Index

_

__call__() (panoptica.utils.edge_case_handling.EdgeCaseResult method) (panoptica.utils.edge_case_handling.MetricZeroTPEdgeCaseHandling method) (panoptica.utils.label_group._LabelGroupAny method) (panoptica.utils.label_group.LabelMergeGroup method) __eq__() (panoptica.utils.constants._Enum_Compare method) (panoptica.utils.edge_case_handling.MetricZeroTPEdgeCaseHandling method) __group_dictionary (panoptica.utils.segmentation_class._NoSegmentationClassGroups attribute) (panoptica.utils.segmentation_class.SegmentationClassGroups attribute) __labelmap (panoptica.utils.instancelabelmap.InstanceLabelMap attribute) __labels (panoptica.utils.segmentation_class.SegmentationClassGroups attribute) __repr__() (panoptica.utils.constants._Enum_Compare method) __str__() (panoptica.utils.constants._Enum_Compare method) (panoptica.utils.edge_case_handling.MetricZeroTPEdgeCaseHandling method) __surface_distances() (in module panoptica.metrics.assd) _abc_impl (panoptica.instance_approximator.ConnectedComponentsInstanceApproximator attribute) (panoptica.instance_approximator.InstanceApproximator attribute) (panoptica.instance_approximator.OneHotConnectedComponentsInstanceApproximator attribute) (panoptica.instance_matcher.InstanceMatchingAlgorithm attribute) (panoptica.instance_matcher.MaxBipartiteMatching attribute) (panoptica.instance_matcher.MaximizeMergeMatching attribute) (panoptica.instance_matcher.NaiveThresholdMatching attribute) (panoptica.instance_matcher.ThresholdBasedMatching attribute) (panoptica.utils.processing_pair._ProcessingPair attribute) (panoptica.utils.processing_pair._ProcessingPairInstanced attribute) (panoptica.utils.processing_pair.MatchedInstancePair attribute) (panoptica.utils.processing_pair.SemanticPair attribute) (panoptica.utils.processing_pair.UnmatchedInstancePair attribute) _approximate_instances() (panoptica.instance_approximator.ConnectedComponentsInstanceApproximator method) (panoptica.instance_approximator.InstanceApproximator method) (panoptica.instance_approximator.OneHotConnectedComponentsInstanceApproximator method) _average_surface_distance() (in module panoptica.metrics.assd) _average_symmetric_surface_distance() (in module panoptica.metrics.assd) _calculate_matching_metric_pairs() (panoptica.instance_matcher.InstanceMatchingAlgorithm method) _check_array_integrity() (in module panoptica.utils.processing_pair) _compute_centerline_dice() (in module panoptica.metrics.cldice) _compute_centerline_dice_coefficient() (in module panoptica.metrics.cldice) _compute_dice_coefficient() (in module panoptica.metrics.dice) _compute_instance_average_symmetric_surface_distance() (in module panoptica.metrics.assd) _compute_instance_iou() (in module panoptica.metrics.iou) _compute_instance_relative_volume_difference() (in module panoptica.metrics.relative_volume_difference) _compute_instance_volumetric_dice() (in module panoptica.metrics.dice) _compute_iou() (in module panoptica.metrics.iou) _compute_relative_volume_difference() (in module panoptica.metrics.relative_volume_difference) _count_unique_without_zeros() (in module panoptica.utils.numpy_utils) _create_cost_matrix() (panoptica.instance_matcher.MaxBipartiteMatching method) _distance_transform_edt() (in module panoptica.metrics.assd) _Enum_Compare (class in panoptica.utils.constants) _get_bbox_nd() (in module panoptica.utils.numpy_utils) _get_daemon() (panoptica.utils.parallel_processing.NoDaemonProcess method) _get_skeleton() (in module panoptica.metrics.cldice)

