def convert_dicom_to_raw_nii(scan_folder_name):
ret = data_customs.convert_dicom_to_nifti(
os.path.join(rootconfig.dms.folder_temp, 'DICOM'),
os.path.join(rootconfig.dms.folder_temp, 'NII'))
if ret == 0:
logging.info('{} Successfully converted {}'.format(
clock.now(), scan_folder_name))
else:
logging.error('{} Error converting scan {} with return code {}'.format(
clock.now(), scan_folder_name, ret))
with open(os.path.join(rootconfig.dms.folder_temp, 'NII',
'scan_info.json')) as f:
jsonObject = json.load(f)
print('Subject ID: %s' % jsonObject['Patient']['ID'])
try:
# shutil.copytree(os.path.join(rootconfig.dms.folder_temp, 'NII'), os.path.join(rootconfig.dms.folder_rawnii, scan_folder_name))
os.system('robocopy /S "{}" "{}"'.format(
os.path.join(rootconfig.dms.folder_temp, 'NII'),
os.path.join(rootconfig.dms.folder_rawnii, scan_folder_name)))
# remove temp folder
os.system('rmdir /S /Q "{}"'.format(rootconfig.dms.folder_temp))
except FileExistsError as e:
logging.error('{} Destination already exists.\n{}'.format(
clock.now(), e))
exit()
except PermissionError as e:
print('PermissionError')
print(e)
logging.error('{} PermissionError.\n{}'.format(clock.now(), e))
exit()
logging.info('{} raw nii moved to NAS and temp folder removed'.format(
clock.now()))
def extract_modalities(scan_folder_name):
worker = data_customs.MRIScanImporter(
os.path.join(rootconfig.dms.folder_rawnii),
os.path.join(rootconfig.dms.folder_mridata),
cls_niftigetter=data_customs.ChanggungNiftiGetter)
logging.info('{} Extracting modalities...'.format(clock.now()))
modalities_coverage = worker.copy_one_nifti(scan_folder_name)
logging.info('{} Extracting modalities finished with coverage: {}'.format(
clock.now(), modalities_coverage))
return modalities_coverage
def compress_dicom(scan_folder_name):
"""
compress local dicom folder as a zip and move to NAS
"""
logging.info('{} Compressing...'.format(clock.now()))
shutil.make_archive(
os.path.join(rootconfig.dms.folder_temp, scan_folder_name), 'zip',
os.path.join(rootconfig.dms.folder_temp, 'DICOM'))
os.system('robocopy "{}" "{}" {}'.format(
rootconfig.dms.folder_temp, rootconfig.dms.folder_dicom,
'{}.zip'.format(scan_folder_name)))
logging.info('{} Compressed'.format(clock.now()))
def copy_dicom_from_CD():
"""
copy dicom from CD to local temp folder
dcm2niix conversion is faster on local
"""
try:
# shutil.make_archive(os.path.join(rootconfig.dms.folder_dicom, scan_folder_name), 'zip', rootconfig.dms.CD_dicom_path)
# shutil.copytree(rootconfig.dms.CD_dicom_path, os.path.join(rootconfig.dms.folder_temp, 'DICOM'))
os.system('robocopy /S "{}" "{}"'.format(
rootconfig.dms.CD_dicom_path,
os.path.join(rootconfig.dms.folder_temp, 'DICOM')))
except FileExistsError as e:
logging.error('{} Destination already exists.\n{}'.format(
clock.now(), e))
exit()
logging.info('{} Dicom copied.'.format(clock.now()))
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--name',
help='name of the subject.',
required=True,
default='')
parser.add_argument('--zh',
help='name_zh of the subject.',
required=True,
default='')
parser.add_argument('--date',
help='scanning date',
required=True,
default='')
args = parser.parse_args()
subject_name = args.name
name_zh = args.zh
scan_date = args.date
scan_folder_name = '%s_%s' % (subject_name, scan_date)
logging.basicConfig(filename='import_changgung.log', level=logging.DEBUG)
logging.info('{} New Run {}'.format(clock.now(), scan_folder_name))
copy_dicom_from_CD()
compress_dicom(scan_folder_name)
convert_dicom_to_raw_nii(scan_folder_name)
modalities_coverage = extract_modalities(scan_folder_name)
update_sql_database(scan_folder_name, modalities_coverage)
update_PMAR_database(scan_folder_name, name_zh)
def run1(f, argvec, processes=None):
"""Run function f len(argvec) times, each time use one arg in argvec."""
