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<h1 id="index">Index</h1>
<div class="genindex-jumpbox">
<a href="#_"><strong>_</strong></a>
| <a href="#A"><strong>A</strong></a>
| <a href="#B"><strong>B</strong></a>
| <a href="#C"><strong>C</strong></a>
| <a href="#D"><strong>D</strong></a>
| <a href="#E"><strong>E</strong></a>
| <a href="#F"><strong>F</strong></a>
| <a href="#G"><strong>G</strong></a>
| <a href="#H"><strong>H</strong></a>
| <a href="#I"><strong>I</strong></a>
| <a href="#K"><strong>K</strong></a>
| <a href="#L"><strong>L</strong></a>
| <a href="#M"><strong>M</strong></a>
| <a href="#N"><strong>N</strong></a>
| <a href="#O"><strong>O</strong></a>
| <a href="#P"><strong>P</strong></a>
| <a href="#R"><strong>R</strong></a>
| <a href="#S"><strong>S</strong></a>
| <a href="#T"><strong>T</strong></a>
| <a href="#V"><strong>V</strong></a>
</div>
<h2 id="_">_</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.data.Coordinates.html#deepof.data.Coordinates.__init__">__init__() (deepof.data.Coordinates method)</a>, <a href="_generated/deepof.data.Coordinates.html#id0">[1]</a>
<ul>
<li><a href="_generated/deepof.data.Project.html#deepof.data.Project.__init__">(deepof.data.Project method)</a>, <a href="_generated/deepof.data.Project.html#id0">[1]</a>
</li>
<li><a href="_generated/deepof.data.TableDict.html#deepof.data.TableDict.__init__">(deepof.data.TableDict method)</a>, <a href="_generated/deepof.data.TableDict.html#id0">[1]</a>
</li>
<li><a href="_generated/deepof.hypermodels.Contrastive.html#deepof.hypermodels.Contrastive.__init__">(deepof.hypermodels.Contrastive method)</a>, <a href="_generated/deepof.hypermodels.Contrastive.html#id0">[1]</a>
</li>
<li><a href="_generated/deepof.hypermodels.VaDE.html#deepof.hypermodels.VaDE.__init__">(deepof.hypermodels.VaDE method)</a>, <a href="_generated/deepof.hypermodels.VaDE.html#id0">[1]</a>
</li>
<li><a href="_generated/deepof.hypermodels.VQVAE.html#deepof.hypermodels.VQVAE.__init__">(deepof.hypermodels.VQVAE method)</a>, <a href="_generated/deepof.hypermodels.VQVAE.html#id0">[1]</a>
</li>
<li><a href="_generated/deepof.model_utils.ClusterControl.html#deepof.model_utils.ClusterControl.__init__">(deepof.model_utils.ClusterControl method)</a>, <a href="_generated/deepof.model_utils.ClusterControl.html#id0">[1]</a>
</li>
<li><a href="_generated/deepof.model_utils.CustomStopper.html#deepof.model_utils.CustomStopper.__init__">(deepof.model_utils.CustomStopper method)</a>, <a href="_generated/deepof.model_utils.CustomStopper.html#id0">[1]</a>
</li>
<li><a href="_generated/deepof.model_utils.ExponentialLearningRate.html#deepof.model_utils.ExponentialLearningRate.__init__">(deepof.model_utils.ExponentialLearningRate method)</a>, <a href="_generated/deepof.model_utils.ExponentialLearningRate.html#id0">[1]</a>
</li>
<li><a href="_generated/deepof.model_utils.ProbabilisticDecoder.html#deepof.model_utils.ProbabilisticDecoder.__init__">(deepof.model_utils.ProbabilisticDecoder method)</a>, <a href="_generated/deepof.model_utils.ProbabilisticDecoder.html#id0">[1]</a>
</li>
<li><a href="_generated/deepof.model_utils.TransformerDecoder.html#deepof.model_utils.TransformerDecoder.__init__">(deepof.model_utils.TransformerDecoder method)</a>, <a href="_generated/deepof.model_utils.TransformerDecoder.html#id0">[1]</a>
</li>
<li><a href="_generated/deepof.model_utils.TransformerDecoderLayer.html#deepof.model_utils.TransformerDecoderLayer.__init__">(deepof.model_utils.TransformerDecoderLayer method)</a>, <a href="_generated/deepof.model_utils.TransformerDecoderLayer.html#id0">[1]</a>
</li>
<li><a href="_generated/deepof.model_utils.TransformerEncoder.html#deepof.model_utils.TransformerEncoder.__init__">(deepof.model_utils.TransformerEncoder method)</a>, <a href="_generated/deepof.model_utils.TransformerEncoder.html#id0">[1]</a>
</li>