_get_smallest_fitting_uint() (in module panoptica.utils.numpy_utils) _intermediatesteps (panoptica.utils.processing_pair.IntermediateStepsData attribute) _LabelGroupAny (class in panoptica.utils.label_group) _load_from_config() (in module panoptica.utils.config) _load_from_config_by_name() (in module panoptica.utils.config) _load_from_config_by_path() (in module panoptica.utils.config) _load_yaml() (in module panoptica.utils.config) _match_instances() (panoptica.instance_matcher.InstanceMatchingAlgorithm method) (panoptica.instance_matcher.MaxBipartiteMatching method) (panoptica.instance_matcher.MaximizeMergeMatching method) (panoptica.instance_matcher.NaiveThresholdMatching method) (panoptica.instance_matcher.ThresholdBasedMatching method) _Metric (class in panoptica.metrics.metrics) _metric_function (panoptica.metrics.metrics._Metric attribute), [1] _NoSegmentationClassGroups (class in panoptica.utils.segmentation_class) _one_hot() (panoptica.instance_approximator.OneHotConnectedComponentsInstanceApproximator method) _original_n_preds (panoptica.utils.processing_pair._ProcessingPair property) (panoptica.utils.processing_pair._ProcessingPairInstanced property) _original_n_refs (panoptica.utils.processing_pair._ProcessingPair property) (panoptica.utils.processing_pair._ProcessingPairInstanced property) _ProcessingPair (class in panoptica.utils.processing_pair) _ProcessingPairInstanced (class in panoptica.utils.processing_pair) _register_class_to_yaml() (in module panoptica.utils.config) _register_helper_classes() (in module panoptica.utils.config) _register_permanently() (panoptica.utils.config.SupportsConfig class method) (panoptica.utils.constants._Enum_Compare class method) _save_to_config() (in module panoptica.utils.config) _save_to_config_by_name() (in module panoptica.utils.config) _save_to_config_by_path() (in module panoptica.utils.config) _save_yaml() (in module panoptica.utils.config) _set_daemon() (panoptica.utils.parallel_processing.NoDaemonProcess method) _solve_bipartite_matching() (panoptica.instance_matcher.MaxBipartiteMatching method) _unique_without_zeros() (in module panoptica.utils.numpy_utils) _yaml_repr() (panoptica.instance_approximator.ConnectedComponentsInstanceApproximator class method) (panoptica.instance_approximator.InstanceApproximator method) (panoptica.instance_approximator.OneHotConnectedComponentsInstanceApproximator class method) (panoptica.instance_matcher.InstanceMatchingAlgorithm method) (panoptica.instance_matcher.MaxBipartiteMatching class method) (panoptica.instance_matcher.MaximizeMergeMatching class method) (panoptica.instance_matcher.NaiveThresholdMatching class method) (panoptica.instance_matcher.ThresholdBasedMatching class method) (panoptica.utils.config.SupportsConfig class method) (panoptica.utils.edge_case_handling.EdgeCaseHandler class method) (panoptica.utils.edge_case_handling.EdgeCaseHandler method) (panoptica.utils.edge_case_handling.MetricZeroTPEdgeCaseHandling class method) (panoptica.utils.edge_case_handling.MetricZeroTPEdgeCaseHandling method) (panoptica.utils.label_group._LabelGroupAny class method) (panoptica.utils.label_group.LabelGroup class method) (panoptica.utils.segmentation_class._NoSegmentationClassGroups class method) (panoptica.utils.segmentation_class.SegmentationClassGroups class method)

A

add_intermediate_arr_data() (panoptica.utils.processing_pair.IntermediateStepsData method) add_intermediate_data() (panoptica.utils.processing_pair.IntermediateStepsData method) add_labelmap_entry() (panoptica.utils.instancelabelmap.InstanceLabelMap method), [1] ALL (panoptica.metrics.metrics.MetricMode attribute)

allow_many_to_one (panoptica.instance_matcher.NaiveThresholdMatching attribute) approximate_instances() (panoptica.instance_approximator.InstanceApproximator method) args (panoptica.utils.parallel_processing.NoDaemonProcess attribute) ASSD (panoptica.metrics.metrics.Metric attribute) AVG (panoptica.metrics.metrics.MetricMode attribute)

