def zip_resource(res_obj, directory, resource, no_delete=False, no_big=False):
"""
Zip the files in the resource.
:param res_obj: resource Eobject from pyxnat
:param directory: directory to save temp files
:param resource: resource label
:param no_delete: do not delete the files zipped
:param no_big: do not zip big resources
"""
_warn = ' - warning: %s'
fzip = '%s.zip' % resource
if len(res_obj.files().get()) > 1:
print(" --> downloading %s ..." % resource)
fpaths = XnatUtils.download_files_from_obj(directory, res_obj)
if not fpaths:
msg = '%s -- no files.' % resource
print(_warn % msg)
else:
# If the resource.zip file exists, exit
if res_obj.file(fzip).exists():
msg = '%s -- zip file already on XNAT but zipped files not \
deleted.' % resource
print(_warn % msg)
else:
# Zip the resource if more than one
print(' --> zipping files.')
resource_dir = os.path.dirname(fpaths[0])
# Get init directory
init_dir = os.getcwd()
# Zip all the files in the directory
os.chdir(resource_dir)
os.system('zip -r %s * > /dev/null' % fzip)
# return to the initial directory:
os.chdir(init_dir)
# upload
_fzip = os.path.join(resource_dir, fzip)
if os.path.exists(_fzip):
# Check the size:
size_file = int(os.stat(_fzip).st_size) / (1024 * 1024)
if size_file >= LIMIT_SIZE:
msg = '%s too big.' % resource
print(_warn % msg)
if no_big and size_file >= LIMIT_SIZE:
msg = '%s too big. Skipping.' % resource
print(_warn % msg)
return
print(' --> uploading zip file')
res_obj.put_zip(_fzip, overwrite=True, extract=False)
if no_delete:
print(' --> not deleting original files(two copies).')
else:
print(' --> deleting original files and keeping zipfile.')
delete_resources(res_obj, fzip)
# clean tmp folder
XnatUtils.clean_directory(directory)
def convert_DICOM():
"""Loop through the project scans to convert DICOM to NIFTI."""
list_scans = XnatUtils.list_project_scans(XNAT, OPTIONS.project)
# filter the list to keep scans with DICOM and no NIFTI
if not OPTIONS.force:
print "Filtering list of scans to keep scans with DICOM but no NIFTI."
list_scans = filter(
lambda x: 'DICOM' in x['resources'] and 'NIFTI' not in x['resources'],
list_scans)
else:
print "Filtering list of scans to keep scans with DICOM."
list_scans = filter(lambda x: 'DICOM' in x['resources'], list_scans)
# if sessions, filter:
if OPTIONS.sessions:
list_scans = filter(
lambda x: x['session_label'] in OPTIONS.sessions.split(','),
list_scans)
number_scans = len(list_scans)
print "Converting the %s scans found." % (number_scans)
for index, scan in enumerate(sorted(list_scans,
key=lambda k: k['session_label'])):
message = ' * {index}/{total} -- Session: {session} -- Scan: {scan}'
print message.format(index=index+1,
total=number_scans,
session=scan['session_label'],
scan=scan['ID'])
need_to_zip = False
scan_obj = XnatUtils.get_full_object(XNAT, scan)
if scan_obj.exists() and \
len(scan_obj.resource('DICOM').files().get()) > 0:
print " --> downloading DICOM ..."
fpaths = XnatUtils.download_files_from_obj(
OPTIONS.directory,
scan_obj.resource("DICOM"))
if not fpaths:
print ' - warning: DICOM -- no files.'
