/**
* Returns an ImageProcessor for the specified slice, were 1<=n<=nslices. Returns null if the
* stack is empty.
*/
public ImageProcessor getProcessor(int n) {
ImageProcessor ip;
if (n < 1 || n > nSlices) throw new IllegalArgumentException(outOfRange + n);
if (nSlices == 0) return null;
if (stack[0] == null) throw new IllegalArgumentException("Pixel array is null");
if (stack[0] instanceof byte[]) ip = new ByteProcessor(width, height, null, cm);
else if (stack[0] instanceof short[]) ip = new ShortProcessor(width, height, null, cm);
else if (stack[0] instanceof int[]) ip = new ColorProcessor(width, height, null);
else if (stack[0] instanceof float[]) ip = new FloatProcessor(width, height, null, cm);
else throw new IllegalArgumentException("Unknown stack type");
ip.setPixels(stack[n - 1]);
if (min != Double.MAX_VALUE && ip != null && !(ip instanceof ColorProcessor))
ip.setMinAndMax(min, max);
if (cTable != null) ip.setCalibrationTable(cTable);
return ip;
}
void setCalibration(ImagePlus imp) {
if (fi.fileType == FileInfo.GRAY16_SIGNED) {
if (IJ.debugMode) IJ.log("16-bit signed");
double[] coeff = new double[2];
coeff[0] = -32768.0;
coeff[1] = 1.0;
imp.getLocalCalibration().setFunction(Calibration.STRAIGHT_LINE, coeff, "gray value");
}
Properties props = decodeDescriptionString(fi);
Calibration cal = imp.getCalibration();
boolean calibrated = false;
if (fi.pixelWidth > 0.0 && fi.unit != null) {
cal.pixelWidth = fi.pixelWidth;
cal.pixelHeight = fi.pixelHeight;
cal.pixelDepth = fi.pixelDepth;
cal.setUnit(fi.unit);
calibrated = true;
}
if (fi.valueUnit != null) {
int f = fi.calibrationFunction;
if ((f >= Calibration.STRAIGHT_LINE && f <= Calibration.RODBARD2 && fi.coefficients != null)
|| f == Calibration.UNCALIBRATED_OD) {
boolean zeroClip = props != null && props.getProperty("zeroclip", "false").equals("true");
cal.setFunction(f, fi.coefficients, fi.valueUnit, zeroClip);
calibrated = true;
}
}
if (calibrated) checkForCalibrationConflict(imp, cal);
if (fi.frameInterval != 0.0) cal.frameInterval = fi.frameInterval;
if (props == null) return;
cal.xOrigin = getDouble(props, "xorigin");
cal.yOrigin = getDouble(props, "yorigin");
cal.zOrigin = getDouble(props, "zorigin");
cal.info = props.getProperty("info");
cal.fps = getDouble(props, "fps");
cal.loop = getBoolean(props, "loop");
cal.frameInterval = getDouble(props, "finterval");
cal.setTimeUnit(props.getProperty("tunit", "sec"));
double displayMin = getDouble(props, "min");
double displayMax = getDouble(props, "max");
if (!(displayMin == 0.0 && displayMax == 0.0)) {
int type = imp.getType();
ImageProcessor ip = imp.getProcessor();
if (type == ImagePlus.GRAY8 || type == ImagePlus.COLOR_256)
ip.setMinAndMax(displayMin, displayMax);
else if (type == ImagePlus.GRAY16 || type == ImagePlus.GRAY32) {
if (ip.getMin() != displayMin || ip.getMax() != displayMax)
ip.setMinAndMax(displayMin, displayMax);
}
}
int stackSize = imp.getStackSize();
if (stackSize > 1) {
int channels = (int) getDouble(props, "channels");
int slices = (int) getDouble(props, "slices");
int frames = (int) getDouble(props, "frames");
if (channels == 0) channels = 1;
if (slices == 0) slices = 1;
if (frames == 0) frames = 1;
// IJ.log("setCalibration: "+channels+" "+slices+" "+frames);
if (channels * slices * frames == stackSize) {
imp.setDimensions(channels, slices, frames);
if (getBoolean(props, "hyperstack")) imp.setOpenAsHyperStack(true);
}
}
}