def run(self, scan_info, scan_obj):
""" main function to run on scan """
if not len(scan_obj.resource(self.resourcename).files().get()) > 0:
LOGGER.warn('Preview NIFTI -- '+scan_info['scan_id']+' -- No file(s) for '+self.resourcename)
else:
LOGGER.debug("downloading "+self.resourcename+"...")
fpath = XnatUtils.download_biggest_file_from_obj(self.directory, scan_obj.resource(self.resourcename))
if not os.path.exists(fpath):
LOGGER.warn('Preview NIFTI -- '+scan_info['scan_id']+' -- '+self.resourcename+' file size is zero.')
else:
sm_gif = str(os.path.join(self.directory, os.path.splitext(os.path.basename(fpath))[0] + "_sm.gif"))
lg_gif = str(os.path.join(self.directory, os.path.splitext(os.path.basename(fpath))[0] + "_lg.gif"))
# Generate preview from the nifti file
self.generate_preview(fpath, sm_gif, lg_gif)
if os.path.isfile(sm_gif):
LOGGER.debug('GIF Made / upload ...')
scan_obj.resource('SNAPSHOTS').file('snap_t.gif').put(sm_gif, 'GIF', 'THUMBNAIL')
scan_obj.resource('SNAPSHOTS').file('snap.gif').put(lg_gif, 'GIF', 'ORIGINAL')
else:
LOGGER.error('Preview NIFTI -- '+scan_info['scan_id']+' -- GIF FAILED')
self.log_warning_error('GIF failed for NIFTI', scan_info, error=True)
self.clean_directory()
def make_preview_nifti(xnat, options):
"""generate previewe for a project on XNAT."""
# make directory
if not os.path.exists(options.directory):
os.makedirs(options.directory)
# list of scans for the project
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 scans to keep scans with NIFTI but no SNAPSHOTS."
list_scans = filter(lambda x: 'NIFTI' in x['resources'] and
'SNAPSHOTS' not 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)
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'])
scan_obj = XnatUtils.get_full_object(xnat, scan)
res_obj = scan_obj.resource(options.resource)
if res_obj.exists() and len(res_obj.files().get()) > 0:
if options.force and scan_obj.resource("SNAPSHOTS").exists():
scan_obj.resource("SNAPSHOTS").delete()
print " --> downloading "+options.resource+" ..."
filename = XnatUtils.download_biggest_file_from_obj(
options.directory, res_obj)
if not filename:
print ' - warning: '+options.resource+' -- no files.'
else:
if filename.endswith('.nii.gz'):
os.system('gzip -d '+filename)
filename = filename[:-3]
fname = os.path.basename(filename).split('.')[0] + "_sm.gif"
smgif = os.path.join(options.directory, fname)
fname = os.path.basename(filename).split('.')[0] + "_lg.gif"
lggif = os.path.join(options.directory, fname)
status = generate_preview(filename, smgif, lggif)
if not status:
print ' --> GIF FAILED'
else:
if os.path.isfile(smgif):
print ' --> GIF Made / upload to XNAT...'
scan_obj.resource('SNAPSHOTS').file('snap_t.gif')\
.put(smgif, 'GIF', 'THUMBNAIL')
scan_obj.resource('SNAPSHOTS').file('snap.gif')\
.put(lggif, 'GIF', 'ORIGINAL')
else:
print ' --> GIF FAILED'
if os.path.isfile(smgif):
os.remove(smgif)
os.remove(lggif)
if os.path.isfile(filename):
os.remove(filename)
else:
print(" - ERROR : issue with resource %s: no file or resource. "
% (options.resource))
for SCAN in SCANS:
NEED_PAR = False
NEED_REC = True
sys.stdout.write('Checking scan %s in session %s\n' % (SCAN['ID'], SCAN['session_label']))
if 'DICOM' not in SCAN['resources'] and 'secondary' in SCAN['resources'] and SCAN['ID'] not in KNOWN_IGNORE_LIST \
and 'superpacs' not in SCAN['type'].lower():
sys.stdout.write(' -DICOM not found. Checking to see if PAR and REC do\n')
if 'PAR' not in SCAN['resources']:
sys.stdout.write(' -PAR not found. Marked for upload\n')
NEED_PAR = True
if 'REC' not in SCAN['resources']:
sys.stdout.write(' -REC not found. Marked for upload\n')
NEED_REC = True
SCAN_OBJECT = XnatUtils.get_full_object(XNAT, SCAN)
if SCAN_OBJECT.exists():
DL_FILE = XnatUtils.download_biggest_file_from_obj('/tmp', SCAN_OBJECT.resource('secondary'))
ZIP_FILE_NAME = DL_FILE.replace('.dcm', '.ZIP')
os.rename(DL_FILE, ZIP_FILE_NAME)
sys.stdout.write(' -Got file %s\n' % ZIP_FILE_NAME)
TEMP_DIR_LOCATION = os.path.join('/tmp', '-x-'.join([SCAN['session_label'], SCAN['ID']]))
if not os.path.isdir(TEMP_DIR_LOCATION):
os.makedirs(TEMP_DIR_LOCATION)
else:
shutil.rmtree(TEMP_DIR_LOCATION)
os.makedirs(TEMP_DIR_LOCATION)
TMP_DIR_LIST.append(TEMP_DIR_LOCATION)
sys.stdout.write(' -Extracting all resources to %s\n' % TEMP_DIR_LOCATION)
try:
ZIP_FILE = zipfile.ZipFile(ZIP_FILE_NAME)