byte[] getJar(String address) {
// System.out.println("getJar: "+address);
byte[] data;
try {
URL url = new URL(address);
IJ.showStatus("Connecting to " + IJ.URL);
URLConnection uc = url.openConnection();
int len = uc.getContentLength();
if (IJ.debugMode) IJ.log("Updater (url): " + address + " " + len);
if (len <= 0) return null;
String name = address.contains("wsr") ? "daily build (" : "ij.jar (";
IJ.showStatus("Downloading " + name + IJ.d2s((double) len / 1048576, 1) + "MB)");
InputStream in = uc.getInputStream();
data = new byte[len];
int n = 0;
while (n < len) {
int count = in.read(data, n, len - n);
if (count < 0) throw new EOFException();
n += count;
IJ.showProgress(n, len);
}
in.close();
} catch (IOException e) {
if (IJ.debugMode) IJ.log("" + e);
return null;
}
if (IJ.debugMode) IJ.wait(6000);
return data;
}
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;
}
/** Reads the pixel data from an image described by a FileInfo object. */
Object readPixels(FileInfo fi) {
Object pixels = null;
try {
InputStream is = createInputStream(fi);
if (is == null) return null;
ImageReader reader = new ImageReader(fi);
pixels = reader.readPixels(is);
minValue = reader.min;
maxValue = reader.max;
is.close();
} catch (Exception e) {
if (!Macro.MACRO_CANCELED.equals(e.getMessage())) IJ.handleException(e);
}
return pixels;
}
String openUrlAsString(String address, int maxLines) {
StringBuffer sb;
try {
URL url = new URL(address);
InputStream in = url.openStream();
BufferedReader br = new BufferedReader(new InputStreamReader(in));
sb = new StringBuffer();
int count = 0;
String line;
while ((line = br.readLine()) != null && count++ < maxLines) sb.append(line + "\n");
in.close();
} catch (IOException e) {
sb = null;
}
return sb != null ? new String(sb) : null;
}
/** Opens a stack of images. */
ImagePlus openStack(ColorModel cm, boolean show) {
ImageStack stack = new ImageStack(fi.width, fi.height, cm);
long skip = fi.getOffset();
Object pixels;
try {
ImageReader reader = new ImageReader(fi);
InputStream is = createInputStream(fi);
if (is == null) return null;
IJ.resetEscape();
for (int i = 1; i <= fi.nImages; i++) {
if (!silentMode) IJ.showStatus("Reading: " + i + "/" + fi.nImages);
if (IJ.escapePressed()) {
IJ.beep();
IJ.showProgress(1.0);
silentMode = false;
return null;
}
pixels = reader.readPixels(is, skip);
if (pixels == null) break;
stack.addSlice(null, pixels);
skip = fi.gapBetweenImages;
if (!silentMode) IJ.showProgress(i, fi.nImages);
}
is.close();
} catch (Exception e) {
IJ.log("" + e);
} catch (OutOfMemoryError e) {
IJ.outOfMemory(fi.fileName);
stack.trim();
}
if (!silentMode) IJ.showProgress(1.0);
if (stack.getSize() == 0) return null;
if (fi.sliceLabels != null && fi.sliceLabels.length <= stack.getSize()) {
for (int i = 0; i < fi.sliceLabels.length; i++) stack.setSliceLabel(fi.sliceLabels[i], i + 1);
}
ImagePlus imp = new ImagePlus(fi.fileName, stack);
if (fi.info != null) imp.setProperty("Info", fi.info);
if (show) imp.show();
imp.setFileInfo(fi);
setCalibration(imp);
ImageProcessor ip = imp.getProcessor();
if (ip.getMin() == ip.getMax()) // find stack min and max if first slice is blank
setStackDisplayRange(imp);
if (!silentMode) IJ.showProgress(1.0);
silentMode = false;
return imp;
}
public static byte[] download(String urlString, String name) {
int maxLength = 52428800; // 50MB
URL url = null;
boolean unknownLength = false;
byte[] data = null;
;
int n = 0;
try {
url = new URL(urlString);
if (IJ.debugMode) IJ.log("PluginInstaller: " + urlString + " " + url);
if (url == null) return null;
URLConnection uc = url.openConnection();
