update doc

README.rst

@@ -21,7 +21,7 @@ directly from the DICOM files.
 
 
 * Free software: MIT license
-* Documentation: https://okapy.readthedocs.io.
+* Documentation: https://voreille.github.io/okapy/
 
 
 Features

docs/_build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 89954e14a676554ecc745cb9085f966e
+config: b5eb7e0f69dddc75ad5eeaa5c74b9ccd
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_build/html/_modules/index.html

@@ -197,6 +197,8 @@
         <article role="main">
           <h1>All modules for which code is available</h1>
 <ul><li><a href="okapy/dicomconverter/converter.html">okapy.dicomconverter.converter</a></li>
+<li><a href="okapy/dicomconverter/dicom_walker.html">okapy.dicomconverter.dicom_walker</a></li>
+<li><a href="okapy/dicomconverter/study.html">okapy.dicomconverter.study</a></li>
 </ul>
         </article>
       </div>

docs/_build/html/_modules/okapy/dicomconverter/converter.html

@@ -356,7 +356,7 @@ <h1>Source code for okapy.dicomconverter.converter</h1><div class="highlight"><p
 <span class="sd">    This class represents an instance used for converting a folder containing DICOM files</span>
 <span class="sd">    to NIfTI files. The DICOM files are initially sorted using okapy.dicomconverter.dicom_walker.DicomWalker.</span>
 <span class="sd">    Subsequently, the files are organized based on StudyInstanceUID, creating instances of</span>
-<span class="sd">    okapy.dicomconverter.study.Study. The processing is then carried out sequentially on each Study instances.</span>
+<span class="sd">    :class:`okapy.dicomconverter.study.Study`. The processing is then carried out sequentially on each Study instances.</span>
 <span class="sd">    This approach allows for application of the same segmentation (in the form of RTSTRUCT or SEG)</span>
 <span class="sd">    across different modalities within the same study.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
@@ -480,12 +480,16 @@ <h1>Source code for okapy.dicomconverter.converter</h1><div class="highlight"><p
 <span class="sd">    The `params_path` is a path pointing to a .yaml file containing all the relevant parameters.</span>
 <span class="sd">    An example of a parameters file can be found in the parameters/ folder.</span>
 
-<span class="sd">    Example usage:</span>
-<span class="sd">    ```python</span>
-<span class="sd">    params_path = &quot;path/to/parameters.yaml&quot;</span>
-<span class="sd">    converter = okapy.dicomconverter.converter.ExtractorConverter.from_params(params_path)</span>
-<span class="sd">    results = converter(folder_path)</span>
-<span class="sd">    ```</span>
+<span class="sd">    Once the features are extracted, the NIfTI files are deleted. By default they are stored in a temp</span>
+<span class="sd">    folder using the python function :mod:`tempfile.mkdtemp`.</span>
+
+<span class="sd">    Example usage::</span>
+
+<span class="sd">        from okapy.dicomconverter.converter import ExtractorConverter</span>
+
+<span class="sd">        params_path = &quot;path/to/parameters.yaml&quot; </span>
+<span class="sd">        converter = ExtractorConverter.from_params(params_path)</span>
+<span class="sd">        results = converter(folder_path)</span>
 <span class="sd">    </span>
 <span class="sd">    `results` is a pandas dataframe with the features values for each different images and modalities.</span>
 

docs/_build/html/_sources/index.rst.txt

@@ -2,7 +2,7 @@ Welcome to OkaPy's documentation!
 ======================================
 
 .. toctree::
-   :maxdepth: 6
+   :maxdepth: 2
    :caption: Contents:
 
    readme

docs/_build/html/_sources/installation.rst.txt

@@ -16,11 +16,13 @@ You can either clone the public repository:
 
     $ git clone git://github.com/voreille/okapy
 
-Once you have a copy of the source, you can install it with:
+Once you have a copy of the source open a terminal within the okapy director
+and  you can install it with:
 
 .. code-block:: console
 
-    $ python setup.py install
+    $ pip install numpy # if not already installed
+    $ pip install -e .
 
