Exemplo n.º 1
0
 private void openDirectory(File f, String path) {
   if (path == null) return;
   if (!(path.endsWith(File.separator) || path.endsWith("/"))) path += File.separator;
   String[] names = f.list();
   names = (new FolderOpener()).trimFileList(names);
   if (names == null) return;
   String msg = "Open all " + names.length + " images in \"" + f.getName() + "\" as a stack?";
   GenericDialog gd = new GenericDialog("Open Folder");
   gd.setInsets(10, 5, 0);
   gd.addMessage(msg);
   gd.setInsets(15, 35, 0);
   gd.addCheckbox("Convert to RGB", convertToRGB);
   gd.setInsets(0, 35, 0);
   gd.addCheckbox("Use Virtual Stack", virtualStack);
   gd.enableYesNoCancel();
   gd.showDialog();
   if (gd.wasCanceled()) return;
   if (gd.wasOKed()) {
     convertToRGB = gd.getNextBoolean();
     virtualStack = gd.getNextBoolean();
     String options = " sort";
     if (convertToRGB) options += " convert_to_rgb";
     if (virtualStack) options += " use";
     IJ.run("Image Sequence...", "open=[" + path + "]" + options);
     DirectoryChooser.setDefaultDirectory(path);
   } else {
     for (int k = 0; k < names.length; k++) {
       IJ.redirectErrorMessages();
       if (!names[k].startsWith(".")) (new Opener()).open(path + names[k]);
     }
   }
   IJ.register(DragAndDrop.class);
 }
Exemplo n.º 2
0
  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
Exemplo n.º 3
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);
 }
Exemplo n.º 4
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);
   }
 }
Exemplo n.º 5
0
 public Zipper<Map<Integer, MZipper<RoiContainer>>> exec(
     Zipper<Map<Integer, MZipper<RoiContainer>>> z, int frame) {
   JFileChooser fc = new JFileChooser();
   int returnVal = fc.showOpenDialog(WindowManager.getCurrentWindow().getCanvas());
   Map<Integer, MZipper<RoiContainer>> newRois;
   if (returnVal == JFileChooser.APPROVE_OPTION) {
     try {
       FileInputStream f = new FileInputStream(fc.getSelectedFile().getCanonicalPath());
       MroiLisp parser = new MroiLisp(f);
       parser.ReInit(f);
       newRois = parser.roiFile();
       //				z.rights.clear();
       //				z.rights.add(newRois);
       //				z = z.right();
       //				return z;
       return z.insertAndStep(newRois);
     } catch (IOException e) {
       IJ.error("Couldn't open from " + fc.getSelectedFile().getName() + ": " + e.getMessage());
     } catch (mroi.ParseException e) {
       IJ.error("Failed in parsing: " + e.getMessage());
     } catch (Exception e) {
       IJ.error("Malformed input file: " + e.getMessage());
     }
   }
   return z;
 }
Exemplo n.º 6
0
  /** 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());
  }
Exemplo n.º 7
0
 void write16BitStack(OutputStream out, Object[] stack) throws IOException {
   showProgressBar = false;
   for (int i = 0; i < fi.nImages; i++) {
     IJ.showStatus("Writing: " + (i + 1) + "/" + fi.nImages);
     write16BitImage(out, (short[]) stack[i]);
     IJ.showProgress((double) (i + 1) / fi.nImages);
   }
 }
Exemplo n.º 8
0
 public void dragOver(DropTargetDragEvent e) {
   if (IJ.debugMode) IJ.log("DragOver: " + e.getLocation());
   Point loc = e.getLocation();
   int buttonSize = Toolbar.getButtonSize();
   int width = IJ.getInstance().getSize().width;
   openAsVirtualStack = width - loc.x <= buttonSize;
   if (openAsVirtualStack) IJ.showStatus("<<Open as Virtual Stack>>");
   else IJ.showStatus("<<Drag and Drop>>");
 }
Exemplo n.º 9
0
 void write16BitVirtualStack(OutputStream out, VirtualStack virtualStack) throws IOException {
   showProgressBar = false;
   boolean flip = "FlipTheseImages".equals(fi.fileName);
   for (int i = 1; i <= fi.nImages; i++) {
     IJ.showStatus("Writing: " + i + "/" + fi.nImages);