int len = uc.getContentLength();
unknownLength = len < 0;
if (unknownLength) len = maxLength;
if (name != null) IJ.showStatus("Downloading " + url.getFile());
InputStream in = uc.getInputStream();
data = new byte[len];
int lenk = len / 1024;
while (n < len) {
int count = in.read(data, n, len - n);
if (count < 0) break;
n += count;
if (name != null)
IJ.showStatus("Downloading " + name + " (" + (n / 1024) + "/" + lenk + "k)");
IJ.showProgress(n, len);
}
in.close();
} catch (Exception e) {
String msg = "" + e;
if (!msg.contains("://")) msg += "\n " + urlString;
IJ.error("Plugin Installer", msg);
return null;
} finally {
IJ.showProgress(1.0);
}
if (name != null) IJ.showStatus("");
if (unknownLength) {
byte[] data2 = data;
data = new byte[n];
for (int i = 0; i < n; i++) data[i] = data2[i];
}
return data;
}
float[] read64bitImage(InputStream in) throws IOException {
int pixelsRead;
byte[] buffer = new byte[bufferSize];
float[] pixels = new float[nPixels];
long totalRead = 0L;
int base = 0;
int count, value;
int bufferCount;
long tmp;
long b1, b2, b3, b4, b5, b6, b7, b8;
while (totalRead < byteCount) {
if ((totalRead + bufferSize) > byteCount) bufferSize = (int) (byteCount - totalRead);
bufferCount = 0;
while (bufferCount < bufferSize) { // fill the buffer
count = in.read(buffer, bufferCount, bufferSize - bufferCount);
if (count == -1) {
if (bufferCount > 0) for (int i = bufferCount; i < bufferSize; i++) buffer[i] = 0;
totalRead = byteCount;
eofError();
break;
}
bufferCount += count;
}
totalRead += bufferSize;
showProgress(totalRead, byteCount);
pixelsRead = bufferSize / bytesPerPixel;
int j = 0;
for (int i = base; i < (base + pixelsRead); i++) {
b1 = buffer[j + 7] & 0xff;
b2 = buffer[j + 6] & 0xff;
b3 = buffer[j + 5] & 0xff;
b4 = buffer[j + 4] & 0xff;
b5 = buffer[j + 3] & 0xff;
b6 = buffer[j + 2] & 0xff;
b7 = buffer[j + 1] & 0xff;
b8 = buffer[j] & 0xff;
if (fi.intelByteOrder)
tmp =
(long)
((b1 << 56) | (b2 << 48) | (b3 << 40) | (b4 << 32) | (b5 << 24) | (b6 << 16)
| (b7 << 8) | b8);
else
tmp =
(long)
((b8 << 56) | (b7 << 48) | (b6 << 40) | (b5 << 32) | (b4 << 24) | (b3 << 16)
| (b2 << 8) | b1);
pixels[i] = (float) Double.longBitsToDouble(tmp);
j += 8;
}
base += pixelsRead;
}
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;
}
public Properties decodeDescriptionString(FileInfo fi) {
if (fi.description == null || fi.description.length() < 7) return null;
if (IJ.debugMode) IJ.log("Image Description: " + new String(fi.description).replace('\n', ' '));
if (!fi.description.startsWith("ImageJ")) return null;
Properties props = new Properties();
InputStream is = new ByteArrayInputStream(fi.description.getBytes());
try {
props.load(is);
is.close();
} catch (IOException e) {
return null;
}
fi.unit = props.getProperty("unit", "");
Double n = getNumber(props, "cf");
if (n != null) fi.calibrationFunction = n.intValue();
double c[] = new double[5];
int count = 0;
for (int i = 0; i < 5; i++) {
n = getNumber(props, "c" + i);
if (n == null) break;
c[i] = n.doubleValue();
count++;
}
if (count >= 2) {
fi.coefficients = new double[count];
for (int i = 0; i < count; i++) fi.coefficients[i] = c[i];
}
fi.valueUnit = props.getProperty("vunit");
n = getNumber(props, "images");
if (n != null && n.doubleValue() > 1.0) fi.nImages = (int) n.doubleValue();
if (fi.nImages > 1) {
double spacing = getDouble(props, "spacing");
if (spacing != 0.0) {
if (spacing < 0) spacing = -spacing;
fi.pixelDepth = spacing;
}
}
return props;
}
byte[] getJar(String address) {
byte[] data;
boolean gte133 = version().compareTo("1.33u") >= 0;
try {
URL url = new URL(address);
