int[] readPlanarRGB(InputStream in) throws IOException {
if (fi.compression > FileInfo.COMPRESSION_NONE) return readCompressedPlanarRGBImage(in);
DataInputStream dis = new DataInputStream(in);
int planeSize = nPixels; // 1/3 image size
byte[] buffer = new byte[planeSize];
int[] pixels = new int[nPixels];
int r, g, b;
startTime = 0L;
showProgress(10, 100);
dis.readFully(buffer);
for (int i = 0; i < planeSize; i++) {
r = buffer[i] & 0xff;
pixels[i] = 0xff000000 | (r << 16);
}
showProgress(40, 100);
dis.readFully(buffer);
for (int i = 0; i < planeSize; i++) {
g = buffer[i] & 0xff;
pixels[i] |= g << 8;
}
showProgress(70, 100);
dis.readFully(buffer);
for (int i = 0; i < planeSize; i++) {
b = buffer[i] & 0xff;
pixels[i] |= b;
}
showProgress(90, 100);
return pixels;
}
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;
}
float[] read24bitImage(InputStream in) throws IOException {
byte[] buffer = new byte[width * 3];
float[] pixels = new float[nPixels];
int b1, b2, b3;
DataInputStream dis = new DataInputStream(in);
for (int y = 0; y < height; y++) {
// IJ.log("read24bitImage: ");
dis.readFully(buffer);
int b = 0;
for (int x = 0; x < width; x++) {
b1 = buffer[b++] & 0xff;
b2 = buffer[b++] & 0xff;
b3 = buffer[b++] & 0xff;
pixels[x + y * width] = (b3 << 16) | (b2 << 8) | b1;
}
}
return pixels;
}
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;
}
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;
}
byte[] read1bitImage(InputStream in) throws IOException {
if (fi.compression == FileInfo.LZW)
throw new IOException("ImageJ cannot open 1-bit LZW compressed TIFFs");
int scan = (int) Math.ceil(width / 8.0);
int len = scan * height;
byte[] buffer = new byte[len];
byte[] pixels = new byte[nPixels];
DataInputStream dis = new DataInputStream(in);
dis.readFully(buffer);
int value1, value2, offset, index;
for (int y = 0; y < height; y++) {
offset = y * scan;
index = y * width;
for (int x = 0; x < scan; x++) {
value1 = buffer[offset + x] & 0xff;
for (int i = 7; i >= 0; i--) {
value2 = (value1 & (1 << i)) != 0 ? 255 : 0;
if (index < pixels.length) pixels[index++] = (byte) value2;
}
}
}
return pixels;
}
short[] read12bitImage(InputStream in) throws IOException {
int bytesPerLine = (int) (width * 1.5);
if ((width & 1) == 1) bytesPerLine++; // add 1 if odd
byte[] buffer = new byte[bytesPerLine * height];
short[] pixels = new short[nPixels];
DataInputStream dis = new DataInputStream(in);
dis.readFully(buffer);
for (int y = 0; y < height; y++) {
int index1 = y * bytesPerLine;
int index2 = y * width;
int count = 0;
while (count < width) {
pixels[index2 + count] =
(short) (((buffer[index1] & 0xff) * 16) + ((buffer[index1 + 1] >> 4) & 0xf));
count++;
if (count == width) break;
pixels[index2 + count] =
(short) (((buffer[index1 + 1] & 0xf) * 256) + (buffer[index1 + 2] & 0xff));
count++;
index1 += 3;
}
}
return pixels;
}