deploy: 8faa13e

Author: jeffjennings

tutorials/SpectralCubeReprojectExample.html

@@ -390,6 +390,7 @@ <h2>Step 1: Download the data<a class="headerlink" href="#step-1-download-the-da
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
 <span class="kn">from</span><span class="w"> </span><span class="nn">astropy.utils.data</span><span class="w"> </span><span class="kn">import</span> <span class="n">download_file</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">astroquery</span>
 </pre></div>
 </div>
 </div>
@@ -479,37 +480,19 @@ <h2>Step 2: Load the cubes<a class="headerlink" href="#step-2-load-the-cubes" ti
 <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WARNING: ExperimentalImplementationWarning: The line-finding routine is experimental.  Please report bugs on the Issues page: https://github.com/radio-astro-tools/spectral-cube/issues [spectral_cube.spectral_cube]
 </pre></div>
 </div>
-<div class="output traceback highlight-ipythontb notranslate"><div class="highlight"><pre><span></span><span class="gt">---------------------------------------------------------------------------</span>
-<span class="ne">ModuleNotFoundError</span><span class="g g-Whitespace">                       </span>Traceback (most recent call last)
-<span class="n">Cell</span> <span class="n">In</span><span class="p">[</span><span class="mi">7</span><span class="p">],</span> <span class="n">line</span> <span class="mi">1</span>
-<span class="ne">----&gt; </span><span class="mi">1</span> <span class="n">cube1</span><span class="o">.</span><span class="n">find_lines</span><span class="p">(</span><span class="n">chemical_name</span><span class="o">=</span><span class="s2">&quot; H2CS &quot;</span><span class="p">)</span><span class="o">.</span><span class="n">show_in_notebook</span><span class="p">()</span>
-
-<span class="nn">File /opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/spectral_cube/spectral_cube.py:2620,</span> in <span class="ni">BaseSpectralCube.find_lines</span><span class="nt">(self, velocity_offset, velocity_convention, rest_value, **kwargs)</span>
-<span class="g g-Whitespace">   </span><span class="mi">2597</span><span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
-<span class="g g-Whitespace">   </span><span class="mi">2598</span><span class="sd"> Using astroquery&#39;s splatalogue interface, search for lines within the</span>
-<span class="g g-Whitespace">   </span><span class="mi">2599</span><span class="sd"> spectral band.  See `astroquery.splatalogue.Splatalogue` for</span>
-<span class="sd">   (...)   2613     `with_spectral_unit`</span>
-<span class="g g-Whitespace">   </span><span class="mi">2614</span><span class="sd"> &quot;&quot;&quot;</span>
-<span class="g g-Whitespace">   </span><span class="mi">2615</span> <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s2">&quot;The line-finding routine is experimental.  Please &quot;</span>
-<span class="g g-Whitespace">   </span><span class="mi">2616</span>               <span class="s2">&quot;report bugs on the Issues page: &quot;</span>
-<span class="g g-Whitespace">   </span><span class="mi">2617</span>               <span class="s2">&quot;https://github.com/radio-astro-tools/spectral-cube/issues&quot;</span><span class="p">,</span>
-<span class="g g-Whitespace">   </span><span class="mi">2618</span>               <span class="n">ExperimentalImplementationWarning</span>
-<span class="g g-Whitespace">   </span><span class="mi">2619</span>              <span class="p">)</span>
-<span class="ne">-&gt; </span><span class="mi">2620</span> <span class="kn">from</span><span class="w"> </span><span class="nn">astroquery.splatalogue</span><span class="w"> </span><span class="kn">import</span> <span class="n">Splatalogue</span>
-<span class="g g-Whitespace">   </span><span class="mi">2621</span> <span class="k">if</span> <span class="n">velocity_convention</span> <span class="ow">in</span> <span class="n">DOPPLER_CONVENTIONS</span><span class="p">:</span>
-<span class="g g-Whitespace">   </span><span class="mi">2622</span>     <span class="n">velocity_convention</span> <span class="o">=</span> <span class="n">DOPPLER_CONVENTIONS</span><span class="p">[</span><span class="n">velocity_convention</span><span class="p">]</span>
-
-<span class="ne">ModuleNotFoundError</span>: No module named &#39;astroquery&#39;
-</pre></div>
-</div>
-</div>
