ashs.py 3.0 KB

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  1. """
  2. Read hippocampal subfield volumes computed by ASHS
  3. https://sites.google.com/site/hipposubfields/home
  4. >>> from freesurfer_volume_reader.ashs import HippocampalSubfieldsVolumeFile
  5. >>>
  6. >>> for volume_file in HippocampalSubfieldsVolumeFile('/my/ashs/subjects'):
  7. >>> print(volume_file.subject, volume_file.hemisphere, volume_file.correction)
  8. >>> print(volume_file.read_volumes_mm3())
  9. >>> print(volume_file.read_volumes_dataframe())
  10. """
  11. import os
  12. import re
  13. import typing
  14. import pandas
  15. import freesurfer_volume_reader
  16. class IntracranialVolumeFile(freesurfer_volume_reader.VolumeFile):
  17. FILENAME_REGEX = re.compile(r'^(?P<s>\w+)_icv.txt$')
  18. def __init__(self, path: str):
  19. self._absolute_path = os.path.abspath(path)
  20. filename_match = self.FILENAME_REGEX.match(os.path.basename(path))
  21. assert filename_match, self._absolute_path
  22. self.subject = filename_match.groupdict()['s']
  23. @property
  24. def absolute_path(self):
  25. return self._absolute_path
  26. class HippocampalSubfieldsVolumeFile(freesurfer_volume_reader.SubfieldVolumeFile):
  27. # https://sites.google.com/site/hipposubfields/tutorial#TOC-Viewing-ASHS-Segmentation-Results
  28. FILENAME_PATTERN = r'^(?P<s>\w+)_(?P<h>left|right)' \
  29. r'_(heur|corr_(?P<c>nogray|usegray))_volumes.txt$'
  30. FILENAME_REGEX = re.compile(FILENAME_PATTERN)
  31. def __init__(self, path: str):
  32. self._absolute_path = os.path.abspath(path)
  33. filename_match = self.FILENAME_REGEX.match(os.path.basename(path))
  34. assert filename_match, self._absolute_path
  35. filename_groups = filename_match.groupdict()
  36. self.subject = filename_groups['s']
  37. self.hemisphere = filename_groups['h']
  38. self.correction = filename_groups['c']
  39. @property
  40. def absolute_path(self):
  41. return self._absolute_path
  42. def read_volumes_mm3(self) -> typing.Dict[str, float]:
  43. subfield_volumes = {}
  44. with open(self.absolute_path, 'r') as volume_file:
  45. for line in volume_file.read().rstrip().split('\n'):
  46. # > echo $ASHS_SUBJID $side $SUB $NBODY $VSUB >> $FNBODYVOL
  47. # https://github.com/pyushkevich/ashs/blob/515ff7c2f50928adabc4e64bded9a7e76fc750b1/bin/ashs_extractstats_qsub.sh#L94
  48. subject, hemisphere, subfield_name, slices_number_str, volume_mm3_str \
  49. = line.split(' ')
  50. assert self.subject == subject
  51. assert self.hemisphere == hemisphere
  52. assert int(slices_number_str) >= 0
  53. subfield_volumes[subfield_name] = float(volume_mm3_str)
  54. return subfield_volumes
  55. def read_volumes_dataframe(self) -> pandas.DataFrame:
  56. volumes_frame = pandas.DataFrame([
  57. {'subfield': s, 'volume_mm^3': v}
  58. for s, v in self.read_volumes_mm3().items()
  59. ])
  60. volumes_frame['subject'] = self.subject
  61. volumes_frame['hemisphere'] = self.hemisphere
  62. volumes_frame['correction'] = self.correction
  63. return volumes_frame