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))
logging.info('###USER : %s' % (user))
subs = bg.MyDirsDialog(prompt='Choose Subjects ', indir='%s/' % root)
roid = pp.roilabels_fromcsv(roifile)
alld = {}
return
roid = {}
for row in csv.reader(open(infile)):
if 'SUBID' in row:
continue
roid[row[0]] = row[1:]
if dict.has_key(subid):
print 'duplicate for %s'%subid
else:
dict[subid] = roid
if __name__ == '__main__':
# specify if subjects will have more than one visit
app = wx.App()
data_dir = bg.SimpleDirDialog(prompt='Choose PIB data dir',
indir='/home/jagust')
if 'UCD_Project' in data_dir:
visit = False
else:
visit = True
_, datadir_nme = os.path.split(data_dir)
#data_dir ='/home/jagust/UCD_Project/pet'
#data_dir = '/home/jagust/bacs_pet/PIB'
globstr = os.path.join(data_dir, 'B*/pib/dvr/PIB*')
allpi = glob(globstr)
allpi.sort()
allsd = {}
for f in allpi:
get_data(allsd, f, visit=visit)
import logging, logging.config
from time import asctime
if __name__ == '__main__':
"""sets up subject directory structure
Select subs from ARDA,
1. creates output dirs
2. copies pet data to Raw
3. converts
"""
# start wx gui app
app = wx.App()
arda = '/home/jagust/arda/lblid'
root = bg.SimpleDirDialog(prompt='Choose project data dir',
indir='/home/jagust')
mridir = bg.SimpleDirDialog(prompt='Choose Freesurfer data dir',
indir='/home/jagust')
cleantime = asctime().replace(' ', '-').replace(':', '-')
_, scriptnme = os.path.split(__file__)
logfile = os.path.join(root, 'logs', '%s_%s.log' % (scriptnme, cleantime))
log_settings = pp.get_logging_configdict(logfile)
logging.config.dictConfig(log_settings)
tracer = 'FDG'
user = os.environ['USER']
logging.info('###START Setup Directory :::')
logging.info('###TRACER Setup %s :::' % (tracer))
logging.info('###USER : %s' % (user))
import sys, os, shutil
import wx
from glob import glob
sys.path.insert(0, '/home/jagust/cindeem/CODE/PetProcessing')
import preprocessing as pp
import base_gui as bg
import logging, logging.config
from time import asctime
import tempfile
if __name__ == '__main__':
# start wx gui app
app = wx.App()
fsdir = bg.SimpleDirDialog(prompt='Choose Freesurfer DIR',
indir='/home/jagust')
cleantime = asctime().replace(' ', '-').replace(':', '-')
logfile = os.path.join(fsdir, 'seedfs_logs',
'%s%s.log' % (__file__, cleantime))
log_settings = pp.get_logging_configdict(logfile)
logging.config.dictConfig(log_settings)
user = os.environ['USER']
logging.info('###START %s :::' % __file__)
logging.info('###USER : %s' % (user))
tgz = bg.FilesDialog(prompt='Choose mri .tgz file',
indir='/home/jagust/arda/lblid')
try:
m = pp.re.search('B[0-9]{2}-[0-9]{3}', tgz[0])
