Morphology-Classification
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Contents

  • Installation
    • Basic
    • Check the Installation
    • Development
    • Why an Installation Script?
      • 1. Install the morphoclass package as usual
      • 2. Install/re-install torch manually
      • 3. Install torch-geometric manually
    • DeepWalk and CleanLab
  • Project Tree
  • Docker
  • Building the Documentation
  • CLI
    • Overview
    • Subcommands
  • DVC
    • Data pre-processing
    • Feature extraction
    • Training
      • Example model config
      • Example splitter config
      • Output of the morphoclass train command
    • Evaluation
    • Outdated stages
    • DVC Cache
  • Data
    • Loading Datasets
      • From a list of paths
      • From a CSV file
      • From a structured directory
    • Data Objects
    • Filters
    • Transforms
      • Pre-Processing and Augmentation
      • Feature Extraction and Adjacency Matrix
      • Feature Scalers
    • Persistence Images and Diagrams
  • Models - GNNs
    • Loading Data
    • Training
    • Evaluating
  • Models - CNNs
    • Loading Data
    • Training
    • Evaluating
  • Models - PersLay
    • Data Loading
    • Training
    • Evaluation
  • Custom Models and Layers
    • Layers
      • Graph Convolution Layers
      • PersLay Layer
      • Pooling Layers
      • Other Layers
    • Models
    • Example
  • Example - Design a GNN
    • Data
    • The Net
    • The Training Loop
    • Visualizing Results

