LICENSE.md
README.md
pyproject.toml
setup.py
htc/__init__.py
htc/cli.py
htc/run_info.py
htc/settings.py
htc/settings_seg.py
htc/cluster/ClusterConnection.py
htc/cluster/RunGenerator.py
htc/cluster/UpdateCluster.py
htc/cluster/__init__.py
htc/cluster/utils.py
htc/cpp/ParallelExecution.h
htc/cpp/__init__.py
htc/cpp/bindings.cpp
htc/cpp/colorchecker_automask.cpp
htc/cpp/evaluate_superpixels.cpp
htc/cpp/hierarchical_bootstrapping.h
htc/cpp/kfold_combinations.cpp
htc/cpp/map_label_image.cpp
htc/cpp/nunique.cpp
htc/cpp/segmentation_mask.cpp
htc/cpp/tensor_mapping.h
htc/data_exploration/__init__.py
htc/data_processing/DatasetIteration.py
htc/data_processing/__init__.py
htc/data_processing/run_l1_normalization.py
htc/data_processing/run_median_spectra.py
htc/data_processing/run_parameter_images.py
htc/data_processing/run_raw16.py
htc/data_processing/run_standardization.py
htc/data_processing/run_superpixel_prediction.py
htc/evaluation/__init__.py
htc/evaluation/analyze_tfevents.py
htc/evaluation/evaluate_images.py
htc/evaluation/evaluate_superpixels.py
htc/evaluation/ranking.py
htc/evaluation/run_compare_runs.py
htc/evaluation/run_ranking_lr.py
htc/evaluation/run_table_generation.py
htc/evaluation/utils.py
htc/evaluation/metrics/BrierScore.py
htc/evaluation/metrics/ECE.py
htc/evaluation/metrics/NSDToleranceEstimation.py
htc/evaluation/metrics/__init__.py
htc/evaluation/metrics/scores.py
htc/evaluation/model_comparison/__init__.py
htc/evaluation/model_comparison/dataset_size.py
htc/evaluation/model_comparison/paper_runs.py
htc/evaluation/model_comparison/run_challengeR_table.py
htc/fonts/__init__.py
htc/fonts/set_font.py
htc/model_processing/ImageConsumer.py
htc/model_processing/Predictor.py
htc/model_processing/Runner.py
htc/model_processing/SinglePredictionTable.py
htc/model_processing/SinglePredictor.py
htc/model_processing/TestEnsemble.py
htc/model_processing/TestLeaveOneOutPredictor.py
htc/model_processing/TestPredictor.py
htc/model_processing/ValidationPredictor.py
htc/model_processing/__init__.py
htc/model_processing/run_image_figures.py
htc/model_processing/run_inference.py
htc/model_processing/run_median_test_table.py
htc/model_processing/run_multiple.py
htc/model_processing/run_tables.py
htc/models/__init__.py
htc/models/run_dataset_size.py
htc/models/run_generate_configs.py
htc/models/run_inference_timeit.py
htc/models/run_model_comparison.py
htc/models/run_pretrained_semantic_models.py
htc/models/run_seed_variations.py
htc/models/run_training.py
htc/models/common/ChannelWeights.py
htc/models/common/EvaluationMixin.py
htc/models/common/ForwardHookPromise.py
htc/models/common/HSI3dChannel.py
htc/models/common/HTCDataset.py
htc/models/common/HTCDatasetStream.py
htc/models/common/HTCLightning.py
htc/models/common/HTCModel.py
htc/models/common/Heads.py
htc/models/common/HierarchicalSampler.py
htc/models/common/MetricAggregation.py
htc/models/common/MetricAggregationClassification.py
htc/models/common/SharedMemoryDatasetMixin.py
htc/models/common/StreamDataLoader.py
htc/models/common/StreamImageDataLoader.py
htc/models/common/__init__.py
htc/models/common/class_weights.py
htc/models/common/distance_correlation.py
htc/models/common/functions.py
htc/models/common/loss.py
htc/models/common/torch_helpers.py
htc/models/common/transforms.py
htc/models/common/utils.py
htc/models/data/DataSpecification.py
htc/models/data/SpecsGeneration.py
htc/models/data/__init__.py
htc/models/data/pigs_semantic-only_5foldsV2.json
htc/models/data/pigs_semantic-only_dataset-size_repetitions=5V2.json
htc/models/data/run_pig_dataset.py
htc/models/data/run_size_dataset.py
htc/models/image/DatasetImage.py
htc/models/image/DatasetImageBatch.py
htc/models/image/DatasetImageStream.py
htc/models/image/LightningImage.py
htc/models/image/ModelImage.py
htc/models/image/__init__.py
htc/models/image/configs/default.json
htc/models/image/configs/default_parameters.json
htc/models/image/configs/default_rgb.json
htc/models/image/configs/spxs.json
htc/models/median_pixel/DatasetMedianPixel.py
htc/models/median_pixel/LightningMedianPixel.py
htc/models/median_pixel/__init__.py
htc/models/median_pixel/configs/default.json
