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IJ-OpenCV plugins
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‎Plugins/IJ-OpenCV.zip‎

18.9 MB
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‎Plugins/src/Adaptive_ThresholdJ_.java‎

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import ij.IJ;
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import ij.ImagePlus;
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import ij.gui.GenericDialog;
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import ij.plugin.PlugIn;
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import ijopencv.ImageConverter;
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import org.bytedeco.javacpp.opencv_core;
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import static org.bytedeco.javacpp.opencv_imgproc.ADAPTIVE_THRESH_GAUSSIAN_C;
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import static org.bytedeco.javacpp.opencv_imgproc.ADAPTIVE_THRESH_MEAN_C;
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import static org.bytedeco.javacpp.opencv_imgproc.THRESH_BINARY;
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import static org.bytedeco.javacpp.opencv_imgproc.THRESH_BINARY_INV;
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import static org.bytedeco.javacpp.opencv_imgproc.adaptiveThreshold;
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/*
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* To change this license header, choose License Headers in Project Properties.
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* To change this template file, choose Tools | Templates
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* and open the template in the editor.
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*/
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/**
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*
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* @author jonathan
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*/
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public class Adaptive_ThresholdJ_ implements PlugIn {
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String method;
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String thresholdmethod;
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int maxValue=255;
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int blockSize=3;
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@Override
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public void run(String arg) {
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ImagePlus imp = IJ.getImage();
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// Converter
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ImageConverter ic = new ImageConverter();
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opencv_core.Mat m = ic.convertTo(imp);
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// opencv_imgproc.cvtColor(m, m, opencv_imgproc.COLOR_BGR2GRAY);
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opencv_core.Mat res = new opencv_core.Mat();
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if (!showDialog()) {
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return;
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}
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int adaptiveMethod;
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if(method=="Mean"){
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adaptiveMethod = ADAPTIVE_THRESH_MEAN_C;
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}else{
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adaptiveMethod = ADAPTIVE_THRESH_GAUSSIAN_C;
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}
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int thresType;
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if(thresholdmethod=="Binary"){
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thresType = THRESH_BINARY;
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}else{
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thresType = THRESH_BINARY_INV;
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}
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adaptiveThreshold(m, res, maxValue, adaptiveMethod, thresType, blockSize, 2);
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ImagePlus imp2 = ic.convertFrom(res);
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imp2.show();
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}
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private boolean showDialog() {
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GenericDialog gd = new GenericDialog("Adaptive Threshold");
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String[] items = {"Mean","Gaussian"};
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String[] itemsThreshold = {"Binary","Binary Inv"};
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gd.addChoice("Method", items, items[0]);
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gd.addChoice("Threshold Type", itemsThreshold, itemsThreshold[0]);
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gd.addNumericField("Max Value", maxValue, 0);
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gd.addNumericField("Block size", blockSize, 0);
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//gd.addNumericField("Gaussian Kernel width:", gaussianKernelWidth, 0);
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gd.showDialog();
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if (gd.wasCanceled()) {
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return false;
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}
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method = gd.getNextChoice();
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thresholdmethod = gd.getNextChoice();
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maxValue = (int) gd.getNextNumber();
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blockSize = (int) gd.getNextNumber();
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return true;
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}
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}

‎Plugins/src/BGR_Histogram_ComparisonJ_.java‎

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import ij.IJ;
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import ij.ImagePlus;
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import ij.gui.GenericDialog;
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import ij.plugin.PlugIn;
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import ij.text.TextWindow;
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import ijopencv.ImageStackConverter;
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import java.util.ArrayList;
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import org.bytedeco.javacpp.FloatPointer;
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import org.bytedeco.javacpp.IntPointer;
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import org.bytedeco.javacpp.PointerPointer;
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import org.bytedeco.javacpp.opencv_core;
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import org.bytedeco.javacpp.opencv_imgproc;
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import static org.bytedeco.javacpp.opencv_imgproc.calcHist;
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/*
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* To change this license header, choose License Headers in Project Properties.
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* To change this template file, choose Tools | Templates
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* and open the template in the editor.
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*/
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/**
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*
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* @author jonathan
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*/
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public class BGR_Histogram_ComparisonJ_ implements PlugIn {
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int blueBins = 8;
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int greenBins = 8;
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int redBins = 8;
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@Override
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public void run(String arg) {
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ImagePlus imp = IJ.getImage();
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int stacksize = imp.getStack().getSize();
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if (imp.getStack().getSize() == 1) {
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IJ.error("You need a stack of images");
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return;
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}
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// Converter
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ImageStackConverter isc = new ImageStackConverter();
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opencv_core.MatVector mvec = isc.convertTo(imp);
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if (!showDialog()) {
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return;
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}
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double[][] comparison = new double[4][stacksize * (stacksize - 1) / 2];
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opencv_core.Mat mask = new opencv_core.Mat();
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IntPointer intPtrChannels = new IntPointer(0, 1, 2);
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IntPointer intPtrHistSize = new IntPointer(blueBins, greenBins, redBins);
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FloatPointer fltPtrRanges = new FloatPointer(0.0f, 255.0f, 0.0f, 255.0f, 0.0f, 255.0f);
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PointerPointer ptptranges = new PointerPointer(fltPtrRanges, fltPtrRanges, fltPtrRanges);
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opencv_core.Mat hist1 = new opencv_core.Mat();
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opencv_core.Mat hist2 = new opencv_core.Mat();
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int n = 0;
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for (int i = 0; i < mvec.size() - 1; i++) {
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calcHist(mvec.get(i), 1, intPtrChannels, mask, hist1, 3, intPtrHistSize, ptptranges, true, false);
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opencv_core.normalize(hist1, hist1);
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for (int j = i + 1; j < mvec.size(); j++) {
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calcHist(mvec.get(j), 1, intPtrChannels, mask, hist2, 3, intPtrHistSize, ptptranges, true, false);
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opencv_core.normalize(hist2, hist2);
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comparison[0][n] = opencv_imgproc.compareHist(hist1, hist2, opencv_imgproc.CV_COMP_CORREL);
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comparison[1][n] = opencv_imgproc.compareHist(hist1, hist2, opencv_imgproc.CV_COMP_CHISQR);
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comparison[2][n] = opencv_imgproc.compareHist(hist1, hist2, opencv_imgproc.CV_COMP_INTERSECT);
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comparison[3][n] = opencv_imgproc.compareHist(hist1, hist2, opencv_imgproc.CV_COMP_BHATTACHARYYA);
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n++;
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}
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}
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String headings = "Method\t";
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for (int i = 0; i < mvec.size() - 1; i++) {
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for (int j = i + 1; j < mvec.size(); j++) {
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headings = headings + (i + 1) + "-" + (j + 1) + "\t";
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}
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}
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headings = headings.substring(0, headings.lastIndexOf("\t"));
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ArrayList list = new ArrayList();
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String row1 = "Correlation\t";
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String row2 = "CHI Square\t";
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String row3 = "Intersection\t";
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String row4 = "BHATTACHARYYA\t";
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for (int i = 0; i < comparison[0].length - 1; i++) {
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row1 = row1 + comparison[0][i] + "\t";
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row2 = row2 + comparison[1][i] + "\t";
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row3 = row3 + comparison[2][i] + "\t";
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row4 = row4 + comparison[3][i] + "\t";
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}
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row1 = row1 + comparison[0][comparison[0].length - 1] ;
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row2 = row2 + comparison[1][comparison[0].length - 1];
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row3 = row3 + comparison[2][comparison[0].length - 1];
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row4 = row4 + comparison[3][comparison[0].length - 1];
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list.add(row1);
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list.add(row2);
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list.add(row3);
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list.add(row4);
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TextWindow textWindow = new TextWindow("Similarity Table", headings, list, 600, 400);
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textWindow.setVisible(true);
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}
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private boolean showDialog() {
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GenericDialog gd = new GenericDialog("BGR Histogram Comparison");
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gd.addNumericField("Blue bins", blueBins, 0);
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gd.addNumericField("Green bins", greenBins, 0);
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gd.addNumericField("Red bins", redBins, 0);
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//gd.addNumericField("Gaussian Kernel width:", gaussianKernelWidth, 0);
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gd.showDialog();
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if (gd.wasCanceled()) {
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return false;
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}
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blueBins = (int) gd.getNextNumber();
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if (blueBins < 1) {
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blueBins = 1;
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}
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if (blueBins > 255) {
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blueBins = 255;
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}
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greenBins = (int) gd.getNextNumber();
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if (greenBins < 1) {
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greenBins = 1;
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}
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if (greenBins > 255) {
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greenBins = 255;
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}
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redBins = (int) gd.getNextNumber();
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if (redBins < 1) {
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redBins = 1;
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}
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if (redBins > 255) {
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redBins = 255;
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}
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return true;
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}
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}

