Skip to content

Commit

Permalink
Added the class..
Browse files Browse the repository at this point in the history
  • Loading branch information
@tjrantal
tjrantal committed Feb 28, 2012
1 parent d296d71 commit 17afcdc
Showing 1 changed file with 187 additions and 0 deletions.
187 changes: 187 additions & 0 deletions src/org/doube/bonej/pqct/utils/ResultsImage.java
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,187 @@
/*
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
N.B. the above text was copied from http://www.gnu.org/licenses/gpl.html
unmodified. I have not attached a copy of the GNU license to the source...
Results image creator for ImageJ density distribution analysis plugin
Copyright (C) 2011 Timo Rantalainen
*/

package org.doube.bonej.pqct.utils;
import ij.ImagePlus; //Image creation
import ij.IJ; //Image rotation
import ij.measure.Calibration; //Image calibration
import ij.process.FloatProcessor; //Float Images
import ij.process.ImageConverter; //Convert float to RGB
import java.awt.Color; //Color class
import java.util.Vector; //Vector

public class ResultsImage{

/*Get image into which we'll start adding stuff*/
public static ImagePlus getRGBResultImage(double[] values,int width,int height){
ImagePlus tempImage = new ImagePlus("Visual results");
tempImage.setProcessor(new FloatProcessor(width,height,values));
new ImageConverter(tempImage).convertToRGB();
return tempImage;
}

public static ImagePlus addScale(ImagePlus tempImage, double pixelSpacing){
Calibration cal = new Calibration();
cal.setUnit("mm");
cal.pixelWidth = cal.pixelHeight = pixelSpacing;
tempImage.setCalibration(cal);
tempImage.getProcessor().setColor(new Color(255,0,0));
tempImage.getProcessor().drawLine(5, 5, (int)(5.0+10.0/pixelSpacing), 5);
tempImage.getProcessor().drawString("1 cm", 5, 20);
return tempImage;
}
/*Add soft sieve*/
public static ImagePlus addSoftTissueSieve(ImagePlus tempImage, byte[] sieve){
for (int y = 0; y < tempImage.getHeight();++y) {
for (int x = 0; x < tempImage.getWidth();++x) {
if (sieve[x+y*tempImage.getWidth()] == 2){ //Tint fat area with yellow
int value = tempImage.getProcessor().getPixel(x,y);
int[] rgb = new int[3];
for (int i = 0; i<3;++i){
rgb[i] = (value >>(i*8))& 0XFF;
}
tempImage.getProcessor().setColor(new Color(rgb[2],rgb[1],0));
tempImage.getProcessor().drawPixel(x,y);
}
if (sieve[x+y*tempImage.getWidth()] == 3){ //Tint muscle area with red
int value = tempImage.getProcessor().getPixel(x,y);
int[] rgb = new int[3];
for (int i = 0; i<3;++i){
rgb[i] = (value >>(i*8))& 0XFF;
}
tempImage.getProcessor().setColor(new Color(rgb[2],0,0));
tempImage.getProcessor().drawPixel(x,y);
}
if (sieve[x+y*tempImage.getWidth()] == 4){ //Tint intra fat area with green
int value = tempImage.getProcessor().getPixel(x,y);
int[] rgb = new int[3];
for (int i = 0; i<3;++i){
rgb[i] = (value >>(i*8))& 0XFF;
}
tempImage.getProcessor().setColor(new Color(0,rgb[1],0));
tempImage.getProcessor().drawPixel(x,y);
}
if (sieve[x+y*tempImage.getWidth()] == 5){ //Tint subcut fat area with purple
int value = tempImage.getProcessor().getPixel(x,y);
int[] rgb = new int[3];
for (int i = 0; i<3;++i){
rgb[i] = (value >>(i*8))& 0XFF;
}
tempImage.getProcessor().setColor(new Color(rgb[2],0,rgb[0]));
tempImage.getProcessor().drawPixel(x,y);
}
}
}
//tempImage.setProcessor(tempImage.getProcessor().resize(1000));
return tempImage;
}

