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Merge pull request #286 from VUIIS/pk
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Update BIDSMapping and XnatToBids
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@bud42
bud42 authored Jul 21, 2020
2 parents 0293590 + 31b23b0 commit 88fa3e5
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128 changes: 67 additions & 61 deletions bin/Xnat_tools/BIDSMapping
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ from dax import XnatUtils
from datetime import datetime

DESCRIPTION = """What is the script doing :
*Uploads BIDS datatype, tasktype and repitition time mapping to XNAT project level using the \
*Uploads BIDS datatype, tasktype, repitition time and run number mapping to XNAT project level using the \
different OPTIONS.
Examples:
Expand All @@ -41,7 +41,7 @@ Examples:
*Download the current mapping on XNAT:
BIDSMapping -p PID --xnatinfo scan_type --type datatype --download /tmp/download.csv
*Download the scan_types on project on XNAT:
BIDSMapping -p PID --template /tmp/scan_type_template.csv
BIDSMapping -p PID --template /tmp/scan_type_template.csv --xnatinfo scan_types
"""

def add_parser_args():
Expand Down Expand Up @@ -200,15 +200,15 @@ def template():
# Get all the unique scans in the project
scans_list_global = XNAT.get_project_scans(project)
for sd in scans_list_global:
sd_list.append(sd['scan_type'])
sd_list.append(sd[xnat_type])
sd_set = set(sd_list)
uniq_sd = [_f for _f in list(sd_set) if _f]
# Write the list to directory given by the user
with open(template_dir, "w+") as f:
wr = csv.writer(f)
for row in uniq_sd:
wr.writerow([row])
LOGGER.info('Template with scan_type at %s', template_dir)
LOGGER.info('Template with %s is uploaded at %s' % (xnat_type, template_dir))

def default():
"""
Expand All @@ -218,44 +218,46 @@ def default():
"""
new_mapping = dict()
new_mapping[project] = {}
# Since Repetition time should be given by user, it has no default mapping
if mapping_type == 'repetition_time_sec':
LOGGER.info('Repetition time does not have default mapping, use --create')
# Since Repetition time and Run number should be given by user, it has no default mapping
if mapping_type == 'repetition_time_sec' or mapping_type == 'run_number':
LOGGER.info('%s does not have default mapping, use --create' % mapping_type)

else:
# Get the scan type from LANDMAN and use regex to create mapping for those scans and BIDS datatype
if mapping_type == 'datatype':
scans_list_global = XNAT.get_project_scans('LANDMAN')
# Get the scan type/series description from project ID and
# use regex to create mapping for those scans and BIDS datatype
scans_list_global = XNAT.get_project_scans(project)

for sd in scans_list_global:
c = re.search('T1|T2|T1W', sd['scan_type'])
c = re.search('T1|T2|T1W', sd[xnat_type])
if not c == None:
sd_anat = sd['scan_type']
sd_anat = sd[xnat_type]
new_mapping[project][sd_anat] = "anat"

for sd in scans_list_global:
c = re.search('rest|Resting state', sd['scan_type'], flags=re.IGNORECASE)
c = re.search('rest|Resting state', sd[xnat_type], flags=re.IGNORECASE)
if not c == None:
sd_func = sd['scan_type']
new_mapping[project][sd_func] = "func"

for sd in scans_list_global:
c = re.search('dwi|dti', sd['scan_type'], flags=re.IGNORECASE)
c = re.search('dwi|dti', sd[xnat_type], flags=re.IGNORECASE)
if not c == None:
sd_dwi = sd['scan_type']
new_mapping[project][sd_dwi] = "dwi"

for sd in scans_list_global:
c = re.search('Field', sd['scan_type'], flags=re.IGNORECASE)
c = re.search('Field', sd[xnat_type], flags=re.IGNORECASE)
if not c == None:
sd_fmap = sd['scan_type']
new_mapping[project][sd_fmap] = "fmap"