     ImageProcessor ip = virtualStack.getProcessor(i);
     if (flip) ip.flipVertical();
     short[] pixels = (short[]) ip.getPixels();
     write16BitImage(out, pixels);
     IJ.showProgress((double) i / fi.nImages);
   }
 }
Exemplo n.º 10
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);
 }
Exemplo n.º 11
0
 public void drop(DropTargetDropEvent dtde) {
   dtde.acceptDrop(DnDConstants.ACTION_COPY);
   DataFlavor[] flavors = null;
   try {
     Transferable t = dtde.getTransferable();
     iterator = null;
     flavors = t.getTransferDataFlavors();
     if (IJ.debugMode) IJ.log("DragAndDrop.drop: " + flavors.length + " flavors");
     for (int i = 0; i < flavors.length; i++) {
       if (IJ.debugMode) IJ.log("  flavor[" + i + "]: " + flavors[i].getMimeType());
       if (flavors[i].isFlavorJavaFileListType()) {
         Object data = t.getTransferData(DataFlavor.javaFileListFlavor);
         iterator = ((List) data).iterator();
         break;
       } else if (flavors[i].isFlavorTextType()) {
         Object ob = t.getTransferData(flavors[i]);
         if (!(ob instanceof String)) continue;
         String s = ob.toString().trim();
         if (IJ.isLinux() && s.length() > 1 && (int) s.charAt(1) == 0) s = fixLinuxString(s);
         ArrayList list = new ArrayList();
         if (s.indexOf("href=\"") != -1 || s.indexOf("src=\"") != -1) {
           s = parseHTML(s);
           if (IJ.debugMode) IJ.log("  url: " + s);
           list.add(s);
           this.iterator = list.iterator();
           break;
         }
         BufferedReader br = new BufferedReader(new StringReader(s));
         String tmp;
         while (null != (tmp = br.readLine())) {
           tmp = java.net.URLDecoder.decode(tmp.replaceAll("\\+", "%2b"), "UTF-8");
           if (tmp.startsWith("file://")) tmp = tmp.substring(7);
           if (IJ.debugMode) IJ.log("  content: " + tmp);
           if (tmp.startsWith("http://")) list.add(s);
           else list.add(new File(tmp));
         }
         this.iterator = list.iterator();
         break;
       }
     }
     if (iterator != null) {
       Thread thread = new Thread(this, "DrawAndDrop");
       thread.setPriority(Math.max(thread.getPriority() - 1, Thread.MIN_PRIORITY));
       thread.start();
     }
   } catch (Exception e) {
     dtde.dropComplete(false);
     return;
   }
   dtde.dropComplete(true);
   if (flavors == null || flavors.length == 0) {
     if (IJ.isMacOSX())
       IJ.error(
           "First drag and drop ignored. Please try again. You can avoid this\n"
               + "problem by dragging to the toolbar instead of the status bar.");
     else IJ.error("Drag and drop failed");
   }
 }
Exemplo n.º 12
0
 public void run(String arg) {
   ImageJ ij = IJ.getInstance();
   ij.setDropTarget(null);
   new DropTarget(ij, this);
   new DropTarget(Toolbar.getInstance(), this);
   new DropTarget(ij.getStatusBar(), this);
 }
Exemplo n.º 13
0
 void updateMenus() {
   if (IJ.debugMode) {
     long start = System.currentTimeMillis();
     Menus.updateImageJMenus();
     IJ.log("Refresh Menus: " + (System.currentTimeMillis() - start) + " ms");
   } else Menus.updateImageJMenus();
 }
Exemplo n.º 14
0
 /** Opens a stack of images. */
 ImagePlus openStack(ColorModel cm, boolean show) {
   ImageStack stack = new ImageStack(fi.width, fi.height, cm);
   long skip = fi.getOffset();
   Object pixels;
   try {
     ImageReader reader = new ImageReader(fi);
     InputStream is = createInputStream(fi);
     if (is == null) return null;
     IJ.resetEscape();
     for (int i = 1; i <= fi.nImages; i++) {
       if (!silentMode) IJ.showStatus("Reading: " + i + "/" + fi.nImages);
       if (IJ.escapePressed()) {
         IJ.beep();
         IJ.showProgress(1.0);
