Adding 'All steps' tutorial

ghislainv · Jun 20, 2022 · 1be9583 · 1be9583
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diff --git a/.gitignore b/.gitignore
@@ -5,6 +5,7 @@ notes.org
 docsrc/notebooks/data
 docsrc/notebooks/outputs_makemap
 docsrc/notebooks/outputs_MDG
+docsrc/notebooks/outputs_steps
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

diff --git a/docs/_images/fcc123.png b/docs/_images/fcc123.png
diff --git a/docs/_images/fcc1231.png b/docs/_images/fcc1231.png
diff --git a/docs/_images/perc_dist1.png b/docs/_images/perc_dist1.png
diff --git a/docs/_images/plot_dist.png b/docs/_images/plot_dist.png
diff --git a/docs/_images/pred_obs.png b/docs/_images/pred_obs.png
diff --git a/docs/_images/riskmap.png b/docs/_images/riskmap.png
diff --git a/docs/_images/riskmap_ws5_ei.png b/docs/_images/riskmap_ws5_ei.png
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
@@ -57,6 +57,7 @@ <h3>Navigation</h3>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../index.html">Home</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../notebooks/get_started.html">Get Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../articles.html">Articles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../reference.html">Python API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../indices.html">Indices and tables</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>

diff --git a/docs/_sources/articles.rst.txt b/docs/_sources/articles.rst.txt
@@ -0,0 +1,10 @@
+Articles
+========
+
+.. toctree::
+   :maxdepth: 1
+
+   notebooks/get_started
+   notebooks/steps
+
+
diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt
@@ -8,6 +8,7 @@ Table of contents
 
    Home <self>
    notebooks/get_started
+   articles
    reference
    indices
    changelog

diff --git a/docs/_sources/notebooks/get_started.rst.txt b/docs/_sources/notebooks/get_started.rst.txt
@@ -95,7 +95,7 @@ We derive the deforestation risk map using the ``makemap()`` function. This func
     results_makemap = rmj.makemap(
         fcc_file=fcc_file,
         time_interval=[10, 10],
-        output_dir="outputs_makemap",
+        output_dir=out_dir,
         clean=False,
         dist_bins=np.arange(0, 1080, step=30),
         win_sizes=np.arange(5, 48, 16),
@@ -157,7 +157,7 @@ We also have access to a plot showing how the cumulative percentage of deforesta
 
 .. code:: python
 
-    ofile = "outputs_makemap/perc_dist.png"
+    ofile = os.path.join(out_dir, "perc_dist.png")
     ofile
 
 .. _fig:perc_dist:
@@ -190,7 +190,7 @@ We identify the moving window size and the slicing algorithm of the best model.
 
 .. code:: python
 
-    ofile = "outputs_makemap/pred_obs_ws5_ei.png"
+    ofile = os.path.join(out_dir, "pred_obs_ws5_ei.png")
     ofile
 
 .. _fig:pred_obs:
@@ -208,7 +208,7 @@ We plot the risk map using the ``plot.riskmap()`` function.
 
 .. code:: python
 
-    ofile = os.path.join("outputs_makemap", "riskmap_ws5_ei.png")
+    ofile = os.path.join(out_dir, "riskmap_ws5_ei.png")
     riskmap_fig = rmj.plot.riskmap(
         input_risk_map="outputs_makemap/riskmap_ws5_ei.tif",
         maxpixels=1e8,

