Merge pull request #161 from yt-project/sph-diagram-interactive

[ci skip]

This build is based on
04a9eb7.

This commit was created by the following CI build and job:
https://github.com/yt-project/yt-4.0-paper/commit/04a9eb7f09be21b07f86135f0e4c4d0df51749ed/checks
https://github.com/yt-project/yt-4.0-paper/actions/runs/6947153996

README.md

@@ -1,7 +1,7 @@
 # Output directory containing the formatted manuscript
 
 The [`gh-pages`](https://github.com/yt-project/yt-4.0-paper/tree/gh-pages) branch hosts the contents of this directory at <https://yt-project.github.io/yt-4.0-paper/>.
-The permalink for this webpage version is <https://yt-project.github.io/yt-4.0-paper/v/f24c12087aff187ded08b836953ef110b4b7faed/>.
+The permalink for this webpage version is <https://yt-project.github.io/yt-4.0-paper/v/04a9eb7f09be21b07f86135f0e4c4d0df51749ed/>.
 To redirect to the permalink for the latest manuscript version at anytime, use the link <https://yt-project.github.io/yt-4.0-paper/v/freeze/>.
 
 ## Files
@@ -35,4 +35,4 @@ Verifying timestamps with the `ots verify` command requires running a local bitc
 ## Source
 
 The manuscripts in this directory were built from
-[`f24c12087aff187ded08b836953ef110b4b7faed`](https://github.com/yt-project/yt-4.0-paper/commit/f24c12087aff187ded08b836953ef110b4b7faed).
+[`04a9eb7f09be21b07f86135f0e4c4d0df51749ed`](https://github.com/yt-project/yt-4.0-paper/commit/04a9eb7f09be21b07f86135f0e4c4d0df51749ed).

images/sph_ray_tracing.js

@@ -0,0 +1,81 @@
+var particles = [
+    { cx:65, cy:135, r:50},
+    { cx:150, cy:175, r:35 },
+    { cx:185, cy:130, r:7},
+    { cx:160, cy:115, r:10},
+    { cx:235, cy:90, r:40},
+    { cx:215, cy:30, r:20},
+    { cx:425, cy:45, r:40},
+    { cx:280, cy:140, r:25 },
+    { cx:350, cy:125, r:20 },
+    { cx:410, cy:150, r:30},
+    { cx:330, cy:180, r:35},
+    { cx:255, cy:315, r:55},
+    { cx:475, cy:240, r:60},
+    { cx:650, cy:215, r:85},
+    { cx:570, cy:45, r:45},
+    { cx:705, cy:45, r:35},
+];
+const hitOptions = {
+	segments: true,
+	stroke: true,
+	fill: true,
+	tolerance: 5
+};
+function recalculateIntersections() {
+    for (const particle of particleGroup.children) {
+        if (rayLine.intersects(particle)) {
+            particle.fillColor.gradient.stops = ['red','white'];
+            particle.data.line.lastSegment.point = rayLine.getNearestPoint(particle.position);
+            particle.data.line.strokeColor = 'black';
+        } else {
+            particle.fillColor.gradient.stops = ['black', 'white'];
+            particle.data.line.strokeColor = null;
+        }
+    }
+}
+
+const particleGroup = new Group();
+
+for (i = 0; i< particles.length; i++) {
+    const particle = particles[i];
+    var myCircle = new Path.Circle(new Point(particle.cx, particle.cy), particle.r);
+    myCircle.data.line = new Path.Line(myCircle.position, myCircle.position + new Point(0, particle.r))
+    myCircle.data.line.strokeWidth = 3;
+    myCircle.data.radius = particle.r;
+    myCircle.fillColor = {
+        gradient: {
+            stops: ['black', 'white'],
+        radial: true},
+
+        origin: myCircle.position,
+        destination: myCircle.bounds.rightCenter
+    };
+    particleGroup.addChild(myCircle);
+}
+
+const rayPoints = [new Point(50, 50), new Point(200, 50)];
+const rayLine = new Path.Line(rayPoints[0], rayPoints[1]);
+const rayStart = new Path.Circle(rayPoints[0], 8);
+const rayStop = new Path.Circle(rayPoints[1], 8);
+rayLine.strokeColor = 'darkgray';
+rayLine.strokeWidth = 3;
+rayStart.fillColor = 'red';
+rayStop.fillColor = 'red';
+
+function dragCircle(event) {
+    event.target.position += event.delta;
+    rayLine.firstSegment.point = rayStart.position;
+    rayLine.lastSegment.point = rayStop.position;
+    recalculateIntersections();
+}
+
+rayStart.onMouseDrag = rayStop.onMouseDrag = dragCircle;
+
+function dragLine(event) {
+    event.target.position += event.delta;
+    rayStart.position = rayLine.firstSegment.point;
+    rayStop.position = rayLine.lastSegment.point;
+    recalculateIntersections();
+}
+rayLine.onMouseDrag = dragLine;