         silentMode = false;
         return null;
       }
       pixels = reader.readPixels(is, skip);
       if (pixels == null) break;
       stack.addSlice(null, pixels);
       skip = fi.gapBetweenImages;
       if (!silentMode) IJ.showProgress(i, fi.nImages);
     }
     is.close();
   } catch (Exception e) {
     IJ.log("" + e);
   } catch (OutOfMemoryError e) {
     IJ.outOfMemory(fi.fileName);
     stack.trim();
   }
   if (!silentMode) IJ.showProgress(1.0);
   if (stack.getSize() == 0) return null;
   if (fi.sliceLabels != null && fi.sliceLabels.length <= stack.getSize()) {
     for (int i = 0; i < fi.sliceLabels.length; i++) stack.setSliceLabel(fi.sliceLabels[i], i + 1);
   }
   ImagePlus imp = new ImagePlus(fi.fileName, stack);
   if (fi.info != null) imp.setProperty("Info", fi.info);
   if (show) imp.show();
   imp.setFileInfo(fi);
   setCalibration(imp);
   ImageProcessor ip = imp.getProcessor();
   if (ip.getMin() == ip.getMax()) // find stack min and max if first slice is blank
   setStackDisplayRange(imp);
   if (!silentMode) IJ.showProgress(1.0);
   silentMode = false;
   return imp;
 }
Exemplo n.º 15
0
 /**
  * Reads the image from a URL and returns the pixel array (byte, short, int or float). Returns
  * null if there was an IO exception.
  */
 public Object readPixels(String url) {
   java.net.URL theURL;
   InputStream is;
   try {
     theURL = new URL(url);
   } catch (MalformedURLException e) {
     IJ.log("" + e);
     return null;
   }
   try {
     is = theURL.openStream();
   } catch (IOException e) {
     IJ.log("" + e);
     return null;
   }
   return readPixels(is);
 }
Exemplo n.º 16
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 public FileOpener(FileInfo fi) {
   this.fi = fi;
   if (fi != null) {
     width = fi.width;
     height = fi.height;
   }
   if (IJ.debugMode) IJ.log("FileInfo: " + fi);
 }
Exemplo n.º 17
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 public String getInfo() {
   return version()
       + System.getProperty("os.name")
       + " "
       + System.getProperty("os.version")
       + "; "
       + IJ.freeMemory();
 }
Exemplo n.º 18
0
 byte[] getJar(String address) {
   // System.out.println("getJar: "+address);
   byte[] data;
   try {
     URL url = new URL(address);
     IJ.showStatus("Connecting to " + IJ.URL);
     URLConnection uc = url.openConnection();
     int len = uc.getContentLength();
     if (IJ.debugMode) IJ.log("Updater (url): " + address + " " + len);
     if (len <= 0) return null;
     String name = address.contains("wsr") ? "daily build (" : "ij.jar (";
     IJ.showStatus("Downloading " + name + IJ.d2s((double) len / 1048576, 1) + "MB)");
     InputStream in = uc.getInputStream();
     data = new byte[len];
     int n = 0;
     while (n < len) {
       int count = in.read(data, n, len - n);
       if (count < 0) throw new EOFException();
       n += count;
       IJ.showProgress(n, len);
     }
     in.close();
   } catch (IOException e) {
     if (IJ.debugMode) IJ.log("" + e);
     return null;
   }
   if (IJ.debugMode) IJ.wait(6000);
   return data;
 }
Exemplo n.º 19
0
 private String version() {
   return "ImageJ "
       + VERSION
       + BUILD
       + "; "
       + "Java "
       + System.getProperty("java.version")
       + (IJ.is64Bit() ? " [64-bit]; " : " [32-bit]; ");
 }
Exemplo n.º 20
0
 byte[] download(File f) {
   if (!f.exists()) {
     IJ.error("Plugin Installer", "File not found: " + f);
     return null;
   }
   byte[] data = null;
   try {
     int len = (int) f.length();
     InputStream in = new BufferedInputStream(new FileInputStream(f));
     DataInputStream dis = new DataInputStream(in);
     data = new byte[len];
     dis.readFully(data);