<li><a href="_generated/deepof.model_utils.TransformerEncoderLayer.html#deepof.model_utils.TransformerEncoderLayer.__init__">(deepof.model_utils.TransformerEncoderLayer method)</a>, <a href="_generated/deepof.model_utils.TransformerEncoderLayer.html#id0">[1]</a>
</li>
<li><a href="_generated/deepof.models.Classifier.html#deepof.models.Classifier.__init__">(deepof.models.Classifier method)</a>, <a href="_generated/deepof.models.Classifier.html#id0">[1]</a>
</li>
<li><a href="_generated/deepof.models.Contrastive.html#deepof.models.Contrastive.__init__">(deepof.models.Contrastive method)</a>, <a href="_generated/deepof.models.Contrastive.html#id0">[1]</a>
</li>
<li><a href="_generated/deepof.models.GaussianMixtureLatent.html#deepof.models.GaussianMixtureLatent.__init__">(deepof.models.GaussianMixtureLatent method)</a>, <a href="_generated/deepof.models.GaussianMixtureLatent.html#id0">[1]</a>
</li>
<li><a href="_generated/deepof.models.VaDE.html#deepof.models.VaDE.__init__">(deepof.models.VaDE method)</a>, <a href="_generated/deepof.models.VaDE.html#id0">[1]</a>
</li>
<li><a href="_generated/deepof.models.VectorQuantizer.html#deepof.models.VectorQuantizer.__init__">(deepof.models.VectorQuantizer method)</a>, <a href="_generated/deepof.models.VectorQuantizer.html#id0">[1]</a>
</li>
<li><a href="_generated/deepof.models.VQVAE.html#deepof.models.VQVAE.__init__">(deepof.models.VQVAE method)</a>, <a href="_generated/deepof.models.VQVAE.html#id0">[1]</a>
</li>
</ul></li>
</ul></td>
</tr></table>
<h2 id="A">A</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.post_hoc.align_deepof_kinematics_with_unsupervised_labels.html#deepof.post_hoc.align_deepof_kinematics_with_unsupervised_labels">align_deepof_kinematics_with_unsupervised_labels() (in module deepof.post_hoc)</a>
</li>
<li><a href="_generated/deepof.utils.align_trajectories.html#deepof.utils.align_trajectories">align_trajectories() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.utils.angle.html#deepof.utils.angle">angle() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.visuals.animate_skeleton.html#deepof.visuals.animate_skeleton">animate_skeleton() (in module deepof.visuals)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.post_hoc.annotate_time_chunks.html#deepof.post_hoc.annotate_time_chunks">annotate_time_chunks() (in module deepof.post_hoc)</a>
</li>
<li><a href="_generated/deepof.visuals.annotate_video.html#deepof.visuals.annotate_video">annotate_video() (in module deepof.visuals)</a>
</li>
<li><a href="_generated/deepof.utils.arena_parameter_extraction.html#deepof.utils.arena_parameter_extraction">arena_parameter_extraction() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.utils.automatically_recognize_arena.html#deepof.utils.automatically_recognize_arena">automatically_recognize_arena() (in module deepof.utils)</a>
</li>
</ul></td>
</tr></table>
<h2 id="B">B</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.utils.bp2polar.html#deepof.utils.bp2polar">bp2polar() (in module deepof.utils)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.utils.bpart_distance.html#deepof.utils.bpart_distance">bpart_distance() (in module deepof.utils)</a>
</li>
</ul></td>
</tr></table>
<h2 id="C">C</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.post_hoc.chunk_cv_splitter.html#deepof.post_hoc.chunk_cv_splitter">chunk_cv_splitter() (in module deepof.post_hoc)</a>
</li>
<li><a href="_generated/deepof.post_hoc.chunk_summary_statistics.html#deepof.post_hoc.chunk_summary_statistics">chunk_summary_statistics() (in module deepof.post_hoc)</a>
</li>
<li><a href="_generated/deepof.models.Classifier.html#deepof.models.Classifier">Classifier (class in deepof.models)</a>
</li>
<li><a href="_generated/deepof.annotation_utils.climb_wall.html#deepof.annotation_utils.climb_wall">climb_wall() (in module deepof.annotation_utils)</a>
</li>
<li><a href="_generated/deepof.annotation_utils.close_double_contact.html#deepof.annotation_utils.close_double_contact">close_double_contact() (in module deepof.annotation_utils)</a>
</li>
