private ImagePlus openImage(String directory, String name, String path) {
    Object o = tryOpen(directory, name, path);
    // if an image was returned, assume success
    if (o instanceof ImagePlus) return (ImagePlus) o;

    // try opening the file with LOCI Bio-Formats plugin - always check this last!
    // Do not call Bio-Formats if File>Import>Image Sequence is opening this file.
    if (o == null
        && (IJ.getVersion().compareTo("1.38j") < 0 || !IJ.redirectingErrorMessages())
        && (new File(path).exists())) {
      Object loci = IJ.runPlugIn("loci.plugins.LociImporter", path);
      if (loci != null) {
        // plugin exists and was launched
        try {
          // check whether plugin was successful
          Class c = loci.getClass();
          boolean success = c.getField("success").getBoolean(loci);
          boolean canceled = c.getField("canceled").getBoolean(loci);
          if (success || canceled) {
            width = IMAGE_OPENED;
            return null;
          }
        } catch (Exception exc) {
        }
      }
    }

    return null;
  } // openImage
  /** Called from io/Opener.java. */
  public void run(String path) {
    if (path.equals("")) return;
    File theFile = new File(path);
    String directory = theFile.getParent();
    String fileName = theFile.getName();
    if (directory == null) directory = "";

    // Try and recognise file type and load the file if recognised
    ImagePlus imp = openImage(directory, fileName, path);
    if (imp == null) {
      IJ.showStatus("");
      return; // failed to load file or plugin has opened and displayed it
    }
    ImageStack stack = imp.getStack();
    // get the title from the stack (falling back to the fileName)
    String title = imp.getTitle().equals("") ? fileName : imp.getTitle();
    // set the stack of this HandleExtraFileTypes object
    // to that attached to the ImagePlus object returned by openImage()
    setStack(title, stack);
    // copy over the calibration info since it doesn't come with the ImageProcessor
    setCalibration(imp.getCalibration());
    // also copy the Show Info field over if it exists
    if (imp.getProperty("Info") != null) setProperty("Info", imp.getProperty("Info"));
    // copy the FileInfo
    setFileInfo(imp.getOriginalFileInfo());
    // copy dimensions
    if (IJ.getVersion().compareTo("1.38s") >= 0)
      setDimensions(imp.getNChannels(), imp.getNSlices(), imp.getNFrames());
    if (IJ.getVersion().compareTo("1.41o") >= 0) setOpenAsHyperStack(imp.getOpenAsHyperStack());
  }
Example #3
0
 void loadTransformation(String filename, ResultsTable res) {
   try {
     String line;
     FileReader fr = new FileReader(filename);
     BufferedReader br = new BufferedReader(fr);
     if (!br.readLine().equals(" 	Z-Step	Raw Width minus Heigh	Calibration Width minus Height")) {
       IJ.error("File does not seam to be an Astigmatism calibration file");
       return;
     }
     // java.lang.String [] elements = new java.lang.String [3];
     java.lang.String[] elements;
     int counter = 1;
     res.reset();
     while ((line = br.readLine()) != null) {
       IJ.showStatus("Loading element " + counter + "... sit back and relax.");
       counter++;
       line.trim();
       elements = line.split("\t");
       res.incrementCounter();
       res.addValue("Z-Step", Double.parseDouble(elements[1]));
       res.addValue("Raw Width minus Heigh", Double.parseDouble(elements[2]));
       res.addValue("Calibration Width minus Height", Double.parseDouble(elements[3]));
     }
     fr.close();
   } catch (FileNotFoundException e) {
     IJ.error("File not found exception" + e);
     return;
   } catch (IOException e) {
     IJ.error("IOException exception" + e);
     return;
   } catch (NumberFormatException e) {
     IJ.error("Number format exception" + e);
     return;
   }
 }
Example #4
0
  public void run(String arg) {
    ImagePlus imp = WindowManager.getCurrentImage();
    if (imp == null) {
      IJ.noImage();
      return;
    }

    ImageStack stack1 = imp.getStack();
    String fileName = imp.getTitle();
    int endslice = stack1.getSize();

    ImagePlus imp2 = duplicateStack(imp);
    imp2.show();
    String duplicateName = imp2.getTitle();
    // IJ.showMessage("Box",fileName);
    ImageStack stack2 = imp2.getStack();
    stack1.deleteSlice(1);
    stack2.deleteSlice(endslice);

