Update docs to reflect themove to pip from conda

Author: allevitan

_sources/installation.rst.txt

@@ -13,20 +13,22 @@ The repository remains under active development as of late 2024.
 Step 2: Install Dependencies
 ----------------------------
 
-CDTools requires python 3.7 or greater.
+CDTools is regularly tested with Python versions 3.8 to 3.12, so it is recommended to use one of these versions. In general, CDTools requires Python 3.7 or higher.
 
 The major dependency for CDTools is pytorch (version 1.9.0 or greater). Because the details of the installation can vary depending on platform, GPU availability, etc, it is recommended that you follow the install instructions on `the pytorch site`_ to install pytorch before installing the remaining dependencies.
 
 .. _`the pytorch site`: https://pytorch.org/get-started/locally/
 
-If you manage your environment with conda, the remaining dependencies can be installed by running the following command in the top level directory of the package:
+pytorch stopped supporting installation using conda for installation, so it is recommended continue the installation using pip.
 
 .. code:: bash
 	  
-   $ conda install --file requirements.txt -c conda-forge
+   $ pip install -r requirements.txt
+
+This will install all required dependencies and verify that they meet the pytorch version requirements. Additionally, several optional dependencies used for testing and documentation will also be installed. The full set of dependencies and minimum requirements are listed below is listed below.
+
+CDTools is reguarly tested with the latest versions of the packages shown below.   
 
-This will install all required dependencies *except for pytorch*, as well as several optional dependencies which are used for the tests and documentation. The full set of dependencies are noted below.
-   
 Required dependencies:
 
    * `numpy <http://www.numpy.org>`_ >= 1.0

_sources/intro.rst.txt

@@ -7,9 +7,7 @@ Introduction to CDTools
    Introduction to CDTools
    -----------------------
 
-`CDTools`_ is an open source python library for ptychography and CDI reconstructions, using an automatic differentiation based approach. It is distributed under an MIT (a.k.a. Expat) license.
-
-.. _`CDTools`: https://github.com/cdtools-developers/cdtools
+CDTools is an open source python library for ptychography and CDI reconstructions, using an automatic differentiation based approach. It is distributed under an MIT (a.k.a. Expat) license.
 
 .. code-block:: python
 

datasets.html

@@ -74,6 +74,9 @@
 <li class="toctree-l3"><a class="reference internal" href="#cdtools.datasets.Ptycho2DDataset.plot_mean_pattern"><code class="docutils literal notranslate"><span class="pre">Ptycho2DDataset.plot_mean_pattern()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#cdtools.datasets.Ptycho2DDataset.split"><code class="docutils literal notranslate"><span class="pre">Ptycho2DDataset.split()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#cdtools.datasets.Ptycho2DDataset.pad"><code class="docutils literal notranslate"><span class="pre">Ptycho2DDataset.pad()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#cdtools.datasets.Ptycho2DDataset.downsample"><code class="docutils literal notranslate"><span class="pre">Ptycho2DDataset.downsample()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#cdtools.datasets.Ptycho2DDataset.remove_translations_mask"><code class="docutils literal notranslate"><span class="pre">Ptycho2DDataset.remove_translations_mask()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#cdtools.datasets.Ptycho2DDataset.crop_translations"><code class="docutils literal notranslate"><span class="pre">Ptycho2DDataset.crop_translations()</span></code></a></li>
 </ul>
 </li>
 </ul>
@@ -472,6 +475,71 @@
 </dl>
 </dd></dl>
 
