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BrainLesion · Aug 20, 2024 · 6aaf04a · 6aaf04a
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Showing 5 changed files with 59 additions and 17 deletions.
diff --git a/examples/example_spine_semantic.py b/examples/example_spine_semantic.py
@@ -26,7 +26,9 @@
 
 def main():
     with cProfile.Profile() as pr:
-        result, intermediate_steps_data = evaluator.evaluate(prediction_mask, reference_mask)["ungrouped"]
+        result, intermediate_steps_data = evaluator.evaluate(
+            prediction_mask, reference_mask
+        )["ungrouped"]
 
         # To print the results, just call print
         print(result)
@@ -35,8 +37,12 @@ def main():
         intermediate_steps_data.original_prediction_arr  # Input prediction array, untouched
         intermediate_steps_data.original_reference_arr  # Input reference array, untouched
 
-        intermediate_steps_data.prediction_arr(InputType.MATCHED_INSTANCE)  # Prediction array after instances have been matched
-        intermediate_steps_data.reference_arr(InputType.MATCHED_INSTANCE)  # Reference array after instances have been matched
+        intermediate_steps_data.prediction_arr(
+            InputType.MATCHED_INSTANCE
+        )  # Prediction array after instances have been matched
+        intermediate_steps_data.reference_arr(
+            InputType.MATCHED_INSTANCE
+        )  # Reference array after instances have been matched
 
     pr.dump_stats(directory + "/semantic_example.log")
     return result, intermediate_steps_data

diff --git a/panoptica/panoptica_evaluator.py b/panoptica/panoptica_evaluator.py
@@ -226,11 +226,19 @@ def panoptic_evaluate(
     # Crops away unecessary space of zeroes
     input_pair.crop_data()
 
-    processing_pair: SemanticPair | UnmatchedInstancePair | MatchedInstancePair | EvaluateInstancePair | PanopticaResult = input_pair.copy()
+    processing_pair: (
+        SemanticPair
+        | UnmatchedInstancePair
+        | MatchedInstancePair
+        | EvaluateInstancePair
+        | PanopticaResult
+    ) = input_pair.copy()
 
     # First Phase: Instance Approximation
     if isinstance(processing_pair, SemanticPair):
-        intermediate_steps_data.add_intermediate_arr_data(processing_pair.copy(), InputType.SEMANTIC)
+        intermediate_steps_data.add_intermediate_arr_data(
+            processing_pair.copy(), InputType.SEMANTIC
+        )
         assert (
             instance_approximator is not None
         ), "Got SemanticPair but not InstanceApproximator"
@@ -243,7 +251,9 @@ def panoptic_evaluate(
 
     # Second Phase: Instance Matching
     if isinstance(processing_pair, UnmatchedInstancePair):
-        intermediate_steps_data.add_intermediate_arr_data(processing_pair.copy(), InputType.UNMATCHED_INSTANCE)
+        intermediate_steps_data.add_intermediate_arr_data(
+            processing_pair.copy(), InputType.UNMATCHED_INSTANCE
+        )
         processing_pair = _handle_zero_instances_cases(
             processing_pair,
             eval_metrics=instance_metrics,
@@ -266,7 +276,9 @@ def panoptic_evaluate(
 
     # Third Phase: Instance Evaluation
     if isinstance(processing_pair, MatchedInstancePair):
-        intermediate_steps_data.add_intermediate_arr_data(processing_pair.copy(), InputType.MATCHED_INSTANCE)
+        intermediate_steps_data.add_intermediate_arr_data(
+            processing_pair.copy(), InputType.MATCHED_INSTANCE
+        )
         processing_pair = _handle_zero_instances_cases(
             processing_pair,
             eval_metrics=instance_metrics,

diff --git a/panoptica/utils/processing_pair.py b/panoptica/utils/processing_pair.py
@@ -343,7 +343,9 @@ def __init__(self, original_input: _ProcessingPair | None):
         self._original_input = original_input
         self._intermediatesteps: dict[str, _ProcessingPair] = {}
 
