def get_default_manager():
"""Get the default tool manager, configured using tools_config.json."""
toolsconffile = os.path.join(rootconfig.path.tools, 'ui_programs',
'tools_config.json')
toolsconf = load_json(toolsconffile)
manager = ToolManager()
manager.load(toolsconf)
return manager
def get_old(atlasname):
"""Get an atlasobj with name.
This is typically what you want when to get a atlas object.
"""
jsonFileName = atlasname + '.json'
jsonFilePath = os.path.join(rootconfig.path.atlas, jsonFileName)
atlasconf = loadsave.load_json(jsonFilePath)
return Atlas(atlasconf)
def insert_mrirow(self, scan, hasT1, hasT2, hasBOLD, hasDWI):
"""Insert one mriscan record."""
# check if scan already exist
try:
ret = self.session.query(
exists().where(MRIScan.filename == scan)).scalar()
if ret:
# record exists
return 0
except MultipleResultsFound:
print('Error when importing: multiple scan records found for %s' %
scan)
return 1
mrifolder = rootconfig.dms.folder_mridata
scaninfo = load_json(os.path.join(mrifolder, scan, 'scan_info.json'))
machine = self.add_and_get_mrimachine(scaninfo['Machine'])
name, date = name_date(scan)
dateobj = clock.simple_to_time(date)
db_mriscan = MRIScan(date=dateobj,
hasT1=hasT1,
hasT2=hasT2,
hasBOLD=hasBOLD,
hasDWI=hasDWI,
filename=scan)
machine.mriscans.append(db_mriscan)
try:
ret = self.session.query(exists().where(
and_(Person.name == name,
Person.patientid == scaninfo['Patient']['ID']))).scalar()
if ret:
self.session.add(db_mriscan)
person = self.session.query(Person).filter_by(name=name).one()
person.mriscans.append(db_mriscan)
self.session.commit()
print('Old patient new scan %s inserted' % scan)
return 0
except MultipleResultsFound:
print(
'Error when importing: multiple person records found for %s' %
name)
return 2
db_person = self.build_person(name, scaninfo)
self.db_people[name] = db_person
self.session.add(db_person)
self.db_people[name].mriscans.append(db_mriscan)
self.session.commit()
print('New patient new scan %s inserted' % scan)
def update_PMAR_database(scan_folder_name, name_zh):
scan_info = loadsave.load_json(
os.path.join(rootconfig.dms.folder_mridata, scan_folder_name,
'scan_info.json'))
search_res = pmar.search_patients(name=name_zh)
print(search_res)
if len(search_res) < 1:
# new patient
search_res = pmar.add_patient(name_zh, scan_info['Patient']['Birth'],
scan_info['Patient']['Gender'],
scan_info['Patient']['ID'])
else:
assert len(search_res) == 1
search_res = search_res[0]
ret = pmar.add_scan(search_res['id'],
scan_info['StudyDate'].replace(' ', 'T'))
print('update PMAR result: ', ret)
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 update_patient_scan():
scan_dict = loadsave.load_csv_to_dict('I:/new_data_mapping.csv', 'en')
for name, data_dict in scan_dict.items():
if data_dict['en'] != 'wangguojun':
continue
scan = name + '_' + data_dict['date']
scan_info = loadsave.load_json('X:/MRIData/%s/scan_info.json' % scan)
print(scan, data_dict['zh'], data_dict['id'],
scan_info['Patient']['ID'], scan_info['Patient']['Birth'],
scan_info['Patient']['Gender'])
search_res = search_patients(name=data_dict['zh'])
print(search_res)
if len(search_res) < 1:
# new patient
search_res = add_patient(data_dict['zh'],
scan_info['Patient']['Birth'],
scan_info['Patient']['Gender'],
scan_info['Patient']['ID'])
else:
assert len(search_res) == 1
search_res = search_res[0]
add_scan(search_res['id'], scan_info['StudyDate'].replace(' ', 'T'))
def check_RSN(self):
if not hasattr(self, 'RSNConfig'):
self.RSNConfig = loadsave.load_json(
self.fullpath('RSN_%s.json' % self.name))
"""
self.check_RSN()
return self.RSNConfig['RSN order']
def adjust_vec_Circos(self, vec):
vec_adjusted = np.zeros(vec.shape)
self.set_brainparts('default')
