Exemple #1
0
 /** Quit using a separate thread, hopefully avoiding thread deadlocks. */
 public void run() {
   quitting = true;
   boolean changes = false;
   int[] wList = WindowManager.getIDList();
   if (wList != null) {
     for (int i = 0; i < wList.length; i++) {
       ImagePlus imp = WindowManager.getImage(wList[i]);
       if (imp != null && imp.changes == true) {
         changes = true;
         break;
       }
     }
   }
   Frame[] frames = WindowManager.getNonImageWindows();
   if (frames != null) {
     for (int i = 0; i < frames.length; i++) {
       if (frames[i] != null && (frames[i] instanceof Editor)) {
         if (((Editor) frames[i]).fileChanged()) {
           changes = true;
           break;
         }
       }
     }
   }
   if (windowClosed
       && !changes
       && Menus.window.getItemCount() > Menus.WINDOW_MENU_ITEMS
       && !(IJ.macroRunning() && WindowManager.getImageCount() == 0)) {
     GenericDialog gd = new GenericDialog("ImageJ", this);
     gd.addMessage("Are you sure you want to quit ImageJ?");
     gd.showDialog();
     quitting = !gd.wasCanceled();
     windowClosed = false;
   }
   if (!quitting) return;
   if (!WindowManager.closeAllWindows()) {
     quitting = false;
     return;
   }
   // IJ.log("savePreferences");
   if (applet == null) {
     saveWindowLocations();
     Prefs.savePreferences();
   }
   IJ.cleanup();
   // setVisible(false);
   // IJ.log("dispose");
   dispose();
   if (exitWhenQuitting) System.exit(0);
 }
Exemple #2
0
 /** Handles CheckboxMenuItem state changes. */
 public void itemStateChanged(ItemEvent e) {
   MenuItem item = (MenuItem) e.getSource();
   MenuComponent parent = (MenuComponent) item.getParent();
   String cmd = e.getItem().toString();
   if ((Menu) parent == Menus.window) WindowManager.activateWindow(cmd, item);
   else doCommand(cmd);
 }
 /** Sets the color used used for the ROI Manager "Show All" mode. */
 public static void setShowAllColor(Color c) {
   if (c == null) return;
   showAllColor = c;
   labelColor = null;
   ImagePlus img = WindowManager.getCurrentImage();
   if (img != null) {
     ImageCanvas ic = img.getCanvas();
     if (ic != null && ic.getShowAllROIs()) img.draw();
   }
 }
  private boolean showDialog() {
    String[] types = {"RAW", "JPEG", "ZLIB"};
    GenericDialog gd = new GenericDialog("Generate Bricks");
    gd.addChoice("FileType", types, filetype);
    gd.addNumericField("JPEG quality", jpeg_quality, 0);
    gd.addNumericField("Max file size (MB)", bdsizelimit, 0);

    int[] wlist = WindowManager.getIDList();
    if (wlist == null) return false;

    String[] titles = new String[wlist.length];
    for (int i = 0; i < wlist.length; i++) titles[i] = "";

    int tnum = 0;
    for (int i = 0; i < wlist.length; i++) {
      ImagePlus imp = WindowManager.getImage(wlist[i]);
      if (imp != null) {
        titles[tnum] = imp.getTitle();
        tnum++;
      }
    }
    gd.addChoice("Source image: ", titles, titles[0]);

    gd.showDialog();
    if (gd.wasCanceled()) return false;

    filetype = types[gd.getNextChoiceIndex()];
    jpeg_quality = (int) gd.getNextNumber();
    if (jpeg_quality > 100) jpeg_quality = 100;
    if (jpeg_quality < 0) jpeg_quality = 0;
    bdsizelimit = (int) gd.getNextNumber();

    int id = gd.getNextChoiceIndex();
    lvImgTitle = new ArrayList<String>();
    lvImgTitle.add(titles[id]);

    Prefs.set("filetype.string", filetype);
    Prefs.set("jpeg_quality.int", jpeg_quality);
    Prefs.set("bdsizelimit.int", bdsizelimit);

