def test_sub_kwargs():
""" Test creating a sub workspace with kwargs """
wsp = Workspace()
wsp.sub("child", wibble="squid", pudding=4)
assert(isinstance(wsp.child, Workspace))
assert(wsp.child.wibble == "squid")
assert(wsp.child.pudding == 4)
def test_sub():
""" Test sub-workspaces """
wsp = Workspace()
wsp.sub("child")
assert(isinstance(wsp.child, Workspace))
assert(wsp.child.wibble is None)
assert(wsp.child.log == wsp.log)
def test_default_wsp_multiple():
""" Test multiple default sub-workspaces for search """
wsp = Workspace(defaults=["plants", "trees"])
wsp.daffodil = 9
wsp.larch = 1
wsp.sub("trees")
wsp.trees.oak = 3
wsp.trees.larch = 2
wsp.trees.apple = 7
assert(wsp.daffodil == 9)
assert(wsp.larch == 1)
assert(wsp.oak == 3)
assert(wsp.apple == 7)
assert(wsp.trees.larch == 2)
assert(wsp.trees.oak == 3)
assert(wsp.trees.daffodil is None)
assert(wsp.trees.apple == 7)
wsp.sub("plants")
wsp.plants.lily = 4
wsp.plants.oak = 5
assert(wsp.daffodil == 9)
assert(wsp.larch == 1)
assert(wsp.lily == 4)
assert(wsp.oak == 5)
assert(wsp.apple == 7)
assert(wsp.trees.oak == 3)
assert(wsp.trees.lily is None)
assert(wsp.plants.daffodil is None)
assert(wsp.plants.lily == 4)
assert(wsp.plants.oak == 5)
def test_sub_inherit_wsp():
""" Test sub workspaces can inherit sub-workspaces from their parent """
wsp = Workspace()
wsp.sub("child1")
wsp.child1.wibble = 7
wsp.sub("child2")
assert(wsp.child2.child1 is not None)
assert(wsp.child2.child1.wibble == 7)
def test_sub_inherit():
""" Test sub workspaces can inherit values from their parent """
wsp = Workspace()
wsp.wibble = 7
wsp.wobble = 6
wsp.sub("child")
wsp.child.wobble = 5
assert(wsp.child.wibble == 7)
assert(wsp.child.wobble == 5)
def main():
""" Simple test case """
from fsl.data.image import Image
from oxasl import Workspace
wsp = Workspace(savedir="epi_py_out", debug=True)
wsp.sub("reg")
wsp.regfrom = Image(sys.argv[1])
wsp.fslanat = sys.argv[2]
struc.init(wsp)
result = epi_reg(wsp, wsp.regfrom)
wsp.imgreg, wsp.img2struc = result["out.nii.gz"], result["out"]
def test_savedir_sub():
""" Test sub-workspace have subdirs created """
tempdir = tempfile.mktemp("_oxasl")
try:
log = StringIO()
wsp = Workspace(savedir=tempdir, log=log)
wsp.sub("quark")
path = os.path.join(tempdir, "quark")
assert(wsp.quark.savedir == path)
assert(os.path.isdir(path))
assert("WARNING" not in log.getvalue())
finally:
shutil.rmtree(tempdir)
def main():
"""
Entry point for OXASL_DEBLUR command line application
"""
try:
parser = AslOptionParser(
usage="oxasl_deblur -i <ASL input file> [options...]",
version=__version__)
if hasattr(image, "Options"):
parser.add_category(image.Options())
else:
parser.add_category(image.AslImageOptions())
parser.add_category(Options())
parser.add_category(basil.BasilOptions())
#parser.add_category(calib.CalibOptions())
parser.add_category(GenericOptions())
options, _ = parser.parse_args()
if not options.output:
options.output = "oxasl_deblur"
if not options.asldata:
sys.stderr.write("Input ASL data not specified\n")
parser.print_help()
sys.exit(1)
print("OXASL_DEBLUR %s (%s)\n" % (__version__, __timestamp__))
wsp = Workspace(savedir=options.output,
auto_asldata=True,
**vars(options))
wsp.asldata.summary()
wsp.sub("reg")
wsp.reg.nativeref = wsp.asldata.perf_weighted()
wsp.sub("output")
run(wsp, output_wsp=wsp.output)
if wsp.save_kernel:
wsp.output.kernel = wsp.deblur.kernel
if wsp.save_residuals:
wsp.output.residuals = wsp.deblur.residuals
if not wsp.debug:
wsp.deblur = None
wsp.input = None
print('\nOXASL_DEBLUR - DONE - output is in %s' % options.output)
except RuntimeError as e:
print("ERROR: " + str(e) + "\n")
sys.exit(1)
def test_default_wsp():
""" Test default sub-workspaces for search """
wsp = Workspace(defaults=["cars"])
assert(wsp.cars is None)
wsp.ferrari = 9
wsp.merc = 8
wsp.sub("cars")
wsp.cars.porsche = 6
wsp.cars.ferrari = 4
assert(wsp.cars is not None)
assert(wsp.ferrari == 9)
assert(wsp.porsche == 6)
assert(wsp.merc == 8)
assert(wsp.cars.porsche == 6)
assert(wsp.cars.ferrari == 4)
assert(wsp.cars.merc is None)
