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clatlab

clatlab is a bridge between Matlab and clij2.

For scripting clatlab it's recommended to use CLIJ2-assistant and its matlab code generator.

Image

Installation

Download the following files, removed the numbers from their file endings and put them all in the `<HOME_DIR>/Documents/MATLAB folder:

Test the installation by executing this script from matlab:

clij2 = init_clatlab();
% print out name of used GPU:
clij2.getGPUName()

Example code

Examples are available in the matlab folder.

Clatlab provides two entry points for processing:

  • clij2 is the entry point to clijs image processing operations. Read the clij2 reference to see which operations are available. Replace clij.op(). with clijx in order to make it run in matlab. For example a Gaussian blur can be applied like this:
clij2.gaussianBlur(imageIn, imageOut, 5, 5);
Command Matlab expresson clij2 counter part
push(a) c = clij2.pushMat(a);
pull(a) c = clij2.pullMat(a);
plus(a,b) c = a + b clij2.addImages(a, b, c);
minus(a,b) c = a - b clij2.subtractImages(a, b, c);
uminus(a) c = -a clij2.invert(a, c);
transpose(a) c = a.' clij2.transposeXY(a, c);
times(a,b) c = a .* b clij2.multiplyImages(a, b, c);
mtimes(a,b) c = a * b clij2.multiplyMatrix(a, b, c);
rdivide(a,b) c = a ./ b clij2.divideImages(a, b, c);
ldivide(a,b) c = b ./ b clij2.divideImages(b, a, c);
power(a,b) c = a .^ b clij2.powerImages(a, b, c);
lt(a,b) c = a < b clij2.smaller(a, b, c);
gt(a,b) c = a > b clij2.greater(a, b, c);
le(a,b) c = a <= b clij2.smallerOrEqual(a, b, c);
ge(a,b) c = a >= b clij2.greaterOrEqual(a, b, c);
ne(a,b) c = a ~= b clij2.notEqual(a, b, c);
eq(a,b) c = a == b clij2.equal(a, b, c);
and(a,b) c = a & b clij2.binaryAnd(a, b, c);
or(a,b) c = a I b clij2.binaryOr(a, b, c);
not(a) c = ~b clij2.binaryNot(a, c);
imhist(a) [c,x] = imhist(a) clij2.fillHistogram(a, c);
fliplr(a) c = fliplr(a) clij2.flip(a, c, true, false, false);
min(a) c = min(a) c = clij2.minimumOfAllPixels(a);
max(a) c = max(a) c = clij2.maximumOfAllPixels(a);
mean(a) c = mean(a) c = clij2.meanOfAllPixels(a);
ones(a) c = ones(a) clij2.create(a); clij2.set(a, 1);
zeros(a) c = zeros(a) clij2.create(a); clij2.set(a, 0);
size(a) c = size(a) c = clij2.getDimensions()
colon(a,b) c = [a:b] c = clij2.create(b-a); clij2.setRampX(c);

How to develop clatlab

Clone this repository and build it using maven. Afterwards, you find the clatlab.jar in the target directory. Copy it to your clatlab/matlab java classpath.

git clone https://github.com/clij/clatlab
cd clatlab
mvn package
cp target/clatlab*.jar classpath/

Back to CLIJ documentation

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GPU-accelerated image processing in Matlab using CLIJ

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