/** * 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); } } }