Update documentation

2025-12-25 20:34:30 -08:00 · 2021-03-17 11:26:14 -04:00
parent 638a2aaf93
commit 2f2d0fe7ee
37 changed files with 1260 additions and 1382 deletions
--- a/07_plot.html
+++ b/07_plot.html
@@ -57,7 +57,7 @@
    <script async="async" src="_static/sphinx-thebe.js"></script>
    <link rel="index" title="Index" href="genindex.html" />
    <link rel="search" title="Search" href="search.html" />
-    <link rel="prev" title="Photometry" href="06_photo.html" />
+    <link rel="prev" title="6. Photometry" href="06_photo.html" />

    <meta name="viewport" content="width=device-width, initial-scale=1" />
    <meta name="docsearch:language" content="en" />
@@ -118,12 +118,12 @@
 </li>
 <li class="toctree-l1">
  <a class="reference internal" href="05_join.html">
-   Joining Tables
+   5. Joining Tables
  </a>
 </li>
 <li class="toctree-l1">
  <a class="reference internal" href="06_photo.html">
-   Photometry
+   6. Photometry
  </a>
 </li>
 <li class="toctree-l1 current active">
@@ -404,7 +404,7 @@
 <li><p>In the design of this figure, can you identify 1-2 choices the authors made that you think are effective?  Think about big-picture elements, like the number of panels and how they are arranged, as well as details like the choice of typeface.</p></li>
 <li><p>Can you identify 1-2 elements that could be improved, or that you might have done differently?</p></li>
 </ol>
-<div class="cell docutils container">
+<div class="cell tag_hide-cell docutils container">
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Solution</span>

@@ -450,7 +450,7 @@
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">os</span>
 <span class="kn">from</span> <span class="nn">wget</span> <span class="kn">import</span> <span class="n">download</span>

-<span class="n">filename</span> <span class="o">=</span> <span class="s1">&#39;gd1_merged.hdf5&#39;</span>
+<span class="n">filename</span> <span class="o">=</span> <span class="s1">&#39;gd1_data.hdf&#39;</span>
 <span class="n">path</span> <span class="o">=</span> <span class="s1">&#39;https://github.com/AllenDowney/AstronomicalData/raw/main/data/&#39;</span>

 <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
@@ -463,7 +463,7 @@
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>