URLConnection uc = url.openConnection();
int len = uc.getContentLength();
String name = address.endsWith("ij/ij.jar") ? "daily build" : "ij.jar";
IJ.showStatus("Downloading ij.jar (" + IJ.d2s((double) len / 1048576, 1) + "MB)");
InputStream in = uc.getInputStream();
data = new byte[len];
int n = 0;
while (n < len) {
int count = in.read(data, n, len - n);
if (count < 0) throw new EOFException();
n += count;
if (gte133) IJ.showProgress(n, len);
}
in.close();
} catch (IOException e) {
return null;
}
return data;
}
/** Reads a 16-bit image. Signed pixels are converted to unsigned by adding 32768. */
short[] read16bitImage(InputStream in) throws IOException {
if (fi.compression > FileInfo.COMPRESSION_NONE
|| (fi.stripOffsets != null && fi.stripOffsets.length > 1)
&& fi.fileType != FileInfo.RGB48_PLANAR) return readCompressed16bitImage(in);
int pixelsRead;
byte[] buffer = new byte[bufferSize];
short[] pixels = new short[nPixels];
long totalRead = 0L;
int base = 0;
int count, value;
int bufferCount;
while (totalRead < byteCount) {
if ((totalRead + bufferSize) > byteCount) bufferSize = (int) (byteCount - totalRead);
bufferCount = 0;
while (bufferCount < bufferSize) { // fill the buffer
count = in.read(buffer, bufferCount, bufferSize - bufferCount);
if (count == -1) {
if (bufferCount > 0) for (int i = bufferCount; i < bufferSize; i++) buffer[i] = 0;
totalRead = byteCount;
eofError();
break;
}
bufferCount += count;
}
totalRead += bufferSize;
showProgress(totalRead, byteCount);
pixelsRead = bufferSize / bytesPerPixel;
if (fi.intelByteOrder) {
if (fi.fileType == FileInfo.GRAY16_SIGNED)
for (int i = base, j = 0; i < (base + pixelsRead); i++, j += 2)
pixels[i] = (short) ((((buffer[j + 1] & 0xff) << 8) | (buffer[j] & 0xff)) + 32768);
else
for (int i = base, j = 0; i < (base + pixelsRead); i++, j += 2)
pixels[i] = (short) (((buffer[j + 1] & 0xff) << 8) | (buffer[j] & 0xff));
} else {
if (fi.fileType == FileInfo.GRAY16_SIGNED)
for (int i = base, j = 0; i < (base + pixelsRead); i++, j += 2)
pixels[i] = (short) ((((buffer[j] & 0xff) << 8) | (buffer[j + 1] & 0xff)) + 32768);
else
for (int i = base, j = 0; i < (base + pixelsRead); i++, j += 2)
pixels[i] = (short) (((buffer[j] & 0xff) << 8) | (buffer[j + 1] & 0xff));
}
base += pixelsRead;
}
return pixels;
}
byte[] read8bitImage(InputStream in) throws IOException {
if (fi.compression > FileInfo.COMPRESSION_NONE) return readCompressed8bitImage(in);
byte[] pixels = new byte[nPixels];
// assume contiguous strips
int count, actuallyRead;
int totalRead = 0;
while (totalRead < byteCount) {
if (totalRead + bufferSize > byteCount) count = (int) (byteCount - totalRead);
else count = bufferSize;
actuallyRead = in.read(pixels, totalRead, count);
if (actuallyRead == -1) {
eofError();
break;
}
totalRead += actuallyRead;
showProgress(totalRead, byteCount);
}
return pixels;
}
void skip(InputStream in) throws IOException {
if (skipCount > 0) {
long bytesRead = 0;
int skipAttempts = 0;
long count;
while (bytesRead < skipCount) {
count = in.skip(skipCount - bytesRead);
skipAttempts++;
if (count == -1 || skipAttempts > 5) break;
bytesRead += count;
// IJ.log("skip: "+skipCount+" "+count+" "+bytesRead+" "+skipAttempts);
}
}
byteCount = ((long) width) * height * bytesPerPixel;
if (fi.fileType == FileInfo.BITMAP) {
int scan = width / 8, pad = width % 8;
if (pad > 0) scan++;
byteCount = scan * height;
}
nPixels = width * height;
bufferSize = (int) (byteCount / 25L);
if (bufferSize < 8192) bufferSize = 8192;
else bufferSize = (bufferSize / 8192) * 8192;
}
float[] read32bitImage(InputStream in) throws IOException {
