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
Example #2
0
 void createSelectionFromMask(ImagePlus imp) {
   ImageProcessor ip = imp.getProcessor();
   if (ip.getMinThreshold() != ImageProcessor.NO_THRESHOLD) {
     IJ.runPlugIn("ij.plugin.filter.ThresholdToSelection", "");
     return;
   }
   if (!ip.isBinary()) {
     IJ.error(
         "Create Selection",
         "This command creates a composite selection from\n"
             + "a mask (8-bit binary image with white background)\n"
             + "or from an image that has been thresholded using\n"
             + "the Image>Adjust>Threshold tool. The current\n"
             + "image is not a mask and has not been thresholded.");
     return;
   }
   int threshold = ip.isInvertedLut() ? 255 : 0;
   ip.setThreshold(threshold, threshold, ImageProcessor.NO_LUT_UPDATE);
   IJ.runPlugIn("ij.plugin.filter.ThresholdToSelection", "");
 }
 /**
  * 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;
 }
Example #4
0
  /** Restores original disk or network version of image. */
  public void revertToSaved(ImagePlus imp) {
    Image img;
    ProgressBar pb = IJ.getInstance().getProgressBar();
    ImageProcessor ip;
    String path = fi.directory + fi.fileName;

    if (fi.fileFormat == fi.GIF_OR_JPG) {
      // restore gif or jpg
      img = Toolkit.getDefaultToolkit().createImage(path);
      imp.setImage(img);
      if (imp.getType() == ImagePlus.COLOR_RGB) Opener.convertGrayJpegTo8Bits(imp);
      return;
    }

    if (fi.fileFormat == fi.DICOM) {
      // restore DICOM
      ImagePlus imp2 = (ImagePlus) IJ.runPlugIn("ij.plugin.DICOM", path);
      if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
      return;
    }

    if (fi.fileFormat == fi.BMP) {
      // restore BMP
      ImagePlus imp2 = (ImagePlus) IJ.runPlugIn("ij.plugin.BMP_Reader", path);
      if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
      return;
    }

    if (fi.fileFormat == fi.PGM) {
      // restore PGM
      ImagePlus imp2 = (ImagePlus) IJ.runPlugIn("ij.plugin.PGM_Reader", path);
      if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
      return;
    }

    if (fi.fileFormat == fi.ZIP_ARCHIVE) {
      // restore ".zip" file
      ImagePlus imp2 = (new Opener()).openZip(path);
      if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
      return;
    }

    // restore PNG or another image opened using ImageIO
    if (fi.fileFormat == fi.IMAGEIO) {
      ImagePlus imp2 = (new Opener()).openUsingImageIO(path);
      if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
      return;
    }

    if (fi.nImages > 1) return;

    ColorModel cm;
    if (fi.url == null || fi.url.equals("")) IJ.showStatus("Loading: " + path);
    else IJ.showStatus("Loading: " + fi.url + fi.fileName);
    Object pixels = readPixels(fi);
    if (pixels == null) return;
    cm = createColorModel(fi);
    switch (fi.fileType) {
      case FileInfo.GRAY8:
      case FileInfo.COLOR8:
      case FileInfo.BITMAP:
        ip = new ByteProcessor(width, height, (byte[]) pixels, cm);
        imp.setProcessor(null, ip);
        break;
      case FileInfo.GRAY16_SIGNED:
      case FileInfo.GRAY16_UNSIGNED:
      case FileInfo.GRAY12_UNSIGNED:
        ip = new ShortProcessor(width, height, (short[]) pixels, cm);
        imp.setProcessor(null, ip);
        break;
      case FileInfo.GRAY32_INT:
      case FileInfo.GRAY32_FLOAT:
        ip = new FloatProcessor(width, height, (float[]) pixels, cm);
        imp.setProcessor(null, ip);
        break;
      case FileInfo.RGB:
      case FileInfo.BGR:
      case FileInfo.ARGB:
      case FileInfo.ABGR:
      case FileInfo.RGB_PLANAR:
        img =
            Toolkit.getDefaultToolkit()
                .createImage(new MemoryImageSource(width, height, (int[]) pixels, 0, width));
        imp.setImage(img);
        break;
    }
  }
Example #5
0
  /**
   * If 'applet' is not null, creates a new ImageJ frame that runs as an applet. If 'mode' is
   * ImageJ.EMBEDDED and 'applet is null, creates an embedded (non-standalone) version of ImageJ.
   */
  public ImageJ(java.applet.Applet applet, int mode) {
    super("ImageJ");
    if ((mode & DEBUG) != 0) IJ.setDebugMode(true);
    mode = mode & 255;
    if (IJ.debugMode) IJ.log("ImageJ starting in debug mode: " + mode);
    embedded = applet == null && (mode == EMBEDDED || mode == NO_SHOW);
    this.applet = applet;
    String err1 = Prefs.load(this, applet);
    setBackground(backgroundColor);
    Menus m = new Menus(this, applet);
    String err2 = m.addMenuBar();
    m.installPopupMenu(this);
    setLayout(new BorderLayout());

