def test_find_raw_files(): tmpdir = tempfile.mkdtemp() reg.function_logger(tmpdir) logger = logging.getLogger('antsregister.pstask') logger.info(os.getenv('USER')) logger.info(__file__) subid = 'B00-000' files = ['{0}_brainmask.nii.gz'.format(subid), '{0}_aparcaseg.nii.gz'.format(subid), '{0}_4d_func.nii.gz'.format(subid)] allfiles = [os.path.join(tmpdir, x) for x in files] anat, aparc, func = find_raw_files(tmpdir, subid, logger) assert anat is None for tf in allfiles: os.system('touch %s'%tf) anat, aparc, func = find_raw_files(tmpdir, subid, logger) assert all([anat, aparc, func]) #Cleanup os.system('rm -rf %s'%(tmpdir))
if __name__ == '__main__': try: datadirectory = sys.argv[1] globstr = sys.argv[2] except: raise IndexError('please pass a subjects datadir') dirs = sorted(glob(os.path.join(datadirectory, '{0}*'.format(globstr)))) try: taskid = os.environ['SGE_TASK_ID'] except: raise IOError('Are you using SGE??') datadir = dirs[int(taskid) - 1] reg.function_logger(datadir) logger = logging.getLogger('antsregister.pstask') logger.info(os.getenv('USER')) logger.info(__file__) rundirsstr = os.path.join(datadir, 'run*') rundirs = sorted(glob(rundirsstr)) _, sid = os.path.split(datadir) for r in rundirs: if 'run3' in r: run3 = r rundirs.remove(r) else: continue
sys.path.insert(0, os.path.split(__file__)[0]) import register as reg import transform as xfm if __name__ =='__main__': rootdir = '/home/jagust/fmri-pstask/pilot/ANTS/example_data_pstask/B13-005' #'/home/jagust/fmri-pstask/pilot/B13-004/pstask' #allseries = sorted(glob(os.path.join(rootdir, 'series_*'))) allseries = [rootdir,] reg.function_logger(rootdir) logger = logging.getLogger('antsregister.wrapper') for datadir in allseries: logger.info(datadir) globstr = os.path.join(datadir, 'B13-005_sess*.nii.gz') allf = sorted(glob(globstr)) target = allf[0] basedir, _ = os.path.split(target) reg.function_logger(basedir) allmove = [] allmoved = [target] for movin in allf[1:3]: tmpaff = reg.affine_register_cc(target, movin) if tmpaff is None: continue displacement, translate, angles = xfm.params_from_ants(tmpaff)