    return true;
  }
Exemple #5
0
 void saveWindowLocations() {
   Frame frame = WindowManager.getFrame("B&C");
   if (frame != null) Prefs.saveLocation(ContrastAdjuster.LOC_KEY, frame.getLocation());
   frame = WindowManager.getFrame("Threshold");
   if (frame != null) Prefs.saveLocation(ThresholdAdjuster.LOC_KEY, frame.getLocation());
   frame = WindowManager.getFrame("Results");
   if (frame != null) {
     Prefs.saveLocation(TextWindow.LOC_KEY, frame.getLocation());
     Dimension d = frame.getSize();
     Prefs.set(TextWindow.WIDTH_KEY, d.width);
     Prefs.set(TextWindow.HEIGHT_KEY, d.height);
   }
   frame = WindowManager.getFrame("Log");
   if (frame != null) {
     Prefs.saveLocation(TextWindow.LOG_LOC_KEY, frame.getLocation());
     Dimension d = frame.getSize();
     Prefs.set(TextWindow.LOG_WIDTH_KEY, d.width);
     Prefs.set(TextWindow.LOG_HEIGHT_KEY, d.height);
   }
 }
 private boolean checkImage() {
   imp = WindowManager.getCurrentImage();
   if (imp == null) {
     IJ.beep();
     IJ.showStatus("No image");
     return false;
   }
   ip = setup(imp);
   if (ip == null) return false;
   return true;
 }
Exemple #7
0
 private boolean ignoreArrowKeys(ImagePlus imp) {
   Frame frame = WindowManager.getFrontWindow();
   String title = frame.getTitle();
   if (title != null && title.equals("ROI Manager")) return true;
   // Control Panel?
   if (frame != null && frame instanceof javax.swing.JFrame) return true;
   ImageWindow win = imp.getWindow();
   // LOCI Data Browser window?
   if (imp.getStackSize() > 1 && win != null && win.getClass().getName().startsWith("loci"))
     return true;
   return false;
 }
Exemple #8
0
 void saveWindowLocations() {
   Window win = WindowManager.getWindow("B&C");
   if (win != null) Prefs.saveLocation(ContrastAdjuster.LOC_KEY, win.getLocation());
   win = WindowManager.getWindow("Threshold");
   if (win != null) Prefs.saveLocation(ThresholdAdjuster.LOC_KEY, win.getLocation());
   win = WindowManager.getWindow("Results");
   if (win != null) {
     Prefs.saveLocation(TextWindow.LOC_KEY, win.getLocation());
     Dimension d = win.getSize();
     Prefs.set(TextWindow.WIDTH_KEY, d.width);
     Prefs.set(TextWindow.HEIGHT_KEY, d.height);
   }
   win = WindowManager.getWindow("Log");
   if (win != null) {
     Prefs.saveLocation(TextWindow.LOG_LOC_KEY, win.getLocation());
     Dimension d = win.getSize();
     Prefs.set(TextWindow.LOG_WIDTH_KEY, d.width);
     Prefs.set(TextWindow.LOG_HEIGHT_KEY, d.height);
   }
   win = WindowManager.getWindow("ROI Manager");
   if (win != null) Prefs.saveLocation(RoiManager.LOC_KEY, win.getLocation());
 }
Exemple #9
0
 void checkForCalibrationConflict(ImagePlus imp, Calibration cal) {
   Calibration gcal = imp.getGlobalCalibration();
   if (gcal == null || !showConflictMessage || IJ.isMacro()) return;
   if (cal.pixelWidth == gcal.pixelWidth && cal.getUnit().equals(gcal.getUnit())) return;
   GenericDialog gd = new GenericDialog(imp.getTitle());
   gd.addMessage("The calibration of this image conflicts\nwith the current global calibration.");
   gd.addCheckbox("Disable_Global Calibration", true);
   gd.addCheckbox("Disable_these Messages", false);
   gd.showDialog();
   if (gd.wasCanceled()) return;
   boolean disable = gd.getNextBoolean();
   if (disable) {
     imp.setGlobalCalibration(null);
     imp.setCalibration(cal);
     WindowManager.repaintImageWindows();
   }
   boolean dontShow = gd.getNextBoolean();
   if (dontShow) showConflictMessage = false;
 }
Exemple #10
0
  public void keyPressed(KeyEvent e) {
    // if (e.isConsumed()) return;
    int keyCode = e.getKeyCode();
    IJ.setKeyDown(keyCode);
    hotkey = false;
    if (keyCode == KeyEvent.VK_CONTROL || keyCode == KeyEvent.VK_SHIFT) return;
    char keyChar = e.getKeyChar();
    int flags = e.getModifiers();
    if (IJ.debugMode)
      IJ.log(
          "keyPressed: code="
              + keyCode
              + " ("
              + KeyEvent.getKeyText(keyCode)
              + "), char=\""
              + keyChar
              + "\" ("
              + (int) keyChar
              + "), flags="
              + KeyEvent.getKeyModifiersText(flags));
    boolean shift = (flags & KeyEvent.SHIFT_MASK) != 0;
    boolean control = (flags & KeyEvent.CTRL_MASK) != 0;
    boolean alt = (flags & KeyEvent.ALT_MASK) != 0;
    boolean meta = (flags & KeyEvent.META_MASK) != 0;
    String cmd = null;
    ImagePlus imp = WindowManager.getCurrentImage();
    boolean isStack = (imp != null) && (imp.getStackSize() > 1);

    if (imp != null
        && !control
        && ((keyChar >= 32 && keyChar <= 255) || keyChar == '\b' || keyChar == '\n')) {
      Roi roi = imp.getRoi();
      if (roi instanceof TextRoi) {
        if ((flags & KeyEvent.META_MASK) != 0 && IJ.isMacOSX()) return;
        if (alt) {
          switch (keyChar) {
            case 'u':
            case 'm':
              keyChar = IJ.micronSymbol;
              break;
            case 'A':
              keyChar = IJ.angstromSymbol;
              break;
            default:
          }
        }
        ((TextRoi) roi).addChar(keyChar);
        return;
      }
    }

    // Handle one character macro shortcuts
    if (!control && !meta) {
      Hashtable macroShortcuts = Menus.getMacroShortcuts();
      if (macroShortcuts.size() > 0) {
        if (shift) cmd = (String) macroShortcuts.get(new Integer(keyCode + 200));
        else cmd = (String) macroShortcuts.get(new Integer(keyCode));
        if (cmd != null) {
          // MacroInstaller.runMacroCommand(cmd);
          commandName = cmd;
          MacroInstaller.runMacroShortcut(cmd);
          return;
        }
      }
    }

    if ((!Prefs.requireControlKey || control || meta) && keyChar != '+') {
      Hashtable shortcuts = Menus.getShortcuts();
      if (shift) cmd = (String) shortcuts.get(new Integer(keyCode + 200));
      else cmd = (String) shortcuts.get(new Integer(keyCode));
    }

    if (cmd == null) {
      switch (keyChar) {
        case '<':
        case ',':
          if (isStack) cmd = "Previous Slice [<]";
          break;
        case '>':
        case '.':
        case ';':
          if (isStack) cmd = "Next Slice [>]";
          break;
        case '+':
        case '=':
          cmd = "In [+]";
          break;
        case '-':
          cmd = "Out [-]";
          break;
        case '/':
          cmd = "Reslice [/]...";
          break;
        default:
      }
    }

