Create a core submodule (#290)

kaiko-ai · Mar 18, 2024 · 879b51e · 879b51e
1 parent dbcbb94
commit 879b51e
Show file tree

Hide file tree

Showing 153 changed files with 389 additions and 306 deletions.
diff --git a/configs/core/tests/offline/embeddings.yaml b/configs/core/tests/offline/embeddings.yaml
@@ -47,18 +47,18 @@ data:
   init_args:
     datasets:
       train:
-        class_path: eva.data.datasets.classification.EmbeddingsDataset
+        class_path: eva.datasets.EmbeddingsClassificationDataset
         init_args: &DATASET_ARGS
           root: ${oc.env:TESTS_ROOT, tests/eva}/assets/core/datasets/embeddings
           manifest_file: manifest.csv
           split: train
       val:
-        class_path: eva.data.datasets.classification.EmbeddingsDataset
+        class_path: eva.datasets.EmbeddingsClassificationDataset
         init_args:
           <<: *DATASET_ARGS
           split: val
       test:
-        class_path: eva.data.datasets.classification.EmbeddingsDataset
+        class_path: eva.datasets.EmbeddingsClassificationDataset
         init_args:
           <<: *DATASET_ARGS
           split: test

diff --git a/configs/vision/dino_vit/offline/bach.yaml b/configs/vision/dino_vit/offline/bach.yaml
@@ -29,7 +29,7 @@ trainer:
             0: train
             1: val
           backbone:
-            class_path: eva.models.networks.wrappers.ModelFromFunction
+            class_path: eva.models.ModelFromFunction
             init_args:
               path: torch.hub.load
               arguments:
@@ -74,13 +74,13 @@ data:
   init_args:
     datasets:
       train:
-        class_path: eva.data.datasets.classification.EmbeddingsDataset
+        class_path: eva.datasets.EmbeddingsClassificationDataset
         init_args: &DATASET_ARGS
           root: *DATASET_EMBEDDINGS_ROOT
           manifest_file: manifest.csv
           split: train
       val:
-        class_path: eva.data.datasets.classification.EmbeddingsDataset
+        class_path: eva.datasets.EmbeddingsClassificationDataset
         init_args:
           <<: *DATASET_ARGS
           split: val

diff --git a/configs/vision/dino_vit/offline/crc.yaml b/configs/vision/dino_vit/offline/crc.yaml
@@ -29,7 +29,7 @@ trainer:
             0: train
             1: val
           backbone:
-            class_path: eva.models.networks.wrappers.ModelFromFunction
+            class_path: eva.models.ModelFromFunction
             init_args:
               path: torch.hub.load
               arguments:
@@ -74,13 +74,13 @@ data:
   init_args:
     datasets:
       train:
-        class_path: eva.data.datasets.classification.EmbeddingsDataset
+        class_path: eva.datasets.EmbeddingsClassificationDataset
         init_args: &DATASET_ARGS
           root: *DATASET_EMBEDDINGS_ROOT
           manifest_file: manifest.csv
           split: train
       val:
-        class_path: eva.data.datasets.classification.EmbeddingsDataset
+        class_path: eva.datasets.EmbeddingsClassificationDataset
         init_args:
           <<: *DATASET_ARGS
           split: val

diff --git a/configs/vision/dino_vit/offline/mhist.yaml b/configs/vision/dino_vit/offline/mhist.yaml
@@ -29,7 +29,7 @@ trainer:
             0: train
             1: test
           backbone:
-            class_path: eva.models.networks.wrappers.ModelFromFunction
+            class_path: eva.models.ModelFromFunction
             init_args:
               path: torch.hub.load
               arguments:
@@ -72,15 +72,15 @@ data:
   init_args:
     datasets:
       train:
-        class_path: eva.data.datasets.classification.EmbeddingsDataset
+        class_path: eva.datasets.EmbeddingsClassificationDataset
         init_args: &DATASET_ARGS
           root: *DATASET_EMBEDDINGS_ROOT
           manifest_file: manifest.csv
           split: train
           target_transforms:
-            class_path: eva.vision.data.transforms.common.ArrayToFloatTensor
+            class_path: eva.core.data.transforms.ArrayToFloatTensor
       val:
-        class_path: eva.data.datasets.classification.EmbeddingsDataset
+        class_path: eva.datasets.EmbeddingsClassificationDataset
         init_args:
           <<: *DATASET_ARGS
           split: test

diff --git a/configs/vision/dino_vit/offline/patch_camelyon.yaml b/configs/vision/dino_vit/offline/patch_camelyon.yaml
@@ -30,7 +30,7 @@ trainer:
             1: val
             2: test
           backbone:
-            class_path: eva.models.networks.wrappers.ModelFromFunction
+            class_path: eva.models.ModelFromFunction
             init_args:
               path: torch.hub.load
               arguments:
@@ -73,20 +73,20 @@ data:
   init_args:
     datasets:
       train:
-        class_path: eva.data.datasets.classification.EmbeddingsDataset
+        class_path: eva.datasets.EmbeddingsClassificationDataset
         init_args: &DATASET_ARGS
           root: *DATASET_EMBEDDINGS_ROOT
           manifest_file: manifest.csv
           split: train
           target_transforms:
-            class_path: eva.vision.data.transforms.common.ArrayToFloatTensor
+            class_path: eva.core.data.transforms.ArrayToFloatTensor
       val:
-        class_path: eva.data.datasets.classification.EmbeddingsDataset
+        class_path: eva.datasets.EmbeddingsClassificationDataset
         init_args:
           <<: *DATASET_ARGS
           split: val
       test:
-        class_path: eva.data.datasets.classification.EmbeddingsDataset
+        class_path: eva.datasets.EmbeddingsClassificationDataset
         init_args:
           <<: *DATASET_ARGS
           split: test

diff --git a/configs/vision/dino_vit/online/bach.yaml b/configs/vision/dino_vit/online/bach.yaml
@@ -30,7 +30,7 @@ model:
   class_path: eva.HeadModule
   init_args:
     backbone:
-      class_path: eva.models.networks.wrappers.ModelFromFunction
+      class_path: eva.models.ModelFromFunction
       init_args:
         path: torch.hub.load
         arguments:

diff --git a/configs/vision/dino_vit/online/crc.yaml b/configs/vision/dino_vit/online/crc.yaml
@@ -30,7 +30,7 @@ model:
   class_path: eva.HeadModule
   init_args:
     backbone:
-      class_path: eva.models.networks.wrappers.ModelFromFunction
+      class_path: eva.models.ModelFromFunction
       init_args:
         path: torch.hub.load
         arguments:

diff --git a/configs/vision/dino_vit/online/mhist.yaml b/configs/vision/dino_vit/online/mhist.yaml
@@ -30,7 +30,7 @@ model:
   class_path: eva.HeadModule
   init_args:
     backbone:
-      class_path: eva.models.networks.wrappers.ModelFromFunction
+      class_path: eva.models.ModelFromFunction
       init_args:
         path: torch.hub.load
         arguments:
@@ -76,7 +76,7 @@ data:
               mean: ${oc.env:NORMALIZE_MEAN, [0.485, 0.456, 0.406]} 
               std: ${oc.env:NORMALIZE_STD, [0.229, 0.224, 0.225]}
           target_transforms:
-            class_path: eva.vision.data.transforms.common.ArrayToFloatTensor
+            class_path: eva.core.data.transforms.ArrayToFloatTensor
       val:
         class_path: eva.vision.datasets.MHIST
         init_args:

diff --git a/configs/vision/dino_vit/online/patch_camelyon.yaml b/configs/vision/dino_vit/online/patch_camelyon.yaml
@@ -30,7 +30,7 @@ model:
   class_path: eva.HeadModule
   init_args:
     backbone:
-      class_path: eva.models.networks.wrappers.ModelFromFunction
+      class_path: eva.models.ModelFromFunction
       init_args:
         path: torch.hub.load
         arguments:
@@ -81,7 +81,7 @@ data:
               mean: ${oc.env:NORMALIZE_MEAN, [0.485, 0.456, 0.406]} 
               std: ${oc.env:NORMALIZE_STD, [0.229, 0.224, 0.225]}
           target_transforms:
-            class_path: eva.vision.data.transforms.common.ArrayToFloatTensor
+            class_path: eva.core.data.transforms.ArrayToFloatTensor
       val:
         class_path: eva.vision.datasets.PatchCamelyon
         init_args:

