CLIJ2

Logo

GPU accelerated image processing for everyone

CLIJ2 home

median3DSphere

Computes the local median of a pixels spherical neighborhood.

The spheres size is specified by its half-width, half-height and half-depth (radius).

For technical reasons, the volume of the sphere must contain less than 1000 voxels.

Categories: Noise, Filter

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_median3DSphere(Image source, Image destination, Number radiusX, Number radiusY, Number radiusZ);

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);
int radiusX = 10;
int radiusY = 20;
int radiusZ = 30;
// Execute operation on GPU
clij2.median3DSphere(source, destination, radiusX, radiusY, radiusZ);
// 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);
radiusX = 10;
radiusY = 20;
radiusZ = 30;
% Execute operation on GPU
clij2.median3DSphere(source, destination, radiusX, radiusY, radiusZ);
% 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);
radiusX = 10;
radiusY = 20;
radiusZ = 30;
// Execute operation on GPU
clij2.median3DSphere(source, destination, radiusX, radiusY, radiusZ);
// show result
destination_sequence = clij2.pullSequence(destination)
Icy.addSequence(destination_sequence);
// cleanup memory on GPU
clij2.release(source);
clij2.release(destination);

Back to CLIJ2 reference Back to CLIJ2 documentation

Imprint