From a16c397fd31629dbeb98321c556edfd004c3aabd Mon Sep 17 00:00:00 2001 From: PierreAuriau Date: Thu, 31 Oct 2024 10:57:28 +0100 Subject: [PATCH 1/3] fix bug on params --- deep_folding/brainvisa/resample_files.py | 15 +++------------ 1 file changed, 3 insertions(+), 12 deletions(-) diff --git a/deep_folding/brainvisa/resample_files.py b/deep_folding/brainvisa/resample_files.py index 29ba594..3634df4 100644 --- a/deep_folding/brainvisa/resample_files.py +++ b/deep_folding/brainvisa/resample_files.py @@ -761,9 +761,7 @@ 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, @@ -771,18 +769,11 @@ def parse_args(argv): 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 params.pop('output_dir') From c242566ba08e9e533f2a44258b21c1c21ca0892c Mon Sep 17 00:00:00 2001 From: PierreAuriau Date: Thu, 31 Oct 2024 11:02:23 +0100 Subject: [PATCH 2/3] change filenames --- deep_folding/brainvisa/resample_files.py | 38 ++++++++++++------------ 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/deep_folding/brainvisa/resample_files.py b/deep_folding/brainvisa/resample_files.py index 3634df4..44270bf 100644 --- a/deep_folding/brainvisa/resample_files.py +++ b/deep_folding/brainvisa/resample_files.py @@ -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 @@ -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, @@ -554,7 +554,7 @@ 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' @@ -562,10 +562,10 @@ def __init__(self, src_dir, resampled_dir, transform_dir, 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, @@ -612,7 +612,7 @@ 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' @@ -620,10 +620,10 @@ def __init__(self, src_dir, resampled_dir, transform_dir, 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, @@ -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, @@ -773,7 +773,7 @@ def parse_args(argv): params['resampled_dir'] = args.output_dir # Checks if nb_subjects is either the string "all" or a positive integer params['nb_subjects'] = get_number_subjects(args.nb_subjects) - + # Removes renamed params # So that we can use params dictionary directly as function arguments params.pop('output_dir') From 942f9c13749397489b29a9e2b5789ea12d716293 Mon Sep 17 00:00:00 2001 From: PierreAuriau Date: Thu, 31 Oct 2024 11:07:25 +0100 Subject: [PATCH 3/3] upgrade documentation and helpers --- deep_folding/brainvisa/resample_files.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/deep_folding/brainvisa/resample_files.py b/deep_folding/brainvisa/resample_files.py index 44270bf..be4abe2 100644 --- a/deep_folding/brainvisa/resample_files.py +++ b/deep_folding/brainvisa/resample_files.py @@ -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 : ".nii.gz") + (format : "_.nii.gz") output_filename : name of generated files - (format : ".nii.gz") + (format : "_.nii.gz") """ super(SkeletonResampler, self).__init__( src_dir=src_dir, resampled_dir=resampled_dir, @@ -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 : ".nii.gz") + (format : "_.nii.gz") output_filename : name of generated files - (format : ".nii.gz") + (format : "_.nii.gz") """ super(FoldLabelResampler, self).__init__( src_dir=src_dir, resampled_dir=resampled_dir, @@ -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 : ".nii.gz") + (format : "_.nii.gz") output_filename : name of generated files - (format : ".nii.gz") + (format : "_.nii.gz") """ super(ExtremitiesResampler, self).__init__( src_dir=src_dir, resampled_dir=resampled_dir, @@ -744,7 +744,7 @@ def parse_args(argv): parser.add_argument( "-f", "--src_filename", type=str, default=_SKELETON_FILENAME, help='Filename of sources files. ' - 'Format is : ".nii.gz" ' + 'Format is : "_.nii.gz" ' 'Default is : ' + _SKELETON_FILENAME) parser.add_argument( "-e", @@ -752,7 +752,7 @@ def parse_args(argv): type=str, default=_RESAMPLED_SKELETON_FILENAME, help='Filename of output files. ' - 'Format is : ".nii.gz" ' + 'Format is : "_.nii.gz" ' 'Default is : ' + _RESAMPLED_SKELETON_FILENAME) parser.add_argument(