     dis.close();
   } catch (Exception e) {
     IJ.error("Plugin Installer", "" + e);
     data = null;
   }
   return data;
 }
Exemplo n.º 21
0
 short[] readCompressed16bitImage(InputStream in) throws IOException {
   if (IJ.debugMode) IJ.log("ImageReader.read16bit, offset=" + fi.stripOffsets[0]);
   short[] pixels = new short[nPixels];
   int base = 0;
   short last = 0;
   for (int k = 0; k < fi.stripOffsets.length; k++) {
     // IJ.log("seek: "+fi.stripOffsets[k]+" "+fi.stripLengths[k]+"  "+(in instanceof
     // RandomAccessStream));
     if (in instanceof RandomAccessStream) ((RandomAccessStream) in).seek(fi.stripOffsets[k]);
     else if (k > 0) {
       long skip =
           (fi.stripOffsets[k] & 0xffffffffL)
               - (fi.stripOffsets[k - 1] & 0xffffffffL)
               - fi.stripLengths[k - 1];
       if (skip > 0L) in.skip(skip);
     }
     byte[] byteArray = new byte[fi.stripLengths[k]];
     int read = 0, left = byteArray.length;
     while (left > 0) {
       int r = in.read(byteArray, read, left);
       if (r == -1) {
         eofError();
         break;
       }
       read += r;
       left -= r;
     }
     byteArray = uncompress(byteArray);
     int pixelsRead = byteArray.length / bytesPerPixel;
     pixelsRead = pixelsRead - (pixelsRead % fi.width);
     int pmax = base + pixelsRead;
     if (pmax > nPixels) pmax = nPixels;
     if (fi.intelByteOrder) {
       for (int i = base, j = 0; i < pmax; i++, j += 2)
         pixels[i] = (short) (((byteArray[j + 1] & 0xff) << 8) | (byteArray[j] & 0xff));
     } else {
       for (int i = base, j = 0; i < pmax; i++, j += 2)
         pixels[i] = (short) (((byteArray[j] & 0xff) << 8) | (byteArray[j + 1] & 0xff));
     }
     if (fi.compression == FileInfo.LZW_WITH_DIFFERENCING) {
       for (int b = base; b < pmax; b++) {
         pixels[b] += last;
         last = b % fi.width == fi.width - 1 ? 0 : pixels[b];
       }
     }
     base += pixelsRead;
     showProgress(k + 1, fi.stripOffsets.length);
   }
   if (fi.fileType == FileInfo.GRAY16_SIGNED) {
     // convert to unsigned
     for (int i = 0; i < nPixels; i++) pixels[i] = (short) (pixels[i] + 32768);
   }
   return pixels;
 }
Exemplo n.º 22
0
 boolean savePlugin(File f, byte[] data) {
   try {
     FileOutputStream out = new FileOutputStream(f);
     out.write(data, 0, data.length);
     out.close();
   } catch (IOException e) {
     IJ.error("Plugin Installer", "" + e);
     return false;
   }
   return true;
 }
Exemplo n.º 23
0
 String[] openUrlAsList(String address) {
   IJ.showStatus("Connecting to " + IJ.URL);
   Vector v = new Vector();
   try {
     URL url = new URL(address);
     InputStream in = url.openStream();
     BufferedReader br = new BufferedReader(new InputStreamReader(in));
     String line;
     while (true) {
       line = br.readLine();
       if (line == null) break;
       if (!line.equals("")) v.addElement(line);
     }
     br.close();
   } catch (Exception e) {
   }
   String[] lines = new String[v.size()];
   v.copyInto((String[]) lines);
   IJ.showStatus("");
   return lines;
 }
Exemplo n.º 24
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 public void run(String arg) {
   OpenDialog od = new OpenDialog("Install Plugin, Macro or Script...", arg);
   String directory = od.getDirectory();
   String name = od.getFileName();
   if (name == null) return;
   if (!validExtension(name)) {
     IJ.error("Plugin Installer", errorMessage());
     return;
   }
   String path = directory + name;
   install(path);
 }
Exemplo n.º 25
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();
 }
Exemplo n.º 26
0
 /**
  * Open a file. If it's a directory, ask to open all images as a sequence in a stack or
  * individually.