 
 .. _Github repo: https://github.com/voreille/okapy

docs/_build/html/_sources/modules.rst.txt

@@ -1,5 +1,21 @@
 Modules
 =======
 
+okapy.dicomconverter.converter
+------------------------------
+
 .. automodule:: okapy.dicomconverter.converter
    :members:
+
+
+okapy.dicomconverter.dicom_walker
+---------------------------------
+
+.. automodule:: okapy.dicomconverter.dicom_walker
+   :members:
+
+okapy.dicomconverter.study
+---------------------------------
+
+.. automodule:: okapy.dicomconverter.study
+   :members:

docs/_build/html/_sources/usage.rst.txt

@@ -2,6 +2,17 @@
 Usage
 =====
 
-To use OkaPy in a project::
+OkaPy is designed for processing 3D DICOM images.
+
+There are two primary use cases for OkaPy:
+
+1. **Conversion to NIfTI Files:**
+   OkaPy allows you to convert unsorted DICOM files to NIfTI files, specifically handling 3D images.
+
+2. **Feature Extraction from DICOM Files:**
+   Another usage involves extracting features directly from unsorted DICOM files. In this scenario, OkaPy first converts the DICOM files to NIfTI format and then utilizes `PyRadiomics <https://www.radiomics.io/pyradiomics.html>`_ to perform feature extraction.
+
+
+Example of the first usage::
 
     import okapy

docs/_build/html/authors.html

@@ -159,10 +159,7 @@
 <li class="toctree-l1"><a class="reference internal" href="readme.html">OkaPy</a></li>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage.html">Usage</a></li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="modules.html">Modules</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of Modules</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
-<li class="toctree-l2"><a class="reference internal" href="generated/okapy.html">okapy</a></li>
-</ul>
-</li>
+<li class="toctree-l1"><a class="reference internal" href="modules.html">Modules</a></li>
 <li class="toctree-l1"><a class="reference internal" href="contributing.html">Contributing</a></li>
 <li class="toctree-l1 current current-page"><a class="current reference internal" href="#">Credits</a></li>
 <li class="toctree-l1"><a class="reference internal" href="history.html">History</a></li>

docs/_build/html/contributing.html

@@ -3,7 +3,7 @@
   <head><meta charset="utf-8"/>
     <meta name="viewport" content="width=device-width,initial-scale=1"/>
     <meta name="color-scheme" content="light dark"><meta name="viewport" content="width=device-width, initial-scale=1" />
-<link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="search.html" /><link rel="next" title="Credits" href="authors.html" /><link rel="prev" title="okapy" href="generated/okapy.html" />
+<link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="search.html" /><link rel="next" title="Credits" href="authors.html" /><link rel="prev" title="Modules" href="modules.html" />
 
     <!-- Generated with Sphinx 7.2.6 and Furo 2023.09.10 -->
         <title>Contributing - OkaPy 0.1.0 documentation</title>
@@ -159,10 +159,7 @@
 <li class="toctree-l1"><a class="reference internal" href="readme.html">OkaPy</a></li>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage.html">Usage</a></li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="modules.html">Modules</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of Modules</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
-<li class="toctree-l2"><a class="reference internal" href="generated/okapy.html">okapy</a></li>
-</ul>
-</li>
+<li class="toctree-l1"><a class="reference internal" href="modules.html">Modules</a></li>
 <li class="toctree-l1 current current-page"><a class="current reference internal" href="#">Contributing</a></li>
 <li class="toctree-l1"><a class="reference internal" href="authors.html">Credits</a></li>
 <li class="toctree-l1"><a class="reference internal" href="history.html">History</a></li>
@@ -335,14 +332,14 @@ <h2>Deploying<a class="headerlink" href="#deploying" title="Link to this heading
               </div>
               <svg class="furo-related-icon"><use href="#svg-arrow-right"></use></svg>
             </a>
-          <a class="prev-page" href="generated/okapy.html">
+          <a class="prev-page" href="modules.html">
               <svg class="furo-related-icon"><use href="#svg-arrow-right"></use></svg>
               <div class="page-info">
                 <div class="context">
                   <span>Previous</span>
                 </div>
 