    // Tool bar
    toolbar = new Toolbar();
    toolbar.addKeyListener(this);
    add("Center", toolbar);

    // Status bar
    statusBar = new Panel();
    statusBar.setLayout(new BorderLayout());
    statusBar.setForeground(Color.black);
    statusBar.setBackground(backgroundColor);
    statusLine = new JLabel();
    statusLine.setFont(new Font("SansSerif", Font.PLAIN, 13));
    statusLine.addKeyListener(this);
    statusLine.addMouseListener(this);
    statusBar.add("Center", statusLine);
    progressBar = new ProgressBar(120, 20);
    progressBar.addKeyListener(this);
    progressBar.addMouseListener(this);
    statusBar.add("East", progressBar);
    add("South", statusBar);

    IJ.init(this, applet);
    addKeyListener(this);
    addWindowListener(this);
    setFocusTraversalKeysEnabled(false);
    m.installStartupMacroSet(); // add custom tools
    runStartupMacro();

    Point loc = getPreferredLocation();
    Dimension tbSize = toolbar.getPreferredSize();
    setCursor(Cursor.getDefaultCursor()); // work-around for JDK 1.1.8 bug
    if (mode != NO_SHOW) {
      if (IJ.isWindows())
        try {
          setIcon();
        } catch (Exception e) {
        }
      setLocation(loc.x, loc.y);
      setResizable(!IJ.isMacOSX());
      pack();
      setVisible(true);
    }
    if (err1 != null) IJ.error(err1);
    if (err2 != null) {
      IJ.error(err2);
      IJ.runPlugIn("ij.plugin.ClassChecker", "");
    }
    if (IJ.isMacintosh() && applet == null) {
      Object qh = null;
      qh = IJ.runPlugIn("MacAdapter", "");
      if (qh == null) IJ.runPlugIn("QuitHandler", "");
    }
    if (applet == null) IJ.runPlugIn("ij.plugin.DragAndDrop", "");
    String str = m.getMacroCount() == 1 ? " macro" : " macros";
    IJ.showStatus(version() + m.getPluginCount() + " commands; " + m.getMacroCount() + str);
    configureProxy();
    if (applet == null) loadCursors();
  }
Example #6
0
  /**
   * If 'applet' is not null, creates a new ImageJ frame that runs as an applet. If 'mode' is
   * ImageJ.EMBEDDED and 'applet is null, creates an embedded (non-standalone) version of ImageJ.
   */
  public ImageJ(java.applet.Applet applet, int mode) {
    super("ImageJ");
    embedded = applet == null && (mode == EMBEDDED || mode == NO_SHOW);
    this.applet = applet;
    String err1 = Prefs.load(this, applet);
    if (IJ.isLinux()) {
      backgroundColor = new Color(240, 240, 240);
      setBackground(backgroundColor);
    }
    Menus m = new Menus(this, applet);
    String err2 = m.addMenuBar();
    m.installPopupMenu(this);
    setLayout(new GridLayout(2, 1));

    // Tool bar
    toolbar = new Toolbar();
    toolbar.addKeyListener(this);
    add(toolbar);

    // Status bar
    statusBar = new Panel();
    statusBar.setLayout(new BorderLayout());
    statusBar.setForeground(Color.black);
    statusBar.setBackground(backgroundColor);
    statusLine = new Label();
    statusLine.setFont(SansSerif12);
    statusLine.addKeyListener(this);
    statusLine.addMouseListener(this);
    statusBar.add("Center", statusLine);
    progressBar = new ProgressBar(120, 20);
    progressBar.addKeyListener(this);
    progressBar.addMouseListener(this);
    statusBar.add("East", progressBar);
    statusBar.setSize(toolbar.getPreferredSize());
    add(statusBar);

