Bugfix in GeneralizedDiceScore move segmentation metrics to `eva.vi…

…sion` (#653)
kaiko-ai · Oct 1, 2024 · 8e9eda4 · 8e9eda4
1 parent ed73bb0
commit 8e9eda4
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Showing 31 changed files with 276 additions and 163 deletions.
diff --git a/configs/vision/pathology/offline/segmentation/bcss.yaml b/configs/vision/pathology/offline/segmentation/bcss.yaml
@@ -80,13 +80,13 @@ model:
       common:
         - class_path: eva.metrics.AverageLoss
       evaluation:
-        - class_path: eva.core.metrics.defaults.MulticlassSegmentationMetrics
+        - class_path: eva.vision.metrics.defaults.MulticlassSegmentationMetrics
           init_args:
             num_classes: *NUM_CLASSES
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.core.metrics.GeneralizedDiceScore
+              class_path: eva.vision.metrics.GeneralizedDiceScore
               init_args:
                 num_classes: *NUM_CLASSES
                 weight_type: linear

diff --git a/configs/vision/pathology/offline/segmentation/consep.yaml b/configs/vision/pathology/offline/segmentation/consep.yaml
@@ -80,13 +80,13 @@ model:
       common:
         - class_path: eva.metrics.AverageLoss
       evaluation:
-        - class_path: eva.core.metrics.defaults.MulticlassSegmentationMetrics
+        - class_path: eva.vision.metrics.defaults.MulticlassSegmentationMetrics
           init_args:
             num_classes: *NUM_CLASSES
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.core.metrics.GeneralizedDiceScore
+              class_path: eva.vision.metrics.GeneralizedDiceScore
               init_args:
                 num_classes: *NUM_CLASSES
                 weight_type: linear

diff --git a/configs/vision/pathology/offline/segmentation/monusac.yaml b/configs/vision/pathology/offline/segmentation/monusac.yaml
@@ -82,14 +82,14 @@ model:
       common:
         - class_path: eva.metrics.AverageLoss
       evaluation:
-        - class_path: eva.core.metrics.defaults.MulticlassSegmentationMetrics
+        - class_path: eva.vision.metrics.defaults.MulticlassSegmentationMetrics
           init_args:
             num_classes: *NUM_CLASSES
             ignore_index: *IGNORE_INDEX
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.core.metrics.GeneralizedDiceScore
+              class_path: eva.vision.metrics.GeneralizedDiceScore
               init_args:
                 num_classes: *NUM_CLASSES
                 weight_type: linear

diff --git a/configs/vision/pathology/offline/segmentation/total_segmentator_2d.yaml b/configs/vision/pathology/offline/segmentation/total_segmentator_2d.yaml
@@ -79,13 +79,13 @@ model:
       common:
         - class_path: eva.metrics.AverageLoss
       evaluation:
-        - class_path: eva.core.metrics.defaults.MulticlassSegmentationMetrics
+        - class_path: eva.vision.metrics.defaults.MulticlassSegmentationMetrics
           init_args:
             num_classes: *NUM_CLASSES
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.core.metrics.GeneralizedDiceScore
+              class_path: eva.vision.metrics.GeneralizedDiceScore
               init_args:
                 num_classes: *NUM_CLASSES
                 weight_type: linear

diff --git a/configs/vision/pathology/online/segmentation/bcss.yaml b/configs/vision/pathology/online/segmentation/bcss.yaml
@@ -73,13 +73,13 @@ model:
       common:
         - class_path: eva.metrics.AverageLoss
       evaluation:
-        - class_path: eva.core.metrics.defaults.MulticlassSegmentationMetrics
+        - class_path: eva.vision.metrics.defaults.MulticlassSegmentationMetrics
           init_args:
             num_classes: *NUM_CLASSES
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.core.metrics.GeneralizedDiceScore
+              class_path: eva.vision.metrics.GeneralizedDiceScore
               init_args:
                 num_classes: *NUM_CLASSES
                 weight_type: linear

diff --git a/configs/vision/pathology/online/segmentation/consep.yaml b/configs/vision/pathology/online/segmentation/consep.yaml
@@ -73,13 +73,13 @@ model:
       common:
         - class_path: eva.metrics.AverageLoss
       evaluation:
-        - class_path: eva.core.metrics.defaults.MulticlassSegmentationMetrics
+        - class_path: eva.vision.metrics.defaults.MulticlassSegmentationMetrics
           init_args:
             num_classes: *NUM_CLASSES
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.core.metrics.GeneralizedDiceScore
+              class_path: eva.vision.metrics.GeneralizedDiceScore
               init_args:
                 num_classes: *NUM_CLASSES
                 weight_type: linear

