def get_all_gradients(session_label, dti_stack, decimals=None):
"""
Parses a list of dti sidecar files for subject.
Returns
=======
list of np.array
"""
gradients_per_frame = list()
gradients_as_array = np.asanyarray([])
error_xml_path_list=[]
error_msg=""
for xml_path in dti_stack:
xml_sidecar = read_xml_sidecar(xml_path)
try:
gradients_per_frame.append(get_gradient_table(xml_sidecar,
decimals=decimals))
gradients_as_array = np.asanyarray(gradients_per_frame)
except Exception as e:
error_xml_path_list.append(xml_path)
error_msg=str(e)
if error_xml_path_list != [] :
slog.info(session_label,
'ERROR: Could not get gradient table from xml sidecar',
script='xnat/check_gradient_tables.py',
sidecar=str(xml_sidecar),
error_xml_path_list=str(error_xml_path_list),
error_msg=error_msg)
return gradients_as_array
def verify_image_count(session, session_label, scan, scantype, manufacturer,
images_created):
if manufacturer in expected_images.keys():
if scantype in expected_images[manufacturer].keys():
imgrange = expected_images[manufacturer][scantype]
if not images_created in imgrange:
error = 'WARNING: Number of frames in archive differ from the standard'
slog.info(session_label, error,
session=session,
scan_number=scan,
scan_type=scantype,
actual_frame_number=images_created,
manufacturer=manufacturer,
expected_frame_number=str(expected_images[manufacturer][scantype]))
def export_to_nifti(interface, project, subject, session, session_label,
manufacturer, scanner_model, scan, scantype, verbose=False):
if verbose:
print "Starting export of nifti files for ", project, subject, session, session_label, scan, scantype
error_msg = []
# logfile_resource = '%s_%s/dcm2image.log' % (scan, scantype)
# xnat_log = interface.select.project(project).subject(subject).experiment(session).resource('nifti').file(logfile_resource)
# To test gradient directions without having to delete nifti files in xnat just uncomment this line
# and comment out the proceeding one
# if not xnat_log.exists() or 'dti60b1000' in scantype:
# if not xnat_log.exists():
match = re.match('.*(/fs/storage/XNAT/.*)scan_.*_catalog.xml.*',
interface.select.experiment(session).scan(scan).get(),
re.DOTALL)
if match:
dicom_path = match.group(1)
if not os.path.exists(dicom_path):
dicom_path = re.sub('storage/XNAT', 'ncanda-xnat', dicom_path)
if not os.path.exists(dicom_path):
error_msg.append(
"Path %s does not exist - export_to_nifti failed for SID:"
"%s EID:%s Label: %s!" % (dicom_path, subject, session,
session_label))
return error_msg,0
# if nifti files were created make sure that they are newer than dicom file otherwise recreate them
nifti_log_search = glob.glob(re.sub('/DICOM/','_%s/dcm2image.log' % (scantype),re.sub( '/SCANS/', '/RESOURCES/nifti/', dicom_path)))
if nifti_log_search != [] :
# we changed code here from *.* to avoid getting errors of not finding dicom files for sessions such as
# NCANDA_E01386 / B-00454-M-9-20140214 - scan 1 /ncanda-localizer-v1
dicom_file_pattern = dicom_path + '*'
dicom_file_list = glob.glob(dicom_file_pattern)
# ommit xml file - so that only dicom files are left - xml file is updated every time somebody changes something in the gui for that session - which has no meaning for xml file
dicom_file_list = [x for x in dicom_file_list if '.xml' not in x ]
# if dicom file is not there something odd is going on
if dicom_file_list == [] :
slog.info(session_label, "Error: could not find dicom files ",
session=session,
subject=subject,
scan_number=scan,
scan_type=scantype,
dicom_log_file=dicom_file_pattern)
return error_msg,0
# check time stamp - if newer than there is nothing to do
nifti_time = time.strftime('%Y-%m-%d %H:%m:%S',time.gmtime(os.path.getmtime(nifti_log_search[0])))
dicom_time = time.strftime('%Y-%m-%d %H:%m:%S',time.gmtime(os.path.getmtime(dicom_file_list[0])))
if nifti_time > dicom_time :
if verbose:
print("... nothing to do as nifti files are up to date")
return error_msg,0
slog.info(session_label + "_" + scan, "Warning: nifti seem outdated (dicom > nifti time) so they are recreated!",
session=session,
subject=subject,
check_nifti = str(nifti_time) + " " + str(nifti_log_search[0]),
check_dicom = str(dicom_time) + " " + str(dicom_file_list[0]),
info = "If the issue reappears then simply open up the session in XNAT, go to 'Manage Files', delete the directory 'Resources/nifti/" + scantype + "', and run the script again. If it still reappears then repeat the previous procedure and afterwards delete the directory that the log file in check_nifti is located!")
