Ejemplo n.º 1
0
  public boolean beadCalibration3d() {
    imp = IJ.getImage();
    if (imp == null) {
      IJ.noImage();
      return false;
    } else if (imp.getStackSize() == 1) {
      IJ.error("Stack required");
      return false;
    } else if (imp.getType() != ImagePlus.GRAY8 && imp.getType() != ImagePlus.GRAY16) {
      // In order to support 32bit images, pict[] must be changed to float[], and  getPixel(x, y);
      // requires a Float.intBitsToFloat() conversion
      IJ.error("8 or 16 bit greyscale image required");
      return false;
    }
    width = imp.getWidth();
    height = imp.getHeight();
    nslices = imp.getStackSize();
    imtitle = imp.getTitle();

    models[0] = "*None*";
    models[1] = "line";
    models[2] = "2nd degree polynomial";
    models[3] = "3rd degree polynomial";
    models[4] = "4th degree polynomial";

    GenericDialog gd = new GenericDialog("3D PALM calibration");
    gd.addNumericField("Maximum FWHM (in px)", prefs.get("QuickPALM.3Dcal_fwhm", 20), 0);
    gd.addNumericField(
        "Particle local threshold (% maximum intensity)", prefs.get("QuickPALM.pthrsh", 20), 0);
    gd.addNumericField("Z-spacing (nm)", prefs.get("QuickPALM.z-step", 10), 2);
    gd.addNumericField("Calibration Z-smoothing (radius)", prefs.get("QuickPALM.window", 1), 0);
    gd.addChoice("Model", models, prefs.get("QuickPALM.model", models[3]));
    gd.addCheckbox(
        "Show divergence of bead positions against model",
        prefs.get("QuickPALM.3Dcal_showDivergence", false));
    gd.addCheckbox("Show extra particle info", prefs.get("QuickPALM.3Dcal_showExtraInfo", false));
    gd.addMessage("\n\nDon't forget to save the table in the end...");
    gd.showDialog();
    if (gd.wasCanceled()) return false;
    fwhm = gd.getNextNumber();
    prefs.set("QuickPALM.QuickPALM.3Dcal_fwhm", fwhm);
    pthrsh = gd.getNextNumber() / 100;
    prefs.set("QuickPALM.pthrsh", pthrsh * 100);
    cal_z = gd.getNextNumber();
    prefs.set("QuickPALM.z-step", cal_z);
    window = (int) gd.getNextNumber();
    prefs.set("QuickPALM.window", window);
    model = gd.getNextChoice();
    prefs.set("QuickPALM.model", model);
    part_divergence = gd.getNextBoolean();
    prefs.set("QuickPALM.3Dcal_showDivergence", part_divergence);
    part_extrainfo = gd.getNextBoolean();
    prefs.set("QuickPALM.3Dcal_showExtraInfo", part_extrainfo);
    return true;
  }
Ejemplo n.º 2
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);
 }
Ejemplo n.º 3
0
  public boolean analyseParticles(MyFunctions f) {
    GenericDialog gd = new GenericDialog("Analyse PALM/STORM Particles");
    gd.addNumericField("Minimum SNR", prefs.get("QuickPALM.snr", 5), 2);
    gd.addNumericField("Maximum FWHM (in px)", prefs.get("QuickPALM.fwhm", 4), 0);
    gd.addNumericField("Image plane pixel size (nm)", prefs.get("QuickPALM.pixelsize", 106), 2);
    gd.addCheckbox("Smart SNR", prefs.get("QuickPALM.smartsnr", true));
    gd.addCheckbox(
        "3D PALM (astigmatism) - will require calibration file",
        prefs.get("QuickPALM.is3d", false));
    gd.addCheckbox("Online rendering", prefs.get("QuickPALM.view", true));
    gd.addCheckbox("Attach to running acquisition", prefs.get("QuickPALM.attach", false));
    gd.addCheckbox("Stream particle info directly into file", prefs.get("QuickPALM.stream", true));
    gd.addMessage("\n");
    // -----------------------------------------
    gd.addMessage("-- Online rendering settings (used only if selected) --");
    gd.addMessage("\n");
    gd.addNumericField("Pixel size of rendered image (nm)", 30, 2);
    gd.addNumericField("Accumulate last (0 to accumulate all frames)", 0, 0);
    gd.addNumericField("Update every (frames)", 10, 0);
    // gd.addNumericField("Allow color saturation (%)", 50, 0);
    gd.addMessage("\n");
    // -----------------------------------------
    gd.addMessage("-- Attach to running acquisition settings (used only if selected) --");
    gd.addMessage("\n");
    gd.addStringField(
        "_Image name pattern (NN...NN represents the numerical change)",
        prefs.get("QuickPALM.pattern", "imgNNNNNNNNN.tif"),
        20);
    gd.addNumericField("Start NN...NN with", 0, 0);
    gd.addNumericField("In acquisition max. wait time for new image (ms)", 50, 0);
    gd.addMessage("\n");
    // -----------------------------------------
    gd.addMessage("-- Advanced settings (don't normally need to be changed) --");
    gd.addMessage("\n");
    gd.addNumericField("_Minimum symmetry (%)", prefs.get("QuickPALM.symmetry", 50), 0);
    gd.addNumericField(
        "Local threshold (% maximum intensity)", prefs.get("QuickPALM.lthreshold", 20), 0);
    gd.addNumericField("_Maximum iterations per frame", prefs.get("QuickPALM.maxiter", 1000), 0);
    gd.addNumericField(
        "Threads (each takes ~3*[frame size] in memory)", prefs.get("QuickPALM.nthreads", 50), 0);
    gd.addMessage("\n\nDon't forget to save the table in the end...");