if mapping_type == 'tasktype':
scans_list_global = XNAT.get_project_scans('LANDMAN')
scans_list_global = XNAT.get_project_scans(project)
for sd in scans_list_global:
c = re.search('rest', sd['scan_type'], flags=re.IGNORECASE)
c = re.search('rest', sd[xnat_type], flags=re.IGNORECASE)
if not c == None:
sd_func = sd['scan_type']
sd_func = sd[xnat_type]
new_mapping[project][sd_func] = "rest"

new_json_name = d_m_y + '_' + mapping_type + '.json'
Expand Down Expand Up @@ -301,6 +303,8 @@ def create():
new_mapping[project][sd] = rows['tasktype']
elif mapping_type == 'repetition_time_sec':
new_mapping[project][sd] = rows['repetition_time_sec']
elif mapping_type == 'run_number':
new_mapping[project][sd] = rows['run_number']
LOGGER.info('date %s' % (date.strftime("%d-%m-%y-%H:%M:%S")))

# If mapping is not present upload the new_mapping from the CSV, if not throw an error
Expand Down Expand Up @@ -350,6 +354,8 @@ def update_or_replace():
new_mapping[project][sd] = rows['tasktype']
elif mapping_type == 'repetition_time_sec':
new_mapping[project][sd] = rows['repetition_time_sec']
elif mapping_type == 'run_number':
new_mapping[project][sd] = rows['run_number']
# Get the json mapping from XNAT
if len(XNAT.select(res_files).get()) > 1:
for res in XNAT.select(res_files).get():
Expand Down Expand Up @@ -383,7 +389,7 @@ def csv_check(src_path):
with open(src_path, 'r') as csvFile:
csvReader = csv.DictReader(csvFile)
if csvReader.fieldnames[0] in ["scan_type","series_description"] and csvReader.fieldnames[1] in \
["datatype", "tasktype", "repetition_time_sec"] and csvReader.fieldnames[0] == xnat_type and csvReader.fieldnames[1] == mapping_type:
["datatype", "tasktype", "repetition_time_sec", "run_number"] and csvReader.fieldnames[0] == xnat_type and csvReader.fieldnames[1] == mapping_type:
if csvReader.fieldnames[1] == "datatype":
for rows in csvReader:
if rows['datatype'] not in ["anat", "dwi", "func", "fmap"]:
Expand All @@ -394,7 +400,7 @@ def csv_check(src_path):
LOGGER.info("CSV mapping format is good")
else:
LOGGER.error("ERROR in CSV column headers. Check 1) if the xnat_info and column header match, 2) if the type and column header match, "
"3) column headers should be series_description or scan_type and datatype, tasktype or repetition_time_sec")
"3) column headers should be series_description or scan_type and datatype, tasktype, repetition_time_sec, or run_number")
sys.exit()