diff --git a/configs/vision/pathology/online/segmentation/monusac.yaml b/configs/vision/pathology/online/segmentation/monusac.yaml
@@ -74,14 +74,14 @@ model:
       common:
         - class_path: eva.metrics.AverageLoss
       evaluation:
-        - class_path: eva.core.metrics.defaults.MulticlassSegmentationMetrics
+        - class_path: eva.vision.metrics.defaults.MulticlassSegmentationMetrics
           init_args:
             num_classes: *NUM_CLASSES
             ignore_index: *IGNORE_INDEX
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.core.metrics.GeneralizedDiceScore
+              class_path: eva.vision.metrics.GeneralizedDiceScore
               init_args:
                 num_classes: *NUM_CLASSES
                 weight_type: linear

diff --git a/configs/vision/pathology/online/segmentation/total_segmentator_2d.yaml b/configs/vision/pathology/online/segmentation/total_segmentator_2d.yaml
@@ -72,13 +72,13 @@ model:
       common:
         - class_path: eva.metrics.AverageLoss
       evaluation:
-        - class_path: eva.core.metrics.defaults.MulticlassSegmentationMetrics
+        - class_path: eva.vision.metrics.defaults.MulticlassSegmentationMetrics
           init_args:
             num_classes: *NUM_CLASSES
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.core.metrics.GeneralizedDiceScore
+              class_path: eva.vision.metrics.GeneralizedDiceScore
               init_args:
                 num_classes: *NUM_CLASSES
                 weight_type: linear

diff --git a/configs/vision/radiology/offline/segmentation/lits.yaml b/configs/vision/radiology/offline/segmentation/lits.yaml
@@ -79,13 +79,13 @@ model:
       common:
         - class_path: eva.metrics.AverageLoss
       evaluation:
-        - class_path: eva.core.metrics.defaults.MulticlassSegmentationMetrics
+        - class_path: eva.vision.metrics.defaults.MulticlassSegmentationMetrics
           init_args:
             num_classes: *NUM_CLASSES
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: torchmetrics.segmentation.GeneralizedDiceScore
+              class_path: eva.vision.metrics.GeneralizedDiceScore
               init_args:
                 num_classes: *NUM_CLASSES
                 weight_type: linear

diff --git a/configs/vision/radiology/offline/segmentation/lits_balanced.yaml b/configs/vision/radiology/offline/segmentation/lits_balanced.yaml
@@ -79,13 +79,13 @@ model:
       common:
         - class_path: eva.metrics.AverageLoss
       evaluation:
-        - class_path: eva.core.metrics.defaults.MulticlassSegmentationMetrics
+        - class_path: eva.vision.metrics.defaults.MulticlassSegmentationMetrics
           init_args:
             num_classes: *NUM_CLASSES
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: torchmetrics.segmentation.GeneralizedDiceScore
+              class_path: eva.vision.metrics.GeneralizedDiceScore
               init_args:
                 num_classes: *NUM_CLASSES
                 weight_type: linear

diff --git a/configs/vision/radiology/online/segmentation/lits.yaml b/configs/vision/radiology/online/segmentation/lits.yaml
@@ -72,13 +72,13 @@ model:
       common:
         - class_path: eva.metrics.AverageLoss
       evaluation:
-        - class_path: eva.core.metrics.defaults.MulticlassSegmentationMetrics
+        - class_path: eva.vision.metrics.defaults.MulticlassSegmentationMetrics
           init_args:
             num_classes: *NUM_CLASSES
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: torchmetrics.segmentation.GeneralizedDiceScore
+              class_path: eva.vision.metrics.GeneralizedDiceScore
               init_args:
                 num_classes: *NUM_CLASSES
                 weight_type: linear

diff --git a/configs/vision/radiology/online/segmentation/lits_balanced.yaml b/configs/vision/radiology/online/segmentation/lits_balanced.yaml
@@ -72,13 +72,13 @@ model:
       common:
         - class_path: eva.metrics.AverageLoss
       evaluation:
-        - class_path: eva.core.metrics.defaults.MulticlassSegmentationMetrics
+        - class_path: eva.vision.metrics.defaults.MulticlassSegmentationMetrics
           init_args:
             num_classes: *NUM_CLASSES
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: torchmetrics.segmentation.GeneralizedDiceScore
+              class_path: eva.vision.metrics.GeneralizedDiceScore
               init_args:
                 num_classes: *NUM_CLASSES
                 weight_type: linear