+<dl class="py method">
+<dt class="sig sig-object py" id="cdtools.datasets.Ptycho2DDataset.downsample">
+<span class="sig-name descname"><span class="pre">downsample</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">factor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cdtools.datasets.Ptycho2DDataset.downsample" title="Link to this definition"></a></dt>
+<dd><p>Downsamples all diffraction patterns by the specified factor</p>
+<p>This is an easy way to shrink the amount of data you need to work with
+if the speckle size is much larger than the detector pixel size.</p>
+<p>The downsampling factor must be an integer. The size of the output
+patterns are reduced by the specified factor, with each output pixel
+equal to the sum of a &lt;factor&gt; x &lt;factor&gt; region of pixels in the
+input pattern. This summation is done by pytorch.functional.avg_pool2d.</p>
+<p>Any mask and background data which is stored with the dataset is
+downsampled with the data. The background is downsampled using the same
+method as the data. The mask is expanded so that any output pixel
+containing a masked pixel will be masked.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>factor</strong> (<em>int</em>) – Default 2, the factor to downsample by</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="cdtools.datasets.Ptycho2DDataset.remove_translations_mask">
+<span class="sig-name descname"><span class="pre">remove_translations_mask</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mask_remove</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cdtools.datasets.Ptycho2DDataset.remove_translations_mask" title="Link to this definition"></a></dt>
+<dd><p>Removes one or more translation positions, and their associated
+properties, from the dataset using logical indexing.</p>
+<p>This takes a 1D mask (boolean torch tensor) with the length
+self.translations.shape[0] (i.e., the number of individual
+translated points). Patterns, translations, and intensities
+associated with indices that are “True” will be removed.</p>
+<section id="parameters">
+<h2>Parameters:<a class="headerlink" href="#parameters" title="Link to this heading"></a></h2>
+<dl class="simple">
+<dt>mask_remove<span class="classifier">1D torch.tensor(dtype=torch.bool)</span></dt><dd><p>The boolean mask indicating which elements are to be removed from
+the dataset. True indicates that the corresponding element will be
+removed.</p>
+</dd>
+</dl>
+</section>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="cdtools.datasets.Ptycho2DDataset.crop_translations">
+<span class="sig-name descname"><span class="pre">crop_translations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">roi</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cdtools.datasets.Ptycho2DDataset.crop_translations" title="Link to this definition"></a></dt>
+<dd><p>Shrinks the range of translation positions that are analyzed</p>
+<p>This deletes all diffraction patterns associated with x- and
+y-translations that lie outside of a specified rectangular
+region of interest. In essence, this operation crops the “relative
+displacement map” (shown in self.inspect()) down to the region of
+interest.</p>
+<section id="id1">
+<h2>Parameters:<a class="headerlink" href="#id1" title="Link to this heading"></a></h2>
+<dl class="simple">
+<dt>roi<span class="classifier">tuple(float, float, float, float)</span></dt><dd><p>The translation-x and -y coordinates that define the rectangular
+region of interest as (in units of meters)
+(left, right, bottom, top). The definition of these bounds are
+based on how an image is normally displayed with matplotlib’s
+imshow. The order in which these elements are defined in roi
+do not matter as long as roi[:2] and roi[2:] correspond with
+the x and y coordinates, respectively.</p>
+</dd>
+</dl>
+</section>
+</dd></dl>
+
 </dd></dl>
 
 </section>

genindex.html

@@ -87,6 +87,7 @@ <h1 id="index">Index</h1>
  | <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>
@@ -303,6 +304,16 @@ <h2 id="C">C</h2>
       <li><a href="tools/image_processing.html#cdtools.tools.image_processing.convolve_1d">convolve_1d() (in module cdtools.tools.image_processing)</a>
 </li>
       <li><a href="tools/data.html#cdtools.tools.data.create_cxi">create_cxi() (in module cdtools.tools.data)</a>
+</li>
+      <li><a href="datasets.html#cdtools.datasets.Ptycho2DDataset.crop_translations">crop_translations() (cdtools.datasets.Ptycho2DDataset method)</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="datasets.html#cdtools.datasets.Ptycho2DDataset.downsample">downsample() (cdtools.datasets.Ptycho2DDataset method)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -553,10 +564,12 @@ <h2 id="R">R</h2>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="models.html#cdtools.models.RPI.random_init">random_init() (cdtools.models.RPI method)</a>
 </li>
-      <li><a href="models.html#cdtools.models.CDIModel.report">report() (cdtools.models.CDIModel method)</a>
+      <li><a href="datasets.html#cdtools.datasets.Ptycho2DDataset.remove_translations_mask">remove_translations_mask() (cdtools.datasets.Ptycho2DDataset method)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="models.html#cdtools.models.CDIModel.report">report() (cdtools.models.CDIModel method)</a>
+</li>
       <li><a href="models.html#cdtools.models.RPI">RPI (class in cdtools.models)</a>
 </li>
       <li><a href="tools/interactions.html#cdtools.tools.interactions.RPI_interaction">RPI_interaction() (in module cdtools.tools.interactions)</a>

