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OrientationJ/src/orientation/OrientationProcess.java
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OrientationProcess.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 orientation;
import java.awt.Color;
import java.io.File;
import java.io.FileWriter;
import java.util.Vector;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import additionaluserinterface.WalkBar;
import ij.IJ;
import ij.ImagePlus;
import ij.gui.Plot;
import ij.measure.ResultsTable;
import imageware.FMath;
import imageware.ImageWare;
public class OrientationProcess extends Thread {
private GroupImage gim;
private OrientationParameters params;
private WalkBar walk;
private ImageWare source;
public OrientationProcess(ImageWare source, OrientationParameters params) {
this.walk = new WalkBar("", false, false, false, 100);
this.source = source;
this.params = params;
}
public OrientationProcess(WalkBar walk, ImageWare source, OrientationParameters params) {
this.walk = walk;
this.source = source;
this.params = params;
}
public OrientationProcess(GroupImage gim, OrientationParameters params) {
this.walk = new WalkBar();
this.source = gim.source;
this.gim = gim;
this.params = params;
}
public GroupImage getGroupImage() {
return gim;
}
public void run() {
walk.reset();
gim = new GroupImage(walk, source, params);
if (params.gradient == OrientationParameters.HESSIAN)
new Hessian(walk, gim, params).run();
else
new Gradient(walk, gim, params).run();
StructureTensor st = new StructureTensor(walk, gim, params);
ExecutorService executor = Executors.newFixedThreadPool(1);
executor.execute(st);
executor.shutdown();
while (!executor.isTerminated()) {}
walk.finish();
}
/**
*/
public double[][] distribution() {
double cohmin = params.minCoherency / 100.0;
double enemin = params.minEnergy / 100.0;
gim.selectedOrientation = gim.orientation.replicate();
gim.selectedOrientation.fillConstant(-1.0);
gim.selectedMask = gim.coherency.replicate();
gim.selectedEnergy = gim.energy.duplicate();
gim.selectedEnergy.rescale(0, 1);
int nz = gim.coherency.getSizeZ();
double histo[][] = new double[nz][180];
double angles[][] = new double[nz][180];
for(int z=0; z<nz; z++)
for(int a=0; a<180; a++)
angles[z][a] = a-90;
int nx = gim.nx;
int ny = gim.ny;
double r = 180.0/Math.PI;
for(int z=0; z<nz; z++)
for(int x=0; x<nx; x++)
for(int y=0; y<ny; y++) {
double coh = gim.coherency.getPixel(x, y, z);
if (cohmin <= coh) {
double ene = gim.selectedEnergy.getPixel(x, y, z);
if (enemin <= ene) {
double ori = 90.0 + gim.orientation.getPixel(x, y, z) * r;
gim.selectedOrientation.putPixel(x, y, z, ori);
gim.selectedMask.putPixel(x, y, z, 1.0);
int a = FMath.floor(ori);
double da = ori-a;
int a1 = a;
a1 = (a1 < 0 ? 180+a1 : (a1 >= 180 ? a1-180 : a1));
histo[z][a1] += (1f - da) * coh;
int a2 = a+1;
a2 = (a2+1 < 0 ? 180+a2 : (a2 >= 180 ? a2-180 : a2));
histo[z][a2] += da * coh;
}
}
}
return histo;
}
public void saveDistribution(OrientationParameters params, double[][] histo) {
if (params.pathSaveDistribution != "") {
IJ.log("Saved the distribution in the file: " + params.pathSaveDistribution);
File file = new File(params.pathSaveDistribution);
try {
FileWriter fw = new FileWriter(file);
for(int a=0; a<180; a++) {
fw.write("" + (a-90) + "\t" + (histo[0][a]) + "\n");
}
fw.close();
}
catch (Exception ex) {
IJ.log("Error to write into the file: " + params.pathSaveDistribution);
}
}
}
public Vector<ImagePlus> show(int countRun) {
Vector<ImagePlus> list = new Vector<ImagePlus>();
int feature = OrientationParameters.GRADIENT_VERTICAL;
feature = OrientationParameters.GRADIENT_HORIZONTAL;
