Reorganize datasets and metrics in pathology

docs/source/apps.rst

@@ -77,7 +77,7 @@ Clara MMARs
 `Pathology`
 -----------
 
-.. automodule:: monai.apps.pathology.datasets
+.. automodule:: monai.apps.pathology.data
 .. autoclass:: PatchWSIDataset
     :members:
 .. autoclass:: SmartCachePatchWSIDataset

monai/apps/pathology/__init__.py

@@ -9,7 +9,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from .datasets import MaskedInferenceWSIDataset, PatchWSIDataset, SmartCacheDataset
+from .data import MaskedInferenceWSIDataset, PatchWSIDataset, SmartCachePatchWSIDataset
 from .handlers import ProbMapProducer
 from .metrics import LesionFROC
 from .transforms.stain.array import ExtractHEStains, NormalizeHEStains

monai/apps/pathology/data/__init__.py

@@ -0,0 +1,12 @@
+# Copyright 2020 - 2021 MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from .datasets import MaskedInferenceWSIDataset, PatchWSIDataset, SmartCachePatchWSIDataset

monai/apps/pathology/metrics/__init__.py

@@ -0,0 +1,12 @@
+# Copyright 2020 - 2021 MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from .lesion_froc import LesionFROC

tests/test_masked_inference_wsi_dataset.py

@@ -17,7 +17,7 @@
 from numpy.testing import assert_array_equal
 from parameterized import parameterized
 
-from monai.apps.pathology.datasets import MaskedInferenceWSIDataset
+from monai.apps.pathology.data import MaskedInferenceWSIDataset
 from monai.apps.utils import download_url
 from monai.utils import optional_import
 from tests.utils import skip_if_quick

tests/test_patch_wsi_dataset.py

@@ -17,7 +17,7 @@
 from numpy.testing import assert_array_equal
 from parameterized import parameterized
 
-from monai.apps.pathology.datasets import PatchWSIDataset
+from monai.apps.pathology.data import PatchWSIDataset
 from monai.apps.utils import download_url
 from monai.utils import optional_import
 

tests/test_smartcache_patch_wsi_dataset.py

@@ -17,7 +17,7 @@
 from numpy.testing import assert_array_equal
 from parameterized import parameterized
 
-from monai.apps.pathology.datasets import SmartCachePatchWSIDataset
+from monai.apps.pathology.data import SmartCachePatchWSIDataset
 from monai.apps.utils import download_url
 from monai.utils import optional_import