    if (cmd == null) {
      switch (keyCode) {
        case KeyEvent.VK_TAB:
          WindowManager.putBehind();
          return;
        case KeyEvent.VK_BACK_SPACE: // delete
          if (deleteOverlayRoi(imp)) return;
          cmd = "Clear";
          hotkey = true;
          break;
          // case KeyEvent.VK_BACK_SLASH: cmd=IJ.altKeyDown()?"Animation Options...":"Start
          // Animation"; break;
        case KeyEvent.VK_EQUALS:
          cmd = "In [+]";
          break;
        case KeyEvent.VK_MINUS:
          cmd = "Out [-]";
          break;
        case KeyEvent.VK_SLASH:
        case 0xbf:
          cmd = "Reslice [/]...";
          break;
        case KeyEvent.VK_COMMA:
        case 0xbc:
          if (isStack) cmd = "Previous Slice [<]";
          break;
        case KeyEvent.VK_PERIOD:
        case 0xbe:
          if (isStack) cmd = "Next Slice [>]";
          break;
        case KeyEvent.VK_LEFT:
        case KeyEvent.VK_RIGHT:
        case KeyEvent.VK_UP:
        case KeyEvent.VK_DOWN: // arrow keys
          if (imp == null) return;
          Roi roi = imp.getRoi();
          if (IJ.shiftKeyDown() && imp == Orthogonal_Views.getImage()) return;
          boolean stackKey = imp.getStackSize() > 1 && (roi == null || IJ.shiftKeyDown());
          boolean zoomKey = roi == null || IJ.shiftKeyDown() || IJ.controlKeyDown();
          if (stackKey && keyCode == KeyEvent.VK_RIGHT) cmd = "Next Slice [>]";
          else if (stackKey && keyCode == KeyEvent.VK_LEFT) cmd = "Previous Slice [<]";
          else if (zoomKey
              && keyCode == KeyEvent.VK_DOWN
              && !ignoreArrowKeys(imp)
              && Toolbar.getToolId() < Toolbar.SPARE6) cmd = "Out [-]";
          else if (zoomKey
              && keyCode == KeyEvent.VK_UP
              && !ignoreArrowKeys(imp)
              && Toolbar.getToolId() < Toolbar.SPARE6) cmd = "In [+]";
          else if (roi != null) {
            if ((flags & KeyEvent.ALT_MASK) != 0) roi.nudgeCorner(keyCode);
            else roi.nudge(keyCode);
            return;
          }
          break;
        case KeyEvent.VK_ESCAPE:
          abortPluginOrMacro(imp);
          return;
        case KeyEvent.VK_ENTER:
          WindowManager.toFront(this);
          return;
        default:
          break;
      }
    }

    if (cmd != null && !cmd.equals("")) {
      commandName = cmd;
      if (cmd.equals("Fill") || cmd.equals("Draw")) hotkey = true;
      if (cmd.charAt(0) == MacroInstaller.commandPrefix) MacroInstaller.runMacroShortcut(cmd);
      else {
        doCommand(cmd);
        keyPressedTime = System.currentTimeMillis();
        lastKeyCommand = cmd;
      }
    }
  }
Exemple #11
0
 public void mousePressed(MouseEvent e) {
   Undo.reset();
   if (!Prefs.noClickToGC) System.gc();
   IJ.showStatus(version() + IJ.freeMemory());
   if (IJ.debugMode) IJ.log("Windows: " + WindowManager.getWindowCount());
 }
  public void build_bricks() {

    ImagePlus imp;
    ImagePlus orgimp;
    ImageStack stack;
    FileInfo finfo;

    if (lvImgTitle.isEmpty()) return;
    orgimp = WindowManager.getImage(lvImgTitle.get(0));
    imp = orgimp;

    finfo = imp.getFileInfo();
    if (finfo == null) return;

    int[] dims = imp.getDimensions();
    int imageW = dims[0];
    int imageH = dims[1];
    int nCh = dims[2];
    int imageD = dims[3];
    int nFrame = dims[4];
    int bdepth = imp.getBitDepth();
    double xspc = finfo.pixelWidth;
    double yspc = finfo.pixelHeight;
    double zspc = finfo.pixelDepth;
    double z_aspect = Math.max(xspc, yspc) / zspc;

    int orgW = imageW;
    int orgH = imageH;
    int orgD = imageD;
    double orgxspc = xspc;
    double orgyspc = yspc;
    double orgzspc = zspc;

    lv = lvImgTitle.size();
    if (filetype == "JPEG") {
      for (int l = 0; l < lv; l++) {
        if (WindowManager.getImage(lvImgTitle.get(l)).getBitDepth() != 8) {
          IJ.error("A SOURCE IMAGE MUST BE 8BIT GLAYSCALE");
          return;
        }
      }
    }

    // calculate levels
    /*		int baseXY = 256;
    		int baseZ = 256;

    		if (z_aspect < 0.5) baseZ = 128;
    		if (z_aspect > 2.0) baseXY = 128;
    		if (z_aspect >= 0.5 && z_aspect < 1.0) baseZ = (int)(baseZ*z_aspect);
    		if (z_aspect > 1.0 && z_aspect <= 2.0) baseXY = (int)(baseXY/z_aspect);