diff --git a/configs/vision/owkin/phikon/offline/bach.yaml b/configs/vision/owkin/phikon/offline/bach.yaml
@@ -29,11 +29,11 @@ trainer:
             0: train
             1: val
           backbone:
-            class_path: eva.models.networks.wrappers.HuggingFaceModel
+            class_path: eva.models.HuggingFaceModel
             init_args:
               model_name_or_path: owkin/phikon
               tensor_transforms: 
-                class_path: eva.models.networks.transforms.ExtractCLSFeatures
+                class_path: eva.core.models.networks.transforms.ExtractCLSFeatures
     logger:
       - class_path: pytorch_lightning.loggers.TensorBoardLogger
         init_args:
@@ -70,15 +70,15 @@ data:
   init_args:
     datasets:
       train:
-        class_path: eva.data.datasets.classification.EmbeddingsDataset
+        class_path: eva.datasets.EmbeddingsClassificationDataset
         init_args: &DATASET_ARGS
           root: *EMBEDDINGS_DIR
           manifest_file: manifest.csv
           split: train
           column_mapping:
             path: embedding
       val:
-        class_path: eva.data.datasets.classification.EmbeddingsDataset
+        class_path: eva.datasets.EmbeddingsClassificationDataset
         init_args:
           <<: *DATASET_ARGS
           split: val

diff --git a/configs/vision/owkin/phikon/offline/crc.yaml b/configs/vision/owkin/phikon/offline/crc.yaml
@@ -29,11 +29,11 @@ trainer:
             0: train
             1: val
           backbone:
-            class_path: eva.models.networks.wrappers.HuggingFaceModel
+            class_path: eva.models.HuggingFaceModel
             init_args:
               model_name_or_path: owkin/phikon
               tensor_transforms: 
-                class_path: eva.models.networks.transforms.ExtractCLSFeatures
+                class_path: eva.core.models.networks.transforms.ExtractCLSFeatures
     logger:
       - class_path: pytorch_lightning.loggers.TensorBoardLogger
         init_args:
@@ -70,15 +70,15 @@ data:
   init_args:
     datasets:
       train:
-        class_path: eva.data.datasets.classification.EmbeddingsDataset
+        class_path: eva.datasets.EmbeddingsClassificationDataset
         init_args: &DATASET_ARGS
           root: *EMBEDDINGS_DIR
           manifest_file: manifest.csv
           split: train
           column_mapping:
             path: embedding
       val:
-        class_path: eva.data.datasets.classification.EmbeddingsDataset
+        class_path: eva.datasets.EmbeddingsClassificationDataset
         init_args:
           <<: *DATASET_ARGS
           split: val

diff --git a/configs/vision/owkin/phikon/offline/mhist.yaml b/configs/vision/owkin/phikon/offline/mhist.yaml
@@ -29,11 +29,11 @@ trainer:
             0: train
             1: test
           backbone:
-            class_path: eva.models.networks.wrappers.HuggingFaceModel
+            class_path: eva.models.HuggingFaceModel
             init_args:
               model_name_or_path: owkin/phikon
               tensor_transforms: 
-                class_path: eva.models.networks.transforms.ExtractCLSFeatures
+                class_path: eva.core.models.networks.transforms.ExtractCLSFeatures
     logger:
       - class_path: pytorch_lightning.loggers.TensorBoardLogger
         init_args:
@@ -68,17 +68,17 @@ data:
   init_args:
     datasets:
       train:
-        class_path: eva.data.datasets.classification.EmbeddingsDataset
+        class_path: eva.datasets.EmbeddingsClassificationDataset
         init_args: &DATASET_ARGS
           root: *EMBEDDINGS_DIR
           manifest_file: manifest.csv
           split: train
           column_mapping:
             path: embedding
           target_transforms:
-            class_path: eva.vision.data.transforms.common.ArrayToFloatTensor
+            class_path: eva.core.data.transforms.ArrayToFloatTensor
       val:
-        class_path: eva.data.datasets.classification.EmbeddingsDataset
+        class_path: eva.datasets.EmbeddingsClassificationDataset
         init_args:
           <<: *DATASET_ARGS
           split: test