index.html

@@ -66,7 +66,7 @@
   <meta name="author" content="John H. Wise" />
   <meta name="author" content="Shin-Rong Tsai" />
   <meta name="author" content="Add Yourself" />
-  <meta name="dcterms.date" content="2023-11-20" />
+  <meta name="dcterms.date" content="2023-11-21" />
   <meta name="keywords" content="markdown, publishing, manubot" />
   <title>Introducing yt 4.0: Analysis and Visualization of Volumetric Data</title>
   <style>
@@ -174,11 +174,11 @@
   <meta name="citation_title" content="Introducing yt 4.0: Analysis and Visualization of Volumetric Data" />
   <meta property="og:title" content="Introducing yt 4.0: Analysis and Visualization of Volumetric Data" />
   <meta property="twitter:title" content="Introducing yt 4.0: Analysis and Visualization of Volumetric Data" />
-  <meta name="dc.date" content="2023-11-20" />
-  <meta name="citation_publication_date" content="2023-11-20" />
-  <meta property="article:published_time" content="2023-11-20" />
-  <meta name="dc.modified" content="2023-11-20T01:28:29+00:00" />
-  <meta property="article:modified_time" content="2023-11-20T01:28:29+00:00" />
+  <meta name="dc.date" content="2023-11-21" />
+  <meta name="citation_publication_date" content="2023-11-21" />
+  <meta property="article:published_time" content="2023-11-21" />
+  <meta name="dc.modified" content="2023-11-21T17:04:59+00:00" />
+  <meta property="article:modified_time" content="2023-11-21T17:04:59+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -388,9 +388,9 @@
   <meta name="citation_fulltext_html_url" content="https://yt-project.github.io/yt-4.0-paper/" />
   <meta name="citation_pdf_url" content="https://yt-project.github.io/yt-4.0-paper/manuscript.pdf" />
   <link rel="alternate" type="application/pdf" href="https://yt-project.github.io/yt-4.0-paper/manuscript.pdf" />
-  <link rel="alternate" type="text/html" href="https://yt-project.github.io/yt-4.0-paper/v/f24c12087aff187ded08b836953ef110b4b7faed/" />
-  <meta name="manubot_html_url_versioned" content="https://yt-project.github.io/yt-4.0-paper/v/f24c12087aff187ded08b836953ef110b4b7faed/" />
-  <meta name="manubot_pdf_url_versioned" content="https://yt-project.github.io/yt-4.0-paper/v/f24c12087aff187ded08b836953ef110b4b7faed/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://yt-project.github.io/yt-4.0-paper/v/04a9eb7f09be21b07f86135f0e4c4d0df51749ed/" />
+  <meta name="manubot_html_url_versioned" content="https://yt-project.github.io/yt-4.0-paper/v/04a9eb7f09be21b07f86135f0e4c4d0df51749ed/" />
+  <meta name="manubot_pdf_url_versioned" content="https://yt-project.github.io/yt-4.0-paper/v/04a9eb7f09be21b07f86135f0e4c4d0df51749ed/manuscript.pdf" />
   <meta property="og:type" content="article" />
   <meta property="twitter:card" content="summary_large_image" />
   <link rel="icon" type="image/png" sizes="192x192" href="https://manubot.org/favicon-192x192.png" />
@@ -508,10 +508,10 @@ <h1 class="title">Introducing yt 4.0: Analysis and Visualization of Volumetric D
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://yt-project.github.io/yt-4.0-paper/v/f24c12087aff187ded08b836953ef110b4b7faed/">permalink</a>)
+(<a href="https://yt-project.github.io/yt-4.0-paper/v/04a9eb7f09be21b07f86135f0e4c4d0df51749ed/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/yt-project/yt-4.0-paper/tree/f24c12087aff187ded08b836953ef110b4b7faed">yt-project/yt-4.0-paper@f24c120</a>
-on November 20, 2023.
+from <a href="https://github.com/yt-project/yt-4.0-paper/tree/04a9eb7f09be21b07f86135f0e4c4d0df51749ed">yt-project/yt-4.0-paper@04a9eb7</a>
+on November 21, 2023.
 </em></small></p>
