def create_anat_json(bxh_file, full_output):
logging.info('---START: create_anat_json---')
with open(bxh_file) as fd:
bxh_contents = xmltodict.parse(fd.read())
#Put together dictionary of things to write to the sidecar .json file
#Make sure the anat field template file is where it should be
here = os.path.dirname(os.path.realpath(__file__))
anat_field_file = os.path.join(here, 'info_field_files', 'anat_info_fields.json')
if not os.path.exists(anat_field_file):
logging.error('Anatomical image sidecar template file cannot be found!')
logging.error('It should be here: '+str(anat_field_file))
raise RuntimeError('Missing anatomical sidecar template file!')
out_dict = bxh_pick_fields.bxh_pick(anat_field_file, bxh_as_dict=bxh_contents)
#Make sure echo time is in seconds
et = out_dict['EchoTime']
if et > 1:
logging.info('Echo Time is greater than 1, assuming it is in ms.')
et = et/1000
out_dict['EchoTime'] = et
out_string = json.dumps(out_dict, indent=4)
logging.info('Writing sidecar anat file: '+str(full_output))
with open(full_output, 'w') as out_file:
out_file.write(out_string)
logging.info('---FINISHED: create_anat_json---')
def create_ncanda_json(bxh_file, full_output):
logging.info('---START: create_ncanda_fmap_json---')
with open(bxh_file) as fd:
bxh_contents = xmltodict.parse(fd.read())
#Put together dictionary of things to write to the sidecar .json file
#Make sure the fmap field template file is where it should be
here = os.path.dirname(os.path.realpath(__file__))
fmap_field_file = os.path.join(here, 'info_field_files',
'fmap_info_fields.json')
if not os.path.exists(fmap_field_file):
logging.error('Fmap image sidecar template file cannot be found!')
logging.error('It should be here: ' + str(fmap_field_file))
raise RuntimeError('Missing fmap sidecar template file!')
out_dict = bxh_pick_fields.bxh_pick(fmap_field_file,
bxh_as_dict=bxh_contents)
#Pull apart the two echo times and make sure they are in seconds
et = out_dict['EchoTime']
if not (len(et.split(' ')) > 1):
logging.error('Only one TE found in .bxh header for ncanda fmap!')
logging.error('There should be exactly two!')
logging.error('Header entry as read by .bxh_pick: ' + str(et))
logging.error('.bxh file: ' + str(bxh_file))
raise RuntimeError('One TE found in ncanda .bxh header!')
et_one = float(et.split(' ')[0])
et_two = float(et.split(' ')[1])
if et_one > 1:
logging.info('Echo Time is greater than 1, assuming it is in ms.')
et_one = et_one / 1000
out_dict['EchoTime1'] = et_one
if et_two > 1:
logging.info('Echo Time is greater than 1, assuming it is in ms.')
et_two = et_two / 1000
out_dict['EchoTime2'] = et_two
#Remove the old EchoTime dictionary entry, quietly
out_dict['EchoTime'] = None
out_dict.pop('EchoTime')
out_string = json.dumps(out_dict, indent=4)
logging.info('Writing sidecar fmap file: ' + str(full_output))
with open(full_output, 'w') as out_file:
out_file.write(out_string)
logging.info('---FINISHED: create_ncanda_fmap_json---')
def create_dwi_json(bxh_file, full_output):
logging.info('---START: create_dwi_json---')
with open(bxh_file) as fd:
bxh_contents = xmltodict.parse(fd.read())
#Pull the task name out of the output file name
taskname = os.path.split(full_output)[-1].split('task-')[-1].split('_')[0]
##TODO: Clean this up! Probably move all these to a template file.
#Calculate total readout time
#Put together dictionary of things to write to the sidecar .json file
#Make sure the func field template file is where it should be
here = os.path.dirname(os.path.realpath(__file__))
func_field_file = os.path.join(here, 'info_field_files',
'dwi_info_fields.json')
if not os.path.exists(func_field_file):
logging.error('DWI image sidecar template file cannot be found!')
logging.error('It should be here: ' + str(func_field_file))
raise RuntimeError('Missing functional sidecar template file!')
out_dict = bxh_pick_fields.bxh_pick(func_field_file,
bxh_as_dict=bxh_contents)
#Make sure the tr is in seconds
tr = out_dict['RepetitionTime']
if tr > 50:
logging.info(
'TR in bxh file is greater than 50, assuming it is in ms.')
tr = tr / 1000
out_dict['RepetitionTime'] = tr
#Make sure echo time is in seconds
et = out_dict['EchoTime']
if et > 1:
logging.info('Echo Time is greater than 1, assuming it is in ms.')
et = et / 1000
out_dict['EchoTime'] = et
out_string = json.dumps(out_dict, indent=4)
logging.info('Writing sidecar func file: ' + str(full_output))
with open(full_output, 'w') as out_file:
out_file.write(out_string)
logging.info('---FINISHED: create_dwi_json---')
def create_bold_json(bxh_file, full_output):
logging.info('---START: create_bold_json---')
with open(bxh_file) as fd:
bxh_contents = xmltodict.parse(fd.read())
#Pull the task name out of the output file name
taskname = os.path.split(full_output)[-1].split('task-')[-1].split('_')[0]
##TODO: Clean this up! Probably move all these to a template file.
#Calculate total readout time
#Look for the TR
try:
tr = float(bxh_contents['bxh']['acquisitiondata']['tr'])
except:
logging.error('TR could not be found in passed .bxh!')
logging.error('bxh_file: '+str(bxh_file))
raise RuntimeError('TR could not be found in .bxh.')
#Put together dictionary of things to write to the sidecar .json file
#Make sure the func field template file is where it should be
here = os.path.dirname(os.path.realpath(__file__))
func_field_file = os.path.join(here, 'info_field_files', 'func_info_fields.json')
if not os.path.exists(func_field_file):
logging.error('Functional image sidecar template file cannot be found!')
logging.error('It should be here: '+str(func_field_file))
raise RuntimeError('Missing functional sidecar template file!')
out_dict = bxh_pick_fields.bxh_pick(func_field_file, bxh_as_dict=bxh_contents)
#Make sure the tr is in seconds
tr = out_dict['RepetitionTime']
if tr > 50:
logging.info('TR in bxh file is greater than 50, assuming it is in ms.')
tr = tr/1000
out_dict['RepetitionTime'] = tr
#Make sure echo time is in seconds
et = out_dict['EchoTime']
if et > 1:
logging.info('Echo Time is greater than 1, assuming it is in ms.')
et = et/1000
out_dict['EchoTime'] = et
#Calculate slice timing
for element in bxh_contents['bxh']['datarec']['dimension']:
if element['@type'] == 'z':
slice_order_list = element['datapoints']['#text']
num_slices = float(element['size'])
factor = tr/num_slices
st = []
for s in slice_order_list.split(' '):
st.append(factor * (int(s)-1))
out_dict['TaskName'] = taskname
out_dict['SliceTiming'] = st
out_string = json.dumps(out_dict, indent=4)
logging.info('Writing sidecar func file: '+str(full_output))
with open(full_output, 'w') as out_file:
out_file.write(out_string)
logging.info('---FINISHED: create_bold_json---')