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actions-user committed Feb 14, 2024
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8 changes: 4 additions & 4 deletions api/configs.html
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Expand Up @@ -290,7 +290,7 @@ <h2 id="architectureconfigs">ArchitectureConfigs<a class="headerlink" href="#arc
<blockquote>
<div><dl class="py class">
<dt class="sig sig-object py" id="dacapo.experiments.architectures.CNNectomeUNetConfig">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">dacapo.experiments.architectures.</span></span><span class="sig-name descname"><span class="pre">CNNectomeUNetConfig</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">input_shape</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmaps_out</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmaps_in</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_fmaps</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmap_inc_factor</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">downsample_factors</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">kernel_size_down</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">kernel_size_up</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">eval_shape_increase</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">upsample_factors</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">constant_upsample</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">padding</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'valid'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_attention</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#dacapo.experiments.architectures.CNNectomeUNetConfig" title="Link to this definition"></a></dt>
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">dacapo.experiments.architectures.</span></span><span class="sig-name descname"><span class="pre">CNNectomeUNetConfig</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">input_shape</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmaps_out</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmaps_in</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_fmaps</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmap_inc_factor</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">downsample_factors</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">kernel_size_down</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">kernel_size_up</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">eval_shape_increase</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">upsample_factors</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">constant_upsample</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">padding</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'valid'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#dacapo.experiments.architectures.CNNectomeUNetConfig" title="Link to this definition"></a></dt>
<dd><p>This class configures the CNNectomeUNet based on
<a class="reference external" href="https://github.com/saalfeldlab/CNNectome/blob/master/CNNectome/networks/unet_class.py">https://github.com/saalfeldlab/CNNectome/blob/master/CNNectome/networks/unet_class.py</a></p>
<p>Includes support for super resolution via the upsampling factors.</p>
Expand Down Expand Up @@ -321,7 +321,7 @@ <h2 id="taskconfigs">TaskConfigs<a class="headerlink" href="#taskconfigs" title=
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="dacapo.experiments.tasks.AffinitiesTaskConfig">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">dacapo.experiments.tasks.</span></span><span class="sig-name descname"><span class="pre">AffinitiesTaskConfig</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">neighborhood</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lsds</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lsds_to_affs_weight_ratio</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">affs_weight_clipmin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">affs_weight_clipmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.95</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lsd_weight_clipmin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lsd_weight_clipmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.95</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#dacapo.experiments.tasks.AffinitiesTaskConfig" title="Link to this definition"></a></dt>
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">dacapo.experiments.tasks.</span></span><span class="sig-name descname"><span class="pre">AffinitiesTaskConfig</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">neighborhood</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lsds</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lsds_to_affs_weight_ratio</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#dacapo.experiments.tasks.AffinitiesTaskConfig" title="Link to this definition"></a></dt>
<dd><p>This is a Affinities task config used for generating and
evaluating voxel affinities for instance segmentations.</p>
<dl class="py attribute">
Expand All @@ -332,7 +332,7 @@ <h2 id="taskconfigs">TaskConfigs<a class="headerlink" href="#taskconfigs" title=
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="dacapo.experiments.tasks.DistanceTaskConfig">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">dacapo.experiments.tasks.</span></span><span class="sig-name descname"><span class="pre">DistanceTaskConfig</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">channels</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">clip_distance</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tol_distance</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale_factor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mask_distances</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">clipmin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">clipmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.95</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#dacapo.experiments.tasks.DistanceTaskConfig" title="Link to this definition"></a></dt>
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">dacapo.experiments.tasks.</span></span><span class="sig-name descname"><span class="pre">DistanceTaskConfig</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">channels</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">clip_distance</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tol_distance</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale_factor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mask_distances</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#dacapo.experiments.tasks.DistanceTaskConfig" title="Link to this definition"></a></dt>
<dd><p>This is a Distance task config used for generating and
evaluating signed distance transforms as a way of generating
segmentations.</p>
Expand All @@ -353,7 +353,7 @@ <h2 id="trainerconfigs">TrainerConfigs<a class="headerlink" href="#trainerconfig
<blockquote>
<div><dl class="py class">
<dt class="sig sig-object py" id="dacapo.experiments.trainers.GunpowderTrainerConfig">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">dacapo.experiments.trainers.</span></span><span class="sig-name descname"><span class="pre">GunpowderTrainerConfig</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">batch_size</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">learning_rate</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_data_fetchers</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">augments</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">_Nothing.NOTHING</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">snapshot_interval</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_masked</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.15</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">clip_raw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#dacapo.experiments.trainers.GunpowderTrainerConfig" title="Link to this definition"></a></dt>
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">dacapo.experiments.trainers.</span></span><span class="sig-name descname"><span class="pre">GunpowderTrainerConfig</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">batch_size</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">learning_rate</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_data_fetchers</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">augments</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">_Nothing.NOTHING</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">snapshot_interval</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_masked</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.15</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">clip_raw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">add_predictor_nodes_to_dataset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#dacapo.experiments.trainers.GunpowderTrainerConfig" title="Link to this definition"></a></dt>
<dd><dl class="py attribute">
<dt class="sig sig-object py" id="dacapo.experiments.trainers.GunpowderTrainerConfig.trainer_type">
<span class="sig-name descname"><span class="pre">trainer_type</span></span><a class="headerlink" href="#dacapo.experiments.trainers.GunpowderTrainerConfig.trainer_type" title="Link to this definition"></a></dt>
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