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OrientationJ/src/riesz/RieszTransform.java
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RieszTransform.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 riesz;
import fft.ComplexSignal;
import ij.IJ;
import imageware.Builder;
import imageware.ImageWare;
public class RieszTransform {
private int nx;
private int ny;
private RieszFilter filter;
public RieszTransform(int nx, int ny, int order, boolean cancelDC) {
this.nx = nx;
this.ny = ny;
filter = new RieszFilter(nx, ny, order, cancelDC);
}
/**
*/
public ImageWare[] analysis(ImageWare image) {
int N = filter.getChannels();
double[] in = (image.convert(ImageWare.DOUBLE)).getSliceDouble(0);
ComplexSignal sin = new ComplexSignal(in, nx, ny);
ComplexSignal fin = fft.FFT2D.transform(sin);
ImageWare channelsReal[] = new ImageWare[N];
for(int k=0; k<N; k++) {
channelsReal[k] = Builder.create(nx, ny, 1, ImageWare.DOUBLE);
ComplexSignal fcurr = filter.getAnalysis(k);
ComplexSignal fg = ComplexSignal.multiply(fin, fcurr);
ComplexSignal g = fft.FFT2D.inverse(fg);
storeReal(g, channelsReal[k]);
}
return channelsReal;
}
/**
*/
public ImageWare synthesis(ImageWare channels[]) {
int N = filter.getChannels();
if (N != channels.length) {
IJ.error("Not compatible stack of images for inverting Riesz Transform");
return null;
}
ComplexSignal csum = new ComplexSignal(nx, ny);
for(int k=0; k<N; k++) {
ComplexSignal fc = new ComplexSignal(channels[k].getSliceDouble(0), nx, ny);
ComplexSignal fg = fft.FFT2D.transform(fc);
ComplexSignal fi = ComplexSignal.multiply(fg, filter.getSynthesis(k));
for(int i=0; i<nx*ny; i++) {
csum.real[i] += fi.real[i];
csum.imag[i] += fi.imag[i];
}
}
ComplexSignal rsum = fft.FFT2D.inverse(csum);
ImageWare out = Builder.create(nx, ny, 1, ImageWare.DOUBLE);
storeReal(rsum, out);
return out;
}
/**
*/
public RieszFilter getFilters() {
return filter;
}
/**
*/
private void storeReal(ComplexSignal signal, ImageWare channel) {
int nx = channel.getWidth();
int ny = channel.getHeight();
double data[] = channel.getSliceDouble(0);
System.arraycopy(signal.real, 0, data, 0, nx*ny);
}
}
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