Merge remote-tracking branch 'origin/main' into 624-add-support-for-k…

…its23-dataset
kaiko-ai · Dec 9, 2024 · ce76b0e · ce76b0e
2 parents 5e738e2 + 453a12e
commit ce76b0e
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Showing 36 changed files with 495 additions and 100 deletions.
diff --git a/configs/vision/pathology/offline/segmentation/bcss.yaml b/configs/vision/pathology/offline/segmentation/bcss.yaml
@@ -21,7 +21,7 @@ trainer:
           filename: best
           save_last: true
           save_top_k: 1
-          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/GeneralizedDiceScore}
+          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}
       - class_path: lightning.pytorch.callbacks.EarlyStopping
         init_args:
@@ -87,11 +87,18 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.GeneralizedDiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: *NUM_CLASSES
-                weight_type: linear
-                per_class: true
+                reduction: none
+            labels:
+              - outside_roi
+              - tumor
+              - stroma
+              - inflammatory
+              - necrosis
+              - other
 data:
   class_path: eva.DataModule
   init_args:

diff --git a/configs/vision/pathology/offline/segmentation/consep.yaml b/configs/vision/pathology/offline/segmentation/consep.yaml
@@ -21,7 +21,7 @@ trainer:
           filename: best
           save_last: true
           save_top_k: 1
-          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/GeneralizedDiceScore}
+          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}
       - class_path: lightning.pytorch.callbacks.EarlyStopping
         init_args:
@@ -87,11 +87,17 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.GeneralizedDiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: *NUM_CLASSES
-                weight_type: linear
-                per_class: true
+                reduction: none
+            labels:
+              - background
+              - other
+              - inflammatory
+              - epithelial
+              - spindle-shaped
 data:
   class_path: eva.DataModule
   init_args:

diff --git a/configs/vision/pathology/offline/segmentation/monusac.yaml b/configs/vision/pathology/offline/segmentation/monusac.yaml
@@ -24,7 +24,7 @@ trainer:
           filename: best
           save_last: true
           save_top_k: 1
-          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/GeneralizedDiceScore}
+          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}
       - class_path: lightning.pytorch.callbacks.EarlyStopping
         init_args:
@@ -90,12 +90,19 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.GeneralizedDiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: 6
-                weight_type: linear
+                reduction: none
                 ignore_index: *IGNORE_INDEX
-                per_class: true
+            labels:
+              - background
+              - epithelial
+              - lymphocyte
+              - neutrophil
+              - macrophage
+              - ambiguous
 data:
   class_path: eva.DataModule
   init_args:

diff --git a/configs/vision/pathology/online/segmentation/bcss.yaml b/configs/vision/pathology/online/segmentation/bcss.yaml
@@ -22,7 +22,7 @@ trainer:
           filename: best
           save_last: true
           save_top_k: 1
-          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/GeneralizedDiceScore}
+          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}
       - class_path: lightning.pytorch.callbacks.EarlyStopping
         init_args:
@@ -80,11 +80,18 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.GeneralizedDiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: *NUM_CLASSES
-                weight_type: linear
-                per_class: true
+                reduction: none
+            labels:
+              - outside_roi
+              - tumor
+              - stroma
+              - inflammatory
+              - necrosis
+              - other
 data:
   class_path: eva.DataModule
   init_args:

diff --git a/configs/vision/pathology/online/segmentation/consep.yaml b/configs/vision/pathology/online/segmentation/consep.yaml
@@ -22,7 +22,7 @@ trainer:
           filename: best
           save_last: true
           save_top_k: 1
-          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/GeneralizedDiceScore}
+          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}
       - class_path: lightning.pytorch.callbacks.EarlyStopping
         init_args:
@@ -80,11 +80,17 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.GeneralizedDiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: *NUM_CLASSES
-                weight_type: linear
-                per_class: true
+                reduction: none
+            labels:
+              - background
+              - other
+              - inflammatory
+              - epithelial
+              - spindle-shaped
 data:
   class_path: eva.DataModule
   init_args:
@@ -110,7 +116,7 @@ data:
       train:
         batch_size: &BATCH_SIZE ${oc.env:BATCH_SIZE, 64}
         num_workers: &N_DATA_WORKERS ${oc.env:N_DATA_WORKERS, 4}
-        shuffle: true
+        shuffle: false
       val:
         batch_size: *BATCH_SIZE
         num_workers: *N_DATA_WORKERS
diff --git a/configs/vision/pathology/online/segmentation/monusac.yaml b/configs/vision/pathology/online/segmentation/monusac.yaml
@@ -22,7 +22,7 @@ trainer:
           filename: best
           save_last: true
           save_top_k: 1
-          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/GeneralizedDiceScore}
+          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}
       - class_path: lightning.pytorch.callbacks.EarlyStopping
         init_args:
@@ -82,12 +82,19 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.GeneralizedDiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: 6
-                weight_type: linear
+                reduction: none
                 ignore_index: *IGNORE_INDEX
-                per_class: true
+            labels:
+              - background
+              - epithelial
+              - lymphocyte
+              - neutrophil
+              - macrophage
+              - ambiguous
 data:
   class_path: eva.DataModule
   init_args:

diff --git a/configs/vision/radiology/offline/segmentation/lits.yaml b/configs/vision/radiology/offline/segmentation/lits.yaml
@@ -19,7 +19,7 @@ trainer:
           filename: best
           save_last: true
           save_top_k: 1
-          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/GeneralizedDiceScore}
+          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}
       - class_path: lightning.pytorch.callbacks.EarlyStopping
         init_args:
@@ -84,11 +84,15 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.GeneralizedDiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: *NUM_CLASSES
-                weight_type: linear
-                per_class: true
+                reduction: none
+            labels:
+              - background
+              - liver
+              - tumor
 data:
   class_path: eva.DataModule
   init_args:

diff --git a/configs/vision/radiology/offline/segmentation/lits_balanced.yaml b/configs/vision/radiology/offline/segmentation/lits_balanced.yaml
@@ -20,7 +20,7 @@ trainer:
           filename: best
           save_last: true
           save_top_k: 1
-          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/GeneralizedDiceScore}
+          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}
       - class_path: lightning.pytorch.callbacks.EarlyStopping
         init_args:
@@ -85,11 +85,15 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.GeneralizedDiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: *NUM_CLASSES
-                weight_type: linear
-                per_class: true
+                reduction: none
+            labels:
+              - background
+              - liver
+              - tumor
 data:
   class_path: eva.DataModule
   init_args:

diff --git a/...ne/segmentation/total_segmentator_2d.yaml → ...ne/segmentation/total_segmentator_2d.yaml b/...ne/segmentation/total_segmentator_2d.yaml → ...ne/segmentation/total_segmentator_2d.yaml
@@ -21,7 +21,7 @@ trainer:
           filename: best
           save_last: true
           save_top_k: 1
-          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/GeneralizedDiceScore}
+          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}
       - class_path: lightning.pytorch.callbacks.EarlyStopping
         init_args:
@@ -86,11 +86,11 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.GeneralizedDiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: *NUM_CLASSES
-                weight_type: linear
-                per_class: true
+                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
@@ -22,7 +22,7 @@ trainer:
           filename: best
           save_last: true
           save_top_k: 1
-          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/GeneralizedDiceScore}
+          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}
       - class_path: lightning.pytorch.callbacks.EarlyStopping
         init_args:
@@ -78,11 +78,15 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.GeneralizedDiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: *NUM_CLASSES
-                weight_type: linear
-                per_class: true
+                reduction: none
+            labels:
+              - background
+              - liver
+              - tumor
 data:
   class_path: eva.DataModule
   init_args:

diff --git a/configs/vision/radiology/online/segmentation/lits_balanced.yaml b/configs/vision/radiology/online/segmentation/lits_balanced.yaml
@@ -22,7 +22,7 @@ trainer:
           filename: best
           save_last: true
           save_top_k: 1
-          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/GeneralizedDiceScore}
+          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}
       - class_path: lightning.pytorch.callbacks.EarlyStopping
         init_args:
@@ -78,11 +78,15 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.GeneralizedDiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: *NUM_CLASSES
-                weight_type: linear
-                per_class: true
+                reduction: none
+            labels:
+              - background
+              - liver
+              - tumor
 data:
   class_path: eva.DataModule
   init_args:

diff --git a/...ne/segmentation/total_segmentator_2d.yaml → ...ne/segmentation/total_segmentator_2d.yaml b/...ne/segmentation/total_segmentator_2d.yaml → ...ne/segmentation/total_segmentator_2d.yaml
@@ -21,7 +21,7 @@ trainer:
           filename: best
           save_last: true
           save_top_k: 1
-          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, val/GeneralizedDiceScore}
+          monitor: &MONITOR_METRIC ${oc.env:MONITOR_METRIC, 'val/MonaiDiceScore'}
           mode: &MONITOR_METRIC_MODE ${oc.env:MONITOR_METRIC_MODE, max}
       - class_path: lightning.pytorch.callbacks.EarlyStopping
         init_args:
@@ -79,11 +79,11 @@ model:
         - class_path: torchmetrics.ClasswiseWrapper
           init_args:
             metric:
-              class_path: eva.vision.metrics.GeneralizedDiceScore
+              class_path: eva.vision.metrics.MonaiDiceScore
               init_args:
+                include_background: true
                 num_classes: *NUM_CLASSES
-                weight_type: linear
-                per_class: true
+                reduction: none
 data:
   class_path: eva.DataModule
   init_args: