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Merge pull request #216 from mianalysis/develop
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31 files changed

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‎mia-algorithms/pom.xml

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<parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>pom-mia</artifactId>
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<version>1.7.4</version>
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<version>1.7.5</version>
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</parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>mia-algorithms</artifactId>
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<version>1.7.4</version>
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<version>1.7.5</version>
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<packaging>jar</packaging>
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<name>mia-algorithms</name>
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<url>https://github.com/mianalysis/mia</url>

‎mia-algorithms/src/main/java/io/github/mianalysis/mia/process/houghtransform/accumulators/AbstractAccumulator.java

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return parameters;
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}
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public Indexer getIndexer() {
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return indexer;
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}
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// ABSTRACT METHODS
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‎mia-algorithms/src/main/java/io/github/mianalysis/mia/process/houghtransform/accumulators/LineAccumulator.java

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package io.github.mianalysis.mia.process.houghtransform.accumulators;
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import java.util.ArrayList;
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import ij.IJ;
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import ij.ImagePlus;
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import ij.gui.Line;
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import ij.gui.Overlay;
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import io.github.mianalysis.mia.process.voxel.MidpointCircle;
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public class LineAccumulator extends AbstractAccumulator {
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public LineAccumulator(int[][] parameters) {
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super(parameters);
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}
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@Override
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public void addDetectedObjectsOverlay(ImagePlus ipl, ArrayList<double[]> objects) {
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// Adding overlay showing detected circles
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Overlay overlay = ipl.getOverlay();
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if (overlay == null)
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overlay = new Overlay();
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for (int i = 0; i < objects.size(); i++) {
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double R = objects.get(i)[0];
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double thetaD = objects.get(i)[1];
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double thetaR = Math.toRadians(thetaD);
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int y0 = (int) Math.round(R / (Math.sin(thetaR)));
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int y1 = (int) Math.round((R - ipl.getWidth() * Math.cos(thetaR)) / (Math.sin(thetaR)));
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Line roi = new Line(0, y0, ipl.getWidth(), y1);
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overlay.add(roi);
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}
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ipl.setOverlay(overlay);
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}
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@Override
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public void addPoints(int[] indices, double value, int[][] points) {
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for (int i = 0; i < points.length; i++) {
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int iR = parameters[0][indices[0]] + points[i][0] - parameters[0][0];
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int iThetaD = parameters[1][indices[1]] + points[i][1] - parameters[1][0];
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int idx = indexer.getIndex(new int[] { iR, iThetaD });
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if (idx == -1)
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continue;
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// Adding the current value and incrementing the count
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accumulator[idx] = accumulator[idx] + value;
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counts[idx]++;
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}
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}
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@Override
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public ArrayList<double[]> getObjects(double minScore, int exclusionR) {
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// Creating an ArrayList to store the points
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ArrayList<double[]> objects = new ArrayList<>();
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// Getting relative coordinates for exclusion zone
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MidpointCircle midpointCircle = new MidpointCircle(exclusionR);
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int[] x = midpointCircle.getXCircleFill();
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int[] y = midpointCircle.getYCircleFill();
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// Identifying the brightest point in the accumulator
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int maxIdx = getLargestScorePixelIndex();
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if (maxIdx == -1)
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return objects;