if (fi.compression > FileInfo.COMPRESSION_NONE
|| (fi.stripOffsets != null && fi.stripOffsets.length > 1))
return readCompressed32bitImage(in);
int pixelsRead;
byte[] buffer = new byte[bufferSize];
float[] pixels = new float[nPixels];
long totalRead = 0L;
int base = 0;
int count, value;
int bufferCount;
int tmp;
while (totalRead < byteCount) {
if ((totalRead + bufferSize) > byteCount) bufferSize = (int) (byteCount - totalRead);
bufferCount = 0;
while (bufferCount < bufferSize) { // fill the buffer
count = in.read(buffer, bufferCount, bufferSize - bufferCount);
if (count == -1) {
if (bufferCount > 0) for (int i = bufferCount; i < bufferSize; i++) buffer[i] = 0;
totalRead = byteCount;
eofError();
break;
}
bufferCount += count;
}
totalRead += bufferSize;
showProgress(totalRead, byteCount);
pixelsRead = bufferSize / bytesPerPixel;
int pmax = base + pixelsRead;
if (pmax > nPixels) pmax = nPixels;
int j = 0;
if (fi.intelByteOrder)
for (int i = base; i < pmax; i++) {
tmp =
(int)
(((buffer[j + 3] & 0xff) << 24)
| ((buffer[j + 2] & 0xff) << 16)
| ((buffer[j + 1] & 0xff) << 8)
| (buffer[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;
j += 4;
}
else
for (int i = base; i < pmax; i++) {
tmp =
(int)
(((buffer[j] & 0xff) << 24)
| ((buffer[j + 1] & 0xff) << 16)
| ((buffer[j + 2] & 0xff) << 8)
| (buffer[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;
j += 4;
}
base += pixelsRead;
}
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;
}
int[] readChunkyRGB(InputStream in) throws IOException {
if (fi.compression == FileInfo.JPEG) return readJPEG(in);
else if (fi.compression > FileInfo.COMPRESSION_NONE
|| (fi.stripOffsets != null && fi.stripOffsets.length > 1))
return readCompressedChunkyRGB(in);
int pixelsRead;
bufferSize = 24 * width;
byte[] buffer = new byte[bufferSize];
int[] pixels = new int[nPixels];
long totalRead = 0L;
int base = 0;
int count, value;
int bufferCount;
int r, g, b, a;
while (totalRead < byteCount) {
if ((totalRead + bufferSize) > byteCount) bufferSize = (int) (byteCount - totalRead);
bufferCount = 0;
while (bufferCount < bufferSize) { // fill the buffer
count = in.read(buffer, bufferCount, bufferSize - bufferCount);
if (count == -1) {
if (bufferCount > 0) for (int i = bufferCount; i < bufferSize; i++) buffer[i] = 0;
totalRead = byteCount;
eofError();
break;
}
bufferCount += count;
}
totalRead += bufferSize;
showProgress(totalRead, byteCount);
pixelsRead = bufferSize / bytesPerPixel;
boolean bgr = fi.fileType == FileInfo.BGR;
int j = 0;
for (int i = base; i < (base + pixelsRead); i++) {
if (bytesPerPixel == 4) {
if (fi.fileType == FileInfo.BARG) { // MCID
b = buffer[j++] & 0xff;
j++; // ignore alfa byte
r = buffer[j++] & 0xff;
g = buffer[j++] & 0xff;
} else if (fi.fileType == FileInfo.ABGR) {
b = buffer[j++] & 0xff;
g = buffer[j++] & 0xff;
r = buffer[j++] & 0xff;
j++; // ignore alfa byte
} else if (fi.fileType == FileInfo.CMYK) {
r = buffer[j++] & 0xff; // c
g = buffer[j++] & 0xff; // m
b = buffer[j++] & 0xff; // y
a = buffer[j++] & 0xff; // k
if (a > 0) { // if k>0 then c=c*(1-k)+k
r = ((r * (256 - a)) >> 8) + a;
g = ((g * (256 - a)) >> 8) + a;
b = ((b * (256 - a)) >> 8) + a;
} // else r=1-c, g=1-m and b=1-y, which IJ does by inverting image
} else { // ARGB
r = buffer[j++] & 0xff;
g = buffer[j++] & 0xff;
b = buffer[j++] & 0xff;
j++; // ignore alfa byte
}
} else {
r = buffer[j++] & 0xff;
g = buffer[j++] & 0xff;
b = buffer[j++] & 0xff;
}
if (bgr) pixels[i] = 0xff000000 | (b << 16) | (g << 8) | r;
else pixels[i] = 0xff000000 | (r << 16) | (g << 8) | b;
}
base += pixelsRead;
}
