def bb_basic_QC(subject, fileConfig):
keysToPop = []
global logger
logger = LT.initLogging(__file__, subject)
idealConfigFile = os.environ[
'BB_BIN_DIR'] + '/bb_data/ideal_config_sizes.json'
with open(idealConfigFile, 'r') as f:
idealConfig = json.load(f)
os.chdir(subject)
fd_fileName = "logs/file_descriptor.json"
for fileN in fileConfig:
if not isinstance(fileConfig[fileN], list):
if bb_path.isImage(fileConfig[fileN]):
fils = bb_path.removeImageExt(fileConfig[fileN])
if os.path.isfile(fils + "_orig.nii.gz"):
fileList = [fils + "_orig.nii.gz"]
else:
fileList = [fileConfig[fileN]]
else:
fileList = [fileConfig[fileN]]
else:
fileList = fileConfig[fileN]
for fileName in fileList:
if os.path.isfile(fileName):
if fileN in idealConfig:
img = nib.load(fileName)
dims = img.header['dim'][1:5]
if not np.all(dims == idealConfig[fileN]['dims']):
keysToPop.append(fileN)
#make_unusable(fileName, idealConfig[fileName]['dep_dirs'])
f = open('info_basic_QC.txt', 'a')
f.write('Problem in file ' + fileName + '\n')
f.close()
for keyToPop in keysToPop:
fileConfig.pop(keyToPop, None)
fd = open(fd_fileName, "w")
json.dump(fileConfig, fd, sort_keys=True, indent=4)
fd.close()
os.chdir("..")
return fileConfig
def main():
parser = MyParser(description='BioBank Pipeline Manager')
parser.add_argument("subjectFolder", help='Subject Folder')
argsa = parser.parse_args()
subject = argsa.subjectFolder
subject = subject.strip()
if subject[-1] == '/':
subject = subject[0:len(subject) - 1]
logger = LT.initLogging(__file__, subject)
logger.info('Running file manager')
fileConfig = bb_file_manager(subject)
fileConfig = bb_basic_QC(subject, fileConfig)
logger.info("File configuration after running file manager: " +
str(fileConfig))
# runTopup ==> Having fieldmap
if not ((('AP' in fileConfig) and (fileConfig['AP'] != '')) and
(('PA' in fileConfig) and (fileConfig['PA'] != ''))):
logger.error(
"There is no proper DWI data. Thus, the B0 file cannot be generated in order to run topup"
)
runTopup = False
else:
runTopup = True
# Default value for job id. SGE does not wait for a job with this id.
jobSTEP1 = "-1"
jobSTEP2 = "-1"
jobSTEP3 = "-1"
jobSTEP1 = bb_pipeline_struct(subject, runTopup, fileConfig)
if runTopup:
jobSTEP2 = bb_pipeline_func(subject, jobSTEP1, fileConfig)
jobSTEP3 = bb_pipeline_diff(subject, jobSTEP1, fileConfig)
jobSTEP4 = bb_IDP(subject, jobSTEP1 + "," + jobSTEP2 + "," + jobSTEP3,
fileConfig)
LT.finishLogging(logger)
def main():
parser = MyParser(description='BioBank basic QC tool')
parser.add_argument("subjectFolder", help='Subject Folder')
argsa = parser.parse_args()
subject = argsa.subjectFolder
subject = subject.strip()
if subject[-1] == '/':
subject = subject[0:len(subject) - 1]
logger = LT.initLogging(__file__, subject)
logger.info('Running file manager')
idealConfigFile = os.environ['BB_BIN_DIR'] + '/bb_data/ideal_config.json'
with open(idealConfigFile, 'r') as f:
fileConfig = json.load(f)
fileConfig = bb_basic_QC(subject, fileConfig)
def main():
global logger
parser = MyParser(description='BioBank Pipeline FILE Manager')
parser.add_argument("subjectFolder", help='Subject Folder')
argsa = parser.parse_args()
subject = argsa.subjectFolder
subject = subject.strip()
if subject[-1] == '/':
subject = subject[0:len(subject) - 1]
logger = LT.initLogging(__file__, subject)
logger.info('Running UK Biobank to BIDS converter')
bb_UKBB_to_BIDS_converter(subject)
LT.finishLogging(logger)
def main():
parser = MyParser(description='BioBank Pipeline FILE Manager')
parser.add_argument("subjectFolder", help='Subject Folder')
argsa = parser.parse_args()
subject = argsa.subjectFolder
subject = subject.strip()
if subject[-1] == '/':
subject = subject[0:len(subject) - 1]
logger = LT.initLogging(__file__, subject)
logger.info('Running file manager')
fileConfig = bb_file_manager(subject)
logger.info("File configuration after running file manager: \n" +
str(fileConfig))
LT.finishLogging(logger)
def bb_file_manager(subject):
global logger
global idealConfig
global fileConfig
logger = LT.initLogging(__file__, subject)
idealConfigFile = os.environ['BB_BIN_DIR'] + '/bb_data/ideal_config.json'
with open(idealConfigFile, 'r') as f:
idealConfig = json.load(f)
directories = [
"delete", "unclassified", "raw", "T1", "T2_FLAIR", "SWI",
"SWI/PHA_TE1", "SWI/PHA_TE2", "SWI/MAG_TE1", "SWI/MAG_TE2",
"SWI/unclassified", "dMRI", "dMRI/raw", "fMRI", "fieldmap"
]
patterns_actions = [[["*.*"], capitalize_and_clean],
[["dicom", "DICOM"], move_to, "delete/"],
[["T1*.nii.gz"], manage_struct, "T1"],
[["T2*FLAIR*.nii.gz"], manage_struct, "T2"],
[["*FMRI*RESTING*.nii.gz", "MB8*RESTING*.nii.gz"],
manage_fMRI, "rfMRI"],
[["*FMRI*TASK*.nii.gz", "MB8*TASK*.nii.gz"],
manage_fMRI, "tfMRI"], [["SWI*nii.gz"], manage_SWI],
[["DIFF_*", "MB3_*"], manage_DWI],
[["SWI*.*"], move_to, "SWI/unclassified/"],
[["*.*"], move_to, "unclassified/"]]
os.chdir(subject)
fd_fileName = "logs/file_descriptor.json"
#Check if the subject has already been managed
if (os.path.isfile(fd_fileName)):
with open(fd_fileName, 'r') as f:
fileConfig = json.load(f)
else:
for directory in directories:
if not os.path.isdir(directory):
os.mkdir(directory)
listFiles = glob.glob("*.*")
listFiles.sort()
# Organize the files in sets
for patterns_action in patterns_actions:
patterns = patterns_action[0]
action = patterns_action[1]
args = patterns_action[2:]
listFiles = []
for fileTy in patterns:
listFiles.extend(
[x for x in glob.glob(fileTy) if x not in listFiles])
logger.info("Performing action " + action.__name__ +
" on files with patterns " + str(patterns))
action(listFiles, *args)
# Create file descriptor
fd = open(fd_fileName, "w")
json.dump(fileConfig, fd, sort_keys=True, indent=4)
fd.close()
os.chdir("..")
fileConfigFormatted = formatFileConfig()
return fileConfig