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

    snr = (int) gd.getNextNumber();
    prefs.set("QuickPALM.snr", snr);
    fwhm = gd.getNextNumber();
    prefs.set("QuickPALM.fwhm", fwhm);
    pixelsize = gd.getNextNumber();
    prefs.set("QuickPALM.pixelsize", pixelsize);

    smartsnr = gd.getNextBoolean();
    prefs.set("QuickPALM.smartsnr", smartsnr);
    is3d = gd.getNextBoolean();
    prefs.set("QuickPALM.is3d", is3d);
    view = gd.getNextBoolean();
    prefs.set("QuickPALM.view", view);
    attach = gd.getNextBoolean();
    prefs.set("QuickPALM.attach", attach);

    if (gd.getNextBoolean()) {
      f.psave = new ParticleSaver();
      f.psave.setup();
      prefs.set("QuickPALM.stream", true);
    } else prefs.set("QuickPALM.stream", false);
    // --

    magn = pixelsize / gd.getNextNumber();
    viewer_accumulate = (int) gd.getNextNumber();
    viewer_update = (int) gd.getNextNumber();

    // --
    pattern = gd.getNextString().trim();
    prefs.set("QuickPALM.pattern", pattern);
    prefix = pattern.substring(0, pattern.indexOf("N"));
    sufix = pattern.substring(pattern.lastIndexOf("N") + 1, pattern.length());
    nimchars = pattern.split("N").length - 1;
    nimstart = (int) gd.getNextNumber();
    waittime = (int) gd.getNextNumber();

    // --

    symmetry = gd.getNextNumber() / 100;
    prefs.set("QuickPALM.symmetry", symmetry);
    pthrsh = gd.getNextNumber() / 100;
    prefs.set("QuickPALM.lthreshold", pthrsh * 100);
    maxpart = (int) gd.getNextNumber();
    prefs.set("QuickPALM.maxiter", maxpart);
    threads = (int) gd.getNextNumber();
    prefs.set("QuickPALM.nthreads", threads);

    return true;
  }
Ejemplo n.º 4
0
  public boolean reconstructDataset() {

    view_modes[0] = "3D color";
    view_modes[1] = "2D histogram";
    view_modes[2] = "2D particle intensity (16-bit)";
    view_modes[3] = "2D particle intensity (8-bit)";

