/** 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;
}
/** 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;
}
/** Attemps to open a tiff file as a stack. Returns an ImagePlus object if successful. */
public ImagePlus openTiffStack(FileInfo[] info) {
if (info.length > 1 && !allSameSizeAndType(info)) return null;
FileInfo fi = info[0];
if (fi.nImages > 1) return new FileOpener(fi).open(false); // open contiguous images as stack
else {
ColorModel cm = createColorModel(fi);
ImageStack stack = new ImageStack(fi.width, fi.height, cm);
Object pixels = null;
long skip = fi.getOffset();
int imageSize = fi.width * fi.height * fi.getBytesPerPixel();
if (info[0].fileType == FileInfo.GRAY12_UNSIGNED) {
imageSize = (int) (fi.width * fi.height * 1.5);
if ((imageSize & 1) == 1) imageSize++; // add 1 if odd
}
if (info[0].fileType == FileInfo.BITMAP) {
int scan = (int) Math.ceil(fi.width / 8.0);
imageSize = scan * fi.height;
}
long loc = 0L;
int nChannels = 1;
try {
InputStream is = createInputStream(fi);
ImageReader reader = new ImageReader(fi);
IJ.resetEscape();
for (int i = 0; i < info.length; i++) {
nChannels = 1;
Object[] channels = null;
if (!silentMode) IJ.showStatus("Reading: " + (i + 1) + "/" + info.length);
if (IJ.escapePressed()) {
IJ.beep();
IJ.showProgress(1.0);
return null;
}
fi.stripOffsets = info[i].stripOffsets;
fi.stripLengths = info[i].stripLengths;
int bpp = info[i].getBytesPerPixel();
if (info[i].samplesPerPixel > 1 && !(bpp == 3 || bpp == 4 || bpp == 6)) {
nChannels = fi.samplesPerPixel;
channels = new Object[nChannels];
for (int c = 0; c < nChannels; c++) {
pixels = reader.readPixels(is, c == 0 ? skip : 0L);
channels[c] = pixels;
}
} else pixels = reader.readPixels(is, skip);
if (pixels == null && channels == null) break;
loc += imageSize * nChannels + skip;
if (i < (info.length - 1)) {
skip = info[i + 1].getOffset() - loc;
if (info[i + 1].compression >= FileInfo.LZW) skip = 0;
if (skip < 0L) {
IJ.error("Opener", "Unexpected image offset");
break;
}
}
if (fi.fileType == FileInfo.RGB48) {
Object[] pixels2 = (Object[]) pixels;
stack.addSlice(null, pixels2[0]);
stack.addSlice(null, pixels2[1]);
stack.addSlice(null, pixels2[2]);
isRGB48 = true;
} else if (nChannels > 1) {
for (int c = 0; c < nChannels; c++) {
if (channels[c] != null) stack.addSlice(null, channels[c]);
}
} else stack.addSlice(null, pixels);
IJ.showProgress(i, info.length);
}
is.close();
} catch (Exception e) {
IJ.handleException(e);
} catch (OutOfMemoryError e) {
IJ.outOfMemory(fi.fileName);
stack.deleteLastSlice();
stack.deleteLastSlice();
}
IJ.showProgress(1.0);
if (stack.getSize() == 0) return null;
if (fi.fileType == FileInfo.GRAY16_UNSIGNED
|| fi.fileType == FileInfo.GRAY12_UNSIGNED
|| fi.fileType == FileInfo.GRAY32_FLOAT
|| fi.fileType == FileInfo.RGB48) {
ImageProcessor ip = stack.getProcessor(1);
ip.resetMinAndMax();
stack.update(ip);
}
// if (fi.whiteIsZero)
// new StackProcessor(stack, stack.getProcessor(1)).invert();
ImagePlus imp = new ImagePlus(fi.fileName, stack);
new FileOpener(fi).setCalibration(imp);
imp.setFileInfo(fi);
if (fi.info != null) imp.setProperty("Info", fi.info);
if (fi.description != null && fi.description.contains("order=zct"))
new HyperStackConverter().shuffle(imp, HyperStackConverter.ZCT);
int stackSize = stack.getSize();
if (nChannels > 1 && (stackSize % nChannels) == 0) {
imp.setDimensions(nChannels, stackSize / nChannels, 1);
imp = new CompositeImage(imp, IJ.COMPOSITE);
imp.setOpenAsHyperStack(true);
} else if (imp.getNChannels() > 1) imp = makeComposite(imp, fi);
IJ.showProgress(1.0);
return imp;
}
}