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])