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affineTransform2D

By Robert Haase and Peter Haub based on work by Martin Weigert

Applies an affine transform to a 2D image. Individual transforms must be separated by spaces.

Supported transforms:

Example transform: transform = “center scale=2 rotate=45 -center”;

Category: Transformations

affineTransform2D often follows after

affineTransform2D is often followed by

Usage in ImageJ macro

Ext.CLIJ2_affineTransform2D(Image source, Image destination, String transform);

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);
destination = clij2.create(source);
// Execute operation on GPU
clij2.affineTransform2D(source, destination, transform);
// show result
destinationImagePlus = clij2.pull(destination);
destinationImagePlus.show();

// cleanup memory on GPU
clij2.release(source);
clij2.release(destination);
Matlab
% init CLIJ and GPU
clij2 = init_clatlab();

% get input parameters
source = clij2.pushMat(source_matrix);
destination = clij2.create(source);
% Execute operation on GPU
clij2.affineTransform2D(source, destination, transform);
% show result
destination = clij2.pullMat(destination)

% cleanup memory on GPU
clij2.release(source);
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);
destination = clij2.create(source);
// Execute operation on GPU
clij2.affineTransform2D(source, destination, transform);
// show result
destination_sequence = clij2.pullSequence(destination)
Icy.addSequence(destination_sequence);
// cleanup memory on GPU
clij2.release(source);
clij2.release(destination);

Example notebooks

applyVectorFieldMD
rotate_comparison_IJ_CLIJ

Example scripts

affineTransform.ijm
applyVectorField.ijm
applyVectorFieldMD.ijm
motionCorrection.ijm
motionCorrection_compare_stackreg.ijm
rotate_comparison_IJ_CLIJ.ijm
affineTransform.py
applyVectorField.py
rotateFree.py
rotateOverwriteOiginal.py

License terms

adapted from: https://github.com/maweigert/gputools/blob/master/gputools/transforms/kernels/transformations.cl

Copyright (c) 2016, Martin Weigert
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS”
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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