C

cc3d (panoptica.utils.constants.CCABackend attribute) cca_backend (panoptica.instance_approximator.ConnectedComponentsInstanceApproximator attribute) CCABackend (class in panoptica.utils.constants) CEDI (panoptica.metrics.metrics.Metric attribute) cl_score() (in module panoptica.metrics.cldice) clDSC (panoptica.metrics.metrics.Metric attribute) config_by_name() (in module panoptica.utils.filepath) config_dir_by_name() (in module panoptica.utils.filepath) ConnectedComponentsInstanceApproximator (class in panoptica.instance_approximator)

contains_and() (panoptica.utils.instancelabelmap.InstanceLabelMap method), [1] contains_or() (panoptica.utils.instancelabelmap.InstanceLabelMap method), [1] contains_pred() (panoptica.utils.instancelabelmap.InstanceLabelMap method), [1] contains_ref() (panoptica.utils.instancelabelmap.InstanceLabelMap method), [1] copy() (panoptica.utils.processing_pair._ProcessingPair method) (panoptica.utils.processing_pair._ProcessingPairInstanced method) (panoptica.utils.processing_pair.MatchedInstancePair method) crop (panoptica.utils.processing_pair._ProcessingPair attribute) crop_data() (panoptica.utils.processing_pair._ProcessingPair method)

D

daemon (panoptica.utils.parallel_processing.NoDaemonProcess attribute) (panoptica.utils.parallel_processing.NoDaemonProcess property) decreasing (panoptica.metrics.metrics._Metric attribute), [1] (panoptica.metrics.metrics.Metric property)

default_result (panoptica.utils.edge_case_handling.MetricZeroTPEdgeCaseHandling attribute) DirectValueMeta (class in panoptica.metrics.metrics) DSC (panoptica.metrics.metrics.Metric attribute)

E

EdgeCaseHandler (class in panoptica.utils.edge_case_handling) EdgeCaseResult (class in panoptica.utils.edge_case_handling) EdgeCaseZeroTP (class in panoptica.utils.edge_case_handling) empty_list_std (panoptica.utils.edge_case_handling.EdgeCaseHandler attribute) EMPTY_PRED (panoptica.utils.edge_case_handling.EdgeCaseZeroTP attribute), [1] empty_prediction_result (panoptica.utils.edge_case_handling.MetricZeroTPEdgeCaseHandling attribute)

EMPTY_REF (panoptica.utils.edge_case_handling.EdgeCaseZeroTP attribute), [1] empty_reference_result (panoptica.utils.edge_case_handling.MetricZeroTPEdgeCaseHandling attribute) EvaluateInstancePair (class in panoptica.utils.processing_pair) Evaluation_List_Metric (class in panoptica.metrics.metrics) Evaluation_Metric (class in panoptica.metrics.metrics) extract_label() (panoptica.utils.label_group.LabelGroup method) (panoptica.utils.label_group.LabelPartGroup method)

F

from_yaml() (panoptica.utils.config.SupportsConfig class method) (panoptica.utils.config.SupportsConfig method) (panoptica.utils.constants._Enum_Compare class method) (panoptica.utils.constants._Enum_Compare method)

G

get_metadata() (panoptica.utils.processing_pair._ProcessingPair method) get_metric_zero_tp_handle() (panoptica.utils.edge_case_handling.EdgeCaseHandler method), [1] get_one_to_one_dictionary() (panoptica.utils.instancelabelmap.InstanceLabelMap method), [1]

get_pred_labels_matched_to_ref() (panoptica.utils.instancelabelmap.InstanceLabelMap method), [1] get_result_key() (panoptica.metrics.metrics.Metric method) GLOBAL (panoptica.metrics.metrics.MetricType attribute) group (panoptica.utils.parallel_processing.NoDaemonProcess attribute)

H

handle_empty_list_std() (panoptica.utils.edge_case_handling.EdgeCaseHandler method), [1] handle_zero_tp() (panoptica.utils.edge_case_handling.EdgeCaseHandler method), [1] has_defined_labels_for() (panoptica.utils.segmentation_class._NoSegmentationClassGroups method) (panoptica.utils.segmentation_class.SegmentationClassGroups method)