/*Add bone sieve*/
public static ImagePlus addBoneSieve(ImagePlus tempImage, byte[] sieve,double[] scaledImage, double marrowThreshold){
for (int y = 0; y < tempImage.getHeight();++y) {
for (int x = 0; x < tempImage.getWidth();++x) {
if (sieve[x+y*tempImage.getWidth()] == 1){ //Tint bone area with purple
int value = tempImage.getProcessor().getPixel(x,y);
int[] rgb = new int[3];
for (int i = 0; i<3;++i){
rgb[i] = (value >>(i*8))& 0XFF;
}
tempImage.getProcessor().setColor(new Color(rgb[2],0,rgb[0]));
tempImage.getProcessor().drawPixel(x,y);
}
if (sieve[x+y*tempImage.getWidth()] == 1 && scaledImage[x+y*tempImage.getWidth()] <=marrowThreshold){ //Tint marrow area with green
int value = tempImage.getProcessor().getPixel(x,y);
int[] rgb = new int[3];
for (int i = 0; i<3;++i){
rgb[i] = (value >>(i*8))& 0XFF;
}
if (rgb[0] < 255-50){
rgb[0]+=50;
}
tempImage.getProcessor().setColor(new Color(0,0,rgb[0]));
tempImage.getProcessor().drawPixel(x,y);
}
}
}
return tempImage;
}

/*addDenstiyDistribution*/
public static ImagePlus addRadii(ImagePlus tempImage,double alfa,double[] marrowCenter,Vector<Integer> pindColor,
double[] R, double[] R2, double[] Theta){
//Draw unrotated radii
for(int i = 0; i< 360;i++) {//45;i++) {//
int x = ((int) (marrowCenter[0]+R[i]*Math.cos(Theta[i])));
int y = ((int) (marrowCenter[1]+R[i]*Math.sin(Theta[i])));
double colorScale = ((double) pindColor.get(i))/359.0;
tempImage.getProcessor().setColor(new Color((int) (255.0*colorScale),0,(int) (255.0*(1.0-colorScale))));
tempImage.getProcessor().drawPixel(x,y);
x = ((int) (marrowCenter[0]+R2[i]*Math.cos(Theta[i])));
y = ((int) (marrowCenter[1]+R2[i]*Math.sin(Theta[i])));
tempImage.getProcessor().setColor(new Color(0,(int) (255.0*colorScale),(int) (255.0*(1.0-colorScale))));
tempImage.getProcessor().drawPixel(x,y);
}
return tempImage;
}

public static ImagePlus addMarrowCenter(ImagePlus tempImage,double alfa,double[] marrowCenter){
/*plot marrowCenter*/
for(int i = 0; i< 10;i++) {//45;i++) {//
int x = ((int) (marrowCenter[0]+i));
int y = ((int) (marrowCenter[1]));
tempImage.getProcessor().setColor(new Color(0,255,255));
tempImage.getProcessor().drawPixel(x,y);
x = (int) (marrowCenter[0]);
y = (int) (marrowCenter[1]+i);
tempImage.getProcessor().setColor(new Color(255,0,255));
tempImage.getProcessor().drawPixel(x,y);
/*Plot rotated axes...*/
x = ((int) ((double) marrowCenter[0]+((double) i)*Math.cos(-alfa/180*Math.PI)));
y = ((int) ((double) marrowCenter[1]+((double) i)*Math.sin(-alfa/180*Math.PI)));
tempImage.getProcessor().setColor(new Color(0,255,0));
tempImage.getProcessor().drawPixel(x,y);
x = ((int) ((double) marrowCenter[0]+((double) -i)*Math.sin(-alfa/180*Math.PI)));
y = ((int) ((double) marrowCenter[1]+((double) i)*Math.cos(-alfa/180*Math.PI)));
tempImage.getProcessor().setColor(new Color(0,0,255));
tempImage.getProcessor().drawPixel(x,y);
}
return tempImage;
}

public static ImagePlus addRotate(ImagePlus tempImage,double alfa){
tempImage.getProcessor().setBackgroundValue(0.0);
IJ.run(tempImage, "Arbitrarily...", "angle=" + alfa + " grid=1 interpolation=Bilinear enlarge");
return tempImage;
}

/*Concentric rings distribution result image*/
public static ImagePlus addPeriRadii(ImagePlus tempImage,double[] marrowCenter,Vector<Integer> pindColor, double[] R, double[] Theta){
//Draw unrotated radii
for(int i = 0; i< Theta.length;i++) {//45;i++) {//
int x = ((int) (marrowCenter[0]+R[i]*Math.cos(Theta[i])));
int y = ((int) (marrowCenter[1]+R[i]*Math.sin(Theta[i])));
double colorScale = ((double) pindColor.get(i))/359.0;
tempImage.getProcessor().setColor(new Color(0,(int) (255.0*colorScale),(int) (255.0*(1.0-colorScale))));
tempImage.getProcessor().drawPixel(x,y);
}
return tempImage;
}
}

0 comments on commit 17afcdc

Please sign in to comment.