+<script type="application/vnd.jupyter.widget-view+json">{"version_major": 2, "version_minor": 0, "model_id": "b5a507dafc8548b192d544e0dc59b9d0"}</script></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="n">cube2</span><span class="o">.</span><span class="n">find_lines</span><span class="p">(</span><span class="n">chemical_name</span><span class="o">=</span><span class="s2">&quot;SiO&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">show_in_notebook</span><span class="p">()</span>
 </pre></div>
 </div>
 </div>
+<div class="cell_output docutils container">
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WARNING: ExperimentalImplementationWarning: The line-finding routine is experimental.  Please report bugs on the Issues page: https://github.com/radio-astro-tools/spectral-cube/issues [spectral_cube.spectral_cube]
+</pre></div>
+</div>
+<script type="application/vnd.jupyter.widget-view+json">{"version_major": 2, "version_minor": 0, "model_id": "125fd5e4a9fb4683959d200b12009f91"}</script></div>
 </div>
 </section>
 <section id="step-3-convert-cubes-from-frequency-to-velocity">
@@ -531,6 +514,14 @@ <h2>Step 3: Convert cubes from frequency to velocity<a class="headerlink" href="
 </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>SpectralCube with shape=(75, 250, 250) and unit=Jy / beam:
+ n_x:    250  type_x: RA---SIN  unit_x: deg    range:   266.534072 deg:  266.554577 deg
+ n_y:    250  type_y: DEC--SIN  unit_y: deg    range:   -28.713958 deg:  -28.695975 deg
+ n_s:     75  type_s: VRAD      unit_s: km / s  range:      -43.509 km / s:     104.685 km / s
+</pre></div>
+</div>
+</div>
 </div>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
@@ -541,6 +532,14 @@ <h2>Step 3: Convert cubes from frequency to velocity<a class="headerlink" href="
 </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>SpectralCube with shape=(478, 420, 420) and unit=Jy / beam:
+ n_x:    420  type_x: RA---SIN  unit_x: deg    range:   266.537002 deg:  266.551600 deg
+ n_y:    420  type_y: DEC--SIN  unit_y: deg    range:   -28.711371 deg:  -28.698569 deg
+ n_s:    478  type_s: VRAD      unit_s: km / s  range:     -118.278 km / s:     203.359 km / s
+</pre></div>
+</div>
+</div>
 </div>
 <p>From the shape of the cube, we can see the H2CS cube is narrower in velocity, so we’ll use that as the target spectral reprojection.  However, the SiO cube is the smaller footprint on the sky.</p>
 <section id="create-spatial-maps-of-the-peak-intensity-to-quickly-explore-the-cubes">
@@ -553,6 +552,46 @@ <h3>Create spatial maps of the peak intensity to quickly explore the cubes:<a cl
 </pre></div>
 </div>
 </div>
+<div class="cell_output docutils container">
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WARNING: PossiblySlowWarning: This function (&lt;function BaseSpectralCube.max at 0x7fd9ed7b79c0&gt;) requires loading the entire cube into memory and may therefore be slow. [spectral_cube.utils]
+/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/spectral_cube/spectral_cube.py:440: RuntimeWarning: All-NaN slice encountered
+  out = function(self._get_filled_data(fill=fill,
+</pre></div>
+</div>
+<div class="output traceback highlight-ipythontb notranslate"><div class="highlight"><pre><span></span><span class="gt">---------------------------------------------------------------------------</span>
+<span class="ne">ModuleNotFoundError</span><span class="g g-Whitespace">                       </span>Traceback (most recent call last)
+<span class="nn">File /opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/spectral_cube/lower_dimensional_structures.py:430,</span> in <span class="ni">Projection.quicklook</span><span class="nt">(self, filename, use_aplpy, aplpy_kwargs)</span>
+<span class="g g-Whitespace">    </span><span class="mi">429</span> <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;FITSFigure&#39;</span><span class="p">):</span>
+<span class="ne">--&gt; </span><span class="mi">430</span>     <span class="kn">import</span><span class="w"> </span><span class="nn">aplpy</span>
+<span class="g g-Whitespace">    </span><span class="mi">431</span>     <span class="bp">self</span><span class="o">.</span><span class="n">FITSFigure</span> <span class="o">=</span> <span class="n">aplpy</span><span class="o">.</span><span class="n">FITSFigure</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">hdu</span><span class="p">,</span>
