def main():
header_msg = '%s - v%s' % (os.path.basename(sys.argv[0]), __version__)
if len(sys.argv) != 5:
print '[error] No valid arguments supplied (%s)' % header_msg
sys.exit(1)
usr_pwd = sys.argv[1]
hostname = sys.argv[2]
expID = sys.argv[3]
in_directory = sys.argv[4]
#basic checkings
if not os.path.isdir(in_directory):
print '[error] Input data location specified is not a valid directory (%s)' % in_directory
sys.exit(1)
try:
with xnatLibrary.XNAT(hostname, usr_pwd) as xnat_connection:
get_scans_details(xnat_connection, expID, in_directory)
except xnatLibrary.XNATException as xnatErr:
print '[error] XNAT-related issue(%s): %s' % (header_msg, xnatErr)
sys.exit(1)
except Exception as e:
print '[Error]', e
print(traceback.format_exc())
sys.exit(1)
def main(argument_list):
header_msg = '%s - v%s' % (os.path.basename(argument_list[0]), __version__)
if len(argument_list) != 7:
print '[error] No valid arguments supplied (%s)' % header_msg
sys.exit(1)
# input argument list
usr_pwd = argument_list[1]
hostname = argument_list[2]
project = argument_list[3]
subject = argument_list[4]
session = argument_list[5]
csv_input_file = argument_list[6]
# check the main XML element type (XNAT datatype)
xml_element_type = 'AMCZ0:qMRIData'
# parse out data from CSV file containing results generated by qMRI run
parsed_results = parse_csv_file(csv_input_file)
#parsed_results = fix_results_type(parsed_results)
# connect to XNAT
try:
with xnatLibrary.XNAT(hostname, usr_pwd) as xnat_connection:
# for each entry (row) in the results file, create an XML object instantiating an XNAT assessment/experiment
for scan_results in parsed_results:
xml_element = create_xml_obj(scan_results, xml_element_type)
# Do some magic :: upload xml object into XNAT (instantiate a new dataType object)
assessment_label = normalize_string(
session + '_' + xml_element_type.split(':')[1])
assessment_uid = upload_to_XNAT(xnat_connection, project,
subject, session,
assessment_label,
etree.tostring(xml_element),
xml_element_type)
# quality control image upload
output_directory = os.path.dirname(
os.path.realpath(csv_input_file))
qc_image_file = os.path.join(output_directory, 'qmri_fits.png')
if os.path.isfile(qc_image_file):
upload_snapshot_resource(xnat_connection, project, subject,
session, assessment_uid,
qc_image_file)
except xnatLibrary.XNATException as xnatErr:
print '[error] XNAT-related issue(%s): %s' % (header_msg, xnatErr)
sys.exit(1)
except Exception as e:
print '[error]', e
print(traceback.format_exc())
sys.exit(1)
def main():
header_msg = '%s - v%s' % (os.path.basename(sys.argv[0]), __version__)
if len(sys.argv) != 8:
print '[error] No valid arguments supplied (%s)' % header_msg
sys.exit(1)
usr_pwd = sys.argv[1]
hostname = sys.argv[2]
project = sys.argv[3]
subjectID = sys.argv[4]
experimentID = sys.argv[5]
required_type = sys.argv[6]
output_directory = sys.argv[7]
resource_format = 'DICOM,NIFTI'
#basic checkings on output directory status
if not os.path.isdir(output_directory):
print '[error] Download location specified is not a valid directory (%s)' % header_msg
sys.exit(1)
# connect to XNAT
try:
with xnatLibrary.XNAT(hostname, usr_pwd) as xnat_connection:
# get a list of affected scans for the given imaging session
process_scan_list = get_scans_list(xnat_connection, project,
subjectID, experimentID,
required_type)
# if the list is empty, no valid scans found for the given imaging session, close and exit
if not process_scan_list:
print '[error] Unable to find a suitable %s scan for %s (%s)' % (
required_type, experimentID, header_msg)
sys.exit(1)
# retrieve the scans from XNAT
download_scan_list_files(xnat_connection, experimentID,
process_scan_list, resource_format,
output_directory)
except xnatLibrary.XNATException as xnatErr:
print '[error] XNAT-related issue(%s): %s' % (header_msg, xnatErr)
sys.exit(1)
except Exception as e:
print '[Error]', e
print(traceback.format_exc())
sys.exit(1)
# compose the HTTP basic authentication credentials string
if args['password'] is None :
password = getpass.getpass('Password for user %s:' %args['username'])
else :
password = args['password']
usr_pwd = args['username']+':'+password
print ''
try:
#if args['csvFile'] is not None and not os.path.isfile(args['csvFile']) :
# raise Exception('CSV file %s not found' %args['csvFile'])
# connect to XNAT
with xnatLibrary.XNAT(args['hostname'],usr_pwd) as XNAT :
if args['verbose'] : print ' [Info] session %s opened' %XNAT.jsession
# check if XNAT project exists
if XNAT.resourceExist('%s/data/projects/%s' %(XNAT.host,args['project'])).status != 200 :
raise xnatLibrary.XNATException('project ("%s") is unreachable at: %s' % (args['project'], XNAT.host) )