-<span class="n">selected2</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_hdf</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s1">&#39;selected2&#39;</span><span class="p">)</span>
+<span class="n">winner_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_hdf</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s1">&#39;winner_df&#39;</span><span class="p">)</span>
 </pre></div>
 </div>
 </div>
@@ -491,7 +491,7 @@
 <div class="cell docutils container">
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">(</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span><span class="mf">2.5</span><span class="p">))</span>
-<span class="n">plot_second_selection</span><span class="p">(</span><span class="n">selected2</span><span class="p">)</span>
+<span class="n">plot_second_selection</span><span class="p">(</span><span class="n">winner_df</span><span class="p">)</span>
 </pre></div>
 </div>
 </div>
@@ -702,6 +702,15 @@
 </div>
 <p>You might have to install a package that contains the fonts LaTeX needs.  On some systems, the packages <code class="docutils literal notranslate"><span class="pre">texlive-latex-extra</span></code> or <code class="docutils literal notranslate"><span class="pre">cm-super</span></code> might be what you need.  <a class="reference external" href="https://stackoverflow.com/questions/11354149/python-unable-to-render-tex-in-matplotlib">See here for more help with this</a>.</p>
 <p>In case you are curious, <code class="docutils literal notranslate"><span class="pre">cm</span></code> stands for <a class="reference external" href="https://en.wikipedia.org/wiki/Computer_Modern">Computer Modern</a>, the font LaTeX uses to typeset math.</p>
+<p>Before we go on, let’s put things back where we found them.</p>
+<div class="cell docutils container">
+<div class="cell_input docutils container">
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">plt</span><span class="o">.</span><span class="n">rcParams</span><span class="p">[</span><span class="s1">&#39;text.usetex&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">False</span>
+<span class="n">plt</span><span class="o">.</span><span class="n">style</span><span class="o">.</span><span class="n">use</span><span class="p">(</span><span class="s1">&#39;default&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
 </div>
 <div class="section" id="multiple-panels">
 <h2>Multiple panels<a class="headerlink" href="#multiple-panels" title="Permalink to this headline">¶</a></h2>
@@ -720,21 +729,7 @@
 <p>To make the panel in the upper right, we have to reload <code class="docutils literal notranslate"><span class="pre">centerline_df</span></code>.</p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
-<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">os</span>
-
-<span class="n">filename</span> <span class="o">=</span> <span class="s1">&#39;gd1_dataframe.hdf5&#39;</span>
-<span class="n">path</span> <span class="o">=</span> <span class="s1">&#39;https://github.com/AllenDowney/AstronomicalData/raw/main/data/&#39;</span>
-
-<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
-    <span class="nb">print</span><span class="p">(</span><span class="n">download</span><span class="p">(</span><span class="n">path</span><span class="o">+</span><span class="n">filename</span><span class="p">))</span>
-</pre></div>
-</div>
-</div>
-</div>
-<div class="cell docutils container">
-<div class="cell_input docutils container">
-<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
-
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">filename</span> <span class="o">=</span> <span class="s1">&#39;gd1_data.hdf&#39;</span>
 <span class="n">centerline_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_hdf</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s1">&#39;centerline_df&#39;</span><span class="p">)</span>
 </pre></div>
 </div>
@@ -802,10 +797,7 @@
 <p>Here’s what the new version of the figure looks like.  We’ve changed the labels on the axes to be consistent with the paper.</p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
-<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">plt</span><span class="o">.</span><span class="n">rcParams</span><span class="p">[</span><span class="s1">&#39;text.usetex&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">False</span>
-<span class="n">plt</span><span class="o">.</span><span class="n">style</span><span class="o">.</span><span class="n">use</span><span class="p">(</span><span class="s1">&#39;default&#39;</span><span class="p">)</span>
-
-<span class="n">plot_proper_motion</span><span class="p">(</span><span class="n">centerline_df</span><span class="p">)</span>
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">plot_proper_motion</span><span class="p">(</span><span class="n">centerline_df</span><span class="p">)</span>
 </pre></div>
 </div>
 </div>
@@ -819,23 +811,7 @@
 <p>Now let’s work on the panel in the upper left. We have to reload <code class="docutils literal notranslate"><span class="pre">candidates</span></code>.</p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
-<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">os</span>
-
-<span class="n">filename</span> <span class="o">=</span> <span class="s1">&#39;gd1_candidates.hdf5&#39;</span>
-<span class="n">path</span> <span class="o">=</span> <span class="s1">&#39;https://github.com/AllenDowney/AstronomicalData/raw/main/data/&#39;</span>
-
-<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
-    <span class="nb">print</span><span class="p">(</span><span class="n">download</span><span class="p">(</span><span class="n">path</span><span class="o">+</span><span class="n">filename</span><span class="p">))</span>
-</pre></div>
-</div>
-</div>
-</div>
-<div class="cell docutils container">
-<div class="cell_input docutils container">
-<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
-
-<span class="n">filename</span> <span class="o">=</span> <span class="s1">&#39;gd1_candidates.hdf5&#39;</span>
-
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">filename</span> <span class="o">=</span> <span class="s1">&#39;gd1_data.hdf&#39;</span>
 <span class="n">candidate_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_hdf</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s1">&#39;candidate_df&#39;</span><span class="p">)</span>
 </pre></div>
 </div>
@@ -867,25 +843,13 @@
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="_images/07_plot_61_0.png" src="_images/07_plot_61_0.png" />
+<img alt="_images/07_plot_60_0.png" src="_images/07_plot_60_0.png" />
 </div>
 </div>
 </div>
 <div class="section" id="lower-right">
 <h2>Lower right<a class="headerlink" href="#lower-right" title="Permalink to this headline">¶</a></h2>
-<p>For the figure in the lower right, we need to reload the merged <code class="docutils literal notranslate"><span class="pre">DataFrame</span></code>, which contains data from Gaia and photometry data from Pan-STARRS.</p>
-<div class="cell docutils container">
-<div class="cell_input docutils container">
-<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
-
-<span class="n">filename</span> <span class="o">=</span> <span class="s1">&#39;gd1_merged.hdf5&#39;</span>
-
-<span class="n">merged</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_hdf</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s1">&#39;merged&#39;</span><span class="p">)</span>
-</pre></div>
-</div>
-</div>
-</div>
-<p>From the previous notebook, here’s the function that plots the color-magnitude diagram.</p>
+<p>For the figure in the lower right, we’ll use this function to plots the color-magnitude diagram.</p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
@@ -910,35 +874,22 @@
 </div>
 </div>
 </div>
-<p>And here’s what it looks like.</p>
+<p>Here’s what it looks like.</p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
-<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">plot_cmd</span><span class="p">(</span><span class="n">merged</span><span class="p">)</span>
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">plot_cmd</span><span class="p">(</span><span class="n">candidate_df</span><span class="p">)</span>
 </pre></div>
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="_images/07_plot_67_0.png" src="_images/07_plot_67_0.png" />
-</div>
-</div>
-<p>The following cell downloads an HDF file that contains the polygon we used to select starts in the color-magnitude diagram, if it doesn’t already exist.</p>
-<div class="cell docutils container">
-<div class="cell_input docutils container">
-<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">os</span>
-
-<span class="n">filename</span> <span class="o">=</span> <span class="s1">&#39;gd1_polygon.hdf5&#39;</span>
-<span class="n">path</span> <span class="o">=</span> <span class="s1">&#39;https://github.com/AllenDowney/AstronomicalData/raw/main/data/&#39;</span>
-
-<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
-    <span class="nb">print</span><span class="p">(</span><span class="n">download</span><span class="p">(</span><span class="n">path</span><span class="o">+</span><span class="n">filename</span><span class="p">))</span>
-</pre></div>
-</div>
+<img alt="_images/07_plot_64_0.png" src="_images/07_plot_64_0.png" />
 </div>
 </div>
 <p>And here’s how we read it back.</p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
-<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">loop_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_hdf</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s1">&#39;loop_df&#39;</span><span class="p">)</span>
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">filename</span> <span class="o">=</span> <span class="s1">&#39;gd1_data.hdf&#39;</span>
+<span class="n">loop_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_hdf</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s1">&#39;loop_df&#39;</span><span class="p">)</span>
 <span class="n">loop_df</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
 </pre></div>
 </div>
@@ -1033,10 +984,10 @@
 <span class="n">plot_proper_motion</span><span class="p">(</span><span class="n">centerline_df</span><span class="p">)</span>