adjustedTicks, nodeCount = self.brainparts.get_region_list()
for i in range(self.count):
realpos = self.ticks.index(adjustedTicks[i])
vec_adjusted[i] = vec[realpos]
return vec_adjusted
brodmann_lr = Atlas(
loadsave.load_json(os.path.join(rootconfig.path.atlas,
'brodmann_lr.json')))
brodmann_lrce = Atlas(
loadsave.load_json(
os.path.join(rootconfig.path.atlas, 'brodmann_lrce.json')))
aal = Atlas(loadsave.load_json(os.path.join(rootconfig.path.atlas,
'aal.json')))
aal2 = Atlas(
loadsave.load_json(os.path.join(rootconfig.path.atlas, 'aal2.json')))
aicha = Atlas(
loadsave.load_json(os.path.join(rootconfig.path.atlas, 'aicha.json')))
bnatlas = Atlas(
loadsave.load_json(os.path.join(rootconfig.path.atlas, 'bnatlas.json')))
def get(atlasname, suppress=True):
if not suppress:
"""Run a job."""
import sys, os
import argparse
from mmdps.proc import job
from mmdps.util import loadsave
from mmdps.util import path
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('--config', help='job config json file', required=True)
parser.add_argument('--folder',
help='job run in this folder',
default=None)
args = parser.parse_args()
print('Runjob Folder:', args.folder)
configfile = path.fullfile(args.config)
print('Runjob File:', configfile)
configdict = loadsave.load_json(configfile)
currentJob = job.create_from_dict(configdict)
job.runjob(currentJob, args.folder)
sys.stdin.close()
sys.stdout.close()
sys.stderr.close()
# print(self.get_total_time_points())
for start in range(0, self.get_total_time_points()-self.windowLength+1, self.stepSize):
ts = self.gen_timeseries(start)
if ts is None:
# print(start,)
raise Exception('Dynamic sliding window exceeds total time points')
save_csvmat(self.outpath('timeseries-%d-%d.csv' % (start, start+self.windowLength)), ts)
tscorr = np.corrcoef(ts)
save_csvmat(self.outpath('corrcoef-%d-%d.csv' % (start, start+self.windowLength)), tscorr)
def run(self):
self.gen_net()
if __name__=="__main__":
atlasobj = path.curatlas()
volumename = '3mm'
img = load_nii(os.path.join(path.curparent(), 'pBOLD.nii'))
json_path = path.fullfile("inter_attr_dynamic.json")
argsDict = load_json(json_path)
outfolder = os.path.join(os.getcwd(),'bold_net','dynamic_'+str(argsDict['stepSize'])+"_"+str(argsDict['windowLength']))
os.makedirs(outfolder, exist_ok = True)
# c = Calc(atlasobj, volumename, img, outfolder)
# c.run()
# atlasobj, volumename, img, outfolder, windowLength = 100, stepSize = 3
# print(outfolder)
# print(volumename)
cal = Calc(atlasobj = atlasobj, volumename = volumename, img = img, outfolder = outfolder,windowLength=argsDict['windowLength'],stepSize=argsDict['stepSize'])
cal.run()
def from_json(self, json_name):
self.argsDict = load_json(json_name)
pass
def loadconf(confname):
return load_json(os.path.join(ConfDir, confname+'.json'))
"""Run a Para."""
import sys
import argparse
from mmdps.proc import para
from mmdps.util.loadsave import load_json
from mmdps.util import path
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('--config', help='para config json file', required=True)
args = parser.parse_args()
configpath = path.fullfile(args.config)
print('Runpara: configpath', configpath)
configDict = load_json(configpath)
currentPara = para.load(configDict)
currentPara.run()
sys.stdin.close()
sys.stdout.close()
sys.stderr.close()
def get_brainparts_config(self, name='default'):
circosfile = 'circosparts_{}.json'.format(name)
return loadsave.load_json(os.path.join(self.circosfolder, circosfile))
def load_from_file(configfile):
"""Load a job from file."""
configDict = load_json(configfile)
return create_from_dict(configDict)
def insert_mrirow(self,
scan,
hasT1,
hasT2,
hasBOLD,
hasDWI,
mrifolder=rootconfig.dms.folder_mridata):
"""Insert one mriscan record."""