# if all went OK, proceed to the main processing stage
main(XNAT,args)
# disconnect from XNAT
if args['verbose'] : print ' [Info] session %s closed' %XNAT.jsession
except xnatLibrary.XNATException as xnatErr:
print ' [Error] XNAT-related issue:', xnatErr
except Exception as e:
parser.add_argument('-t','--type', dest="e_type", help='Entity type/level where to create resource; can either be: {projects,subjects,experiments}', required=True)
parser.add_argument('-id','--identifier', dest="e_name", help='Entity name/identifier where to create resource', required=True)
parser.add_argument('-i','--input', dest="input", help='Input file/directory location', required=True)
parser.add_argument('-rc','--resource_collection', dest="resource_collection", default=None, help='Resource collection name (optional)', required=False)
parser.add_argument('-v','--verbose', dest="verbose", action='store_true', default=False, help='Display verbosal information (optional)', required=False)
args = vars(parser.parse_args())
# compose the HTTP basic authentication credentials string
password = getpass.getpass('Password for user %s:' %args['username'])
usr_pwd = args['username']+':'+password
print ''
try:
# connect to XNAT
with xnatLibrary.XNAT(args['hostname'],usr_pwd) as xnat_connection :
if args['verbose'] : print '[Info] session %s opened' %xnat_connection.jsession
main(xnat_connection,args)
if args['verbose'] : print '[Info] session %s closed' %xnat_connection.jsession
# disconnect from XNAT
except xnatLibrary.XNATException as xnatErr:
print '[Error] XNAT-related issue:', xnatErr
sys.exit(1)
except Exception as e:
print '[Error]', e
print(traceback.format_exc())
sys.exit(1)
def main(argument_list):
header_msg = '%s - v%s' % (os.path.basename(argument_list[0]), __version__)
if len(argument_list) != 7:
print '[error] No valid arguments supplied (%s)' % header_msg
sys.exit(1)
# input argument list
usr_pwd = argument_list[1]
hostname = argument_list[2]
project = argument_list[3]
csv_input_file = argument_list[4]
qap_analysis_type = argument_list[5] # either {temporal, spatial}
scan_type = argument_list[6] # either {anat, func}
# check the main XML element type (XNAT datatype)
if 'anat' in scan_type.lower():
xml_element_type = 'AMCZ0:anatQA'
elif 'func' in scan_type.lower():
if qap_analysis_type.lower() == 'spatial':
xml_element_type = 'AMCZ0:fspatQA'
elif qap_analysis_type.lower() == 'temporal':
xml_element_type = 'AMCZ0:ftempQA'
if xml_element_type not in [
'AMCZ0:anatQA', 'AMCZ0:fspatQA', 'AMCZ0:ftempQA'
]:
print '[error] No valid QAP or scan type recognized (%s)' % header_msg
sys.exit(1)
# parse out data from CSV file containing results generated by QAP run
parsed_results = parse_csv_file(csv_input_file)
parsed_results = fix_results_type(parsed_results)
# connect to XNAT
try:
with xnatLibrary.XNAT(hostname, usr_pwd) as xnat_connection:
# for each entry (row) in the results file, create an XML object instantiating an XNAT assessment/experiment
for scan_results in parsed_results:
scan_id = scan_results['scan'].split('_')[1]
scan_type = xnat_scan_type = get_scan_type_xnat(
xnat_connection, project, scan_results['subject'],
scan_results['session'], scan_id)
xml_element = create_xml_obj(scan_results, xml_element_type,
scan_id, scan_type)
# Do some magic :: upload xml object into XNAT (instantiate a new dataType object)
#assessment_label = normalize_string( scan_results['subject'] + '_' + scan_results['session'] + '_s' + scan_results['scan'].split('_')[1] + '_' + xml_element_type.split(':')[1] )
#let's shorten it, subject info is not required (session label should suffice)
assessment_label = normalize_string(
scan_results['session'] + '_s' +
scan_results['scan'].split('_')[1] + '_' +
xml_element_type.split(':')[1])
assessment_uid = upload_to_XNAT(xnat_connection, project,
scan_results['subject'],
scan_results['session'],
assessment_label,
etree.tostring(xml_element),
xml_element_type)
# snapshot images generation and upload
qap_output_directory = os.path.dirname(
os.path.realpath(csv_input_file))
matched_results = qap_snapshot_creator.find_pdf_files(
qap_output_directory, scan_results['scan'])
if matched_results:
for pdf_file in matched_results:
png_file = qap_snapshot_creator.convert_to_img(
pdf_file)
qap_snapshot_creator.upload_snapshot_resource(
xnat_connection, project, scan_results['subject'],
scan_results['session'], assessment_uid, png_file)
os.remove(png_file)
except xnatLibrary.XNATException as xnatErr:
print '[error] XNAT-related issue(%s): %s' % (header_msg, xnatErr)
sys.exit(1)
except Exception as e:
print '[error]', e
print(traceback.format_exc())
sys.exit(1)