Bugfix and GUI refactoring

Author: ppouchin

src/main/java/fr/igred/nucleus/autocrop/AutoCrop.java

@@ -59,6 +59,7 @@
 import java.util.TreeMap;
 import java.util.concurrent.ExecutionException;
 
+import static fr.igred.nucleus.utils.Thresholding.binarize;
 import static fr.igred.nucleus.utils.Thresholding.contrastAnd8bits;
 
 
@@ -270,7 +271,7 @@ public void thresholdKernels(String typeThresholding) {
 			}
 		}
 		this.otsuThreshold = thresh;
-		this.imageSeg = generateSegmentedImage(imageSeg, thresh);
+		binarize(imageSeg, thresh);
 	}
 
 
@@ -566,34 +567,6 @@ public List<String> getFileCoordinates() {
 	}
 
 
-	/**
-	 * Create binary image with the threshold value gave in input
-	 *
-	 * @param imagePlusInput ImagePlus raw image to binarize
-	 * @param threshold      integer threshold value
-	 *
-	 * @return The segmented binary image.
-	 */
-	private static ImagePlus generateSegmentedImage(ImagePlus imagePlusInput, int threshold) {
-		ImageStack imageStackInput     = imagePlusInput.getStack();
-		ImagePlus  imagePlusSegmented  = imagePlusInput.duplicate();
-		ImageStack imageStackSegmented = imagePlusSegmented.getStack();
-		for (int k = 0; k < imagePlusInput.getStackSize(); ++k) {
-			for (int i = 0; i < imagePlusInput.getWidth(); ++i) {
-				for (int j = 0; j < imagePlusInput.getHeight(); ++j) {
-					double voxelValue = imageStackInput.getVoxel(i, j, k);
-					if (voxelValue >= threshold) {
-						imageStackSegmented.setVoxel(i, j, k, 255);
-					} else {
-						imageStackSegmented.setVoxel(i, j, k, 0);
-					}
-				}
-			}
-		}
-		return imagePlusSegmented;
-	}
-	
-	
 	/**
 	 * Crop of the bounding box on 3D image. The coordinates are inputs of this methods
 	 *

src/main/java/fr/igred/nucleus/autocrop/Box.java

@@ -49,8 +49,7 @@ public class Box {
 	 * @param zMin: coordinate z min of the Box
 	 * @param zMax: coordinate z max of the Box
 	 */
-	public Box(short xMin, short xMax, short yMin, short yMax, short zMin,
-	           short zMax) {
+	public Box(short xMin, short xMax, short yMin, short yMax, short zMin, short zMax) {
 		this.xMin = xMin;
 		this.xMax = xMax;
 		this.yMin = yMin;

src/main/java/fr/igred/nucleus/autocrop/RectangleIntersection.java

@@ -70,7 +70,7 @@ public class RectangleIntersection {
 	 * Constructor getting list of boxes computed in autocrop class. Initialisation of a list of 2D rectangles and a
 	 * list of Z stack associated (zMin-zMax).
 	 *
-	 * @param boxes              List of boxes
+	 * @param boxes  List of boxes
 	 * @param params Autocrop parameters
 	 */
 	public RectangleIntersection(Map<Double, Box> boxes, AutocropParameters params) {
@@ -114,12 +114,13 @@ public static double percentOf2Rectangles(Rectangle2D r1, Rectangle2D r2) {
 	 */
 	public void runRectangleRecompilation() {
 		this.newBoxesAdded = true;
-		int tours = 0;
+		int i = 0;
 		while (newBoxesAdded) {
-			tours++;
 			computeIntersection();
 			rectangleRegroup();
 			recompileRectangle();
+			i++;
+			LOGGER.trace("Iteration {}: {} boxes detected", i, listRectangle.size());
 		}
 	}
 