 <span class="n">plt</span><span class="o">.</span><span class="n">subplot2grid</span><span class="p">(</span><span class="n">shape</span><span class="p">,</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
-<span class="n">plot_second_selection</span><span class="p">(</span><span class="n">selected2</span><span class="p">)</span>
+<span class="n">plot_second_selection</span><span class="p">(</span><span class="n">winner_df</span><span class="p">)</span>

 <span class="n">plt</span><span class="o">.</span><span class="n">subplot2grid</span><span class="p">(</span><span class="n">shape</span><span class="p">,</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span>
-<span class="n">plot_cmd</span><span class="p">(</span><span class="n">merged</span><span class="p">)</span>
+<span class="n">plot_cmd</span><span class="p">(</span><span class="n">candidate_df</span><span class="p">)</span>
 <span class="n">poly</span> <span class="o">=</span> <span class="n">Polygon</span><span class="p">(</span><span class="n">loop_df</span><span class="p">,</span> <span class="n">closed</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> 
               <span class="n">facecolor</span><span class="o">=</span><span class="s1">&#39;C1&#39;</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.4</span><span class="p">)</span>
 <span class="n">plt</span><span class="o">.</span><span class="n">gca</span><span class="p">()</span><span class="o">.</span><span class="n">add_patch</span><span class="p">(</span><span class="n">poly</span><span class="p">)</span>
@@ -1046,7 +997,7 @@
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="_images/07_plot_75_0.png" src="_images/07_plot_75_0.png" />
+<img alt="_images/07_plot_70_0.png" src="_images/07_plot_70_0.png" />
 </div>
 </div>
 <p>We use <a class="reference external" href="https://matplotlib.org/3.3.1/tutorials/intermediate/tight_layout_guide.html"><code class="docutils literal notranslate"><span class="pre">plt.tight_layout</span></code></a> at the end, which adjusts the sizes of the panels to make sure the titles and axis labels don’t overlap.</p>
@@ -1071,10 +1022,10 @@
 <span class="n">plot_proper_motion</span><span class="p">(</span><span class="n">centerline_df</span><span class="p">)</span>

