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OrientationJ/src/OrientationJ_Distribution.java
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OrientationJ_Distribution.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 ij.Macro;
import ij.plugin.PlugIn;
import imageware.ImageWare;
import orientation.GroupImage;
import orientation.OrientationParameters;
import orientation.OrientationProcess;
import orientation.OrientationService;
import orientationj.AnalysisDialog;
public class OrientationJ_Distribution implements PlugIn {
public static void main(String arg[]) {
new OrientationJ_Test_Image().run("");
new OrientationJ_Distribution().run("");
}
public void run(String arg) {
if (Macro.getOptions() == null) {
AnalysisDialog orientation = new AnalysisDialog(OrientationService.DISTRIBUTION);
orientation.showDialog();
}
else {
OrientationParameters params = new OrientationParameters(OrientationService.DISTRIBUTION);
params.getMacroParameters(Macro.getOptions());
ImageWare source = GroupImage.getCurrentImage();
if (source == null) {
return;
}
OrientationProcess process = new OrientationProcess(source, params);
process.run();
process.show(1);
float[] histo = process.distribution();
process.showDistribution(1, histo);
process.saveDistribution(params, histo);
}
}
}
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