@@ -133,9 +134,7 @@ public void computeIntersection() {
 				if (i != y &&
 				    !rectangleIntersect.contains(i + "-" + y) &&
 				    !rectangleIntersect.contains(y + "-" + i)) {
-					
 					if (listRectangle.get(i).intersects(listRectangle.get(y))) {
-						
 						if (percentOf2Rectangles(listRectangle.get(i), listRectangle.get(y)) >
 						    autocropParameters.getBoxesSurfacePercent() ||
 						    percentOf2Rectangles(listRectangle.get(y), listRectangle.get(i)) >
@@ -211,28 +210,28 @@ public void recompileRectangle() {
 		List<Rectangle> rectanglesToRemove   = new ArrayList<>();
 		for (String value : finalListRectangle) {
 			String[] splitList2       = value.split("-");
-			double   xMixNewRectangle = 0;
-			double   yMinNewRectangle = 0;
-			double   maxWidth         = 0;
-			double   maxHeight        = 0;
+			int      xMixNewRectangle = 0;
+			int      yMinNewRectangle = 0;
+			int      maxWidth         = 0;
+			int      maxHeight        = 0;
 			int      minZSlice        = 0;
 			int      maxZSlice        = 0;
 			if (splitList2.length > 1) {
 				for (String s : splitList2) {
 					int tmp = Integer.parseInt(s);
 					if (listRectangle.get(tmp).getX() < xMixNewRectangle || xMixNewRectangle == 0) {
-						xMixNewRectangle = listRectangle.get(tmp).getX();
+						xMixNewRectangle = listRectangle.get(tmp).x;
 					}
 					if (listRectangle.get(tmp).getY() < yMinNewRectangle || yMinNewRectangle == 0) {
-						yMinNewRectangle = listRectangle.get(tmp).getY();
+						yMinNewRectangle = listRectangle.get(tmp).y;
 					}
 					if (listRectangle.get(tmp).getX() + listRectangle.get(tmp).getWidth() > maxWidth ||
 					    maxWidth == 0) {
-						maxWidth = listRectangle.get(tmp).getX() + listRectangle.get(tmp).getWidth();
+						maxWidth = listRectangle.get(tmp).x + listRectangle.get(tmp).width;
 					}
 					if (listRectangle.get(tmp).getY() + listRectangle.get(tmp).getHeight() > maxHeight ||
 					    maxHeight == 0) {
-						maxHeight = listRectangle.get(tmp).getY() + listRectangle.get(tmp).getHeight();
+						maxHeight = listRectangle.get(tmp).y + listRectangle.get(tmp).height;
 					}
 
 					String[] zSliceTMP = zSlices.get(tmp).split("-");
@@ -242,20 +241,14 @@ public void recompileRectangle() {
 					if (Integer.parseInt(zSliceTMP[0] + Integer.valueOf(zSliceTMP[1])) > maxZSlice || maxZSlice == 0) {
 						maxZSlice = Integer.parseInt(zSliceTMP[0]) + Integer.parseInt(zSliceTMP[1]);
 					}
-					rectanglesToRemove.add(new Rectangle((int) listRectangle.get(tmp).getX(),
-					                                     (int) listRectangle.get(tmp).getY(),
-					                                     (int) listRectangle.get(tmp).getWidth(),
-					                                     (int) listRectangle.get(tmp).getHeight()));
+					rectanglesToRemove.add(new Rectangle(listRectangle.get(tmp)));
 				}
 
 				maxZSlice -= minZSlice;
 				rectangleZSliceToAdd.add(minZSlice + "-" + maxZSlice);
-				maxWidth = (int) maxWidth - (int) xMixNewRectangle;
-				maxHeight = (int) maxHeight - (int) yMinNewRectangle;
-				rectanglesToAdd.add(new Rectangle((int) xMixNewRectangle,
-				                                  (int) yMinNewRectangle,
-				                                  (int) maxWidth,
-				                                  (int) maxHeight));
+				maxWidth -= xMixNewRectangle;
+				maxHeight -= yMinNewRectangle;
+				rectanglesToAdd.add(new Rectangle(xMixNewRectangle, yMinNewRectangle, maxWidth, maxHeight));
 			}
 		}
 		LOGGER.debug("{} boxes will be merged in {} new boxes",
@@ -287,18 +280,16 @@ public Map<Double, Box> getNewBoxes() {
 
 		for (int i = 0; i < listRectangle.size(); i++) {
 			String[] zSliceTMP = zSlices.get(i).split("-");
-			short    tmpXMax   = (short) (listRectangle.get(i).getX() + listRectangle.get(i).getWidth());
-			short    tmpYMax   = (short) (listRectangle.get(i).getY() + listRectangle.get(i).getHeight());
-			short    tmpZMax   = (short) (Short.parseShort(zSliceTMP[0]) + Short.parseShort(zSliceTMP[1]));
-			if (tmpZMax == 0) {
-				tmpZMax = 1;
+			short    xMin   = (short) listRectangle.get(i).x;
+			short    yMin   = (short) listRectangle.get(i).y;
+			short    zMin   = Short.parseShort(zSliceTMP[0]);
+			short    xMax   = (short) (xMin + listRectangle.get(i).width);
+			short    yMax   = (short) (yMin + listRectangle.get(i).height);
+			short    zMax   = (short) (zMin + Short.parseShort(zSliceTMP[1]));
+			if (zMax == 0) {
+				zMax = 1;
 			}
-			Box box = new Box((short) listRectangle.get(i).getX(),
-			                  tmpXMax,
-			                  (short) listRectangle.get(i).getY(),
-			                  tmpYMax,
-			                  Short.parseShort(zSliceTMP[0]),
-			                  tmpZMax);
+			Box box = new Box(xMin, xMax, yMin, yMax, zMin, zMax);
 			boxes.put((double) i, box);
 		}
 		return boxes;

