예제 #1
0
  /* TODO: sorted */
  public static MenuItem installPlugin(String menuPath, String name, String command) {
    if (Menus.getCommands().get(name) != null) {
      IJ.log("The user plugin " + name + " would override an existing command!");
      return null;
    }

    MenuItem item = null;
    if (IJ.getInstance() != null) {
      int croc = menuPath.lastIndexOf('>');
      Menu menu = getMenu(menuPath);
      item = new MenuItem(name);
      menu.add(item);
      item.addActionListener(IJ.getInstance());
    }
    Menus.getCommands().put(name, command);
    return item;
  }
예제 #2
0
  /** Install the plugins now */
  public void run(String arg) {
    if ("update".equals(arg)) {
      Menus.updateImageJMenus();
      ClassLoader loader = IJ.getClassLoader();
      if (loader != null && (loader instanceof FijiClassLoader)) return;
    }
    FijiClassLoader classLoader = new FijiClassLoader(true);
    try {
      classLoader.addPath(path);
    } catch (IOException e) {
    }

    try {
      // IJ.setClassLoader(classLoader);
      Class ij = Class.forName("ij.IJ");
      java.lang.reflect.Method method =
          ij.getDeclaredMethod("setClassLoader", new Class[] {ClassLoader.class});
      method.setAccessible(true);
      method.invoke(null, new Object[] {classLoader});
    } catch (Exception e) {
      e.printStackTrace();
    }

    installScripts();
    installPlugins(path, ".", menuPath);
    /* make sure "Update Menus" runs _this_ plugin */
    Menus.getCommands().put("Update Menus", "fiji.User_Plugins(\"update\")");
    Menus.getCommands().put("Refresh Menus", "fiji.User_Plugins(\"update\")");
    Menus.getCommands().put("Compile and Run...", "fiji.Compile_and_Run");
    if (IJ.getInstance() != null) {
      Menu help = Menus.getMenuBar().getHelpMenu();
      for (int i = help.getItemCount() - 1; i >= 0; i--) {
        MenuItem item = help.getItem(i);
        String name = item.getLabel();
        if (name.equals("Update Menus")) item.setLabel("Refresh Menus");
      }
    }

    // make sure "Edit>Options>Memory & Threads runs Fiji's plugin
    Menus.getCommands().put("Memory & Threads...", "fiji.Memory");

    SampleImageLoader.install();
    Main.installRecentCommands();
  }
예제 #3
0
  @Override
  public Map<String, Throwable> findPlugins(final List<PluginInfo<?>> plugins) {
    final Map<String, MenuPath> menuTable = parseMenus(IJ.getInstance());
    final Hashtable<?, ?> commands = Menus.getCommands();
    final int startSize = plugins.size();
    for (final Object key : commands.keySet()) {
      final PluginInfo<Command> pe = createEntry(key, commands, menuTable);
      if (pe != null) plugins.add(pe);
    }
    final int pluginCount = plugins.size() - startSize;
    final int ignoredCount = commands.size() - pluginCount;
    log.info("Found " + pluginCount + " legacy plugins (plus " + ignoredCount + " ignored).");

    return null;
  }
예제 #4
0
 public void run(String arg) {
   if (arg.equals("menus")) {
     updateMenus();
     return;
   }
   if (IJ.getApplet() != null) return;
   // File file = new File(Prefs.getHomeDir() + File.separator + "ij.jar");
   // if (isMac() && !file.exists())
   //	file = new File(Prefs.getHomeDir() + File.separator +
   // "ImageJ.app/Contents/Resources/Java/ij.jar");
   URL url = getClass().getResource("/ij/IJ.class");
   String ij_jar = url == null ? null : url.toString().replaceAll("%20", " ");
   if (ij_jar == null || !ij_jar.startsWith("jar:file:")) {
     error("Could not determine location of ij.jar");
     return;
   }
   int exclamation = ij_jar.indexOf('!');
   ij_jar = ij_jar.substring(9, exclamation);
   if (IJ.debugMode) IJ.log("Updater: " + ij_jar);
   File file = new File(ij_jar);
   if (!file.exists()) {
     error("File not found: " + file.getPath());
     return;
   }
   if (!file.canWrite()) {
     String msg = "No write access: " + file.getPath();
     if (IJ.isVista()) msg += Prefs.vistaHint;
     error(msg);
     return;
   }
   String[] list = openUrlAsList(IJ.URL + "/download/jars/list.txt");
   int count = list.length + 2;
   String[] versions = new String[count];
   String[] urls = new String[count];
   String uv = getUpgradeVersion();
   if (uv == null) return;
   versions[0] = "v" + uv;
   urls[0] = IJ.URL + "/upgrade/ij.jar";
   if (versions[0] == null) return;
   for (int i = 1; i < count - 1; i++) {
     String version = list[i - 1];
     versions[i] = version.substring(0, version.length() - 1); // remove letter
     urls[i] =
         IJ.URL + "/download/jars/ij" + version.substring(1, 2) + version.substring(3, 6) + ".jar";
   }
   versions[count - 1] = "daily build";
   urls[count - 1] = IJ.URL + "/ij.jar";
   int choice = showDialog(versions);
   if (choice == -1) return;
   if (!versions[choice].startsWith("daily")
       && versions[choice].compareTo("v1.39") < 0
       && Menus.getCommands().get("ImageJ Updater") == null) {
     String msg =
         "This command is not available in versions of ImageJ prior\n"
             + "to 1.39 so you will need to install the plugin version at\n"
             + "<"
             + IJ.URL
             + "/plugins/imagej-updater.html>.";
     if (!IJ.showMessageWithCancel("Update ImageJ", msg)) return;
   }
   byte[] jar = getJar(urls[choice]);
   // file.renameTo(new File(file.getParent()+File.separator+"ij.bak"));
   if (version().compareTo("1.37v") >= 0) Prefs.savePreferences();
   // if (!renameJar(file)) return; // doesn't work on Vista
   saveJar(file, jar);
   if (choice < count - 1) // force macro Function Finder to download fresh list
   new File(IJ.getDirectory("macros") + "functions.html").delete();
   System.exit(0);
 }
예제 #5
0
  private Object tryOpen(String directory, String name, String path) {
    // set up a stream to read in 132 bytes from the file header
    // These can be checked for "magic" values which are diagnostic
    // of some image types
    InputStream is;
    byte[] buf = new byte[132];
    try {
      if (0 == path.indexOf("http://")) is = new java.net.URL(path).openStream();
      else is = new FileInputStream(path);
      is.read(buf, 0, 132);
      is.close();
    } catch (IOException e) {
      // couldn't open the file for reading
      return null;
    }
    name = name.toLowerCase();
    width = PLUGIN_NOT_FOUND;

    // Temporarily suppress "plugin not found" errors if LOCI Bio-Formats plugin is installed
    if (Menus.getCommands().get("Bio-Formats Importer") != null
        && IJ.getVersion().compareTo("1.37u") >= 0) IJ.suppressPluginNotFoundError();

    // OK now we get to the interesting bit

    // GJ: added Biorad PIC confocal file handler
    // ------------------------------------------
    // These make 12345 if you read them as the right kind of short
    // and should have this value in every Biorad PIC file
    if (buf[54] == 57 && buf[55] == 48) {
      return tryPlugIn("Biorad_Reader", path);
    }
    // GJ: added Gatan Digital Micrograph DM3 handler
    // ----------------------------------------------
    // check if the file ends in .DM3 or .dm3,
    // and bytes make an int value of 3 which is the DM3 version number
    if (name.endsWith(".dm3") && buf[0] == 0 && buf[1] == 0 && buf[2] == 0 && buf[3] == 3) {
      return tryPlugIn("DM3_Reader", path);
    }

    // IPLab file handler
    // Little-endian IPLab files start with "iiii" or "mmmm".
    if (name.endsWith(".ipl")
        || (buf[0] == 105 && buf[1] == 105 && buf[2] == 105 && buf[3] == 105)
        || (buf[0] == 109 && buf[1] == 109 && buf[2] == 109 && buf[3] == 109)) {
      return tryPlugIn("IPLab_Reader", path);
    }

    // Packard InstantImager format (.img) handler -> check HERE
    // before Analyze check below!
    // Check extension and signature bytes KAJ_
    if (name.endsWith(".img") && buf[0] == 75 && buf[1] == 65 && buf[2] == 74 && buf[3] == 0) {
      return tryPlugIn("InstantImager_Reader", path);
    }

    // Analyze format (.img/.hdr) handler
    // Opens the file using the Nifti_Reader if it is installed,
    // otherwise the Analyze_Reader is used. Note that
    // the Analyze_Reader plugin opens and displays the
    // image and does not implement the ImagePlus class.
    if (name.endsWith(".img") || name.endsWith(".hdr")) {
      if (Menus.getCommands().get("NIfTI-Analyze") != null) return tryPlugIn("Nifti_Reader", path);
      else return tryPlugIn("Analyze_Reader", path);
    }

    // NIFTI format (.nii) handler
    if (name.endsWith(".nii") || name.endsWith(".nii.gz") || name.endsWith(".nii.z")) {
      return tryPlugIn("Nifti_Reader", path);
    }

    // Image Cytometry Standard (.ics) handler
    // http://valelab.ucsf.edu/~nico/IJplugins/Ics_Opener.html
    if (name.endsWith(".ics")) {
      return tryPlugIn("Ics_Opener", path);
    }

    // Princeton Instruments SPE image file (.spe) handler
    // http://rsb.info.nih.gov/ij/plugins/spe.html
    if (name.endsWith(".spe")) {
      return tryPlugIn("OpenSPE_", path);
    }

    // Zeiss Confocal LSM 510 image file (.lsm) handler
    // http://rsb.info.nih.gov/ij/plugins/lsm-reader.html
    if (name.endsWith(".lsm")) {
      Object obj = tryPlugIn("LSM_Reader", path);
      if (obj == null && Menus.getCommands().get("Show LSMToolbox") != null)
        obj = tryPlugIn("LSM_Toolbox", "file=" + path);
      return obj;
    }

