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affineTransform3D

By Robert Haase based on work by Martin Weigert

Applies an affine transform to a 3D image.

The transform describes how coordinates in the target image are transformed to coordinates in the source image. This may appear unintuitive and will be changed in the next major release. The replacement affineTransform (currently part of CLIJx) will apply inverted transforms compared to this operation. Individual transforms must be separated by spaces.

Parameters

source : Image The input image to be processed. destination : Image The output image where results are written into. transform : String A space-separated list of individual transforms. Syntrax see below.

Supported transforms:

  • -center: translate the coordinate origin to the center of the image
  • center: translate the coordinate origin back to the initial origin
  • rotate=[angle]: rotate in X/Y plane (around Z-axis) by the given angle in degrees
  • rotateX=[angle]: rotate in Y/Z plane (around X-axis) by the given angle in degrees
  • rotateY=[angle]: rotate in X/Z plane (around Y-axis) by the given angle in degrees
  • rotateZ=[angle]: rotate in X/Y plane (around Z-axis) by the given angle in degrees
  • scale=[factor]: isotropic scaling according to given zoom factor
  • scaleX=[factor]: scaling along X-axis according to given zoom factor
  • scaleY=[factor]: scaling along Y-axis according to given zoom factor
  • scaleZ=[factor]: scaling along Z-axis according to given zoom factor
  • shearXY=[factor]: shearing along X-axis in XY plane according to given factor
  • shearXZ=[factor]: shearing along X-axis in XZ plane according to given factor
  • shearYX=[factor]: shearing along Y-axis in XY plane according to given factor
  • shearYZ=[factor]: shearing along Y-axis in YZ plane according to given factor
  • shearZX=[factor]: shearing along Z-axis in XZ plane according to given factor
  • shearZY=[factor]: shearing along Z-axis in YZ plane according to given factor
  • translateX=[distance]: translate along X-axis by distance given in pixels
  • translateY=[distance]: translate along X-axis by distance given in pixels
  • translateZ=[distance]: translate along X-axis by distance given in pixels

Example transform: transform = "-center scale=2 rotate=45 center";

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_affineTransform3D(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.affineTransform3D(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.affineTransform3D(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.affineTransform3D(source, destination, transform);

// show result
destination_sequence = clij2.pullSequence(destination)
Icy.addSequence(destination_sequence);
// cleanup memory on GPU
clij2.release(source);
clij2.release(destination);
clEsperanto Python (experimental) 
import pyclesperanto_prototype as cle

cle.affine_transform(source, destination, transform)

Example notebooks

affine_transforms.ipynb
affine_transforms.ipynb

Example scripts

affineTransform3D.ijm
interactiveCylinderProjection.py
interactiveSphereProjection.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:

  • Redistributions of source code must retain the above copyright notice, this
    list of conditions and the following disclaimer.

  • Redistributions in binary form must reproduce the above copyright notice,
    this list of conditions and the following disclaimer in the documentation
    and/or other materials provided with the distribution.

  • Neither the name of gputools nor the names of its
    contributors may be used to endorse or promote products derived from
    this software without specific prior written permission.

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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