htc/models/median_pixel/configs/median_18classes.json
htc/models/patch/DatasetPatchImage.py
htc/models/patch/DatasetPatchStream.py
htc/models/patch/LightningPatch.py
htc/models/patch/__init__.py
htc/models/patch/configs/default.json
htc/models/patch/configs/default_64.json
htc/models/patch/configs/default_64_parameters.json
htc/models/patch/configs/default_64_rgb.json
htc/models/patch/configs/default_parameters.json
htc/models/patch/configs/default_rgb.json
htc/models/pixel/DatasetPixelStream.py
htc/models/pixel/LightningPixel.py
htc/models/pixel/ModelPixel.py
htc/models/pixel/ModelPixelRGB.py
htc/models/pixel/__init__.py
htc/models/pixel/configs/default.json
htc/models/pixel/configs/default_parameters.json
htc/models/pixel/configs/default_rgb.json
htc/models/superpixel_classification/DatasetSuperpixelImage.py
htc/models/superpixel_classification/DatasetSuperpixelStream.py
htc/models/superpixel_classification/LightningSuperpixelClassification.py
htc/models/superpixel_classification/ModelSuperpixelClassification.py
htc/models/superpixel_classification/__init__.py
htc/models/superpixel_classification/configs/default.json
htc/models/superpixel_classification/configs/default_parameters.json
htc/models/superpixel_classification/configs/default_rgb.json
htc/rater_variability/__init__.py
htc/rater_variability/rater_evaluation.py
htc/rater_variability/run_nsd_thresholds.py
htc/special/__init__.py
htc/special/run_python_versions.py
htc/tivita/DataPath.py
htc/tivita/DataPathMultiorgan.py
htc/tivita/DataPathMultiorganNamed.py
htc/tivita/DataPathReference.py
htc/tivita/DataPathSepsis.py
htc/tivita/DataPathTivita.py
htc/tivita/DatasetSettings.py
htc/tivita/__init__.py
htc/tivita/colorscale.py
htc/tivita/hsi.py
htc/tivita/metadata.py
htc/tivita/rgb.py
htc/utils/AdvancedJSONEncoder.py
htc/utils/ColorcheckerReader.py
htc/utils/Config.py
htc/utils/Datasets.py
htc/utils/DelayedFileHandler.py
htc/utils/DomainMapper.py
htc/utils/DuplicateFilter.py
htc/utils/JSONSchemaMeta.py
htc/utils/LDA.py
htc/utils/LabelMapping.py
htc/utils/MeasureTime.py
htc/utils/MultiPath.py
htc/utils/PathHashMapper.py
htc/utils/SLICWrapper.py
htc/utils/SpectrometerReader.py
htc/utils/Task.py
htc/utils/_MedianTableHelper.py
htc/utils/__init__.py
htc/utils/blosc_compression.py
htc/utils/colors.py
htc/utils/docs_helpers.py
htc/utils/file_transfer.py
htc/utils/general.py
htc/utils/helper_functions.py
htc/utils/import_extra.py
htc/utils/parallel.py
htc/utils/paths.py
htc/utils/renderjson.js
htc/utils/run_system_monitor.py
htc/utils/specular_highlights.py
htc/utils/sqldf.py
htc/utils/test_helpers.py
htc/utils/type_from_string.py
htc/utils/unify_path.py
htc/utils/visualization.py
htc/utils/mitk/PathAnnotations.py
htc/utils/mitk/__init__.py
htc/utils/mitk/mitk_masks.py
htc/utils/mitk/run_mitk_dataset.py
htc/utils/mitk/run_mitk_task_list.py
htc_projects/__init__.py
htc_projects/atlas/__init__.py
htc_projects/atlas/settings_atlas.py
htc_projects/atlas/tables.py
htc_projects/atlas/data/__init__.py
htc_projects/atlas/data/run_atlas_dataset.py
htc_projects/atlas/data/tissue-atlas_loocv_test-8_seed-0_cam-118.json
htc_projects/atlas/model_processing/__init__.py
htc_projects/atlas/model_processing/run_test_table_generation.py
htc_projects/atlas_open/__init__.py
htc_projects/atlas_open/profiles.py
htc_projects/atlas_open/run_label_profiles.py
htc_projects/atlas_open/run_readme_gif.py
htc_projects/benchmarking/__init__.py
htc_projects/benchmarking/run_benchmark.py
htc_projects/benchmarking/settings_benchmarking.py
htc_projects/benchmarking/configs/blosc.json
htc_projects/benchmarking/configs/fp16.json
htc_projects/benchmarking/configs/gpu-aug.json
htc_projects/benchmarking/configs/original.json
htc_projects/benchmarking/configs/ring-buffer.json
htc_projects/benchmarking/data/__init__.py
htc_projects/benchmarking/data/pigs_semantic-all_train-only.json
htc_projects/benchmarking/data/run_benchmarking_dataset.py
htc_projects/benchmarking/models/LightningImageBench.py
htc_projects/benchmarking/models/__init__.py
htc_projects/context/__init__.py
htc_projects/context/context_transforms.py
htc_projects/context/settings_context.py