diff --git a/docs/_sources/notebooks/steps.rst.txt b/docs/_sources/notebooks/steps.rst.txt
diff --git a/docs/_static/riskmapjnr-example.png b/docs/_static/riskmapjnr-example.png
diff --git a/docs/articles.html b/docs/articles.html
@@ -0,0 +1,142 @@
+
+<!DOCTYPE html>
+
+<html lang="en">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+
+    <title>Articles &#8212; riskmapjnr — Map of deforestation risk following JNR methodology</title>
+    <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
+    <link rel="stylesheet" type="text/css" href="_static/alabaster.css" />
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+    <link rel="shortcut icon" href="_static/favicon.ico"/>
+    <link rel="index" title="Index" href="genindex.html" />
+    <link rel="search" title="Search" href="search.html" />
+    <link rel="next" title="All steps" href="notebooks/steps.html" />
+    <link rel="prev" title="Get Started" href="notebooks/get_started.html" />
+
+  <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+
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+  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
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+    <img class="logo" src="_static/logo-riskmapjnr.svg" alt="Logo"/>
+
+    <h1 class="logo logo-name">riskmapjnr</h1>
+
+  </a>
+</p>
+
+
+
+<p class="blurb">Map of deforestation risk following JNR methodology</p>
+
+
+
+
+<p>
+<iframe src="https://ghbtns.com/github-btn.html?user=ghislainv&repo=riskmapjnr&type=star&count=true&size=large&v=2"
+  allowtransparency="true" frameborder="0" scrolling="0" width="200px" height="35px"></iframe>
+</p>
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="index.html">Home</a></li>
+<li class="toctree-l1"><a class="reference internal" href="notebooks/get_started.html">Get Started</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Articles</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/get_started.html">Get Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/steps.html">All steps</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="reference.html">Python API</a></li>
+<li class="toctree-l1"><a class="reference internal" href="indices.html">Indices and tables</a></li>
+<li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
+<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
+</ul>
+
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+  <li><a href="index.html">Documentation overview</a><ul>
+      <li>Previous: <a href="notebooks/get_started.html" title="previous chapter">Get Started</a></li>
+      <li>Next: <a href="notebooks/steps.html" title="next chapter">All steps</a></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">
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
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+    </form>
+    </div>
+</div>
+<script>document.getElementById('searchbox').style.display = "block"</script>
+
+
+
+
+
+
+
+
+        </div>
+      </div>
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+
+
+          <div class="body" role="main">
+
+  <section id="articles">
+<h1>Articles<a class="headerlink" href="#articles" title="Permalink to this heading">¶</a></h1>
+<div class="toctree-wrapper compound">
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="notebooks/get_started.html">Get Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="notebooks/steps.html">All steps</a></li>
+</ul>
+</div>
+</section>
+
+
+          </div>
+
+        </div>
+      </div>
+    <div class="clearer"></div>
+  </div>
+    <div class="footer">
+      &copy;2022, Ghislain Vieilledent.
+
+      |
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 5.0.1</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+
+      |
+      <a href="_sources/articles.rst.txt"
+          rel="nofollow">Page source</a>
+    </div>
+
+
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+
+  </body>
+</html>
diff --git a/docs/changelog.html b/docs/changelog.html
@@ -60,6 +60,7 @@ <h3>Navigation</h3>
 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="index.html">Home</a></li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks/get_started.html">Get Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="articles.html">Articles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="reference.html">Python API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="indices.html">Indices and tables</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Changelog</a><ul>

diff --git a/docs/code_of_conduct.html b/docs/code_of_conduct.html
@@ -58,6 +58,7 @@ <h3>Navigation</h3>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="index.html">Home</a></li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks/get_started.html">Get Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="articles.html">Articles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="reference.html">Python API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="indices.html">Indices and tables</a></li>
 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>

diff --git a/docs/contributing.html b/docs/contributing.html
@@ -58,6 +58,7 @@ <h3>Navigation</h3>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="index.html">Home</a></li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks/get_started.html">Get Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="articles.html">Articles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="reference.html">Python API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="indices.html">Indices and tables</a></li>
 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>

diff --git a/docs/genindex.html b/docs/genindex.html
@@ -57,6 +57,7 @@ <h3>Navigation</h3>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="index.html">Home</a></li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks/get_started.html">Get Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="articles.html">Articles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="reference.html">Python API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="indices.html">Indices and tables</a></li>
 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>

diff --git a/docs/index.html b/docs/index.html
@@ -59,6 +59,7 @@ <h3>Navigation</h3>
 <ul class="current">
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Home</a></li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks/get_started.html">Get Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="articles.html">Articles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="reference.html">Python API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="indices.html">Indices and tables</a></li>
 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
@@ -265,6 +266,11 @@ <h2>Table of contents<a class="headerlink" href="#table-of-contents" title="Perm
 <li class="toctree-l2"><a class="reference internal" href="notebooks/get_started.html#results">3 Results</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="articles.html">Articles</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/get_started.html">Get Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/steps.html">All steps</a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="reference.html">Python API</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="reference.html#module-riskmapjnr">Main functions</a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference.html#module-riskmapjnr.plot">Plot functions</a></li>

diff --git a/docs/indices.html b/docs/indices.html
@@ -60,6 +60,7 @@ <h3>Navigation</h3>
 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="index.html">Home</a></li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks/get_started.html">Get Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="articles.html">Articles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="reference.html">Python API</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Indices and tables</a></li>
 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>

diff --git a/docs/license.html b/docs/license.html
@@ -59,6 +59,7 @@ <h3>Navigation</h3>
 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="index.html">Home</a></li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks/get_started.html">Get Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="articles.html">Articles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="reference.html">Python API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="indices.html">Indices and tables</a></li>
 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>

diff --git a/docs/notebooks/get_started.html b/docs/notebooks/get_started.html
@@ -20,7 +20,7 @@
     <link rel="shortcut icon" href="../_static/favicon.ico"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="Python API" href="../reference.html" />
+    <link rel="next" title="Articles" href="../articles.html" />
     <link rel="prev" title="riskmapjnr Python package" href="../index.html" />
 
