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Merge pull request #42 from argyelan/master
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participants.tsv and keys in dict handled better
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@jmtyszka
jmtyszka authored Sep 28, 2018
2 parents 68303e9 + 7d74d58 commit 7af856e
Showing 1 changed file with 99 additions and 77 deletions.
176 changes: 99 additions & 77 deletions dcm2bids.py
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Original file line number Diff line number Diff line change
Expand Up @@ -153,10 +153,8 @@ def main():

# Initialize BIDS source directory contents
if not first_pass:
participants_fd = bids_init(bids_src_dir, overwrite)
else:
participants_fd = []

bids_init(bids_src_dir, overwrite)

# Loop over subject directories in DICOM root
for dcm_sub_dir in glob(dcm_root_dir + '/*/'):

Expand Down Expand Up @@ -227,17 +225,16 @@ def main():
dcm_info = bids_dcm_info(dcm_dir)

# Add line to participants TSV file
participants_fd.write("sub-%s\t%s\t%s\n" % (SID, dcm_info['Sex'], dcm_info['Age']))

#participants_fd.write("sub-%s\t%s\t%s\n" % (SID, dcm_info['Sex'], dcm_info['Age']))
add_participant_record(bids_src_dir, SID, dcm_info['Age'], dcm_info['Sex'])

# Run dcm2niix output to BIDS source conversions
bids_run_conversion(work_conv_dir, first_pass, prot_dict, bids_src_ses_dir, SID, SES, overwrite)

if first_pass:
# Create a template protocol dictionary
bids_create_prot_dict(prot_dict_json, prot_dict)
else:
# Close participants TSV file
participants_fd.close()


# Clean exit
sys.exit(0)
Expand Down Expand Up @@ -304,53 +301,58 @@ def bids_run_conversion(conv_dir, first_pass, prot_dict, src_dir, SID, SES, over
print('* JSON sidecar not found : %s' % src_json_fname)
break

if prot_dict[info['SerDesc']][0].startswith('EXCLUDE'):

# Skip excluded protocols
print('* Excluding protocol ' + str(info['SerDesc']))

else:
if info['SerDesc'] in prot_dict.keys():

if prot_dict[info['SerDesc']][0].startswith('EXCLUDE'):

print(' Organizing ' + str(info['SerDesc']))
# Skip excluded protocols
print('* Excluding protocol ' + str(info['SerDesc']))

# Use protocol dictionary to determine purpose folder, BIDS filename suffix and fmap linking
bids_purpose, bids_suffix, bids_intendedfor = prot_dict[info['SerDesc']]
else:

# Safely add run-* key to BIDS suffix
bids_suffix = bids_add_run_number(bids_suffix, run_no[fc])
print(' Organizing ' + str(info['SerDesc']))

# Create BIDS purpose directory
bids_purpose_dir = os.path.join(src_dir, bids_purpose)
safe_mkdir(bids_purpose_dir)
# Use protocol dictionary to determine purpose folder, BIDS filename suffix and fmap linking
bids_purpose, bids_suffix, bids_intendedfor = prot_dict[info['SerDesc']]

# Complete BIDS filenames for image and sidecar
if SES:
bids_prefix = 'sub-' + SID + '_ses-' + SES + '_'
else:
bids_prefix = 'sub-' + SID + '_'
# Safely add run-* key to BIDS suffix
bids_suffix = bids_add_run_number(bids_suffix, run_no[fc])

# Construct BIDS source Nifti and JSON filenames
bids_nii_fname = os.path.join(bids_purpose_dir, bids_prefix + bids_suffix + '.nii.gz')
bids_json_fname = bids_nii_fname.replace('.nii.gz','.json')
# Create BIDS purpose directory
bids_purpose_dir = os.path.join(src_dir, bids_purpose)
safe_mkdir(bids_purpose_dir)

# Add prefix and suffix to IntendedFor values
if not 'UNASSIGNED' in bids_intendedfor:
if isinstance(bids_intendedfor, str):
# Single linked image
bids_intendedfor = bids_build_intendedfor(SID, SES, bids_intendedfor)
# Complete BIDS filenames for image and sidecar
if SES:
bids_prefix = 'sub-' + SID + '_ses-' + SES + '_'
else:
# Loop over all linked images
for ifc, ifstr in enumerate(bids_intendedfor):
# Avoid multiple substitutions
if not '.nii.gz' in ifstr:
bids_intendedfor[ifc] = bids_build_intendedfor(SID, SES, ifstr)

# Special handling for specific purposes (anat, func, fmap, etc)
# This function populates BIDS structure with the image and adjusted sidecar
bids_purpose_handling(bids_purpose, bids_intendedfor, info['SeqName'],
src_nii_fname, src_json_fname,
bids_nii_fname, bids_json_fname,
overwrite)
bids_prefix = 'sub-' + SID + '_'

# Construct BIDS source Nifti and JSON filenames
bids_nii_fname = os.path.join(bids_purpose_dir, bids_prefix + bids_suffix + '.nii.gz')
bids_json_fname = bids_nii_fname.replace('.nii.gz','.json')