processes = get_processes(processes)
with multiprocessing.Pool(processes) as p:
m = multiprocessing.Manager()
q = m.Queue()
fwrap = FWrap(f, q)
result = p.map_async(fwrap.run, argvec)
ntotal = len(argvec)
print('Begin proc, {} cpus, {} left, start at {}'.format(
processes, ntotal, clock.now()))
nfinished = 0
while True:
if result.ready():
break
else:
res = q.get()
nfinished += 1
print('{} just finished. {} left, at {}'.format(
res, ntotal - nfinished, clock.now()))
print('End proc, end at {}'.format(clock.now()))
outputs = result.get()
return outputs
rets = []
ret = self.work_attr(mriscan)
rets.extend(ret)
#ret = self.work_net(mriscan)
#rets.extend(ret)
return rets
def flattenlist(ll):
ls = []
for l in ll:
ls.extend(l)
return ls
if __name__ == '__main__':
atlasobj = atlas.getbyenv('aal')
fu = fusion.create_by_folder(atlasobj,
'E:/MMDPSoftware/mmdps/pipeline/Fusion')
mriscans = fu.groups['entire'].mriscans
foreach_scan = MRIScanReport(fu, mriscans)
funcslist = foreach_scan.run()
funcs = flattenlist(funcslist)
print(len(funcs))
print(clock.now())
parabase.run_callfunc(funcs)
## for func in funcs:
## func()
print(clock.now())
def run(f, argvec, processes=None):
"""Run function f len(argvec) times, each time use one arg in argvec."""
processes = get_processes(processes)
estimated_task_time_cost = -1
with multiprocessing.Pool(processes) as pool:
manager = multiprocessing.Manager()
managerQueue = manager.Queue()
fwrap = FWrap(f, managerQueue)
result = pool.map_async(fwrap.run, argvec)
ntotal = len(argvec)
nError = 0
errorList = []
print('Begin proc, {} cpus, {} left, start at {}'.format(
processes, ntotal, clock.now()))
nfinished = 0
while True:
if result.ready():
break
else:
try:
ret = managerQueue.get(timeout=1)
except queue.Empty:
continue
else:
nfinished += 1
elapsed_time = time.time() - ret['start_time']
if estimated_task_time_cost < 0:
estimated_task_time_cost = elapsed_time
else:
estimated_task_time_cost = 0.75 * estimated_task_time_cost + 0.25 * elapsed_time
res = ret['message']
retCode = int(res[res.find('res: ') + 5:])
if retCode != 0:
nError += 1
errorList.append(res)
print(
'{} just finished with error after {:1.2f} s execution. {} left, at {}. Estimated time left: {} (HMS)'
.format(
res, elapsed_time, ntotal - nfinished,
clock.now(),
str(
datetime.timedelta(
seconds=(ntotal - nfinished) *
estimated_task_time_cost))))
else:
print(
'{} just finished after {:1.2f} s execution. {} left, at {}. Estimated time left: {} (HMS)'
.format(
res, elapsed_time, ntotal - nfinished,
clock.now(),
str(
datetime.timedelta(
seconds=(ntotal - nfinished) *
estimated_task_time_cost))))
print('End proc, end at {}. {} error.'.format(clock.now(), nError))
if nError != 0:
print('Listing errs')
for err in errorList:
print(err)
outputs = result.get()
# print(outputs) # a list of return codes, should be all zero
return outputs
def genlogfilename(info=''):
"""Generate a log file name base on current time and supplied info."""
path.makedirs('log')
timestr = clock.now()
return 'log/log_{}_{}.txt'.format(timestr, info)
import os
import argparse
import logging
from mmdps.dms import converter, importer, dbgen
from mmdps.util.loadsave import load_txt
from mmdps import rootconfig
from mmdps.util import clock
logging.basicConfig(filename='import_changgung.log', level=logging.DEBUG)
logging.info('New Run: {}'.format(clock.now()))
def apppath(s):
return os.path.join(WORKING_FOLDER, s)
class ChanggungNiftiGetter(converter.NiftiGetter):
def __init__(self, niftifolder):
super().__init__(niftifolder)
def get_T1(self):
return self.fnmatch_one('*OSag_3D_T1BRAVO*.nii.gz')
def get_T2(self):
return self.fnmatch_one('*OAx_T2_PROPELLER*.nii.gz')
def get_BOLD(self):
return self.fnmatch_one('*BOLD-rest*.nii.gz')
def get_DWI(self):
nii = self.fnmatch_one('*DTI_24_Directions*.nii.gz')