   <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -67,6 +67,7 @@ <h3>Navigation</h3>
 <li class="toctree-l2"><a class="reference internal" href="#results">3 Results</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="../articles.html">Articles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../reference.html">Python API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../indices.html">Indices and tables</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
@@ -78,7 +79,7 @@ <h3>Related Topics</h3>
 <ul>
   <li><a href="../index.html">Documentation overview</a><ul>
       <li>Previous: <a href="../index.html" title="previous chapter"><code class="docutils literal notranslate"><span class="pre">riskmapjnr</span></code> Python package</a></li>
-      <li>Next: <a href="../reference.html" title="next chapter">Python API</a></li>
+      <li>Next: <a href="../articles.html" title="next chapter">Articles</a></li>
   </ul></li>
 </ul>
 </div>
@@ -180,7 +181,7 @@ <h2>2 Derive the deforestation risk map<a class="headerlink" href="#derive-the-d
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">results_makemap</span> <span class="o">=</span> <span class="n">rmj</span><span class="o">.</span><span class="n">makemap</span><span class="p">(</span>
     <span class="n">fcc_file</span><span class="o">=</span><span class="n">fcc_file</span><span class="p">,</span>
     <span class="n">time_interval</span><span class="o">=</span><span class="p">[</span><span class="mi">10</span><span class="p">,</span> <span class="mi">10</span><span class="p">],</span>
-    <span class="n">output_dir</span><span class="o">=</span><span class="s2">&quot;outputs_makemap&quot;</span><span class="p">,</span>
+    <span class="n">output_dir</span><span class="o">=</span><span class="n">out_dir</span><span class="p">,</span>
     <span class="n">clean</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
     <span class="n">dist_bins</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1080</span><span class="p">,</span> <span class="n">step</span><span class="o">=</span><span class="mi">30</span><span class="p">),</span>
     <span class="n">win_sizes</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">5</span><span class="p">,</span> <span class="mi">48</span><span class="p">,</span> <span class="mi">16</span><span class="p">),</span>
@@ -280,7 +281,7 @@ <h3>3.1 Deforestation risk and distance to forest edge<a class="headerlink" href
 </tbody>
 </table>
 <p>We also have access to a plot showing how the cumulative percentage of deforestation increases with the distance to forest edge.</p>
-<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">ofile</span> <span class="o">=</span> <span class="s2">&quot;outputs_makemap/perc_dist.png&quot;</span>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">ofile</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">out_dir</span><span class="p">,</span> <span class="s2">&quot;perc_dist.png&quot;</span><span class="p">)</span>
 <span class="n">ofile</span>
 </pre></div>
 </div>
@@ -307,7 +308,7 @@ <h3>3.2 Best model<a class="headerlink" href="#best-model" title="Permalink to t
 </section>
 <section id="validation">
 <h3>3.3 Validation<a class="headerlink" href="#validation" title="Permalink to this heading">¶</a></h3>
-<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">ofile</span> <span class="o">=</span> <span class="s2">&quot;outputs_makemap/pred_obs_ws5_ei.png&quot;</span>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">ofile</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">out_dir</span><span class="p">,</span> <span class="s2">&quot;pred_obs_ws5_ei.png&quot;</span><span class="p">)</span>
 <span class="n">ofile</span>
 </pre></div>
 </div>
@@ -321,7 +322,7 @@ <h3>3.3 Validation<a class="headerlink" href="#validation" title="Permalink to t
 <section id="risk-map-of-deforestation">
 <h3>3.4 Risk map of deforestation<a class="headerlink" href="#risk-map-of-deforestation" title="Permalink to this heading">¶</a></h3>
 <p>We plot the risk map using the <code class="docutils literal notranslate"><span class="pre">plot.riskmap()</span></code> function.</p>
-<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">ofile</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="s2">&quot;outputs_makemap&quot;</span><span class="p">,</span> <span class="s2">&quot;riskmap_ws5_ei.png&quot;</span><span class="p">)</span>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">ofile</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">out_dir</span><span class="p">,</span> <span class="s2">&quot;riskmap_ws5_ei.png&quot;</span><span class="p">)</span>
 <span class="n">riskmap_fig</span> <span class="o">=</span> <span class="n">rmj</span><span class="o">.</span><span class="n">plot</span><span class="o">.</span><span class="n">riskmap</span><span class="p">(</span>
     <span class="n">input_risk_map</span><span class="o">=</span><span class="s2">&quot;outputs_makemap/riskmap_ws5_ei.tif&quot;</span><span class="p">,</span>
     <span class="n">maxpixels</span><span class="o">=</span><span class="mf">1e8</span><span class="p">,</span>