def edit_session_date(xnat, session_info):
date = session_info['label'].split('_')[-1]
date = '{}-{}-{}'.format(date[:4], date[4:6], date[6:])
print("%s - %s" % (session_info['label'], date))
if session_info['date'] == date:
print ' already set up.'
else:
session_obj = XnatUtils.get_full_object(xnat, session_info)
session_obj.attrs.set('date', date)
def sessions_delete():
"""Delete sessions on XNAT."""
for session in LI_SESSIONS:
print ' - deleting session: %s' % session['label']
session_obj = XnatUtils.get_full_object(XNAT, session)
if session_obj.exists():
try:
session_obj.delete()
except:
print "exception but let's continue"
def set_session_age(session_info):
"""Set age for session."""
if not session_info['age'] or ARGS.force:
session_obj = XnatUtils.get_full_object(XNAT, session_info)
xsitype_sess = session_obj.attrs.get('xsiType')
yob = session_obj.parent().attrs.get('yob')
if not yob:
print 'Skipping the session because yob not set.'
else:
yob = "%s-01-01" % yob
years = years_between(yob, session_info['date'])
age = '%.2f' % years
session_obj.attrs.set('%s/%s' % (xsitype_sess, 'age'), age)
print 'Age set to %s for %s.' % (age, session['label'])
else:
print 'Already set to %s for %s' % (session_info['age'],
session['label'])
def zip_resources(xnat, args):
"""
Loop through the project scans to zip files.
:param xnat: interface from dax related to pyxnat
:param args: arguments from parse_args
"""
# set a directory where the files are download
directory = os.path.abspath(XnatUtils.makedir(args.directory))
list_scans = XnatUtils.list_project_scans(xnat, args.project)
print("INFO: Filtering list of scans to keep scans with resources.")
if not args.force:
for resource in args.resources.split(','):
list_scans = filter(lambda x: resource in x['resources'],
list_scans)
# if sessions, filter:
if args.sessions:
list_scans = filter(
lambda x: x['session_label'] in args.sessions.split(','),
list_scans)
# filtering last sessions:
list_scans = sorted(list_scans, key=lambda k: k['session_label'])
if args.lastsess:
list_scans = remove_sessions_processed(list_scans, args.lastsess)
number_scans = len(list_scans)
print("INFO: Converting the %s scans found." % (number_scans))
for index, scan in enumerate(list_scans):
message = ' * {ind}/{tot} -- Session: {sess} -- Scan: {scan}'
print(message.format(ind=index + 1,
tot=number_scans,
sess=scan['session_label'],
scan=scan['ID']))
scan_obj = XnatUtils.get_full_object(xnat, scan)
if scan_obj.exists():
for resource in args.resources.split(','):
zip_resource(scan_obj.resource(resource), directory,
resource, args.no_delete, args.no_big)
if args.subjects:
li_scans = XnatUtils.filter_list_dicts_regex(
li_scans, 'subject_label', args.subjects.split(','))
li_scans = sorted(li_scans, key=lambda k: k['session_label'])
for scan_d in li_scans:
if scan_d['ID'] == 'n004':
print (' -> converting session: %s /scan: %s'
% (scan_d['session_label'], scan_d['ID']))
if 'IMG' in scan_d['resources']:
if 'NIFTI' not in scan_d['resources'] or args.force:
tmp_dir = os.path.join(args.directory,
scan_d['session_label'],
scan_d['ID'])
if not os.path.isdir(tmp_dir):
os.makedirs(tmp_dir)
scan_obj = XnatUtils.get_full_object(xnat, scan_d)
# Download:
files = XnatUtils.download_files_from_obj(
tmp_dir, scan_obj.resource('IMG'))
if len(files) > 1 and args.zip_fdf:
zipping_files(scan_obj, os.path.dirname(files[0]))
if len(files) == 1 and files[0].endswith('.zip'):
fdf_dir = os.path.dirname(files[0])
os.system('unzip -d %s -j %s > /dev/null'
% (fdf_dir, files[0]))
os.remove(files[0])
files = get_files_list(fdf_dir, '.fdf',
add_procpar=True)
# Convert:
try:
xnat = XnatUtils.get_interface(host=HOST)
if ASSESSOR:
li_assessors = [XnatUtils.select_assessor(xnat, ASSESSOR)]
sys.stdout.write('Renaming resources %s to %s for assessor %s'
% (OLD_RESOURCE, NEW_RESOURCE, ASSESSOR))
else:
li_assessors = XnatUtils.list_project_assessors(xnat, PROJECT)
sys.stdout.write('Renaming resources %s to %s for assessor type %s\n'
% (OLD_RESOURCE, NEW_RESOURCE, ASSESSOR_TYPE))
for assessor in li_assessors:
sys.stdout.write(' - assessor: %s ...\n' % assessor['label'])
assessors = XnatUtils.get_full_object(xnat, assessor)
old_res = assessors.resource(OLD_RESOURCE)
files = None
if old_res.exists():
files = XnatUtils.download_files_from_obj(TMP_DIR, old_res)
if files:
new_res = assessors.resource(NEW_RESOURCE)
XnatUtils.upload_files_to_obj(files, new_res)
if new_res.exists():
old_res.delete()
sys.stdout.write(' renamed.\n')
for f in files:
os.remove(f)
print "DONE -- See y'all"
except Exception as e:
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))
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: \
li_scans = [scan for scan in li_scans
if scan['type'] == '1946_PET_NAC_DYNAMIC_0_60MIN']
row = list()
for scan in li_scans:
if scan['session_label'] not in li_sessions:
msg = 'Download scan number %s for session %s'
print msg % (scan['ID'], scan['session_label'])
# data_dir = os.path.join(args.directory, scan['subject_label'],
# scan['session_label'], 'scans',
# '1946_PET_NAC_DYNAMIC_0_60MIN')
data_dir = os.path.join(args.directory, scan['session_label'])
if os.path.exists(data_dir):
print ' --> Folder present. Already downloaded?'
