CNN Module

• CNN
  • CNN Model Class
    • build_cnn_network()
  • CNN Train Module
    • train_cnn()
  • CNN Trainer Wrapper
    • CNNTrainer
• CNN Model
  • Convolutions Modules
    • GeLU
      • GeLU.forward()
    • convolution()
    • SingleConvolution
    • DoubleConvolution
    • RecurrentDoubleConvolution
      • RecurrentDoubleConvolution.forward()
  • Generalize Encoder Module
    • EncoderBlock
      • EncoderBlock.dropout
      • EncoderBlock.forward()
    • build_encoder()
  • Generalize Decoder Module
    • DecoderBlockCNN
      • DecoderBlockCNN.dropout
      • DecoderBlockCNN.deconv_module
      • DecoderBlockCNN.forward()
    • DecoderBlockRCNN
      • DecoderBlockRCNN.dropout
      • DecoderBlockRCNN.deconv_res_module
      • DecoderBlockRCNN.forward()
    • DecoderBlockUnet3Plus
      • DecoderBlockUnet3Plus.dropout
      • DecoderBlockUnet3Plus.deconv
      • DecoderBlockUnet3Plus.forward()
    • build_decoder()
  • Weight Initialization
    • weights_init_kaiming()
    • init_weights()
• DataLoader
  • Image Augmentation
    • CenterCrop
    • RandomFlip
    • RandomRotation
    • ComposeRandomTransformation
    • preprocess()
  • DataLoader
    • CNNDataset
    • PredictionDataset
  • Dataset Builder
    • build_train_dataset()
    • load_img_mask_data()
    • error_log_build_data()
• Data processing
  • Image patching - Image trimming
    • trim_with_stride()
    • trim_label_mask()
  • Image patching - Image stitching
    • StitchImages
    • generate_grid()
  • Utils
    • interpolate_generator()
    • interpolation()
    • draw_instances()
    • draw_semantic_membrane()
    • draw_instances_membrane()
    • draw_mask()
    • draw_circle()
    • draw_sphere()
    • scale_image()
    • nn_scaling()
    • linear_scaling()
    • area_scaling()
    • fourier_scaling()
• Utils
  • CNN Builder
    • BasicCNN
      • BasicCNN.update_patch_size()
      • BasicCNN.build_cnn_model()
    • UNet
      • UNet.forward()
    • ResUNet
      • ResUNet.forward()
    • UNet3Plus
      • UNet3Plus.encoder
      • UNet3Plus.decoder
      • UNet3Plus.dot_product()
      • UNet3Plus.forward()
    • FNet
      • FNet.update_patch_size()
      • FNet.build_cnn_model()
      • FNet.forward()
  • CNN Utils
    • number_of_features_per_level()
    • max_number_of_conv_layer()
    • normalize_image()
    • check_model_dict()

DIST Module

• DIST
  • DIST Model Class
    • BasicDIST
      • BasicDIST.embed_input()
      • BasicDIST.forward()
    • DIST
    • CDIST
    • build_dist_network()
  • DIST Train Module
    • train_dist()
  • DIST Trainer Wrapper
    • SparseDistTrainer
    • DistTrainer
    • CDistTrainer
• DIST Model
  • DIST layer wrapper
    • DistStack
      • DistStack.forward()
    • DistLayer
      • DistLayer.update_nodes()
      • DistLayer.update_edges()
      • DistLayer.forward()
  • DIST graph update-modules
    • PairBiasSelfAttention
      • PairBiasSelfAttention.forward()
    • ComparisonLayer
      • ComparisonLayer.forward()
    • TriangularEdgeUpdate
      • TriangularEdgeUpdate.forward()
    • QuadraticEdgeUpdate
      • QuadraticEdgeUpdate.forward()
    • MultiHeadAttention
      • MultiHeadAttention.reset_parameters()
      • MultiHeadAttention.forward()
    • SelfAttention2D
      • SelfAttention2D.forward()
    • GeluFeedForward
      • GeluFeedForward.forward()
  • Feature embedding
    • NodeEmbedding
      • NodeEmbedding.forward()
    • EdgeEmbedding
      • EdgeEmbedding.forward()
• DataLoader
  • General DataLoader
    • BasicDataset
      • BasicDataset.save_temp()
      • BasicDataset.load_temp()
      • BasicDataset.list_to_tensor()
  • Specialized DataLoader’s
    • Filament structure DataSet
      • FilamentDataset
      • PartnetDataset
    • ScanNet V2 synthetic DataSet
      • ScannetDataset
    • ScanNet V2 with RGB values synthetic DataSet
      • ScannetColorDataset
    • Stanford S3DIS DataSet
      • Stanford3DDataset
  • Helper Functions
    • Build dataloader
      • build_dataset()
    • Point Cloud Augmentation
      • preprocess_data()
      • BuildGraph
      • Crop2D3D
        • Crop2D3D.get_xyz_position()
      • upsample_pc()
    • Patch dataset
      • PatchDataSet
        • PatchDataSet.boundary_box()
        • PatchDataSet.center_patch()
        • PatchDataSet.points_in_patch()
        • PatchDataSet.optimal_patches()
        • PatchDataSet.normalize_idx()
        • PatchDataSet.output_format()
        • PatchDataSet.patched_dataset()
• Utils
  • Build point cloud from image
    • BuildPointCloud
      • BuildPointCloud.check_data()
      • BuildPointCloud.build_point_cloud()
    • draw_line()
    • quadratic_bezier()
    • draw_curved_line()
    • draw_circle()
    • draw_sphere()
    • draw_sheet()
    • create_simulated_dataset()
  • Segment point cloud from graph
    • PropGreedyGraphCut
      • PropGreedyGraphCut.preprocess_connections()
      • PropGreedyGraphCut.patch_to_segment()
  • General Utils
    • pc_median_dist()
    • point_in_bb()
    • DownSampling
      • DownSampling.pc_down_sample()
    • VoxelDownSampling
      • VoxelDownSampling.pc_down_sample()
    • RandomDownSampling
      • RandomDownSampling.pc_down_sample()
    • check_model_dict()

