sys.path.insert(0, '/home/jagust/cindeem/CODE/PetProcessing/pvc')
import metzler
import logging, logging.config
from time import asctime
if __name__ == '__main__':
"""Uses specified subject dir
finds dvr dir
find aparc_aseg in pet space
fins pons normed fdg
"""
# start wx gui app
app = wx.App()
roifile = bg.FileDialog(prompt='Choose fsroi csv file',
indir='/home/jagust/cindeem/CODE/PetProcessing')
arda = '/home/jagust/arda/lblid'
root = bg.SimpleDirDialog(prompt='Choose FDG data dir',
indir='/home/jagust')
cleantime = asctime().replace(' ', '-').replace(':', '-')
logfile = os.path.join(root, 'logs', '%s_%s.log' % (__file__, cleantime))
log_settings = pp.get_logging_configdict(logfile)
logging.config.dictConfig(log_settings)
tracer = 'FDG'
user = os.environ['USER']
logging.info('###START %s %s :::' % (tracer, __file__))
logging.info('###TRACER %s :::' % (tracer))
roifile = bg.FilesDialog(
prompt='Choose roifile',
indir='/home/jagust/cindeem/CODE/PetProcessing/pib')
nifti = bg.FilesDialog(prompt='Choose realigned ', indir='%s/' % root)
try:
m = pp.re.search('B[0-9]{2}-[0-9]{3}', nifti[0])
subid = m.group()
except:
logging.error('cant find ID in %s' % (nifti[0]))
raise IOError('cant find ID in %s' % (nifti[0]))
realigned_dir, _ = os.path.split(nifti[0])
pth, _ = os.path.split(realigned_dir)
# get ref and brainmask
rbrainmask = bg.FileDialog(prompt='Choose rbrainmask', indir=pth)
if rbrainmask is None:
logging.error('%s missing, skipping' % (globstr))
raise IOError('%s missing, skipping' % (globstr))
rcere = bg.FileDialog(prompt='Choose refregion', indir=pth)
if rcere is None:
logging.error('%s missing, skipping' % (globstr))
# get timing file
sub, _ = os.path.split(pth)
timingf = bg.FileDialog(prompt='Select Timing File', indir=pth)
if len(timingf) < 1:
logging.error('%s missing, skipping' % (globstr))
raise IOError('%s missing, skipping' % (globstr))
timingf = timingf
ft = ft.read_frametimes(timingf)