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rugeli committed Jun 11, 2024
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87 changes: 54 additions & 33 deletions _modules/cellpack/autopack/Analysis.html

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7 changes: 5 additions & 2 deletions _modules/cellpack/autopack/Environment.html
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Expand Up @@ -185,7 +185,11 @@ <h1>Source code for cellpack.autopack.Environment</h1><div class="highlight"><pr
<span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>
<span class="bp">self</span><span class="o">.</span><span class="n">version</span> <span class="o">=</span> <span class="n">recipe</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;version&quot;</span><span class="p">,</span> <span class="s2">&quot;default&quot;</span><span class="p">)</span>
<span class="c1"># saving/pickle option</span>
<span class="bp">self</span><span class="o">.</span><span class="n">saveResult</span> <span class="o">=</span> <span class="s2">&quot;out&quot;</span> <span class="ow">in</span> <span class="n">config</span>
<span class="bp">self</span><span class="o">.</span><span class="n">saveResult</span> <span class="o">=</span> <span class="p">(</span>
<span class="s2">&quot;out&quot;</span> <span class="ow">in</span> <span class="n">config</span>
<span class="ow">and</span> <span class="ow">not</span> <span class="n">config</span><span class="p">[</span><span class="s2">&quot;save_analyze_result&quot;</span><span class="p">]</span>
<span class="ow">and</span> <span class="ow">not</span> <span class="n">config</span><span class="p">[</span><span class="s2">&quot;number_of_packings&quot;</span><span class="p">]</span> <span class="o">&gt;</span> <span class="mi">1</span>
<span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">out_folder</span> <span class="o">=</span> <span class="n">create_output_dir</span><span class="p">(</span><span class="n">config</span><span class="p">[</span><span class="s2">&quot;out&quot;</span><span class="p">],</span> <span class="n">name</span><span class="p">,</span> <span class="n">config</span><span class="p">[</span><span class="s2">&quot;place_method&quot;</span><span class="p">])</span>
<span class="bp">self</span><span class="o">.</span><span class="n">base_name</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">config</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">]</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">version</span><span class="si">}</span><span class="s2">&quot;</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_file_out</span> <span class="o">=</span> <span class="p">(</span>
Expand Down Expand Up @@ -2422,7 +2426,6 @@ <h1>Source code for cellpack.autopack.Environment</h1><div class="highlight"><pr
<span class="n">pbar</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">log</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">&quot;time to fill </span><span class="si">%d</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">t2</span> <span class="o">-</span> <span class="n">t1</span><span class="p">)</span>
<span class="n">all_objects</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">prep_molecules_for_save</span><span class="p">(</span><span class="n">distances</span><span class="p">,</span> <span class="n">free_points</span><span class="p">,</span> <span class="n">nbFreePoints</span><span class="p">)</span>

<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">saveResult</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">save_result</span><span class="p">(</span>
<span class="n">free_points</span><span class="p">,</span>
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131 changes: 131 additions & 0 deletions _modules/cellpack/autopack/upy/simularium/plots.html
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@@ -0,0 +1,131 @@
<!DOCTYPE html>

<html lang="en" data-content_root="../../../../../">
<head>
<meta charset="utf-8" />
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<title>cellpack.autopack.upy.simularium.plots &#8212; cellPack 1.0.8 documentation</title>
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<h1>Source code for cellpack.autopack.upy.simularium.plots</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">from</span> <span class="nn">simulariumio</span> <span class="kn">import</span> <span class="n">ScatterPlotData</span><span class="p">,</span> <span class="n">HistogramPlotData</span>


<div class="viewcode-block" id="PlotData">
<a class="viewcode-back" href="../../../../../cellpack.autopack.upy.simularium.html#cellpack.autopack.upy.simularium.plots.PlotData">[docs]</a>
<span class="k">class</span> <span class="nc">PlotData</span><span class="p">:</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">plot_list</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># list of tuples</span>

<span class="k">def</span> <span class="nf">_add_plot</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">plot</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">plot_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">plot</span><span class="p">)</span>

<div class="viewcode-block" id="PlotData.add_scatter">
<a class="viewcode-back" href="../../../../../cellpack.autopack.upy.simularium.html#cellpack.autopack.upy.simularium.plots.PlotData.add_scatter">[docs]</a>
<span class="k">def</span> <span class="nf">add_scatter</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">title</span><span class="p">,</span> <span class="n">xaxis_title</span><span class="p">,</span> <span class="n">yaxis_title</span><span class="p">,</span> <span class="n">xtrace</span><span class="p">,</span> <span class="n">ytraces</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_add_plot</span><span class="p">(</span>
<span class="p">(</span>
<span class="s2">&quot;scatter&quot;</span><span class="p">,</span>
<span class="n">ScatterPlotData</span><span class="p">(</span>
<span class="n">title</span><span class="o">=</span><span class="n">title</span><span class="p">,</span>
<span class="n">xaxis_title</span><span class="o">=</span><span class="n">xaxis_title</span><span class="p">,</span>
<span class="n">yaxis_title</span><span class="o">=</span><span class="n">yaxis_title</span><span class="p">,</span>
<span class="n">xtrace</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">xtrace</span><span class="p">),</span>
<span class="n">ytraces</span><span class="o">=</span><span class="p">{</span><span class="n">key</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">value</span><span class="p">)</span> <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">ytraces</span><span class="o">.</span><span class="n">items</span><span class="p">()},</span>
<span class="p">),</span>
<span class="p">)</span>
<span class="p">)</span></div>


