fixed element and timepoint deletion

javacImageJ

@@ -5,11 +5,12 @@ cd src
 # javac -target 1.1 -deprecation View5D_.java
 cp view5d/View5D_.java view5d/aaa.class
 rm view5d/*.class
-javac -target 1.8 -source 1.8 -deprecation -classpath ".:/usr/local/ImageJ/ij.jar" view5d/View5D_.java view5d/View5D.java  # -target 1.4 -source 1.2
+javac -target 1.8 -source 1.8 -deprecation -classpath ".:/usr/share/java/ij.jar" view5d/View5D_.java view5d/View5D.java  # -target 1.4 -source 1.2
 # javac -deprecation -classpath "." View5D_.java
-jar -cf View5D_.jar view5d/*.class plugins.config
+jar -cf /tmp/View5D_.jar view5d/*.class plugins.config
+cp /tmp/View5D_.jar .
 # cp /*.class /usr/local/ImageJ/plugins/View5D/
-cp View5D_.jar /mnt/c/Users/pi96doc/Desktop/Fiji.app/plugins/View5D_-2.3.7.jar
+cp View5D_.jar /mnt/c/Users/pi96doc/Desktop/UserPrograms/fiji-win64/Fiji.app/plugins/View5D_-2.3.8.jar
 
 # cp View5D_.jar /usr/local/ImageJ/plugins/View5D/
 # cp View5D_.jar /windows/C/DriveF/JavaProgs/ImageJ/plugins/View5D/

javacPython

@@ -6,9 +6,11 @@ cd src
 cp view5d/View5D_.java view5d/aaa.class
 rm view5d/*.class
 # javac -target 1.5 -source 1.5 -deprecation -classpath ".:/usr/local/ImageJ/ij.jar" view5d/View5D_.java view5d/View5D.java  # -target 1.4 -source 1.2
-javac -target 1.6 -source 1.6 -deprecation -classpath ".:/usr/local/ImageJ/ij.jar" view5d/View5D_.java view5d/View5D.java  # -target 1.4 -source 1.2
+# javac -target 1.6 -source 1.6 -deprecation -classpath ".:/usr/local/ImageJ/ij.jar" view5d/View5D_.java view5d/View5D.java  # -target 1.4 -source 1.2
+javac -target 1.6 -source 1.6 -deprecation -classpath ".:/usr/share/java/ij.jar" view5d/View5D_.java view5d/View5D.java  # -target 1.4 -source 1.2
 # javac -deprecation -classpath "." View5D_.java
-jar -cf View5D_.jar view5d/*.class plugins.config
+jar -cf /tmp/View5D_.jar view5d/*.class plugins.config
+cp /tmp/View5D_.jar .
 cp View5D_.jar ../../../PythonScripts/FromWeb/nanoimagingpack/NanoImagingPack/resources/
 cp View5D_.jar "/mnt/c/NoBackup/DeconvCompileTest/DIPlib_3_2017/share/DIPimage/private/View5D.jar"
 cp View5D_.jar "/mnt/c/NoBackup/DeconvCompileTest/DIPlib_3_2019/share/DIPimage/private/View5D.jar"
@@ -19,8 +21,8 @@ cp View5D_.jar "C:\Program Files\DIPlib_3_2019\share\DIPimage\private\View5D.jar
 cp View5D_.jar " C:\NoBackup\DeconvCompileTest\DIPlib_3_2019\share\DIPimage\private\View5D.jar"
 cp View5D_.jar " C:\NoBackup\DeconvCompileTest\DIPlib_3_2017\share\DIPimage\private\View5D.jar"
 cd ..
-cp View5D.jar "View5D_v2.3.7.jar"
-tar -czf "View5D_v2.3.7-jar.tar.gz" "View5D_v2.3.7.jar"
+cp View5D.jar "View5D_v2.3.8.jar"
+tar -czf "View5D_v2.3.8-jar.tar.gz" "View5D_v2.3.8.jar"
 # cp /*.class /usr/local/ImageJ/plugins/View5D/
 #cp View5D_.jar /usr/local/ImageJ/plugins/View5D/
 # cp View5D_.jar /windows/C/DriveF/JavaProgs/ImageJ/plugins/View5D/

src/view5d/Bundle.java

@@ -334,7 +334,7 @@ public void GenCMap() {
 
     public static int AddLookUpTable(int TableSize, byte reds[], byte greens[], byte blues[])
     {
-        MapSizes.addElement(new Integer(TableSize));
+        MapSizes.addElement(Integer.valueOf(TableSize));
         RedMaps.addElement(reds);
         GreenMaps.addElement(greens);
         BlueMaps.addElement(blues);

src/view5d/ImageCanvas.java

@@ -58,6 +58,8 @@ public class ImageCanvas extends Canvas implements ImageObserver,MouseListener,M
 