    GenericDialog gd = new GenericDialog("Reconstruct PALM/STORM Dataset");
    gd.addNumericField(
        "Target pixel size for the rendered image (nm)",
        prefs.get("QuickPALM.viewer_tpixelsize", 30),
        2);
    gd.addNumericField("Original image width (px)", prefs.get("QuickPALM.viewer_owidth", 512), 2);
    gd.addNumericField("Original image height (px)", prefs.get("QuickPALM.viewer_oheight", 512), 2);
    gd.addChoice("View mode", view_modes, prefs.get("QuickPALM.view_mode", view_modes[1]));
    // gd.addNumericField("Allow image saturation (%)", prefs.get("QuickPALM.saturation", 50), 0);

    gd.addCheckbox(
        "Simulate sub-difraction spot (gaussian convolution - only 2D)",
        prefs.get("QuickPALM.viewer_doConvolve", true));
    // gd.addCheckbox("Make 3D stack", prefs.get("QuickPALM.viewer_do3d", false));
    // gd.addCheckbox("Make movie", prefs.get("QuickPALM.viewer_doMovie", false));
    gd.addCheckbox("Make 3D stack", false);
    gd.addCheckbox("Make movie", false);
    // gd.addCheckbox("Save only and don't show", prefs.get("QuickPALM.viewer_doSave", false));
    gd.addMessage("\n");

    // -----------------------------------------
    gd.addMessage("-- Simulate sub-difraction spot settings (used only if selected) --");
    gd.addNumericField("FWHM of the spot", prefs.get("QuickPALM.viewer_fwhm", 30), 2);
    gd.addMessage("\n");

    // -----------------------------------------
    gd.addMessage("-- Make 3D stack settings (used only if selected) --");
    gd.addNumericField("Z-spacing between slices (nm)", prefs.get("QuickPALM.viewer_zstep", 50), 2);
    gd.addNumericField(
        "Merge particle Z-position above (nm - 0 for full Z range)",
        prefs.get("QuickPALM.viewer_mergeabove", 0),
        2);
    gd.addNumericField(
        "Merge particle Z-position bellow (nm - 0 for full Z range)",
        prefs.get("QuickPALM.viewer_mergebellow", 0),
        2);
    gd.addMessage("\n");

    // -----------------------------------------
    gd.addMessage("-- Make movie settings (used only if selected) --");
    gd.addNumericField(
        "Make a reconstruction in every N frames", prefs.get("QuickPALM.viewer_update", 10), 0);
    gd.addNumericField(
        "Accumulate N neighboring frames for each reconstruction\n(set to 0 to accumulate all the preceding frames)",
        prefs.get("QuickPALM.viewer_accumulate", 100),
        0);

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

    viewer_tpixelsize = gd.getNextNumber();
    prefs.set("QuickPALM.viewer_tpixelsize", viewer_tpixelsize);
    viewer_owidth = (int) gd.getNextNumber();
    prefs.set("QuickPALM.viewer_owidth", viewer_owidth);
    viewer_oheight = (int) gd.getNextNumber();
    prefs.set("QuickPALM.viewer_oheight", viewer_oheight);
    view_mode = gd.getNextChoice();
    prefs.set("QuickPALM.view_mode", view_mode);

    viewer_doConvolve = gd.getNextBoolean();
    prefs.set("QuickPALM.viewer_doConvolve", viewer_doConvolve);
    viewer_do3d = gd.getNextBoolean();
    prefs.set("QuickPALM.viewer_do3d", viewer_do3d);
    viewer_doMovie = gd.getNextBoolean();
    prefs.set("QuickPALM.viewer_doMovie", viewer_doMovie);
    // viewer_doSave = gd.getNextBoolean();
    // prefs.set("QuickPALM.viewer_doSave", viewer_doSave);

    // -- Simulate sub-difraction spot
    viewer_fwhm = gd.getNextNumber();
    prefs.set("QuickPALM.viewer_fwhm", viewer_fwhm);

    // -- Show B&W
    // viewer_is8bit = gd.getNextBoolean();
    // prefs.set("QuickPALM.viewer_is8bit", viewer_is8bit);

    // -- Make 3D stack
    viewer_zstep = gd.getNextNumber();
    prefs.set("QuickPALM.viewer_zstep", viewer_zstep);
    viewer_mergeabove = gd.getNextNumber();
    prefs.set("QuickPALM.viewer_mergeabove", viewer_mergeabove);
    viewer_mergebellow = gd.getNextNumber();
    prefs.set("QuickPALM.viewer_mergebellow", viewer_mergebellow);

