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2 changes: 1 addition & 1 deletion _modules/index.html
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<head>
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<title>myria3d.callbacks.comet_callbacks &mdash; myria3d 3.5.2 documentation</title>
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<title>myria3d.callbacks.finetuning_callbacks &mdash; myria3d 3.5.2 documentation</title>
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12 changes: 7 additions & 5 deletions _modules/myria3d/models/interpolation.html
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<head>
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<title>myria3d.models.interpolation &mdash; myria3d 3.5.2 documentation</title>
<title>myria3d.models.interpolation &mdash; myria3d 3.6.0 documentation</title>
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Expand Down Expand Up @@ -220,16 +220,17 @@ <h1>Source code for myria3d.models.interpolation</h1><div class="highlight"><pre
<span class="bp">self</span><span class="o">.</span><span class="n">logits</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="n">torch</span><span class="o">.</span><span class="n">Tensor</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">idx_in_full_cloud_list</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>

<div class="viewcode-block" id="Interpolator.load_full_las_for_update"><a class="viewcode-back" href="../../../apidoc/myria3d.model.html#myria3d.models.interpolation.Interpolator.load_full_las_for_update">[docs]</a> <span class="k">def</span> <span class="nf">load_full_las_for_update</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">src_las</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">:</span>
<div class="viewcode-block" id="Interpolator.load_full_las_for_update"><a class="viewcode-back" href="../../../apidoc/myria3d.model.html#myria3d.models.interpolation.Interpolator.load_full_las_for_update">[docs]</a> <span class="k">def</span> <span class="nf">load_full_las_for_update</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">src_las</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">epsg</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Loads a LAS and adds necessary extradim.</span>

<span class="sd"> Args:</span>
<span class="sd"> filepath (str): Path to LAS for which predictions are made.</span>
<span class="sd"> epsg (str): epsg to force the reading with</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="c1"># We do not reset the dims we create channel.</span>
<span class="c1"># Slight risk of interaction with previous values, but it is expected that all non-artefacts values are updated.</span>

<span class="n">pipeline</span> <span class="o">=</span> <span class="n">get_pdal_reader</span><span class="p">(</span><span class="n">src_las</span><span class="p">)</span>
<span class="n">pipeline</span> <span class="o">=</span> <span class="n">get_pdal_reader</span><span class="p">(</span><span class="n">src_las</span><span class="p">,</span> <span class="n">epsg</span><span class="p">)</span>
<span class="k">for</span> <span class="n">proba_channel_to_create</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">probas_to_save</span><span class="p">:</span>
<span class="n">pipeline</span> <span class="o">|=</span> <span class="n">pdal</span><span class="o">.</span><span class="n">Filter</span><span class="o">.</span><span class="n">ferry</span><span class="p">(</span><span class="n">dimensions</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;=&gt;</span><span class="si">{</span><span class="n">proba_channel_to_create</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="n">pipeline</span> <span class="o">|=</span> <span class="n">pdal</span><span class="o">.</span><span class="n">Filter</span><span class="o">.</span><span class="n">assign</span><span class="p">(</span><span class="n">value</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">proba_channel_to_create</span><span class="si">}</span><span class="s2">=0&quot;</span><span class="p">)</span>
Expand Down Expand Up @@ -280,14 +281,15 @@ <h1>Source code for myria3d.models.interpolation</h1><div class="highlight"><pre
<span class="k">return</span> <span class="n">reduced_logits</span><span class="p">[</span><span class="n">idx_in_full_cloud</span><span class="p">],</span> <span class="n">idx_in_full_cloud</span></div>

<div class="viewcode-block" id="Interpolator.reduce_predictions_and_save"><a class="viewcode-back" href="../../../apidoc/myria3d.model.html#myria3d.models.interpolation.Interpolator.reduce_predictions_and_save">[docs]</a> <span class="nd">@torch</span><span class="o">.</span><span class="n">no_grad</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">reduce_predictions_and_save</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">raw_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">output_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
<span class="k">def</span> <span class="nf">reduce_predictions_and_save</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">raw_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">output_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">epsg</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Interpolate all predicted probabilites to their original points in LAS file, and save.</span>

<span class="sd"> Args:</span>
<span class="sd"> interpolation (torch.Tensor, torch.Tensor): output of _interpolate, of which we need the logits.</span>
<span class="sd"> basename: str: file basename to save it with the same one</span>
<span class="sd"> output_dir (Optional[str], optional): Directory to save output LAS with new predicted classification, entropy,</span>
<span class="sd"> and probabilities. Defaults to None.</span>
<span class="sd"> epsg (str): epsg to force the reading with</span>
<span class="sd"> Returns:</span>
<span class="sd"> str: path of the updated, saved LAS file.</span>

Expand All @@ -306,7 +308,7 @@ <h1>Source code for myria3d.models.interpolation</h1><div class="highlight"><pre
<span class="k">del</span> <span class="n">logits</span>

