void setStackDisplayRange(ImagePlus imp) {
ImageStack stack = imp.getStack();
double min = Double.MAX_VALUE;
double max = -Double.MAX_VALUE;
int n = stack.getSize();
for (int i = 1; i <= n; i++) {
if (!silentMode) IJ.showStatus("Calculating stack min and max: " + i + "/" + n);
ImageProcessor ip = stack.getProcessor(i);
ip.resetMinAndMax();
if (ip.getMin() < min) min = ip.getMin();
if (ip.getMax() > max) max = ip.getMax();
}
imp.getProcessor().setMinAndMax(min, max);
imp.updateAndDraw();
}
/** 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;
}
/** Opens the image. Displays it if 'show' is true. Returns an ImagePlus object if successful. */
public ImagePlus open(boolean show) {
ImagePlus imp = null;
Object pixels;
ProgressBar pb = null;
ImageProcessor ip;
ColorModel cm = createColorModel(fi);
if (fi.nImages > 1) {
return openStack(cm, show);
}
switch (fi.fileType) {
case FileInfo.GRAY8:
case FileInfo.COLOR8:
case FileInfo.BITMAP:
pixels = readPixels(fi);
if (pixels == null) return null;
ip = new ByteProcessor(width, height, (byte[]) pixels, cm);
imp = new ImagePlus(fi.fileName, ip);
break;
case FileInfo.GRAY16_SIGNED:
case FileInfo.GRAY16_UNSIGNED:
case FileInfo.GRAY12_UNSIGNED:
pixels = readPixels(fi);
if (pixels == null) return null;
ip = new ShortProcessor(width, height, (short[]) pixels, cm);
imp = new ImagePlus(fi.fileName, ip);
break;
case FileInfo.GRAY32_INT:
case FileInfo.GRAY32_UNSIGNED:
case FileInfo.GRAY32_FLOAT:
case FileInfo.GRAY24_UNSIGNED:
case FileInfo.GRAY64_FLOAT:
pixels = readPixels(fi);
if (pixels == null) return null;
ip = new FloatProcessor(width, height, (float[]) pixels, cm);
imp = new ImagePlus(fi.fileName, ip);
break;
case FileInfo.RGB:
case FileInfo.BGR:
case FileInfo.ARGB:
case FileInfo.ABGR:
case FileInfo.BARG:
case FileInfo.RGB_PLANAR:
pixels = readPixels(fi);
if (pixels == null) return null;
ip = new ColorProcessor(width, height, (int[]) pixels);
imp = new ImagePlus(fi.fileName, ip);
break;
case FileInfo.RGB48:
case FileInfo.RGB48_PLANAR:
boolean planar = fi.fileType == FileInfo.RGB48_PLANAR;
Object[] pixelArray = (Object[]) readPixels(fi);
if (pixelArray == null) return null;
ImageStack stack = new ImageStack(width, height);
stack.addSlice("Red", pixelArray[0]);
stack.addSlice("Green", pixelArray[1]);
stack.addSlice("Blue", pixelArray[2]);
imp = new ImagePlus(fi.fileName, stack);
imp.setDimensions(3, 1, 1);
if (planar) imp.getProcessor().resetMinAndMax();
imp.setFileInfo(fi);
int mode = CompositeImage.COMPOSITE;
if (fi.description != null) {
if (fi.description.indexOf("mode=color") != -1) mode = CompositeImage.COLOR;
else if (fi.description.indexOf("mode=gray") != -1) mode = CompositeImage.GRAYSCALE;
}
imp = new CompositeImage(imp, mode);
if (!planar && fi.displayRanges == null) {
for (int c = 1; c <= 3; c++) {
imp.setPosition(c, 1, 1);
imp.setDisplayRange(minValue, maxValue);
}
imp.setPosition(1, 1, 1);
}
break;
}
imp.setFileInfo(fi);
setCalibration(imp);
if (fi.info != null) imp.setProperty("Info", fi.info);
if (fi.sliceLabels != null && fi.sliceLabels.length == 1 && fi.sliceLabels[0] != null)
imp.setProperty("Label", fi.sliceLabels[0]);
if (show) imp.show();
return imp;
}