    		IJ.log("Z_aspect: " + z_aspect);
    		IJ.log("BaseXY: " + baseXY);
    		IJ.log("BaseZ: " + baseZ);
    */

    int baseXY = 256;
    int baseZ = 128;
    int dbXY = Math.max(orgW, orgH) / baseXY;
    if (Math.max(orgW, orgH) % baseXY > 0) dbXY *= 2;
    int dbZ = orgD / baseZ;
    if (orgD % baseZ > 0) dbZ *= 2;
    lv = Math.max(log2(dbXY), log2(dbZ)) + 1;

    int ww = orgW;
    int hh = orgH;
    int dd = orgD;
    for (int l = 0; l < lv; l++) {
      int bwnum = ww / baseXY;
      if (ww % baseXY > 0) bwnum++;
      int bhnum = hh / baseXY;
      if (hh % baseXY > 0) bhnum++;
      int bdnum = dd / baseZ;
      if (dd % baseZ > 0) bdnum++;

      if (bwnum % 2 == 0) bwnum++;
      if (bhnum % 2 == 0) bhnum++;
      if (bdnum % 2 == 0) bdnum++;

      int bw = (bwnum <= 1) ? ww : ww / bwnum + 1 + (ww % bwnum > 0 ? 1 : 0);
      int bh = (bhnum <= 1) ? hh : hh / bhnum + 1 + (hh % bhnum > 0 ? 1 : 0);
      int bd = (bdnum <= 1) ? dd : dd / bdnum + 1 + (dd % bdnum > 0 ? 1 : 0);

      bwlist.add(bw);
      bhlist.add(bh);
      bdlist.add(bd);

      IJ.log("LEVEL: " + l);
      IJ.log("  width: " + ww);
      IJ.log("  hight: " + hh);
      IJ.log("  depth: " + dd);
      IJ.log("  bw: " + bw);
      IJ.log("  bh: " + bh);
      IJ.log("  bd: " + bd);

      int xyl2 = Math.max(ww, hh) / baseXY;
      if (Math.max(ww, hh) % baseXY > 0) xyl2 *= 2;
      if (lv - 1 - log2(xyl2) <= l) {
        ww /= 2;
        hh /= 2;
      }
      IJ.log("  xyl2: " + (lv - 1 - log2(xyl2)));

      int zl2 = dd / baseZ;
      if (dd % baseZ > 0) zl2 *= 2;
      if (lv - 1 - log2(zl2) <= l) dd /= 2;
      IJ.log("  zl2: " + (lv - 1 - log2(zl2)));

      if (l < lv - 1) {
        lvImgTitle.add(lvImgTitle.get(0) + "_level" + (l + 1));
        IJ.selectWindow(lvImgTitle.get(0));
        IJ.run(
            "Scale...",
            "x=- y=- z=- width="
                + ww
                + " height="
                + hh
                + " depth="
                + dd
                + " interpolation=Bicubic average process create title="
                + lvImgTitle.get(l + 1));
      }
    }

    for (int l = 0; l < lv; l++) {
      IJ.log(lvImgTitle.get(l));
    }

    Document doc = newXMLDocument();
    Element root = doc.createElement("BRK");
    root.setAttribute("version", "1.0");
    root.setAttribute("nLevel", String.valueOf(lv));
    root.setAttribute("nChannel", String.valueOf(nCh));
    root.setAttribute("nFrame", String.valueOf(nFrame));
    doc.appendChild(root);

    for (int l = 0; l < lv; l++) {
      IJ.showProgress(0.0);

      int[] dims2 = imp.getDimensions();
      IJ.log(
          "W: "
              + String.valueOf(dims2[0])
              + " H: "
              + String.valueOf(dims2[1])
              + " C: "
              + String.valueOf(dims2[2])
              + " D: "
              + String.valueOf(dims2[3])
              + " T: "
              + String.valueOf(dims2[4])
              + " b: "
              + String.valueOf(bdepth));

      bw = bwlist.get(l).intValue();
      bh = bhlist.get(l).intValue();
      bd = bdlist.get(l).intValue();

      boolean force_pow2 = false;
      /*			if(IsPowerOf2(bw) && IsPowerOf2(bh) && IsPowerOf2(bd)) force_pow2 = true;

      			if(force_pow2){
      				//force pow2
      				if(Pow2(bw) > bw) bw = Pow2(bw)/2;
      				if(Pow2(bh) > bh) bh = Pow2(bh)/2;
      				if(Pow2(bd) > bd) bd = Pow2(bd)/2;
      			}

      			if(bw > imageW) bw = (Pow2(imageW) == imageW) ? imageW : Pow2(imageW)/2;
      			if(bh > imageH) bh = (Pow2(imageH) == imageH) ? imageH : Pow2(imageH)/2;
      			if(bd > imageD) bd = (Pow2(imageD) == imageD) ? imageD : Pow2(imageD)/2;

      */
      if (bw > imageW) bw = imageW;
      if (bh > imageH) bh = imageH;
      if (bd > imageD) bd = imageD;

      if (bw <= 1 || bh <= 1 || bd <= 1) break;

      if (filetype == "JPEG" && (bw < 8 || bh < 8)) break;

      Element lvnode = doc.createElement("Level");
      lvnode.setAttribute("lv", String.valueOf(l));
      lvnode.setAttribute("imageW", String.valueOf(imageW));
      lvnode.setAttribute("imageH", String.valueOf(imageH));
      lvnode.setAttribute("imageD", String.valueOf(imageD));
      lvnode.setAttribute("xspc", String.valueOf(xspc));
      lvnode.setAttribute("yspc", String.valueOf(yspc));
      lvnode.setAttribute("zspc", String.valueOf(zspc));
      lvnode.setAttribute("bitDepth", String.valueOf(bdepth));
      root.appendChild(lvnode);

      Element brksnode = doc.createElement("Bricks");
      brksnode.setAttribute("brick_baseW", String.valueOf(bw));
      brksnode.setAttribute("brick_baseH", String.valueOf(bh));
      brksnode.setAttribute("brick_baseD", String.valueOf(bd));
      lvnode.appendChild(brksnode);

