http://imagej.273.s1.nabble.com/histogram-of-a-surrounding-sphere-tp3693546p3693550.html
So obvious... Thanks a lot, the plugin works perfectly!
Just a question: how getting the mean value directly instead of the full tab values?
> Date: Sun, 22 Feb 2009 12:04:35 +0100
> From:
[hidden email]
> Subject: Re: histogram of a surrounding sphere
> To:
[hidden email]
>
> Hi,
>
> You need first to rename your file to the same name as the class :
> HistoPixel3D_.java
>
> let's assume ij.jar and ij3d-bin.jar and the HistoPixel3D_.java file are
> in the same folder :
>
> javac -cp ij.jar:ij3d-bin.jar HistoPixel_.java
> use ; instead of : with Windows
>
> Thomas
>
>> 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
>> public class HistoPixel3D_ implements PlugInFilter {
>> Many thanksMilan
>>
>>
>>> 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
>>> /*****************************************************/
>>>
>>>
>>>
>>>
>>
>> _________________________________________________________________
>> 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
> /*****************************************************/
>
>
>