-    def add_intermediate_arr_data(self, processing_pair: _ProcessingPair, inputtype: InputType):
+    def add_intermediate_arr_data(
+        self, processing_pair: _ProcessingPair, inputtype: InputType
+    ):
         type_name = inputtype.name
         self.add_intermediate_data(type_name, processing_pair)
 
@@ -353,26 +355,36 @@ def add_intermediate_data(self, key, value):
 
     @property
     def original_prediction_arr(self):
-        assert self._original_input is not None, "Original prediction_arr is None, there are no intermediate steps"
+        assert (
+            self._original_input is not None
+        ), "Original prediction_arr is None, there are no intermediate steps"
         return self._original_input.prediction_arr
 
     @property
     def original_reference_arr(self):
-        assert self._original_input is not None, "Original reference_arr is None, there are no intermediate steps"
+        assert (
+            self._original_input is not None
+        ), "Original reference_arr is None, there are no intermediate steps"
         return self._original_input.reference_arr
 
     def prediction_arr(self, inputtype: InputType):
         type_name = inputtype.name
         procpair = self[type_name]
-        assert isinstance(procpair, _ProcessingPair), f"step {type_name} is not a processing pair, error"
+        assert isinstance(
+            procpair, _ProcessingPair
+        ), f"step {type_name} is not a processing pair, error"
         return procpair.prediction_arr
 
     def reference_arr(self, inputtype: InputType):
         type_name = inputtype.name
         procpair = self[type_name]
-        assert isinstance(procpair, _ProcessingPair), f"step {type_name} is not a processing pair, error"
+        assert isinstance(
+            procpair, _ProcessingPair
+        ), f"step {type_name} is not a processing pair, error"
         return procpair.reference_arr
 
     def __getitem__(self, key):
-        assert key in self._intermediatesteps, f"key {key} not in intermediate steps, maybe the step was skipped?"
+        assert (
+            key in self._intermediatesteps
+        ), f"key {key} not in intermediate steps, maybe the step was skipped?"
         return self._intermediatesteps[key]
diff --git a/unit_tests/test_config.py b/unit_tests/test_config.py
@@ -21,7 +21,11 @@
     MetricZeroTPEdgeCaseHandling,
     EdgeCaseHandler,
 )
-from panoptica import ConnectedComponentsInstanceApproximator, NaiveThresholdMatching, Panoptica_Evaluator
+from panoptica import (
+    ConnectedComponentsInstanceApproximator,
+    NaiveThresholdMatching,
+    Panoptica_Evaluator,
+)
 from pathlib import Path
 import numpy as np
 import random
@@ -105,7 +109,9 @@ def test_SegmentationClassGroups_config_by_name(self):
 
         configname = "test_file.yaml"
         t.save_to_config_by_name(configname)
-        d: SegmentationClassGroups = SegmentationClassGroups.load_from_config_name(configname)
+        d: SegmentationClassGroups = SegmentationClassGroups.load_from_config_name(
+            configname
+        )
 
         testfile_d = config_by_name(configname)
         os.remove(testfile_d)

diff --git a/unit_tests/test_datatype.py b/unit_tests/test_datatype.py
@@ -11,7 +11,11 @@
     MetricMode,
     MetricCouldNotBeComputedException,
 )
-from panoptica.utils.edge_case_handling import EdgeCaseResult, EdgeCaseHandler, MetricZeroTPEdgeCaseHandling
+from panoptica.utils.edge_case_handling import (
+    EdgeCaseResult,
+    EdgeCaseHandler,
+    MetricZeroTPEdgeCaseHandling,
+)
 
 
 class Test_EdgeCaseHandler(unittest.TestCase):
@@ -24,7 +28,9 @@ def test_edgecasehandler_simple(self):
 
         print()
         # print(handler.get_metric_zero_tp_handle(ListMetric.IOU))
-        r = handler.handle_zero_tp(Metric.IOU, tp=0, num_pred_instances=1, num_ref_instances=1)
+        r = handler.handle_zero_tp(
+            Metric.IOU, tp=0, num_pred_instances=1, num_ref_instances=1
+        )
         print(r)
 
         iou_test = MetricZeroTPEdgeCaseHandling(