diff --git a/src/eva/core/metrics/__init__.py b/src/eva/core/metrics/__init__.py
@@ -3,17 +3,13 @@
 from eva.core.metrics.average_loss import AverageLoss
 from eva.core.metrics.binary_balanced_accuracy import BinaryBalancedAccuracy
 from eva.core.metrics.defaults import BinaryClassificationMetrics, MulticlassClassificationMetrics
-from eva.core.metrics.generalized_dice import GeneralizedDiceScore
-from eva.core.metrics.mean_iou import MeanIoU
 from eva.core.metrics.structs import Metric, MetricCollection, MetricModule, MetricsSchema
 
 __all__ = [
     "AverageLoss",
     "BinaryBalancedAccuracy",
     "BinaryClassificationMetrics",
     "MulticlassClassificationMetrics",
-    "GeneralizedDiceScore",
-    "MeanIoU",
     "Metric",
     "MetricCollection",
     "MetricModule",

diff --git a/src/eva/core/metrics/defaults/__init__.py b/src/eva/core/metrics/defaults/__init__.py
@@ -4,10 +4,8 @@
     BinaryClassificationMetrics,
     MulticlassClassificationMetrics,
 )
-from eva.core.metrics.defaults.segmentation import MulticlassSegmentationMetrics
 
 __all__ = [
     "MulticlassClassificationMetrics",
     "BinaryClassificationMetrics",
-    "MulticlassSegmentationMetrics",
 ]
diff --git a/src/eva/core/metrics/mean_iou.py b/src/eva/core/metrics/mean_iou.py
diff --git a/src/eva/vision/metrics/__init__.py b/src/eva/vision/metrics/__init__.py
@@ -0,0 +1,11 @@
+"""Default metric collections API."""
+
+from eva.vision.metrics.defaults.segmentation import MulticlassSegmentationMetrics
+from eva.vision.metrics.segmentation.generalized_dice import GeneralizedDiceScore
+from eva.vision.metrics.segmentation.mean_iou import MeanIoU
+
+__all__ = [
+    "MulticlassSegmentationMetrics",
+    "GeneralizedDiceScore",
+    "MeanIoU",
+]
diff --git a/src/eva/vision/metrics/defaults/__init__.py b/src/eva/vision/metrics/defaults/__init__.py
@@ -0,0 +1,7 @@
+"""Default metric collections API."""
+
+from eva.vision.metrics.defaults.segmentation import MulticlassSegmentationMetrics
+
+__all__ = [
+    "MulticlassSegmentationMetrics",
+]
diff --git a/...metrics/defaults/segmentation/__init__.py → ...metrics/defaults/segmentation/__init__.py b/...metrics/defaults/segmentation/__init__.py → ...metrics/defaults/segmentation/__init__.py
@@ -1,5 +1,5 @@
 """Default segmentation metric collections API."""
 
-from eva.core.metrics.defaults.segmentation.multiclass import MulticlassSegmentationMetrics
+from eva.vision.metrics.defaults.segmentation.multiclass import MulticlassSegmentationMetrics
 
 __all__ = ["MulticlassSegmentationMetrics"]
diff --git a/...trics/defaults/segmentation/multiclass.py → ...trics/defaults/segmentation/multiclass.py b/...trics/defaults/segmentation/multiclass.py → ...trics/defaults/segmentation/multiclass.py
@@ -1,6 +1,7 @@
 """Default metric collection for multiclass semantic segmentation tasks."""
 
-from eva.core.metrics import generalized_dice, mean_iou, structs
+from eva.core.metrics import structs
+from eva.vision.metrics.segmentation import generalized_dice, mean_iou
 
 
 class MulticlassSegmentationMetrics(structs.MetricCollection):

diff --git a/src/eva/vision/metrics/segmentation/BUILD b/src/eva/vision/metrics/segmentation/BUILD
@@ -0,0 +1 @@
+python_sources()
diff --git a/src/eva/vision/metrics/segmentation/__init__.py b/src/eva/vision/metrics/segmentation/__init__.py
@@ -0,0 +1,9 @@
+"""Segmentation metrics API."""
+
+from eva.vision.metrics.segmentation.generalized_dice import GeneralizedDiceScore
+from eva.vision.metrics.segmentation.mean_iou import MeanIoU
+
+__all__ = [
+    "GeneralizedDiceScore",
+    "MeanIoU",
+]