def revert():
Expand Down Expand Up @@ -512,49 +518,49 @@ if __name__ == '__main__':
LOGGER.info("WARNING: Project is require. Use --project")
else:
project = OPTIONS.project
if OPTIONS.template:
template()
# Put the XNAT type info at project level in xnat_type.txt
xnat_type_file = XNAT.select('/data/projects/' + project + '/resources/BIDS_xnat_type/files/xnat_type.txt')
if not OPTIONS.xnatinfo:
LOGGER.info("WARNING: Xnatinfo is required. Use --xnatinfo")
elif OPTIONS.xnatinfo not in ["scan_type", "series_description"]:
LOGGER.error("ERROR: Type must be scan_type or series_description")
else:
# Put the XNAT type info at project level in xnat_type.txt
xnat_type_file = XNAT.select('/data/projects/' + project + '/resources/BIDS_xnat_type/files/xnat_type.txt')
if not OPTIONS.xnatinfo:
LOGGER.info("WARNING: Xnatinfo is required. Use --xnatinfo")
elif OPTIONS.xnatinfo not in ["scan_type", "series_description"]:
LOGGER.error("ERROR: Type must be scan_type or series_description")
xnat_type = OPTIONS.xnatinfo
LOGGER.info("The info used from XNAT is " + xnat_type)
xnat_type_file.put(src=xnat_type, overwrite=True)
XNAT.select(os.path.join('/data/projects/' + project + '/resources/', 'LOGFILE.txt'))
if OPTIONS.template:
template()
sys.exit()
if not OPTIONS.type:
LOGGER.info("WARNING: Type is required. Use --type")
elif OPTIONS.type not in ["datatype", "tasktype", "repetition_time_sec", "run_number"]:
LOGGER.error("ERROR: Type must be datatype or tasktype or repetition_time_sec or run_number")
else:
xnat_type = OPTIONS.xnatinfo
LOGGER.info("The info used from XNAT is " + xnat_type)
xnat_type_file.put(src=xnat_type, overwrite=True)
XNAT.select(os.path.join('/data/projects/' + project + '/resources/', 'LOGFILE.txt'))
if not OPTIONS.type:
LOGGER.info("WARNING: Type is required. Use --type")
elif OPTIONS.type not in ["datatype", "tasktype", "repetition_time_sec"]:
LOGGER.error("ERROR: Type must be datatype or tasktype or repetition_time_sec")
else:
mapping_type = OPTIONS.type
CSVWRITER = None
res_files = '/data/projects/' + project + '/resources/BIDS_' + mapping_type + '/files'
xnat_logfile = XNAT.select(os.path.join(res_files, 'LOGFILE.txt'))
if not xnat_logfile.exists():
# If LOGFILE does not exist revert cant be done
if OPTIONS.revert:
LOGGER.error('Cannot perform --revert. Create mapping with --create option first')
sys.exit()
xnat_logfile.put(src="Logfile\n")
LOGFILE = xnat_logfile.get()
csvfilewrite = open(LOGFILE, 'a')
CSVWRITER = csv.writer(csvfilewrite, delimiter=',')
if OPTIONS.create:
create()
if OPTIONS.create_default:
default()
if OPTIONS.update or OPTIONS.replace:
update_or_replace()
mapping_type = OPTIONS.type
CSVWRITER = None
res_files = '/data/projects/' + project + '/resources/BIDS_' + mapping_type + '/files'
xnat_logfile = XNAT.select(os.path.join(res_files, 'LOGFILE.txt'))
if not xnat_logfile.exists():
# If LOGFILE does not exist revert cant be done
if OPTIONS.revert:
revert()
if OPTIONS.download:
mapping_download()

csvfilewrite.close()
XNAT.select(os.path.join(res_files, 'LOGFILE.txt')).put(src=LOGFILE, overwrite=True)
LOGGER.error('Cannot perform --revert. Create mapping with --create option first')
sys.exit()
xnat_logfile.put(src="Logfile\n")
LOGFILE = xnat_logfile.get()
csvfilewrite = open(LOGFILE, 'a')
CSVWRITER = csv.writer(csvfilewrite, delimiter=',')
if OPTIONS.create:
create()
if OPTIONS.create_default:
default()
if OPTIONS.update or OPTIONS.replace:
update_or_replace()
if OPTIONS.revert:
revert()
if OPTIONS.download:
mapping_download()

csvfilewrite.close()
XNAT.select(os.path.join(res_files, 'LOGFILE.txt')).put(src=LOGFILE, overwrite=True)

52 changes: 40 additions & 12 deletions dax/XnatToBids.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,8 @@ def transform_to_bids(XNAT, DIRECTORY, project, BIDS_DIR, LOGGER):
subj_idx = subj_idx + 1
LOGGER.info("\t>Removing XNAT subject %s folder" % (subj))
os.rmdir(os.path.join(DIRECTORY, proj, subj))
dataset_description_file(BIDS_DIR, XNAT, project)
BIDS_PROJ_DIR = os.path.join(BIDS_DIR, project)
dataset_description_file(BIDS_PROJ_DIR, XNAT, project)