-                <div class="title">okapy</div>
+                <div class="title">Modules</div>
 
               </div>
             </a>

docs/_build/html/generated/okapy.dicomconverter.dicom_walker.html

@@ -159,10 +159,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../readme.html">OkaPy</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../usage.html">Usage</a></li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="../modules.html">Modules</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of Modules</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
-<li class="toctree-l2"><a class="reference internal" href="okapy.html">okapy</a></li>
-</ul>
-</li>
+<li class="toctree-l1"><a class="reference internal" href="../modules.html">Modules</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../contributing.html">Contributing</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../authors.html">Credits</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../history.html">History</a></li>

docs/_build/html/generated/okapy.dicomconverter.html

@@ -159,10 +159,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../readme.html">OkaPy</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../usage.html">Usage</a></li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="../modules.html">Modules</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of Modules</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
-<li class="toctree-l2"><a class="reference internal" href="okapy.html">okapy</a></li>
-</ul>
-</li>
+<li class="toctree-l1"><a class="reference internal" href="../modules.html">Modules</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../contributing.html">Contributing</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../authors.html">Credits</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../history.html">History</a></li>

docs/_build/html/generated/okapy.html

@@ -3,7 +3,7 @@
   <head><meta charset="utf-8"/>
     <meta name="viewport" content="width=device-width,initial-scale=1"/>
     <meta name="color-scheme" content="light dark"><meta name="viewport" content="width=device-width, initial-scale=1" />
-<link rel="index" title="Index" href="../genindex.html" /><link rel="search" title="Search" href="../search.html" /><link rel="next" title="Contributing" href="../contributing.html" /><link rel="prev" title="Modules" href="../modules.html" />
+<link rel="index" title="Index" href="../genindex.html" /><link rel="search" title="Search" href="../search.html" />
 
     <!-- Generated with Sphinx 7.2.6 and Furo 2023.09.10 -->
         <title>okapy - OkaPy 0.1.0 documentation</title>
@@ -155,14 +155,11 @@
 </form>
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
   <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
-<ul class="current">
+<ul>
 <li class="toctree-l1"><a class="reference internal" href="../readme.html">OkaPy</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../usage.html">Usage</a></li>
-<li class="toctree-l1 current has-children"><a class="reference internal" href="../modules.html">Modules</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of Modules</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul class="current">
-<li class="toctree-l2 current current-page"><a class="current reference internal" href="#">okapy</a></li>
-</ul>
-</li>
+<li class="toctree-l1"><a class="reference internal" href="../modules.html">Modules</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../contributing.html">Contributing</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../authors.html">Credits</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../history.html">History</a></li>
@@ -210,26 +207,8 @@
       <footer>
 
         <div class="related-pages">
-          <a class="next-page" href="../contributing.html">
-              <div class="page-info">
-                <div class="context">
-                  <span>Next</span>
-                </div>
-                <div class="title">Contributing</div>
-              </div>
-              <svg class="furo-related-icon"><use href="#svg-arrow-right"></use></svg>
-            </a>
-          <a class="prev-page" href="../modules.html">
-              <svg class="furo-related-icon"><use href="#svg-arrow-right"></use></svg>
-              <div class="page-info">
-                <div class="context">
-                  <span>Previous</span>
-                </div>
-
-                <div class="title">Modules</div>
-
-              </div>
-            </a>
+
+
         </div>
         <div class="bottom-of-page">
           <div class="left-details">