    String calculatorstring =
        ("image1='"
            + fileName
            + "' operation=Subtract image2="
            + imp2.getTitle()
            + " create stack");

    IJ.run("Image Calculator...", calculatorstring);
    ImagePlus imp3 = WindowManager.getCurrentImage();
    imp3.setTitle(fileName + " DeltaF up");
    imp2.getWindow().close();
    imp.getWindow().close();
  }
Example #5
0
 /** Handle menu events. */
 public void actionPerformed(ActionEvent e) {
   if ((e.getSource() instanceof MenuItem)) {
     MenuItem item = (MenuItem) e.getSource();
     String cmd = e.getActionCommand();
     commandName = cmd;
     ImagePlus imp = null;
     if (item.getParent() == Menus.getOpenRecentMenu()) {
       new RecentOpener(cmd); // open image in separate thread
       return;
     } else if (item.getParent() == Menus.getPopupMenu()) {
       Object parent = Menus.getPopupMenu().getParent();
       if (parent instanceof ImageCanvas) imp = ((ImageCanvas) parent).getImage();
     }
     int flags = e.getModifiers();
     hotkey = false;
     actionPerformedTime = System.currentTimeMillis();
     long ellapsedTime = actionPerformedTime - keyPressedTime;
     if (cmd != null && (ellapsedTime >= 200L || !cmd.equals(lastKeyCommand))) {
       if ((flags & Event.ALT_MASK) != 0) IJ.setKeyDown(KeyEvent.VK_ALT);
       if ((flags & Event.SHIFT_MASK) != 0) IJ.setKeyDown(KeyEvent.VK_SHIFT);
       new Executer(cmd, imp);
     }
     lastKeyCommand = null;
     if (IJ.debugMode) IJ.log("actionPerformed: time=" + ellapsedTime + ", " + e);
   }
 }
    public synchronized void adjustmentValueChanged(AdjustmentEvent e) {

      if (!checkImage()) {
        IJ.beep();
        IJ.showStatus("No Image");
        return;
      }

      if (e.getSource() == minSlider) {
        adjustMinHue((int) minSlider.getValue());
      } else if (e.getSource() == maxSlider) {
        adjustMaxHue((int) maxSlider.getValue());
      } else if (e.getSource() == minSlider2) {
        adjustMinSat((int) minSlider2.getValue());
      } else if (e.getSource() == maxSlider2) {
        adjustMaxSat((int) maxSlider2.getValue());
      } else if (e.getSource() == minSlider3) {
        adjustMinBri((int) minSlider3.getValue());
      } else if (e.getSource() == maxSlider3) {
        adjustMaxBri((int) maxSlider3.getValue());
      }
      originalB.setEnabled(true);
      updateLabels();
      updatePlot();
      notify();
    }
Example #7
0
 /** Called by ImageJ when the user selects Quit. */
 public void quit() {
   quitMacro = IJ.macroRunning();
   Thread thread = new Thread(this, "Quit");
   thread.setPriority(Thread.NORM_PRIORITY);
   thread.start();
   IJ.wait(10);
 }
Example #8
0
  public Channels() {
    super("Channels");
    if (instance != null) {
      instance.toFront();
      return;
    }
    WindowManager.addWindow(this);
    instance = this;
    GridBagLayout gridbag = new GridBagLayout();
    GridBagConstraints c = new GridBagConstraints();
    setLayout(gridbag);
    int y = 0;
    c.gridx = 0;
    c.gridy = y++;
    c.gridwidth = 1;
    c.fill = GridBagConstraints.BOTH;
    c.anchor = GridBagConstraints.CENTER;
    int margin = 32;
    if (IJ.isMacOSX()) margin = 20;
    c.insets = new Insets(10, margin, 10, margin);
    choice = new Choice();
    for (int i = 0; i < modes.length; i++) choice.addItem(modes[i]);
    choice.select(0);
    choice.addItemListener(this);
    add(choice, c);