def bids_yaml(XNAT, project, scan_id, subj, res_dir, scan_file, uri, sess, nii_file, sess_idx, subj_idx):
Expand Down Expand Up @@ -198,18 +199,25 @@ def yaml_bids_filename(XNAT, data_type, scan_id, subj, sess, project, scan_file,
'Use BidsMapping tool. Func folder not created' % xnat_mapping_type))
print("ERROR: BIDS Conversion not complete")
sys.exit()
bids_fname = "sub-" + subj_idx + '_' + "ses-" + sess_idx + '_task-' + task_type + '_acq-' + scan_id + '_run-01' \
+ '_' + 'bold' + '.' + ".".join(scan_file.split('.')[1:])
# Get the run_number for the scan
rn_dict = sd_run_mapping(XNAT, project)
# Map scan and with run_number, if run_number
# not present for scan then 01 is used
run_number = rn_dict.get(xnat_mapping_type, "01")
bids_fname = "sub-" + subj_idx + '_' + "ses-" + sess_idx + '_task-' + task_type + '_acq-' + scan_id + '_run-' \
+ run_number + '_bold' + '.' + ".".join(scan_file.split('.')[1:])
return bids_fname

elif data_type == "dwi":
rn_dict = sd_run_mapping(XNAT, project)
run_number = rn_dict.get(xnat_mapping_type, "01")
if scan_file.endswith('bvec.txt'):
bids_fname = "sub-" + subj_idx + '_' + "ses-" + sess_idx + '_acq-' + scan_id + '_run-' + scan_id + '_' + 'dwi' + '.' + 'bvec'
bids_fname = "sub-" + subj_idx + '_' + "ses-" + sess_idx + '_acq-' + scan_id + '_run-' + run_number + '_dwi.bvec'

elif scan_file.endswith('bval.txt'):
bids_fname = "sub-" + subj_idx + '_' + "ses-" + sess_idx + '_acq-' + scan_id + '_run-' + scan_id + '_' + 'dwi' + '.' + 'bval'
bids_fname = "sub-" + subj_idx + '_' + "ses-" + sess_idx + '_acq-' + scan_id + '_run-' + run_number + '_dwi.bval'
else:
bids_fname = "sub-" + subj_idx + '_' + "ses-" + sess_idx + '_acq-' + scan_id + '_run-' + scan_id + '_' + 'dwi' + \
bids_fname = "sub-" + subj_idx + '_' + "ses-" + sess_idx + '_acq-' + scan_id + '_run-' + run_number + '_dwi' + \
'.' + ".".join(scan_file.split('.')[1:])
return bids_fname

Expand Down Expand Up @@ -450,10 +458,31 @@ def sd_tasktype_mapping(XNAT, project):
return tk_dict


def dataset_description_file(BIDS_DIR, XNAT, project):
def sd_run_mapping(XNAT, project):
"""
Method to get the Run number mapping at Project level
:param XNAT: XNAT interface
:param project: XNAT Project ID
:return: Dictonary with scan_type/series_description and run number mapping
"""
rn_dict = {}
if XNAT.select('/data/projects/' + project + '/resources/BIDS_run_number').exists():
for res in XNAT.select('/data/projects/' + project + '/resources/BIDS_run_number/files').get():
if res.endswith('.json'):
with open(XNAT.select('/data/projects/' + project + '/resources/BIDS_run_number/files/'
+ res).get(), "r+") as f:
datatype_mapping = json.load(f)
rn_dict = datatype_mapping[project]

else:
print("\t\t>WARNING: No Run number mapping at project level. Using 01 as run number")

return rn_dict

def dataset_description_file(BIDS_PROJ_DIR, XNAT, project):
"""
Build BIDS dataset description json file
:param BIDS_DIR: BIDS directory
:param BIDS_PROJ_DIR: Project BIDS directory
:param XNAT: XNAT interface
:param project: XNAT Project
"""
Expand All @@ -469,8 +498,7 @@ def dataset_description_file(BIDS_DIR, XNAT, project):
dataset_description['Author'] = PI_element[0][1].text, PI_element[0][0].text
else:
dataset_description['Author'] = "No Author defined on XNAT"
dd_file = os.path.join(BIDS_DIR, project)
if not os.path.exists(dd_file):
os.makedirs(dd_file)
with open(os.path.join(dd_file, 'dataset_description.json'), 'w+') as f:
if not os.path.exists(BIDS_PROJ_DIR):
os.makedirs(BIDS_PROJ_DIR)
with open(os.path.join(BIDS_PROJ_DIR, 'dataset_description.json'), 'w+') as f:
json.dump(dataset_description, f, indent=2)

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