<li><a href="_generated/deepof.annotation_utils.close_single_contact.html#deepof.annotation_utils.close_single_contact">close_single_contact() (in module deepof.annotation_utils)</a>
</li>
<li><a href="_generated/deepof.utils.closest_side.html#deepof.utils.closest_side">closest_side() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.model_utils.cluster_frequencies_regularizer.html#deepof.model_utils.cluster_frequencies_regularizer">cluster_frequencies_regularizer() (in module deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.utils.cluster_transition_matrix.html#deepof.utils.cluster_transition_matrix">cluster_transition_matrix() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.model_utils.ClusterControl.html#deepof.model_utils.ClusterControl">ClusterControl (class in deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.utils.compute_animal_presence_mask.html#deepof.utils.compute_animal_presence_mask">compute_animal_presence_mask() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.utils.compute_areas.html#deepof.utils.compute_areas">compute_areas() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.utils.compute_dist.html#deepof.utils.compute_dist">compute_dist() (in module deepof.utils)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.model_utils.compute_kmeans_loss.html#deepof.model_utils.compute_kmeans_loss">compute_kmeans_loss() (in module deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.model_utils.compute_shannon_entropy.html#deepof.model_utils.compute_shannon_entropy">compute_shannon_entropy() (in module deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.post_hoc.compute_steady_state.html#deepof.post_hoc.compute_steady_state">compute_steady_state() (in module deepof.post_hoc)</a>
</li>
<li><a href="_generated/deepof.post_hoc.compute_transition_matrix_per_condition.html#deepof.post_hoc.compute_transition_matrix_per_condition">compute_transition_matrix_per_condition() (in module deepof.post_hoc)</a>
</li>
<li><a href="_generated/deepof.post_hoc.compute_UMAP.html#deepof.post_hoc.compute_UMAP">compute_UMAP() (in module deepof.post_hoc)</a>
</li>
<li><a href="_generated/deepof.post_hoc.condition_distance_binning.html#deepof.post_hoc.condition_distance_binning">condition_distance_binning() (in module deepof.post_hoc)</a>
</li>
<li><a href="_generated/deepof.utils.connect_mouse.html#deepof.utils.connect_mouse">connect_mouse() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.hypermodels.Contrastive.html#deepof.hypermodels.Contrastive">Contrastive (class in deepof.hypermodels)</a>
<ul>
<li><a href="_generated/deepof.models.Contrastive.html#deepof.models.Contrastive">(class in deepof.models)</a>
</li>
</ul></li>
<li><a href="_generated/deepof.data.Coordinates.html#deepof.data.Coordinates">Coordinates (class in deepof.data)</a>
</li>
<li><a href="_generated/deepof.model_utils.create_look_ahead_mask.html#deepof.model_utils.create_look_ahead_mask">create_look_ahead_mask() (in module deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.model_utils.create_masks.html#deepof.model_utils.create_masks">create_masks() (in module deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.model_utils.create_padding_mask.html#deepof.model_utils.create_padding_mask">create_padding_mask() (in module deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.model_utils.CustomStopper.html#deepof.model_utils.CustomStopper">CustomStopper (class in deepof.model_utils)</a>
</li>
</ul></td>
</tr></table>
<h2 id="D">D</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.model_utils.dcl_loss.html#deepof.model_utils.dcl_loss">dcl_loss() (in module deepof.model_utils)</a>
</li>
<li>
deepof
<ul>
<li><a href="deepof.html#module-deepof">module</a>
</li>
</ul></li>
<li>
deepof.annotation_utils
<ul>
<li><a href="_generated/deepof.annotation_utils.html#module-deepof.annotation_utils">module</a>
</li>
</ul></li>
<li>
deepof.data
<ul>
<li><a href="_generated/deepof.data.html#module-deepof.data">module</a>
