Merge pull request #215 from clEsperanto/release-0.19.3

Release 0.19.3

README.md

@@ -15,20 +15,20 @@
 [![DOI](https://zenodo.org/badge/248206619.svg)](https://zenodo.org/badge/latestdoi/248206619)
 
 py-clesperanto is a prototype for [clesperanto](http://clesperanto.net) - a multi-platform multi-language framework for GPU-accelerated image processing. 
-We mostly use it in the life sciences for analysing 3/4-dimensional microsopy data, e.g. as we face it developmental biology when segmenting cells and studying
+We mostly use it in the life sciences for analysing 3- and 4-dimensional microsopy data, e.g. as we face it developmental biology when segmenting cells and studying
 their individual properties as well as properties of compounds of cells forming tissues.
 
 ![](https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/banner.png)
-<small>Image data source: Daniela Vorkel, Myers lab, MPI-CBG, rendered using [napari](https://github.com/napari/napari) </small>
+Image data source: Daniela Vorkel, Myers lab, MPI-CBG, rendered using [napari](https://github.com/napari/napari)
 
 clesperanto uses [OpenCL kernels](https://github.com/clEsperanto/clij-opencl-kernels/tree/development/src/main/java/net/haesleinhuepf/clij/kernels) from [CLIJ](http://clij.github.io/).
-Since version 0.11.1 py-clesperanto comes with a yet experimental [cupy](https://cupy.dev)-based [CUDA](https://en.wikipedia.org/wiki/CUDA) backend.
 
 For users convenience, there are code generators available for [napari](https://clesperanto.github.io/napari_pyclesperanto_assistant/) and [Fiji](https://clij.github.io/assistant/).
 Also check out the [napari workflow optimizer](https://github.com/haesleinhuepf/napari-workflow-optimizer) for semi-automatic parameter tuning of clesperanto-functions.
 
 ## Reference
-The [full reference](https://clij.github.io/clij2-docs/reference__pyclesperanto) is available as part of the CLIJ2 documentation.
+The preliminary API reference is available [here](https://clesperanto.github.io/pyclesperanto_prototype/docs/_build/html/).
+Furthermore, parts of the [reference](https://clij.github.io/clij2-docs/reference__pyclesperanto) are also available within the CLIJ2 documentation.
 
 ## Installation
 * Get a conda/python environment, e.g. via [mini-conda](https://docs.conda.io/en/latest/miniconda.html). If you never used python/conda environments before, please follow the instructions [here](https://biapol.github.io/blog/johannes_mueller/anaconda_getting_started/) first.

docs/_build/html/genindex.html

@@ -309,6 +309,8 @@ <h2 id="C">C</h2>
       <li><a href="index.html#pyclesperanto_prototype.create_zyx">create_zyx() (in module pyclesperanto_prototype)</a>
 </li>
       <li><a href="index.html#pyclesperanto_prototype.crop">crop() (in module pyclesperanto_prototype)</a>, <a href="reference.html#pyclesperanto_prototype.crop">[1]</a>
+</li>
+      <li><a href="index.html#pyclesperanto_prototype.crop_border">crop_border() (in module pyclesperanto_prototype)</a>, <a href="reference.html#pyclesperanto_prototype.crop_border">[1]</a>
 </li>
       <li><a href="index.html#pyclesperanto_prototype.cubic_root">cubic_root() (in module pyclesperanto_prototype)</a>, <a href="reference.html#pyclesperanto_prototype.cubic_root">[1]</a>
 </li>

docs/_build/html/py-modindex.html

@@ -82,7 +82,7 @@ <h1>Python Module Index</h1>
      <tr>
        <td></td>
        <td>
-       <a href="index.html#module-pyclesperanto_prototype"><code class="xref">pyclesperanto_prototype</code></a></td><td>
+       <a href="reference.html#module-pyclesperanto_prototype"><code class="xref">pyclesperanto_prototype</code></a></td><td>
        <em></em></td></tr>
    </table>
 

docs/_build/html/reference.html

@@ -1927,6 +1927,28 @@ <h1>Reference<a class="headerlink" href="#reference" title="Permalink to this he
 </dl>
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="pyclesperanto_prototype.crop_border">
+<span class="sig-prename descclassname"><span class="pre">pyclesperanto_prototype.</span></span><span class="sig-name descname"><span class="pre">crop_border</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_image</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Union</span><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">OCLArray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Image</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">_OCLImage</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">destination_image</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Union</span><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">OCLArray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Image</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">_OCLImage</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">border_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1</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">Union</span><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">OCLArray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Image</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">_OCLImage</span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#pyclesperanto_prototype.crop_border" title="Permalink to this definition"></a></dt>
+<dd><p>Crops an image by removing the outer pixels, per default 1.</p>
+<p class="rubric">Notes</p>
+<ul class="simple">
+<li><p>To make sure the output image has the right size, provide destination_image=None.</p></li>
+</ul>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>input_image</strong> (<em>Image</em>) – </p></li>
+<li><p><strong>destination_image</strong> (<em>Image</em>) – </p></li>
+<li><p><strong>border_size</strong> (<em>int</em>) – </p></li>
+</ul>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p>destination_image</p>
+</dd>
+</dl>
+</dd></dl>
+
 <dl class="py function">
 <dt class="sig sig-object py" id="pyclesperanto_prototype.cubic_root">
 <span class="sig-prename descclassname"><span class="pre">pyclesperanto_prototype.</span></span><span class="sig-name descname"><span class="pre">cubic_root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Union</span><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">OCLArray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Image</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">_OCLImage</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">destination</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Union</span><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">OCLArray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Image</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">_OCLImage</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</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">Union</span><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">OCLArray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Image</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">_OCLImage</span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#pyclesperanto_prototype.cubic_root" title="Permalink to this definition"></a></dt>

docs/index.html

@@ -0,0 +1 @@
+<meta http-equiv="refresh" content="0; url=./_build/html/index.html" />

docs/readme.md

@@ -21,3 +21,6 @@ make.bat html
 make.bat clean
 ```
 
+## See also
+
+https://biapol.github.io/blog/johannes_mueller/entry_sphinx/

pyclesperanto_prototype/__init__.py

@@ -10,5 +10,5 @@
 from ._tier10 import *
 from ._tier11 import *
 
-__version__ = "0.19.2"
+__version__ = "0.19.3"
 __common_alias__ = "cle"

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = pyclesperanto_prototype
-version = 0.19.2
+version = 0.19.3
 author = Robert Haase
 author_email = [email protected]
 url = https://github.com/clEsperanto/pyclesperanto_prototype