Colocalization GUI cleaned up a little - now it is able to handle n-channels instead of fixed 2

src/main/java/mosaic/bregman/GUI/GenericGUI.java

@@ -23,15 +23,20 @@ import javax.swing.JFileChooser;
 import javax.swing.JLabel;
 import javax.swing.JPanel;
 
+import org.apache.log4j.Logger;
+
 import ij.IJ;
 import ij.ImagePlus;
 import ij.gui.GenericDialog;
 import mosaic.bregman.Parameters;
 import mosaic.core.GUI.HelpGUI;
 import mosaic.plugins.BregmanGLM_Batch.RunMode;
+import mosaic.utils.ImgUtils;
 
 
 public class GenericGUI {
+    private static final Logger logger = Logger.getLogger(GenericGUI.class);
+    
     // Input params
     protected final Parameters iParameters;
     protected ImagePlus iInputImage;
@@ -39,11 +44,11 @@ public class GenericGUI {
     private boolean iIsConfigReadFromArguments;
 
     private String iInputField = "";
-    protected ImagePlus imgch2; // TODO: it is not used currently (never assigned)
     
     public GenericGUI(ImagePlus aInputImg, boolean aUseGui, Parameters aParameters, boolean aIsConfigReadFromArguments) {
         iParameters = aParameters;
         iInputImage = aInputImg;
+        logger.info("GUI input image: " + ImgUtils.getImageInfo(aInputImg));
         iUseGui = aUseGui;
         iIsConfigReadFromArguments = aIsConfigReadFromArguments;
     }
@@ -95,7 +100,7 @@ public class GenericGUI {
         addButton(p, "Options", new ActionListener() {
             @Override
             public void actionPerformed(ActionEvent arg0) {
-                final ColocalizationGUI gds = new ColocalizationGUI(iInputImage, imgch2, iParameters);
+                final ColocalizationGUI gds = new ColocalizationGUI(iInputImage, iParameters);
                 gds.run();
             }
         });  
@@ -128,7 +133,7 @@ public class GenericGUI {
         if (!iUseGui && !iIsConfigReadFromArguments) {
             BackgroundSubGUI.getParameters(iParameters);
             SegmentationGUI.getParameters(iParameters);
-            new ColocalizationGUI(iInputImage, imgch2, iParameters).run();
+            new ColocalizationGUI(iInputImage, iParameters).run();
             VisualizationGUI.getParameters(iParameters);
         }
         iInputField = gd.getNextString();
@@ -176,14 +181,11 @@ public class GenericGUI {
 
         @Override
         public void actionPerformed(ActionEvent e) {
+            // close previosuly opened images
             if (iInputImage != null) {
                 iInputImage.close();
                 iInputImage = null;
             }
-            if (imgch2 != null) {
-                imgch2.close();
-                imgch2 = null;
-            }// close previosuly opened images
 
             final JFileChooser fc = new JFileChooser();
             fc.setFileSelectionMode(JFileChooser.FILES_AND_DIRECTORIES);

src/main/java/mosaic/bregman/Mask.java

@@ -39,7 +39,7 @@ public class Mask {
         double minNorm = iGlobalMin;
         double maxNorm = iGlobalMax;
         if (iGlobalMax == 0) {
-            MinMax<Double> mm = ImgUtils.findMinMax(aImage);
+            MinMax<Double> mm = ImgUtils.findMinMax(aImage, 1, 1);
             minNorm = mm.getMin();
             maxNorm = mm.getMax();
         }
@@ -47,7 +47,7 @@ public class Mask {
     }
     
     private boolean[][][] generateMask(final ImagePlus aImage, double aNormalizationMin, double aNormalizationMax, double aMaskThreshold) {
-        ImagePlus mask = Mask.createBinaryCellMask(aImage, "Cell mask", aMaskThreshold * (aNormalizationMax - aNormalizationMin) + aNormalizationMin);
+        ImagePlus mask = Mask.createBinaryCellMask(aImage, "Cell mask", aMaskThreshold * (aNormalizationMax - aNormalizationMin) + aNormalizationMin, 1);
         return ImgUtils.imgToZXYbinaryArray(mask);
     }
     
@@ -97,13 +97,13 @@ public class Mask {
         return ((inside / size) > InsideThreshold);
     }
 
-    public static ImagePlus createBinaryCellMask(ImagePlus aInputImage, String aTitle, double aThreshold) {
+    public static ImagePlus createBinaryCellMask(ImagePlus aInputImage, String aTitle, double aThreshold, int aChannel) {
         int ni = aInputImage.getWidth();
         int nj = aInputImage.getHeight();
         int nz = aInputImage.getNSlices();
         final ImageStack maskStack = new ImageStack(ni, nj);
         for (int z = 0; z < nz; z++) {
-            aInputImage.setSlice(z + 1);
+            aInputImage.setPosition(aChannel, z, 1);
             ImageProcessor ip = aInputImage.getProcessor();
             final byte[] mask = new byte[ni * nj];
             for (int i = 0; i < ni; i++) {

src/main/java/mosaic/bregman/RScript.java

@@ -6,7 +6,6 @@ import java.io.IOException;
 import java.io.InputStream;
 import java.io.PrintWriter;
 import java.util.ArrayList;
-import java.util.Iterator;
 import java.util.List;
 import java.util.Scanner;
 