     int		imgw = -1;
     int		imgh = -1;
+    int defaultTimeElementChoice=1; // Time is the default direction to delete
+
     //int		xoff = 0;
     //int		yoff = 0;
     double	scale = 1.0;  // will be changed in init
@@ -1127,7 +1129,7 @@ public void mousePressed(MouseEvent e) {
           else  // just a mouse pressed in the empty image area
           {
               // e.isAltGraphDown() ||  // This does not work with matlab
-            if ( e.isMetaDown() || e.getClickCount()>1 || (e.getModifiers() & Event.ALT_MASK) != 0)
+            if ( e.isMetaDown() || e.getClickCount()>1 || (e.getModifiersEx() & InputEvent.ALT_DOWN_MASK) != 0)
                 ImgDragStarted = true;
             if (ImgDragStarted)  // Only drag the image but do not change coordinates
             {
@@ -1614,7 +1616,20 @@ public boolean checkProceed(String txt) { // calls a user dialog to see if the u
         AGenericDialog question= new AGenericDialog("Warning!");
         question.addMessage(txt + " modifies the data.\nDo you really want to proceed?");
         question.showDialog();
-        return ! question.wasCanceled();
+        // System.out.println("Dialog was "+!question.wasCanceled()+"\n");
+        return (!question.wasCanceled());
+}
+
+public int checkChoice(String txt, String [] choices, String default_choice) { // calls a user dialog to see if the user really wants to proceed
+    int choice=0;
+    AGenericDialog question= new AGenericDialog("Delete Element or Timepoint");
+    question.addMessage(txt);
+    question.addChoice("Delete", choices, default_choice);
+    question.showDialog();
+    choice = question.getNextChoiceIndex();
+    if (question.wasCanceled())
+        choice = -1;
+    return choice;
 }
 
 
@@ -1627,9 +1642,28 @@ public void ProcessKey(char myChar) {
 	    centerCursor();
 	    return;
     case 'D':
-        if (checkProceed("Delete Element"))
-            my3ddata.DeleteActElement();
-	    UpdateAllPanels();
+        if (my3ddata.Elements > 1)
+            if (my3ddata.Times <= 1)
+                {if (checkProceed("Delete Element"))
+                    my3ddata.DeleteActElement();}
+            else
+                {
+                String [] choices = {"Element", "Time"};
+                int choice = checkChoice("Deleting Element/Timepoint modifies the data. Do you really want to proceed?", choices, choices[defaultTimeElementChoice]);
+                if (choice == 0)
+                    my3ddata.DeleteActElement();
+                if (choice == 1)
+                    my3ddata.DeleteActTime();
+                defaultTimeElementChoice=choice; // store the default for the next call
+                myPanel.CheckScrollBar();
+                }
+            else if ((my3ddata.Times > 1))
+                {if (checkProceed("Delete Timepoint"))
+                    my3ddata.DeleteActTime();
+                myPanel.CheckScrollBar();
+                }
+
+UpdateAllPanels();
 	return;
     case 'f':  // upcast datatype to float
         my3ddata.CloneFloat();

src/view5d/My3DData.java

@@ -2182,10 +2182,12 @@ public void DeleteActElement()  // what, if another dublicate exists?
         for (int t=0;t<Times;t++) {
             DeleteActElement(ElementsAtTime(t));
             try {
-                TimesColorInfo.get(t).removeElement(ActiveElement);
+                if (TimesColorInfo != null && TimesColorInfo.get(t) != null)
+                    TimesColorInfo.get(t).removeElement(ActiveElement);
             }
-            catch(Exception e)
+            catch (Exception e)
             {
+                // System.out.println("Exception "+e+"\n");
                 // ignore this
             }
         }
@@ -2202,6 +2204,38 @@ public void DeleteActElement()  // what, if another dublicate exists?
         InvalidateColor();
         }
     }
+
+    public void DeleteActTime()  // what, if another dublicate exists?
+    {
+        if (Times > 1) // The last time must not be deleted
+        {  
+            for (int e=0;e<Elements;e++) {
+                ElementsAtTime(ActiveTime).removeElementAt(0);
+                // System.out.println("Time is "+ActiveTime+", Delting Element: "+e+"\n");
+
+                try {
+                    if (TimesColorInfo != null && TimesColorInfo.size() > ActiveTime && TimesColorInfo.get(ActiveTime) != null)
+                        TimesColorInfo.get(ActiveTime).removeElement(0);
+                }
+                catch(Exception ex)
+                {
+                    // System.out.println("Exception "+ex+"\n");
+                    // ignore this
+                }
+            }
+            MyTimeProj.removeElementAt(ActiveTime);
+            MyTimeColorProj.removeElementAt(ActiveTime);
+            MyTimes.removeElementAt(ActiveTime);  // However, all times use the same list of elements.
+            Times --;
+
+            if (ActiveTime >= Times)
+                ActiveTime = Times-1;
+            InvalidateSlices();
+            InvalidateColor();
+            MyElements = ElementsAtTime(ActiveTime);
+            sizes[4]=Times;
+        }
+    }
 
     public Color GetMarkerColor(int e) {
       int Red=0,Green=0,Blue=0;
@@ -2514,8 +2548,8 @@ else if (dir==1)
         }
 
