本文整理汇总了Python中dax.XnatUtils.download_file_from_obj方法的典型用法代码示例。如果您正苦于以下问题：Python XnatUtils.download_file_from_obj方法的具体用法？Python XnatUtils.download_file_from_obj怎么用？Python XnatUtils.download_file_from_obj使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类dax.XnatUtils的用法示例。
在下文中一共展示了XnatUtils.download_file_from_obj方法的4个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: pre_run
# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import download_file_from_obj [as 别名]
def pre_run(self):
"""Method to download data from XNAT.
:param argument_parse: argument parser object return by parse_args()
"""
resource = 'ACQ' # resource to download from the scan on XNAT
folder = os.path.join(self.jobdir, 'inputs')
os.makedirs(folder)
assessor_label = '-x-'.join([self.xnat_project,
self.xnat_subject,
self.xnat_session,
self.proctype])
xnat = XnatUtils.get_interface()
a = xnat.select('/projects/%s/subjects/%s/experiments/%s/assessors/%s'
% (self.xnat_project, self.xnat_subject,
self.xnat_session, assessor_label))
for nb_acq in range(1, self.nb_acquisition+1):
res_name = '%s%d' % (resource, nb_acq)
self.time_writer('Download resource: %s' % res_name)
file_gzip = XnatUtils.download_file_from_obj(
folder, a.out_resource(res_name))
self.time_writer('Unzip file: %s' % file_gzip)
XnatUtils.gunzip_file(file_gzip)
self.inputs[nb_acq] = file_gzip[:-3]
sc = XnatUtils.get_good_scans(a.parent(), DICOM_SCAN_TYPE)[0]
dcm_file = XnatUtils.download_file_from_obj(
folder, sc.resource('DICOM'))
self.inputs['dcm'] = dcm_file
xnat.disconnect()示例2: pre_run
# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import download_file_from_obj [as 别名]
def pre_run(self):
"""Method to download data from XNAT.
:param argument_parse: argument parser object return by parse_args()
"""
# Make directory
input_folder = XnatUtils.makedir(os.path.join(self.jobdir, 'inputs'),
subdir=False)
# Download scans:
self.time_writer('Connection to XNAT')
xnat = XnatUtils.get_interface(host=self.host,
user=self.user,
pwd=self.pwd)
# Download NIFTIs
index = 1
for scan_id in self.scans_id:
scan_info = {}
scan_dir = XnatUtils.makedir(os.path.join(input_folder, scan_id),
subdir=False)
self.time_writer('Downloading scan ID %s ...' % scan_id)
scan = XnatUtils.select_obj(xnat,
self.xnat_project,
self.xnat_subject,
self.xnat_session,
scan_id)
snii_obj = scan.resource('NIFTI')
scan_info['4D'] = XnatUtils.download_file_from_obj(scan_dir,
snii_obj)
# Download DICOMs
sdcm_obj = scan.resource('DICOM')
self.time_writer('Downloading DICOM for scan ID %s ...'
% scan_id)
scan_info['dicom'] = XnatUtils.download_file_from_obj(scan_dir,
sdcm_obj)
scan_info['type'] = scan.attrs.get('type')
scan_info['ID'] = scan_id
if 'b3000' in scan_info['type'].lower() and \
len([o for o in self.acquisitions.get(index, list())
if 'b3000' in o['type'].lower()]) > 0:
index += 1
if index in self.acquisitions:
self.acquisitions[index].append(scan_info)
else:
self.acquisitions[index] = [scan_info]
xnat.disconnect()
self.time_writer('Disconnection of XNAT')示例3: sorted
# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import download_file_from_obj [as 别名]
if args.sessions:
li_scans = XnatUtils.filter_list_dicts_regex(
li_scans, 'session_label', args.sessions.split(','))
li_scans = sorted(li_scans, key=lambda k: k['session_label'])
for scan_d in li_scans:
# If type is unknown or empty, run:
if scan_d['type'] == 'unknown' or not scan_d['type']:
if 'DICOM' in scan_d['resources']:
print (" - setting type for %s/%s"
% (scan_d['session_label'], scan_d['ID']))
tmp_dir = os.path.join(directory, scan_d['session_label'],
scan_d['ID'])
if not os.path.isdir(tmp_dir):
os.makedirs(tmp_dir)
# Download the dicom and read the header:
scan_obj = XnatUtils.get_full_object(xnat, scan_d)
dicom_file = XnatUtils.download_file_from_obj(
tmp_dir, scan_obj.resource('DICOM'))
# for dicom_path in dicom_files:
print " file: %s " % dicom_file
dcm = dicom.read_file(dicom_file)
# Get the protocol name
protocol = dcm.ProtocolName
if protocol is not None:
# Set it to the scan
scan_obj.attrs.mset({'type': protocol,
'series_description': protocol})
finally:
xnat.disconnect()
示例4: pre_run
# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import download_file_from_obj [as 别名]
def pre_run(self):
"""Method to download data from XNAT.
:param argument_parse: argument parser object return by parse_args()
"""
# Make directory
input_folder = XnatUtils.makedir(os.path.join(self.jobdir, 'inputs'),
subdir=False)
# Target
target_folder = XnatUtils.makedir(os.path.join(input_folder,
ARGS.target_id),
subdir=False)
target_dcm = XnatUtils.makedir(os.path.join(target_folder, 'DICOM'),
subdir=False)
self.time_writer('Connection to XNAT')
xnat = XnatUtils.get_interface(host=self.host,
user=self.user,
pwd=self.pwd)
self.time_writer('Downloading target %s ...' % ARGS.target_id)
target_scan = XnatUtils.select_obj(xnat,
ARGS.proj_label,
ARGS.subj_label,
ARGS.sess_label,
ARGS.target_id)
tnii_obj = target_scan.resource('NIFTI')
self.target['nii'] = XnatUtils.download_file_from_obj(target_folder,
tnii_obj)
tdcm_obj = target_scan.resource('DICOM')
self.target['dcm'] = XnatUtils.download_files_from_obj(target_dcm,
tdcm_obj)
self.target['type'] = target_scan.attrs.get('type')
self.target['ID'] = ARGS.target_id
# Sources
sources_list = XnatUtils.get_input_list(ARGS.sources_id, list())
self.time_writer('Downloading sources %s ...' % sources_list)
for scan_id in sources_list:
# Make directories
spath = os.path.join(input_folder, scan_id)
source_folder = XnatUtils.makedir(spath, subdir=False)
dpath = os.path.join(source_folder, 'DICOM')
source_dcm = XnatUtils.makedir(dpath, subdir=False)
source_scan = XnatUtils.select_obj(xnat,
ARGS.proj_label,
ARGS.subj_label,
ARGS.sess_label,
scan_id)
snii_obj = source_scan.resource('NIFTI')
nii_list = XnatUtils.download_file_from_obj(source_folder,
snii_obj)
sdcm_obj = source_scan.resource('DICOM')
dcm_list = XnatUtils.download_file_from_obj(source_dcm, sdcm_obj)
self.sources[scan_id] = dict()
self.sources[scan_id]['nii'] = nii_list
self.sources[scan_id]['dcm'] = dcm_list
self.sources[scan_id]['type'] = source_scan.attrs.get('type')
self.sources[scan_id]['ID'] = scan_id
xnat.disconnect()
self.time_writer('Disconnection of XNAT')