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)