diff --git a/configs/vision/owkin/phikon/offline/patch_camelyon.yaml b/configs/vision/owkin/phikon/offline/patch_camelyon.yaml
@@ -30,11 +30,11 @@ trainer:
             1: val
             2: test
           backbone:
-            class_path: eva.models.networks.wrappers.HuggingFaceModel
+            class_path: eva.models.HuggingFaceModel
             init_args:
               model_name_or_path: owkin/phikon
               tensor_transforms: 
-                class_path: eva.models.networks.transforms.ExtractCLSFeatures
+                class_path: eva.core.models.networks.transforms.ExtractCLSFeatures
     logger:
       - class_path: pytorch_lightning.loggers.TensorBoardLogger
         init_args:
@@ -69,22 +69,22 @@ data:
   init_args:
     datasets:
       train:
-        class_path: eva.data.datasets.classification.EmbeddingsDataset
+        class_path: eva.datasets.EmbeddingsClassificationDataset
         init_args: &DATASET_ARGS
           root: *EMBEDDINGS_DIR
           manifest_file: manifest.csv
           split: train
           column_mapping:
             path: embedding
           target_transforms:
-            class_path: eva.vision.data.transforms.common.ArrayToFloatTensor
+            class_path: eva.core.data.transforms.ArrayToFloatTensor
       val:
-        class_path: eva.data.datasets.classification.EmbeddingsDataset
+        class_path: eva.datasets.EmbeddingsClassificationDataset
         init_args:
           <<: *DATASET_ARGS
           split: val
       test:
-        class_path: eva.data.datasets.classification.EmbeddingsDataset
+        class_path: eva.datasets.EmbeddingsClassificationDataset
         init_args:
           <<: *DATASET_ARGS
           split: test

diff --git a/configs/vision/tests/offline/patch_camelyon.yaml b/configs/vision/tests/offline/patch_camelyon.yaml
@@ -15,7 +15,7 @@ trainer:
             1: val
             2: test
           backbone:
-            class_path: eva.models.networks.wrappers.ModelFromFunction
+            class_path: eva.core.models.networks.wrappers.ModelFromFunction
             init_args:
               path: torch.hub.load
               arguments:
@@ -65,15 +65,15 @@ data:
   init_args:
     datasets:
       train:
-        class_path: eva.data.datasets.classification.EmbeddingsDataset
+        class_path: eva.datasets.EmbeddingsClassificationDataset
         init_args: &DATASET_ARGS
           root: *DATASET_EMBEDDINGS_ROOT
           manifest_file: manifest.csv
           split: train
           target_transforms:
-            class_path: eva.vision.data.transforms.common.ArrayToFloatTensor
+            class_path: eva.core.data.transforms.ArrayToFloatTensor
       val:
-        class_path: eva.data.datasets.classification.EmbeddingsDataset
+        class_path: eva.datasets.EmbeddingsClassificationDataset
         init_args:
           <<: *DATASET_ARGS
           split: val

diff --git a/configs/vision/tests/online/patch_camelyon.yaml b/configs/vision/tests/online/patch_camelyon.yaml
@@ -48,7 +48,7 @@ data:
               mean: ${oc.env:NORMALIZE_MEAN, [0.485, 0.456, 0.406]} 
               std: ${oc.env:NORMALIZE_STD, [0.229, 0.224, 0.225]}
           target_transforms:
-            class_path: eva.vision.data.transforms.common.ArrayToFloatTensor
+            class_path: eva.core.data.transforms.ArrayToFloatTensor
       val:
         class_path: eva.vision.datasets.PatchCamelyon
         init_args: