Chris Oswald
commited on
Commit
•
a803284
1
Parent(s):
9c6a8c8
modified patient id generation
Browse files
SPIDER.py
CHANGED
@@ -328,9 +328,7 @@ class SPIDER(datasets.GeneratorBasedBuilder):
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# Generate train/validate/test partitions of patient IDs
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patient_ids = np.unique([file.split('_')[0] for file in image_files])
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print(f'Number of patients: {len(patient_ids)}')
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partition = np.random.choice(
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['train', 'dev', 'test'],
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p=[train_share, validate_share, test_share],
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@@ -341,13 +339,6 @@ class SPIDER(datasets.GeneratorBasedBuilder):
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test_ids = set(patient_ids[partition == 'test'])
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assert len(train_ids.union(validate_ids, test_ids)) == len(patient_ids)
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print(f'# of training ids: {len(train_ids)}')
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print(f'# of validation ids: {len(validate_ids)}')
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print(f'# of testing ids: {len(test_ids)}')
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print(f'Length of image file list: {len(image_files)}')
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# Subset train/validation/test partition images and mask files
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train_image_files = subset_file_list(image_files, train_ids)
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validate_image_files = subset_file_list(image_files, validate_ids)
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@@ -361,12 +352,6 @@ class SPIDER(datasets.GeneratorBasedBuilder):
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assert len(validate_image_files) == len(validate_mask_files)
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assert len(test_image_files) == len(test_mask_files)
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print(f'# of training images: {len(train_image_files)}')
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print(f'# of validation images: {len(validate_image_files)}')
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print(f'# of testing images: {len(test_image_files)}')
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print([x for x in image_files if x not in train_image_files + validate_image_files + test_image_files])
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# Import patient/scanner data and radiological gradings data
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overview_data = import_csv_data(paths_dict['overview'])
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grades_data = import_csv_data(paths_dict['gradings'])
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]
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# Generate train/validate/test partitions of patient IDs
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+
patient_ids = np.unique([file.split('_')[0] for file in image_files])
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partition = np.random.choice(
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['train', 'dev', 'test'],
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p=[train_share, validate_share, test_share],
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test_ids = set(patient_ids[partition == 'test'])
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assert len(train_ids.union(validate_ids, test_ids)) == len(patient_ids)
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# Subset train/validation/test partition images and mask files
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train_image_files = subset_file_list(image_files, train_ids)
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validate_image_files = subset_file_list(image_files, validate_ids)
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assert len(validate_image_files) == len(validate_mask_files)
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assert len(test_image_files) == len(test_mask_files)
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# Import patient/scanner data and radiological gradings data
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overview_data = import_csv_data(paths_dict['overview'])
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grades_data = import_csv_data(paths_dict['gradings'])
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