    // -- Make Movie
    viewer_update = (int) gd.getNextNumber();
    prefs.set("QuickPALM.viewer_update", viewer_update);
    viewer_accumulate = (int) gd.getNextNumber();
    prefs.set("QuickPALM.viewer_accumulate", viewer_accumulate);

    return true;
  }
Ejemplo n.º 5
0
  /** Ask for parameters and then execute. */
  public void run(String arg) {
    // 1 - Obtain the currently active image:
    ImagePlus imp = IJ.getImage();

    if (null == imp) {
      IJ.showMessage("There must be at least one image open");
      return;
    }

    if (imp.getBitDepth() != 8) {
      IJ.showMessage("Error", "Only 8-bit images are supported");
      return;
    }

    // 2 - Ask for parameters:
    GenericDialog gd = new GenericDialog("Auto Local Threshold");
    String[] methods = {
      "Try all",
      "Bernsen",
      "Contrast",
      "Mean",
      "Median",
      "MidGrey",
      "Niblack",
      "Otsu",
      "Phansalkar",
      "Sauvola"
    };
    gd.addMessage("Auto Local Threshold v1.5");
    gd.addChoice("Method", methods, methods[0]);
    gd.addNumericField("Radius", 15, 0);
    gd.addMessage("Special paramters (if different from default)");
    gd.addNumericField("Parameter_1", 0, 0);
    gd.addNumericField("Parameter_2", 0, 0);
    gd.addCheckbox("White objects on black background", true);
    if (imp.getStackSize() > 1) {
      gd.addCheckbox("Stack", false);
    }
    gd.addMessage("Thresholded result is always shown in white [255].");
    gd.showDialog();
    if (gd.wasCanceled()) return;

    // 3 - Retrieve parameters from the dialog
    String myMethod = gd.getNextChoice();
    int radius = (int) gd.getNextNumber();
    double par1 = (double) gd.getNextNumber();
    double par2 = (double) gd.getNextNumber();
    boolean doIwhite = gd.getNextBoolean();
    boolean doIstack = false;

    int stackSize = imp.getStackSize();
    if (stackSize > 1) doIstack = gd.getNextBoolean();

    // 4 - Execute!
    // long start = System.currentTimeMillis();
    if (myMethod.equals("Try all")) {
      ImageProcessor ip = imp.getProcessor();
      int xe = ip.getWidth();
      int ye = ip.getHeight();
      int ml = methods.length;
      ImagePlus imp2, imp3;
      ImageStack tstack = null, stackNew;
      if (stackSize > 1 && doIstack) {
        boolean doItAnyway = true;
        if (stackSize > 25) {
          YesNoCancelDialog d =
              new YesNoCancelDialog(
                  IJ.getInstance(),
                  "Auto Local Threshold",
                  "You might run out of memory.\n \nDisplay "
                      + stackSize
                      + " slices?\n \n \'No\' will process without display and\noutput results to the log window.");
          if (!d.yesPressed()) {
            //						doIlog=true; //will show in the log window
            doItAnyway = false;
          }
          if (d.cancelPressed()) return;
        }

        for (int j = 1; j <= stackSize; j++) {
          imp.setSlice(j);
          ip = imp.getProcessor();
          tstack = new ImageStack(xe, ye);
          for (int k = 1; k < ml; k++) tstack.addSlice(methods[k], ip.duplicate());
          imp2 = new ImagePlus("Auto Threshold", tstack);
          imp2.updateAndDraw();

          for (int k = 1; k < ml; k++) {
            imp2.setSlice(k);
            Object[] result = exec(imp2, methods[k], radius, par1, par2, doIwhite);
          }
          // if (doItAnyway){
          CanvasResizer cr = new CanvasResizer();
          stackNew = cr.expandStack(tstack, (xe + 2), (ye + 18), 1, 1);
          imp3 = new ImagePlus("Auto Threshold", stackNew);
          imp3.updateAndDraw();
          MontageMaker mm = new MontageMaker();
          mm.makeMontage(imp3, 3, 3, 1.0, 1, (ml - 1), 1, 0, true); // 3 columns and 3 rows
        }
        imp.setSlice(1);
        // if (doItAnyway)
        IJ.run("Images to Stack", "method=[Copy (center)] title=Montage");
        return;
      } else { // single image try all
        tstack = new ImageStack(xe, ye);
        for (int k = 1; k < ml; k++) tstack.addSlice(methods[k], ip.duplicate());
        imp2 = new ImagePlus("Auto Threshold", tstack);
        imp2.updateAndDraw();