Analysis Module

• Analysis
  • Analysis -> Analysis wrappers
    • analyse_filaments()
    • save_analysis()
    • analyse_filaments_list()
    • analyse_mt_classes()
  • Analysis -> Filament Structure
    • assign_filaments_to_poles()
  • Analysis -> Geometry metrics
    • curvature()
    • curvature_list()
    • tortuosity()
    • tortuosity_list()
    • total_length()
    • length_list()
    • angle_between_vectors()
    • intensity()
    • pixel_intensity()
    • thicken_line_coordinates()
    • intensity_list()
• MT classification
  • MT Classification - Main
    • MicrotubuleClassifier
      • MicrotubuleClassifier.get_vertices_file()
      • MicrotubuleClassifier.get_filament_file()
      • MicrotubuleClassifier.get_poles_file()
      • MicrotubuleClassifier.correct_data()
      • MicrotubuleClassifier.get_filament_endpoints()
      • MicrotubuleClassifier.assign_to_kmts()
      • MicrotubuleClassifier.kmts_inside_outside()
      • MicrotubuleClassifier.assign_to_mid_mt()
      • MicrotubuleClassifier.assign_to_int_mt()
      • MicrotubuleClassifier.assign_to_bridge_mt()
      • MicrotubuleClassifier.assign_mt_with_crossing()
      • MicrotubuleClassifier.classified_MTs()
      • MicrotubuleClassifier.get_classified_indices()
      • MicrotubuleClassifier.get_classified_fibers()
      • MicrotubuleClassifier.get_filaments()
      • MicrotubuleClassifier.get_vertices()
      • MicrotubuleClassifier.get_poles()
  • MT Classification - Utils
    • count_true_groups()
    • distances_of_ends_to_surface()
    • distance_to_the_pole()
    • divide_into_sequences()
    • fill_gaps()
    • pick_pole_to_surfaces()
    • points_on_mesh_knn()
    • select_mt_ids_within_bb()
    • assign_filaments_to_poles()
• Filament Utils
  • resample_filament()
  • sort_segments()
  • sort_segment()
  • reorder_segments_id()
  • smooth_spline()
  • sort_by_length()
  • cut_150_degree()
  • Analysis -> Spatial Graph Utils
    • FilterConnectedNearSegments
      • FilterConnectedNearSegments.splines_direction()
      • FilterConnectedNearSegments.marge_splines()
    • FilterSpatialGraph
    • SpatialGraphCompare
    • ComputeConfidenceScore
      • ComputeConfidenceScore.normalized_length()
      • ComputeConfidenceScore.combined_smoothness()
    • compare_splines_probability()

