Update documentation

2025-12-25 20:34:30 -08:00 · 2021-03-18 08:34:28 -04:00
parent 2f2d0fe7ee
commit 1683afba03
19 changed files with 421 additions and 9505 deletions
--- a/07_plot.html
+++ b/07_plot.html
@@ -5,7 +5,7 @@
  <head>
    <meta charset="utf-8" />
    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Visualization &#8212; Astronomical Data in Python</title>
+    <title>7. Visualization &#8212; Astronomical Data in Python</title>
    
  <link rel="stylesheet" href="_static/css/index.d431a4ee1c1efae0e38bdfebc22debff.css">

@@ -128,7 +128,7 @@
 </li>
 <li class="toctree-l1 current active">
  <a class="current reference internal" href="#">
-   Visualization
+   7. Visualization
  </a>
 </li>
 </ul>
@@ -242,6 +242,11 @@
   Outline
  </a>
 </li>
+ <li class="toc-h2 nav-item toc-entry">
+  <a class="reference internal nav-link" href="#installing-libraries">
+   Installing libraries
+  </a>
+ </li>
 <li class="toc-h2 nav-item toc-entry">
  <a class="reference internal nav-link" href="#making-figures-that-tell-a-story">
   Making Figures That Tell a Story
@@ -364,7 +369,7 @@
              <div>
                
  <div class="section" id="visualization">
-<h1>Visualization<a class="headerlink" href="#visualization" title="Permalink to this headline">¶</a></h1>
+<h1>7. Visualization<a class="headerlink" href="#visualization" title="Permalink to this headline">¶</a></h1>
 <p>This is the seventh in a series of notebooks related to astronomy data.</p>
 <p>As a continuing example, we will replicate part of the analysis in a recent paper, “<a class="reference external" href="https://arxiv.org/abs/1805.00425">Off the beaten path: Gaia reveals GD-1 stars outside of the main stream</a>” by Adrian M. Price-Whelan and Ana Bonaca.</p>
 <p>In the previous notebook we selected photometry data from Pan-STARRS and used it to identify stars we think are likely to be in GD-1</p>
@@ -384,6 +389,24 @@
 <li><p>Generate a figure with multiple subplots.</p></li>
 </ul>
 </div>
+<div class="section" id="installing-libraries">
+<h2>Installing libraries<a class="headerlink" href="#installing-libraries" title="Permalink to this headline">¶</a></h2>
+<p>If you are running this notebook on Colab, you can run the following cell to install the libraries we’ll use.</p>
+<p>If you are running this notebook on your own computer, you might have to install these libraries yourself.  See the instructions in the preface.</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="c1"># If we&#39;re running on Colab, install libraries</span>
+
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="n">IN_COLAB</span> <span class="o">=</span> <span class="s1">&#39;google.colab&#39;</span> <span class="ow">in</span> <span class="n">sys</span><span class="o">.</span><span class="n">modules</span>
+
+<span class="k">if</span> <span class="n">IN_COLAB</span><span class="p">:</span>
+    <span class="o">!</span>pip install wget
+</pre></div>
+</div>
+</div>
+</div>
+</div>
 <div class="section" id="making-figures-that-tell-a-story">
 <h2>Making Figures That Tell a Story<a class="headerlink" href="#making-figures-that-tell-a-story" title="Permalink to this headline">¶</a></h2>
 <p>So far the figure we’ve made have been “quick and dirty”.  Mostly we have used Matplotlib’s default style, although we have adjusted a few parameters, like <code class="docutils literal notranslate"><span class="pre">markersize</span></code> and <code class="docutils literal notranslate"><span class="pre">alpha</span></code>, to improve legibility.</p>
@@ -406,36 +429,7 @@
 </ol>
 <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>
-
-<span class="c1"># Some topics that might come up in this discussion:</span>
-
-<span class="c1"># 1. The primary result is that the multiple stages of selection </span>
-<span class="c1"># make it possible to separate likely candidates from the </span>
-<span class="c1"># background more effectively than in previous work, which makes </span>
-<span class="c1"># it possible to see the structure of GD-1 in &quot;unprecedented detail&quot;.</span>
-
-<span class="c1"># 2. The figure documents the selection process as a sequence of </span>
-<span class="c1"># steps.  Reading right-to-left, top-to-bottom, we see selection </span>
-<span class="c1"># based on proper motion, the results of the first selection, </span>
-<span class="c1"># selection based on color and magnitude, and the results of the </span>
-<span class="c1"># second selection.  So this figure documents the methodology and </span>
-<span class="c1"># presents the primary result.</span>
-
-<span class="c1"># 3. It&#39;s mostly black and white, with minimal use of color, so </span>
