tools/accuracy_checker/accuracy_checker/annotation_converters/brats.py

   1 """
   2 Copyright (c) 2019 Intel Corporation
   3
   4 Licensed under the Apache License, Version 2.0 (the "License");
   5 you may not use this file except in compliance with the License.
   6 You may obtain a copy of the License at
   7
   8       http://www.apache.org/licenses/LICENSE-2.0
   9
  10 Unless required by applicable law or agreed to in writing, software
  11 distributed under the License is distributed on an "AS IS" BASIS,
  12 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  13 See the License for the specific language governing permissions and
  14 limitations under the License.
  15 """
  16 from pathlib import Path
  17
  18 from ..representation import BrainTumorSegmentationAnnotation
  19 from ..utils import get_path
  20 from ..config import StringField
  21 from .format_converter import BaseFormatConverter, DirectoryBasedAnnotationConverterConfig
  22
  23
  24 class BratsConverterConfig(DirectoryBasedAnnotationConverterConfig):
  25     image_folder = StringField(optional=True)
  26     mask_folder = StringField(optional=True)
  27
  28
  29 class BratsConverter(BaseFormatConverter):
  30     __provider__ = 'brats'
  31
  32     _config_validator_type = BratsConverterConfig
  33
  34     def configure(self):
  35         self.data_dir = self.config['data_dir']
  36         self.image_folder = self.config.get('image_folder', 'imagesTr')
  37         self.mask_folder = self.config.get('mask_folder', 'labelsTr')
  38
  39     def convert(self):
  40         mask_folder = Path(self.mask_folder)
  41         image_folder = Path(self.image_folder)
  42         image_dir = get_path(self.data_dir / image_folder, is_directory=True)
  43
  44         annotations = []
  45         for file_in_dir in image_dir.iterdir():
  46             annotation = BrainTumorSegmentationAnnotation(
  47                 str(image_folder / file_in_dir.parts[-1]),
  48                 str(mask_folder / file_in_dir.parts[-1]),
  49             )
  50
  51             annotations.append(annotation)
  52
  53         return annotations, None