 <span class="n">plt</span><span class="o">.</span><span class="n">subplot2grid</span><span class="p">(</span><span class="n">shape</span><span class="p">,</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span> <span class="n">colspan</span><span class="o">=</span><span class="mi">3</span><span class="p">)</span>
-<span class="n">plot_second_selection</span><span class="p">(</span><span class="n">selected2</span><span class="p">)</span>
+<span class="n">plot_second_selection</span><span class="p">(</span><span class="n">winner_df</span><span class="p">)</span>

 <span class="n">plt</span><span class="o">.</span><span class="n">subplot2grid</span><span class="p">(</span><span class="n">shape</span><span class="p">,</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">))</span>
-<span class="n">plot_cmd</span><span class="p">(</span><span class="n">merged</span><span class="p">)</span>
+<span class="n">plot_cmd</span><span class="p">(</span><span class="n">candidate_df</span><span class="p">)</span>
 <span class="n">poly</span> <span class="o">=</span> <span class="n">Polygon</span><span class="p">(</span><span class="n">loop_df</span><span class="p">,</span> <span class="n">closed</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> 
               <span class="n">facecolor</span><span class="o">=</span><span class="s1">&#39;C1&#39;</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.4</span><span class="p">)</span>
 <span class="n">plt</span><span class="o">.</span><span class="n">gca</span><span class="p">()</span><span class="o">.</span><span class="n">add_patch</span><span class="p">(</span><span class="n">poly</span><span class="p">)</span>
@@ -1084,14 +1035,14 @@
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="_images/07_plot_78_0.png" src="_images/07_plot_78_0.png" />
+<img alt="_images/07_plot_73_0.png" src="_images/07_plot_73_0.png" />
 </div>
 </div>
 <p>This is looking more and more like the figure in the paper.</p>
 <div class="section" id="id4">
 <h3>Exercise<a class="headerlink" href="#id4" title="Permalink to this headline">¶</a></h3>
 <p>In this example, the ratio of the widths of the panels is 3:1.  How would you adjust it if you wanted the ratio to be 3:2?</p>
-<div class="cell docutils container">
+<div class="cell tag_hide-cell docutils container">
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Solution</span>

@@ -1105,10 +1056,10 @@
 <span class="c1"># plot_proper_motion(centerline_df)</span>

 <span class="c1"># plt.subplot2grid(shape, (1, 0), colspan=3)</span>
-<span class="c1"># plot_second_selection(selected2)</span>
+<span class="c1"># plot_second_selection(winner_df)</span>

 <span class="c1"># plt.subplot2grid(shape, (1, 3), colspan=2)       # CHANGED</span>
-<span class="c1"># plot_cmd(merged)</span>
+<span class="c1"># plot_cmd(candidate_df)</span>
 <span class="c1"># poly = Polygon(coords, closed=True, </span>
 <span class="c1">#                facecolor=&#39;C1&#39;, alpha=0.4)</span>
 <span class="c1"># plt.gca().add_patch(poly)</span>
@@ -1164,7 +1115,7 @@
    
    <div class='prev-next-bottom'>
        
-    <a class='left-prev' id="prev-link" href="06_photo.html" title="previous page">Photometry</a>
+    <a class='left-prev' id="prev-link" href="06_photo.html" title="previous page">6. Photometry</a>

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