      ArrayList<Brick> bricks = new ArrayList<Brick>();
      int mw, mh, md, mw2, mh2, md2;
      double tx0, ty0, tz0, tx1, ty1, tz1;
      double bx0, by0, bz0, bx1, by1, bz1;
      for (int k = 0; k < imageD; k += bd) {
        if (k > 0) k--;
        for (int j = 0; j < imageH; j += bh) {
          if (j > 0) j--;
          for (int i = 0; i < imageW; i += bw) {
            if (i > 0) i--;
            mw = Math.min(bw, imageW - i);
            mh = Math.min(bh, imageH - j);
            md = Math.min(bd, imageD - k);

            if (force_pow2) {
              mw2 = Pow2(mw);
              mh2 = Pow2(mh);
              md2 = Pow2(md);
            } else {
              mw2 = mw;
              mh2 = mh;
              md2 = md;
            }

            if (filetype == "JPEG") {
              if (mw2 < 8) mw2 = 8;
              if (mh2 < 8) mh2 = 8;
            }

            tx0 = i == 0 ? 0.0d : ((mw2 - mw + 0.5d) / mw2);
            ty0 = j == 0 ? 0.0d : ((mh2 - mh + 0.5d) / mh2);
            tz0 = k == 0 ? 0.0d : ((md2 - md + 0.5d) / md2);

            tx1 = 1.0d - 0.5d / mw2;
            if (mw < bw) tx1 = 1.0d;
            if (imageW - i == bw) tx1 = 1.0d;

            ty1 = 1.0d - 0.5d / mh2;
            if (mh < bh) ty1 = 1.0d;
            if (imageH - j == bh) ty1 = 1.0d;

            tz1 = 1.0d - 0.5d / md2;
            if (md < bd) tz1 = 1.0d;
            if (imageD - k == bd) tz1 = 1.0d;

            bx0 = i == 0 ? 0.0d : (i + 0.5d) / (double) imageW;
            by0 = j == 0 ? 0.0d : (j + 0.5d) / (double) imageH;
            bz0 = k == 0 ? 0.0d : (k + 0.5d) / (double) imageD;

            bx1 = Math.min((i + bw - 0.5d) / (double) imageW, 1.0d);
            if (imageW - i == bw) bx1 = 1.0d;

            by1 = Math.min((j + bh - 0.5d) / (double) imageH, 1.0d);
            if (imageH - j == bh) by1 = 1.0d;

            bz1 = Math.min((k + bd - 0.5d) / (double) imageD, 1.0d);
            if (imageD - k == bd) bz1 = 1.0d;

            int x, y, z;
            x = i - (mw2 - mw);
            y = j - (mh2 - mh);
            z = k - (md2 - md);
            bricks.add(
                new Brick(
                    x, y, z, mw2, mh2, md2, 0, 0, tx0, ty0, tz0, tx1, ty1, tz1, bx0, by0, bz0, bx1,
                    by1, bz1));
          }
        }
      }

      Element fsnode = doc.createElement("Files");
      lvnode.appendChild(fsnode);

      stack = imp.getStack();

      int totalbricknum = nFrame * nCh * bricks.size();
      int curbricknum = 0;
      for (int f = 0; f < nFrame; f++) {
        for (int ch = 0; ch < nCh; ch++) {
          int sizelimit = bdsizelimit * 1024 * 1024;
          int bytecount = 0;
          int filecount = 0;
          int pd_bufsize = Math.max(sizelimit, bw * bh * bd * bdepth / 8);
          byte[] packed_data = new byte[pd_bufsize];
          String base_dataname =
              basename
                  + "_Lv"
                  + String.valueOf(l)
                  + "_Ch"
                  + String.valueOf(ch)
                  + "_Fr"
                  + String.valueOf(f);
          String current_dataname = base_dataname + "_data" + filecount;

          Brick b_first = bricks.get(0);
          if (b_first.z_ != 0) IJ.log("warning");
          int st_z = b_first.z_;
          int ed_z = b_first.z_ + b_first.d_;
          LinkedList<ImageProcessor> iplist = new LinkedList<ImageProcessor>();
          for (int s = st_z; s < ed_z; s++)
            iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));

          //					ImagePlus test;
          //					ImageStack tsst;
          //					test = NewImage.createByteImage("test", imageW, imageH, imageD,
          // NewImage.FILL_BLACK);
          //					tsst = test.getStack();
          for (int i = 0; i < bricks.size(); i++) {
            Brick b = bricks.get(i);

            if (ed_z > b.z_ || st_z < b.z_ + b.d_) {
              if (b.z_ > st_z) {
                for (int s = 0; s < b.z_ - st_z; s++) iplist.pollFirst();
                st_z = b.z_;
              } else if (b.z_ < st_z) {
                IJ.log("warning");
                for (int s = st_z - 1; s > b.z_; s--)
                  iplist.addFirst(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
                st_z = b.z_;
              }

              if (b.z_ + b.d_ > ed_z) {
                for (int s = ed_z; s < b.z_ + b.d_; s++)
                  iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
                ed_z = b.z_ + b.d_;
              } else if (b.z_ + b.d_ < ed_z) {
                IJ.log("warning");
                for (int s = 0; s < ed_z - (b.z_ + b.d_); s++) iplist.pollLast();
                ed_z = b.z_ + b.d_;
              }
            } else {
              IJ.log("warning");
              iplist.clear();
              st_z = b.z_;
              ed_z = b.z_ + b.d_;
              for (int s = st_z; s < ed_z; s++)
                iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
            }

            if (iplist.size() != b.d_) {
              IJ.log("Stack Error");
              return;
            }

            //						int zz = st_z;

            int bsize = 0;
            byte[] bdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8];
            Iterator<ImageProcessor> ipite = iplist.iterator();
            while (ipite.hasNext()) {

              //							ImageProcessor tsip = tsst.getProcessor(zz+1);

