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OrientationJ/src/OrientationJ_Dominant_Direction.java
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OrientationJ_Dominant_Direction.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)
//
//==============================================================================
import java.awt.Dimension;
import java.text.DecimalFormat;
import additionaluserinterface.NumericTable;
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.WindowManager;
import ij.measure.ResultsTable;
import ij.plugin.PlugIn;
import ij.process.ImageProcessor;
import imageware.Builder;
import imageware.ImageWare;
public class OrientationJ_Dominant_Direction implements PlugIn {
public static void main(String arg[]) {
new OrientationJ_Test_Image().run("");
new OrientationJ_Dominant_Direction().run("");
}
public void run(String arg) {
if (IJ.versionLessThan("1.21a")) {
return;
}
ImagePlus imp = WindowManager.getCurrentImage();
if (imp == null) {
IJ.error("No open image.");
return;
}
if (imp.getType() != ImagePlus.GRAY8 && imp.getType() != ImagePlus.GRAY16 && imp.getType() != ImagePlus.GRAY32) {
IJ.error("Only processed 8-bits, 16-bits, or 32 bits images.");
return;
}
ImageStack stack = imp.getStack();
int nt = stack.getSize();
IJ.log("Frame, Orientation [Degrees], Coherency [%]");
String formats[] = {"#0.00", "#0.0000", "#0.00000"};
double data[][] = new double[nt][3];
ResultsTable table = new ResultsTable();
for (int i=1; i<=nt; i++) {
imp.setSlice(i);
ImageProcessor ip = imp.getProcessor().crop();
ip.crop();
ImageWare input = Builder.create(new ImagePlus("", ip), ImageWare.DOUBLE);
double res[] = compute(input);
data[i-1][0] = i;
data[i-1][1] = res[0];
data[i-1][2] = res[1];
String s1 = (new DecimalFormat(formats[0])).format(i);
String s2 = (new DecimalFormat(formats[1])).format(res[0]);
String s3 = (new DecimalFormat(formats[2])).format(res[1]);
IJ.log(s1 + ", " + s2 + ", " + s3);
table.incrementCounter();
table.addValue("Frame", imp.getStack().getSliceLabel(i));
table.addValue("Orientation [Degrees]", s2);
table.addValue("Coherency [%]", s3);
}
table.show("Results Orientation");
}
/**
*/
public double[] compute(ImageWare image) {
int nx = image.getWidth();
int ny = image.getHeight();
double[] in = image.getSliceDouble(0);
double dy = 0;
double dx = 0;
double vxy = 0;
double vxx = 0;
double vyy = 0;
int k;
int area = (nx-2)*(ny-2);
for(int y=1; y<ny-1; y++)
for(int x=1; x<nx-1; x++) {
k = x+y*nx;
dx = in[k-1] - in[k+1];
dy = in[k-nx] - in[k+nx];
vxx += dx * dx;
vyy += dy * dy;
vxy += dx * dy;
}
vxy /= area;
vxx /= area;
vyy /= area;
double orientation = Math.toDegrees(0.5*Math.atan2(2.0*vxy, vyy-vxx));
double d = vyy - vxx;
double coherency = 0.0;
if (vxx+vyy > 1) {
coherency = Math.sqrt(d*d + vxy*vxy*4.0)/(vxx+vyy);
}
return new double[] {orientation, coherency};
}
}
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