def store_as_nifti(
image: np.ndarray,
header: ImageHeader,
file_name: PathOrString,
image_type: Union[str, type, np.dtype],
scale: bool = False,
input_range: Optional[Iterable[Union[int, float]]] = None,
output_range: Optional[Iterable[Union[int, float]]] = None) -> Path:
"""
Saves an image in nifti format (uploading to Azure also if an online Run), and performs the following operations:
1) transpose the image back into X,Y,Z from Z,Y,X
2) if scale is true, then performs a linear scaling to either the input/output range or
byte range (0,255) as default.
3) cast the image values to the given type before saving
:param image: 3D image in shape: Z x Y x X.
:param header: The image header
:param file_name: The name of the file for this image.
:param scale: Should perform linear scaling of the image, to desired output range or byte range by default.
:param input_range: The input range the image belongs to.
:param output_range: The output range to scale the image to.
:param image_type: The type to save the image in.
:return: the path to the saved image
"""
if image.ndim != 3:
raise Exception("Image must have 3 dimensions, found: {}".format(
len(image.shape)))
if image_type is None:
raise Exception("You must specify a valid image type.")
if scale and ((input_range is not None and output_range is None) or
(input_range is None and output_range is not None)):
raise Exception(
"You must provide both input and output ranges to apply custom linear scaling."
)
# rescale image for visualization in the app
if scale:
if input_range is not None and output_range is not None:
# noinspection PyTypeChecker
image = LinearTransform.transform(
data=image,
input_range=input_range, # type: ignore
output_range=tuple(output_range) # type: ignore
)
else:
image = (image + 1) * 255
image = sitk.GetImageFromArray(image.astype(image_type))
image.SetSpacing(sitk.VectorDouble(reverse_tuple_float3(
header.spacing))) # Spacing needs to be X Y Z
image.SetOrigin(header.origin)
image.SetDirection(header.direction)
sitk.WriteImage(image, str(file_name))
return Path(file_name)
