def _gen_outfilename(self, name):
if name == 'out_file':
out_file = self.inputs.out_file
if isdefined(out_file) and isdefined(self.inputs.input_file):
_, _, ext = split_filename(self.inputs.input_file)
out_file = self.inputs.out_file + ext
if not isdefined(out_file) and isdefined(self.inputs.input_file):
pth, fname, ext = split_filename(self.inputs.input_file)
print(pth, fname, ext)
out_file = os.path.join(pth, fname + '_bet' + ext)
elif name == 'out_mask':
out_file = self.inputs.out_file
if isdefined(out_file) and isdefined(self.inputs.input_file):
_, _, ext = split_filename(self.inputs.input_file)
out_file = self.inputs.out_file + '_mask' + ext
# if isdefined(out_file):
# pth, fname, ext = split_filename(out_file)
# out_file = os.path.join(pth, fname+'_bet_mask'+ext)
elif not isdefined(out_file) and isdefined(self.inputs.input_file):
pth, fname, ext = split_filename(self.inputs.input_file)
print(pth, fname, ext)
out_file = os.path.join(pth, fname + '_bet_mask' + ext)
return os.path.abspath(out_file)
def _gen_outfilename(self):
out_file = self.inputs.out_file
if isdefined(out_file) and isdefined(self.inputs.t1):
_, _, ext = split_filename(self.inputs.t1)
out_file = self.inputs.out_file + ext
if not isdefined(out_file) and isdefined(self.inputs.t1):
pth, _, ext = split_filename(self.inputs.t1)
print(pth, ext)
out_file = os.path.join(pth, 'segmentation' + ext)
return os.path.abspath(out_file)
def __init__(self, toConvert, clean=False, bin_path=''):
print('Started image format conversion...')
self.basedir, self.filename, _ = split_filename(toConvert)
self.filename = self.filename.split('.')[0]
self.toConvert = toConvert
self.clean = clean
self.bin_path = bin_path
def __init__(self, image, mask=None, prefix=None):
print('\nStarting image cropping...')
self.image = image
self.mask = mask
imagePath, imageFilename, imageExt = split_filename(image)
filename = imageFilename.split('.')[0]
if mask is not None:
_, maskFilename, maskExt = split_filename(mask)
maskFilename = maskFilename.replace('.', '_')
self.maskOutname = os.path.join(
imagePath, maskFilename + '_cropped') + maskExt
if prefix is None and mask is not None:
self.imageOutname = os.path.join(imagePath,
filename + '_cropped') + imageExt
elif prefix is None and mask is None:
self.imageOutname = os.path.join(imagePath, filename + '_cropped')
elif prefix is not None and mask is None:
self.imageOutname = os.path.join(imagePath, prefix + '_cropped')
elif prefix is not None and mask is not None:
self.imageOutname = os.path.join(imagePath,
prefix + '_cropped') + imageExt
def _run_interface(self, runtime):
images = self.inputs.images
if images:
new_dir = os.path.abspath('data_prepared')
os.mkdir(os.path.abspath('data_prepared'))
for i, image in enumerate(images):
_, _, ext = split_filename(image)
shutil.copy2(
image,
os.path.join(new_dir,
'subject1_{}'.format(str(i).zfill(4)) + ext))
else:
raise Exception('No images provided!Please check.')
return runtime
def put(project,
subject,
sessions,
sub_folder,
config=None,
url=None,
pwd=None,
user=None,
processed=False):
if config is not None:
interface = Interface(config)
else:
interface = Interface(server=url,
user=user,
password=pwd,
proxy='www-int2:80')
uri = '/data/projects/%s/subjects/%s' % (project, subject)
response = interface.put(uri)
subject_uid = response.content
print('New subject %s created!' % subject_uid)
xnat_subs = interface.select.project(project).subjects()
xnat_sub = [x for x in xnat_subs if x.label() == subject][0]
sub_id = interface.select.project(project).subject(xnat_sub.id())
for session in sessions:
print('Processing session {}'.format(session))
session_folder = os.path.join(sub_folder, session)
scans = [
x for x in sorted(glob.glob(session_folder + '/*'))
if os.path.isfile(x)
]
match = session_modality_re.match(session)
proc = ''
if match is None and processed:
experiment_type = 'xnat:mrSessionData'
scan_type = 'xnat:mrScanData'
proc = '_processed'
elif match.group(1) == 'MR':
experiment_type = 'xnat:mrSessionData'
scan_type = 'xnat:mrScanData'
elif match.group(1) == 'CT' or match.group(1) == 'CTREF':
experiment_type = 'xnat:ctSessionData'
scan_type = 'xnat:ctScanData'
elif match.group(1) == 'RT':
experiment_type = 'xnat:rtSessionData'
scan_type = 'xnat:rtScanData'
experiment = sub_id.experiment('%s_%s%s' %
(xnat_sub.label(), session, proc))
if not experiment.exists():
try:
experiment.create(experiments=experiment_type)
except DatabaseError:
experiment.create(experiments=experiment_type)
print('New experiment %s created!' % experiment.id())
for scan in scans:
_, scan_name, extention = split_filename(scan)
res_format = get_resource_name(scan)
# scan_name = scan.split('/')[-1].split('.')[0]
print('Uploading {}...'.format(scan_name))
xnat_scan = experiment.scan(scan_name)
if not xnat_scan.exists():
done = False
z = 1
while not done:
try:
xnat_scan.create(scans=scan_type)
done = True
except DatabaseError:
print('Same Database error: {} times'.format(z))
z = z + 1
# xnat_scan.create(scans=scan_type)
print('New scan %s created!' % xnat_scan.id())
resource = xnat_scan.resource(res_format)
if not resource.exists():
try:
resource.create()
except DatabaseError:
resource.create()
print('New resource %s created!' % resource.id())
else:
print('Resource %s already in the repository!' %
resource.id())
xnat_resource = resource.file(scan_name + extention)
response = xnat_resource.put(src=scan,
format=res_format,
content=res_format,
extract=False,
overwrite=True)
else:
print('Scan %s already in the repository!' % xnat_scan.id())