Exemplo n.º 1
0
 /** Opens the nth image of the specified TIFF stack. */
 public ImagePlus openTiff(String path, int n) {
   TiffDecoder td = new TiffDecoder(getDir(path), getName(path));
   if (IJ.debugMode) td.enableDebugging();
   FileInfo[] info = null;
   try {
     info = td.getTiffInfo();
   } catch (IOException e) {
     String msg = e.getMessage();
     if (msg == null || msg.equals("")) msg = "" + e;
     IJ.error("Open TIFF", msg);
     return null;
   }
   if (info == null) return null;
   FileInfo fi = info[0];
   if (info.length == 1 && fi.nImages > 1) {
     if (n < 1 || n > fi.nImages)
       throw new IllegalArgumentException("N out of 1-" + fi.nImages + " range");
     long size = fi.width * fi.height * fi.getBytesPerPixel();
     fi.longOffset = fi.getOffset() + (n - 1) * (size + fi.gapBetweenImages);
     fi.offset = 0;
     fi.nImages = 1;
   } else {
     if (n < 1 || n > info.length)
       throw new IllegalArgumentException("N out of 1-" + info.length + " range");
     fi.longOffset = info[n - 1].getOffset();
     fi.offset = 0;
     fi.stripOffsets = info[n - 1].stripOffsets;
     fi.stripLengths = info[n - 1].stripLengths;
   }
   FileOpener fo = new FileOpener(fi);
   return fo.open(false);
 }
Exemplo n.º 2
0
 /** Deserialize a byte array that was serialized using the FileSaver.serialize(). */
 public ImagePlus deserialize(byte[] bytes) {
   ByteArrayInputStream stream = new ByteArrayInputStream(bytes);
   TiffDecoder decoder = new TiffDecoder(stream, "Untitled");
   if (IJ.debugMode) decoder.enableDebugging();
   FileInfo[] info = null;
   try {
     info = decoder.getTiffInfo();
   } catch (IOException e) {
     return null;
   }
   FileOpener opener = new FileOpener(info[0]);
   ImagePlus imp = opener.open(false);
   if (imp == null) return null;
   imp.setTitle(info[0].fileName);
   imp = makeComposite(imp, info[0]);
   return imp;
 }
Exemplo n.º 3
0
 ImagePlus openTiff2(FileInfo[] info) {
   if (info == null) return null;
   ImagePlus imp = null;
   if (IJ.debugMode) // dump tiff tags
   IJ.log(info[0].debugInfo);
   if (info.length > 1) { // try to open as stack
     imp = openTiffStack(info);
     if (imp != null) return imp;
   }
   FileOpener fo = new FileOpener(info[0]);
   imp = fo.open(false);
   if (imp == null) return null;
   int[] offsets = info[0].stripOffsets;
   if (offsets != null && offsets.length > 1 && offsets[offsets.length - 1] < offsets[0])
     ij.IJ.run(imp, "Flip Vertically", "stack");
   imp = makeComposite(imp, info[0]);
   if (imp.getBitDepth() == 32 && imp.getTitle().startsWith("FFT of")) return openFFT(imp);
   else return imp;
 }
Exemplo n.º 4
0
 /**
  * Attempts to open the specified file as a tiff, bmp, dicom, fits, pgm, gif or jpeg image.
  * Returns an ImagePlus object if successful. Modified by Gregory Jefferis to call
  * HandleExtraFileTypes plugin if the file type is unrecognised.
  *
  * @see ij.IJ#openImage(String)
  */
 public ImagePlus openImage(String directory, String name) {
   ImagePlus imp;
   FileOpener.setSilentMode(silentMode);
   if (directory.length() > 0 && !(directory.endsWith("/") || directory.endsWith("\\")))
     directory += Prefs.separator;
   String path = directory + name;
   fileType = getFileType(path);
   if (IJ.debugMode) IJ.log("openImage: \"" + types[fileType] + "\", " + path);
   switch (fileType) {
     case TIFF:
       imp = openTiff(directory, name);
       return imp;
     case DICOM:
       imp = (ImagePlus) IJ.runPlugIn("ij.plugin.DICOM", path);
       if (imp.getWidth() != 0) return imp;
       else return null;
     case TIFF_AND_DICOM:
       // "hybrid" files created by GE-Senographe 2000 D */
       imp = openTiff(directory, name);
       ImagePlus imp2 = (ImagePlus) IJ.runPlugIn("ij.plugin.DICOM", path);
       if (imp != null && imp2 != null) {
         imp.setProperty("Info", imp2.getProperty("Info"));
         imp.setCalibration(imp2.getCalibration());
       }
       if (imp == null) imp = imp2;
       return imp;
     case FITS:
       imp = (ImagePlus) IJ.runPlugIn("ij.plugin.FITS_Reader", path);
       if (imp.getWidth() != 0) return imp;
       else return null;
     case PGM:
       imp = (ImagePlus) IJ.runPlugIn("ij.plugin.PGM_Reader", path);
       if (imp.getWidth() != 0) {
         if (imp.getStackSize() == 3 && imp.getBitDepth() == 16)
           imp = new CompositeImage(imp, IJ.COMPOSITE);
         return imp;
       } else return null;
     case JPEG:
       imp = openJpegOrGif(directory, name);
       if (imp != null && imp.getWidth() != 0) return imp;
       else return null;
     case GIF:
       imp = (ImagePlus) IJ.runPlugIn("ij.plugin.GIF_Reader", path);
       if (imp != null && imp.getWidth() != 0) return imp;
       else return null;
     case PNG:
       imp = openUsingImageIO(directory + name);
       if (imp != null && imp.getWidth() != 0) return imp;
       else return null;
     case BMP:
       imp = (ImagePlus) IJ.runPlugIn("ij.plugin.BMP_Reader", path);
       if (imp.getWidth() != 0) return imp;
       else return null;
     case ZIP:
       return openZip(path);
     case AVI:
       AVI_Reader reader = new AVI_Reader();
       reader.displayDialog(!IJ.macroRunning());
       reader.run(path);
       return reader.getImagePlus();
     case UNKNOWN:
     case TEXT:
       // Call HandleExtraFileTypes plugin to see if it can handle unknown format
       int[] wrap = new int[] {fileType};
       imp = openWithHandleExtraFileTypes(path, wrap);
       if (imp != null && imp.getNChannels() > 1) imp = new CompositeImage(imp, IJ.COLOR);
       fileType = wrap[0];
       if (imp == null && fileType == UNKNOWN && IJ.getInstance() == null)
         IJ.error("Opener", "Unsupported format or not found");
       return imp;
     default:
       return null;
   }
 }