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;
}
public void run(String arg) {
GenericDialog gd = new GenericDialog("Options");
double sfreq = 20000.0;
gd.addNumericField("Sampling Frequency?", sfreq, 1, 10, null);
String[] psfchoice = {"3D Gaussian", "Gaus-Lorentz^2", "2D Gaussian"};
gd.addChoice("PSF Type?", psfchoice, psfchoice[0]);
String[] filetypechoice = {
"Confocor 3 raw", "Short binary trajectory", "PlotWindow trajectory", "Ascii Text File"
};
gd.addChoice("File Type?", filetypechoice, filetypechoice[0]);
boolean ch2green = true;
gd.addCheckbox("Ch2 is green?", ch2green);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
sfreq = gd.getNextNumber();
int psfflag = gd.getNextChoiceIndex();
int fileflag = gd.getNextChoiceIndex();
ch2green = gd.getNextBoolean();
int nfiles = 0;
Object[] histograms = null;
int xmax = 0;
int ymax = 0;
String[] names = null;
if (fileflag < 2) {
jdataio ioclass = new jdataio();
File[] filearray = ioclass.openfiles(OpenDialog.getDefaultDirectory(), IJ.getInstance());
if (filearray.length == 0) {
return;
}
String dir = filearray[0].getAbsolutePath();
int sepindex = dir.lastIndexOf(File.separator);
String newdir = dir.substring(0, sepindex + 1);
OpenDialog.setDefaultDirectory(newdir);
nfiles = filearray.length / 2;
if (nfiles > 25) {
nfiles = 25;
}
histograms = new Object[nfiles];
names = organize_c3_files(filearray);
for (int i = 0; i < nfiles; i++) {
try {
int length1 = (int) (((double) filearray[2 * i].length() - 128.0) / 4.0);
int length2 = (int) (((double) filearray[2 * i + 1].length() - 128.0) / 4.0);
int length3 = (int) (((double) filearray[2 * i].length()) / 2.0);
int length4 = (int) (((double) filearray[2 * i + 1].length()) / 2.0);
InputStream instream = new BufferedInputStream(new FileInputStream(filearray[2 * i]));
InputStream instream2 =
new BufferedInputStream(new FileInputStream(filearray[2 * i + 1]));
if (fileflag == 0) {
int[] pmdata = new int[length1];
int[] pmdata2 = new int[length2];
if (!ioclass.skipstreambytes(instream, 128)) {
showioerror();
instream.close();
return;
}
if (!ioclass.skipstreambytes(instream2, 128)) {
showioerror();
instream2.close();
return;
}
if (!ioclass.readintelintfile(instream, length1, pmdata)) {
showioerror();
instream.close();
return;
}
if (!ioclass.readintelintfile(instream2, length2, pmdata2)) {
showioerror();
instream2.close();
return;
}
if (ch2green) {
histograms[i] = (new pmodeconvert()).pm2pch(pmdata2, pmdata, sfreq, 20000000);
} else {
histograms[i] = (new pmodeconvert()).pm2pch(pmdata, pmdata2, sfreq, 20000000);
}
} else {
float[] tmdata = new float[length3];
float[] tmdata2 = new float[length4];
if (!ioclass.readintelshortfile(instream, length3, tmdata)) {
showioerror();
instream.close();
return;
}
if (!ioclass.readintelshortfile(instream2, length4, tmdata2)) {
showioerror();
instream2.close();
return;
}
if (ch2green) {
histograms[i] = (new pmodeconvert()).create_2Dhistogram(tmdata2, tmdata);
} else {
histograms[i] = (new pmodeconvert()).create_2Dhistogram(tmdata, tmdata2);
}
}
if (((float[][]) histograms[i]).length > xmax) {
xmax = ((float[][]) histograms[i]).length;
}
if (((float[][]) histograms[i])[0].length > ymax) {
ymax = ((float[][]) histograms[i])[0].length;
}
instream.close();
instream2.close();
} catch (IOException e) {
showioerror();
return;
}
}
} else {
if (fileflag == 2) {
ImageWindow iw = WindowManager.getCurrentWindow();
float[][] trajectories = (float[][]) jutils.runPW4VoidMethod(iw, "getYValues");
float[][] tempxvals = (float[][]) jutils.runPW4VoidMethod(iw, "getXValues");
sfreq = 1.0 / ((double) tempxvals[0][1]);