<span class="c1"># Read las after fetching all information to write into it</span>
<span class="n">las</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_full_las_for_update</span><span class="p">(</span><span class="n">src_las</span><span class="o">=</span><span class="n">raw_path</span><span class="p">)</span>
<span class="n">las</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_full_las_for_update</span><span class="p">(</span><span class="n">raw_path</span><span class="p">,</span> <span class="n">epsg</span><span class="p">)</span>

<span class="k">for</span> <span class="n">idx</span><span class="p">,</span> <span class="n">class_name</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classification_dict</span><span class="o">.</span><span class="n">values</span><span class="p">()):</span>
<span class="k">if</span> <span class="n">class_name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">probas_to_save</span><span class="p">:</span>
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2 changes: 1 addition & 1 deletion _modules/myria3d/models/model.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>myria3d.models.model &mdash; myria3d 3.5.2 documentation</title>
<title>myria3d.models.model &mdash; myria3d 3.6.0 documentation</title>
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<head>
<meta charset="utf-8" />
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<title>myria3d.models.modules.pyg_randla_net &mdash; myria3d 3.5.2 documentation</title>
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<head>
<meta charset="utf-8" />
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<title>myria3d.pctl.dataloader.dataloader &mdash; myria3d 3.5.2 documentation</title>
<title>myria3d.pctl.dataloader.dataloader &mdash; myria3d 3.6.0 documentation</title>
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6 changes: 5 additions & 1 deletion _modules/myria3d/pctl/datamodule/hdf5.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>myria3d.pctl.datamodule.hdf5 &mdash; myria3d 3.5.2 documentation</title>
<title>myria3d.pctl.datamodule.hdf5 &mdash; myria3d 3.6.0 documentation</title>
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Expand Down Expand Up @@ -194,6 +194,7 @@ <h1>Source code for myria3d.pctl.datamodule.hdf5</h1><div class="highlight"><pre
<span class="n">data_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
<span class="n">split_csv_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
<span class="n">hdf5_file_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
<span class="n">epsg</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
<span class="n">points_pre_transform</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">Callable</span><span class="p">[[</span><span class="n">ArrayLike</span><span class="p">],</span> <span class="n">Data</span><span class="p">]]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
<span class="n">pre_filter</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">Callable</span><span class="p">[[</span><span class="n">Data</span><span class="p">],</span> <span class="nb">bool</span><span class="p">]]</span> <span class="o">=</span> <span class="n">pre_filter_below_n_points</span><span class="p">,</span>
<span class="n">tile_width</span><span class="p">:</span> <span class="n">Number</span> <span class="o">=</span> <span class="mi">1000</span><span class="p">,</span>
Expand All @@ -209,6 +210,7 @@ <h1>Source code for myria3d.pctl.datamodule.hdf5</h1><div class="highlight"><pre
<span class="bp">self</span><span class="o">.</span><span class="n">split_csv_path</span> <span class="o">=</span> <span class="n">split_csv_path</span>
<span class="bp">self</span><span class="o">.</span><span class="n">data_dir</span> <span class="o">=</span> <span class="n">data_dir</span>
<span class="bp">self</span><span class="o">.</span><span class="n">hdf5_file_path</span> <span class="o">=</span> <span class="n">hdf5_file_path</span>
<span class="bp">self</span><span class="o">.</span><span class="n">epsg</span> <span class="o">=</span> <span class="n">epsg</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_dataset</span> <span class="o">=</span> <span class="kc">None</span> <span class="c1"># will be set by self.dataset property</span>
<span class="bp">self</span><span class="o">.</span><span class="n">las_paths_by_split_dict</span> <span class="o">=</span> <span class="p">{}</span> <span class="c1"># Will be set from split_csv</span>

Expand Down Expand Up @@ -292,6 +294,7 @@ <h1>Source code for myria3d.pctl.datamodule.hdf5</h1><div class="highlight"><pre

<span class="bp">self</span><span class="o">.</span><span class="n">_dataset</span> <span class="o">=</span> <span class="n">HDF5Dataset</span><span class="p">(</span>
<span class="bp">self</span><span class="o">.</span><span class="n">hdf5_file_path</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">epsg</span><span class="p">,</span>
<span class="n">las_paths_by_split_dict</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">las_paths_by_split_dict</span><span class="p">,</span>
<span class="n">points_pre_transform</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">points_pre_transform</span><span class="p">,</span>
<span class="n">tile_width</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">tile_width</span><span class="p">,</span>
Expand Down Expand Up @@ -331,6 +334,7 @@ <h1>Source code for myria3d.pctl.datamodule.hdf5</h1><div class="highlight"><pre
<span class="k">def</span> <span class="nf">_set_predict_data</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">las_file_to_predict</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">predict_dataset</span> <span class="o">=</span> <span class="n">InferenceDataset</span><span class="p">(</span>
<span class="n">las_file_to_predict</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">epsg</span><span class="p">,</span>
<span class="n">points_pre_transform</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">points_pre_transform</span><span class="p">,</span>
<span class="n">pre_filter</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">pre_filter</span><span class="p">,</span>
<span class="n">transform</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">predict_transform</span><span class="p">,</span>
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