deploy: 6e7d464

index.html

@@ -396,6 +396,20 @@ <h2 id="usage">Usage</h2>
 3          0           0  87.333336  49.666668  80.0
 4          0           0  76.000000  82.000000  80.0
 </code></pre></div>
+<p>Annotations made in the <a href="https://bio3d.colorado.edu/imod/doc/3dmodHelp/slicer.html">slicer window</a> are stored in the IMOD binary file with both centerpoints and angles.</p>
+<p>These annotations can be read in by setting <code>annotation='slan'</code> when calling <code>imodmodel.read()</code></p>
+<div class="highlight"><pre><span></span><code><span class="kn">import</span> <span class="nn">imodmodel</span>
+
+<span class="n">df</span> <span class="o">=</span> <span class="n">imodmodel</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="s1">&#39;file_with_slicer_angles.mod&#39;</span><span class="p">,</span> <span class="n">annotation</span><span class="o">=</span><span class="s1">&#39;slan&#39;</span><span class="p">)</span>
+</code></pre></div>
+<div class="highlight"><pre><span></span><code>In [3]: df.head()
+Out[3]:
+   object_id  slan_id  time      x_rot  y_rot      z_rot    center_x    center_y  center_z label
+0          0        0     1  13.100000    0.0 -30.200001  235.519577  682.744141     302.0
+0          0        1     1 -41.400002    0.0 -47.700001  221.942444  661.193237     327.0
+0          0        2     1 -41.400002    0.0 -41.799999  232.790726  671.332031     327.0
+0          0        3     1 -35.500000    0.0 -36.000000  240.129181  679.927795     324.0
+</code></pre></div>
 <p>That's it!</p>
 <h2 id="installation">Installation</h2>
 <p><code>imodmodel</code> can be installed from the <a href="https://pypi.org/">Python Package Index</a> (PyPI)</p>

search/search_index.json

@@ -1 +1 @@
-{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"Overview","text":"<p>Read IMOD model files  as pandas dataframes  in Python.</p>"},{"location":"#usage","title":"Usage","text":"<pre><code>import imodmodel\n\ndf = imodmodel.read('my_model_file.mod')\n</code></pre> <pre><code>In [3]: df.head()\nOut[3]: \n   object_id  contour_id          x          y     z\n0          0           0  64.333336  64.666664  80.0\n1          0           0  47.000000  77.333336  80.0\n2          0           0  51.333332  45.666668  80.0\n3          0           0  87.333336  49.666668  80.0\n4          0           0  76.000000  82.000000  80.0\n</code></pre> <p>That's it!</p>"},{"location":"#installation","title":"Installation","text":"<p><code>imodmodel</code> can be installed from the Python Package Index (PyPI)</p> <pre><code>pip install imodmodel\n</code></pre> <p>We recommend installing into a clean virtual environment.</p>"}]}
+{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"Overview","text":"<p>Read IMOD model files  as pandas dataframes  in Python.</p>"},{"location":"#usage","title":"Usage","text":"<pre><code>import imodmodel\n\ndf = imodmodel.read('my_model_file.mod')\n</code></pre> <pre><code>In [3]: df.head()\nOut[3]: \n   object_id  contour_id          x          y     z\n0          0           0  64.333336  64.666664  80.0\n1          0           0  47.000000  77.333336  80.0\n2          0           0  51.333332  45.666668  80.0\n3          0           0  87.333336  49.666668  80.0\n4          0           0  76.000000  82.000000  80.0\n</code></pre> <p>Annotations made in the slicer window are stored in the IMOD binary file with both centerpoints and angles.</p> <p>These annotations can be read in by setting <code>annotation='slan'</code> when calling <code>imodmodel.read()</code></p> <pre><code>import imodmodel\n\ndf = imodmodel.read('file_with_slicer_angles.mod', annotation='slan')\n</code></pre> <pre><code>In [3]: df.head()\nOut[3]:\n   object_id  slan_id  time      x_rot  y_rot      z_rot    center_x    center_y  center_z label\n0          0        0     1  13.100000    0.0 -30.200001  235.519577  682.744141     302.0\n0          0        1     1 -41.400002    0.0 -47.700001  221.942444  661.193237     327.0\n0          0        2     1 -41.400002    0.0 -41.799999  232.790726  671.332031     327.0\n0          0        3     1 -35.500000    0.0 -36.000000  240.129181  679.927795     324.0\n</code></pre> <p>That's it!</p>"},{"location":"#installation","title":"Installation","text":"<p><code>imodmodel</code> can be installed from the Python Package Index (PyPI)</p> <pre><code>pip install imodmodel\n</code></pre> <p>We recommend installing into a clean virtual environment.</p>"}]}

sitemap.xml

@@ -2,7 +2,7 @@
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
     <url>
          <loc>https://teamtomo.org/imodmodel/</loc>
-         <lastmod>2024-06-07</lastmod>
+         <lastmod>2024-06-08</lastmod>
          <changefreq>daily</changefreq>
     </url>
 </urlset>