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;
}
byte[] readCompressed8bitImage(InputStream in) throws IOException {
byte[] pixels = new byte[nPixels];
int current = 0;
byte last = 0;
for (int i = 0; i < fi.stripOffsets.length; i++) {
if (in instanceof RandomAccessStream) ((RandomAccessStream) in).seek(fi.stripOffsets[i]);
else if (i > 0) {
long skip =
(fi.stripOffsets[i] & 0xffffffffL)
- (fi.stripOffsets[i - 1] & 0xffffffffL)
- fi.stripLengths[i - 1];
if (skip > 0L) in.skip(skip);
}
byte[] byteArray = new byte[fi.stripLengths[i]];
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 length = byteArray.length;
length = length - (length % fi.width);
if (fi.compression == FileInfo.LZW_WITH_DIFFERENCING) {
for (int b = 0; b < length; b++) {
byteArray[b] += last;
last = b % fi.width == fi.width - 1 ? 0 : byteArray[b];
}
}
if (current + length > pixels.length) length = pixels.length - current;
System.arraycopy(byteArray, 0, pixels, current, length);
current += length;
showProgress(i + 1, fi.stripOffsets.length);
}
return pixels;
}
int[] readCompressedChunkyRGB(InputStream in) throws IOException {
int[] pixels = new int[nPixels];
int base = 0;
int lastRed = 0, lastGreen = 0, lastBlue = 0;
int nextByte;
int red = 0, green = 0, blue = 0, alpha = 0;
boolean bgr = fi.fileType == FileInfo.BGR;
boolean cmyk = fi.fileType == FileInfo.CMYK;
boolean differencing = fi.compression == FileInfo.LZW_WITH_DIFFERENCING;
for (int i = 0; i < fi.stripOffsets.length; i++) {
if (in instanceof RandomAccessStream) ((RandomAccessStream) in).seek(fi.stripOffsets[i]);
else if (i > 0) {
long skip =
(fi.stripOffsets[i] & 0xffffffffL)
- (fi.stripOffsets[i - 1] & 0xffffffffL)
- fi.stripLengths[i - 1];
if (skip > 0L) in.skip(skip);
}
byte[] byteArray = new byte[fi.stripLengths[i]];
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);
if (differencing) {
for (int b = 0; b < byteArray.length; b++) {
if (b / bytesPerPixel % fi.width == 0) continue;
byteArray[b] += byteArray[b - bytesPerPixel];
}
}
int k = 0;
int pixelsRead = byteArray.length / bytesPerPixel;
pixelsRead = pixelsRead - (pixelsRead % fi.width);
int pmax = base + pixelsRead;
if (pmax > nPixels) pmax = nPixels;
for (int j = base; j < pmax; j++) {
if (bytesPerPixel == 4) {
red = byteArray[k++] & 0xff;
green = byteArray[k++] & 0xff;
blue = byteArray[k++] & 0xff;
alpha = byteArray[k++] & 0xff;
if (cmyk && alpha > 0) {
red = ((red * (256 - alpha)) >> 8) + alpha;
green = ((green * (256 - alpha)) >> 8) + alpha;
blue = ((blue * (256 - alpha)) >> 8) + alpha;
}
} else {
red = byteArray[k++] & 0xff;
green = byteArray[k++] & 0xff;
blue = byteArray[k++] & 0xff;
}
if (bgr) pixels[j] = 0xff000000 | (blue << 16) | (green << 8) | red;
else pixels[j] = 0xff000000 | (red << 16) | (green << 8) | blue;
}
base += pixelsRead;
showProgress(i + 1, fi.stripOffsets.length);
}
return pixels;
}
float[] readCompressed32bitImage(InputStream in) throws IOException {
float[] pixels = new float[nPixels];
int base = 0;
float last = 0;
for (int k = 0; k < fi.stripOffsets.length; k++) {
// IJ.log("seek: "+fi.stripOffsets[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;
int tmp;
if (fi.intelByteOrder) {
for (int i = base, j = 0; i < pmax; i++, j += 4) {
tmp =
(int)
(((byteArray[j + 3] & 0xff) << 24)
| ((byteArray[j + 2] & 0xff) << 16)
| ((byteArray[j + 1] & 0xff) << 8)
| (byteArray[j] & 0xff));
if (fi.fileType == FileInfo.GRAY32_FLOAT) pixels[i] = Float.intBitsToFloat(tmp);
else if (fi.fileType == FileInfo.GRAY32_UNSIGNED) pixels[i] = (float) (tmp & 0xffffffffL);
else pixels[i] = tmp;
}
} else {
for (int i = base, j = 0; i < pmax; i++, j += 4) {
tmp =
(int)
(((byteArray[j] & 0xff) << 24)
| ((byteArray[j + 1] & 0xff) << 16)
| ((byteArray[j + 2] & 0xff) << 8)
| (byteArray[j + 3] & 0xff));
if (fi.fileType == FileInfo.GRAY32_FLOAT) pixels[i] = Float.intBitsToFloat(tmp);
else if (fi.fileType == FileInfo.GRAY32_UNSIGNED) pixels[i] = (float) (tmp & 0xffffffffL);
else pixels[i] = tmp;
}
}
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);
}
return pixels;
}