deleted cfos example, updated speedtest

BrainLesion · Jan 15, 2024 · df6e9b3 · df6e9b3
1 parent 91fc758
commit df6e9b3
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Showing 6 changed files with 10 additions and 280 deletions.
diff --git a/benchmark/modules_speedtest.py b/benchmark/modules_speedtest.py
@@ -9,6 +9,8 @@
     ConnectedComponentsInstanceApproximator,
     NaiveThresholdMatching,
     SemanticPair,
+    UnmatchedInstancePair, 
+    MatchedInstancePair,
 )
 from panoptica.instance_evaluator import evaluate_matched_instance
 from time import perf_counter
@@ -80,16 +82,16 @@ def test_input(processing_pair: SemanticPair):
     processing_pair.crop_data()
     #
     start1 = perf_counter()
-    processing_pair = instance_approximator.approximate_instances(processing_pair)
+    unmatched_instance_pair = instance_approximator.approximate_instances(semantic_pair=processing_pair)
     time1 = perf_counter() - start1
     #
     start2 = perf_counter()
-    processing_pair = instance_matcher.match_instances(processing_pair)
+    matched_instance_pair = instance_matcher.match_instances(unmatched_instance_pair=unmatched_instance_pair)
     time2 = perf_counter() - start2
     #
     start3 = perf_counter()
-    processing_pair = evaluate_matched_instance(
-        processing_pair, matching_threshold=iou_threshold
+    result = evaluate_matched_instance(
+        matched_instance_pair, decision_threshold=iou_threshold,
     )
     time3 = perf_counter() - start3
     return time1, time2, time3

diff --git a/examples/example_cfos_3d.py b/examples/example_cfos_3d.py
diff --git a/panoptica/__init__.py b/panoptica/__init__.py
@@ -3,7 +3,7 @@
     CCABackend,
 )
 from panoptica.instance_matcher import NaiveThresholdMatching
-from panoptica.evaluator import Panoptic_Evaluator
+from panoptica.panoptic_evaluator import Panoptic_Evaluator
 from panoptica.panoptic_result import PanopticaResult
 from panoptica.utils.processing_pair import (
     SemanticPair,

diff --git a/panoptica/evaluator.py b/panoptica/evaluator.py
diff --git a/panoptica/instance_evaluator.py b/panoptica/instance_evaluator.py
@@ -16,8 +16,8 @@
 
 def evaluate_matched_instance(
     matched_instance_pair: MatchedInstancePair,
-    eval_metrics: list[_MatchingMetric],
-    decision_metric: _MatchingMetric | None = None,
+    eval_metrics: list[_MatchingMetric] = [Metrics.DSC, Metrics.IOU, Metrics.ASSD],
+    decision_metric: _MatchingMetric | None = Metrics.IOU,
     decision_threshold: float | None = None,
     edge_case_handler: EdgeCaseHandler | None = None,
     **kwargs,

diff --git a/unit_tests/test_panoptic_evaluator.py b/unit_tests/test_panoptic_evaluator.py
@@ -6,7 +6,7 @@
 import os
 import numpy as np
 
-from panoptica.evaluator import Panoptic_Evaluator
+from panoptica.panoptic_evaluator import Panoptic_Evaluator
 from panoptica.instance_approximator import ConnectedComponentsInstanceApproximator
 from panoptica.instance_matcher import NaiveThresholdMatching