updated yaml configs

kaiko-ai · Nov 29, 2024 · ab69fcc · ab69fcc
1 parent 0766787
commit ab69fcc
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Showing 13 changed files with 39 additions and 25 deletions.
diff --git a/configs/vision/pathology/offline/segmentation/bcss.yaml b/configs/vision/pathology/offline/segmentation/bcss.yaml
@@ -86,10 +86,11 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.DiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: *NUM_CLASSES
-                average: none
+                reduction: none
             labels:
               - outside_roi
               - tumor

diff --git a/configs/vision/pathology/offline/segmentation/consep.yaml b/configs/vision/pathology/offline/segmentation/consep.yaml
@@ -86,10 +86,11 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.DiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: *NUM_CLASSES
-                average: none
+                reduction: none
             labels:
               - background
               - other

diff --git a/configs/vision/pathology/offline/segmentation/monusac.yaml b/configs/vision/pathology/offline/segmentation/monusac.yaml
@@ -89,10 +89,11 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.DiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: 6
-                average: none
+                reduction: none
                 ignore_index: *IGNORE_INDEX
             labels:
               - background

diff --git a/configs/vision/pathology/online/segmentation/bcss.yaml b/configs/vision/pathology/online/segmentation/bcss.yaml
@@ -79,10 +79,11 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.DiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: *NUM_CLASSES
-                average: none
+                reduction: none
             labels:
               - outside_roi
               - tumor

diff --git a/configs/vision/pathology/online/segmentation/consep.yaml b/configs/vision/pathology/online/segmentation/consep.yaml
@@ -79,10 +79,11 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.DiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: *NUM_CLASSES
-                average: none
+                reduction: none
             labels:
               - background
               - other

diff --git a/configs/vision/pathology/online/segmentation/monusac.yaml b/configs/vision/pathology/online/segmentation/monusac.yaml
@@ -81,10 +81,11 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.DiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: 6
-                average: none
+                reduction: none
                 ignore_index: *IGNORE_INDEX
             labels:
               - background

diff --git a/configs/vision/radiology/offline/segmentation/lits.yaml b/configs/vision/radiology/offline/segmentation/lits.yaml
@@ -84,10 +84,11 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.DiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: *NUM_CLASSES
-                average: none
+                reduction: none
             labels:
               - background
               - liver

diff --git a/configs/vision/radiology/offline/segmentation/lits_balanced.yaml b/configs/vision/radiology/offline/segmentation/lits_balanced.yaml
@@ -84,10 +84,11 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.DiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: *NUM_CLASSES
-                average: none
+                reduction: none
             labels:
               - background
               - liver

diff --git a/configs/vision/radiology/offline/segmentation/total_segmentator_2d.yaml b/configs/vision/radiology/offline/segmentation/total_segmentator_2d.yaml
@@ -85,10 +85,11 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.DiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: *NUM_CLASSES
-                average: none
+                reduction: none
 data:
   class_path: eva.DataModule
   init_args:

diff --git a/configs/vision/radiology/online/segmentation/lits.yaml b/configs/vision/radiology/online/segmentation/lits.yaml
@@ -77,10 +77,11 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.DiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: *NUM_CLASSES
-                average: none
+                reduction: none
             labels:
               - background
               - liver

diff --git a/configs/vision/radiology/online/segmentation/lits_balanced.yaml b/configs/vision/radiology/online/segmentation/lits_balanced.yaml
@@ -77,10 +77,11 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.DiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: *NUM_CLASSES
-                average: none
+                reduction: none
             labels:
               - background
               - liver

diff --git a/configs/vision/radiology/online/segmentation/total_segmentator_2d.yaml b/configs/vision/radiology/online/segmentation/total_segmentator_2d.yaml
@@ -78,10 +78,11 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.DiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: *NUM_CLASSES
-                average: none
+                reduction: none
 data:
   class_path: eva.DataModule
   init_args:

diff --git a/src/eva/vision/metrics/__init__.py b/src/eva/vision/metrics/__init__.py
@@ -4,10 +4,12 @@
 from eva.vision.metrics.segmentation.dice import DiceScore
 from eva.vision.metrics.segmentation.generalized_dice import GeneralizedDiceScore
 from eva.vision.metrics.segmentation.mean_iou import MeanIoU
+from eva.vision.metrics.segmentation.monai_dice import MonaiDiceScore
 
 __all__ = [
     "DiceScore",
     "GeneralizedDiceScore",
-    "MulticlassSegmentationMetrics",
     "MeanIoU",
+    "MonaiDiceScore",
+    "MulticlassSegmentationMetrics",
 ]