docs/_build/html/genindex.html

@@ -197,8 +197,18 @@
 
 <section class="genindex-section">
   <h1 id="index">Index</h1>
-  <div class="genindex-jumpbox"><a href="#E"><strong>E</strong></a> | <a href="#M"><strong>M</strong></a> | <a href="#N"><strong>N</strong></a> | <a href="#O"><strong>O</strong></a></div>
+  <div class="genindex-jumpbox"><a href="#D"><strong>D</strong></a> | <a href="#E"><strong>E</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="#S"><strong>S</strong></a></div>
 </section>
+<section id="D" class="genindex-section">
+  <h2>D</h2>
+  <table style="width: 100%" class="indextable genindextable"><tr>
+    <td style="width: 33%; vertical-align: top;"><ul>
+        <li><a href="modules.html#okapy.dicomconverter.dicom_walker.DicomWalker">DicomWalker (class in okapy.dicomconverter.dicom_walker)</a>
+</li>
+    </ul></td>
+  </tr></table>
+</section>
+
 <section id="E" class="genindex-section">
   <h2>E</h2>
   <table style="width: 100%" class="indextable genindextable"><tr>
@@ -223,7 +233,9 @@ <h2>M</h2>
 </li>
           <li><a href="modules.html#module-okapy.dicomconverter.converter">okapy.dicomconverter.converter</a>
 </li>
-          <li><a href="generated/okapy.dicomconverter.dicom_walker.html#module-okapy.dicomconverter.dicom_walker">okapy.dicomconverter.dicom_walker</a>
+          <li><a href="generated/okapy.dicomconverter.dicom_walker.html#module-okapy.dicomconverter.dicom_walker">okapy.dicomconverter.dicom_walker</a>, <a href="modules.html#module-okapy.dicomconverter.dicom_walker">[1]</a>
+</li>
+          <li><a href="modules.html#module-okapy.dicomconverter.study">okapy.dicomconverter.study</a>
 </li>
         </ul></li>
     </ul></td>
@@ -258,22 +270,39 @@ <h2>O</h2>
           <li><a href="generated/okapy.dicomconverter.html#module-okapy.dicomconverter">module</a>
 </li>
         </ul></li>
-    </ul></td>
-    <td style="width: 33%; vertical-align: top;"><ul>
         <li>
     okapy.dicomconverter.converter
 
         <ul>
           <li><a href="modules.html#module-okapy.dicomconverter.converter">module</a>
 </li>
         </ul></li>
+    </ul></td>
+    <td style="width: 33%; vertical-align: top;"><ul>
         <li>
     okapy.dicomconverter.dicom_walker
 
         <ul>
-          <li><a href="generated/okapy.dicomconverter.dicom_walker.html#module-okapy.dicomconverter.dicom_walker">module</a>
+          <li><a href="generated/okapy.dicomconverter.dicom_walker.html#module-okapy.dicomconverter.dicom_walker">module</a>, <a href="modules.html#module-okapy.dicomconverter.dicom_walker">[1]</a>
 </li>
         </ul></li>
+        <li>
+    okapy.dicomconverter.study
+
+        <ul>
+          <li><a href="modules.html#module-okapy.dicomconverter.study">module</a>
+</li>
+        </ul></li>
+    </ul></td>
+  </tr></table>
+</section>
+
+<section id="S" class="genindex-section">
+  <h2>S</h2>
+  <table style="width: 100%" class="indextable genindextable"><tr>
+    <td style="width: 33%; vertical-align: top;"><ul>
+        <li><a href="modules.html#okapy.dicomconverter.study.Study">Study (class in okapy.dicomconverter.study)</a>
+</li>
     </ul></td>
   </tr></table>
 </section>

docs/_build/html/history.html

@@ -159,10 +159,7 @@
 <li class="toctree-l1"><a class="reference internal" href="readme.html">OkaPy</a></li>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage.html">Usage</a></li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="modules.html">Modules</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of Modules</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
-<li class="toctree-l2"><a class="reference internal" href="generated/okapy.html">okapy</a></li>
-</ul>
-</li>
+<li class="toctree-l1"><a class="reference internal" href="modules.html">Modules</a></li>
 <li class="toctree-l1"><a class="reference internal" href="contributing.html">Contributing</a></li>
 <li class="toctree-l1"><a class="reference internal" href="authors.html">Credits</a></li>
 <li class="toctree-l1 current current-page"><a class="current reference internal" href="#">History</a></li>