Object readRGB48(InputStream in) throws IOException {
if (fi.compression > FileInfo.COMPRESSION_NONE) return readCompressedRGB48(in);
int channels = fi.samplesPerPixel;
short[][] stack = new short[channels][nPixels];
DataInputStream dis = new DataInputStream(in);
int pixel = 0;
int min = 65535, max = 0;
if (fi.stripLengths == null) {
fi.stripLengths = new int[fi.stripOffsets.length];
fi.stripLengths[0] = width * height * bytesPerPixel;
}
for (int i = 0; i < fi.stripOffsets.length; i++) {
if (i > 0) {
long skip =
(fi.stripOffsets[i] & 0xffffffffL)
- (fi.stripOffsets[i - 1] & 0xffffffffL)
- fi.stripLengths[i - 1];
if (skip > 0L) dis.skip(skip);
}
int len = fi.stripLengths[i];
int bytesToGo = (nPixels - pixel) * channels * 2;
if (len > bytesToGo) len = bytesToGo;
byte[] buffer = new byte[len];
dis.readFully(buffer);
int value;
int channel = 0;
boolean intel = fi.intelByteOrder;
for (int base = 0; base < len; base += 2) {
if (intel) value = ((buffer[base + 1] & 0xff) << 8) | (buffer[base] & 0xff);
else value = ((buffer[base] & 0xff) << 8) | (buffer[base + 1] & 0xff);
if (value < min) min = value;
if (value > max) max = value;
stack[channel][pixel] = (short) (value);
channel++;
if (channel == channels) {
channel = 0;
pixel++;
}
}
showProgress(i + 1, fi.stripOffsets.length);
}
this.min = min;
this.max = max;
return stack;
}
Object readCompressedRGB48(InputStream in) throws IOException {
if (fi.compression == FileInfo.LZW_WITH_DIFFERENCING)
throw new IOException("ImageJ cannot open 48-bit LZW compressed TIFFs with predictor");
int channels = 3;
short[][] stack = new short[channels][nPixels];
DataInputStream dis = new DataInputStream(in);
int pixel = 0;
int min = 65535, max = 0;
for (int i = 0; i < fi.stripOffsets.length; i++) {
if (i > 0) {
long skip =
(fi.stripOffsets[i] & 0xffffffffL)
- (fi.stripOffsets[i - 1] & 0xffffffffL)
- fi.stripLengths[i - 1];
if (skip > 0L) dis.skip(skip);
}
int len = fi.stripLengths[i];
byte[] buffer = new byte[len];
dis.readFully(buffer);
buffer = uncompress(buffer);
len = buffer.length;
if (len % 2 != 0) len--;
int value;
int channel = 0;
boolean intel = fi.intelByteOrder;
for (int base = 0; base < len && pixel < nPixels; base += 2) {
if (intel) value = ((buffer[base + 1] & 0xff) << 8) | (buffer[base] & 0xff);
else value = ((buffer[base] & 0xff) << 8) | (buffer[base + 1] & 0xff);
if (value < min) min = value;
if (value > max) max = value;
stack[channel][pixel] = (short) (value);
channel++;
if (channel == channels) {
channel = 0;
pixel++;
}
}
showProgress(i + 1, fi.stripOffsets.length);
}
this.min = min;
this.max = max;
return stack;
}