    IJ.init(this, applet);
    addKeyListener(this);
    addWindowListener(this);
    setFocusTraversalKeysEnabled(false);

    Point loc = getPreferredLocation();
    Dimension tbSize = toolbar.getPreferredSize();
    int ijWidth = tbSize.width + 10;
    int ijHeight = 100;
    setCursor(Cursor.getDefaultCursor()); // work-around for JDK 1.1.8 bug
    if (mode != NO_SHOW) {
      if (IJ.isWindows())
        try {
          setIcon();
        } catch (Exception e) {
        }
      setBounds(loc.x, loc.y, ijWidth, ijHeight); // needed for pack to work
      setLocation(loc.x, loc.y);
      pack();
      setResizable(!(IJ.isMacintosh() || IJ.isWindows())); // make resizable on Linux
      show();
    }
    if (err1 != null) IJ.error(err1);
    if (err2 != null) {
      IJ.error(err2);
      IJ.runPlugIn("ij.plugin.ClassChecker", "");
    }
    m.installStartupMacroSet();
    if (IJ.isMacintosh() && applet == null) {
      Object qh = null;
      qh = IJ.runPlugIn("MacAdapter", "");
      if (qh == null) IJ.runPlugIn("QuitHandler", "");
    }
    if (applet == null) IJ.runPlugIn("ij.plugin.DragAndDrop", "");
    String str = m.getMacroCount() == 1 ? " macro" : " macros";
    IJ.showStatus(version() + m.getPluginCount() + " commands; " + m.getMacroCount() + str);
    // if (applet==null && !embedded && Prefs.runSocketListener)
    //	new SocketListener();
    configureProxy();
    if (applet == null) loadCursors();
  }
 public boolean install(String path) {
   boolean isURL = path.contains("://");
   String lcPath = path.toLowerCase();
   if (isURL) path = Opener.updateUrl(path);
   boolean isTool =
       lcPath.endsWith("tool.ijm")
           || lcPath.endsWith("tool.txt")
           || lcPath.endsWith("tool.class")
           || lcPath.endsWith("tool.jar");
   boolean isMacro = lcPath.endsWith(".txt") || lcPath.endsWith(".ijm");
   byte[] data = null;
   String name = path;
   if (isURL) {
     int index = path.lastIndexOf("/");
     if (index != -1 && index <= path.length() - 1) name = path.substring(index + 1);
     data = download(path, name);
   } else {
     File f = new File(path);
     name = f.getName();
     data = download(f);
   }
   if (data == null) return false;
   if (name.endsWith(".txt") && !name.contains("_"))
     name = name.substring(0, name.length() - 4) + ".ijm";
   if (name.endsWith(".zip")) {
     if (!name.contains("_")) {
       IJ.error("Plugin Installer", "No underscore in file name:\n \n  " + name);
       return false;
     }
     name = name.substring(0, name.length() - 4) + ".jar";
   }
   String dir = null;
   boolean isLibrary = name.endsWith(".jar") && !name.contains("_");
   if (isLibrary) {
     dir = Menus.getPlugInsPath() + "jars";
     File f = new File(dir);
     if (!f.exists()) {
       boolean ok = f.mkdir();
       if (!ok) dir = Menus.getPlugInsPath();
     }
   }
   if (isTool) {
     dir = Menus.getPlugInsPath() + "Tools" + File.separator;
     File f = new File(dir);
     if (!f.exists()) {
       boolean ok = f.mkdir();
       if (!ok) dir = null;
     }
     if (dir != null && isMacro) {
       String name2 = getToolName(data);
       if (name2 != null) name = name2;
     }
   }
   if (dir == null) {
     SaveDialog sd =
         new SaveDialog("Save Plugin, Macro or Script...", Menus.getPlugInsPath(), name, null);
     String name2 = sd.getFileName();
     if (name2 == null) return false;
     dir = sd.getDirectory();
   }
   // IJ.log(dir+"   "+Menus.getPlugInsPath());
   if (!savePlugin(new File(dir, name), data)) return false;
   if (name.endsWith(".java")) IJ.runPlugIn("ij.plugin.Compiler", dir + name);
   Menus.updateImageJMenus();
   if (isTool) {
     if (isMacro) IJ.runPlugIn("ij.plugin.Macro_Runner", "Tools/" + name);
     else if (name.endsWith(".class")) {
       name = name.replaceAll("_", " ");
       name = name.substring(0, name.length() - 6);
       IJ.run(name);
     }
   }
   return true;
 }