nfiles = trajectories.length / 2;
if (nfiles > 25) {
nfiles = 25;
}
names = new String[nfiles + 1];
names[nfiles] = "avg";
histograms = new Object[nfiles];
for (int i = 0; i < nfiles; i++) {
names[i] = "trajectory " + (i + 1);
if (ch2green) {
histograms[i] =
(new pmodeconvert())
.create_2Dhistogram(trajectories[2 * i + 1], trajectories[2 * i]);
} else {
histograms[i] =
(new pmodeconvert())
.create_2Dhistogram(trajectories[2 * i], trajectories[2 * i + 1]);
}
if (((float[][]) histograms[i]).length > xmax) {
xmax = ((float[][]) histograms[i]).length;
}
if (((float[][]) histograms[i])[0].length > ymax) {
ymax = ((float[][]) histograms[i])[0].length;
}
}
} else {
// here we read tab delimited lines from files
jdataio ioclass = new jdataio();
File[] filearray = ioclass.openfiles(OpenDialog.getDefaultDirectory(), IJ.getInstance());
if (filearray.length == 0) {
return;
}
String dir = filearray[0].getAbsolutePath();
int sepindex = dir.lastIndexOf(File.separator);
String newdir = dir.substring(0, sepindex + 1);
OpenDialog.setDefaultDirectory(newdir);
nfiles = filearray.length;
if (nfiles > 25) {
nfiles = 25;
}
histograms = new Object[nfiles];
names = new String[nfiles + 1];
names[nfiles] = "avg";
for (int i = 0; i < nfiles; i++) {
try {
names[i] = filearray[i].getName();
BufferedReader d = new BufferedReader(new FileReader(filearray[i]));
String[] lines = new String[256];
int counter = 0;
do {
lines[counter] = d.readLine();
counter++;
} while ((lines[counter - 1] != null && lines[counter - 1] != "") && counter < 256);
int numcolumns = 0;
for (int j = 0; j < counter - 1; j++) {
int temp = getncolumns(lines[j]);
if (temp > numcolumns) {
numcolumns = temp;
}
}
float[][] temphist2 = null;
if (ch2green) {
temphist2 = new float[numcolumns][counter - 1];
} else {
temphist2 = new float[counter - 1][numcolumns];
}
for (int k = 0; k < counter - 1; k++) {
float[] temp = tab_delim2float(lines[k]);
for (int j = 0; j < numcolumns; j++) {
if (ch2green) {
temphist2[j][k] = temp[j];
} else {
temphist2[k][j] = temp[j];
}
}
}
histograms[i] = temphist2;
d.close();
} catch (IOException e) {
showioerror();
return;
}
}
for (int i = 0; i < nfiles; i++) {
if (((float[][]) histograms[i]).length > xmax) {
xmax = ((float[][]) histograms[i]).length;
}
if (((float[][]) histograms[i])[0].length > ymax) {
ymax = ((float[][]) histograms[i])[0].length;
}
}
}
}
// note that here x is green and y is red
float[][][] pch = new float[nfiles][xmax][ymax];
for (int i = 0; i < nfiles; i++) {
for (int j = 0; j < ((float[][]) histograms[i]).length; j++) {
for (int k = 0; k < ((float[][]) histograms[i])[j].length; k++) {
pch[i][j][k] = ((float[][]) histograms[i])[j][k];
}
}
}
final PCH2DFitWindow cw = new PCH2DFitWindow();
cw.init(names, pch, psfflag);
final Frame f = new Frame("PCH 2D Analysis");
f.setLocation(10, 10);
f.addWindowListener(
new WindowAdapter() {
public void windowClosing(WindowEvent e) {
f.dispose();
}
});
f.add(cw);
f.pack();
f.setResizable(false);
Insets ins = f.getInsets();
cw.totalSize.height = PCH2DFitWindow.H + ins.bottom + ins.top + 65;
cw.totalSize.width = PCH2DFitWindow.WR + ins.left + ins.right;
f.setSize(cw.totalSize);
f.setVisible(true);
cw.requestFocus();
}
private Object tryOpen(String directory, String name, String path) {
// set up a stream to read in 132 bytes from the file header
// These can be checked for "magic" values which are diagnostic
// of some image types
InputStream is;
byte[] buf = new byte[132];
try {
if (0 == path.indexOf("http://")) is = new java.net.URL(path).openStream();
else is = new FileInputStream(path);
is.read(buf, 0, 132);
is.close();