# check if scan already exist
try:
ret = self.session.query(
exists().where(tables.MRIScan.filename == scan)).scalar()
if ret:
# record exists
return 0
except MultipleResultsFound:
print('Error when importing: multiple scan records found for %s' %
scan)
return 1
# check MRIMachine
scan_info = loadsave.load_json(
os.path.join(mrifolder, scan, 'scan_info.json'))
ret = self.session.query(exists().where(
and_(
tables.MRIMachine.institution == scan_info['Machine']
['Institution'], tables.MRIMachine.manufacturer ==
scan_info['Machine']['Manufacturer'],
tables.MRIMachine.modelname == scan_info['Machine']
['ManufacturerModelName']))).scalar()
if ret:
machine = self.session.query(tables.MRIMachine).filter(
and_(
tables.MRIMachine.institution == scan_info['Machine']
['Institution'], tables.MRIMachine.manufacturer ==
scan_info['Machine']['Manufacturer'],
tables.MRIMachine.modelname == scan_info['Machine']
['ManufacturerModelName'])).one()
else:
# insert new MRIMachine
machine = tables.MRIMachine(
institution=scan_info['Machine']['Institution'],
manufacturer=scan_info['Machine']['Manufacturer'],
modelname=scan_info['Machine']['ManufacturerModelName'])
# check Person
name = scan_info['Patient']['Name']
try:
dateobj = datetime.datetime.strptime(scan_info['StudyDate'],
'%Y-%m-%d %H:%M:%S')
except ValueError:
dateobj = None
db_mriscan = tables.MRIScan(date=dateobj,
hasT1=hasT1,
hasT2=hasT2,
hasBOLD=hasBOLD,
hasDWI=hasDWI,
filename=scan)
machine.mriscans.append(db_mriscan)
try:
ret = self.session.query(exists().where(
and_(tables.Person.name == name, tables.Person.patientid ==
scan_info['Patient']['ID']))).scalar()
if ret:
person = self.session.query(tables.Person).filter(
and_(tables.Person.name == name, tables.Person.patientid ==
scan_info['Patient']['ID'])).one()
person.mriscans.append(db_mriscan)
self.session.add(db_mriscan)
self.session.commit()
print('Old patient new scan %s inserted' % scan)
return 0
except MultipleResultsFound:
print(
'Error when importing: multiple person records found for %s' %
name)
return 2
db_person = tables.Person.build_person(name, scan_info)
db_person.mriscans.append(db_mriscan)
self.session.add(db_person)
self.session.commit()
print('New patient new scan %s inserted' % scan)
return 0
def set_brainparts(self, name):
from mmdps.vis import braincircos
circosfile = 'circosparts_{}.json'.format(name)
self.brainparts = braincircos.BrainParts(
loadsave.load_json(os.path.join(self.circosfolder, circosfile)))
default=False)
parser.add_argument('--datasource',
help='datasource for MMDPDatabase',
default=None)
parser.add_argument(
'--force',
help='True/False. If overwrite existing feature record',
default=False)
args = parser.parse_args()
if args.modal is not None:
feature_exporter.check_modal(
args.modal,
os.path.join(rootconfig.path.dms, 'export_mainconf.json'))
data_config = loadsave.load_json(
os.path.join(rootconfig.path.dms, 'export_dataconf.json'))
main_config = loadsave.load_json(
os.path.join(rootconfig.path.dms, 'export_mainconf.json'))
if args.modal is not None:
print('Will search default folder for %s' % (args.modal))
if args.database and args.datasource is None:
raise Exception('Datasource unknown')
elif args.database:
print('Will export to database. datasource = %s' % (args.datasource))
if args.force:
print('Force mode. Will overwrite existing features')
exporter = feature_exporter.MRIScanProcExporter(main_config, data_config,
args.modal, args.database,
args.datasource,
