def define_pixel_sizes(args):
"""
Defines the pixel sizes based on metadata file, or CLI flags
:param args: amap argument object
:return: args updated
"""
if None in [args.x_pixel_um, args.y_pixel_um, args.z_pixel_um]:
if args.metadata is None:
raise CommandLineInputError(
"Not all pixel sizes are defined on the command line, but "
"no metadata file has been supplied")
try:
metadata = get_acquisition_metadata(args.metadata)
except NotImplementedError:
raise CommandLineInputError(
"Not all pixel sizes are defined on the command line, but the"
" metadata file cannot be read.")
for dim in ["x", "y", "z"]:
dim_attribute = "{}_pixel_um".format(dim)
if getattr(args, dim_attribute) is None:
try:
setattr(args, dim_attribute, getattr(metadata, dim_attribute))
except ArgumentTypeError:
raise CommandLineInputError(
"No {} pixel size was defined on the command line, and it "
"cannot be parsed from the metadata".format(dim))
return args
def test_mesospim_meta():
metadata = meta.get_acquisition_metadata(mesoSPIM_metadata)
assert isclose(8.23, metadata.x_pixel_um, abs_tol=VOX_DIM_TOLERANCE)
assert isclose(8.23, metadata.y_pixel_um, abs_tol=VOX_DIM_TOLERANCE)
assert isclose(10, metadata.z_pixel_um, abs_tol=VOX_DIM_TOLERANCE)
assert metadata.num_planes == 852
def test_baking_tray_meta():
metadata = meta.get_acquisition_metadata(baking_tray_metadata)
assert isclose(2.19, metadata.x_pixel_um, abs_tol=VOX_DIM_TOLERANCE)
assert isclose(2.14, metadata.y_pixel_um, abs_tol=VOX_DIM_TOLERANCE)
assert isclose(5, metadata.z_pixel_um, abs_tol=VOX_DIM_TOLERANCE)
assert metadata.num_planes == 2000
def test_amap_meta():
metadata = meta.get_acquisition_metadata(amap_metadata)
assert isclose(8, metadata.x_pixel_um, abs_tol=VOX_DIM_TOLERANCE)
assert isclose(8, metadata.y_pixel_um, abs_tol=VOX_DIM_TOLERANCE)
assert isclose(20, metadata.z_pixel_um, abs_tol=VOX_DIM_TOLERANCE)
assert metadata.num_planes == 100
def test_cellfinder_meta():
metadata = meta.get_acquisition_metadata(cellfinder_metadata)
assert isclose(2, metadata.x_pixel_um, abs_tol=VOX_DIM_TOLERANCE)
assert isclose(2, metadata.y_pixel_um, abs_tol=VOX_DIM_TOLERANCE)
assert isclose(5, metadata.z_pixel_um, abs_tol=VOX_DIM_TOLERANCE)
assert metadata.num_planes == 1500
def test_unsupported_meta():
with pytest.raises(NotImplementedError):
assert meta.get_acquisition_metadata(unsupported_metadata)