        for (int k = 1; k < ml; k++) {
          imp2.setSlice(k);
          // IJ.log("analyzing slice with "+methods[k]);
          Object[] result = exec(imp2, methods[k], radius, par1, par2, doIwhite);
        }
        // imp2.setSlice(1);
        CanvasResizer cr = new CanvasResizer();
        stackNew = cr.expandStack(tstack, (xe + 2), (ye + 18), 1, 1);
        imp3 = new ImagePlus("Auto Threshold", stackNew);
        imp3.updateAndDraw();
        MontageMaker mm = new MontageMaker();
        mm.makeMontage(imp3, 3, 3, 1.0, 1, (ml - 1), 1, 0, true);
        return;
      }
    } else { // selected a method
      if (stackSize > 1 && doIstack) { // whole stack
        //				if (doIstackHistogram) {// one global histogram
        //					Object[] result = exec(imp, myMethod, noWhite, noBlack, doIwhite, doIset, doIlog,
        // doIstackHistogram );
        //				}
        //				else{ // slice by slice
        for (int k = 1; k <= stackSize; k++) {
          imp.setSlice(k);
          Object[] result = exec(imp, myMethod, radius, par1, par2, doIwhite);
        }
        //				}
        imp.setSlice(1);
      } else { // just one slice
        Object[] result = exec(imp, myMethod, radius, par1, par2, doIwhite);
      }
      // 5 - If all went well, show the image:
      // not needed here as the source image is binarised
    }
  }
Ejemplo n.º 6
0
 public void itemStateChanged(ItemEvent e) {
   ImagePlus imp = WindowManager.getCurrentImage();
   if (imp == null) return;
   if (!imp.isComposite()) {
     int channels = imp.getNChannels();
     if (channels == 1 && imp.getStackSize() <= 4) channels = imp.getStackSize();
     if (imp.getBitDepth() == 24 || (channels > 1 && channels < CompositeImage.MAX_CHANNELS)) {
       GenericDialog gd = new GenericDialog(imp.getTitle());
       gd.addMessage("Convert to multi-channel composite image?");
       gd.showDialog();
       if (gd.wasCanceled()) return;
       else IJ.doCommand("Make Composite");
     } else {
       IJ.error(
           "Channels",
           "A composite image is required (e.g., "
               + moreLabel
               + " Open HeLa Cells),\nor create one using "
               + moreLabel
               + " Make Composite.");
       return;
     }
   }
   if (!imp.isComposite()) return;
   CompositeImage ci = (CompositeImage) imp;
   Object source = e.getSource();
   if (source == choice) {
     int index = ((Choice) source).getSelectedIndex();
     switch (index) {
       case 0:
         ci.setMode(IJ.COMPOSITE);
         break;
       case 1:
         ci.setMode(IJ.COLOR);
         break;
       case 2:
         ci.setMode(IJ.GRAYSCALE);
         break;
     }
     ci.updateAndDraw();
     if (Recorder.record) {
       String mode = null;
       switch (index) {
         case 0:
           mode = "composite";
           break;
         case 1:
           mode = "color";
           break;
         case 2:
           mode = "grayscale";
           break;
       }
       Recorder.record("Stack.setDisplayMode", mode);
     }
   } else if (source instanceof Checkbox) {
     for (int i = 0; i < checkbox.length; i++) {
       Checkbox cb = (Checkbox) source;
       if (cb == checkbox[i]) {
         if (ci.getMode() == IJ.COMPOSITE) {
           boolean[] active = ci.getActiveChannels();
           active[i] = cb.getState();
           if (Recorder.record) {
             String str = "";
             for (int c = 0; c < ci.getNChannels(); c++) str += active[c] ? "1" : "0";
             Recorder.record("Stack.setActiveChannels", str);
             Recorder.record("//Stack.toggleChannel", imp.getChannel());
           }
         } else {
           imp.setPosition(i + 1, imp.getSlice(), imp.getFrame());
           if (Recorder.record) Recorder.record("Stack.setChannel", i + 1);
         }
         ci.updateAndDraw();
         return;
       }
     }
   }
 }