} catch (IOException e) {
// couldn't open the file for reading
return null;
}
name = name.toLowerCase();
width = PLUGIN_NOT_FOUND;
// Temporarily suppress "plugin not found" errors if LOCI Bio-Formats plugin is installed
if (Menus.getCommands().get("Bio-Formats Importer") != null
&& IJ.getVersion().compareTo("1.37u") >= 0) IJ.suppressPluginNotFoundError();
// OK now we get to the interesting bit
// GJ: added Biorad PIC confocal file handler
// ------------------------------------------
// These make 12345 if you read them as the right kind of short
// and should have this value in every Biorad PIC file
if (buf[54] == 57 && buf[55] == 48) {
return tryPlugIn("Biorad_Reader", path);
}
// GJ: added Gatan Digital Micrograph DM3 handler
// ----------------------------------------------
// check if the file ends in .DM3 or .dm3,
// and bytes make an int value of 3 which is the DM3 version number
if (name.endsWith(".dm3") && buf[0] == 0 && buf[1] == 0 && buf[2] == 0 && buf[3] == 3) {
return tryPlugIn("DM3_Reader", path);
}
// IPLab file handler
// Little-endian IPLab files start with "iiii" or "mmmm".
if (name.endsWith(".ipl")
|| (buf[0] == 105 && buf[1] == 105 && buf[2] == 105 && buf[3] == 105)
|| (buf[0] == 109 && buf[1] == 109 && buf[2] == 109 && buf[3] == 109)) {
return tryPlugIn("IPLab_Reader", path);
}
// Packard InstantImager format (.img) handler -> check HERE
// before Analyze check below!
// Check extension and signature bytes KAJ_
if (name.endsWith(".img") && buf[0] == 75 && buf[1] == 65 && buf[2] == 74 && buf[3] == 0) {
return tryPlugIn("InstantImager_Reader", path);
}
// Analyze format (.img/.hdr) handler
// Opens the file using the Nifti_Reader if it is installed,
// otherwise the Analyze_Reader is used. Note that
// the Analyze_Reader plugin opens and displays the
// image and does not implement the ImagePlus class.
if (name.endsWith(".img") || name.endsWith(".hdr")) {
if (Menus.getCommands().get("NIfTI-Analyze") != null) return tryPlugIn("Nifti_Reader", path);
else return tryPlugIn("Analyze_Reader", path);
}
// NIFTI format (.nii) handler
if (name.endsWith(".nii") || name.endsWith(".nii.gz") || name.endsWith(".nii.z")) {
return tryPlugIn("Nifti_Reader", path);
}
// Image Cytometry Standard (.ics) handler
// http://valelab.ucsf.edu/~nico/IJplugins/Ics_Opener.html
if (name.endsWith(".ics")) {
return tryPlugIn("Ics_Opener", path);
}
// Princeton Instruments SPE image file (.spe) handler
// http://rsb.info.nih.gov/ij/plugins/spe.html
if (name.endsWith(".spe")) {
return tryPlugIn("OpenSPE_", path);
}
// Zeiss Confocal LSM 510 image file (.lsm) handler
// http://rsb.info.nih.gov/ij/plugins/lsm-reader.html
if (name.endsWith(".lsm")) {
Object obj = tryPlugIn("LSM_Reader", path);
if (obj == null && Menus.getCommands().get("Show LSMToolbox") != null)
obj = tryPlugIn("LSM_Toolbox", "file=" + path);
return obj;
}
// BM: added Bruker file handler 29.07.04
if (name.equals("ser")
|| name.equals("fid")
|| name.equals("2rr")
|| name.equals("2ii")
|| name.equals("3rrr")
|| name.equals("3iii")
|| name.equals("2dseq")) {
ij.IJ.showStatus("Opening Bruker " + name + " File");
return tryPlugIn("BrukerOpener", name + "|" + path);
}
// AVI: open AVI files using AVI_Reader plugin
if (name.endsWith(".avi")) {
return tryPlugIn("AVI_Reader", path);
}
// QuickTime: open .mov and .pict files using QT_Movie_Opener plugin
if (name.endsWith(".mov") || name.endsWith(".pict")) {
return tryPlugIn("QT_Movie_Opener", path);
}
// ZVI file handler
// Little-endian ZVI and Thumbs.db files start with d0 cf 11 e0
// so we can only look at the extension.
