Add CBIS-DDSM dataset to TFDS.

The DDSM is a database of 2,620 scanned film mammography studies. It contains normal, benign, and malignant cases with verified pathology information.

The default config is made of patches extracted from the original mammograms, following the description from http://arxiv.org/abs/1708.09427, in order to frame the task to solve in a traditional image classification setting.

PiperOrigin-RevId: 252581171

Author: jpuigcerver

tensorflow_datasets/image/__init__.py

@@ -19,6 +19,7 @@
 from tensorflow_datasets.image.bigearthnet import Bigearthnet
 from tensorflow_datasets.image.caltech import Caltech101
 from tensorflow_datasets.image.cats_vs_dogs import CatsVsDogs
+from tensorflow_datasets.image.cbis_ddsm import CuratedBreastImagingDDSM
 from tensorflow_datasets.image.celeba import CelebA
 from tensorflow_datasets.image.celebahq import CelebAHq
 from tensorflow_datasets.image.chexpert import Chexpert

tensorflow_datasets/image/cbis_ddsm.py

@@ -0,0 +1,10 @@
+N/A
+CLUSTERED
+CLUSTERED-LINEAR
+CLUSTERED-SEGMENTAL
+DIFFUSELY_SCATTERED
+LINEAR
+LINEAR-SEGMENTAL
+REGIONAL
+REGIONAL-REGIONAL
+SEGMENTAL

tensorflow_datasets/image/cbis_ddsm_calc_distributions.txt

@@ -0,0 +1,48 @@
+N/A
+AMORPHOUS
+AMORPHOUS-PLEOMORPHIC
+AMORPHOUS-ROUND_AND_REGULAR
+COARSE
+COARSE-LUCENT_CENTER
+COARSE-PLEOMORPHIC
+COARSE-ROUND_AND_REGULAR
+COARSE-ROUND_AND_REGULAR-LUCENT_CENTER
+COARSE-ROUND_AND_REGULAR-LUCENT_CENTERED
+DYSTROPHIC
+EGGSHELL
+FINE_LINEAR_BRANCHING
+LARGE_RODLIKE
+LARGE_RODLIKE-ROUND_AND_REGULAR
+LUCENT_CENTER
+LUCENT_CENTERED
+LUCENT_CENTER-PUNCTATE
+MILK_OF_CALCIUM
+PLEOMORPHIC
+PLEOMORPHIC-AMORPHOUS
+PLEOMORPHIC-FINE_LINEAR_BRANCHING
+PLEOMORPHIC-PLEOMORPHIC
+PUNCTATE
+PUNCTATE-AMORPHOUS
+PUNCTATE-AMORPHOUS-PLEOMORPHIC
+PUNCTATE-FINE_LINEAR_BRANCHING
+PUNCTATE-LUCENT_CENTER
+PUNCTATE-PLEOMORPHIC
+PUNCTATE-ROUND_AND_REGULAR
+ROUND_AND_REGULAR
+ROUND_AND_REGULAR-AMORPHOUS
+ROUND_AND_REGULAR-EGGSHELL
+ROUND_AND_REGULAR-LUCENT_CENTER
+ROUND_AND_REGULAR-LUCENT_CENTER-DYSTROPHIC
+ROUND_AND_REGULAR-LUCENT_CENTERED
+ROUND_AND_REGULAR-LUCENT_CENTER-PUNCTATE
+ROUND_AND_REGULAR-PLEOMORPHIC
+ROUND_AND_REGULAR-PUNCTATE
+ROUND_AND_REGULAR-PUNCTATE-AMORPHOUS
+SKIN
+SKIN-COARSE-ROUND_AND_REGULAR
+SKIN-PUNCTATE
+SKIN-PUNCTATE-ROUND_AND_REGULAR
+VASCULAR
+VASCULAR-COARSE
+VASCULAR-COARSE-LUCENT_CENTERED
+VASCULAR-COARSE-LUCENT_CENTER-ROUND_AND_REGULAR-PUNCTATE

