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@mogres
mogres committed Jun 13, 2024
1 parent c303496 commit 96a4e5d
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Showing 17 changed files with 348 additions and 63 deletions.
132 changes: 89 additions & 43 deletions _modules/cellpack/autopack.html
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2 changes: 1 addition & 1 deletion _modules/cellpack/autopack/AWSHandler.html
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ <h1>Source code for cellpack.autopack.AWSHandler</h1><div class="highlight"><pre
<span class="bp">self</span><span class="p">,</span>
<span class="n">bucket_name</span><span class="p">,</span>
<span class="n">sub_folder_name</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">region_name</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">region_name</span><span class="o">=</span><span class="s2">&quot;us-west-2&quot;</span><span class="p">,</span>
<span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bucket_name</span> <span class="o">=</span> <span class="n">bucket_name</span>
<span class="bp">self</span><span class="o">.</span><span class="n">folder_name</span> <span class="o">=</span> <span class="n">sub_folder_name</span>
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8 changes: 7 additions & 1 deletion _modules/cellpack/autopack/Analysis.html
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Original file line number Diff line number Diff line change
Expand Up @@ -783,12 +783,13 @@ <h1>Source code for cellpack.autopack.Analysis</h1><div class="highlight"><pre>
<span class="bp">self</span><span class="p">,</span>
<span class="n">seed</span><span class="o">=</span><span class="mi">20</span><span class="p">,</span>
<span class="n">show_plotly_plot</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="o">**</span><span class="n">kwargs</span><span class="p">,</span>
<span class="p">):</span>
<span class="k">if</span> <span class="n">show_plotly_plot</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">plotly</span><span class="o">.</span><span class="n">update_title</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">env</span><span class="o">.</span><span class="n">place_method</span><span class="p">)</span>

<span class="n">t1</span> <span class="o">=</span> <span class="n">time</span><span class="p">()</span>
<span class="n">results</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">env</span><span class="o">.</span><span class="n">pack_grid</span><span class="p">(</span><span class="n">seedNum</span><span class="o">=</span><span class="n">seed</span><span class="p">)</span>
<span class="n">results</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">env</span><span class="o">.</span><span class="n">pack_grid</span><span class="p">(</span><span class="n">seedNum</span><span class="o">=</span><span class="n">seed</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">seed_to_results</span><span class="p">[</span><span class="n">seed</span><span class="p">]</span> <span class="o">=</span> <span class="n">results</span>
<span class="n">t2</span> <span class="o">=</span> <span class="n">time</span><span class="p">()</span>
<span class="n">run_time</span> <span class="o">=</span> <span class="n">t2</span> <span class="o">-</span> <span class="n">t1</span>
Expand Down Expand Up @@ -1137,6 +1138,7 @@ <h1>Source code for cellpack.autopack.Analysis</h1><div class="highlight"><pre>
<span class="n">show_grid</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
<span class="n">plot_figures</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
<span class="n">save_gradient_data_as_image</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
<span class="n">clean_grid_cache</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
<span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Packs one seed of a recipe and returns the recipe object</span>
Expand All @@ -1152,6 +1154,7 @@ <h1>Source code for cellpack.autopack.Analysis</h1><div class="highlight"><pre>
<span class="n">seed</span><span class="o">=</span><span class="n">seed</span><span class="p">,</span>
<span class="c1"># TODO: fix this to disable plotly if using simularium</span>
<span class="n">show_plotly_plot</span><span class="o">=</span><span class="p">(</span><span class="n">show_grid</span> <span class="ow">and</span> <span class="n">two_d</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">use_simularium</span><span class="p">,</span>
<span class="n">clean_grid_cache</span><span class="o">=</span><span class="n">clean_grid_cache</span><span class="p">,</span>
<span class="p">)</span>

<span class="bp">self</span><span class="o">.</span><span class="n">center</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">env</span><span class="o">.</span><span class="n">grid</span><span class="o">.</span><span class="n">getCenter</span><span class="p">()</span>
Expand Down Expand Up @@ -1344,6 +1347,7 @@ <h1>Source code for cellpack.autopack.Analysis</h1><div class="highlight"><pre>
<span class="n">save_gradient_data_as_image</span> <span class="o">=</span> <span class="n">packing_config_data</span><span class="o">.</span><span class="n">get</span><span class="p">(</span>
<span class="s2">&quot;save_gradient_data_as_image&quot;</span><span class="p">,</span> <span class="kc">False</span>
<span class="p">)</span>
<span class="n">clean_grid_cache</span> <span class="o">=</span> <span class="n">packing_config_data</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;clean_grid_cache&quot;</span><span class="p">,</span> <span class="kc">False</span><span class="p">)</span>

<span class="n">seed_list</span> <span class="o">=</span> <span class="n">get_seed_list</span><span class="p">(</span><span class="n">packing_config_data</span><span class="p">,</span> <span class="n">recipe_data</span><span class="p">)</span>
<span class="k">if</span> <span class="n">seed_list</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
Expand Down Expand Up @@ -1406,6 +1410,7 @@ <h1>Source code for cellpack.autopack.Analysis</h1><div class="highlight"><pre>
<span class="n">get_distance_distribution</span><span class="o">=</span><span class="n">get_distance_distribution</span><span class="p">,</span>
<span class="n">image_export_options</span><span class="o">=</span><span class="n">image_export_options</span><span class="p">,</span>
<span class="n">save_gradient_data_as_image</span><span class="o">=</span><span class="n">save_gradient_data_as_image</span><span class="p">,</span>
<span class="n">clean_grid_cache</span><span class="o">=</span><span class="n">clean_grid_cache</span><span class="p">,</span>
<span class="p">)</span>
<span class="p">)</span>
<span class="k">for</span> <span class="n">future</span> <span class="ow">in</span> <span class="n">concurrent</span><span class="o">.</span><span class="n">futures</span><span class="o">.</span><span class="n">as_completed</span><span class="p">(</span><span class="n">futures</span><span class="p">):</span>
Expand Down Expand Up @@ -1448,6 +1453,7 @@ <h1>Source code for cellpack.autopack.Analysis</h1><div class="highlight"><pre>
<span class="n">show_grid</span><span class="o">=</span><span class="n">show_grid</span><span class="p">,</span>
<span class="n">plot_figures</span><span class="o">=</span><span class="n">plot_figures</span><span class="p">,</span>
<span class="n">save_gradient_data_as_image</span><span class="o">=</span><span class="n">save_gradient_data_as_image</span><span class="p">,</span>
<span class="n">clean_grid_cache</span><span class="o">=</span><span class="n">clean_grid_cache</span><span class="p">,</span>
<span class="p">)</span>

<span class="bp">self</span><span class="o">.</span><span class="n">writeJSON</span><span class="p">(</span><span class="n">center_distance_file</span><span class="p">,</span> <span class="n">center_distance_dict</span><span class="p">)</span>
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