    CompositeImage ci = getImage();
    int nCheckBoxes = ci != null ? ci.getNChannels() : 3;
    if (nCheckBoxes > CompositeImage.MAX_CHANNELS) nCheckBoxes = CompositeImage.MAX_CHANNELS;
    checkbox = new Checkbox[nCheckBoxes];
    for (int i = 0; i < nCheckBoxes; i++) {
      checkbox[i] = new Checkbox("Channel " + (i + 1), true);
      c.insets = new Insets(0, 25, i < nCheckBoxes - 1 ? 0 : 10, 5);
      c.gridy = y++;
      add(checkbox[i], c);
      checkbox[i].addItemListener(this);
    }

    c.insets = new Insets(0, 15, 10, 15);
    c.fill = GridBagConstraints.NONE;
    c.gridy = y++;
    moreButton = new Button(moreLabel);
    moreButton.addActionListener(this);
    add(moreButton, c);
    update();

    pm = new PopupMenu();
    for (int i = 0; i < menuItems.length; i++) addPopupItem(menuItems[i]);
    add(pm);

    addKeyListener(IJ.getInstance()); // ImageJ handles keyboard shortcuts
    setResizable(false);
    pack();
    if (location == null) {
      GUI.center(this);
      location = getLocation();
    } else setLocation(location);
    show();
  }
Example #9
0
 public void actionPerformed(ActionEvent e) {
   String command = e.getActionCommand();
   if (command == null) return;
   if (command.equals(moreLabel)) {
     Point bloc = moreButton.getLocation();
     pm.show(this, bloc.x, bloc.y);
   } else if (command.equals("Convert to RGB")) IJ.doCommand("Stack to RGB");
   else IJ.doCommand(command);
 }
  public void run(String arg) {
    ImageWindow iw = WindowManager.getCurrentWindow();
    pw = jutils.getPW4SelCopy(iw);
    String title = pw.getTitle();
    float[][] yvals = pw.getYValues();
    float[][] xvals = pw.getXValues();
    int length = yvals[0].length;
    if (pw.getShowErrors()) errs = pw.getErrors(0, false);
    int[] colors = pw.getColors();
    colors[0] = 0;
    ScriptEngineManager manager = new ScriptEngineManager();
    engine = manager.getEngineByName("js");
    ce = (Compilable) engine;
    // hitcounter=0;

    c2 = 0.0f;
    iterations = 0;
    checkc2 = false;

    double[] stats = new double[3];
    tempx = new float[length];
    tempdata = new float[length];
    System.arraycopy(xvals[0], 0, tempx, 0, length);
    System.arraycopy(yvals[0], 0, tempdata, 0, length);
    pw.addPoints(tempx, new float[tempx.length], false);
    series = pw.getNpts().length - 1;
    double[] params = new double[10];
    int[] fixes = {0, 0, 0, 1, 1, 1, 1, 1, 1, 1};
    init_options(params, fixes);
    if (!init_functions()) {
      return;
    }

    while (showoptions(params, fixes)) {
      NLLSfit_v2 fitclass;
      if (checkc2) {
        fitclass = new NLLSfit_v2(this, 0);
      } else {
        fitclass = new NLLSfit_v2(this, 0.0001, 50, 0.1);
      }
      float[] fit = fitclass.fitdata(params, fixes, constraints, yvals[0], weights, stats, true);
      pw.updateSeries(fit, series, false);
      c2 = (float) stats[1];
      iterations = (int) stats[0];
    }

    IJ.log("Chi Squared = " + (float) stats[1]);
    IJ.log("Iterations = " + (int) stats[0]);
    for (int i = 0; i < 10; i++) {
      IJ.log("P" + (i + 1) + " = " + (float) params[i] + " fixed = " + fixes[i]);
    }
    IJ.log("AIC = " + (float) stats[2]);
    // IJ.log("hits = "+hitcounter);
    set_options(params, fixes);
  }
Example #11
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;
  }
Example #12
0
 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;
 }
Example #13
0
  public void run(String arg) {
    int[] wList = WindowManager.getIDList();
    if (wList == null) {
      IJ.error("No images are open.");
      return;
    }

    double thalf = 0.5;
    boolean keep;