HD (panoptica.metrics.metrics.Metric attribute) HD95 (panoptica.metrics.metrics.Metric attribute)

I

increasing (panoptica.metrics.metrics._Metric property) (panoptica.metrics.metrics.Metric property) INF (panoptica.utils.edge_case_handling.EdgeCaseResult attribute), [1] InputType (class in panoptica.utils.processing_pair) INSTANCE (panoptica.metrics.metrics.MetricType attribute) instance_volume_matched_ref (panoptica.utils.processing_pair.EvaluateInstancePair attribute), [1] instance_volume_unmatched_ref (panoptica.utils.processing_pair.EvaluateInstancePair attribute), [1] instance_voxel_count_matched_ref (panoptica.utils.processing_pair.EvaluateInstancePair attribute), [1] instance_voxel_count_unmatched_ref (panoptica.utils.processing_pair.EvaluateInstancePair attribute), [1]

InstanceApproximator (class in panoptica.instance_approximator) InstanceLabelMap (class in panoptica.utils.instancelabelmap) InstanceMatchingAlgorithm (class in panoptica.instance_matcher) IntermediateStepsData (class in panoptica.utils.processing_pair) IOU (panoptica.metrics.metrics.Metric attribute) is_cropped (panoptica.utils.processing_pair._ProcessingPair attribute) is_part_group (panoptica.instance_matcher.MatchingContext property) items() (panoptica.utils.instancelabelmap.InstanceLabelMap method) (panoptica.utils.segmentation_class.SegmentationClassGroups method)

K

keys() (panoptica.utils.instancelabelmap.InstanceLabelMap method) (panoptica.utils.segmentation_class._NoSegmentationClassGroups method) (panoptica.utils.segmentation_class.SegmentationClassGroups method)

kwargs (panoptica.utils.parallel_processing.NoDaemonProcess attribute)

L

label_group (panoptica.instance_matcher.MatchingContext attribute) LabelGroup (class in panoptica.utils.label_group) labelmap (panoptica.utils.instancelabelmap.InstanceLabelMap attribute) LabelMergeGroup (class in panoptica.utils.label_group) LabelPartGroup (class in panoptica.utils.label_group) labels (panoptica.utils.segmentation_class._NoSegmentationClassGroups property) (panoptica.utils.segmentation_class.SegmentationClassGroups property) list_duplicates() (in module panoptica.utils.segmentation_class) list_metrics (panoptica.utils.processing_pair.EvaluateInstancePair attribute), [1]

listmetric_zeroTP_handling (panoptica.utils.edge_case_handling.EdgeCaseHandler attribute) (panoptica.utils.edge_case_handling.EdgeCaseHandler property) listmetric_zeroTP_handling() (panoptica.utils.edge_case_handling.EdgeCaseHandler method) load_from_config() (panoptica.utils.config.SupportsConfig class method) (panoptica.utils.config.SupportsConfig method) (panoptica.utils.constants._Enum_Compare class method) (panoptica.utils.constants._Enum_Compare method) load_from_config_name() (panoptica.utils.config.SupportsConfig method) (panoptica.utils.constants._Enum_Compare method) long_name (panoptica.metrics.metrics._Metric attribute), [1]

M

map_instance_labels() (in module panoptica.instance_matcher) match_instances() (panoptica.instance_matcher.InstanceMatchingAlgorithm method) (panoptica.instance_matcher.ThresholdBasedMatching method) MATCHED_INSTANCE (panoptica.utils.processing_pair.InputType attribute), [1] matched_instances (panoptica.utils.processing_pair.MatchedInstancePair attribute), [1] MatchedInstancePair (class in panoptica.utils.processing_pair) MATCHING (panoptica.metrics.metrics.MetricType attribute) matching_metric (panoptica.instance_matcher.MaximizeMergeMatching attribute) (panoptica.instance_matcher.NaiveThresholdMatching attribute) matching_threshold (panoptica.instance_matcher.MaximizeMergeMatching attribute) (panoptica.instance_matcher.NaiveThresholdMatching attribute) MatchingContext (class in panoptica.instance_matcher) MAX (panoptica.metrics.metrics.MetricMode attribute) MaxBipartiteMatching (class in panoptica.instance_matcher) MaximizeMergeMatching (class in panoptica.instance_matcher) Metric (class in panoptica.metrics.metrics) MetricCouldNotBeComputedException MetricMode (class in panoptica.metrics.metrics) MetricType (class in panoptica.metrics.metrics) MetricZeroTPEdgeCaseHandling (class in panoptica.utils.edge_case_handling) MIN (panoptica.metrics.metrics.MetricMode attribute)