temp_dir = tempfile.mkdtemp()
zip_path = '%s/%s_%s.zip' % (temp_dir, scan, scantype)
log_filename = '%s/%s_%s/dcm2image.log' % (
temp_dir, scan, scantype)
dcm2image_command = 'cmtk dcm2image --tolerance 1e-3 ' \
'--write-single-slices --no-progress ' \
'-rvxO %s/%s_%s/image%%n.nii %s 2>&1' % (
temp_dir, scan, scantype, dicom_path)
output = ""
try:
output = subprocess.check_output(dcm2image_command,
shell=True)
except:
error_msg.append(
"The following command failed %s with the following output %s" % dcm2image_command,output)
if len(error_msg) == 0:
output_file = open(log_filename, 'w')
try:
output_file.writelines(output)
finally:
output_file.close()
try:
fzip = zipfile.ZipFile(zip_path, 'w')
for src in sorted(glob.glob('%s/*/*' % temp_dir)):
fzip.write(src, re.sub('%s/' % temp_dir, '', src))
fzip.close()
except:
error_msg.append("Could not zip %s" % zip_path)
if os.path.exists(zip_path):
try:
interface.select.project(project).subject(
subject).experiment(session).resource(
'nifti').put_zip(zip_path, overwrite=True,
extract=True)
except:
error_msg.append(
"Unable to upload ZIP file %s to experiment %s" % (
zip_path, session))
# Verify image counts for various series
images_created = len(glob.glob('%s/*/*.nii.gz' % temp_dir))
if images_created > 0:
# only use first part of string so GE Manufacturer is turned into GE
manufacturer_u = manufacturer.split(' ',1)[0].upper()
verify_image_count(session, session_label, scan, scantype,
manufacturer_u, images_created)
if 'dti60b1000' in scantype:
xml_search_string = os.path.join(temp_dir,'%s_%s' % (scan,scantype), 'image*.nii.xml')
xml_file_list = glob.glob(xml_search_string)
cgt.check_diffusion(session_label,session,xml_file_list,manufacturer_u,scanner_model,decimals=2)
# Clean up - remove temp directory
shutil.rmtree(temp_dir)
return error_msg,1
def check_diffusion(session_label,session,xml_file_list,manufacturer,scanner_model,decimals):
if len(xml_file_list) == 0 :
slog.info(session_label,
"Error: check_diffusion : xml_file_list is empty ",
session=session)
return
truth_gradient = np.array(get_ground_truth_gradients(manufacturer,scanner_model,decimals))
if len(truth_gradient) == 0 :
slog.info(session_label,
'ERROR: check_diffusion: scanner is unknown',
session=session,
scanner=manufacturer)
return
xml_file_list.sort()
errorsFrame = list()
errorsExpected = list()
errorsActual = list()
try:
evaluated_gradients = get_all_gradients(session_label,xml_file_list, decimals)
if len(evaluated_gradients) == len(truth_gradient):
for idx, frame in enumerate(evaluated_gradients):
# if there is a frame that doesn't match,
# report it.
if not (truth_gradient[idx] == frame).all():
errorsFrame.append(idx)
errorsActual.append(frame)
errorsExpected.append(truth_gradient[idx])
else:
slog.info(session_label,"ERROR: Incorrect number of frames.",
case_gradients=str(evaluated_gradients),
expected=str(truth_gradient),
session=session)
except AttributeError as error:
slog.info(session_label, "Error: parsing XML files failed.",
xml_file_list=str(xml_file_list),
error_msg=str(error),
session=session)
return
if errorsFrame:
slog.info(session_label,
"Errors in dti601000 gradients for new sessions after comparing with ground_truth.",
frames=str(errorsFrame),
actualGradients=str(errorsActual),
expectedGradients=str(errorsExpected),
session=session)
xml_file = open(xml_file_list[0], 'r')
try:
for line in xml_file:
match = re.match('.*<phaseEncodeDirectionSign>(.+)'
'</phaseEncodeDirectionSign>.*',
line)
if match and match.group(1).upper() != 'NEG':
slog.info(session_label,
"dti601000 has wrong PE sign (expected NEG).",
actual_sign=str(match.group(1).upper()),
session=session)
except AttributeError as error:
slog.info(session_label, "Error: parsing XML files failed.",
xml_file=xml_file_list[0],
error=str(error),
session=session)
finally:
xml_file.close()
return