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