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 pixel_array2.dtype != np.uint16:
pixel_array2 = pixel_array2.astype(np.uint16)
print pixel_array2.max()
print pixel_array2.min()
ds.PixelData = pixel_array2.tostring()
# Save the image
ds.save_as(filename)
if __name__ == '__main__':
args = parse_args()
# Scans on XNAT:
try:
xnat = XnatUtils.get_interface()
li_scans = XnatUtils.list_project_scans(xnat, args.project)
# Filter:
if args.sessions:
li_scans = XnatUtils.filter_list_dicts_regex(
li_scans, 'session_label', args.sessions.split(','))
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,
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: \
help="Directory where the json files are stored.",
required=True)
argp.add_argument('-c', dest='csv',
help="Csv file containing the subject that where already\
downloaded.",
required=True)
return argp.parse_args()
if __name__ == '__main__':
args = parse_args()
row_excel = read_csv(args.csv, header=['subject', 'session'])
li_sessions = [row['session'].strip() for row in row_excel]
XNAT = XnatUtils.get_interface(host=HOST)
li_scans = XnatUtils.list_project_scans(XNAT, '1946')
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:
'MaxMun': 0,
'NYU': 5,
'OHSU': 0,
'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()
if not os.path.isfile(file_not_zipped):
sys.stderr.write('ERROR: could not find file %s to gzip' % file_not_zipped)
else:
file_name_out = '%s.gz' % file_not_zipped
content = open(file_not_zipped, 'rb')
content = content.read()
fout = gzip.open(file_name_out, 'wb')
fout.write(content)
fout.close()
os.remove(file_not_zipped)
return file_name_out
if __name__ == '__main__':
XNAT = XnatUtils.get_interface()
SCANS = XnatUtils.list_project_scans(XNAT, 'SMITH_DOD')
FID = open('/tmp/SMITH_DOD.csv', 'w')
NEEDS_UPLOAD = False
TMP_DIR_LIST = list()
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']:
__author__ = "damons"
__purpose__ = "set the scan quality of a scan on xnat"
from dax import XnatUtils
import sys
if __name__ == "__main__":
XNAT = XnatUtils.get_interface()
SCANS = XnatUtils.list_project_scans(XNAT, "WOODWARD_TCP")
if len(sys.argv) != 4:
print len(sys.argv)
sys.stderr.write("ERROR: args must be <SESSION> <SCAN_ID> <STATUS>")
sys.exit(1)
MY_SESSION = sys.argv[1]
MY_SCAN = sys.argv[2]
STATUS = sys.argv[3]
for SCAN in SCANS:
if SCAN["session_label"] == MY_SESSION and SCAN["ID"] == MY_SCAN:
print "Setting QC of scan %s in session %s to %s" % (MY_SCAN, MY_SESSION, STATUS)
OBJECT = XnatUtils.get_full_object(XNAT, SCAN)
OBJECT.attrs.set("quality", STATUS)
XNAT.disconnect()
from dax import XnatUtils
import os
if __name__ == "__main__":
# Variables:
project = 'DIAN'
types = {'': 'PhoenixZIPReport'}
with XnatUtils.get_interface(host=os.environ['DPUK']) as xnat:
scans = XnatUtils.list_project_scans(xnat, project)
scans = XnatUtils.filter_list_dicts_regex(scans, 'type', types.keys())
for scan in sorted(scans, key=lambda k: k['session_label']):
print "%s - %s - %s - %s" % (scan["session_label"],
scan["ID"],
scan["type"],
scan["series_description"])
scan_obj = XnatUtils.get_full_object(xnat, scan)
scan_obj.attrs.set('type', types[scan['type']])
print(' new type: {}'.format(types[scan['type']]))
__author__ = 'damons'
from dax import XnatUtils
if __name__ == '__main__':
XNAT = XnatUtils.get_interface()
SCANS = XnatUtils.list_project_scans(XNAT,'PHOTON')
print "There are %s scans in the PHOTON project" % str(len(SCANS))
count = 0
for SCAN in SCANS:
if 'SNAPSHOTS' in SCAN['resources']:
count +=1
print "There are %s scans in the PHOTON project with SNAPSHOTS" % str(count)
print "There are %s scans in the PHOTON project WITHOUT SNAPSHOTS" % str((len(SCANS) - count))
XNAT.disconnect()
import os
import sys
from dax import XnatUtils
SCAN = 'T2 Axial'
HOST = 'https://prostate-xnat.cs.ucl.ac.uk'
PROJECT = 'PICTURE'
RESOURCE = 'OsiriX'
OLD_FILE = 'mantonelli_Unnamed.rois_series'
NEW_FILE = 'Mrishta_Unnamed.rois_series'
TMP_DIR = '/Users/byvernault/data/temp_roi_upgrade/'
with XnatUtils.get_interface(host=HOST) as xnat:
li_scans = XnatUtils.list_project_scans(xnat, PROJECT)
li_scans = XnatUtils.filter_list_dicts_regex(li_scans, 'type', SCAN)
li_scans = filter(lambda x: RESOURCE in x['resources'], li_scans)
sys.stdout.write('Renaming file %s to %s for scan type %s\n'
% (OLD_FILE, NEW_FILE, SCAN))
for scan in li_scans:
sys.stdout.write(' - scan: %s / %s ...\n'
% (scan['session_label'], scan['ID']))
scan_obj = XnatUtils.get_full_object(xnat, scan)
res_obj = scan_obj.resource(RESOURCE)
files = None
if res_obj.exists() and OLD_FILE in res_obj.files().get()[:]:
# fpath = XnatUtils.download_file_from_obj(TMP_DIR, res_obj,
# fname=OLD_FILE)
