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Use new BIDS tags to create nifti file names #171

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Use new BIDS tags to create nifti file names #171

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38ba451
Use new BIDS tags to create nifti file names
jeremie-fouquet Jun 19, 2024
ea7105f
Correct BIDS tags order for rec and dir
jeremie-fouquet Jun 21, 2024
6a02a07
feat: change where user-defined run number is inserted
jeremie-fouquet Jun 21, 2024
894eaa2
fix: correct the position of the echo tag
jeremie-fouquet Jun 22, 2024
d4ffb49
fix: add modality to multi-echo BIDS file name
jeremie-fouquet Jun 25, 2024
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6 changes: 4 additions & 2 deletions brkraw/lib/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -402,19 +402,21 @@ def build_bids_json(dset, row, fname, json_path, slope=False, offset=False):
crop = [int(row.Start), int(row.End)]
else:
crop = None
fname = '{}_{}'.format(fname, row.modality)
if dset.is_multi_echo(row.ScanID, row.RecoID): # multi_echo
nii_objs = dset.get_niftiobj(row.ScanID, row.RecoID, crop=crop, slope=slope, offset=offset)
n_echo = len(nii_objs)
n_digit = len(str(n_echo))
for echo, nii in enumerate(nii_objs):
# caught a bug here for multiple echo, changed fname to currentFileName
currentFileName = '{}_echo-{}_{}'.format(fname, echo + 1, row.modality)
currentFileName = fname.replace('echo.index',str(echo + 1).zfill(n_digit))
output_path = os.path.join(row.Dir, currentFileName)
nii.to_filename('{}.nii.gz'.format(output_path))
if json_path:
ref = get_bids_ref_obj(json_path, row)
dset.save_json(row.ScanID, row.RecoID, currentFileName, dir=row.Dir,
metadata=ref, condition=['me', echo])
else:
fname = '{}_{}'.format(fname, row.modality)
dset.save_as(row.ScanID, row.RecoID, fname, dir=row.Dir, crop=crop, slope=slope, offset=offset)
if re.search('dwi', row.modality, re.IGNORECASE):
# DTI parameter (FSL style)
Expand Down
35 changes: 26 additions & 9 deletions brkraw/scripts/brkraw.py
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Original file line number Diff line number Diff line change
Expand Up @@ -391,11 +391,11 @@ def main():

# [220202] make compatible with csv, tsv and xlsx
if 'xlsx' in datasheet_ext:
df = pd.read_excel(datasheet, dtype={'SubjID': str, 'SessID': str, 'run': str})
df = pd.read_excel(datasheet, dtype={'SubjID': str, 'SessID': str, 'run': str, 'inv': str, 'flip': str})
elif 'csv' in datasheet_ext:
df = pd.read_csv(datasheet, dtype={'SubjID': str, 'SessID': str, 'run': str}, index_col=None, header=0, sep=',')
df = pd.read_csv(datasheet, dtype={'SubjID': str, 'SessID': str, 'run': str, 'inv': str, 'flip': str}, index_col=None, header=0, sep=',')
elif 'tsv' in datasheet_ext:
df = pd.read_csv(datasheet, dtype={'SubjID': str, 'SessID': str, 'run': str}, index_col=None, header=0, sep='\t')
df = pd.read_csv(datasheet, dtype={'SubjID': str, 'SessID': str, 'run': str, 'inv': str, 'flip': str}, index_col=None, header=0, sep='\t')
else:
print(f'{datasheet_ext} if not supported format.')
raise InvalidApproach('Invalid input for datasheet!')
Expand Down Expand Up @@ -470,11 +470,11 @@ def main():
if len(md_df) > 1:
conflict_tested = []
for j, sub_row in md_df.iterrows():
# Try to append a run number if it was not already specified
# The run tag might not appear at the right position with this
# strategy
if pd.isnull(sub_row.run):
fname = '{}_run-{}'.format(sub_row.FileName, str(j+1).zfill(2))
else:
_ = bids_validation(df, i, 'run', sub_row.run, 3, dtype=int)
fname = '{}_run-{}'.format(sub_row.FileName, str(sub_row.run).zfill(2)) # [20210822] format error
if fname in conflict_tested:
raise ValueConflictInField('ScanID:[{}] Conflict error. '
'The [run] index value must be unique '
Expand Down Expand Up @@ -696,12 +696,29 @@ def completeFieldsCreateFolders (df, filtered_dset, dset, multi_session, root_pa
if pd.notnull(row.ce):
if bids_validation(df, i, 'ce', row.ce, 5):
fname = '{}_ce-{}'.format(fname, row.ce)
if pd.notnull(row.dir):
if bids_validation(df, i, 'dir', row.dir, 2):
fname = '{}_dir-{}'.format(fname, row.dir)
if pd.notnull(row.rec):
if bids_validation(df, i, 'rec', row.rec, 2):
fname = '{}_rec-{}'.format(fname, row.rec)
if pd.notnull(row.dir):
if bids_validation(df, i, 'dir', row.dir, 2):
fname = '{}_dir-{}'.format(fname, row.dir)
if pd.notnull(row.run):
if bids_validation(df, i, 'run', row.run, 2):
fname = '{}_run-{}'.format(fname, row.run)
if dset.is_multi_echo(row.ScanID, row.RecoID):
fname = '{}_echo-echo.index'.format(fname)
if pd.notnull(row.flip):
if bids_validation(df, i, 'flip', row.flip, 2):
fname = '{}_flip-{}'.format(fname, row.flip)
if pd.notnull(row.inv):
if bids_validation(df, i, 'inv', row.inv, 2):
fname = '{}_inv-{}'.format(fname, row.inv)
if pd.notnull(row.mt):
if bids_validation(df, i, 'mt', row.mt, 3):
fname = '{}_mt-{}'.format(fname, row.mt)
if pd.notnull(row.part):
if bids_validation(df, i, 'part', row.part, 5):
fname = '{}_part-{}'.format(fname, row.part)
filtered_dset.loc[i, 'FileName'] = fname
filtered_dset.loc[i, 'Dir'] = dtype_path
if pd.isnull(row.modality):
Expand Down