the data was written successfully</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pytools.vlsvfile.VlsvWriter.write_velocity_space">
+<span class="sig-name descname"><span class="pre">write_velocity_space</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vlsvReader</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cellid</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">blocks_and_values</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.vlsvfile.VlsvWriter.write_velocity_space" title="Link to this definition"></a></dt>
+<dd><p>Writes given velocity space into vlsv file</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>vlsvReader</strong> – Some open vlsv reader file with velocity space in the given cell id</p></li>
+<li><p><strong>cellid</strong> – Given cellid</p></li>
+<li><p><strong>blocks_and_values</strong> – Blocks and values in list format e.g. [[block1,block2,..], [block1_values, block2_values,..]] where block1_values are velocity block values (list length 64)</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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