missed_prediction_labels (panoptica.utils.processing_pair.MatchedInstancePair attribute), [1] missed_reference_labels (panoptica.utils.processing_pair.MatchedInstancePair attribute), [1] module panoptica.instance_approximator panoptica.instance_matcher panoptica.metrics.assd panoptica.metrics.cldice panoptica.metrics.dice panoptica.metrics.iou panoptica.metrics.metrics panoptica.metrics.relative_volume_difference panoptica.utils.config panoptica.utils.constants panoptica.utils.edge_case_handling panoptica.utils.filepath panoptica.utils.instancelabelmap panoptica.utils.label_group panoptica.utils.numpy_utils panoptica.utils.parallel_processing panoptica.utils.processing_pair panoptica.utils.segmentation_class

N

n_dim (panoptica.utils.processing_pair._ProcessingPair attribute) (panoptica.utils.processing_pair._ProcessingPair property) n_matched_instances (panoptica.utils.processing_pair.MatchedInstancePair property) n_pred_instances (panoptica.utils.processing_pair._ProcessingPairInstanced attribute), [1] (panoptica.utils.processing_pair.EvaluateInstancePair attribute), [1] n_ref_instances (panoptica.utils.processing_pair._ProcessingPairInstanced attribute), [1] (panoptica.utils.processing_pair.EvaluateInstancePair attribute), [1] n_ref_labels (panoptica.instance_matcher.MatchingContext attribute) NaiveThresholdMatching (class in panoptica.instance_matcher) name (panoptica.metrics.metrics._Metric attribute), [1] (panoptica.metrics.metrics.Metric property) (panoptica.utils.parallel_processing.NoDaemonProcess attribute)

NAN (panoptica.utils.edge_case_handling.EdgeCaseResult attribute), [1] new_combination_score() (panoptica.instance_matcher.MaximizeMergeMatching method) NO_INSTANCES (panoptica.utils.edge_case_handling.EdgeCaseZeroTP attribute), [1] no_instances_result (panoptica.utils.edge_case_handling.MetricZeroTPEdgeCaseHandling attribute) NO_PRINT (panoptica.metrics.metrics.MetricType attribute) NoDaemonProcess (class in panoptica.utils.parallel_processing) NonDaemonicPool (class in panoptica.utils.parallel_processing) None (panoptica.instance_approximator.InstanceApproximator attribute) NONE (panoptica.utils.edge_case_handling.EdgeCaseResult attribute), [1] NORMAL (panoptica.utils.edge_case_handling.EdgeCaseZeroTP attribute), [1] normal (panoptica.utils.edge_case_handling.MetricZeroTPEdgeCaseHandling attribute) NSD (panoptica.metrics.metrics.Metric attribute)

O

ONE (panoptica.utils.edge_case_handling.EdgeCaseResult attribute), [1] OneHotConnectedComponentsInstanceApproximator (class in panoptica.instance_approximator)

original_input (panoptica.utils.processing_pair.IntermediateStepsData attribute) original_prediction_arr (panoptica.utils.processing_pair.IntermediateStepsData property) original_reference_arr (panoptica.utils.processing_pair.IntermediateStepsData property)