 <h2 id="authors">Authors</h2>
 <ul>
@@ -2494,11 +2494,15 @@ <h3 id="sec:sph-analysis">SPH Analysis</h3>
 However, with SPH data, the selection methods in 2D and 3D will always include those particles whose spheres of influence, defined by the appropriate smoothing lengths, are within or overlapping with the data selector.
 This is somewhat counter to the expectations set by the grid codes, but aligns with the need to have a fully self-contained data-container for computing field values.
 For instance, this means that a “ray” object (often used to compute, for instance, the column density in a cosmological simulation) will in fact include a set of particles within a (potentially) varying impact parameter.
-This can be seen in diagram form in Figure <a href="#fig:sph_ray_tracing">11</a>.</p>
+This can be seen in diagram form in Figure <a href="#fig:sph_ray_tracing">11</a>.
+We note that, as described in the SPLASH method paper <span class="citation" data-cites="1A6gLV5Q0">[<a href="#ref-1A6gLV5Q0" role="doc-biblioref">8</a>]</span>, the kernel interpolation can be computed using the (dimensionless) ratio between the impact parameter of the ray and the smoothing length of the particle.</p>
+<canvas id="sph-ray-figure" style="width:100%;height:100%;min-height: 500px;" hidpi="true">
+</canvas>
+<script type="text/paperscript" canvas="sph-ray-figure" src="images/sph_ray_tracing.js"></script>
 <div id="fig:sph_ray_tracing" class="fignos">
 <figure>
-<img src="images/sph_ray_tracing_diagram.svg" alt="Figure 11: A cartoon diagram of a ray passing through a collection of particles. The radius of the particle is indicative of its smoothing length (values should not be interpreted to be constant within these circles!). As can be seen, the individual particles each contribute different amounts as a result of their smoothing length, the chord-length as the ray passes through the circle, and the values within each particle." />
-<figcaption aria-hidden="true"><span>Figure 11:</span> A cartoon diagram of a ray passing through a collection of particles. The radius of the particle is indicative of its smoothing length (values should <em>not</em> be interpreted to be constant within these circles!). As can be seen, the individual particles each contribute different amounts as a result of their smoothing length, the chord-length as the ray passes through the circle, and the values within each particle.</figcaption>
+<img src="images/blank.svg" width="1" alt="Figure 11: A cartoon diagram of a ray passing through a collection of particles. The radius of the particle is indicative of its smoothing length. As can be seen, the individual particles each contribute different amounts as a result of their smoothing length, the chord-length as the ray passes through the circle, and the values within each particle." />
+<figcaption aria-hidden="true"><span>Figure 11:</span> A cartoon diagram of a ray passing through a collection of particles. The radius of the particle is indicative of its smoothing length. As can be seen, the individual particles each contribute different amounts as a result of their smoothing length, the chord-length as the ray passes through the circle, and the values within each particle.</figcaption>
 </figure>
 </div>
 <p>Other than these differences, which have been intentionally made to align the results with the expected results from the underlying discretization method, the APIs for access to particle data and finite volume data are identical, and they provide broadly identical functionality, where the disparities are typically in functionality such as volume rendering.