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Fix bugs resample #82

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Fix bugs resample #82

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a16c397
fix bug on params
PierreAuriau Oct 31, 2024
c242566
change filenames
PierreAuriau Oct 31, 2024
942f9c1
upgrade documentation and helpers
PierreAuriau Oct 31, 2024
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65 changes: 28 additions & 37 deletions deep_folding/brainvisa/resample_files.py
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Original file line number Diff line number Diff line change
Expand Up @@ -85,12 +85,12 @@
_SKELETON_DIR_DEFAULT, \
_RESAMPLED_SKELETON_DIR_DEFAULT

_SKELETON_FILENAME = "skeleton_generated_"
_FOLDLABEL_FILENAME = "foldlabel_"
_EXTREMITIES_FILENAME = "extremities_"
_RESAMPLED_SKELETON_FILENAME = "resampled_skeleton_"
_RESAMPLED_FOLDLABEL_FILENAME = "resampled_foldlabel_"
_RESAMPLED_EXTREMITIES_FILENAME = "resampled_extremities_"
_SKELETON_FILENAME = "skeleton_generated"
_FOLDLABEL_FILENAME = "foldlabel"
_EXTREMITIES_FILENAME = "extremities"
_RESAMPLED_SKELETON_FILENAME = "resampled_skeleton"
_RESAMPLED_FOLDLABEL_FILENAME = "resampled_foldlabel"
_RESAMPLED_EXTREMITIES_FILENAME = "resampled_extremities"


# Defines logger
Expand Down Expand Up @@ -471,9 +471,9 @@ def __init__(self, src_dir, resampled_dir, transform_dir,
out_voxel_size: float giving voxel size in mm
parallel: does parallel computation if True
src_filename : name of skeleton files
(format : "<SIDE><src_filename><SUBJECT>.nii.gz")
(format : "<SIDE><src_filename>_<SUBJECT>.nii.gz")
output_filename : name of generated files
(format : "<SIDE><output_filename><SUBJECT>.nii.gz")
(format : "<SIDE><output_filename>_<SUBJECT>.nii.gz")
"""
super(SkeletonResampler, self).__init__(
src_dir=src_dir, resampled_dir=resampled_dir,
Expand All @@ -491,17 +491,17 @@ def __init__(self, src_dir, resampled_dir, transform_dir,
# self.src_dir,
# '%(side)sskeleton_generated_%(subject)s.nii.gz')
self.src_file = join(self.src_dir,
'%(side)s' + src_filename + '%(subject)s.nii.gz')
f'%(side)s{src_filename}_%(subject)s.nii.gz')

# Names of files in function of dictionary: keys -> 'subject' and
# 'side'
self.src_filename = src_filename
self.resampled_file = join(
self.resampled_dir,
'%(side)s' + output_filename + '%(subject)s.nii.gz')
f'%(side)s{output_filename}_%(subject)s.nii.gz')

# subjects are detected as the nifti file names under src_dir
self.expr = '^.' + src_filename + '(.*).nii.gz$'
self.expr = f'^.{src_filename}_(.*).nii.gz$'

@staticmethod
def resample_one_subject(src_file: str,
Expand Down Expand Up @@ -540,9 +540,9 @@ def __init__(self, src_dir, resampled_dir, transform_dir,
out_voxel_size: float giving voxel size in mm
parallel: does parallel computation if True
src_filename : name of fold label files
(format : "<SIDE><src_filename><SUBJECT>.nii.gz")
(format : "<SIDE><src_filename>_<SUBJECT>.nii.gz")
output_filename : name of generated files
(format : "<SIDE><output_filename><SUBJECT>.nii.gz")
(format : "<SIDE><output_filename>_<SUBJECT>.nii.gz")
"""
super(FoldLabelResampler, self).__init__(
src_dir=src_dir, resampled_dir=resampled_dir,
Expand All @@ -554,18 +554,18 @@ def __init__(self, src_dir, resampled_dir, transform_dir,
# Src directory contains either 'R' or 'L' a subdirectory
self.src_file = join(
self.src_dir,
'%(side)s' + src_filename + '%(subject)s.nii.gz')
f'%(side)s{src_filename}_%(subject)s.nii.gz')

# Names of files in function of dictionary: keys -> 'subject' and
# 'side'
self.src_filename = src_filename
self.resampled_dir = self.resampled_dir + "_before_masking"
self.resampled_file = join(
self.resampled_dir,
'%(side)s' + output_filename + '%(subject)s.nii.gz')
f'%(side)s{output_filename}_%(subject)s.nii.gz')