    GenericDialog gd = new GenericDialog("Bleach correction");

    gd.addNumericField("t½:", thalf, 1);
    gd.addCheckbox("Keep source stack:", true);
    gd.showDialog();
    if (gd.wasCanceled()) return;

    long start = System.currentTimeMillis();
    thalf = gd.getNextNumber();
    keep = gd.getNextBoolean();
    if (keep) IJ.run("Duplicate...", "title='Bleach corrected' duplicate");
    ImagePlus imp1 = WindowManager.getCurrentImage();
    int d1 = imp1.getStackSize();
    double v1, v2;
    int width = imp1.getWidth();
    int height = imp1.getHeight();
    ImageProcessor ip1, ip2, ip3;

    int slices = imp1.getStackSize();
    ImageStack stack1 = imp1.getStack();
    ImageStack stack2 = imp1.getStack();
    int currentSlice = imp1.getCurrentSlice();

    for (int n = 1; n <= slices; n++) {
      ip1 = stack1.getProcessor(n);
      ip3 = stack1.getProcessor(1);
      ip2 = stack2.getProcessor(n);
      for (int x = 0; x < width; x++) {
        for (int y = 0; y < height; y++) {
          v1 = ip1.getPixelValue(x, y);
          v2 = ip3.getPixelValue(x, y);

          // =B8/(EXP(-C$7*A8))
          v1 = (v1 / Math.exp(-n * thalf));
          ip2.putPixelValue(x, y, v1);
        }
      }
      IJ.showProgress((double) n / slices);
      IJ.showStatus(n + "/" + slices);
    }

    // stack2.show();
    imp1.updateAndDraw();
  }
 boolean init_functions() {
   GenericDialog gd = new GenericDialog("Fitting Options");
   gd.addStringField("Extra Definitions", exdef, 50);
   gd.addCheckbox("Weight Using Plot Errors", false);
   gd.addStringField("Weighting Equation (y is for data)", weightfunction, 50);
   gd.addStringField("Fit_Equation", function, 50);
   gd.showDialog();
   if (gd.wasCanceled()) {
     return false;
   }
   exdef = gd.getNextString();
   boolean errweights = gd.getNextBoolean();
   weightfunction = gd.getNextString();
   function = gd.getNextString();
   // first initialize the weights
   weights = new float[tempdata.length];
   if (errweights
       || weightfunction.equals("")
       || weightfunction == null
       || weightfunction == "1.0") {
     if (errweights) {
       for (int i = 0; i < tempdata.length; i++) weights[i] = 1.0f / (errs[i] * errs[i]);
     } else {
       for (int i = 0; i < tempdata.length; i++) weights[i] = 1.0f;
     }
   } else {
     for (int i = 0; i < tempdata.length; i++) {
       String script =
           "y =" + tempdata[i] + "; " + "x =" + tempx[i] + "; " + "retval=" + weightfunction + ";";
       Double temp = new Double(0.0);
       try {
         temp = (Double) engine.eval(script);
       } catch (Exception e) {
         IJ.log(e.getMessage());
       }
       if (!(temp.isInfinite() || temp.isNaN())) {
         weights[i] = temp.floatValue();
       }
     }
   }
   // now compile the function script
   try {
     String script1 = exdef + "; retval=" + function + ";";
     cs = ce.compile(script1);
   } catch (Exception e) {
     IJ.log(e.toString());
     return false;
   }
   return true;
 }
Example #15
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);
 }
Example #16
0
    public void actionPerformed(ActionEvent e) {
      Button b = (Button) e.getSource();
      if (b == null) return;

      boolean imageThere = checkImage();

      if (imageThere) {
        if (b == originalB) {
          reset(imp, ip);
          filteredB.setEnabled(true);
        } else if (b == filteredB) {
          apply(imp, ip);
        } else if (b == sampleB) {
          reset(imp, ip);
          sample();
          apply(imp, ip);
        } else if (b == stackB) {
          applyStack();
        } else if (b == helpB) {
          IJ.showMessage(
              "Help",
              "Threshold Colour  v1.0\n \n"
                  + "Modification of Bob Dougherty's BandPass2 plugin by G.Landini to\n"
                  + "threshold 24 bit RGB images based on Hue, Saturation and Brightness\n"
                  + "or Red, Green and Blue components.\n \n"
                  + "Pass: Band-pass filter (anything within range is displayed).\n \n"
                  + "Stop: Band-reject filter (anything within range is NOT displayed).\n \n"
                  + "Original: Shows the original image and updates the buffer when\n"
                  + " switching to another image.\n \n"
                  + "Filtered: Shows the filtered image.\n \n"
                  + "Stack: Processes the rest of the slices in the stack (if any)\n"
                  + " using the current settings.\n \n"
                  + "Threshold: Shows the object/background in the foreground and\n"
                  + " background colours selected in the ImageJ toolbar.\n \n"
                  + "Invert: Swaps the fore/background colours.\n \n"
                  + "Sample: (experimental) Sets the ranges of the filters based on the\n"
                  + " pixel value componentd in a rectangular, user-defined, ROI.\n \n"
                  + "HSB RGB: Selects HSB or RGB space and resets all the filters.\n \n"
                  + "Note that the \'thresholded\' image is RGB, not 8 bit grey.");
        }
        updatePlot();
        updateLabels();
        imp.updateAndDraw();
      } else {
        IJ.beep();
        IJ.showStatus("No Image");
      }
      notify();
    }
Example #17
0
  /**
   * Prepare for processing; also called at the very end with argument 'final' to show any newly
   * created output image.
   */
  public int setup(String arg, ImagePlus imp) {
    if (arg.equals("final")) {
      showOutput();
      return DONE;
    }
    this.imp = imp;
    // 'arg' is processing type; default is 'EDM' (0)
    if (arg.equals("watershed")) {
      processType = WATERSHED;
      flags += KEEP_THRESHOLD;
    } else if (arg.equals("points")) processType = UEP;
    else if (arg.equals("voronoi")) processType = VORONOI;