    // BM: added Bruker file handler 29.07.04
    if (name.equals("ser")
        || name.equals("fid")
        || name.equals("2rr")
        || name.equals("2ii")
        || name.equals("3rrr")
        || name.equals("3iii")
        || name.equals("2dseq")) {
      ij.IJ.showStatus("Opening Bruker " + name + " File");
      return tryPlugIn("BrukerOpener", name + "|" + path);
    }

    // AVI: open AVI files using AVI_Reader plugin
    if (name.endsWith(".avi")) {
      return tryPlugIn("AVI_Reader", path);
    }

    // QuickTime: open .mov and .pict files using QT_Movie_Opener plugin
    if (name.endsWith(".mov") || name.endsWith(".pict")) {
      return tryPlugIn("QT_Movie_Opener", path);
    }

    // ZVI file handler
    // Little-endian ZVI and Thumbs.db files start with d0 cf 11 e0
    // so we can only look at the extension.
    if (name.endsWith(".zvi")) {
      return tryPlugIn("ZVI_Reader", path);
    }

    // University of North Carolina (UNC) file format handler
    // 'magic' numbers are (int) offsets to data structures and
    // may change in future releases.
    if (name.endsWith(".unc")
        || (buf[3] == 117 && buf[7] == -127 && buf[11] == 36 && buf[14] == 32 && buf[15] == -127)) {
      return tryPlugIn("UNC_Reader", path);
    }

    // Amira file handler
    // http://wbgn013.biozentrum.uni-wuerzburg.de/ImageJ/amira-io.html
    if (buf[0] == 0x23
        && buf[1] == 0x20
        && buf[2] == 0x41
        && buf[3] == 0x6d
        && buf[4] == 0x69
        && buf[5] == 0x72
        && buf[6] == 0x61
        && buf[7] == 0x4d
        && buf[8] == 0x65
        && buf[9] == 0x73
        && buf[10] == 0x68
        && buf[11] == 0x20) {
      return tryPlugIn("AmiraMeshReader_", path);
    }

    // Deltavision file handler
    // Open DV files generated on Applied Precision DeltaVision systems
    if (name.endsWith(".dv") || name.endsWith(".r3d")) {
      return tryPlugIn("Deltavision_Opener", path);
    }

    // Albert Cardona: read .mrc files (little endian).
    // Documentation at: http://ami.scripps.edu/prtl_data/mrc_specification.htm.
    // The parsing of the header is a bare minimum of what could be done.
    if (name.endsWith(".mrc")) {
      return tryPlugIn("Open_MRC_Leginon", path);
    }

    // Albert Cardona: read .dat files from the EMMENU software
    if (name.endsWith(".dat") && 1 == buf[1] && 0 == buf[2]) { // 'new format' only
      return tryPlugIn("Open_DAT_EMMENU", path);
    }

    // Timo Rantalainen and Michael Doube: read Stratec pQCT files.
    // File name is IDDDDDDD.MHH, where D is decimal and H is hex.
    if (name.matches("[iI]\\d{7}\\.[mM]\\p{XDigit}{2}")) {
      return tryPlugIn("org.doube.bonej.pqct.Read_Stratec_File", path);
    }

    // Michael Doube: read Scanco ISQ files
    // File name is ADDDDDDD.ISQ;D where D is a decimal and A is a letter
    try {
      String isqMagic = new String(buf, 0, 16, "UTF-8");
      if (name.matches("[a-z]\\d{7}.isq;\\d+") || isqMagic.equals("CTDATA-HEADER_V1"))
        return tryPlugIn("org.bonej.io.ISQReader", path);
    } catch (Exception e) {
    }

    // David Mills: read Queen Mary MCD files
    if (name.endsWith(".mcd")) {
      return tryPlugIn("mcdReader", path);
    }
    // David Mills: read Queen Mary TOM files
    if (name.endsWith(".tom")) {
      return tryPlugIn("tomReader", path);
    }

    // ****************** MODIFY HERE ******************
    // do what ever you have to do to recognise your own file type
    // and then call appropriate plugin using the above as models
    // e.g.:

    /*
    // A. Dent: Added XYZ handler
    // ----------------------------------------------
    // check if the file ends in .xyz, and bytes 0 and 1 equal 42
    if (name.endsWith(".xyz") && buf[0]==42 && buf[1]==42) {
    // Ok we've identified the file type - now load it
    	return tryPlugIn("XYZ_Reader", path);
    }
    */

    return null;
  }
예제 #6
0
 /**
  * Run the command associated with a menu label if there is one
  *
  * @param menuLabel the label of the menu item to run
  */
 public static void runPlugIn(String menuLabel) {
   String className = (String) Menus.getCommands().get(menuLabel);
   if (className != null) IJ.runPlugIn(className, null);
 }
예제 #7
0
파일: Opener.java 프로젝트: kkkkxu/BioImage
 static {
   Hashtable commands = Menus.getCommands();
   bioformats = commands != null && commands.get("Bio-Formats Importer") != null;
 }