# subjects are detected as the nifti file names under src_dir
self.expr = '^.' + src_filename + '(.*).nii.gz$'
self.expr = f'^.{src_filename}_(.*).nii.gz$'

@staticmethod
def resample_one_subject(src_file: str,
Expand Down Expand Up @@ -598,9 +598,9 @@ def __init__(self, src_dir, resampled_dir, transform_dir,
out_voxel_size: float giving voxel size in mm
parallel: does parallel computation if True
src_filename : name of fold label files
(format : "<SIDE><src_filename><SUBJECT>.nii.gz")
(format : "<SIDE><src_filename>_<SUBJECT>.nii.gz")
output_filename : name of generated files
(format : "<SIDE><output_filename><SUBJECT>.nii.gz")
(format : "<SIDE><output_filename>_<SUBJECT>.nii.gz")
"""
super(ExtremitiesResampler, self).__init__(
src_dir=src_dir, resampled_dir=resampled_dir,
Expand All @@ -612,18 +612,18 @@ def __init__(self, src_dir, resampled_dir, transform_dir,
# Src directory contains either 'R' or 'L' a subdirectory
self.src_file = join(
self.src_dir,
'%(side)s' + src_filename + '%(subject)s.nii.gz')
f'%(side)s{src_filename}_%(subject)s.nii.gz')

# Names of files in function of dictionary: keys -> 'subject' and
# 'side'
self.src_filename = src_filename
self.resampled_dir = self.resampled_dir + "_before_masking"
self.resampled_file = join(
self.resampled_dir,
'%(side)s' + output_filename + '%(subject)s.nii.gz')
f'%(side)s{output_filename}_%(subject)s.nii.gz')

# subjects are detected as the nifti file names under src_dir
self.expr = '^.' + src_filename + '(.*).nii.gz$'
self.expr = f'^.{src_filename}_(.*).nii.gz$'

@staticmethod
def resample_one_subject(src_file: str,
Expand Down Expand Up @@ -665,17 +665,17 @@ def __init__(self, src_dir, resampled_dir, transform_dir,
# Src directory contains either 'R' or 'L' a subdirectory
self.src_file = join(
self.src_dir,
'%(side)s' + src_filename + '%(subject)s.nii.gz')
f'%(side)s{src_filename}_%(subject)s.nii.gz')

# Names of files in function of dictionary: keys -> 'subject' and
# 'side'
self.src_filename = src_filename
self.resampled_file = join(
self.resampled_dir,
'%(side)s' + output_filename + '%(subject)s.nii.gz')
f'%(side)s{output_filename}_%(subject)s.nii.gz')

# subjects are detected as the nifti file names under src_dir
self.expr = '^.' + src_filename + '(.*).nii.gz$'
self.expr = f'^.{src_filename}_(.*).nii.gz$'

@staticmethod
def resample_one_subject(src_file: str,
Expand Down Expand Up @@ -744,15 +744,15 @@ def parse_args(argv):
parser.add_argument(
"-f", "--src_filename", type=str, default=_SKELETON_FILENAME,
help='Filename of sources files. '
'Format is : "<SIDE><src_filename><SUBJECT>.nii.gz" '
'Format is : "<SIDE><src_filename>_<SUBJECT>.nii.gz" '
'Default is : ' + _SKELETON_FILENAME)
parser.add_argument(
"-e",
"--output_filename",
type=str,
default=_RESAMPLED_SKELETON_FILENAME,
help='Filename of output files. '
'Format is : "<SIDE><output_filename><SUBJECT>.nii.gz" '
'Format is : "<SIDE><output_filename>_<SUBJECT>.nii.gz" '
'Default is : ' +
_RESAMPLED_SKELETON_FILENAME)
parser.add_argument(
Expand All @@ -761,27 +761,18 @@ def parse_args(argv):
'If no option is provided then logging.INFO is selected. '
'If one option -v (or -vv) or more is provided '
'then logging.DEBUG is selected.')

params = {}


args = parser.parse_args(argv)

setup_log(args,
log_dir=f"{args.output_dir}",
prog_name=basename(__file__),
suffix='right' if args.side == 'R' else 'left')

params['src_dir'] = args.src_dir
params['input_type'] = args.input_type
params = vars(args)
params['resampled_dir'] = args.output_dir
params['transform_dir'] = args.transform_dir
params['side'] = args.side
params['out_voxel_size'] = args.out_voxel_size
params['parallel'] = args.parallel
# Checks if nb_subjects is either the string "all" or a positive integer
params['nb_subjects'] = get_number_subjects(args.nb_subjects)
params['src_filename'] = args.src_filename
params['output_filename'] = args.output_filename

# Removes renamed params
# So that we can use params dictionary directly as function arguments
Expand Down