    // output type
    if (processType != WATERSHED) // Watershed always has output BYTE_OVERWRITE=0
    outImageType = outputType; // otherwise use the static variable from setOutputType
    if (outImageType != BYTE_OVERWRITE) flags |= NO_CHANGES;

    // check image and prepare
    if (imp != null) {
      ImageProcessor ip = imp.getProcessor();
      if (!ip.isBinary()) {
        IJ.error("8-bit binary image (0 and 255) required.");
        return DONE;
      }
      ip.resetRoi();
      // processing routines assume background=0; image may be otherwise
      boolean invertedLut = imp.isInvertedLut();
      background255 =
          (invertedLut && Prefs.blackBackground) || (!invertedLut && !Prefs.blackBackground);
    }
    return flags;
  } // public int setup
Example #18
0
  public void run(String arg) {
    ImagePlus imp = WindowManager.getCurrentImage();
    if (!(imp instanceof Image5D)) {
      IJ.error("Current Image is not an Image5D.");
      return;
    }
    IJ.register(Add_Empty_Slice.class);

    Image5D i5d = (Image5D) imp;
    Image5DWindow win = ((Image5DWindow) i5d.getWindow());
    int n = i5d.getNSlices();

    i5d.expandDimension(3, n + 1, true);

    win.updateSliceSelector();
  }
 public double[] fitfunc(double[] fitparams) {
   Bindings b = engine.createBindings();
   for (int i = 0; i < 10; i++) b.put("P" + (i + 1), fitparams[i]);
   /*String script1="P1="+fitparams[0]+"; "+
   "P2="+fitparams[1]+"; "+
   "P3="+fitparams[2]+"; "+
   "P4="+fitparams[3]+"; "+
   "P5="+fitparams[4]+"; "+
   "P6="+fitparams[5]+"; "+
   "P7="+fitparams[6]+"; "+
   "P8="+fitparams[7]+"; "+
   "P9="+fitparams[8]+"; "+
   "P10="+fitparams[9]+"; "+
   exdef+"; x=";
   String script2="; retval="+function+";";*/
   try {
     double[] temp = new double[tempx.length];
     for (int i = 0; i < tempx.length; i++) {
       // temp[i]=((Double)engine.eval(script1+(double)tempx[i]+script2)).doubleValue();
       b.put("x", tempx[i]);
       b.put("y", tempdata[i]);
       temp[i] = (Double) cs.eval(b);
     }
     return temp;
   } catch (Exception e) {
     IJ.log(e.getMessage());
     return null;
   }
 }
Example #20
0
  public boolean checkBeads() {
    rmanager = RoiManager.getInstance();
    if (IJ.versionLessThan("1.26i")) return false;
    else if (rmanager == null) {
      IJ.error("Add bead ROIs to the RoiManager first (select region then press [t]).");
      return false;
    }

    nrois = rmanager.getCount();
    if (nrois == 0) {
      IJ.error("Add bead ROIs to the RoiManager first (select region then press [t]).");
      return false;
    }
    rois = rmanager.getRoisAsArray();
    return true;
  }
Example #21
0
 public String getInfo() {
   return version()
       + System.getProperty("os.name")
       + " "
       + System.getProperty("os.version")
       + "; "
       + IJ.freeMemory();
 }
Example #22
0
  /**
   * Execute the plugin functionality: duplicate and scale the given image.
   *
   * @return an Object[] array with the name and the scaled ImagePlus. Does NOT show the new, image;
   *     just returns it.
   */
  public Object[] exec(
      ImagePlus imp, String myMethod, int radius, double par1, double par2, boolean doIwhite) {