</li>
</ul></li>
<li>
deepof.deepof_train_embeddings
<ul>
<li><a href="deepof.deepof_train_embeddings.html#module-deepof.deepof_train_embeddings">module</a>
</li>
</ul></li>
<li>
deepof.hypermodels
<ul>
<li><a href="_generated/deepof.hypermodels.html#module-deepof.hypermodels">module</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li>
deepof.model_utils
<ul>
<li><a href="_generated/deepof.model_utils.html#module-deepof.model_utils">module</a>
</li>
</ul></li>
<li>
deepof.models
<ul>
<li><a href="_generated/deepof.models.html#module-deepof.models">module</a>
</li>
</ul></li>
<li>
deepof.post_hoc
<ul>
<li><a href="_generated/deepof.post_hoc.html#module-deepof.post_hoc">module</a>
</li>
</ul></li>
<li>
deepof.utils
<ul>
<li><a href="_generated/deepof.utils.html#module-deepof.utils">module</a>
</li>
</ul></li>
<li>
deepof.visuals
<ul>
<li><a href="_generated/deepof.visuals.html#module-deepof.visuals">module</a>
</li>
</ul></li>
</ul></td>
</tr></table>
<h2 id="E">E</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.utils.edges_to_weighted_adj.html#deepof.utils.edges_to_weighted_adj">edges_to_weighted_adj() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.model_utils.embedding_model_fitting.html#deepof.model_utils.embedding_model_fitting">embedding_model_fitting() (in module deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.model_utils.embedding_per_video.html#deepof.model_utils.embedding_per_video">embedding_per_video() (in module deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.post_hoc.enrichment_across_conditions.html#deepof.post_hoc.enrichment_across_conditions">enrichment_across_conditions() (in module deepof.post_hoc)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.utils.enumerate_all_bridges.html#deepof.utils.enumerate_all_bridges">enumerate_all_bridges() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.post_hoc.explain_clusters.html#deepof.post_hoc.explain_clusters">explain_clusters() (in module deepof.post_hoc)</a>
</li>
<li><a href="_generated/deepof.model_utils.ExponentialLearningRate.html#deepof.model_utils.ExponentialLearningRate">ExponentialLearningRate (class in deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.visuals.export_annotated_video.html#deepof.visuals.export_annotated_video">export_annotated_video() (in module deepof.visuals)</a>
</li>
<li><a href="_generated/deepof.utils.extract_polygonal_arena_coordinates.html#deepof.utils.extract_polygonal_arena_coordinates">extract_polygonal_arena_coordinates() (in module deepof.utils)</a>
</li>
</ul></td>
</tr></table>
<h2 id="F">F</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.model_utils.fc_loss.html#deepof.model_utils.fc_loss">fc_loss() (in module deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.utils.filter_columns.html#deepof.utils.filter_columns">filter_columns() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.utils.filter_short_bouts.html#deepof.utils.filter_short_bouts">filter_short_bouts() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.model_utils.find_learning_rate.html#deepof.model_utils.find_learning_rate">find_learning_rate() (in module deepof.model_utils)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.utils.fit_ellipse_to_polygon.html#deepof.utils.fit_ellipse_to_polygon">fit_ellipse_to_polygon() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.post_hoc.fit_normative_global_model.html#deepof.post_hoc.fit_normative_global_model">fit_normative_global_model() (in module deepof.post_hoc)</a>
</li>
<li><a href="_generated/deepof.annotation_utils.following_path.html#deepof.annotation_utils.following_path">following_path() (in module deepof.annotation_utils)</a>
</li>
<li><a href="_generated/deepof.annotation_utils.frame_corners.html#deepof.annotation_utils.frame_corners">frame_corners() (in module deepof.annotation_utils)</a>
</li>
<li><a href="_generated/deepof.utils.full_outlier_mask.html#deepof.utils.full_outlier_mask">full_outlier_mask() (in module deepof.utils)</a>
