Morphology-Classification
latest
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Outdated stages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
Morphology-Classification
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morphoclass.console.cmd_preprocess_dataset module
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morphoclass.console.cmd_preprocess_dataset module
ΒΆ
The preprocess-dataset subcommand.