app = wx.App()
root = bg.SimpleDirDialog(prompt='Choose PIB data dir',
indir='/home/jagust')
cleantime = asctime().replace(' ', '-').replace(':', '-')
logfile = os.path.join(root, 'logs',
'pib_%s%s.log' % (__file__, cleantime))
log_settings = pp.get_logging_configdict(logfile)
logging.config.dictConfig(log_settings)
tracer = 'PIB'
user = os.environ['USER']
logging.info('###START pib %s :::' % __file__)
logging.info('###TRACER %s :::' % (tracer))
logging.info('###USER : %s' % (user))
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)
meanfile = pp.make_mean(nifti)
logging.info('created %s' % (meanfile))
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 :::' % (__file__))
logging.info('###TRACER %s :::' % (tracer))
logging.info('###USER : %s' % (user))
subs = bg.MyDirsDialog(prompt='Choose Subjects ', indir='%s/' % root)
# choose template
template = bg.FilesDialog(prompt='Choose template',
indir='/home/jagust/cindeem/TEMPLATES')
logging.info('Template: %s' % (template[0]))
template = str(template[0])
_, tname, _ = pp.split_filename(template)
for sub in subs:
_, subid = os.path.split(sub)
logging.info('%s' % subid)
anatdir = os.path.join(sub, 'anatomy')
if not os.path.isdir(anatdir):
logging.error('%s doesnt exist,skipping' % (anatdir))
continue
tracerdir = os.path.join(sub, 'fdg')
if not os.path.isdir(tracerdir):
logging.error('%s doesnt exist,skipping' % (tracerdir))
continue
cleantime = asctime().replace(' ', '-').replace(':', '-')
logfile = os.path.join(root, 'logs',
'pib_%s%s.log' % (__file__, cleantime))
log_settings = pp.get_logging_configdict(logfile)
logging.config.dictConfig(log_settings)
tracer = 'PIB'
user = os.environ['USER']
logging.info('###START pib %s :::' % __file__)
logging.info('###TRACER %s :::' % (tracer))
logging.info('###USER : %s' % (user))
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
corgdir = os.path.join(pth, 'coreg')
globstr = '%s/rbrainmask.nii' % (corgdir)
rbrainmask = pp.find_single_file(globstr)
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])
subid = m.group()
except:
logging.error('cant find ID in %s' % (tgz[0]))
raise IOError('cant find ID in %s' % (tgz[0]))
# create temp dir and untar/unzip dicom files into it
startdir = os.getcwd()
tmpdir = tempfile.mkdtemp()
os.chdir(tmpdir)
tgz = tgz[0]
cmd = 'tar xfvz %s ' % (tgz)
os.system(cmd)
# find first dicom