Global Functions

• AWS
  • AWS API
    • get_benchmark_aws()
    • put_benchmark_aws()
    • get_all_version_aws()
    • get_model_aws()
    • get_weights_aws()
    • aws_check_with_temp()
    • aws_check_pkg_with_temp()
  • Over-the-Air Update API
    • ota_update()
    • main()
• Data Handlers
  • Import data formats
    • ImportDataFromAmira
      • ImportDataFromAmira.get_points()
      • ImportDataFromAmira.get_vertex()
      • ImportDataFromAmira.get_segmented_points()
      • ImportDataFromAmira.get_labels()
      • ImportDataFromAmira.get_image()
      • ImportDataFromAmira.get_pixel_size()
      • ImportDataFromAmira.get_surface()
    • load_tiff()
    • mrc_read_header()
    • mrc_write_header()
    • mrc_mode()
    • load_am()
    • load_am_surf()
    • load_mrc_file()
    • load_nd2_file()
    • load_ply_scannet()
    • load_ply_partnet()
    • load_txt_s3dis()
    • load_s3dis_scene()
    • load_image()
  • Export data formats
    • NumpyToAmira
      • NumpyToAmira.check_3d()
      • NumpyToAmira.export_amira()
    • to_mrc()
    • to_am()
    • to_stl()
  • Image normalization
    • adaptive_threshold()
    • SimpleNormalize
    • MinMaxNormalize
    • MeanStdNormalize
    • RescaleNormalize
    • FFTNormalize
      • FFTNormalize.gmm_fit()
      • FFTNormalize.norm_fit()
• Trainer
  • General NN trainer
    • ISR_LR
      • ISR_LR.load_state_dict()
      • ISR_LR.state_dict()
      • ISR_LR.step()
      • ISR_LR.zero_grad()
      • ISR_LR.get_lr_scale()
    • BasicTrainer
      • BasicTrainer.run_trainer()
  • Loss functions
    • AbstractLoss
      • AbstractLoss.activate()
      • AbstractLoss.ignor_diagonal()
      • AbstractLoss.initialize_tensors()
      • AbstractLoss.forward()
    • AdaptiveDiceLoss
      • AdaptiveDiceLoss.forward()
    • BCELoss
      • BCELoss.forward()
    • BCEGraphWiseLoss
      • BCEGraphWiseLoss.forward()
    • BCEDiceLoss
      • BCEDiceLoss.forward()
    • CELoss
      • CELoss.forward()
    • DiceLoss
      • DiceLoss.forward()
    • LaplacianEigenmapsLoss
      • LaplacianEigenmapsLoss.compute_laplacian()
      • LaplacianEigenmapsLoss.forward()
    • SoftSkeletonization
      • SoftSkeletonization.soft_skel()
      • SoftSkeletonization.forward()
    • ClBCELoss
      • ClBCELoss.forward()
    • ClDiceLoss
      • ClDiceLoss.forward()
    • SigmoidFocalLoss
      • SigmoidFocalLoss.forward()
    • WBCELoss
      • WBCELoss.forward()
    • BCEMSELoss
      • BCEMSELoss.forward()
  • Training metrics
    • compare_dict_metrics()
    • eval_graph_f1()
    • calculate_f1()
    • AP()
    • AP_instance()
    • AUC()
    • IoU()
    • mcov()
    • confusion_matrix()
    • normalize_image()
• Predictor
  • GeneralPredictor
    • GeneralPredictor.eta_predict
    • GeneralPredictor.omit_format
    • GeneralPredictor.create_headers()
    • GeneralPredictor.init_check()
    • GeneralPredictor.build_NN()
    • GeneralPredictor.load_data()
    • GeneralPredictor.predict_cnn()
    • GeneralPredictor.predict_cnn_napari()
    • GeneralPredictor.postprocess_CNN()
    • GeneralPredictor.preprocess_DIST()
    • GeneralPredictor.predict_DIST()
    • GeneralPredictor.postprocess_DIST()
    • GeneralPredictor.get_file_list()
    • GeneralPredictor.log_tardis()
    • GeneralPredictor.save_semantic_mask()
    • GeneralPredictor.save_instance_PC()
  • Predictor
    • Predictor.predict()
• Helper Functions
  • tardis_helper()
• Logger
  • TARDIS log
    • print_progress_bar()
    • is_interactive()
    • TardisLogo
      • TardisLogo.clear_output()
      • TardisLogo.cell_width()
    • ContextFilter
      • ContextFilter.hostname
      • ContextFilter.filter()
  • TARDIS errors
    • standard_error_id()
    • TardisError
      • TardisError.cut_desc()
• Utils Functions
  • Device
    • get_device()
    • device_is_str()
  • Global Utils
    • get_n_params()
    • EarlyStopping
    • check_uint8()
• SetUp Environment
  • Dataset organizers
    • find_filtered_files()
    • move_train_dataset()
    • build_test_dataset()
  • Environment setup
    • build_new_dir()
    • build_temp_dir()
    • clean_up()
    • check_dir()
• Visualizer