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double maxVal = accumulator[maxIdx];
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// Extracting all points
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while (maxVal >= minScore) {
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addBrightestObject(maxIdx, maxVal, objects, x, y);
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// Updating the brightest point
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maxIdx = getLargestScorePixelIndex();
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if (maxIdx == -1)
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break;
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maxVal = accumulator[maxIdx];
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}
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return objects;
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}
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@Override
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public ArrayList<double[]> getNObjects(int nObjects, int exclusionR) {
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// Creating an ArrayList to store the points
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ArrayList<double[]> objects = new ArrayList<>();
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// Getting relative coordinates for exclusion zone
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MidpointCircle midpointCircle = new MidpointCircle(exclusionR);
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int[] x = midpointCircle.getXCircleFill();
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int[] y = midpointCircle.getYCircleFill();
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// Extracting all points
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for (int count = 0; count < nObjects; count++) {
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// Identifying the brightest point in the accumulator
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int maxIdx = getLargestScorePixelIndex();
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if (maxIdx == -1)
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return objects;
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double maxVal = accumulator[maxIdx];
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addBrightestObject(maxIdx, maxVal, objects, x, y);
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}
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return objects;
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}
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void addBrightestObject(int maxIdx, double maxVal, ArrayList<double[]> objects, int[] x, int[] y) {
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// Getting parameters for brightest current spot and adding to ArrayList
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int[] currIndices = indexer.getCoord(maxIdx);
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int RR = parameters[0][currIndices[0]];
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int thetaTheta = parameters[1][currIndices[1]];
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objects.add(new double[] { RR, thetaTheta, maxVal });
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// Setting all pixels within exclusion radius to zero. This is repeated for all
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// slices.
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for (int i = 0; i < x.length; i++) {
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int iR = RR + x[i] - parameters[0][0];
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int iTheta = thetaTheta + y[i] - parameters[1][0];
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int idx = indexer.getIndex(new int[] { iR, iTheta });
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if (idx == -1)
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continue;
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accumulator[idx] = 0;
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}
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}
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@Override
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public ImagePlus getAccumulatorAsImage() {
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int[] dim = indexer.getDim();
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ImagePlus ipl = IJ.createHyperStack("Line_Accumulator", dim[0], dim[1], 1, 1, 1, 32);
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for (int idx = 0; idx < indexer.getLength(); idx++) {
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int[] coord = indexer.getCoord(idx);
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double value = accumulator[idx];
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ipl.getProcessor().putPixelValue(coord[0], coord[1], value);
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}
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return ipl;
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}
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/**
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* Returns the Indexer index for the pixel in the Accumulator with the largest
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* score.
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*
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* @return
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*/
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public int getLargestScorePixelIndex() {
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double maxVal = Double.MIN_VALUE;
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int maxIdx = -1;
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// Iterating over all pixels in the Accumulator. Identifying the brightest.
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for (int i = 0; i < accumulator.length; i++) {
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if (accumulator[i] > maxVal) {
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maxVal = accumulator[i];
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maxIdx = i;
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}
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}
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return maxIdx;
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}
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}

