def __init__(self, niipath, atlasobj, outfolder, json_name):
self.niipath = niipath
self.atlasobj = atlasobj
self.atlas_3mm_path = atlasobj.volumes['3mm']['niifile']
self.outfolder = outfolder
self.exeName = path.fullfile("netcalc_intra_region.exe")
self.from_json(json_name)
def cb_button_Edit(self):
"""Edit the file.
Use fileop.edit to launch the proper edit program, by file ext and file name.
"""
filepath = self.value
fileop.edit(path.fullfile(filepath))
def open_configfile(self, configfile):
configfile = path.fullfile(configfile)
if not os.path.isfile(configfile):
print('cannot open file {}'.format(configfile))
return
self.configfile_path = configfile
configdict = load_json_ordered(configfile)
self.load_configdict(configdict)
def build_fullconfig(self):
"""Build full config.
Search the config file using path.fullfile.
"""
config = path.fullfile(self.config)
if config:
return config
else:
return self.config
def opentool(self, *argv):
"""Open the gui tool."""
pyui = path.fullfile(self.pyui)
assert pyui
cmdlist = [pyui]
if self.argv is not None:
cmdlist.extend([self.argv])
cmdlist.extend(argv)
# print('opentool cmdlist: ', cmdlist)
run.popen_py(cmdlist, sys.platform == 'win32')
def inter_calc():
print(os.getcwd())
corrcoef_path = os.path.join(os.getcwd(), 'bold_net', 'corrcoef.csv')
outfolder = os.path.join(os.getcwd(), 'bold_net_attr_zzl')
json_path = path.fullfile("inter_attr.json")
print(outfolder)
print(corrcoef_path)
if not os.path.isdir(outfolder):
os.mkdir(outfolder)
inter_ac = InterAttrCalc(corrcoef_path, outfolder, json_path)
inter_ac.calc()
def open_configfile(self, configfile):
configfile = path.fullfile(configfile)
if not os.path.isfile(configfile):
print('cannot open file {}'.format(configfile))
return
self.configfile_path = configfile
configdict = load_json_ordered(configfile)
self.rootfield = self.connector.config_to_field(configdict)
self.mainfieldwidget = self.rootfield.build_widget(self.mainframe)
self.set_mainwidget(self.mainfieldwidget)
self.mainfieldwidget.pack()
def inter_calc_dynamic():
# print(os.getcwd())
corrcoef_path = os.path.join(os.getcwd(),'bold_net')
nii_path = os.path.join(path.curparent(), 'pBOLD.nii')
outfolder = os.path.join(os.getcwd(), OUTFOLDER_INTER)
json_path = path.fullfile("inter_attr_dynamic.json")
# print(outfolder)
# print(corrcoef_path)
if not os.path.isdir(outfolder):
os.mkdir(outfolder)
inter_ac = InterAttrCalcDynamic(nii_path,corrcoef_path,outfolder,json_path)
inter_ac.calc()
def build_fullcmd(self):
"""Build full command.
If the cmd is not absolute path, search in path for this cmd.
It is similar to matlabpath, so you do not need to specify the
full cmd path. Just make sure to avoid name clash.
"""
cmd = path.fullfile(self.cmd)
if cmd:
return cmd
else:
return self.cmd
def intra_calc():
print(os.getcwd())
atlasobj = path.curatlas()
volumename = '3mm'
nii_path = os.path.join(path.curparent(), 'pBOLD.nii')
outfolder = os.path.join(os.getcwd(), 'bold_net_attr_zzl')
json_path = path.fullfile("intra_attr.json")
print(nii_path)
print(outfolder)
if not os.path.isdir(outfolder):
os.mkdir(outfolder)
intra_ac = IntraAttrCalc(nii_path, atlasobj, outfolder, json_path)
intra_ac.calc()
def intra_calc_dynamic():
# print(os.getcwd())
atlasobj = path.curatlas()
volumename = '3mm'
nii_path = os.path.join(path.curparent(), 'pBOLD.nii')
outfolder = os.path.join(os.getcwd(), OUTFOLDER_INTRA)
json_path = path.fullfile("intra_attr_dynamic.json")
# print(nii_path)
# print(outfolder)
if not os.path.isdir(outfolder):
os.mkdir(outfolder)
intra_ac = IntraAttrCalcDynamic(nii_path,atlasobj,outfolder,json_path)
intra_ac.calc()
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 __init__(self, corrPath, outfolder, json_name):
self.corrPath = corrPath
self.outfolder = outfolder
self.exeName = path.fullfile("netcalc_inter_region.exe")
self.from_json(json_name)
"""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()
# 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()
"""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()
def __init__(self, niipath, corrPath, outfolder, json_name ):
self.niipath = niipath
self.outfolder = outfolder
self.exeName = path.fullfile("netcalc_inter_region_dynamic.exe")
self.from_json(json_name)
self.corrPath = corrPath+ "\\" +"dynamic_"+str(self.argsDict['stepSize'])+"_"+str(self.argsDict['windowLength'])+"\\"
