def test_preproc_none():
wsp = Workspace()
d = np.random.rand(5, 5, 5, 6)
wsp.asldata = AslImage(d, name="asldata", tis=[1.5], iaf="tc", order="lrt")
preproc.preprocess(wsp)
assert wsp.asldata.ntis == wsp.asldata_preproc.ntis
assert wsp.asldata.tis == wsp.asldata_preproc.tis
assert wsp.asldata.have_plds == wsp.asldata_preproc.have_plds
assert wsp.asldata.rpts == wsp.asldata_preproc.rpts
assert wsp.asldata.ntc == wsp.asldata_preproc.ntc
assert wsp.asldata.order == wsp.asldata_preproc.order
def main():
"""
Entry point for BASIL command line application
"""
try:
parser = AslOptionParser(
usage="basil -i <ASL input file> [options...]",
version=__version__)
parser.add_category(image.AslImageOptions())
parser.add_category(BasilOptions())
parser.add_category(GenericOptions())
options, _ = parser.parse_args(sys.argv)
if not options.output:
options.output = "basil"
if not options.asldata:
sys.stderr.write("Input file not specified\n")
parser.print_help()
sys.exit(1)
asldata = AslImage(options.asldata, **parser.filter(options, "image"))
wsp = Workspace(savedir=options.output, **vars(options))
wsp.asldata = asldata
# Deal with --artonly
if wsp.artonly:
wsp.infertiss = False
wsp.inferart = True
# Adjust number of iterations based on fast option
if not wsp.fast:
num_iter, num_trials, onestep = 20, 10, False
elif wsp.fast == 1:
num_iter, num_trials, onestep = 5, 2, False
elif wsp.fast == 2:
num_iter, num_trials, onestep = 10, 5, True
else:
raise ValueError("Not a valid option for fast: %s" % str(wsp.fast))
wsp.max_iterations = num_iter
wsp.max_trials = num_trials
wsp.onestep = onestep
# Run BASIL processing, passing options as keyword arguments using **
basil(wsp)
except ValueError as exc:
sys.stderr.write("\nERROR: " + str(exc) + "\n")
sys.stderr.write("Use --help for usage information\n")
sys.exit(1)
def main():
"""
Entry point for command line tool
"""
try:
parser = AslOptionParser(usage="asl_mask -i <asl_image> [options...]",
version=__version__)
parser.add_option("--calib",
"-c",
help="Calibration image",
default=None)
parser.add_option(
"--use-pwi",
help=
"Use the perfusion weighted average rather than the timeseries mean",
action="store_true",
default=False)
parser.add_category(image.AslImageOptions())
parser.add_category(struc.StructuralImageOptions())
parser.add_category(GenericOptions())
options, _ = parser.parse_args(sys.argv)
options.mask = None # No point in using command line tool if you already have a mask!
wsp = Workspace(**vars(options))
if not options.asldata:
sys.stderr.write("Input file not specified\n")
parser.print_help()
sys.exit(1)
wsp.asldata = AslImage(wsp.asldata,
**parser.filter(vars(options), "image"))
wsp.asldata.summary()
wsp.generate_mask()
if wsp.output is None:
wsp.output = wsp.asldata.name + "_mask"
wsp.rois.mask.save(wsp.output)
except ValueError as exc:
sys.stderr.write("ERROR: " + str(exc) + "\n")
sys.exit(1)
def qp_oxasl(worker_id, queue, asldata, options):
try:
from fsl.data.image import Image
from oxasl import Workspace, AslImage
from oxasl.oxford_asl import oxasl
for key, value in options.items():
if isinstance(value, QpData):
options[key] = qpdata_to_fslimage(value)
output_monitor = OutputStreamMonitor(queue)
wsp = Workspace(log=output_monitor)
wsp.asldata, _ = qpdata_to_aslimage(asldata)
oxasl(wsp)
print("done")
ret = wsp_to_dict(wsp)
return worker_id, True, ret
except:
import sys, traceback
traceback.print_exc()
return worker_id, False, sys.exc_info()[1]