</li>
</ul></td>
</tr></table>
<h2 id="G">G</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.models.GaussianMixtureLatent.html#deepof.models.GaussianMixtureLatent">GaussianMixtureLatent (class in deepof.models)</a>
</li>
<li><a href="_generated/deepof.post_hoc.get_aggregated_embedding.html#deepof.post_hoc.get_aggregated_embedding">get_aggregated_embedding() (in module deepof.post_hoc)</a>
</li>
<li><a href="_generated/deepof.model_utils.get_angles.html#deepof.model_utils.get_angles">get_angles() (in module deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.utils.get_arenas.html#deepof.utils.get_arenas">get_arenas() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.model_utils.get_callbacks.html#deepof.model_utils.get_callbacks">get_callbacks() (in module deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.model_utils.get_hard_counts.html#deepof.model_utils.get_hard_counts">get_hard_counts() (in module deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.annotation_utils.get_hparameters.html#deepof.annotation_utils.get_hparameters">get_hparameters() (in module deepof.annotation_utils)</a>
</li>
<li><a href="_generated/deepof.model_utils.get_k_nearest_neighbors.html#deepof.model_utils.get_k_nearest_neighbors">get_k_nearest_neighbors() (in module deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.model_utils.get_recurrent_block.html#deepof.model_utils.get_recurrent_block">get_recurrent_block() (in module deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.models.get_recurrent_decoder.html#deepof.models.get_recurrent_decoder">get_recurrent_decoder() (in module deepof.models)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.models.get_recurrent_encoder.html#deepof.models.get_recurrent_encoder">get_recurrent_encoder() (in module deepof.models)</a>
</li>
<li><a href="_generated/deepof.models.get_TCN_decoder.html#deepof.models.get_TCN_decoder">get_TCN_decoder() (in module deepof.models)</a>
</li>
<li><a href="_generated/deepof.models.get_TCN_encoder.html#deepof.models.get_TCN_encoder">get_TCN_encoder() (in module deepof.models)</a>
</li>
<li><a href="_generated/deepof.post_hoc.get_time_on_cluster.html#deepof.post_hoc.get_time_on_cluster">get_time_on_cluster() (in module deepof.post_hoc)</a>
</li>
<li><a href="_generated/deepof.models.get_transformer_decoder.html#deepof.models.get_transformer_decoder">get_transformer_decoder() (in module deepof.models)</a>
</li>
<li><a href="_generated/deepof.models.get_transformer_encoder.html#deepof.models.get_transformer_encoder">get_transformer_encoder() (in module deepof.models)</a>
</li>
<li><a href="_generated/deepof.post_hoc.get_transitions.html#deepof.post_hoc.get_transitions">get_transitions() (in module deepof.post_hoc)</a>
</li>
<li><a href="_generated/deepof.models.get_vade.html#deepof.models.get_vade">get_vade() (in module deepof.models)</a>
</li>
<li><a href="_generated/deepof.models.get_vqvae.html#deepof.models.get_vqvae">get_vqvae() (in module deepof.models)</a>
</li>
<li><a href="_generated/deepof.utils.gmm_compute.html#deepof.utils.gmm_compute">gmm_compute() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.utils.gmm_model_selection.html#deepof.utils.gmm_model_selection">gmm_model_selection() (in module deepof.utils)</a>
</li>
</ul></td>
</tr></table>
<h2 id="H">H</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.model_utils.hard_loss.html#deepof.model_utils.hard_loss">hard_loss() (in module deepof.model_utils)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.visuals.heatmap.html#deepof.visuals.heatmap">heatmap() (in module deepof.visuals)</a>
</li>
<li><a href="_generated/deepof.annotation_utils.huddle.html#deepof.annotation_utils.huddle">huddle() (in module deepof.annotation_utils)</a>
</li>
</ul></td>
</tr></table>