              ImageProcessor ip = ipite.next();
              ip.setRoi(b.x_, b.y_, b.w_, b.h_);
              if (bdepth == 8) {
                byte[] data = (byte[]) ip.crop().getPixels();
                System.arraycopy(data, 0, bdata, bsize, data.length);
                bsize += data.length;
              } else if (bdepth == 16) {
                ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8);
                buffer.order(ByteOrder.LITTLE_ENDIAN);
                short[] data = (short[]) ip.crop().getPixels();
                for (short e : data) buffer.putShort(e);
                System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length);
                bsize += buffer.array().length;
              } else if (bdepth == 32) {
                ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8);
                buffer.order(ByteOrder.LITTLE_ENDIAN);
                float[] data = (float[]) ip.crop().getPixels();
                for (float e : data) buffer.putFloat(e);
                System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length);
                bsize += buffer.array().length;
              }
            }

            String filename =
                basename
                    + "_Lv"
                    + String.valueOf(l)
                    + "_Ch"
                    + String.valueOf(ch)
                    + "_Fr"
                    + String.valueOf(f)
                    + "_ID"
                    + String.valueOf(i);

            int offset = bytecount;
            int datasize = bdata.length;

            if (filetype == "RAW") {
              int dummy = -1;
              // do nothing
            }
            if (filetype == "JPEG" && bdepth == 8) {
              try {
                DataBufferByte db = new DataBufferByte(bdata, datasize);
                Raster raster = Raster.createPackedRaster(db, b.w_, b.h_ * b.d_, 8, null);
                BufferedImage img =
                    new BufferedImage(b.w_, b.h_ * b.d_, BufferedImage.TYPE_BYTE_GRAY);
                img.setData(raster);
                ByteArrayOutputStream baos = new ByteArrayOutputStream();
                ImageOutputStream ios = ImageIO.createImageOutputStream(baos);
                String format = "jpg";
                Iterator<javax.imageio.ImageWriter> iter =
                    ImageIO.getImageWritersByFormatName("jpeg");
                javax.imageio.ImageWriter writer = iter.next();
                ImageWriteParam iwp = writer.getDefaultWriteParam();
                iwp.setCompressionMode(ImageWriteParam.MODE_EXPLICIT);
                iwp.setCompressionQuality((float) jpeg_quality * 0.01f);
                writer.setOutput(ios);
                writer.write(null, new IIOImage(img, null, null), iwp);
                // ImageIO.write(img, format, baos);
                bdata = baos.toByteArray();
                datasize = bdata.length;
              } catch (IOException e) {
                e.printStackTrace();
                return;
              }
            }
            if (filetype == "ZLIB") {
              byte[] tmpdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8];
              Deflater compresser = new Deflater();
              compresser.setInput(bdata);
              compresser.setLevel(Deflater.DEFAULT_COMPRESSION);
              compresser.setStrategy(Deflater.DEFAULT_STRATEGY);
              compresser.finish();
              datasize = compresser.deflate(tmpdata);
              bdata = tmpdata;
              compresser.end();
            }

            if (bytecount + datasize > sizelimit && bytecount > 0) {
              BufferedOutputStream fis = null;
              try {
                File file = new File(directory + current_dataname);
                fis = new BufferedOutputStream(new FileOutputStream(file));
                fis.write(packed_data, 0, bytecount);
              } catch (IOException e) {
                e.printStackTrace();
                return;
              } finally {
                try {
                  if (fis != null) fis.close();
                } catch (IOException e) {
                  e.printStackTrace();
                  return;
                }
              }
              filecount++;
              current_dataname = base_dataname + "_data" + filecount;
              bytecount = 0;
              offset = 0;
              System.arraycopy(bdata, 0, packed_data, bytecount, datasize);
              bytecount += datasize;
            } else {
              System.arraycopy(bdata, 0, packed_data, bytecount, datasize);
              bytecount += datasize;
            }

            Element filenode = doc.createElement("File");
            filenode.setAttribute("filename", current_dataname);
            filenode.setAttribute("channel", String.valueOf(ch));
            filenode.setAttribute("frame", String.valueOf(f));
            filenode.setAttribute("brickID", String.valueOf(i));
            filenode.setAttribute("offset", String.valueOf(offset));
            filenode.setAttribute("datasize", String.valueOf(datasize));
            filenode.setAttribute("filetype", String.valueOf(filetype));

            fsnode.appendChild(filenode);

            curbricknum++;
            IJ.showProgress((double) (curbricknum) / (double) (totalbricknum));
          }
          if (bytecount > 0) {
            BufferedOutputStream fis = null;
            try {
              File file = new File(directory + current_dataname);
              fis = new BufferedOutputStream(new FileOutputStream(file));
              fis.write(packed_data, 0, bytecount);
            } catch (IOException e) {
              e.printStackTrace();
              return;
            } finally {
              try {
                if (fis != null) fis.close();
              } catch (IOException e) {
                e.printStackTrace();
                return;
              }
            }
          }
        }
      }

      for (int i = 0; i < bricks.size(); i++) {
        Brick b = bricks.get(i);
        Element bricknode = doc.createElement("Brick");
        bricknode.setAttribute("id", String.valueOf(i));
        bricknode.setAttribute("st_x", String.valueOf(b.x_));
        bricknode.setAttribute("st_y", String.valueOf(b.y_));
        bricknode.setAttribute("st_z", String.valueOf(b.z_));
        bricknode.setAttribute("width", String.valueOf(b.w_));
        bricknode.setAttribute("height", String.valueOf(b.h_));
        bricknode.setAttribute("depth", String.valueOf(b.d_));
        brksnode.appendChild(bricknode);

        Element tboxnode = doc.createElement("tbox");
        tboxnode.setAttribute("x0", String.valueOf(b.tx0_));
        tboxnode.setAttribute("y0", String.valueOf(b.ty0_));
        tboxnode.setAttribute("z0", String.valueOf(b.tz0_));
        tboxnode.setAttribute("x1", String.valueOf(b.tx1_));
        tboxnode.setAttribute("y1", String.valueOf(b.ty1_));
        tboxnode.setAttribute("z1", String.valueOf(b.tz1_));
        bricknode.appendChild(tboxnode);

