def parse_directory(deriv_dir, work_dir, analysis):
fl_layout = BIDSLayout(
deriv_dir,
config=['bids', 'derivatives', 'fitlins'],
validate=False)
wd_layout = BIDSLayout(
str(Path(work_dir) / 'reportlets' / 'fitlins'),
validate=False)
contrast_svgs = fl_layout.get(extensions='.svg', suffix='contrasts')
analyses = []
for contrast_svg in contrast_svgs:
ents = contrast_svg.entities
ents.pop('suffix')
ents.setdefault('subject', None)
correlation_matrix = fl_layout.get(extensions='.svg', suffix='corr',
**ents)
design_matrix = fl_layout.get(extensions='.svg', suffix='design', **ents)
job_desc = {
'ents': {k: v for k, v in ents.items() if v is not None},
'dataset': analysis.layout.root,
'model_name': analysis.model['name'],
'contrasts_svg': contrast_svg.path,
}
if ents.get('subject'):
job_desc['subject_id'] = ents.get('subject')
if correlation_matrix:
job_desc['correlation_matrix_svg'] = correlation_matrix[0].path
if design_matrix:
job_desc['design_matrix_svg'] = design_matrix[0].path
snippet = wd_layout.get(extensions='.html', suffix='snippet', **ents)
if snippet:
with open(snippet[0].path) as fobj:
job_desc['warning'] = fobj.read()
contrasts = fl_layout.get(extensions='.png', suffix='ortho', **ents)
# TODO: Split contrasts from estimates
job_desc['contrasts'] = [{'image_file': c.path,
'name':
fl_layout.parse_file_entities(
c.path)['contrast']}
for c in contrasts]
analyses.append(job_desc)
return analyses
def _run_interface(self, runtime):
from bids.layout import BIDSLayout
derivatives = self.inputs.derivatives
layout = BIDSLayout(self.inputs.bids_dir, derivatives=derivatives)
bold_files = []
mask_files = []
entities = []
for ents in self.inputs.entities:
selectors = {**self.inputs.selectors, **ents}
bold_file = layout.get(**selectors)
if len(bold_file) == 0:
raise FileNotFoundError(
"Could not find BOLD file in {} with entities {}"
"".format(self.inputs.bids_dir, selectors))
elif len(bold_file) > 1:
raise ValueError(
"Non-unique BOLD file in {} with entities {}.\n"
"Matches:\n\t{}"
"".format(
self.inputs.bids_dir, selectors,
"\n\t".join('{} ({})'.format(
f.path, layout.files[f.path].entities)
for f in bold_file)))
# Select exactly matching mask file (may be over-cautious)
bold_ents = layout.parse_file_entities(bold_file[0].path)
bold_ents['suffix'] = 'mask'
bold_ents['desc'] = 'brain'
bold_ents['extension'] = ['.nii', '.nii.gz']
mask_file = layout.get(**bold_ents)
bold_ents.pop('suffix')
bold_ents.pop('desc')
bold_files.append(bold_file[0].path)
mask_files.append(mask_file[0].path if mask_file else None)
entities.append(bold_ents)
self._results['bold_files'] = bold_files
self._results['mask_files'] = mask_files
self._results['entities'] = entities
return runtime