<h2 id="I">I</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.utils.interpolate_outliers.html#deepof.utils.interpolate_outliers">interpolate_outliers() (in module deepof.utils)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.utils.iterative_imputation.html#deepof.utils.iterative_imputation">iterative_imputation() (in module deepof.utils)</a>
</li>
</ul></td>
</tr></table>
<h2 id="K">K</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.utils.kleinberg.html#deepof.utils.kleinberg">kleinberg() (in module deepof.utils)</a>
</li>
</ul></td>
</tr></table>
<h2 id="L">L</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.data.load_project.html#deepof.data.load_project">load_project() (in module deepof.data)</a>
</li>
<li><a href="_generated/deepof.utils.load_segmentation_model.html#deepof.utils.load_segmentation_model">load_segmentation_model() (in module deepof.utils)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.utils.load_table.html#deepof.utils.load_table">load_table() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.model_utils.log_hyperparameters.html#deepof.model_utils.log_hyperparameters">log_hyperparameters() (in module deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.annotation_utils.look_around.html#deepof.annotation_utils.look_around">look_around() (in module deepof.annotation_utils)</a>
</li>
</ul></td>
</tr></table>
<h2 id="M">M</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.utils.mask_outliers.html#deepof.utils.mask_outliers">mask_outliers() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.annotation_utils.max_behaviour.html#deepof.annotation_utils.max_behaviour">max_behaviour() (in module deepof.annotation_utils)</a>
</li>
<li>
module
<ul>
<li><a href="deepof.html#module-deepof">deepof</a>
</li>
<li><a href="_generated/deepof.annotation_utils.html#module-deepof.annotation_utils">deepof.annotation_utils</a>
</li>
<li><a href="_generated/deepof.data.html#module-deepof.data">deepof.data</a>
</li>
<li><a href="deepof.deepof_train_embeddings.html#module-deepof.deepof_train_embeddings">deepof.deepof_train_embeddings</a>
</li>
<li><a href="_generated/deepof.hypermodels.html#module-deepof.hypermodels">deepof.hypermodels</a>
</li>
<li><a href="_generated/deepof.model_utils.html#module-deepof.model_utils">deepof.model_utils</a>
</li>
<li><a href="_generated/deepof.models.html#module-deepof.models">deepof.models</a>
</li>
<li><a href="_generated/deepof.post_hoc.html#module-deepof.post_hoc">deepof.post_hoc</a>
</li>
<li><a href="_generated/deepof.utils.html#module-deepof.utils">deepof.utils</a>
</li>
<li><a href="_generated/deepof.visuals.html#module-deepof.visuals">deepof.visuals</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.utils.moving_average.html#deepof.utils.moving_average">moving_average() (in module deepof.utils)</a>
</li>
</ul></td>
</tr></table>
<h2 id="N">N</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.model_utils.nce_loss.html#deepof.model_utils.nce_loss">nce_loss() (in module deepof.model_utils)</a>
</li>
</ul></td>
</tr></table>
<h2 id="O">O</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.visuals.output_cluster_video.html#deepof.visuals.output_cluster_video">output_cluster_video() (in module deepof.visuals)</a>
</li>
<li><a href="_generated/deepof.visuals.output_unsupervised_annotated_video.html#deepof.visuals.output_unsupervised_annotated_video">output_unsupervised_annotated_video() (in module deepof.visuals)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.visuals.output_videos_per_cluster.html#deepof.visuals.output_videos_per_cluster">output_videos_per_cluster() (in module deepof.visuals)</a>
</li>
<li><a href="_generated/deepof.annotation_utils.outside_ellipse.html#deepof.annotation_utils.outside_ellipse">outside_ellipse() (in module deepof.annotation_utils)</a>
</li>
</ul></td>
</tr></table>
<h2 id="P">P</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.visuals.plot_arena.html#deepof.visuals.plot_arena">plot_arena() (in module deepof.visuals)</a>
</li>
