deploy: f2e5a45

_autosummary/dpat.data.pmchhg_h5_dataset.PMCHHGH5Dataset.html

@@ -412,7 +412,7 @@ <h2>Parameters<a class="headerlink" href="#parameters" title="Link to this headi
 
 <dl class="py method">
 <dt class="sig sig-object py" id="dpat.data.pmchhg_h5_dataset.PMCHHGH5Dataset.from_pmchhg_data_and_model">
-<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_pmchhg_data_and_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="pre">filename:</span> <span class="pre">str,</span> <span class="pre">dir_name:</span> <span class="pre">~pathlib.Path,</span> <span class="pre">dataset:</span> <span class="pre">~dpat.data.pmc_tile_dataset.PMCHHGImageDataset,</span> <span class="pre">model:</span> <span class="pre">~torch.nn.modules.module.Module,</span> <span class="pre">num_classes:</span> <span class="pre">int,</span> <span class="pre">dsetname_format:</span> <span class="pre">list[str],</span> <span class="pre">transform:</span> <span class="pre">&lt;module</span> <span class="pre">'torchvision.transforms'</span> <span class="pre">from</span> <span class="pre">'/usr/share/miniconda3/envs/dpat/lib/python3.10/site-packages/torchvision/transforms/__init__.py'&gt;</span> <span class="pre">=</span> <span class="pre">None,</span> <span class="pre">cache:</span> <span class="pre">bool</span> <span class="pre">=</span> <span class="pre">False,</span> <span class="pre">mode:</span> <span class="pre">&lt;property</span> <span class="pre">object</span> <span class="pre">at</span> <span class="pre">0x7f274a1257b0&gt;</span> <span class="pre">=</span> <span class="pre">'a',</span> <span class="pre">skip_if_exists:</span> <span class="pre">bool</span> <span class="pre">=</span> <span class="pre">True,</span> <span class="pre">skip_feature_compilation:</span> <span class="pre">bool</span> <span class="pre">=</span> <span class="pre">False,</span> <span class="pre">batch_size:</span> <span class="pre">int</span> <span class="pre">=</span> <span class="pre">32,</span> <span class="pre">num_workers:</span> <span class="pre">int</span> <span class="pre">=</span> <span class="pre">0,</span> <span class="pre">clinical_context:</span> <span class="pre">bool</span> <span class="pre">=</span> <span class="pre">False</span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">T</span></span></span><a class="headerlink" href="#dpat.data.pmchhg_h5_dataset.PMCHHGH5Dataset.from_pmchhg_data_and_model" title="Link to this definition">#</a></dt>
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_pmchhg_data_and_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="pre">filename:</span> <span class="pre">str,</span> <span class="pre">dir_name:</span> <span class="pre">~pathlib.Path,</span> <span class="pre">dataset:</span> <span class="pre">~dpat.data.pmc_tile_dataset.PMCHHGImageDataset,</span> <span class="pre">model:</span> <span class="pre">~torch.nn.modules.module.Module,</span> <span class="pre">num_classes:</span> <span class="pre">int,</span> <span class="pre">dsetname_format:</span> <span class="pre">list[str],</span> <span class="pre">transform:</span> <span class="pre">&lt;module</span> <span class="pre">'torchvision.transforms'</span> <span class="pre">from</span> <span class="pre">'/usr/share/miniconda3/envs/dpat/lib/python3.10/site-packages/torchvision/transforms/__init__.py'&gt;</span> <span class="pre">=</span> <span class="pre">None,</span> <span class="pre">cache:</span> <span class="pre">bool</span> <span class="pre">=</span> <span class="pre">False,</span> <span class="pre">mode:</span> <span class="pre">&lt;property</span> <span class="pre">object</span> <span class="pre">at</span> <span class="pre">0x7f9a8dc698a0&gt;</span> <span class="pre">=</span> <span class="pre">'a',</span> <span class="pre">skip_if_exists:</span> <span class="pre">bool</span> <span class="pre">=</span> <span class="pre">True,</span> <span class="pre">skip_feature_compilation:</span> <span class="pre">bool</span> <span class="pre">=</span> <span class="pre">False,</span> <span class="pre">batch_size:</span> <span class="pre">int</span> <span class="pre">=</span> <span class="pre">32,</span> <span class="pre">num_workers:</span> <span class="pre">int</span> <span class="pre">=</span> <span class="pre">0,</span> <span class="pre">clinical_context:</span> <span class="pre">bool</span> <span class="pre">=</span> <span class="pre">False</span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">T</span></span></span><a class="headerlink" href="#dpat.data.pmchhg_h5_dataset.PMCHHGH5Dataset.from_pmchhg_data_and_model" title="Link to this definition">#</a></dt>
 <dd><p>Build an H5 dataset from PMCHHG dataset with a pretrained model.</p>
 <section id="example-structure">
 <h2>Example structure<a class="headerlink" href="#example-structure" title="Link to this heading">#</a></h2>