‎Plugins/src/BlackHatJ_.java‎

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/*
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* To change this license header, choose License Headers in Project Properties.
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* To change this template file, choose Tools | Templates
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* and open the template in the editor.
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*/
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import ij.IJ;
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import ij.ImagePlus;
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import ij.Prefs;
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import ij.gui.GenericDialog;
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import ij.gui.PointRoi;
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import ij.plugin.PlugIn;
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import static ij.plugin.Thresholder.backgrounds;
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import static ij.plugin.Thresholder.methods;
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import ij.process.AutoThresholder;
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import ijopencv.ImageConverter;
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import ijopencv.KeyPointsConverter;
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import java.awt.Choice;
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import java.awt.event.ItemEvent;
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import java.awt.event.ItemListener;
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import java.util.Vector;
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import org.bytedeco.javacpp.opencv_core;
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import org.bytedeco.javacpp.opencv_core.KeyPointVector;
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import org.bytedeco.javacpp.opencv_core.Mat;
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import org.bytedeco.javacpp.opencv_features2d;
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import static org.bytedeco.javacpp.opencv_features2d.AGAST;
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import static org.bytedeco.javacpp.opencv_features2d.AGAST;
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import static org.bytedeco.javacpp.opencv_features2d.AGAST;
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import org.bytedeco.javacpp.opencv_features2d.Feature2D;
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import org.bytedeco.javacpp.opencv_features2d.KAZE;
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import org.bytedeco.javacpp.opencv_imgproc;
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import static org.bytedeco.javacpp.opencv_imgproc.MORPH_BLACKHAT;
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import static org.bytedeco.javacpp.opencv_imgproc.MORPH_RECT;
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import static org.bytedeco.javacpp.opencv_imgproc.getStructuringElement;
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import static org.bytedeco.javacpp.opencv_imgproc.morphologyEx;
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import org.bytedeco.javacpp.opencv_xfeatures2d;
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/**
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*
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* @author jonathan
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*/
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public class BlackHatJ_ implements PlugIn {
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int xSize, ySize;
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@Override
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public void run(String arg) {
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ImagePlus imp = IJ.getImage();
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// Converter
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ImageConverter ic = new ImageConverter();
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opencv_core.Mat m = ic.convertTo(imp);
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opencv_imgproc.cvtColor(m, m, opencv_imgproc.COLOR_BGR2GRAY);
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Mat res = new opencv_core.Mat();
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if (!showDialog()) {
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return;
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}
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Mat element = getStructuringElement(MORPH_RECT, new opencv_core.Size(xSize, ySize));
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morphologyEx(m, res, MORPH_BLACKHAT, element);
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ImagePlus imp2 = ic.convertFrom(res);
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imp2.show();
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}
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private boolean showDialog() {
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GenericDialog gd = new GenericDialog("Black Hat Kernel");
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gd.addNumericField("X size", xSize, 1);
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gd.addNumericField("Y size", ySize, 1);
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//gd.addNumericField("Gaussian Kernel width:", gaussianKernelWidth, 0);
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gd.showDialog();
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if (gd.wasCanceled()) {
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return false;
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}
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xSize = (int) gd.getNextNumber();
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if (xSize < 1) {
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xSize = 1;
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}
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ySize = (int) gd.getNextNumber();
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if (ySize < 1) {
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ySize = 1;
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}
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return true;
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}
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}

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