else:
scan_obj = XnatUtils.get_full_object(XNAT, scan)
res_obj = scan_obj.resource('DICOM')
if not res_obj.exists():
print ' Error: No DICOM Resources found for scan.'
else:
if len(res_obj.files().get()) > 0:
print ' 1) start download...'
os.makedirs(data_dir)
dl_files = XnatUtils.download_files_from_obj(data_dir,
res_obj)
print ' 2) Files downloaded'
else:
os.makedirs(data_dir)
curl = CCMD.format(path=data_dir,
host=HOST,
project='1946',
__purpose__ = "Renaming attrs for xnat object"
__version__ = '1.0.0'
__modifications__ = '11 September 2015 - Original write'
if __name__ == '__main__':
host = os.environ['XNAT_HOST']
user = os.environ['XNAT_USER']
pwd = os.environ['XNAT_PASS']
subject_type = False
session_type = True
xnat = XnatUtils.get_interface(host=host, user=user, pwd=pwd)
if subject_type:
for subject in XnatUtils.list_subjects(xnat, projectid='INNOVATE'):
subj_obj = XnatUtils.get_full_object(xnat, subject)
if subj_obj.exists():
labels = subject['label'].split('-')
if subject['label'].startswith('INN_'):
sub = subject['label'].replace('_', '-')
labels = sub.split('-')
if len(labels) < 2:
print 'stop - wrong label'
continue
if labels[1].isdigit():
print 'stop - already good label'
continue
if '_' in labels[2]:
fin = '_'+'_'.join(labels[2].split('_')[1:])
labels[2] = labels[2].split('_')[0]
else:
'Olin': 5,
'Pitt': 0,
'SBL': 0,
'SDSU': 0,
'Stanford': 0,
'Trinity': 0,
'UCLA': 0,
'UM': 0,
'USM': 0,
'Yale': 5}
XNAT = XnatUtils.get_interface()
SCANS = XnatUtils.list_project_scans(XNAT, 'ABIDE')
for SCAN in SCANS:
if SCAN_TYPE in SCAN['type']:
OBJECT = XnatUtils.get_full_object(XNAT, SCAN)
dropvols_num = get_num_dropvols(SCAN['session_label'])
sys.stdout.write('Setting dropvols to {dropvols} and slorder '
'to {slorder} for scan id {scanid} for '
'session {session}\n'.format(dropvols=dropvols_num,
slorder='[]',
scanid=SCAN['ID'],
session=SCAN['session_label']))
OBJECT.attrs.set('xnat:mrScanData/parameters/addParam[name=dropvols]/addField', str(dropvols_num))
OBJECT.attrs.set('xnat:mrScanData/parameters/addParam[name=slorder]/addField', '[]')
XNAT.disconnect()
print 'INFO: connection to xnat <%s>:' % (HOST)
XNAT = XnatUtils.get_interface(host=ARGS.host, user=ARGS.username,
pwd=PWD)
li_assessors = XnatUtils.list_project_assessors(XNAT, ARGS.project)
li_assessors = XnatUtils.filter_list_dicts_regex(
li_assessors, 'proctype',
['GIF_Parcellation_v2'])
li_assessors = XnatUtils.filter_list_dicts_regex(
li_assessors, 'procstatus',
['COMPLETE'])
li_assessors = filter(lambda x: 'WHOLEBRAIN' not in x['resources'],
li_assessors)
li_assessors = sorted(li_assessors, key=lambda k: k['session_label'])
start = False
for assessor in li_assessors:
if ARGS.session:
if assessor['session_label'] == ARGS.session:
start = True
else:
start = True
if start:
print '\n<-- Assessor: %s -->' % assessor['label']
assessor_obj = XnatUtils.get_full_object(XNAT, assessor)
brain = generate_bmask_whole(assessor_obj, assessor,
ARGS.tmpdir)
XnatUtils.upload_file_to_obj(
brain, assessor_obj.resource('WHOLEBRAIN'), removeall=True)
finally:
XNAT.disconnect()
XNAT = XnatUtils.get_interface()
ASSESSORS = XnatUtils.list_project_assessors(XNAT, 'WOODWARD_TCP')
if len(sys.argv) != 4:
print len(sys.argv)
sys.stderr.write('ERROR: args must be <ASSESSOR_LABEL> <STATUS> <COMMENTS>')
sys.exit()
MY_ASSESSOR = sys.argv[1]
STATUS = sys.argv[2]
COMMENTS = sys.argv[3]
if STATUS not in XNAT_STATUS_LIST:
sys.stderr.write('ERROR: Status "%s" not in known list: %s\n'
%(STATUS, ','.join(XNAT_STATUS_LIST)))
for ASSESSOR in ASSESSORS:
if ASSESSOR['label'] == MY_ASSESSOR:
print "Setting QC of assessor %s to %s" % (MY_ASSESSOR,
STATUS)
OBJECT = XnatUtils.get_full_object(XNAT, ASSESSOR)
if not MY_ASSESSOR.endswith('-x-FS'):
OBJECT.attrs.set('proc:genProcData/validation/status', STATUS)
OBJECT.attrs.set('proc:genProcData/validation/notes', COMMENTS)
else:
OBJECT.attrs.set('fs:fsData/validation/status', STATUS)
OBJECT.attrs.set('fs:fsData/validation/notes', COMMENTS)
XNAT.disconnect()