P

panoptica.instance_approximator module panoptica.instance_matcher module panoptica.metrics.assd module panoptica.metrics.cldice module panoptica.metrics.dice module panoptica.metrics.iou module panoptica.metrics.metrics module panoptica.metrics.relative_volume_difference module panoptica.utils.config module panoptica.utils.constants module panoptica.utils.edge_case_handling module

panoptica.utils.filepath module panoptica.utils.instancelabelmap module panoptica.utils.label_group module panoptica.utils.numpy_utils module panoptica.utils.parallel_processing module panoptica.utils.processing_pair module panoptica.utils.segmentation_class module part_labels (panoptica.utils.label_group.LabelPartGroup attribute) pred_labels (panoptica.utils.processing_pair._ProcessingPair property) prediction_arr (panoptica.utils.processing_pair._ProcessingPair property) (panoptica.utils.processing_pair.EvaluateInstancePair attribute), [1] prediction_arr() (panoptica.utils.processing_pair.IntermediateStepsData method) Process (panoptica.utils.parallel_processing.NonDaemonicPool attribute) processing_pair_orig_shape (panoptica.instance_matcher.MatchingContext attribute)

R

ref_labels (panoptica.utils.processing_pair._ProcessingPair property) reference_arr (panoptica.utils.processing_pair._ProcessingPair property) (panoptica.utils.processing_pair.EvaluateInstancePair attribute), [1] reference_arr() (panoptica.utils.processing_pair.IntermediateStepsData method)

requires_spatial (panoptica.metrics.metrics._Metric attribute), [1] (panoptica.metrics.metrics.Metric property) RVAE (panoptica.metrics.metrics.Metric attribute) RVD (panoptica.metrics.metrics.Metric attribute)

S

save_to_config() (panoptica.utils.config.SupportsConfig method), [1] (panoptica.utils.constants._Enum_Compare method), [1] save_to_config_by_name() (panoptica.utils.config.SupportsConfig method) scipy (panoptica.utils.constants.CCABackend attribute) score_beats_threshold() (panoptica.metrics.metrics._Metric method) (panoptica.metrics.metrics.Metric method) search_path() (in module panoptica.utils.filepath) SegmentationClassGroups (class in panoptica.utils.segmentation_class) SEMANTIC (panoptica.utils.processing_pair.InputType attribute), [1] SemanticPair (class in panoptica.utils.processing_pair)

set_dtype() (panoptica.utils.processing_pair._ProcessingPair method) single_instance (panoptica.utils.label_group._LabelGroupAny property) (panoptica.utils.label_group.LabelGroup attribute) (panoptica.utils.label_group.LabelGroup property) (panoptica.utils.label_group.LabelPartGroup attribute) STD (panoptica.metrics.metrics.MetricMode attribute) suffix (panoptica.metrics.metrics._Metric property) suffix_override (panoptica.metrics.metrics._Metric attribute) SUM (panoptica.metrics.metrics.MetricMode attribute) SupportsConfig (class in panoptica.utils.config)

T

target (panoptica.utils.parallel_processing.NoDaemonProcess attribute) thing_label (panoptica.utils.label_group.LabelPartGroup property) thing_labels (panoptica.utils.label_group.LabelPartGroup attribute) ThresholdBasedMatching (class in panoptica.instance_matcher)

to_yaml() (panoptica.utils.config.SupportsConfig class method) (panoptica.utils.config.SupportsConfig method) (panoptica.utils.constants._Enum_Compare class method) (panoptica.utils.constants._Enum_Compare method) tp (panoptica.utils.processing_pair.EvaluateInstancePair attribute), [1]

U

uncrop_data() (panoptica.utils.processing_pair._ProcessingPair method) uncropped_shape (panoptica.utils.processing_pair._ProcessingPair attribute)

UNMATCHED_INSTANCE (panoptica.utils.processing_pair.InputType attribute), [1] UnmatchedInstancePair (class in panoptica.utils.processing_pair)

V

value (panoptica.utils.edge_case_handling.EdgeCaseResult property) value() (panoptica.utils.edge_case_handling.EdgeCaseResult method) value_labels (panoptica.utils.label_group._LabelGroupAny property) (panoptica.utils.label_group.LabelGroup attribute) (panoptica.utils.label_group.LabelGroup property) (panoptica.utils.label_group.LabelPartGroup attribute)

values() (panoptica.utils.instancelabelmap.InstanceLabelMap method)

Z

ZERO (panoptica.utils.edge_case_handling.EdgeCaseResult attribute), [1]