-<span class="c1"># it will work well in print.  The annotations in the bottom </span>
-<span class="c1"># left panel guide the reader to the most important results.  </span>
-<span class="c1"># It contains enough technical detail for a professional audience, </span>
-<span class="c1"># but most of it is also comprehensible to a more general audience.  </span>
-<span class="c1"># The two left panels have the same dimensions and their axes are </span>
-<span class="c1"># aligned.</span>
-
-<span class="c1"># 4. Since the panels represent a sequence, it might be better to </span>
-<span class="c1"># arrange them left-to-right.  The placement and size of the axis </span>
-<span class="c1"># labels could be tweaked.  The entire figure could be a little </span>
-<span class="c1"># bigger to match the width and proportion of the caption.  </span>
-<span class="c1"># The top left panel has unnused white space (but that leaves </span>
-<span class="c1"># space for the annotations in the bottom left).</span>
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Solution goes here</span>
 </pre></div>
 </div>
 </div>
@@ -495,9 +489,6 @@
 </pre></div>
 </div>
 </div>
-<div class="cell_output docutils container">
-<img alt="_images/07_plot_14_0.png" src="_images/07_plot_14_0.png" />
-</div>
 </div>
 </div>
 <div class="section" id="annotations">
@@ -519,23 +510,7 @@
 <p>And here is some <a class="reference external" href="https://matplotlib.org/3.3.1/tutorials/text/annotations.html#plotting-guide-annotation">additional information about text and arrows</a>.</p>
 <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>
-
-<span class="c1"># plt.axvline(-55, ls=&#39;--&#39;, color=&#39;gray&#39;, </span>
-<span class="c1">#             alpha=0.4, dashes=(6,4), lw=2)</span>
-<span class="c1"># plt.text(-60, 5.5, &#39;Previously\nundetected&#39;, </span>
-<span class="c1">#          fontsize=&#39;small&#39;, ha=&#39;right&#39;, va=&#39;top&#39;);</span>
-
-<span class="c1"># arrowprops=dict(color=&#39;gray&#39;, shrink=0.05, width=1.5, </span>
-<span class="c1">#                 headwidth=6, headlength=8, alpha=0.4)</span>
-
-<span class="c1"># plt.annotate(&#39;Spur&#39;, xy=(-33, 2), xytext=(-35, 5.5),</span>
-<span class="c1">#              arrowprops=arrowprops,</span>
-<span class="c1">#              fontsize=&#39;small&#39;)</span>
-
-<span class="c1"># plt.annotate(&#39;Gap&#39;, xy=(-22, -1), xytext=(-25, -5.5),</span>
-<span class="c1">#              arrowprops=arrowprops,</span>
-<span class="c1">#              fontsize=&#39;small&#39;)</span>
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Solution goes here</span>
 </pre></div>
 </div>
 </div>
@@ -562,9 +537,7 @@
 <p>Read the documentation of <a class="reference external" href="https://matplotlib.org/3.1.1/api/_as_gen/matplotlib.axes.Axes.tick_params.html"><code class="docutils literal notranslate"><span class="pre">tick_params</span></code></a> and use it to put ticks on the top and right sides of the axes.</p>
 <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>
-
-<span class="c1"># plt.gca().tick_params(top=True, right=True)</span>
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Solution goes here</span>
 </pre></div>
 </div>
 </div>
@@ -581,11 +554,6 @@
 </pre></div>
 </div>
 </div>
-<div class="cell_output docutils container">
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>10.0
-</pre></div>
-</div>
-</div>
 </div>
 <p>And sets it to a new value:</p>
 <div class="cell docutils container">
@@ -610,36 +578,6 @@
 </pre></div>
 </div>
 </div>
-<div class="cell_output docutils container">
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&#39;Solarize_Light2&#39;,
- &#39;_classic_test_patch&#39;,
- &#39;bmh&#39;,
- &#39;classic&#39;,
- &#39;dark_background&#39;,
- &#39;fast&#39;,
- &#39;fivethirtyeight&#39;,
- &#39;ggplot&#39;,
- &#39;grayscale&#39;,
- &#39;seaborn&#39;,
- &#39;seaborn-bright&#39;,
- &#39;seaborn-colorblind&#39;,
- &#39;seaborn-dark&#39;,
- &#39;seaborn-dark-palette&#39;,
- &#39;seaborn-darkgrid&#39;,
- &#39;seaborn-deep&#39;,
- &#39;seaborn-muted&#39;,
- &#39;seaborn-notebook&#39;,
- &#39;seaborn-paper&#39;,
- &#39;seaborn-pastel&#39;,
- &#39;seaborn-poster&#39;,
- &#39;seaborn-talk&#39;,
- &#39;seaborn-ticks&#39;,
- &#39;seaborn-white&#39;,
- &#39;seaborn-whitegrid&#39;,
- &#39;tableau-colorblind10&#39;]
-</pre></div>
-</div>
-</div>
 </div>
 <p>Note that <code class="docutils literal notranslate"><span class="pre">seaborn-paper</span></code>, <code class="docutils literal notranslate"><span class="pre">seaborn-talk</span></code> and <code class="docutils literal notranslate"><span class="pre">seaborn-poster</span></code> are particularly intended to prepare versions of a figure with text sizes and other features that work well in papers, talks, and posters.</p>