        Element bboxnode = doc.createElement("bbox");
        bboxnode.setAttribute("x0", String.valueOf(b.bx0_));
        bboxnode.setAttribute("y0", String.valueOf(b.by0_));
        bboxnode.setAttribute("z0", String.valueOf(b.bz0_));
        bboxnode.setAttribute("x1", String.valueOf(b.bx1_));
        bboxnode.setAttribute("y1", String.valueOf(b.by1_));
        bboxnode.setAttribute("z1", String.valueOf(b.bz1_));
        bricknode.appendChild(bboxnode);
      }

      if (l < lv - 1) {
        imp = WindowManager.getImage(lvImgTitle.get(l + 1));
        int[] newdims = imp.getDimensions();
        imageW = newdims[0];
        imageH = newdims[1];
        imageD = newdims[3];
        xspc = orgxspc * ((double) orgW / (double) imageW);
        yspc = orgyspc * ((double) orgH / (double) imageH);
        zspc = orgzspc * ((double) orgD / (double) imageD);
        bdepth = imp.getBitDepth();
      }
    }

    File newXMLfile = new File(directory + basename + ".vvd");
    writeXML(newXMLfile, doc);

    for (int l = 1; l < lv; l++) {
      imp = WindowManager.getImage(lvImgTitle.get(l));
      imp.changes = false;
      imp.close();
    }
  }
    public BandAdjuster() {

      super("Threshold Colour");
      if (instance != null) {
        instance.toFront();
        return;
      }
      imp = WindowManager.getCurrentImage();
      if (imp == null) {
        IJ.beep();
        IJ.showStatus("No image");
        return;
      }
      IJ.run("Select None");
      thread = new Thread(this, "BandAdjuster");
      WindowManager.addWindow(this);
      instance = this;
      IJ.register(PasteController.class);

      ij = IJ.getInstance();
      Font font = new Font("SansSerif", Font.PLAIN, 10);
      GridBagLayout gridbag = new GridBagLayout();
      GridBagConstraints c = new GridBagConstraints();
      setLayout(gridbag);

      int y = 0;
      c.gridx = 0;
      c.gridy = y;
      c.gridwidth = 1;
      c.weightx = 0;
      c.insets = new Insets(5, 0, 0, 0);
      labelh = new Label("Hue", Label.CENTER);
      add(labelh, c);

      c.gridx = 1;
      c.gridy = y++;
      c.gridwidth = 1;
      c.weightx = 0;
      c.insets = new Insets(7, 0, 0, 0);
      labelf = new Label("Filter type", Label.RIGHT);
      add(labelf, c);

      // plot
      c.gridx = 0;
      c.gridy = y;
      c.gridwidth = 1;
      c.fill = c.BOTH;
      c.anchor = c.CENTER;
      c.insets = new Insets(0, 5, 0, 0);
      add(plot, c);

      // checkboxes
      panelh = new Panel();
      filterTypeH = new CheckboxGroup();
      bandPassH = new Checkbox("Pass");
      bandPassH.setCheckboxGroup(filterTypeH);
      bandPassH.addItemListener(this);
      panelh.add(bandPassH);
      bandStopH = new Checkbox("Stop");
      bandStopH.setCheckboxGroup(filterTypeH);
      bandStopH.addItemListener(this);
      panelh.add(bandStopH);
      bandPassH.setState(true);
      c.gridx = 1;
      c.gridy = y++;
      c.gridwidth = 2;
      c.insets = new Insets(5, 0, 0, 0);
      add(panelh, c);

      // minHue slider
      minSlider = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 1;
      c.weightx = IJ.isMacintosh() ? 90 : 100;
      c.fill = c.HORIZONTAL;
      c.insets = new Insets(5, 5, 0, 0);

      add(minSlider, c);
      minSlider.addAdjustmentListener(this);
      minSlider.setUnitIncrement(1);

      // minHue slider label
      c.gridx = 1;
      c.gridwidth = 1;
      c.weightx = IJ.isMacintosh() ? 10 : 0;
      c.insets = new Insets(5, 0, 0, 0);
      label1 = new Label("       ", Label.LEFT);
      label1.setFont(font);
      add(label1, c);

      // maxHue sliderHue
      maxSlider = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
      c.gridx = 0;
      c.gridy = y;
      c.gridwidth = 1;
      c.weightx = 100;
      c.insets = new Insets(5, 5, 0, 0);
      add(maxSlider, c);
      maxSlider.addAdjustmentListener(this);
      maxSlider.setUnitIncrement(1);

      // maxHue slider label
      c.gridx = 1;
      c.gridwidth = 1;
      c.gridy = y++;
      c.weightx = 0;
      c.insets = new Insets(5, 0, 0, 0);
      label2 = new Label("       ", Label.LEFT);
      label2.setFont(font);
      add(label2, c);

      // =====
      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 1;
      c.weightx = 0;
      c.insets = new Insets(10, 0, 0, 0);
      labels = new Label("Saturation", Label.CENTER);
      add(labels, c);

      // plot
      c.gridx = 0;
      c.gridy = y;
      c.gridwidth = 1;
      c.fill = c.BOTH;
      c.anchor = c.CENTER;
      c.insets = new Insets(0, 5, 0, 0);
      add(splot, c);

      // checkboxes
      panels = new Panel();
      filterTypeS = new CheckboxGroup();
      bandPassS = new Checkbox("Pass");
      bandPassS.setCheckboxGroup(filterTypeS);
      bandPassS.addItemListener(this);
      panels.add(bandPassS);
      bandStopS = new Checkbox("Stop");
      bandStopS.setCheckboxGroup(filterTypeS);
      bandStopS.addItemListener(this);
      panels.add(bandStopS);
      bandPassS.setState(true);
      c.gridx = 1;
      c.gridy = y++;
      c.gridwidth = 2;
      c.insets = new Insets(5, 0, 0, 0);
      add(panels, c);