+<span class="g g-Whitespace">    </span><span class="mi">432</span>                                        <span class="o">**</span><span class="n">aplpy_kwargs</span><span class="p">)</span>
+
+<span class="ne">ModuleNotFoundError</span>: No module named &#39;aplpy&#39;
+
+<span class="n">During</span> <span class="n">handling</span> <span class="n">of</span> <span class="n">the</span> <span class="n">above</span> <span class="n">exception</span><span class="p">,</span> <span class="n">another</span> <span class="n">exception</span> <span class="n">occurred</span><span class="p">:</span>
+
+<span class="ne">ModuleNotFoundError</span><span class="g g-Whitespace">                       </span>Traceback (most recent call last)
+<span class="n">Cell</span> <span class="n">In</span><span class="p">[</span><span class="mi">12</span><span class="p">],</span> <span class="n">line</span> <span class="mi">2</span>
+<span class="g g-Whitespace">      </span><span class="mi">1</span> <span class="n">mx</span> <span class="o">=</span> <span class="n">cube1</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+<span class="ne">----&gt; </span><span class="mi">2</span> <span class="n">mx</span><span class="o">.</span><span class="n">quicklook</span><span class="p">()</span>
+
+<span class="nn">File /opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/spectral_cube/lower_dimensional_structures.py:439,</span> in <span class="ni">Projection.quicklook</span><span class="nt">(self, filename, use_aplpy, aplpy_kwargs)</span>
+<span class="g g-Whitespace">    </span><span class="mi">437</span>             <span class="bp">self</span><span class="o">.</span><span class="n">FITSFigure</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
+<span class="g g-Whitespace">    </span><span class="mi">438</span>     <span class="k">except</span> <span class="p">(</span><span class="n">wcs</span><span class="o">.</span><span class="n">InconsistentAxisTypesError</span><span class="p">,</span> <span class="ne">ImportError</span><span class="p">):</span>
+<span class="ne">--&gt; </span><span class="mi">439</span>         <span class="bp">self</span><span class="o">.</span><span class="n">_quicklook_mpl</span><span class="p">(</span><span class="n">filename</span><span class="o">=</span><span class="n">filename</span><span class="p">)</span>
+<span class="g g-Whitespace">    </span><span class="mi">440</span> <span class="k">else</span><span class="p">:</span>
+<span class="g g-Whitespace">    </span><span class="mi">441</span>     <span class="bp">self</span><span class="o">.</span><span class="n">_quicklook_mpl</span><span class="p">(</span><span class="n">filename</span><span class="o">=</span><span class="n">filename</span><span class="p">)</span>
+
+<span class="nn">File /opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/spectral_cube/lower_dimensional_structures.py:444,</span> in <span class="ni">Projection._quicklook_mpl</span><span class="nt">(self, filename)</span>
+<span class="g g-Whitespace">    </span><span class="mi">443</span> <span class="k">def</span><span class="w"> </span><span class="nf">_quicklook_mpl</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<span class="ne">--&gt; </span><span class="mi">444</span>     <span class="kn">from</span><span class="w"> </span><span class="nn">matplotlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">pyplot</span>
+<span class="g g-Whitespace">    </span><span class="mi">445</span>     <span class="bp">self</span><span class="o">.</span><span class="n">figure</span> <span class="o">=</span> <span class="n">pyplot</span><span class="o">.</span><span class="n">gcf</span><span class="p">()</span>
+<span class="g g-Whitespace">    </span><span class="mi">446</span>     <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">pyplot</span><span class="o">.</span><span class="n">imshow</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">value</span><span class="p">)</span>
+
+<span class="ne">ModuleNotFoundError</span>: No module named &#39;matplotlib&#39;
+</pre></div>
+</div>
+</div>
 </div>
 <p>We can do the same thing all on one line (for the other cube this time):</p>
 <div class="cell docutils container">

tutorials/SpectralCubeReprojectExample.ipynb

@@ -65,7 +65,8 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
-    "from astropy.utils.data import download_file"
+    "from astropy.utils.data import download_file\n",
+    "import astroquery"
    ]
   },
   {