copyImageView.py

This code demonstrates how it is possible to copy a whole ImageView content into another one.

This code demonstrates how it is possible to copy a whole ImageView content into another one.

import iolink
import numpy as np
 
 
 
 
def create_imageview() -> iolink.ImageView:
    shape = iolink.VectorXu64(10, 20, 30)
    dt = iolink.DataTypeId.VEC3_UINT8
    image = iolink.ImageViewFactory.allocate(shape, dt)
 
    # set some properties (not exhaustive)
    image.axes_interpretation = iolink.AxesInterpretationId.IMAGE_SEQUENCE
    image.image_interpretation = iolink.ImageInterpretation.RGB
    image.has_alpha = False
    image.spatial_origin = iolink.Vector3d(1.0, 2.0, 3.0)
    image.spatial_spacing = iolink.Vector3d(0.1, 0.2, 0.3)
    image.spatial_unit = "mm"
 
    # create some metadata
    rootNode = iolink.MetadataNodeFactory.create("root", None)
    iolink.MetadataNodeHelper.create_path(rootNode, "level1/data1", iolink.VariantDataValueFactory.create("value1"))
    iolink.MetadataNodeHelper.create_path(rootNode, "level1/data2", iolink.VariantDataValueFactory.create("value2"))
    iolink.MetadataNodeHelper.create_path(rootNode, "level2/data3", iolink.VariantDataValueFactory.create("value3"))
    image.metadata = rootNode
 
    # write some data (anything)
    fullRegion = iolink.RegionXu64.create_full_region(shape)
    npBuf = np.ones(dtype = 'B', shape=(fullRegion.element_count * image.data_type.byte_count()))
    image.write_region(fullRegion, npBuf)
 
    return image
 
 
def copy_imageview(imageSrc: iolink.ImageView, imageDst:iolink.ImageView):
    # when source image origin is not controlled, we should check if we have READ capability
    # this test is not mandatory, but it is a good practice to check if we can read the source image
    if not imageSrc.support(iolink.ImageCapability.READ):
     raise AttributeError("Source image does not have READ capability")
 
    # check if destination image has WRITE and RESHAPE capability
    if not imageDst.support(iolink.ImageCapability.READ):
        raise AttributeError("Destination image does not have WRITE and RESHAPE capability")
 
    # destination image is reshaped to the same shape and data type as the source image
    imageDst.reshape(imageSrc.shape, imageSrc.data_type)
 
    # properties are copied from source to destination
    imageDst.properties = imageSrc.properties
 
    # metadata are copied from source to destination
    if imageSrc.metadata is not None:
        imageDst.metadata = imageSrc.metadata.clone()
 
    # copy pixels/voxels one shot
    # this is the fastest way to copy the whole image but it can require a lot of memory
    # a copy chunk by chunk could be more memory efficient
    fullRegion = iolink.RegionXu64.create_full_region(imageSrc.shape)
    # dimension a buffer to store the whole image temporarily
    npBuf = np.zeros(dtype = 'B', shape=(imageSrc.data_type.byte_count() * fullRegion.element_count))
    # read/write pixels/voxels
    imageSrc.read_region(fullRegion, npBuf)
    imageDst.write_region(fullRegion, npBuf)
 
# create an ImageView with some content
imageSource = create_imageview()
 
# create an ImageView with any shape and data type
imageDestination = iolink.ImageViewFactory.allocate((1, 1), iolink.DataTypeId.FLOAT)
 
# copy the content of the source image into the destination image
copy_imageview(imageSource, imageDestination)
 
print(imageDestination)
print(imageDestination.properties)
print(imageDestination.metadata)
 
print("SUCCESS")