<div class="viewcode-block" id="PlotData.add_histogram">
<a class="viewcode-back" href="../../../../../cellpack.autopack.upy.simularium.html#cellpack.autopack.upy.simularium.plots.PlotData.add_histogram">[docs]</a>
<span class="k">def</span> <span class="nf">add_histogram</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">title</span><span class="p">,</span> <span class="n">xaxis_title</span><span class="p">,</span> <span class="n">traces</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_add_plot</span><span class="p">(</span>
<span class="p">(</span>
<span class="s2">&quot;histogram&quot;</span><span class="p">,</span>
<span class="n">HistogramPlotData</span><span class="p">(</span>
<span class="n">title</span><span class="o">=</span><span class="n">title</span><span class="p">,</span>
<span class="n">xaxis_title</span><span class="o">=</span><span class="n">xaxis_title</span><span class="p">,</span>
<span class="n">traces</span><span class="o">=</span><span class="p">{</span><span class="n">key</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">value</span><span class="p">)</span> <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">traces</span><span class="o">.</span><span class="n">items</span><span class="p">()},</span>
<span class="p">),</span>
<span class="p">)</span>
<span class="p">)</span></div>
</div>

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Original file line number Diff line number Diff line change
Expand Up @@ -63,6 +63,7 @@ <h1>Source code for cellpack.autopack.upy.simularium.simularium_helper</h1><div
<span class="kn">from</span> <span class="nn">simulariumio.constants</span> <span class="kn">import</span> <span class="n">DISPLAY_TYPE</span><span class="p">,</span> <span class="n">VIZ_TYPE</span>

<span class="kn">from</span> <span class="nn">cellpack.autopack.upy</span> <span class="kn">import</span> <span class="n">hostHelper</span>
<span class="kn">from</span> <span class="nn">cellpack.autopack.upy.simularium.plots</span> <span class="kn">import</span> <span class="n">PlotData</span>
<span class="kn">from</span> <span class="nn">cellpack.autopack.DBRecipeHandler</span> <span class="kn">import</span> <span class="n">DBUploader</span><span class="p">,</span> <span class="n">DBMaintenance</span>
<span class="kn">from</span> <span class="nn">cellpack.autopack.interface_objects.database_ids</span> <span class="kn">import</span> <span class="n">DATABASE_IDS</span>
<span class="kn">import</span> <span class="nn">collada</span>
Expand Down Expand Up @@ -167,6 +168,7 @@ <h1>Source code for cellpack.autopack.upy.simularium.simularium_helper</h1><div
<span class="bp">self</span><span class="o">.</span><span class="n">nogui</span> <span class="o">=</span> <span class="kc">True</span>
<span class="bp">self</span><span class="o">.</span><span class="n">hext</span> <span class="o">=</span> <span class="s2">&quot;dae&quot;</span>
<span class="bp">self</span><span class="o">.</span><span class="n">max_fiber_length</span> <span class="o">=</span> <span class="mi">0</span>
<span class="bp">self</span><span class="o">.</span><span class="n">plot_data</span> <span class="o">=</span> <span class="n">PlotData</span><span class="p">()</span>

<div class="viewcode-block" id="simulariumHelper.format_rgb_color">
<a class="viewcode-back" href="../../../../../cellpack.autopack.upy.simularium.html#cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper.format_rgb_color">[docs]</a>
Expand Down Expand Up @@ -1739,7 +1741,11 @@ <h1>Source code for cellpack.autopack.upy.simularium.simularium_helper</h1><div
<span class="n">time_units</span><span class="o">=</span><span class="n">UnitData</span><span class="p">(</span><span class="s2">&quot;ns&quot;</span><span class="p">),</span> <span class="c1"># nanoseconds</span>
<span class="n">spatial_units</span><span class="o">=</span><span class="n">UnitData</span><span class="p">(</span><span class="s2">&quot;nm&quot;</span><span class="p">),</span> <span class="c1"># nanometers</span>
<span class="p">)</span>
<span class="n">TrajectoryConverter</span><span class="p">(</span><span class="n">converted_data</span><span class="p">)</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="n">file_name</span><span class="p">,</span> <span class="kc">False</span><span class="p">)</span>
<span class="n">converter</span> <span class="o">=</span> <span class="n">TrajectoryConverter</span><span class="p">(</span><span class="n">converted_data</span><span class="p">)</span>
<span class="n">plot_list</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">plot_data</span><span class="o">.</span><span class="n">plot_list</span>
<span class="k">for</span> <span class="nb">type</span><span class="p">,</span> <span class="n">plot</span> <span class="ow">in</span> <span class="n">plot_list</span><span class="p">:</span>
<span class="n">converter</span><span class="o">.</span><span class="n">add_plot</span><span class="p">(</span><span class="n">plot</span><span class="p">,</span> <span class="nb">type</span><span class="p">)</span>
<span class="n">converter</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="n">file_name</span><span class="p">,</span> <span class="kc">False</span><span class="p">)</span>
<span class="k">return</span> <span class="n">file_name</span></div>


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