      // minSat slider
      minSlider2 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 1;
      c.weightx = IJ.isMacintosh() ? 90 : 100;
      c.fill = c.HORIZONTAL;
      c.insets = new Insets(5, 5, 0, 0);
      add(minSlider2, c);
      minSlider2.addAdjustmentListener(this);
      minSlider2.setUnitIncrement(1);

      // minSat slider label
      c.gridx = 1;
      c.gridwidth = 1;
      c.weightx = IJ.isMacintosh() ? 10 : 0;
      c.insets = new Insets(5, 0, 0, 0);
      label3 = new Label("       ", Label.LEFT);
      label3.setFont(font);
      add(label3, c);

      // maxSat slider
      maxSlider2 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 1;
      c.weightx = 100;
      c.insets = new Insets(5, 5, 0, 0);
      add(maxSlider2, c);
      maxSlider2.addAdjustmentListener(this);
      maxSlider2.setUnitIncrement(1);

      // maxSat slider label
      c.gridx = 1;
      c.gridwidth = 1;
      c.weightx = 0;
      c.insets = new Insets(5, 0, 0, 0);
      label4 = new Label("       ", Label.LEFT);
      label4.setFont(font);
      add(label4, c);

      // =====
      c.gridx = 0;
      c.gridwidth = 1;
      c.gridy = y++;
      c.weightx = 0;
      c.insets = new Insets(10, 0, 0, 0);
      labelb = new Label("Brightness", Label.CENTER);
      add(labelb, c);

      c.gridx = 0;
      c.gridwidth = 1;
      c.gridy = y;
      c.fill = c.BOTH;
      c.anchor = c.CENTER;
      c.insets = new Insets(0, 5, 0, 0);
      add(bplot, c);

      // checkboxes
      panelb = new Panel();
      filterTypeB = new CheckboxGroup();
      bandPassB = new Checkbox("Pass");
      bandPassB.setCheckboxGroup(filterTypeB);
      bandPassB.addItemListener(this);
      panelb.add(bandPassB);
      bandStopB = new Checkbox("Stop");
      bandStopB.setCheckboxGroup(filterTypeB);
      bandStopB.addItemListener(this);
      panelb.add(bandStopB);
      bandPassB.setState(true);
      c.gridx = 1;
      c.gridy = y++;
      c.gridwidth = 2;
      c.insets = new Insets(5, 0, 0, 0);
      add(panelb, c);

      // minBri slider
      minSlider3 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 1;
      c.weightx = IJ.isMacintosh() ? 90 : 100;
      c.fill = c.HORIZONTAL;
      c.insets = new Insets(5, 5, 0, 0);
      add(minSlider3, c);
      minSlider3.addAdjustmentListener(this);
      minSlider3.setUnitIncrement(1);

      // minBri slider label
      c.gridx = 1;
      c.gridwidth = 1;
      c.weightx = IJ.isMacintosh() ? 10 : 0;
      c.insets = new Insets(5, 0, 0, 0);
      label5 = new Label("       ", Label.LEFT);
      label5.setFont(font);
      add(label5, c);

      // maxBri slider
      maxSlider3 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 1;
      c.weightx = 100;
      c.insets = new Insets(5, 5, 0, 0);
      add(maxSlider3, c);
      maxSlider3.addAdjustmentListener(this);
      maxSlider3.setUnitIncrement(1);

      // maxBri slider label
      c.gridx = 1;
      c.gridwidth = 1;
      c.weightx = 0;
      c.insets = new Insets(5, 0, 0, 0);
      label6 = new Label("       ", Label.LEFT);
      label6.setFont(font);
      add(label6, c);

      // =====
      panelt = new Panel();
      threshold = new Checkbox("Threshold");
      threshold.addItemListener(this);
      panelt.add(threshold);

      invert = new Checkbox("Invert");
      invert.addItemListener(this);
      panelt.add(invert);

      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 2;
      c.insets = new Insets(0, 0, 0, 0);
      add(panelt, c);

      // buttons
      panel = new Panel();
      // panel.setLayout(new GridLayout(2, 2, 0, 0));
      originalB = new Button("Original");
      originalB.setEnabled(false);
      originalB.addActionListener(this);
      originalB.addKeyListener(ij);
      panel.add(originalB);

      filteredB = new Button("Filtered");
      filteredB.setEnabled(false);
      filteredB.addActionListener(this);
      filteredB.addKeyListener(ij);
      panel.add(filteredB);

      stackB = new Button("Stack");
      stackB.addActionListener(this);
      stackB.addKeyListener(ij);
      panel.add(stackB);

      helpB = new Button("Help");
      helpB.addActionListener(this);
      helpB.addKeyListener(ij);
      panel.add(helpB);

      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 2;
      c.insets = new Insets(0, 0, 0, 0);
      add(panel, c);

      panelMode = new Panel();

      sampleB = new Button("Sample");
      sampleB.addActionListener(this);
      sampleB.addKeyListener(ij);
      panelMode.add(sampleB);

      colourMode = new CheckboxGroup();
      hsb = new Checkbox("HSB");
      hsb.setCheckboxGroup(colourMode);
      hsb.addItemListener(this);
      panelMode.add(hsb);
      hsb.setState(true);
      rgb = new Checkbox("RGB");
      rgb.setCheckboxGroup(colourMode);
      rgb.addItemListener(this);
      panelMode.add(rgb);

      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 2;
      c.insets = new Insets(0, 0, 0, 0);
      add(panelMode, c);

      addKeyListener(ij); // ImageJ handles keyboard shortcuts
      pack();
      GUI.center(this);
      setVisible(true);

      ip = setup(imp);
      if (ip == null) {
        imp.unlock();
        IJ.beep();
        IJ.showStatus("RGB image cannot be thresholded");
        return;
      }
      thread.start();
    }