‎mia-algorithms/src/main/java/io/github/mianalysis/mia/process/houghtransform/pixelarrays/PixelArray.java

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public double getPixelValue(int[] coord) {
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int idx = getIndex(coord);
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return getPixelValue(idx);
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}

‎mia-algorithms/src/main/java/io/github/mianalysis/mia/process/houghtransform/transforms/LineTransform.java

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package io.github.mianalysis.mia.process.houghtransform.transforms;
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import ij.gui.Plot;
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import ij.process.ImageProcessor;
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import io.github.mianalysis.mia.process.houghtransform.accumulators.LineAccumulator;
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import io.github.mianalysis.mia.process.string.CommaSeparatedStringInterpreter;
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import io.github.mianalysis.mia.process.voxel.BresenhamLine;
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/**
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* Created by sc13967 on 05/02/2025.
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*/
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public class LineTransform extends AbstractTransform {
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protected int width = 0;
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protected int height = 0;
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public LineTransform(ImageProcessor ipr, String[] parameterRanges) {
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super(ipr);
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String rRange = CommaSeparatedStringInterpreter.removeInterval(parameterRanges[0]);
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String thetaRange = CommaSeparatedStringInterpreter.removeInterval(parameterRanges[1]);
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int[][] parameters = new int[parameterRanges.length][];
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parameters[0] = CommaSeparatedStringInterpreter.interpretIntegers(rRange, true,
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(int) Math.ceil(Math.sqrt(ipr.getWidth() * ipr.getWidth() + ipr.getHeight() * ipr.getHeight())));
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parameters[1] = CommaSeparatedStringInterpreter.interpretIntegers(thetaRange, true, 179);
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this.accumulator = new LineAccumulator(parameters);
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this.width = ipr.getWidth();
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this.height = ipr.getHeight();
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}
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@Override
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public void run() {
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int[][] parameters = accumulator.getParameters();
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// Setting up the threading system
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// ThreadPoolExecutor pool = new ThreadPoolExecutor(nThreads, nThreads, 0L,
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// TimeUnit.MILLISECONDS,
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// new LinkedBlockingQueue<>());
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// Iterating over all widths, heights and orientations
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int nR = parameters[0].length;
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int nTheta = parameters[1].length;
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// Iterating over R and theta
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for (int iR = 0; iR < nR; iR++) {
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// int finalIR = iR;
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// Runnable task = () -> {
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for (int iTheta = 0; iTheta < nTheta; iTheta++) {
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// Getting current XY values
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int R = parameters[0][iR];
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int thetaD = parameters[1][iTheta];
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// 180 degs causes the system to crash
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if (thetaD == 180)
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continue;
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double thetaR = Math.toRadians(thetaD);
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// Generating coordinates for the points on the line
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int y0 = (int) Math.round(R / (Math.sin(thetaR)));
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int y1 = (int) Math.round((R - (width-1) * Math.cos(thetaR)) / (Math.sin(thetaR)));
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int[][] line = BresenhamLine.getLine(0, width-1, y0, y1);
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// double[] xx = new double[line.length];
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// double[] yy = new double[line.length];
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// int i=0;
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for (int[] point : line) {
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// xx[i] = point[0];
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// yy[i] = point[1];
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if (point[1] >= 0 && point[1] < height) {
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// xx[i] = point[0];
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// yy[i] = point[1];
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double value = pixels.getPixelValue(point);
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accumulator.addPoints(new int[] { iR, iTheta }, value, new int[][]{new int[]{0,0}});
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}
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// i++;
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}
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// Plot pl = new Plot("T", "", "");
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// pl.setLimits(0, 512, 0, 512);
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// pl.add("Line", xx, yy);
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// pl.show();
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}
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}
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// pool.shutdown();
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// try {
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// pool.awaitTermination(Integer.MAX_VALUE, TimeUnit.DAYS); // i.e. never
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// terminate early
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// } catch (InterruptedException e) {
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// e.printStackTrace();
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// }
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}
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}

‎mia-algorithms/src/main/java/io/github/mianalysis/mia/process/string/CommaSeparatedStringInterpreter.java

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public static String removeInterval(String range) {
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// Removes anything after a potential second hyphen
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Pattern pattern = Pattern.compile("-");
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Matcher matcher = pattern.matcher(range);
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Matcher matcher = pattern.matcher(range.substring(1));
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int count = 0;
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while (matcher.find())
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if (count++ > 0)
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return range.substring(0, matcher.start());
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return range.substring(0, matcher.start()+1);
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return range;
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‎mia-bonej/pom.xml

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<parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>pom-mia</artifactId>
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<version>1.7.4</version>
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<version>1.7.5</version>
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</parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>mia-bonej</artifactId>
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<version>1.7.4</version>
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<version>1.7.5</version>
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<packaging>jar</packaging>
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<name>mia-bonej</name>
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<url>https://github.com/mianalysis/mia</url>

‎mia-coordinates/pom.xml

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<parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>pom-mia</artifactId>
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<version>1.7.4</version>
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<version>1.7.5</version>
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</parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>mia-coordinates</artifactId>
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<version>1.7.4</version>
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<version>1.7.5</version>
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<packaging>jar</packaging>
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<name>mia-coordinates</name>
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<url>https://github.com/mianalysis/mia</url>

‎mia-core/pom.xml

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<parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>pom-mia</artifactId>
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<version>1.7.4</version>
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<version>1.7.5</version>
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</parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>mia-core</artifactId>
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<version>1.7.4</version>
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<version>1.7.5</version>
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<packaging>jar</packaging>
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<name>mia-core</name>
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<url>https://github.com/mianalysis/mia</url>

‎mia-core/src/main/java/io/github/mianalysis/mia/module/objects/detect/extensions/ManualExtension.java

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public abstract Status initialiseAfterImageShown(@Nullable ImagePlus displayIpl);
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public abstract Status onFinishAddingObjects();
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protected abstract Parameters initialiseParameters();
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public abstract Parameters updateAndGetParameters();

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