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Merge pull request #345 from CoBrALab/parser
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For multi-parameter options, it is no longer needed to fill every par…
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@Gab-D-G
Gab-D-G authored Dec 15, 2023
2 parents 4eba7a7 + d5e8e9f commit 706d55e
Showing 1 changed file with 20 additions and 5 deletions.
25 changes: 20 additions & 5 deletions rabies/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1064,31 +1064,37 @@ def read_parser(parser, args):
opts.anat_inho_cor = parse_argument(opt=opts.anat_inho_cor,
key_value_pairs = {'method':['Rigid', 'Affine', 'SyN', 'no_reg', 'N4_reg', 'disable'],
'otsu_thresh':['0','1','2','3','4'], 'multiotsu':['true', 'false']},
defaults = {'method': 'SyN', 'otsu_thresh': '2', 'multiotsu': False},
name='anat_inho_cor')

opts.bold_inho_cor = parse_argument(opt=opts.bold_inho_cor,
key_value_pairs = {'method':['Rigid', 'Affine', 'SyN', 'no_reg', 'N4_reg', 'disable'],
'otsu_thresh':['0','1','2','3','4'], 'multiotsu':['true', 'false']},
defaults = {'method': 'Rigid', 'otsu_thresh': '2', 'multiotsu': False},
name='bold_inho_cor')

opts.commonspace_reg = parse_argument(opt=opts.commonspace_reg,
key_value_pairs = {'masking':['true', 'false'], 'brain_extraction':['true', 'false'], 'keep_mask_after_extract':['true', 'false'],
'template_registration':['Rigid', 'Affine', 'SyN', 'no_reg'], 'fast_commonspace':['true', 'false']},
defaults = {'masking':False,'brain_extraction':False,'keep_mask_after_extract':False,'template_registration':'SyN','fast_commonspace':False},
name='commonspace_reg')

opts.bold2anat_coreg = parse_argument(opt=opts.bold2anat_coreg,
key_value_pairs = {'masking':['true', 'false'], 'brain_extraction':['true', 'false'], 'keep_mask_after_extract':['true', 'false'],
'registration':['Rigid', 'Affine', 'SyN', 'no_reg']},
defaults = {'masking':False,'brain_extraction':False,'keep_mask_after_extract':False,'registration':'SyN'},
name='bold2anat_coreg')

opts.anat_robust_inho_cor = parse_argument(opt=opts.anat_robust_inho_cor,
key_value_pairs = {'apply':['true', 'false'], 'masking':['true', 'false'], 'brain_extraction':['true', 'false'], 'keep_mask_after_extract':['true', 'false'],
'template_registration':['Rigid', 'Affine', 'SyN', 'no_reg']},
defaults = {'apply':False,'masking':False,'brain_extraction':False,'keep_mask_after_extract':False,'template_registration':'SyN'},
name='anat_robust_inho_cor')

opts.bold_robust_inho_cor = parse_argument(opt=opts.bold_robust_inho_cor,
key_value_pairs = {'apply':['true', 'false'], 'masking':['true', 'false'], 'brain_extraction':['true', 'false'], 'keep_mask_after_extract':['true', 'false'],
'template_registration':['Rigid', 'Affine', 'SyN', 'no_reg']},
defaults = {'apply':False,'masking':False,'brain_extraction':False,'keep_mask_after_extract':False,'template_registration':'SyN'},
name='bold_robust_inho_cor')

# check that masking/extraction options are well set
Expand All @@ -1105,48 +1111,57 @@ def read_parser(parser, args):
opts.frame_censoring = parse_argument(opt=opts.frame_censoring,
key_value_pairs = {'FD_censoring':['true', 'false'], 'FD_threshold':float, 'DVARS_censoring':['true', 'false'],
'minimum_timepoint':int},
defaults = {'FD_censoring':False,'FD_threshold':0.05,'DVARS_censoring':False,'minimum_timepoint':3},
name='frame_censoring')

opts.ica_aroma = parse_argument(opt=opts.ica_aroma,
key_value_pairs = {'apply':['true', 'false'], 'dim':int, 'random_seed':int},
defaults = {'apply':False,'dim':0,'random_seed':1},
name='ica_aroma')

elif opts.rabies_stage == 'analysis':
opts.group_ica = parse_argument(opt=opts.group_ica,
key_value_pairs = {'apply':['true', 'false'], 'dim':int, 'random_seed':int},
defaults = {'apply':False,'dim':0,'random_seed':1},
name='group_ica')
opts.optimize_NPR = parse_argument(opt=opts.optimize_NPR,
key_value_pairs = {'apply':['true', 'false'], 'window_size':int, 'min_prior_corr':float,
'diff_thresh':float, 'max_iter':int, 'compute_max':['true', 'false']},
defaults = {'apply':False,'window_size':5,'min_prior_corr':0.5,'diff_thresh':0.03,'max_iter':20,'compute_max':False},
name='optimize_NPR')
opts.scan_QC_thresholds = parse_scan_QC_thresholds(opts.scan_QC_thresholds)

return opts

def parse_argument(opt, key_value_pairs, name):
def parse_argument(opt, key_value_pairs, defaults, name):
key_list = list(key_value_pairs.keys())
l = opt.split(',')
opt_dict = {}
for e in l:
if not '=' in e:
raise ValueError(f"Provided option must follow the 'key=value' syntax, {e} was found instead.")
raise ValueError(f"Provided option must follow the 'key=value' syntax, {e} was found instead for --{name}.")
s = e.split('=')
if not len(s)==2:
raise ValueError(f"Provided option must follow the 'key=value' syntax, {e} was found instead.")
raise ValueError(f"Provided option must follow the 'key=value' syntax, {e} was found instead for --{name}.")
[key,value] = s
if not key in key_list:
raise ValueError(f"The provided key {key} is not part of the available options {key_list}.")
raise ValueError(f"The provided key {key} is not part of the available options {key_list} for --{name}.")
if key_value_pairs[key] in [int,float]:
value = key_value_pairs[key](value)
else:
if not value in key_value_pairs[key]:
raise ValueError(f"The provided value {value} is not part of the available options {key_value_pairs[key]} for the key {key}.")
raise ValueError(f"The provided value {value} is not part of the available options {key_value_pairs[key]} for the key {key} for --{name}.")
if value=='true':
value=True
elif value=='false':
value=False
opt_dict[key]=value

for key in key_list:
if not key in list(opt_dict.keys()):
opt_dict[key]=defaults[key]

# double check the format
for key in key_list:
if not key in list(opt_dict.keys()):
raise ValueError(f"The key {key} is missing from the necessary attributes for --{name}.")
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