def __init__(self,
mainconfig,
dataconfig,
modal=None,
database=False,
data_source=None,
force=False):
"""Init the exporter using mainconfig and dataconfig."""
self.mainconfig = mainconfig
self.dataconfig = dataconfig
if mainconfig.get('atlas_list', None) is None or mainconfig.get(
'atlas_list', None) == 'all':
# use default atlas_list
self.atlas_list = load_txt(
os.path.join(rootconfig.path.atlas, 'atlas_list.txt'))
elif type(mainconfig['atlas_list']) is list:
self.atlas_list = mainconfig['atlas_list']
else:
self.atlas_list = load_txt(mainconfig['atlas_list'])
if os.path.isfile(mainconfig['scan_list']):
self.mriscans = load_txt(mainconfig['scan_list'])
elif mainconfig['scan_list'] == 'listdir':
if modal is not None:
self.mriscans = sorted(
os.listdir(mainconfig['input_folders'][modal]))
else:
self.mriscans = sorted(
os.listdir(mainconfig['input_folders']['T1']))
else:
raise Exception('Unrecognized scan_list:', mainconfig['scan_list'])
self.modal = modal
self.database = database
self.data_source = data_source
self.force = force
def combine_txts(outtxt, intxts):
outset = set()
for intxt in intxts:
outset.update(load_txt(intxt))
outlist = list(outset)
outlist.sort()
save_txt(outtxt, outlist)
def __init__(self, api, mriscanstxt, modal, outmainfolder):
"""Construct by api object, mriscanstxt contains mriscans by name_date,
modal or file name, and download the data to outmainfolder.
"""
self.api = api
self.mriscans = load_txt(mriscanstxt)
self.outmainfolder = outmainfolder
self.modal = modal
def cb_copy(self):
scanlist = loadsave.load_txt(self.fmriscanstxt.value)
modal = self.fmodal.value
outfolder = self.foutfolder.value
for scan in scanlist:
os.makedirs(os.path.join(outfolder, scan), exist_ok=True)
os.system('robocopy "{}" "{}" {}'.format(
os.path.join(rootconfig.dms.folder_mridata, scan),
os.path.join(outfolder, scan), modal))
def main():
dbfile = 'E:/mmdpdb.db'
engine = create_engine('sqlite:///' + dbfile)
sessionManager = sessionmaker(bind=engine)
session = sessionManager()
db_group = tables.Group(name='test', description='test desc')
session.add(db_group)
names = loadsave.load_txt(
'E:/Changgung works/20180409_tDCS_14/score_info/control_namelist.txt')
for name in names:
person = session.query(tables.Person).filter_by(name=name).one()
db_group.people.append(person)
scans = loadsave.load_txt(
'E:/Changgung works/20180409_tDCS_14/score_info/control_scanlist-2.txt'
)
for scan in scans:
db_scan = session.query(tables.MRIScan).filter_by(filename=scan).one()
db_group.scans.append(db_scan)
session.commit()
def scanFolder(self):
"""
scan folder to load name/scan list
"""
for filename in sorted(os.listdir(self.folderPath)):
if filename.find('txt') == -1:
continue
if filename.find('scan') == -1 and filename.find('name') == -1:
continue
if filename.find('name') != -1:
group = filename.split('_')[0]
self.nameDict[group] = loadsave.load_txt(
os.path.join(self.folderPath, filename))
elif filename.find('scan') != -1:
group = filename.split('_')[0]
timeCase = filename[filename.find('-') +
1:filename.find('.txt')]
self.scanDict[group + timeCase] = loadsave.load_txt(
os.path.join(self.folderPath, filename))
def run(self):
"""Run the para.
finalfolders is the constructed folder in which to run the job in parallel,
Or sequential if configured that way.
Env MMDPS_NEWLIST_TXT will override folderlist.
Env MMDPS_SECONDLIST_TXT will override secondlist.
"""
if self.folderlist == 'listdir':
originalfolders = path.clean_listdir(self.mainfolder)
else:
originalfolders = loadsave.load_txt(
path.env_override(self.folderlist, 'MMDPS_NEWLIST_TXT'))
folders = [os.path.join(self.mainfolder, f) for f in originalfolders]
if self.bsecond:
finalfolders = []
if type(self.secondlist) is list:
secondfolders = self.secondlist
elif self.secondlist == 'all':
secondfolders = loadsave.load_txt(
os.path.join(rootconfig.path.atlas, 'atlas_list.txt'))
else:
secondfolders = loadsave.load_txt(
path.env_override(self.secondlist, 'MMDPS_SECONDLIST_TXT'))
for folder in folders:
for secondfolder in secondfolders:
newfolder = os.path.join(folder, secondfolder)
path.makedirs(newfolder)
finalfolders.append(newfolder)
else:
finalfolders = folders
currentJob = job.create_from_dict(
loadsave.load_json(path.fullfile(self.jobconfig)))
if self.runmode == 'FirstOnly':
return self.run_seq(currentJob, finalfolders[0:1])
if self.runmode == 'Parallel':
return self.run_para(currentJob, finalfolders)
if self.runmode == 'Sequential':
return self.run_seq(currentJob, finalfolders)
else:
print('Error: no such runmode as', self.runmode)
return None
def insert_grouptable(self, grouptable):
"""Insert one configured group."""
name, desc, txt = grouptable
db_group = Group(name=name, description=desc)
self.session.add(db_group)
people = load_txt(txt)
for person in people:
l = person.split('_')
personname = l[0]
if personname in self.db_people:
db_person = self.db_people[personname]
db_group.people.append(db_person)
def __init__(self,
inMainFolder,
outMainFolder,
mriscanstxt=None,
db_generator=None,
cls_niftigetter=NiftiGetter):
"""
Import from inMainFolder to outMainFolder, for mriscans from mriscanstxt.
