Merge pull request #24 from hi-paris/documentation_page

Add Sphinx documentation
hi-paris · Apr 9, 2024 · d0cb54f · d0cb54f
2 parents 7d42046 + 800a21f
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diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -0,0 +1,35 @@
+name: documentation
+
+on: [push, pull_request, workflow_dispatch]
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs: 
+  # This workflow contains a single job called "build"
+  build: 
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v2
+        with:
+           python-version: "3.10"
+      # Runs a single command using the runners shell
+      - name: Run a one-line script
+        run: echo Hello, world!
+
+      - name: Install dependencies
+        run: | 
+          python -m pip install --upgrade pip
+          pip install ghp-import sphinx sphinx_rtd_theme
+      - name: Build HTML
+        run: | 
+          cd docs/
+          make html
+      - name: Run ghp-import
+        run: | 
+          ghp-import -n -p -f docs/_build/html
diff --git a/.gitignore b/.gitignore
@@ -62,9 +62,6 @@ instance/
 # Scrapy stuff:
 .scrapy
 
-# Sphinx documentation
-docs/_build/
-
 # PyBuilder
 target/
 

diff --git a/README.md b/README.md
@@ -174,6 +174,14 @@ destination_directory="path/where/to/save/results"
 despeckle(image_path, destination_directory, model_name="sar2sar")
 ```
 
+## Documentation
+
+To read a clean documentation of the package, you can generate it using sphinx files in the `docs` folder
+
+1. `cd docs`
+2. `make html `
+3. open `build/index.html`
+
 ## Authors
 
 * [Emanuele Dalsasso](https://emanueledalsasso.github.io/) (Researcher at ECEO, EPFL)

diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
diff --git a/docs/_build/doctrees/modules.doctree b/docs/_build/doctrees/modules.doctree
diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo
@@ -0,0 +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: fdae4d25184fbbee4471ad780e47bfd2
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/_modules/deepdespeckling/denoiser.html b/docs/_build/html/_modules/deepdespeckling/denoiser.html
@@ -0,0 +1,188 @@
+<!DOCTYPE html>
+
+<html lang="English" data-content_root="../../">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>deepdespeckling.denoiser &#8212; deepdespeckling 0.3 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d1102ebc" />
+    <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=12dfc556" />
+    <script src="../../_static/documentation_options.js?v=cb255500"></script>
+    <script src="../../_static/doctools.js?v=888ff710"></script>
+    <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
+    <link rel="index" title="Index" href="../../genindex.html" />
+    <link rel="search" title="Search" href="../../search.html" />
+
+  <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
+
+
+
+
+
+  </head><body>
+
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+
+
+          <div class="body" role="main">
+
+  <h1>Source code for deepdespeckling.denoiser</h1><div class="highlight"><pre>
+<span></span><span class="kn">import</span> <span class="nn">logging</span>
+<span class="kn">import</span> <span class="nn">torch</span>
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
+
+
+<div class="viewcode-block" id="Denoiser">
+<a class="viewcode-back" href="../../modules.html#deepdespeckling.denoiser.Denoiser">[docs]</a>
+<span class="k">class</span> <span class="nc">Denoiser</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Class to share parameters beyond denoising functions</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">device</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_device</span><span class="p">()</span>
+
+<div class="viewcode-block" id="Denoiser.get_device">
+<a class="viewcode-back" href="../../modules.html#deepdespeckling.denoiser.Denoiser.get_device">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_device</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Get torch device to use depending on gpu&#39;s availability</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            device (str): device to be used by torch</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">if</span> <span class="n">torch</span><span class="o">.</span><span class="n">backends</span><span class="o">.</span><span class="n">mps</span><span class="o">.</span><span class="n">is_available</span><span class="p">()</span> <span class="ow">and</span> <span class="n">torch</span><span class="o">.</span><span class="n">backends</span><span class="o">.</span><span class="n">mps</span><span class="o">.</span><span class="n">is_built</span><span class="p">():</span>
+            <span class="n">device</span> <span class="o">=</span> <span class="s2">&quot;mps&quot;</span>
+        <span class="k">elif</span> <span class="n">torch</span><span class="o">.</span><span class="n">cuda</span><span class="o">.</span><span class="n">is_available</span><span class="p">():</span>
+            <span class="n">device</span> <span class="o">=</span> <span class="s2">&quot;cuda:0&quot;</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">device</span> <span class="o">=</span> <span class="s2">&quot;cpu&quot;</span>
+        <span class="n">logging</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">device</span><span class="si">}</span><span class="s2"> device is used by torch&quot;</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">device</span></div>
+
+
+<div class="viewcode-block" id="Denoiser.initialize_axis_range">
+<a class="viewcode-back" href="../../modules.html#deepdespeckling.denoiser.Denoiser.initialize_axis_range">[docs]</a>
+    <span class="k">def</span> <span class="nf">initialize_axis_range</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">image_axis_dim</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">patch_size</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">stride_size</span><span class="p">:</span> <span class="nb">int</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Initialize the convolution range for x or y axis</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            image_axis_dim (int): axis size</span>
+<span class="sd">            patch_size (int): patch size</span>
+<span class="sd">            stride_size (int): stride size</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            axis_range (list) : pixel borders of each convolution</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">if</span> <span class="n">image_axis_dim</span> <span class="o">==</span> <span class="n">patch_size</span><span class="p">:</span>
+            <span class="n">axis_range</span> <span class="o">=</span> <span class="nb">list</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="mi">0</span><span class="p">]))</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">axis_range</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span>
+                <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">image_axis_dim</span> <span class="o">-</span> <span class="n">patch_size</span><span class="p">,</span> <span class="n">stride_size</span><span class="p">))</span>
+            <span class="k">if</span> <span class="p">(</span><span class="n">axis_range</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="n">patch_size</span><span class="p">)</span> <span class="o">&lt;</span> <span class="n">image_axis_dim</span><span class="p">:</span>
+                <span class="n">axis_range</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span>
+                    <span class="nb">range</span><span class="p">(</span><span class="n">image_axis_dim</span> <span class="o">-</span> <span class="n">patch_size</span><span class="p">,</span> <span class="n">image_axis_dim</span> <span class="o">-</span> <span class="n">patch_size</span> <span class="o">+</span> <span class="mi">1</span><span class="p">))</span>
+
+        <span class="k">return</span> <span class="n">axis_range</span></div>
+
+
+<div class="viewcode-block" id="Denoiser.save_despeckled_images">
+<a class="viewcode-back" href="../../modules.html#deepdespeckling.denoiser.Denoiser.save_despeckled_images">[docs]</a>
+    <span class="k">def</span> <span class="nf">save_despeckled_images</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">raise</span> <span class="ne">NotImplementedError</span></div>
+
+
+<div class="viewcode-block" id="Denoiser.denoise_image_kernel">
+<a class="viewcode-back" href="../../modules.html#deepdespeckling.denoiser.Denoiser.denoise_image_kernel">[docs]</a>
+    <span class="k">def</span> <span class="nf">denoise_image_kernel</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">raise</span> <span class="ne">NotImplementedError</span></div>
+
+
+<div class="viewcode-block" id="Denoiser.preprocess_denoised_image">
+<a class="viewcode-back" href="../../modules.html#deepdespeckling.denoiser.Denoiser.preprocess_denoised_image">[docs]</a>
+    <span class="k">def</span> <span class="nf">preprocess_denoised_image</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">raise</span> <span class="ne">NotImplementedError</span></div>
+
+
+<div class="viewcode-block" id="Denoiser.denoise_image">
+<a class="viewcode-back" href="../../modules.html#deepdespeckling.denoiser.Denoiser.denoise_image">[docs]</a>
+    <span class="k">def</span> <span class="nf">denoise_image</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">raise</span> <span class="ne">NotImplementedError</span></div>
+
+
+<div class="viewcode-block" id="Denoiser.denoise_images">
+<a class="viewcode-back" href="../../modules.html#deepdespeckling.denoiser.Denoiser.denoise_images">[docs]</a>
+    <span class="k">def</span> <span class="nf">denoise_images</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">raise</span> <span class="ne">NotImplementedError</span></div>
+</div>
+
+</pre></div>
+
+          </div>
+
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="../../index.html">deepdespeckling</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../../modules.html">deepdespeckling</a></li>
+</ul>
+
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+  <li><a href="../../index.html">Documentation overview</a><ul>
+  <li><a href="../index.html">Module code</a><ul>
+  </ul></li>
+  </ul></li>
+</ul>
+</div>
+<div id="searchbox" style="display: none" role="search">
+  <h3 id="searchlabel">Quick search</h3>
+    <div class="searchformwrapper">
+    <form class="search" action="../../search.html" method="get">
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+      <div class="clearer"></div>
+    </div>
+    <div class="footer">
+      &#169;2024, Hadrien Mariaccia, Emanuele Delsasso.
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