tensorflow_datasets/image/cbis_ddsm_calc_types.txt

@@ -0,0 +1,20 @@
+N/A
+CIRCUMSCRIBED
+CIRCUMSCRIBED-ILL_DEFINED
+CIRCUMSCRIBED-MICROLOBULATED
+CIRCUMSCRIBED-MICROLOBULATED-ILL_DEFINED
+CIRCUMSCRIBED-OBSCURED
+CIRCUMSCRIBED-OBSCURED-ILL_DEFINED
+CIRCUMSCRIBED-SPICULATED
+ILL_DEFINED
+ILL_DEFINED-SPICULATED
+MICROLOBULATED
+MICROLOBULATED-ILL_DEFINED
+MICROLOBULATED-ILL_DEFINED-SPICULATED
+MICROLOBULATED-SPICULATED
+OBSCURED
+OBSCURED-CIRCUMSCRIBED
+OBSCURED-ILL_DEFINED
+OBSCURED-ILL_DEFINED-SPICULATED
+OBSCURED-SPICULATED
+SPICULATED

tensorflow_datasets/image/cbis_ddsm_mass_margins.txt

@@ -0,0 +1,21 @@
+N/A
+ARCHITECTURAL_DISTORTION
+ASYMMETRIC_BREAST_TISSUE
+FOCAL_ASYMMETRIC_DENSITY
+IRREGULAR
+IRREGULAR-ARCHITECTURAL_DISTORTION
+IRREGULAR-ASYMMETRIC_BREAST_TISSUE
+IRREGULAR-FOCAL_ASYMMETRIC_DENSITY
+LOBULATED
+LOBULATED-ARCHITECTURAL_DISTORTION
+LOBULATED-IRREGULAR
+LOBULATED-LYMPH_NODE
+LOBULATED-OVAL
+LYMPH_NODE
+OVAL
+OVAL-LOBULATED
+OVAL-LYMPH_NODE
+ROUND
+ROUND-IRREGULAR-ARCHITECTURAL_DISTORTION
+ROUND-LOBULATED
+ROUND-OVAL

tensorflow_datasets/image/cbis_ddsm_mass_shapes.txt

@@ -0,0 +1,5 @@
+BACKGROUND
+BENING_CALCIFICATION
+BENING_MASS
+MALIGNANT_CALCIFICATION
+MALIGNANT_MASS

tensorflow_datasets/image/cbis_ddsm_patch_labels.txt

@@ -0,0 +1,69 @@
+# coding=utf-8
+# Copyright 2019 The TensorFlow Datasets Authors.
+#
+# 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.
+
+"""Tests for cbis_ddsm dataset module."""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+from tensorflow_datasets import testing
+from tensorflow_datasets.image import cbis_ddsm
+
+
+class CuratedBreastImagingDDSMOriginalCalcTest(testing.DatasetBuilderTestCase):
+  DATASET_CLASS = cbis_ddsm.CuratedBreastImagingDDSM
+  BUILDER_CONFIG_NAMES_TO_TEST = ['original-calc']
+  SPLITS = {
+      'train': 3,  # Abnormalities: 7
+      'test': 2,   # Abnormalities: 4
+  }
+  DL_EXTRACT_RESULT = {
+      'test': 'calc_case_description_test_set.csv',
+      'train': 'calc_case_description_train_set.csv',
+  }
+
+
+class CuratedBreastImagingDDSMOriginalMassTest(testing.DatasetBuilderTestCase):
+  DATASET_CLASS = cbis_ddsm.CuratedBreastImagingDDSM
+  BUILDER_CONFIG_NAMES_TO_TEST = ['original-mass']
+  SPLITS = {
+      'train': 3,  # Abnormalities: 10
+      'test': 2,   # Abnormalities: 4
+  }
+  DL_EXTRACT_RESULT = {
+      'test': 'mass_case_description_test_set.csv',
+      'train': 'mass_case_description_train_set.csv',
+  }
+
+
+class CuratedBreastImagingDDSMPatchesTest(testing.DatasetBuilderTestCase):
+  DATASET_CLASS = cbis_ddsm.CuratedBreastImagingDDSM
+  BUILDER_CONFIG_NAMES_TO_TEST = ['patches']
+  SPLITS = {
+      # Total patches = [(10 + 4 + 7 + 4) + (3 + 2 + 3 + 2)] * 10
+      'train': 280,
+      'validation': 40,
+      'test': 30,
+  }
+  DL_EXTRACT_RESULT = {
+      'calc-test': 'calc_case_description_test_set.csv',
+      'calc-train': 'calc_case_description_train_set.csv',
+      'mass-test': 'mass_case_description_test_set.csv',
+      'mass-train': 'mass_case_description_train_set.csv',
+  }
+
+
+if __name__ == '__main__':
+  testing.test_main()