src/main/java/fr/igred/nucleus/autocrop/package-info.java

@@ -1,2 +1,20 @@
+/*
+ * NucleusJ
+ * Copyright (C) 2025 iGReD
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
 /** This package contains classes and interfaces for the AutoCrop feature in the Nucleus plugin. */
 package fr.igred.nucleus.autocrop;

src/main/java/fr/igred/nucleus/cli/CLIRunAction.java

@@ -127,7 +127,7 @@ private void runSegCC() {
 			            params.getInputFolder(),
 			            params.getSegmentedInputFolder(),
 			            params.getOutputFolder());
-			ccCalling.runSeveralImages2();
+			ccCalling.runSeveralImages();
 		} catch (IOException | FormatException e) {
 			LOGGER.error("An error occurred during chromocenter segmentation.", e);
 		}

src/main/java/fr/igred/nucleus/cli/package-info.java

@@ -1,3 +1,21 @@
+/*
+ * NucleusJ
+ * Copyright (C) 2025 iGReD
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
 /**
  * Package containing classes for command line interface (CLI) actions and options for NucleusJ. This package provides
  * functionality to run various actions such as autocrop, segmentation, and compute parameters through command line

src/main/java/fr/igred/nucleus/core/package-info.java

@@ -1,2 +1,20 @@
+/*
+ * NucleusJ
+ * Copyright (C) 2025 iGReD
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
 /** This package contains classes for analyses. */
 package fr.igred.nucleus.core;

src/main/java/fr/igred/nucleus/dialogs/AutocropConfigDialog.java

@@ -31,30 +31,28 @@
 import java.awt.GridBagConstraints;
 import java.awt.GridBagLayout;
 import java.awt.Insets;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 
 
 public class AutocropConfigDialog extends JFrame implements ItemListener {
-	private final JTextField xCropBoxSize                = new JTextField();
-	private final JTextField yCropBoxSize                = new JTextField();
-	private final JTextField zCropBoxSize                = new JTextField();
-	private final JTextField boxNumberFontSize           = new JTextField();
-	private final JTextField xCalibration                = new JTextField();
-	private final JTextField yCalibration                = new JTextField();
-	private final JTextField zCalibration                = new JTextField();
-	private final JTextField minVolume                   = new JTextField();
-	private final JTextField maxVolume                   = new JTextField();
-	private final JTextField thresholdOTSUComputing      = new JTextField();
-	private final JTextField channelToComputeThreshold   = new JTextField();
-	private final JTextField slicesOTSUComputing = new JTextField();
-	private final JTextField boxesSurfacePercent = new JTextField();
-	private final JCheckBox  regroupBoxes        = new JCheckBox();
-	private final JCheckBox  addCalibrationBox           = new JCheckBox();
+	private final JTextField xCropBoxSize              = new JTextField();
+	private final JTextField yCropBoxSize              = new JTextField();
+	private final JTextField zCropBoxSize              = new JTextField();
+	private final JTextField boxNumberFontSize         = new JTextField();
+	private final JTextField xCalibration              = new JTextField();
+	private final JTextField yCalibration              = new JTextField();
+	private final JTextField zCalibration              = new JTextField();
+	private final JTextField minVolume                 = new JTextField();
+	private final JTextField maxVolume                 = new JTextField();
+	private final JTextField thresholdOTSUComputing    = new JTextField();
+	private final JTextField channelToComputeThreshold = new JTextField();
+	private final JTextField slicesOTSUComputing       = new JTextField();
+	private final JTextField boxesSurfacePercent       = new JTextField();
+	private final JCheckBox  regroupBoxes              = new JCheckBox();
+	private final JCheckBox  addCalibrationBox         = new JCheckBox();
 	private final JPanel     cropBoxPane;
-	private       Boolean    isRegroupBoxesSelected      = true;
+	private       Boolean    isRegroupBoxesSelected    = true;
 	private       JPanel     xCalibrationPanel;
 	private       JPanel     yCalibrationPanel;
 	private       JPanel     zCalibrationPanel;
@@ -266,8 +264,7 @@ public AutocropConfigDialog() {
 
 		super.setVisible(false);
 
-		ActionListener startListener = new StartListener(this);
-		buttonOK.addActionListener(startListener);
+		buttonOK.addActionListener(e -> setVisible(false));
 	}
 
 
@@ -399,21 +396,4 @@ public void itemStateChanged(ItemEvent e) {
 		repaint();
 	}
 
-	
-	private static class StartListener implements ActionListener {
-		AutocropConfigDialog autocropDialog;
-		
-		
-		/** @param autocropDialog  */
-		StartListener(AutocropConfigDialog autocropDialog) {
-			this.autocropDialog = autocropDialog;
-		}
-		
-		
-		public void actionPerformed(ActionEvent actionEvent) {
-			autocropDialog.setVisible(false);
-		}
-		
-	}
-	
 }