htc_projects/context/extra_datasets/__init__.py
htc_projects/context/extra_datasets/run_dataset_tables.py
htc_projects/context/manipulated_datasets/__init__.py
htc_projects/context/manipulated_datasets/run_context_evaluation_table.py
htc_projects/context/manipulated_datasets/utils.py
htc_projects/context/models/ContextEvaluationMixin.py
htc_projects/context/models/LightningImageContext.py
htc_projects/context/models/__init__.py
htc_projects/context/models/context_evaluation.py
htc_projects/context/models/run_baseline_tables.py
htc_projects/context/models/run_context_test_tables.py
htc_projects/context/models/run_glove_baseline_runs.py
htc_projects/context/models/run_pretrained_context_models.py
htc_projects/context/models/run_transform_runs.py
htc_projects/context/models/visualization.py
htc_projects/context/models/configs/context-glove.json
htc_projects/context/models/configs/context.json
htc_projects/context/models/configs/organ_transplantation_0.8.json
htc_projects/context/models/data/__init__.py
htc_projects/context/models/data/pigs_semantic-only_5foldsV2_glove.json
htc_projects/context/models/data/run_glove_dataset.py
htc_projects/context/neighbour/__init__.py
htc_projects/context/neighbour/find_neighbour_valid_pixels.py
htc_projects/context/neighbour/find_normalized_neighbour_matrix.py
htc_projects/rat/__init__.py
htc_projects/rat/settings_rat.py
htc_projects/rat/tables.py
htc_projects/species/ProjectionLearner.py
htc_projects/species/__init__.py
htc_projects/species/apply_transforms_paths.py
htc_projects/species/run_create_projections.py
htc_projects/species/run_pretrained_species_models.py
htc_projects/species/run_species_models.py
htc_projects/species/run_transform_spectra.py
htc_projects/species/settings_species.py
htc_projects/species/species_evaluation.py
htc_projects/species/species_transforms.py
htc_projects/species/tables.py
htc_projects/species/configs/baseline_human.json
htc_projects/species/configs/baseline_pig.json
htc_projects/species/configs/baseline_rat.json
htc_projects/species/configs/projected_pig2pig.json
htc_projects/species/data/__init__.py
htc_projects/species/data/human_semantic-only+pig-p+rat-p_physiological-kidney_5folds_nested-0-2_mapping-12_seed-0.json
htc_projects/species/data/human_semantic-only+pig-p+rat-p_physiological-kidney_5folds_nested-1-2_mapping-12_seed-0.json
htc_projects/species/data/human_semantic-only+pig-p+rat-p_physiological-kidney_5folds_nested-2-2_mapping-12_seed-0.json
htc_projects/species/data/human_semantic-only_physiological-kidney_5folds_nested-0-2_mapping-12_seed-0.json
htc_projects/species/data/human_semantic-only_physiological-kidney_5folds_nested-1-2_mapping-12_seed-0.json
htc_projects/species/data/human_semantic-only_physiological-kidney_5folds_nested-2-2_mapping-12_seed-0.json
htc_projects/species/data/kidney_projection_train=P091,P095,P097,P098.json
htc_projects/species/data/pig_semantic-only_5folds_nested-0-2_mapping-12_seed-0.json
htc_projects/species/data/pig_semantic-only_5folds_nested-1-2_mapping-12_seed-0.json
htc_projects/species/data/pig_semantic-only_5folds_nested-2-2_mapping-12_seed-0.json
htc_projects/species/data/rat_semantic-only_5folds_nested-0-2_mapping-12_seed-0.json
htc_projects/species/data/rat_semantic-only_5folds_nested-1-2_mapping-12_seed-0.json
htc_projects/species/data/rat_semantic-only_5folds_nested-2-2_mapping-12_seed-0.json
htc_projects/species/data/run_human_physiological_dataset.py
htc_projects/species/data/run_kidney_projection_dataset.py
htc_projects/species/data/run_pig_semantic_nested_dataset.py
htc_projects/species/data/run_rat_semantic_dataset.py
htc_projects/species/model_processing/__init__.py
htc_projects/species/model_processing/run_icg_scores.py
htc_projects/species/model_processing/run_kidney_test_scores.py
htc_projects/species/model_processing/run_perfusion_scores.py
htc_projects/species/model_processing/run_physiological_scores.py
imsy_htc.egg-info/PKG-INFO
imsy_htc.egg-info/SOURCES.txt
imsy_htc.egg-info/dependency_links.txt
imsy_htc.egg-info/entry_points.txt
imsy_htc.egg-info/requires.txt
imsy_htc.egg-info/top_level.txt
tests/test_cli.py