<li><a href="_generated/deepof.visuals.plot_cluster_detection_performance.html#deepof.visuals.plot_cluster_detection_performance">plot_cluster_detection_performance() (in module deepof.visuals)</a>
</li>
<li><a href="_generated/deepof.visuals.plot_distance_between_conditions.html#deepof.visuals.plot_distance_between_conditions">plot_distance_between_conditions() (in module deepof.visuals)</a>
</li>
<li><a href="_generated/deepof.visuals.plot_embeddings.html#deepof.visuals.plot_embeddings">plot_embeddings() (in module deepof.visuals)</a>
</li>
<li><a href="_generated/deepof.visuals.plot_enrichment.html#deepof.visuals.plot_enrichment">plot_enrichment() (in module deepof.visuals)</a>
</li>
<li><a href="_generated/deepof.visuals.plot_gantt.html#deepof.visuals.plot_gantt">plot_gantt() (in module deepof.visuals)</a>
</li>
<li><a href="_generated/deepof.visuals.plot_heatmaps.html#deepof.visuals.plot_heatmaps">plot_heatmaps() (in module deepof.visuals)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.model_utils.plot_lr_vs_loss.html#deepof.model_utils.plot_lr_vs_loss">plot_lr_vs_loss() (in module deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.visuals.plot_normative_log_likelihood.html#deepof.visuals.plot_normative_log_likelihood">plot_normative_log_likelihood() (in module deepof.visuals)</a>
</li>
<li><a href="_generated/deepof.visuals.plot_shap_swarm_per_cluster.html#deepof.visuals.plot_shap_swarm_per_cluster">plot_shap_swarm_per_cluster() (in module deepof.visuals)</a>
</li>
<li><a href="_generated/deepof.visuals.plot_stationary_entropy.html#deepof.visuals.plot_stationary_entropy">plot_stationary_entropy() (in module deepof.visuals)</a>
</li>
<li><a href="_generated/deepof.visuals.plot_transitions.html#deepof.visuals.plot_transitions">plot_transitions() (in module deepof.visuals)</a>
</li>
<li><a href="_generated/deepof.model_utils.positional_encoding.html#deepof.model_utils.positional_encoding">positional_encoding() (in module deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.model_utils.ProbabilisticDecoder.html#deepof.model_utils.ProbabilisticDecoder">ProbabilisticDecoder (class in deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.data.Project.html#deepof.data.Project">Project (class in deepof.data)</a>
</li>
</ul></td>
</tr></table>
<h2 id="R">R</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.post_hoc.recluster.html#deepof.post_hoc.recluster">recluster() (in module deepof.post_hoc)</a>
</li>
<li><a href="_generated/deepof.utils.rename_track_bps.html#deepof.utils.rename_track_bps">rename_track_bps() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.utils.retrieve_corners_from_image.html#deepof.utils.retrieve_corners_from_image">retrieve_corners_from_image() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.utils.rolling_speed.html#deepof.utils.rolling_speed">rolling_speed() (in module deepof.utils)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.utils.rolling_window.html#deepof.utils.rolling_window">rolling_window() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.annotation_utils.rotate.html#deepof.annotation_utils.rotate">rotate() (in module deepof.annotation_utils)</a>
<ul>
<li><a href="_generated/deepof.utils.rotate.html#deepof.utils.rotate">(in module deepof.utils)</a>
</li>
</ul></li>
<li><a href="_generated/deepof.utils.rupture_per_experiment.html#deepof.utils.rupture_per_experiment">rupture_per_experiment() (in module deepof.utils)</a>
</li>
</ul></td>
</tr></table>
<h2 id="S">S</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.utils.scale_animal.html#deepof.utils.scale_animal">scale_animal() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.utils.scale_table.html#deepof.utils.scale_table">scale_table() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.model_utils.select_contrastive_loss.html#deepof.model_utils.select_contrastive_loss">select_contrastive_loss() (in module deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.post_hoc.select_time_bin.html#deepof.post_hoc.select_time_bin">select_time_bin() (in module deepof.post_hoc)</a>