         // vecx = 1.0; vecy = 0.0; vecz = 0.0;
-        PlanesS[0].addElement(new Integer(ROIXs));PlanesS[1].addElement(new Integer(ROIYs));PlanesS[2].addElement(new Integer(ROIZs));
-        PlanesD[0].addElement(new Double(vecx));PlanesD[1].addElement(new Double(vecy));PlanesD[2].addElement(new Double(vecz));
+        PlanesS[0].addElement(Integer.valueOf(ROIXs));PlanesS[1].addElement(Integer.valueOf(ROIYs));PlanesS[2].addElement(Integer.valueOf(ROIZs));
+        PlanesD[0].addElement(Double.valueOf(vecx));PlanesD[1].addElement(Double.valueOf(vecy));PlanesD[2].addElement(Double.valueOf(vecz));
         // Just add the starting points to the Polygon
         for (int e=0;e<Elements;e++)
             GetBundleAt(e).TakePlaneROIs(PlanesS,PlanesD);

src/view5d/PositionLabel.java

@@ -182,18 +182,19 @@ void Help() {
         // javax.swing.JOptionPane.showMessageDialog(applet,
         String newtext = "Java 5D image viewer, Version V" + View5D_.serialVersionUID + "." + View5D_.serialSubVersionUID + "." + View5D_.serialSubSubVersionUID + "" +
                 " by Rainer Heintzmann\nLeibniz-IPHT and Friedrich Schiller University of Jena, Germany (heintzmann@gmail.com)\n\n" +
-                "NAVIGATION: Right-click for menu and context menus\nUse mouse click for changing slices or cursor keys (arrows) and next/previous page keys.\n" +
+                "NAVIGATION: Right-click for menu and context menus (individual for panels, colopmap list and text panel)\nUse mouse click for changing slices or cursor keys (arrows) and next/previous page keys.\n" +
+                "Zoom in and out via the mouse wheel. Press `shift` and use the mouse wheel to change the LUT gamma value. `shift middle mouse click resets gamma to one`\n +" +
                 "'e' and 'E' movel along the element- (color-) direction. ',' and '.' along time or between multiple images.\n +" +
-                "'home' positions the cursor in the center.\n" +
-                "shift-drag images for positon or press space bar before draggin with the mouse, zoom by typing 'A' and 'a' or zoom into a ROI by pressing 'Z'\n\n" +
-                "VIEW ADJUSTMENT:'<' and '>' for adjusting display magnificaltion perpendicular to the current display\n" +
-                "'i' for init view, 'c' for change ColorMap, \n" +
-                "1,2,5,6' for lower and '3,4,7,8' for upper Threshold coarse and fine adjustment, 't' and 'T' for automatic contrast adjustment using one or all elements\n" +
-                "'e' : toggle elements (if present), 'C' : toggle multicolor display, 'r','g','b' : select element for respective display\n" +
-                "'R','G','B' : clear respective channel, 'p','P': Toggle Projections (MIP, Avg)\n\n"+
-                "ROIs: Shift and mouse-drag for square ROIs, 'Ctrl-s' toggles ROI modes mouse-drag for multiple line ROIs\n\n"+
+                "'home'/'pos1' positions the cursor at the center for this panel.\n" +
+                "shift-drag images for positon or press space bar before draggin with the mouse, zoom by typing 'A' and 'a' or zoom-fit a ROI by pressing 'Z'\n\n" +
+                "VIEW ADJUSTMENT:'<' and '>' to adjusting display magnification (if aspect is not locked) perpendicular to the current display (like the mouse wheel)\n" +
+                "'i' to initialize view, 'c' to change ColorMap, \n" +
+                "1,2,5,6' for lower and '3,4,7,8' for upper Threshold coarse and fine adjustment, 't' and 'T' for automatic contrast adjustment for one or all elements repectively\n" +
+                "'e': toggle elements (if present), 'C': toggle multicolor display, 'r','g','b': select element for respective display\n" +
+                "'G': set element to gray colormap, 'R': glow red colormap, 'B': rainbow colormap, 'p','P': Toggle Projections (MIP, Avg)\n\n"+
+                "ROIs: 'shift' and mouse-drag for square ROIs, 'Ctrl-s' toggles ROI modes mouse-drag for multiple line ROIs\n\n"+
                 "See the context menus (right click) in the main and element displays for more commands with the respective keys shown in []\n" +
-                "For further Documentation see http://www.nanoimaging.de/View5D/";
+                "For further Documentation and commands see http://www.nanoimaging.de/View5D/";
         if (false) {
             MyText.setText(newtext);
             MyText.setCaretPosition(0);

src/view5d/View5D_.java

@@ -35,7 +35,7 @@
 public class View5D_ extends PlugInFrame implements PlugIn, WindowListener {
     public static final long serialVersionUID = 2;
     public static final long serialSubVersionUID = 3;
-    public static final long serialSubSubVersionUID = 7;
+    public static final long serialSubSubVersionUID = 8;
 	// Panel panel;
 	int previousId;
 	ImagePlus imp;