applyVectorField3D

Deforms an image stack according to distances provided in the given vector image stacks.

It is recommended to use 32-bit image stacks for input, output and vector image stacks.

Parameters

source : Image The input image to be processed. vector_x : Image Pixels in this image describe the distance in X direction pixels should be shifted during warping. vector_y : Image Pixels in this image describe the distance in Y direction pixels should be shifted during warping. vector_z : Image Pixels in this image describe the distance in Z direction pixels should be shifted during warping. destination : Image The output image where results are written into.

Category: Transformations

Availability: Available in Fiji by activating the update sites clij and clij2. This function is part of clij2_-2.5.0.1.jar.

Usage in ImageJ macro

Ext.CLIJ2_applyVectorField3D(Image source, Image vectorX, Image vectorY, Image vectorZ, Image destination);

Usage in object oriented programming languages

Java

// init CLIJ and GPU
import net.haesleinhuepf.clij2.CLIJ2;
import net.haesleinhuepf.clij.clearcl.ClearCLBuffer;
CLIJ2 clij2 = CLIJ2.getInstance();

// get input parameters
ClearCLBuffer source = clij2.push(sourceImagePlus);
ClearCLBuffer vectorX = clij2.push(vectorXImagePlus);
ClearCLBuffer vectorY = clij2.push(vectorYImagePlus);
ClearCLBuffer vectorZ = clij2.push(vectorZImagePlus);
destination = clij2.create(source);

// Execute operation on GPU
clij2.applyVectorField3D(source, vectorX, vectorY, vectorZ, destination);

// show result
destinationImagePlus = clij2.pull(destination);
destinationImagePlus.show();

// cleanup memory on GPU
clij2.release(source);
clij2.release(vectorX);
clij2.release(vectorY);
clij2.release(vectorZ);
clij2.release(destination);

Matlab

% init CLIJ and GPU
clij2 = init_clatlab();

% get input parameters
source = clij2.pushMat(source_matrix);
vectorX = clij2.pushMat(vectorX_matrix);
vectorY = clij2.pushMat(vectorY_matrix);
vectorZ = clij2.pushMat(vectorZ_matrix);
destination = clij2.create(source);

% Execute operation on GPU
clij2.applyVectorField3D(source, vectorX, vectorY, vectorZ, destination);

% show result
destination = clij2.pullMat(destination)

% cleanup memory on GPU
clij2.release(source);
clij2.release(vectorX);
clij2.release(vectorY);
clij2.release(vectorZ);
clij2.release(destination);

Icy JavaScript

// init CLIJ and GPU
importClass(net.haesleinhuepf.clicy.CLICY);
importClass(Packages.icy.main.Icy);

clij2 = CLICY.getInstance();

// get input parameters
source_sequence = getSequence();
source = clij2.pushSequence(source_sequence);
vectorX_sequence = getSequence();
vectorX = clij2.pushSequence(vectorX_sequence);
vectorY_sequence = getSequence();
vectorY = clij2.pushSequence(vectorY_sequence);
vectorZ_sequence = getSequence();
vectorZ = clij2.pushSequence(vectorZ_sequence);
destination = clij2.create(source);

// Execute operation on GPU
clij2.applyVectorField3D(source, vectorX, vectorY, vectorZ, destination);

// show result
destination_sequence = clij2.pullSequence(destination)
Icy.addSequence(destination_sequence);
// cleanup memory on GPU
clij2.release(source);
clij2.release(vectorX);
clij2.release(vectorY);
clij2.release(vectorZ);
clij2.release(destination);

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