else:
if OPTIONS.force and scan_obj.resource('NIFTI').exists():
scan_obj.resource('NIFTI').delete()
dcm_dir = os.path.join(OPTIONS.directory, 'DICOM')
if len(fpaths) > 1:
need_to_zip = True
if len(fpaths) == 1 and fpaths[0].endswith('.zip'):
if not os.path.exists(dcm_dir):
os.makedirs(dcm_dir)
os.system('unzip -d %s -j %s > /dev/null' % (dcm_dir,
fpaths[0]))
os.remove(fpaths[0])
dicom_files = get_dicom_list(dcm_dir)
if dicom_files:
# Check for duplicate dicoms:
if OPTIONS.check_dcm:
check_duplicate_slices_dicom(dicom_files)
# convert dcm to nii
conversion_status = dcm2nii(dicom_files[0])
if not conversion_status:
# Convert dcm via dcmdjpeg
dcmdjpeg(dcm_dir)
# try again dcm2nii
dcm_fpath = os.path.join(dcm_dir, 'final_1.dcm')
conversion_status = dcm2nii(dcm_fpath)
# Check if Nifti created:
nii_li = [f for f in os.listdir(dcm_dir)
if f.endswith('.nii.gz') or f.endswith('.nii')]
if not nii_li:
print " - warning: dcm to nii failed with \
conversion dcmjpeg. no upload."
else:
# UPLOADING THE RESULTS
upload_converted_images(dicom_files, dcm_dir, scan_obj,
need_to_zip)
# clean tmp folder
XnatUtils.clean_directory(OPTIONS.directory)
else:
print " - ERROR : no proper DICOM files \
found from the resource on XNAT. "
else:
print " - ERROR : issue with resource DICOM: \
def run(self, scan_info, scan_obj):
"""run function to convert dicom to parrec to nifti and upload data."""
# clean tmp folder
XnatUtils.clean_directory(self.directory)
if not len(scan_obj.resource('DICOM').files().get()) > 0:
LOGGER.debug('no DICOM files')
elif scan_info['type'] in AVOID_SCANTYPES:
LOGGER.info('avoid this scan type: {}'.format(scan_info['type']))
else:
LOGGER.debug('downloading all DICOMs...')
self.dicom_paths = XnatUtils.download_files_from_obj(
self.directory, scan_obj.resource('DICOM'))
if not self.dicom_paths:
msg = """dcm2nii -- %s -- No proper DICOM found in \
resource DICOM on XNAT"""
LOGGER.error(msg % scan_info['scan_id'])
msg = 'No proper DICOM found in resource DICOM on XNAT'
self.log_warning_error(msg, scan_info, error=True)
else:
# convert dcm to nii
dcm_dir = os.path.dirname(self.dicom_paths[0])
# ZIP the DICOM if more than one
if len(self.dicom_paths) > 1 and self.zip_dicoms:
self.zipping_dicoms(scan_obj, dcm_dir)
# if only one DICOM and it's a zip, unzip
if len(self.dicom_paths) == 1 and \
self.dicom_paths[0].endswith('.zip'):
dcm_dir = os.path.dirname(self.dicom_paths[0])
os.system('unzip -d %s -j %s > /dev/null'
% (dcm_dir, self.dicom_paths[0]))
os.remove(self.dicom_paths[0])
self.dicom_paths = self.get_dicom_list(dcm_dir)
if not self.dcm2nii(self.dicom_paths[0]):
# Convert dcm via dcmdjpeg
dicom_paths_djpeg = self.dcmdjpeg()
# try again dcm2nii
self.dcm2nii(dicom_paths_djpeg[0])
dcm_dir = os.path.dirname(dicom_paths_djpeg[0])
# Check if Nifti created:
nifti_list = [
f for f in os.listdir(dcm_dir)
if f.endswith('.nii.gz') or f.endswith('.nii')]
if not nifti_list:
msg = "dcm2nii -- %s -- DCM --> NII ( preprocess \
dicom with dcmdjpeg ) conversion failure"
LOGGER.warn(msg % scan_info['scan_id'])
msg = 'Fail to convert DICOM to NIFTI '
self.log_warning_error(msg, scan_info)
else:
# UPLOADING THE RESULTS
self.upload_converted_images(
dcm_dir, scan_obj, scan_info)
# clean tmp folder
LOGGER.debug('clean temp directory...')
XnatUtils.clean_directory(self.directory)