@@ -47,7 +46,7 @@ public class RScript {
     * -----------------------------------------------------------------------------------------
     */
     public static void makeRScript(String path, String aObjectsDataFile, String aObjectsColocFile, String aImagesColocFile, List<ChannelPair> aChannelPairs, int[] ImagesPerGroup, String[] GroupNames, String Ch1Name, String Ch2Name) {
-        logger.info("Generateing Rscript with path=[" + path + "] aObjectsDataFile=[" + aObjectsDataFile + "] aObjectsColocFile=[" + aObjectsColocFile + "] aImagesColocFile=[" + aImagesColocFile + "] aChannelPairs=[" + aChannelPairs + "] ImagesPerGroup=[" + Debug.getString(ImagesPerGroup) + "] GroupNames=[" + Debug.getString(GroupNames) + "] Ch1Name=[" + Ch1Name + "] Ch2Name=[" + Ch2Name + "]");
+        logger.info("Generateing Rscript with path=[" + path + "] aObjectsDataFile=[" + aObjectsDataFile + "] aObjectsColocFile=[" + aObjectsColocFile + "] aImagesColocFile=[" + aImagesColocFile + "] aChannelPairs=[" + aChannelPairs + "] ImagesPerGroup=[" + Debug.getString(ImagesPerGroup) + "] GroupNames=[" + Debug.getString((Object[])GroupNames) + "] Ch1Name=[" + Ch1Name + "] Ch2Name=[" + Ch2Name + "]");
         
         try {
             PrintWriter Script = new PrintWriter(path + File.separator + ScriptName);

src/main/java/mosaic/bregman/SamplePearsonCorrelationCoefficient.java

@@ -31,12 +31,12 @@ class SamplePearsonCorrelationCoefficient {
         iImageA = new double[iDepth][iWidth][iHeight];
         double maxA = initImageAndGetMax(aImgA, iImageA);
         double tx = aMaskImgA ? aMaskThresholdA * maxA : -1; 
-        iMaskA = ImgUtils.imgToZXYbinaryArray(Mask.createBinaryCellMask(aImgA, "Channel1", tx));
+        iMaskA = ImgUtils.imgToZXYbinaryArray(Mask.createBinaryCellMask(aImgA, "Channel1", tx, 1));
         
         iImageB = new double[iDepth][iWidth][iHeight];
         double maxB = initImageAndGetMax(aImgB, iImageB);
         double ty = aMaskImgB ? aMaskThresholdB * maxB : -1;
-        iMaskB = ImgUtils.imgToZXYbinaryArray(Mask.createBinaryCellMask(aImgB, "Channel2", ty));
+        iMaskB = ImgUtils.imgToZXYbinaryArray(Mask.createBinaryCellMask(aImgB, "Channel2", ty, 1));
     }
 
     /**

src/main/java/mosaic/bregman/SquasshLauncher.java

@@ -387,7 +387,7 @@ public class SquasshLauncher {
         double max = iGlobalNormalizationMax;
         logger.info("Global min/max: " + min + "/" + max);
         if (iGlobalNormalizationMax == 0) {
-            MinMax<Double> mm = ImgUtils.findMinMax(img);
+            MinMax<Double> mm = ImgUtils.findMinMax(img, 1, 1);
             min = mm.getMin();
             max = mm.getMax();
             logger.info("Global min/max from image: " + min + "/" + max);

src/main/java/mosaic/utils/ImgUtils.java

@@ -402,7 +402,7 @@ public class ImgUtils {
         return aImg.factory().create(dims, aImg.firstElement().copy());
     }
     
-    public static MinMax<Double> findMinMax(ImagePlus img) {
+    public static MinMax<Double> findMinMax(ImagePlus img, int channel, int frame) {
         int ni = img.getWidth();
         int nj = img.getHeight();
         int nz = img.getNSlices();
@@ -410,7 +410,7 @@ public class ImgUtils {
         double max = -Double.MAX_VALUE;
         
         for (int z = 0; z < nz; z++) {
-            img.setSlice(z + 1);
+            img.setPosition(channel, z + 1, frame);
             ImageProcessor imp = img.getProcessor();
             for (int i = 0; i < ni; i++) {
                 for (int j = 0; j < nj; j++) {

src/test/java/mosaic/bregman/ColocalizationAnalysisTest.java

 package mosaic.bregman;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -9,13 +10,16 @@ import java.util.Map;
 
 import org.junit.Test;
 
+import ij.ImagePlus;
 import mosaic.bregman.ColocalizationAnalysis.ChannelPair;
 import mosaic.bregman.ColocalizationAnalysis.ColocResult;
 import mosaic.bregman.ColocalizationAnalysis.RegionColoc;
+import mosaic.bregman.GUI.ColocalizationGUI;
 import mosaic.bregman.segmentation.Pix;
 import mosaic.bregman.segmentation.Region;
+import mosaic.test.framework.CommonBase;
 
-public class ColocalizationAnalysisTest {
+public class ColocalizationAnalysisTest extends CommonBase {
 
     @Test
     public void testSimpleTwoRegions() {
@@ -85,4 +89,15 @@ public class ColocalizationAnalysisTest {
         assertEquals(true, rc10.singleRegionColoc);
     }
 
+    
+    @Test
+    public void testGUI() {
+        ImagePlus iInputImage = loadImagePlus("/Users/gonciarz/1/3C.tif");
+        Parameters iParameters = new Parameters();
+        iParameters.usecellmaskY=true;
+        iParameters.thresholdcellmasky = 0.5;
+        final ColocalizationGUI gds = new ColocalizationGUI(iInputImage, iParameters);
+        gds.run();
+        System.out.println(iParameters);
+    }
 }