# Add prefix and suffix to IntendedFor values
if not 'UNASSIGNED' in bids_intendedfor:
if isinstance(bids_intendedfor, str):
# Single linked image
bids_intendedfor = bids_build_intendedfor(SID, SES, bids_intendedfor)
else:
# Loop over all linked images
for ifc, ifstr in enumerate(bids_intendedfor):
# Avoid multiple substitutions
if not '.nii.gz' in ifstr:
bids_intendedfor[ifc] = bids_build_intendedfor(SID, SES, ifstr)

# Special handling for specific purposes (anat, func, fmap, etc)
# This function populates BIDS structure with the image and adjusted sidecar
bids_purpose_handling(bids_purpose, bids_intendedfor, info['SeqName'],
src_nii_fname, src_json_fname,
bids_nii_fname, bids_json_fname,
overwrite)
else:
# Skip protocols not in the dictionary
print('* Protocol ' + str(info['SerDesc']) + ' is not in the dictionary, did not convert.')

if not first_pass:

Expand Down Expand Up @@ -480,9 +482,9 @@ def bids_purpose_handling(bids_purpose, bids_intendedfor, seq_name,

# Fill DWI bval and bvec working and source filenames
# Non-empty filenames trigger the copy below
work_bval_fname = str(work_json_fname.replace('dwi.json', 'dwi.bval'))
work_bval_fname = str(work_json_fname.replace('.json', '.bval'))
bids_bval_fname = str(bids_json_fname.replace('dwi.json', 'dwi.bval'))
work_bvec_fname = str(work_json_fname.replace('dwi.json', 'dwi.bvec'))
work_bvec_fname = str(work_json_fname.replace('.json', '.bvec'))
bids_bvec_fname = str(bids_json_fname.replace('dwi.json', 'dwi.bvec'))

# Populate BIDS source directory with Nifti images, JSON and DWI sidecars
Expand All @@ -509,15 +511,9 @@ def bids_init(bids_src_dir, overwrite=False):
BIDS source directory
:param overwrite: string
Overwrite flag
:return participants_fd: object
participant TSV file descriptor
:return True
"""

# Create template participant TSV file in BIDS root directory
parts_tsv = os.path.join(bids_src_dir, 'participants.tsv')
participants_fd = open(parts_tsv, 'w')
participants_fd.write('participant_id\tsex\tage\n')

# Create template JSON dataset description
datadesc_json = os.path.join(bids_src_dir, 'dataset_description.json')
meta_dict = dict({'BIDSVersion': "1.0.0",
Expand All @@ -528,8 +524,34 @@ def bids_init(bids_src_dir, overwrite=False):
# Write JSON file
bids_write_json(datadesc_json, meta_dict, overwrite)

return participants_fd

return True

def add_participant_record(studydir, subject, age, sex): #copied from heudiconv, this solution is good b/c it checks if the same subject id is already exists
participants_tsv = os.path.join(studydir, 'participants.tsv')
participant_id = 'sub-%s' % subject

if not create_file_if_missing(participants_tsv,'\t'.join(['participant_id', 'age', 'sex', 'group']) + '\n'):
# check if may be subject record already exists
with open(participants_tsv) as f:
f.readline()
known_subjects = {l.split('\t')[0] for l in f.readlines()}
if participant_id in known_subjects:
return
# Add a new participant
with open(participants_tsv, 'a') as f:
f.write('\t'.join(map(str, [participant_id, age.lstrip('0').rstrip('Y') if age else 'N/A', sex, 'control'])) + '\n')

def create_file_if_missing(filename, content):
"""Create file if missing, so we do not
override any possibly introduced changes"""
if os.path.lexists(filename):
return False
dirname = os.path.dirname(filename)
if not os.path.exists(dirname):
os.makedirs(dirname)
with open(filename, 'w') as f:
f.write(content)
return True

def bids_dcm_info(dcm_dir):
"""
Expand Down Expand Up @@ -689,27 +711,27 @@ def bids_events_template(bold_fname, overwrite=False):
Overwrite flag
:return: Nothing
"""
if "_bold.nii.gz" in bold_fname: #can have sbref.nii.gz here and you do not want overwrite it
events_fname = bold_fname.replace('_bold.nii.gz', '_events.tsv')
events_bname = os.path.basename(events_fname)

events_fname = bold_fname.replace('_bold.nii.gz', '_events.tsv')
events_bname = os.path.basename(events_fname)

if os.path.isfile(events_fname):
if overwrite:
print(' Overwriting previous %s' % events_bname)
create_file = True
if os.path.isfile(events_fname):
if overwrite:
print(' Overwriting previous %s' % events_bname)
create_file = True
else:
print(' Preserving previous %s' % events_bname)
create_file = False
else:
print(' Preserving previous %s' % events_bname)
create_file = False
else:
print(' Creating %s' % events_fname)
create_file = True
print(' Creating %s' % events_fname)
create_file = True

if create_file:
fd = open(events_fname, 'w')
fd.write('onset\tduration\ttrial_type\tresponse_time\n')
fd.write('1.0\t0.5\tgo\t0.555\n')
fd.write('2.5\t0.4\tstop\t0.666\n')
fd.close()
if create_file:
fd = open(events_fname, 'w')
fd.write('onset\tduration\ttrial_type\tresponse_time\n')
#fd.write('1.0\t0.5\tgo\t0.555\n')
#fd.write('2.5\t0.4\tstop\t0.666\n')
fd.close()


def strip_extensions(fname):
Expand Down

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