/** 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);
}
/** 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;
}
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;
}
/**
* 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;
}
}