API

  • morphoclass
    • Subpackages
      • morphoclass.console package
        • Submodules
          • morphoclass.console.cmd_evaluate module
          • morphoclass.console.cmd_extract_features module
          • morphoclass.console.cmd_morphometrics module
          • morphoclass.console.cmd_organise_dataset module
          • morphoclass.console.cmd_performance_table module
          • morphoclass.console.cmd_plot_dataset_stats module
          • morphoclass.console.cmd_preprocess_dataset module
          • morphoclass.console.cmd_train module
          • morphoclass.console.cmd_xai module
          • morphoclass.console.dataset_preprocessor module
          • morphoclass.console.evaluate module
          • morphoclass.console.helpers module
          • morphoclass.console.main module
          • morphoclass.console.outlier_detection module
          • morphoclass.console.performance_table module
          • morphoclass.console.stats_plotter module
          • morphoclass.console.transfer_learning module
        • Module contents
      • morphoclass.data package
        • Submodules
          • morphoclass.data.filters module
          • morphoclass.data.morphology_data module
          • morphoclass.data.morphology_data_loader module
          • morphoclass.data.morphology_dataset module
          • morphoclass.data.tns_dataset module
        • Module contents
      • morphoclass.features package
        • Submodules
          • morphoclass.features.non_graph module
        • Module contents
      • morphoclass.layers package
        • Submodules
          • morphoclass.layers.attention_global_pool module
          • morphoclass.layers.bidirectional_block module
          • morphoclass.layers.bidirectional_res_block module
          • morphoclass.layers.cat module
          • morphoclass.layers.cheb_conv module
          • morphoclass.layers.cheb_conv_separable module
          • morphoclass.layers.perslay module
          • morphoclass.layers.running_std module
          • morphoclass.layers.tree_lstm_pool module
        • Module contents
      • morphoclass.models package
        • Submodules
          • morphoclass.models.bidirectional_net module
          • morphoclass.models.cnnet module
          • morphoclass.models.concatecnnet module
          • morphoclass.models.concatenet module
          • morphoclass.models.coriander_net module
          • morphoclass.models.hbnet module
          • morphoclass.models.man_net module
          • morphoclass.models.man_res_nets module
          • morphoclass.models.multi_adj_net module
        • Module contents
      • morphoclass.morphometrics package
        • Submodules
          • morphoclass.morphometrics.cli module
        • Module contents
      • morphoclass.report package
        • Submodules
          • morphoclass.report.plumbing module
          • morphoclass.report.xai module
        • Module contents
      • morphoclass.training package
        • Subpackages
          • morphoclass.training.reports package
            • Submodules
              • morphoclass.training.reports.transfer_learning_report module
            • Module contents
        • Submodules
          • morphoclass.training.cli module
          • morphoclass.training.rd_dataset_prep module
          • morphoclass.training.tns_utils module
          • morphoclass.training.trainers module
          • morphoclass.training.training_config module
          • morphoclass.training.training_log module
          • morphoclass.training.training_loop_cv module
          • morphoclass.training.training_loop_loo module
          • morphoclass.training.training_loop_regression module
          • morphoclass.training.training_loop_simple module
          • morphoclass.training.transfer_learning module
        • Module contents
      • morphoclass.transforms package
        • Subpackages
          • morphoclass.transforms.augmentors package
            • Submodules
              • morphoclass.transforms.augmentors.add_nodes_at_intervals module
              • morphoclass.transforms.augmentors.add_random_points_to_reduction_mask module
              • morphoclass.transforms.augmentors.add_section_middle_points module
              • morphoclass.transforms.augmentors.apply_node_reduction_masks module
              • morphoclass.transforms.augmentors.branching_only_neurites module
              • morphoclass.transforms.augmentors.branching_only_neuron module
              • morphoclass.transforms.augmentors.equalize_node_counts module
              • morphoclass.transforms.augmentors.extract_branching_node_reduction_masks module
              • morphoclass.transforms.augmentors.orient_apicals module
              • morphoclass.transforms.augmentors.orient_neuron module
              • morphoclass.transforms.augmentors.random_jitter module
              • morphoclass.transforms.augmentors.random_rotation module
              • morphoclass.transforms.augmentors.random_stretching module
            • Module contents
          • morphoclass.transforms.edge_features package
            • Submodules
              • morphoclass.transforms.edge_features.extract_distance_weights module
              • morphoclass.transforms.edge_features.extract_edge_features module
              • morphoclass.transforms.edge_features.extract_edge_index module
            • Module contents
          • morphoclass.transforms.global_features package
            • Submodules
              • morphoclass.transforms.global_features.abstract_global_feature_extractor module
              • morphoclass.transforms.global_features.average_branch_order module
              • morphoclass.transforms.global_features.average_radius module
              • morphoclass.transforms.global_features.extract_maximal_apical_path_length module
              • morphoclass.transforms.global_features.extract_number_branch_points module
              • morphoclass.transforms.global_features.extract_number_leaves module
              • morphoclass.transforms.global_features.total_path_length module
            • Module contents
          • morphoclass.transforms.node_features package
            • Submodules
              • morphoclass.transforms.node_features.extract_branching_angles module
              • morphoclass.transforms.node_features.extract_const_feature module
              • morphoclass.transforms.node_features.extract_coordinates module
              • morphoclass.transforms.node_features.extract_diameters module
              • morphoclass.transforms.node_features.extract_distances module
              • morphoclass.transforms.node_features.extract_node_features module
              • morphoclass.transforms.node_features.extract_node_onehot_properties module
              • morphoclass.transforms.node_features.extract_path_distances module
              • morphoclass.transforms.node_features.extract_radial_distances module
              • morphoclass.transforms.node_features.extract_vertical_distances module
            • Module contents
          • morphoclass.transforms.scalers package
            • Submodules
              • morphoclass.transforms.scalers.abstract_scaler module
              • morphoclass.transforms.scalers.manual_scaler module
              • morphoclass.transforms.scalers.min_max_scaler module
              • morphoclass.transforms.scalers.robust_scaler module
              • morphoclass.transforms.scalers.standard_scaler module
            • Module contents
        • Submodules
          • morphoclass.transforms.add_one_hot_labels module
          • morphoclass.transforms.compose module
          • morphoclass.transforms.extract_tmd_neurites module
          • morphoclass.transforms.extract_tmd_neuron module
          • morphoclass.transforms.global_feature_to_label module
          • morphoclass.transforms.helper module
          • morphoclass.transforms.make_copy module
          • morphoclass.transforms.zero_out_features module
        • Module contents
      • morphoclass.unsupervised package
        • Submodules
          • morphoclass.unsupervised.plotting module
        • Module contents
      • morphoclass.xai package
        • Submodules
          • morphoclass.xai.embedding_extractor module
          • morphoclass.xai.embedding_visualization module
          • morphoclass.xai.grad_cam_explainer module
          • morphoclass.xai.grad_cam_on_models module
          • morphoclass.xai.model_attributions module
          • morphoclass.xai.node_saliency module
        • Module contents
    • Submodules
      • morphoclass.cleanlab module
      • morphoclass.constants module
      • morphoclass.deepwalk module
      • morphoclass.metrics module
      • morphoclass.model_utils module
      • morphoclass.orientation module
      • morphoclass.types module
      • morphoclass.utils module
      • morphoclass.vis module
    • Module contents
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