if (params.view[feature]) {
if (params.isServiceAnalysis()) {
ImagePlus imp = gim.showFeature(OrientationParameters.name[feature], countRun, !params.radian[feature], params);
if (imp != null)
list.add(imp);
}
}
feature = OrientationParameters.GRADIENT_VERTICAL;
if (params.view[feature]) {
if (params.isServiceAnalysis()) {
ImagePlus imp = gim.showFeature(OrientationParameters.name[feature], countRun, !params.radian[feature], params);
if (imp != null)
list.add(imp);
}
}
feature = OrientationParameters.TENSOR_ENERGY;
if (params.view[feature]) {
ImagePlus imp = gim.showFeature(OrientationParameters.name[feature], countRun, !params.radian[feature], params);
if (imp != null)
list.add(imp);
}
feature = OrientationParameters.TENSOR_ORIENTATION;
if (params.view[feature]) {
ImagePlus imp = gim.showFeature(OrientationParameters.name[feature], countRun, !params.radian[feature], params);
if (imp != null)
list.add(imp);
}
feature = OrientationParameters.TENSOR_COHERENCY;
if (params.view[feature]) {
ImagePlus imp = gim.showFeature(OrientationParameters.name[feature], countRun, !params.radian[feature], params);
if (imp != null)
list.add(imp);
}
feature = OrientationParameters.HARRIS;
if (params.view[feature]) {
if (params.isServiceHarris()) {
ImagePlus imp = gim.showFeature(OrientationParameters.name[feature], countRun, !params.radian[feature], params);
if (imp != null)
list.add(imp);
}
}
feature = OrientationParameters.SURVEY;
if (params.view[feature]) {
if (!params.isServiceHarris()) {
ImagePlus imp = gim.showFeature(OrientationParameters.name[feature], countRun, !params.radian[feature], params);
if (imp != null)
list.add(imp);
}
}
return list;
}
public Vector<ImagePlus> showDistribution(int countRun, double histo[][]) {
Vector<ImagePlus> list = new Vector<ImagePlus>();
int feature = 0;
feature = OrientationParameters.DIST_MASK;
if (params.view[feature]) {
ImagePlus imp = gim.showFeature(OrientationParameters.name[feature], countRun, !params.radian[feature], params);
if (imp != null)
list.add(imp);
}
feature = OrientationParameters.DIST_ORIENTATION;
if (params.view[feature]) {
ImagePlus imp = gim.showFeature(OrientationParameters.name[feature], countRun, !params.radian[feature], params);
if (imp != null)
list.add(imp);
}
feature = OrientationParameters.DIST_COLOR;
if (params.view[feature]) {
ImagePlus imp = gim.showFeature(OrientationParameters.name[feature], countRun, !params.radian[feature], params);
if (imp != null)
list.add(imp);
}
feature = OrientationParameters.DIST_HISTO;
if (params.view[feature]) {
ImagePlus imp = plotDistribution(countRun, histo);
if (imp != null)
list.add(imp);
}
return list;
}
public ImagePlus plotDistribution(int countRun, double histo[][]) {
int nz = histo.length;
double max = -Double.MIN_VALUE;
for(int a=0; a<180; a++)
for(int z=0; z<nz; z++) {
if (histo[z][a] > max)
max = histo[z][a];
}
double angles[] = new double[180];
for(int a=0; a<180; a++)
angles[a] = a-90;
String title = OrientationParameters.name[OrientationParameters.DIST_HISTO] + "-" + countRun;
Plot plot = new Plot(title, "Orientation in Degrees", "Distribution of orientation");
for(int z=0; z<nz; z++) {
plot.setColor(Color.getHSBColor(((float)z)/nz, 1, 1));
plot.add("Line", angles, histo[z]);
}
plot.setColor(Color.red);
plot.setLineWidth(1);
plot.setLimits(-90, 90, 0, max);
plot.show();
ResultsTable rt = new ResultsTable();
for(int a=0; a<180; a++) {
rt.incrementCounter();
rt.addValue("Angle", angles[a]);
for(int z=0; z<nz; z++)
rt.addValue("Frame " + (z+1), histo[z][a]);
}
rt.show(title);
return plot.getImagePlus();
}
}
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