 <p>To use any of these style sheets, run <code class="docutils literal notranslate"><span class="pre">plt.style.use</span></code> like this:</p>
@@ -760,14 +698,6 @@
 </pre></div>
 </div>
 </div>
-<div class="cell_output docutils container">
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>array([[-8.9, -2.2],
-       [-8.9,  1. ],
-       [-6.9,  1. ],
-       [-6.9, -2.2]])
-</pre></div>
-</div>
-</div>
 </div>
 <p>The following function takes a <code class="docutils literal notranslate"><span class="pre">DataFrame</span></code> as a parameter, plots the proper motion for each star, and adds a shaded <code class="docutils literal notranslate"><span class="pre">Polygon</span></code> to show the region we selected.</p>
 <div class="cell docutils container">
@@ -801,9 +731,6 @@
 </pre></div>
 </div>
 </div>
-<div class="cell_output docutils container">
-<img alt="_images/07_plot_54_0.png" src="_images/07_plot_54_0.png" />
-</div>
 </div>
 </div>
 <div class="section" id="upper-left">
@@ -842,9 +769,6 @@
 </pre></div>
 </div>
 </div>
-<div class="cell_output docutils container">
-<img alt="_images/07_plot_60_0.png" src="_images/07_plot_60_0.png" />
-</div>
 </div>
 </div>
 <div class="section" id="lower-right">
@@ -881,9 +805,6 @@
 </pre></div>
 </div>
 </div>
-<div class="cell_output docutils container">
-<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">
@@ -894,58 +815,6 @@
 </pre></div>
 </div>
 </div>
-<div class="cell_output docutils container">
-<div class="output text_html"><div>
-<style scoped>
-    .dataframe tbody tr th:only-of-type {
-        vertical-align: middle;
-    }
-
-    .dataframe tbody tr th {
-        vertical-align: top;
-    }
-
-    .dataframe thead th {
-        text-align: right;
-    }
-</style>
-<table border="1" class="dataframe">
-  <thead>
-    <tr style="text-align: right;">
-      <th></th>
-      <th>color_loop</th>
-      <th>mag_loop</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-      <th>0</th>
-      <td>0.632171</td>
-      <td>21.411746</td>
-    </tr>
-    <tr>
-      <th>1</th>
-      <td>0.610238</td>
-      <td>21.322466</td>
-    </tr>
-    <tr>
-      <th>2</th>
-      <td>0.588449</td>
-      <td>21.233380</td>
-    </tr>
-    <tr>
-      <th>3</th>
-      <td>0.566924</td>
-      <td>21.144427</td>
-    </tr>
-    <tr>
-      <th>4</th>
-      <td>0.545461</td>
-      <td>21.054549</td>
-    </tr>
-  </tbody>
-</table>
-</div></div></div>
 </div>
 <div class="section" id="id3">
 <h3>Exercise<a class="headerlink" href="#id3" title="Permalink to this headline">¶</a></h3>
@@ -953,11 +822,7 @@
 <p>Hint: pass <code class="docutils literal notranslate"><span class="pre">coords</span></code> as an argument to <code class="docutils literal notranslate"><span class="pre">Polygon</span></code> and plot it using <code class="docutils literal notranslate"><span class="pre">add_patch</span></code>.</p>
 <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>
-
-<span class="c1"># poly = Polygon(loop_df, closed=True, </span>
-<span class="c1">#                facecolor=&#39;C1&#39;, alpha=0.4)</span>
-<span class="c1"># plt.gca().add_patch(poly)</span>
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Solution goes here</span>
 </pre></div>
 </div>
 </div>
@@ -996,9 +861,6 @@
 </pre></div>
 </div>
 </div>
-<div class="cell_output docutils container">
-<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>
 <p>As an exercise, see what happens if you leave out <code class="docutils literal notranslate"><span class="pre">tight_layout</span></code>.</p>
@@ -1034,9 +896,6 @@
 </pre></div>
 </div>
 </div>
-<div class="cell_output docutils container">
-<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">
@@ -1044,27 +903,7 @@
 <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 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>
-
-<span class="c1"># plt.figure(figsize=(9, 4.5))</span>
-
-<span class="c1"># shape = (2, 5)                                   # CHANGED</span>
-<span class="c1"># plt.subplot2grid(shape, (0, 0), colspan=3)</span>
-<span class="c1"># plot_first_selection(candidate_df)</span>
-
-<span class="c1"># plt.subplot2grid(shape, (0, 3), colspan=2)       # CHANGED</span>
-<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(winner_df)</span>
-
-<span class="c1"># plt.subplot2grid(shape, (1, 3), colspan=2)       # CHANGED</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>
-
-<span class="c1"># plt.tight_layout()</span>
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Solution goes here</span>
 </pre></div>
 </div>
 </div>