diff --git a/docs/source/apps.rst b/docs/source/apps.rst index 959e42d6f9..1a2efeff48 100644 --- a/docs/source/apps.rst +++ b/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 diff --git a/monai/apps/pathology/__init__.py b/monai/apps/pathology/__init__.py index 0ada8fe51b..80f32403ea 100644 --- a/monai/apps/pathology/__init__.py +++ b/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 diff --git a/monai/apps/pathology/data/__init__.py b/monai/apps/pathology/data/__init__.py new file mode 100644 index 0000000000..64556b6f6e --- /dev/null +++ b/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 diff --git a/monai/apps/pathology/datasets.py b/monai/apps/pathology/data/datasets.py similarity index 100% rename from monai/apps/pathology/datasets.py rename to monai/apps/pathology/data/datasets.py diff --git a/monai/apps/pathology/metrics/__init__.py b/monai/apps/pathology/metrics/__init__.py new file mode 100644 index 0000000000..ad62df524a --- /dev/null +++ b/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 diff --git a/monai/apps/pathology/metrics.py b/monai/apps/pathology/metrics/lesion_froc.py similarity index 100% rename from monai/apps/pathology/metrics.py rename to monai/apps/pathology/metrics/lesion_froc.py diff --git a/tests/test_masked_inference_wsi_dataset.py b/tests/test_masked_inference_wsi_dataset.py index 27e64c2d7c..361c17e106 100644 --- a/tests/test_masked_inference_wsi_dataset.py +++ b/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 diff --git a/tests/test_patch_wsi_dataset.py b/tests/test_patch_wsi_dataset.py index 7c34997872..f775f28376 100644 --- a/tests/test_patch_wsi_dataset.py +++ b/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 diff --git a/tests/test_smartcache_patch_wsi_dataset.py b/tests/test_smartcache_patch_wsi_dataset.py index 876a30a3b8..c484e5fc69 100644 --- a/tests/test_smartcache_patch_wsi_dataset.py +++ b/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