# test transform read / write transforms = itk.transformread(transform_filename) fixed_parameters = np.asarray(transforms[0].GetFixedParameters()) parameters = np.asarray(transforms[0].GetParameters()) assert np.allclose(fixed_parameters, baseline_fixed_parameters) assert np.allclose(parameters, baseline_parameters) additional_transform = itk.TranslationTransform[itk.D, 3].New() baseline_additional_transform_params = [3.0, 2.0, 8.0] parameters = additional_transform.GetParameters() parameters[0] = baseline_additional_transform_params[0] parameters[1] = baseline_additional_transform_params[1] parameters[2] = baseline_additional_transform_params[2] additional_transform.SetParameters(parameters) transforms.insert(0, additional_transform) itk.transformwrite(transforms, sys.argv[7], compression=True) transforms = itk.transformread(sys.argv[7]) fixed_parameters = np.asarray(transforms[1].GetFixedParameters()) parameters = np.asarray(transforms[1].GetParameters()) assert np.allclose(fixed_parameters, baseline_fixed_parameters) assert np.allclose(parameters, baseline_parameters) parameters = np.asarray(transforms[0].GetParameters()) assert np.allclose(parameters, np.array(baseline_additional_transform_params)) # pipeline, auto_pipeline and templated class are tested in other files # BridgeNumPy # Images image = itk.imread(filename)
# only float is wrapped as coordinate representation type in TileMontage
montage = itk.TileMontage[type(grayscale_images[0]), itk.F].New()
montage.SetMontageSize(stage_tiles.GetAxisSizes())
for t in range(stage_tiles.LinearSize()):
montage.SetInputTile(t, grayscale_images[t])
print("Computing tile registration transforms")
montage.Update()
print("Writing tile transforms")
actual_tiles = stage_tiles # we will update it later
for t in range(stage_tiles.LinearSize()):
index = stage_tiles.LinearIndexToNDIndex(t)
regTr = montage.GetOutputTransform(index)
tile = stage_tiles.GetTile(t)
itk.transformwrite([regTr], str(output_path / (tile.GetFileName() + ".tfm")))
# calculate updated positions - transform physical into index shift
pos = tile.GetPosition()
for d in range(dimension):
pos[d] -= regTr.GetOffset()[d] / spacing[d]
tile.SetPosition(pos)
actual_tiles.SetTile(t, tile)
actual_tiles.Write(str(output_path / "TileConfiguration.registered.txt"))
print("Producing the mosaic")
resampleF = itk.TileMergeImageFilter[type(color_images[0])].New()
resampleF.SetMontageSize(stage_tiles.GetAxisSizes())
for t in range(stage_tiles.LinearSize()):
resampleF.SetInputTile(t, color_images[t])
index = stage_tiles.LinearIndexToNDIndex(t)