_autosummary/dpat.data.pmchhg_h5_dataset.compile_features.html

@@ -354,7 +354,7 @@
 <h1>dpat.data.pmchhg_h5_dataset.compile_features<a class="headerlink" href="#dpat-data-pmchhg-h5-dataset-compile-features" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="dpat.data.pmchhg_h5_dataset.compile_features">
-<span class="sig-prename descclassname"><span class="pre">dpat.data.pmchhg_h5_dataset.</span></span><span class="sig-name descname"><span class="pre">compile_features</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="pre">model:</span> <span class="pre">~torch.nn.modules.module.Module,</span> <span class="pre">dataset:</span> <span class="pre">~dpat.data.pmc_tile_dataset.PMCHHGImageDataset,</span> <span class="pre">dir_name:</span> <span class="pre">~pathlib.Path,</span> <span class="pre">filename:</span> <span class="pre">str,</span> <span class="pre">dsetname_format:</span> <span class="pre">list[str],</span> <span class="pre">mode:</span> <span class="pre">&lt;property</span> <span class="pre">object</span> <span class="pre">at</span> <span class="pre">0x7f274a1257b0&gt;</span> <span class="pre">=</span> <span class="pre">'a',</span> <span class="pre">skip_if_exists:</span> <span class="pre">bool</span> <span class="pre">=</span> <span class="pre">True,</span> <span class="pre">batch_size:</span> <span class="pre">int</span> <span class="pre">=</span> <span class="pre">32,</span> <span class="pre">num_workers:</span> <span class="pre">int</span> <span class="pre">=</span> <span class="pre">0</span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">Path</span></span></span><a class="headerlink" href="#dpat.data.pmchhg_h5_dataset.compile_features" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">dpat.data.pmchhg_h5_dataset.</span></span><span class="sig-name descname"><span class="pre">compile_features</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="pre">model:</span> <span class="pre">~torch.nn.modules.module.Module,</span> <span class="pre">dataset:</span> <span class="pre">~dpat.data.pmc_tile_dataset.PMCHHGImageDataset,</span> <span class="pre">dir_name:</span> <span class="pre">~pathlib.Path,</span> <span class="pre">filename:</span> <span class="pre">str,</span> <span class="pre">dsetname_format:</span> <span class="pre">list[str],</span> <span class="pre">mode:</span> <span class="pre">&lt;property</span> <span class="pre">object</span> <span class="pre">at</span> <span class="pre">0x7f9a8dc698a0&gt;</span> <span class="pre">=</span> <span class="pre">'a',</span> <span class="pre">skip_if_exists:</span> <span class="pre">bool</span> <span class="pre">=</span> <span class="pre">True,</span> <span class="pre">batch_size:</span> <span class="pre">int</span> <span class="pre">=</span> <span class="pre">32,</span> <span class="pre">num_workers:</span> <span class="pre">int</span> <span class="pre">=</span> <span class="pre">0</span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">Path</span></span></span><a class="headerlink" href="#dpat.data.pmchhg_h5_dataset.compile_features" title="Link to this definition">#</a></dt>
 <dd><p>Compile features vectors to H5 format with metadata.</p>
 <section id="parameters">
 <h2>Parameters<a class="headerlink" href="#parameters" title="Link to this heading">#</a></h2>