    // 0 - Check validity of parameters
    if (null == imp) return null;
    ImageProcessor ip = imp.getProcessor();
    int xe = ip.getWidth();
    int ye = ip.getHeight();

    // int [] data = (ip.getHistogram());

    IJ.showStatus("Thresholding...");
    long startTime = System.currentTimeMillis();
    // 1 Do it
    if (imp.getStackSize() == 1) {
      ip.snapshot();
      Undo.setup(Undo.FILTER, imp);
    }
    // Apply the selected algorithm
    if (myMethod.equals("Bernsen")) {
      Bernsen(imp, radius, par1, par2, doIwhite);
    } else if (myMethod.equals("Contrast")) {
      Contrast(imp, radius, par1, par2, doIwhite);
    } else if (myMethod.equals("Mean")) {
      Mean(imp, radius, par1, par2, doIwhite);
    } else if (myMethod.equals("Median")) {
      Median(imp, radius, par1, par2, doIwhite);
    } else if (myMethod.equals("MidGrey")) {
      MidGrey(imp, radius, par1, par2, doIwhite);
    } else if (myMethod.equals("Niblack")) {
      Niblack(imp, radius, par1, par2, doIwhite);
    } else if (myMethod.equals("Otsu")) {
      Otsu(imp, radius, par1, par2, doIwhite);
    } else if (myMethod.equals("Phansalkar")) {
      Phansalkar(imp, radius, par1, par2, doIwhite);
    } else if (myMethod.equals("Sauvola")) {
      Sauvola(imp, radius, par1, par2, doIwhite);
    }
    // IJ.showProgress((double)(255-i)/255);
    imp.updateAndDraw();
    imp.getProcessor().setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
    // 2 - Return the threshold and the image
    IJ.showStatus("\nDone " + (System.currentTimeMillis() - startTime) / 1000.0);
    return new Object[] {imp};
  }
Example #23
0
 private String version() {
   return "ImageJ "
       + VERSION
       + BUILD
       + "; "
       + "Java "
       + System.getProperty("java.version")
       + (IJ.is64Bit() ? " [64-bit]; " : " [32-bit]; ");
 }
Example #24
0
  void Bernsen(ImagePlus imp, int radius, double par1, double par2, boolean doIwhite) {
    // Bernsen recommends WIN_SIZE = 31 and CONTRAST_THRESHOLD = 15.
    //  1) Bernsen J. (1986) "Dynamic Thresholding of Grey-Level Images"
    //    Proc. of the 8th Int. Conf. on Pattern Recognition, pp. 1251-1255
    //  2) Sezgin M. and Sankur B. (2004) "Survey over Image Thresholding
    //   Techniques and Quantitative Performance Evaluation" Journal of
    //   Electronic Imaging, 13(1): 146-165
    //  http://citeseer.ist.psu.edu/sezgin04survey.html
    // Ported to ImageJ plugin from E Celebi's fourier_0.8 routines
    // This version uses a circular local window, instead of a rectagular one
    ImagePlus Maximp, Minimp;
    ImageProcessor ip = imp.getProcessor(), ipMax, ipMin;
    int contrast_threshold = 15;
    int local_contrast;
    int mid_gray;
    byte object;
    byte backg;
    int temp;

    if (par1 != 0) {
      IJ.log("Bernsen: changed contrast_threshold from :" + contrast_threshold + "  to:" + par1);
      contrast_threshold = (int) par1;
    }

    if (doIwhite) {
      object = (byte) 0xff;
      backg = (byte) 0;
    } else {
      object = (byte) 0;
      backg = (byte) 0xff;
    }