Update database. Use NiftiGetter class from cls_niftigetter.
"""
self.inMainFolder = inMainFolder
self.outMainFolder = outMainFolder
if mriscanstxt is not None:
self.mriscans = loadsave.load_txt(mriscanstxt)
self.db_generator = db_generator
self.cls_niftigetter = cls_niftigetter
self.mriscans = mriscans
def run_mriscan(self, mriscan):
src = os.path.join(self.preprocessedFolder, mriscan,
'Filtered_4DVolume.nii')
if os.path.isfile(src):
dst = os.path.join(self.exportFolder, mriscan, 'pBOLD.nii')
path.makedirs_file(dst)
shutil.copy2(src, dst)
print(mriscan, 'OK')
else:
print(mriscan, 'not found', src)
def run(self):
for mriscan in self.mriscans:
self.run_mriscan(mriscan)
if __name__ == '__main__':
# parser = argparse.ArgumentParser(description='Copy preprocessed BOLD to processing folder')
# parser.add_argument('--mriscanstxt', required=True, help='mriscans list in txt file')
# parser.add_argument('--outfolder', required=True, help='pBOLD output folder for all mriscans')
# args = parser.parse_args()
# exp = ExportBOLD(r'E:\DataProcessing\BOLDPreprocess\Data\FunRawARWSDCF',
# loadsave.load_txt(args.mriscanstxt),
# args.outfolder)
mriscanstxt = 'E:/namelist.txt'
exp = ExportBOLD('E:/DataProcessing/BOLDPreprocess/Data/FunRawARWSDCF',
loadsave.load_txt(mriscanstxt), 'E:/DataProcessing/BOLD/')
exp.run()
def test_newGroupByScans(groupManager):
scans = loadsave.load_txt('E:/Changgung works/20180409_tDCS_14/score_info/control_scanlist-2.txt')
groupManager.newGroupByScans('test control 2', scans)
return
self.exportFolder = exportFolder
self.mriscans = mriscans
def run_mriscan(self, mriscan):
src = os.path.join(self.preprocessedFolder, mriscan, 'Filtered_4DVolume.nii')
if os.path.isfile(src):
dst = os.path.join(self.exportFolder, mriscan, 'pBOLD.nii')
path.makedirs_file(dst)
shutil.copy2(src, dst)
print(mriscan, 'OK')
else:
print(mriscan, 'not found', src)
def run(self):
for mriscan in self.mriscans:
self.run_mriscan(mriscan)
if __name__ == '__main__':
# parser = argparse.ArgumentParser(description='Copy preprocessed BOLD to processing folder')
# parser.add_argument('--mriscanstxt', required=True, help='mriscans list in txt file')
# parser.add_argument('--outfolder', required=True, help='pBOLD output folder for all mriscans')
# args = parser.parse_args()
# exp = ExportBOLD(r'E:\DataProcessing\BOLDPreprocess\Data\FunRawARWSDCF',
# loadsave.load_txt(args.mriscanstxt),
# args.outfolder)
mriscanstxt = 'E:/namelist.txt'
exp = ExportBOLD(r'E:\DataProcessing\BOLDPreprocess\Data\FunRawARWSDCF',
loadsave.load_txt(mriscanstxt),
'E:/DataProcessing/BOLD/')
exp.run()
def load_mriscanstxt(self): """Load the mriscans txt file.""" if not os.path.isfile(self.mriscanstxt): return self.mriscans = load_txt(self.mriscanstxt) self.people = self.build_internals(self.mriscans)
def __init__(self, dcmMainFolder, niftiMainFolder, mriscantxt):
self.dcmMainFolder = dcmMainFolder
self.niftiMainFolder = niftiMainFolder
self.mriscans = load_txt(mriscantxt)
def __init__(self, mmdb, outcsvname, personnamestxt, anonymize=True):
self.mmdb = mmdb
self.outcsvname = outcsvname
self.anonymize = anonymize
self.personnames = loadsave.load_txt(personnamestxt)
volumename = '3mm'
atlasobj = atlas.get(atlasname)
work_path = 'D:/Research/xuquan_FMRI/Dynamic_tfMRI_work/'
outfolder = os.path.join(work_path, subject, atlasname, 'bold_net',
'dynamic_%d_%d' % (stepsize, windowLength))
img = load_nii(os.path.join(work_path, subject, 'pBOLD.nii'))
os.makedirs(outfolder, exist_ok=True)
c = CalcDynamic(atlasobj, volumename, img, outfolder, windowLength,
stepsize)
c.run()
if __name__ == '__main__':
atlasList = ['brodmann_lrce']
mriscanstxt = 'D:/Research/xuquan_FMRI/DPARSFA work/namelist.txt'
subjectList = loadsave.load_txt(mriscanstxt)
windowLength = 10
stepsize = 1
taskList = []
for subject in subjectList:
for atlasname in atlasList:
taskList.append((subject, atlasname, windowLength, stepsize))
taskCount = len(taskList)
totalResult = []
pool = multiprocessing.Pool(processes=4)
manager = multiprocessing.Manager()
managerQueue = manager.Queue()
fwrap = parabase.FWrap(func, managerQueue)
result = pool.map_async(fwrap.run, taskList)
nfinished = 0
while True:
