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OrientationJ/src/orientationj/ColorMapping.java
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ColorMapping.java
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//==============================================================================
//
// Project: Directional Image Analysis - OrientationJ plugin
//
// Author: Daniel Sage
//
// Organization: Biomedical Imaging Group (BIG)
// Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
//
// Information:
// OrientationJ: http://bigwww.epfl.ch/demo/orientation/
// MonogenicJ: http://bigwww.epfl.ch/demo/monogenic/
//
//
// Reference on methods and plugin
// Z. Püspöki, M. Storath, D. Sage, M. Unser
// "Transforms and Operators for Directional Bioimage Analysis: A Survey,"
// Advances in Anatomy, Embryology and Cell Biology, vol. 219, Focus on Bio-Image Informatics,
// Springer International Publishing, ch. 3, pp. 69-93, May 21, 2016.
//
// Reference on applications
// E. Fonck, G.G. Feigl, J. Fasel, D. Sage, M. Unser, D.A. Ruefenacht, N. Stergiopulos
// "Effect of Aging on Elastin Functionality in Human Cerebral Arteries,"
// Stroke, vol. 40, no. 7, pp. 2552-2556, July 2009.
//
// R. Rezakhaniha, A. Agianniotis, J.T.C. Schrauwen, A. Griffa, D. Sage, C.V.C. Bouten, F.N. van de Vosse, M. Unser, N. Stergiopulos
// "Experimental Investigation of Collagen Waviness and Orientation in the Arterial Adventitia Using Confocal Laser Scanning Microscopy,"
// Biomechanics and Modeling in Mechanobiology, vol. 11, no. 3-4, pp. 461-473, 2012.
// Conditions of use: You'll be free to use this software for research purposes,
// but you should not redistribute it without our consent. In addition, we
// expect you to include a citation or acknowledgment whenever you present or
// publish results that are based on it.
//
// History:
// - Updated (Daniel Sage, 24 January 2011)
// - Added the Vector field (Daniel Sage, 1 March 2017)
//
//==============================================================================
package orientationj;
import java.awt.Color;
import ij.ImagePlus;
import ij.ImageStack;
import ij.process.ColorProcessor;
import imageware.ImageWare;
public class ColorMapping {
public static ImagePlus colorHSB(int n, String name, ImageWare hue, ImageWare sat, ImageWare bri) {
int nx = hue.getSizeX();
int ny = hue.getSizeY();
ImageStack stack = new ImageStack(nx, ny);
int size = nx*ny;
for(int k=0; k<n; k++) {
int[] pixels = new int[size];
float[] h = hue.getSliceFloat((k < hue.getSizeZ() ? k : 0));
float[] s = sat.getSliceFloat((k < sat.getSizeZ() ? k : 0));
float[] b = bri.getSliceFloat((k < bri.getSizeZ() ? k : 0));
for (int index=0; index<size; index++) {
pixels[index] = Color.HSBtoRGB(h[index], s[index], b[index]) + (0xFF << 24);
}
stack.addSlice("", new ColorProcessor(nx, ny, pixels));
}
ImagePlus imp = new ImagePlus(name, stack);
imp.show();
return imp;
}
public static ImagePlus colorRGB(int n, String name, ImageWare red, ImageWare green, ImageWare blue) {
int nx = red.getSizeX();
int ny = red.getSizeY();
ImageStack stack = new ImageStack(nx, ny);
int size = nx*ny;
for(int k=0; k<n; k++) {
int[] pixels = new int[size];
float[] r = red.getSliceFloat((k < red.getSizeZ() ? k : 0));
float[] g = green.getSliceFloat((k < green.getSizeZ() ? k : 0));
float[] b = blue.getSliceFloat((k < blue.getSizeZ() ? k : 0));
for (int index=0; index<size; index++) {
int ri = (int)(r[index]*255);
int gi = (int)(g[index]*255);
int bi = (int)(b[index]*255);
pixels[index] = (bi + (gi<<8) + (ri<<16) + (0xFF << 24));
}
stack.addSlice("", new ColorProcessor(nx, ny, pixels));
}
ImagePlus imp = new ImagePlus(name, stack);
imp.show();
return imp;
}
/*
private static void addBar(int bar, float[] r, float[] g, float[] b, int nx, int ny) {
float ratio = 1.0f/(ny/2);
int index;
int len = ny/4;
for(int j=len; j<3*len; j++) {
if (bar == 1) {
for(int i=0; i<5; i++) {
index = i+j*nx; r[index] = (j-len)*ratio; g[index] = 0; b[index] = 0;
}
for(int i=5; i<10; i++) {
index = i+j*nx; r[index] = 0; g[index] = (j-len)*ratio; b[index] = 0;
}
for(int i=10; i<15; i++) {
index = i+j*nx; r[index] = 0; g[index] = 0; b[index] = (j-len)*ratio;
}
}
else {
for(int i=nx-15; i<nx-10; i++) {
index = i+j*nx; r[index] = (j-len)*ratio; g[index] = 0; b[index] = 0;
}
for(int i=nx-10; i<nx-5; i++) {
index = i+j*nx; r[index] = 0; g[index] = (j-len)*ratio; b[index] = 0;
}
for(int i=nx-5; i<nx; i++) {
index = i+j*nx; r[index] = 0; g[index] = 0; b[index] = (j-len)*ratio;
}
}
}
}
*/
/*
private static void addRing(int bar, float[] h, float[] s, float[] b, int nx, int ny) {
if (nx < 16)
return;
if (ny < 16)
return;
int index;
int size = 16;
float norm = (float)Math.sqrt(2)*size;
for(int i=-size; i<=size; i++)
for(int j=-size; j<=size; j++) {
float rad = (float)Math.sqrt(i*i+j*j);
if (rad < size) {
rad /= norm;
float theta = (float)((Math.atan2(i, j)+Math.PI/2) / Math.PI);
if (bar == 1) {
index = (size+i+1) + nx*(j+ny/2-size);
h[index] = theta;
s[index] = rad;
b[index] = 1.0f;
index = (size+i+1) + nx*(j+ny/2+size);
h[index] = theta;
s[index] = 1.0f;
b[index] = rad;
}
else {
index = (nx-size-1+i) + nx*(j+ny/2-size);
h[index] = theta;
s[index] = rad;
b[index] = 1.0f;
index = (nx-size-1+i) + nx*(j+ny/2+size);
h[index] = theta;
s[index] = 1.0f;
b[index] = rad;
}
}
}
}
*/
}
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