</li>
<li><a href="_generated/deepof.post_hoc.separation_between_conditions.html#deepof.post_hoc.separation_between_conditions">separation_between_conditions() (in module deepof.post_hoc)</a>
</li>
<li><a href="_generated/deepof.utils.set_missing_animals.html#deepof.utils.set_missing_animals">set_missing_animals() (in module deepof.utils)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.utils.simplify_polygon.html#deepof.utils.simplify_polygon">simplify_polygon() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.utils.smooth_boolean_array.html#deepof.utils.smooth_boolean_array">smooth_boolean_array() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.utils.smooth_mult_trajectory.html#deepof.utils.smooth_mult_trajectory">smooth_mult_trajectory() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.annotation_utils.sniff_object.html#deepof.annotation_utils.sniff_object">sniff_object() (in module deepof.annotation_utils)</a>
</li>
<li><a href="_generated/deepof.utils.split_with_breakpoints.html#deepof.utils.split_with_breakpoints">split_with_breakpoints() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.utils.str2bool.html#deepof.utils.str2bool">str2bool() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.annotation_utils.supervised_tagging.html#deepof.annotation_utils.supervised_tagging">supervised_tagging() (in module deepof.annotation_utils)</a>
</li>
</ul></td>
</tr></table>
<h2 id="T">T</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.utils.tab2polar.html#deepof.utils.tab2polar">tab2polar() (in module deepof.utils)</a>
</li>
<li><a href="_generated/deepof.data.TableDict.html#deepof.data.TableDict">TableDict (class in deepof.data)</a>
</li>
<li><a href="_generated/deepof.visuals.tag_annotated_frames.html#deepof.visuals.tag_annotated_frames">tag_annotated_frames() (in module deepof.visuals)</a>
</li>
<li><a href="_generated/deepof.annotation_utils.tagged_video_output.html#deepof.annotation_utils.tagged_video_output">tagged_video_output() (in module deepof.annotation_utils)</a>
</li>
<li><a href="_generated/deepof.post_hoc.train_supervised_cluster_detectors.html#deepof.post_hoc.train_supervised_cluster_detectors">train_supervised_cluster_detectors() (in module deepof.post_hoc)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.model_utils.TransformerDecoder.html#deepof.model_utils.TransformerDecoder">TransformerDecoder (class in deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.model_utils.TransformerDecoderLayer.html#deepof.model_utils.TransformerDecoderLayer">TransformerDecoderLayer (class in deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.model_utils.TransformerEncoder.html#deepof.model_utils.TransformerEncoder">TransformerEncoder (class in deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.model_utils.TransformerEncoderLayer.html#deepof.model_utils.TransformerEncoderLayer">TransformerEncoderLayer (class in deepof.model_utils)</a>
</li>
<li><a href="_generated/deepof.model_utils.tune_search.html#deepof.model_utils.tune_search">tune_search() (in module deepof.model_utils)</a>
</li>
</ul></td>
</tr></table>
<h2 id="V">V</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.hypermodels.VaDE.html#deepof.hypermodels.VaDE">VaDE (class in deepof.hypermodels)</a>
<ul>
<li><a href="_generated/deepof.models.VaDE.html#deepof.models.VaDE">(class in deepof.models)</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_generated/deepof.models.VectorQuantizer.html#deepof.models.VectorQuantizer">VectorQuantizer (class in deepof.models)</a>
</li>
<li><a href="_generated/deepof.hypermodels.VQVAE.html#deepof.hypermodels.VQVAE">VQVAE (class in deepof.hypermodels)</a>
<ul>
<li><a href="_generated/deepof.models.VQVAE.html#deepof.models.VQVAE">(class in deepof.models)</a>
</li>
</ul></li>
</ul></td>
</tr></table>
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