    Maximp = duplicateImage(ip);
    ipMax = Maximp.getProcessor();
    RankFilters rf = new RankFilters();
    rf.rank(ipMax, radius, rf.MAX); // Maximum
    // Maximp.show();
    Minimp = duplicateImage(ip);
    ipMin = Minimp.getProcessor();
    rf.rank(ipMin, radius, rf.MIN); // Minimum
    // Minimp.show();
    byte[] pixels = (byte[]) ip.getPixels();
    byte[] max = (byte[]) ipMax.getPixels();
    byte[] min = (byte[]) ipMin.getPixels();

    for (int i = 0; i < pixels.length; i++) {
      local_contrast = (int) ((max[i] & 0xff) - (min[i] & 0xff));
      mid_gray = (int) ((min[i] & 0xff) + (max[i] & 0xff)) / 2;
      temp = (int) (pixels[i] & 0x0000ff);
      if (local_contrast < contrast_threshold)
        pixels[i] = (mid_gray >= 128) ? object : backg; // Low contrast region
      else pixels[i] = (temp >= mid_gray) ? object : backg;
    }
    // imp.updateAndDraw();
    return;
  }
Example #25
0
 void applyStack() {
   // int minKeepH = minHue, maxKeepH = maxHue; //GL not needed?
   // int minKeepS = minSat, maxKeepS = maxSat;
   // int minKeepB = minBri, maxKeepB = maxBri;
   for (int i = 1; i <= numSlices; i++) {
     imp.setSlice(i);
     if (!checkImage()) {
       IJ.beep();
       IJ.showStatus("No Image");
       return;
     }
     //	minHue = minKeepH;
     //	maxHue = maxKeepH;
     //	minSat = minKeepS;
     //	maxSat = maxKeepS;
     //	minBri = minKeepB;
     //	maxBri = maxKeepB;
     apply(imp, ip);
   }
 }
  public void run(String arg) {
    if (IJ.versionLessThan("1.49d")) return;

    if (!showDialog()) return;

    SaveDialog sd = new SaveDialog("Save as Bricks...", "", "");
    basename = sd.getFileName();
    directory = sd.getDirectory();
    if (basename == null || directory == null) return;

    build_bricks();
  }
Example #27
0
 void abortPluginOrMacro(ImagePlus imp) {
   if (imp != null) {
     ImageWindow win = imp.getWindow();
     if (win != null) {
       win.running = false;
       win.running2 = false;
     }
   }
   Macro.abort();
   Interpreter.abort();
   if (Interpreter.getInstance() != null) IJ.beep();
 }
Example #28
0
 /**
  * Called by the PlugInFilterRunner after setup. Asks the user in case of a stack and prepares a
  * separate ouptut stack if required
  */
 public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) {
   this.pfr = pfr;
   int width = imp.getWidth();
   int height = imp.getHeight();
   // ask whether to process all slices of stack & prepare stack
   // (if required) for writing into it in parallel threads
   flags = IJ.setupDialog(imp, flags);
   if ((flags & DOES_STACKS) != 0 && outImageType != BYTE_OVERWRITE) {
     outStack = new ImageStack(width, height, imp.getStackSize());
     maxFinder.setNPasses(imp.getStackSize());
   }
   return flags;
 } // public int showDialog
Example #29
0
 public void run(String arg) {
   ImagePlus imp = WindowManager.getCurrentImage();
   if (imp == null) {
     IJ.noImage();
     return;
   }
   if (imp.getStackSize() > 1) {
     IJ.error("This command requires a montage");
     return;
   }
   GenericDialog gd = new GenericDialog("Stack Maker");
   gd.addNumericField("Images_per_row: ", w, 0);
   gd.addNumericField("Images_per_column: ", h, 0);
   gd.addNumericField("Border width: ", b, 0);
   gd.showDialog();
   if (gd.wasCanceled()) return;
   w = (int) gd.getNextNumber();
   h = (int) gd.getNextNumber();
   b = (int) gd.getNextNumber();
   ImageStack stack = makeStack(imp.getProcessor(), w, h, b);
   new ImagePlus("Stack", stack).show();
 }
Example #30
0
 /**
  * Attempts to open the specified path with the given plugin. If the plugin extends the ImagePlus
  * class (e.g., BioRad_Reader), set extendsImagePlus to true, otherwise (e.g., LSM_Reader) set it
  * to false.
  *
  * @return A reference to the plugin, if it was successful.
  */
 private Object tryPlugIn(String className, String path) {
   Object o = IJ.runPlugIn(className, path);
   if (o instanceof ImagePlus) {
     // plugin extends ImagePlus class
     ImagePlus imp = (ImagePlus) o;
     if (imp.getWidth() == 0) o = null; // invalid image
     else width = IMAGE_OPENED; // success
   } else {
     // plugin does not extend ImagePlus; assume success
     width = IMAGE_OPENED;
   }
   return o;
 }