http://imagej.273.s1.nabble.com/histogram-of-a-surrounding-sphere-tp3693546p3693548.html
Thomas,Thank you for your help! Unfortunately, being not a extremely confortable with java, I just can't compile the plugin (see below), although i use -cp ij.jar & ij3d-bin.jar
/Applications/ImageJ/plugins/My_Plugin.java:25: class HistoPixel3D_ is public, should be declared in a file named HistoPixel3D_.java
> Date: Sat, 21 Feb 2009 18:31:09 +0100
> From:
[hidden email]
> Subject: Re: histogram of a surrounding sphere
> To:
[hidden email]
>
> Hi,
>
> You can use my ij3d API, here a simple plugin to do that (beware a lot
> of text !!) :
>
> compile it using -cp ij.jar and ij3d-bin.jar
>
http://imagejdocu.tudor.lu/doku.php?id=plugin:morphology:3d_binary_morphological_filters:start>
> Hope this helps, tell me if you need more explanations.
>
> Thomas
>
>
>
> import ij.*;
> import ij.gui.*;
> import ij.measure.*;
> import ij.plugin.*;
> import ij.plugin.filter.*;
> import ij.process.*;
>
> import ij3d.image3d.*;
> import ij3d.utils.*;
>
> import java.awt.*;
> import java.awt.event.ItemEvent;
> import java.io.BufferedWriter;
> import java.io.FileWriter;
> import java.io.IOException;
> import java.text.*;
> import java.util.Enumeration;
> import java.util.Vector;
> /**
> * Histogram for each pixel in 3D
> *
> *@author Thomas BOUDIER
> *@created avril 2003
> */
> public class HistoPixel3D_ implements PlugInFilter {
> ImagePlus imp;
> float rad;
>
>
> /**
> * Main processing method for the Median3D_ object
> *
> *@param ip Description of the Parameter
> */
> public void run(ImageProcessor ip) {
> rad = 5;
> if (Dialogue()) {
> TabUtil tab;
> IntImage3D col = new IntImage3D(imp.getStack());
> IJ.resetEscape();
> for (int k = 0; k < col.getSizez(); k++) {
> if (IJ.escapePressed()) {
> break;
> }
> IJ.showStatus("3D Histo Pixel : " + (int) (100 * k /
> col.getSizez()) + "%");
> for (int j = 0; j < col.getSizey(); j++) {
> for (int i = 0; i < col.getSizex(); i++) {
> tab = col.getNeighborhoodSphere(i, j, k, rad,
> rad, rad);
> IJ.write("" + tab);
> }
> }
> }
>
> }
> }
>
>
> /**
> * Description of the Method
> *
> *@return Description of the Return Value
> */
> private boolean Dialogue() {
> GenericDialog gd = new GenericDialog("3D Histo Pixel");
> gd.addNumericField("Radius", rad, 0);
> gd.showDialog();
> rad = (int) gd.getNextNumber();
> return (!gd.wasCanceled());
> }
>
>
> /**
> * Description of the Method
> *
> *@param arg Description of the Parameter
> *@param imp Description of the Parameter
> *@return Description of the Return Value
> */
> public int setup(String arg, ImagePlus imp) {
> this.imp = imp;
> return DOES_8G + DOES_16 + NO_CHANGES;
> }
>
> }
>
>
>
>> Hi,In a 3D 8-bit stack (comes from tomography experiment), I would like to have for each point the histogram of the grey scale value of the surrounding voxels contained in a sphere (of 5 voxel radius for example) centered on the point.Any help is warmly welcome.Thank you
>> Milan
>> _________________________________________________________________
>> Découvrez la nouvelle génération des servives de Windows Live
>>
http://download.live.com>>
>>
>
>
> --
> /*****************************************************/
> Thomas Boudier, MCU Université Pierre et Marie Curie
> UMR 7101 / IFR 83. Bat A 328, Campus Jussieu
> Tél : 01 44 27 35 78 Fax : 01 44 27 25 08
> /*****************************************************/
>
>
>