index.html

@@ -86,7 +86,7 @@
 </div>
 <section id="introduction-to-cdtools">
 <h1>Introduction to CDTools<a class="headerlink" href="#introduction-to-cdtools" title="Link to this heading"></a></h1>
-<p><a class="reference external" href="https://github.com/cdtools-developers/cdtools">CDTools</a> is an open source python library for ptychography and CDI reconstructions, using an automatic differentiation based approach. It is distributed under an MIT (a.k.a. Expat) license.</p>
+<p>CDTools is an open source python library for ptychography and CDI reconstructions, using an automatic differentiation based approach. It is distributed under an MIT (a.k.a. Expat) license.</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">matplotlib</span> <span class="kn">import</span> <span class="n">pyplot</span> <span class="k">as</span> <span class="n">plt</span>
 <span class="kn">from</span> <span class="nn">cdtools.datasets</span> <span class="kn">import</span> <span class="n">Ptycho2DDataset</span>
 <span class="kn">from</span> <span class="nn">cdtools.models</span> <span class="kn">import</span> <span class="n">FancyPtycho</span>

installation.html

@@ -98,13 +98,14 @@ <h2>Step 1: Download<a class="headerlink" href="#step-1-download" title="Link to
 </section>
 <section id="step-2-install-dependencies">
 <h2>Step 2: Install Dependencies<a class="headerlink" href="#step-2-install-dependencies" title="Link to this heading"></a></h2>
-<p>CDTools requires python 3.7 or greater.</p>
+<p>CDTools is regularly tested with Python versions 3.8 to 3.12, so it is recommended to use one of these versions. In general, CDTools requires Python 3.7 or higher.</p>
 <p>The major dependency for CDTools is pytorch (version 1.9.0 or greater). Because the details of the installation can vary depending on platform, GPU availability, etc, it is recommended that you follow the install instructions on <a class="reference external" href="https://pytorch.org/get-started/locally/">the pytorch site</a> to install pytorch before installing the remaining dependencies.</p>
-<p>If you manage your environment with conda, the remaining dependencies can be installed by running the following command in the top level directory of the package:</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$<span class="w"> </span>conda<span class="w"> </span>install<span class="w"> </span>--file<span class="w"> </span>requirements.txt<span class="w"> </span>-c<span class="w"> </span>conda-forge
+<p>pytorch stopped supporting installation using conda for installation, so it is recommended continue the installation using pip.</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>-r<span class="w"> </span>requirements.txt
 </pre></div>
 </div>
-<p>This will install all required dependencies <em>except for pytorch</em>, as well as several optional dependencies which are used for the tests and documentation. The full set of dependencies are noted below.</p>
+<p>This will install all required dependencies and verify that they meet the pytorch version requirements. Additionally, several optional dependencies used for testing and documentation will also be installed. The full set of dependencies and minimum requirements are listed below is listed below.</p>
+<p>CDTools is reguarly tested with the latest versions of the packages shown below.</p>
 <p>Required dependencies:</p>
 <blockquote>
 <div><ul class="simple">

intro.html

@@ -83,7 +83,7 @@
 
   <section id="introduction-to-cdtools">
 <h1>Introduction to CDTools<a class="headerlink" href="#introduction-to-cdtools" title="Link to this heading"></a></h1>
-<p><a class="reference external" href="https://github.com/cdtools-developers/cdtools">CDTools</a> is an open source python library for ptychography and CDI reconstructions, using an automatic differentiation based approach. It is distributed under an MIT (a.k.a. Expat) license.</p>
+<p>CDTools is an open source python library for ptychography and CDI reconstructions, using an automatic differentiation based approach. It is distributed under an MIT (a.k.a. Expat) license.</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">matplotlib</span> <span class="kn">import</span> <span class="n">pyplot</span> <span class="k">as</span> <span class="n">plt</span>
 <span class="kn">from</span> <span class="nn">cdtools.datasets</span> <span class="kn">import</span> <span class="n">Ptycho2DDataset</span>
 <span class="kn">from</span> <span class="nn">cdtools.models</span> <span class="kn">import</span> <span class="n">FancyPtycho</span>