  */
 public void openFile(File f) {
   if (IJ.debugMode) IJ.log("DragAndDrop.openFile: " + f);
   try {
     if (null == f) return;
     String path = f.getCanonicalPath();
     if (f.exists()) {
       if (f.isDirectory()) openDirectory(f, path);
       else {
         if (openAsVirtualStack && (path.endsWith(".tif") || path.endsWith(".TIF")))
           (new FileInfoVirtualStack()).run(path);
         else (new Opener()).openAndAddToRecent(path);
         OpenDialog.setLastDirectory(f.getParent() + File.separator);
         OpenDialog.setLastName(f.getName());
       }
     } else {
       IJ.log("File not found: " + path);
     }
   } catch (Throwable e) {
     if (!Macro.MACRO_CANCELED.equals(e.getMessage())) IJ.handleException(e);
   }
 }
Exemplo n.º 27
0
  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();
  }
  public void run(ImageProcessor ip) {

    dimz = stack.getSize();
    dimy = stack.getWidth();
    dimx = stack.getHeight();

    SaveDialog sd = new SaveDialog("Save Measurements as Text...", "res", ".dat");
    String name = sd.getFileName();
    if (name == null) return;

    String directory = sd.getDirectory();

    nb = calculnb(stack); // -1;
    IJ.showStatus("Measure parameters for the " + nb + " objects ...");
    if (nb < 1) {
      IJ.showMessage("volume must be labeled");
    } else {
      double[] volume_m = new double[nb];
      int[] volume_p = new int[nb];
      double[] surface = new double[nb];
      double[] surfacenb = new double[nb];
      double[][][] I = new double[3][3][nb];
      double[][] J = new double[3][nb];
      double[][][] dir = new double[3][3][nb];
      double[] xg = new double[nb];
      double[] yg = new double[nb];
      double[] zg = new double[nb];
      byte[] bord = new byte[nb];
      //       		double[] a = new double[nb];
      //       		double[] b = new double[nb];
      //       		double[] c = new double[nb];
      //       		double[] Fab = new double[nb];
      //       		double[] Fac = new double[nb];
      //       		double[] Fbc = new double[nb];
      //       		double[] sp = new double[nb];
      double[][] lmin = new double[nb][3];
      double[][] lmax = new double[nb][3];
      IJ.showStatus("Measure surfaces ...");
      calculmarchsurfstack(stack, nb, surface, volume_m);
      calculmarchsurfstacknb(stack, nb, surfacenb);
      // calculvolumestack(stack,nb,volume_p);
      IJ.showStatus("Measure volumes and inertia ...");
      calculcgstack(stack, nb, volume_p, xg, yg, zg);
      calculinertiestack(stack, nb, xg, yg, zg, I);
      inertie(nb, I, J, dir);
      IJ.showStatus("Measure bounding boxes ...");
      boitestack(stack, nb, xg, yg, zg, dir, lmin, lmax);
      borderstack(stack, nb, bord);
      IJ.showStatus("Save results ...");
      sauvegarde(
          volume_p, volume_m, surface, surfacenb, xg, yg, zg, J, dir, nb, bord, lmin, lmax,
          directory, name);
      volume_m = null;
      volume_p = null;
      surface = null;
      xg = null;
      yg = null;
      zg = null;
    }
  }
Exemplo n.º 29
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;
 }
Exemplo n.º 30
0
 private String parseHTML(String s) {
   if (IJ.debugMode) IJ.log("parseHTML:\n" + s);
   int index1 = s.indexOf("src=\"");
   if (index1 >= 0) {
     int index2 = s.indexOf("\"", index1 + 5);
     if (index2 > 0) return s.substring(index1 + 5, index2);
   }
   index1 = s.indexOf("href=\"");
   if (index1 >= 0) {
     int index2 = s.indexOf("\"", index1 + 6);
     if (index2 > 0) return s.substring(index1 + 6, index2);
   }
   return s;
 }