if (name.endsWith(".zvi")) {
return tryPlugIn("ZVI_Reader", path);
}
// University of North Carolina (UNC) file format handler
// 'magic' numbers are (int) offsets to data structures and
// may change in future releases.
if (name.endsWith(".unc")
|| (buf[3] == 117 && buf[7] == -127 && buf[11] == 36 && buf[14] == 32 && buf[15] == -127)) {
return tryPlugIn("UNC_Reader", path);
}
// Amira file handler
// http://wbgn013.biozentrum.uni-wuerzburg.de/ImageJ/amira-io.html
if (buf[0] == 0x23
&& buf[1] == 0x20
&& buf[2] == 0x41
&& buf[3] == 0x6d
&& buf[4] == 0x69
&& buf[5] == 0x72
&& buf[6] == 0x61
&& buf[7] == 0x4d
&& buf[8] == 0x65
&& buf[9] == 0x73
&& buf[10] == 0x68
&& buf[11] == 0x20) {
return tryPlugIn("AmiraMeshReader_", path);
}
// Deltavision file handler
// Open DV files generated on Applied Precision DeltaVision systems
if (name.endsWith(".dv") || name.endsWith(".r3d")) {
return tryPlugIn("Deltavision_Opener", path);
}
// Albert Cardona: read .mrc files (little endian).
// Documentation at: http://ami.scripps.edu/prtl_data/mrc_specification.htm.
// The parsing of the header is a bare minimum of what could be done.
if (name.endsWith(".mrc")) {
return tryPlugIn("Open_MRC_Leginon", path);
}
// Albert Cardona: read .dat files from the EMMENU software
if (name.endsWith(".dat") && 1 == buf[1] && 0 == buf[2]) { // 'new format' only
return tryPlugIn("Open_DAT_EMMENU", path);
}
// Timo Rantalainen and Michael Doube: read Stratec pQCT files.
// File name is IDDDDDDD.MHH, where D is decimal and H is hex.
if (name.matches("[iI]\\d{7}\\.[mM]\\p{XDigit}{2}")) {
return tryPlugIn("org.doube.bonej.pqct.Read_Stratec_File", path);
}
// Michael Doube: read Scanco ISQ files
// File name is ADDDDDDD.ISQ;D where D is a decimal and A is a letter
try {
String isqMagic = new String(buf, 0, 16, "UTF-8");
if (name.matches("[a-z]\\d{7}.isq;\\d+") || isqMagic.equals("CTDATA-HEADER_V1"))
return tryPlugIn("org.bonej.io.ISQReader", path);
} catch (Exception e) {
}
// David Mills: read Queen Mary MCD files
if (name.endsWith(".mcd")) {
return tryPlugIn("mcdReader", path);
}
// David Mills: read Queen Mary TOM files
if (name.endsWith(".tom")) {
return tryPlugIn("tomReader", path);
}
// ****************** MODIFY HERE ******************
// do what ever you have to do to recognise your own file type
// and then call appropriate plugin using the above as models
// e.g.:
/*
// A. Dent: Added XYZ handler
// ----------------------------------------------
// check if the file ends in .xyz, and bytes 0 and 1 equal 42
if (name.endsWith(".xyz") && buf[0]==42 && buf[1]==42) {
// Ok we've identified the file type - now load it
return tryPlugIn("XYZ_Reader", path);
}
*/
return null;
}