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; }
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); } } }
String getInfo(ImagePlus imp, ImageProcessor ip) { String s = new String("\n"); s += "Title: " + imp.getTitle() + "\n"; Calibration cal = imp.getCalibration(); int stackSize = imp.getStackSize(); int channels = imp.getNChannels(); int slices = imp.getNSlices(); int frames = imp.getNFrames(); int digits = imp.getBitDepth() == 32 ? 4 : 0; if (cal.scaled()) { String unit = cal.getUnit(); String units = cal.getUnits(); s += "Width: " + IJ.d2s(imp.getWidth() * cal.pixelWidth, 2) + " " + units + " (" + imp.getWidth() + ")\n"; s += "Height: " + IJ.d2s(imp.getHeight() * cal.pixelHeight, 2) + " " + units + " (" + imp.getHeight() + ")\n"; if (slices > 1) s += "Depth: " + IJ.d2s(slices * cal.pixelDepth, 2) + " " + units + " (" + slices + ")\n"; double xResolution = 1.0 / cal.pixelWidth; double yResolution = 1.0 / cal.pixelHeight; int places = Tools.getDecimalPlaces(xResolution, yResolution); if (xResolution == yResolution) s += "Resolution: " + IJ.d2s(xResolution, places) + " pixels per " + unit + "\n"; else { s += "X Resolution: " + IJ.d2s(xResolution, places) + " pixels per " + unit + "\n"; s += "Y Resolution: " + IJ.d2s(yResolution, places) + " pixels per " + unit + "\n"; } } else { s += "Width: " + imp.getWidth() + " pixels\n"; s += "Height: " + imp.getHeight() + " pixels\n"; if (stackSize > 1) s += "Depth: " + slices + " pixels\n"; } if (stackSize > 1) s += "Voxel size: " + d2s(cal.pixelWidth) + "x" + d2s(cal.pixelHeight) + "x" + d2s(cal.pixelDepth) + " " + cal.getUnit() + "\n"; else s += "Pixel size: " + d2s(cal.pixelWidth) + "x" + d2s(cal.pixelHeight) + " " + cal.getUnit() + "\n"; s += "ID: " + imp.getID() + "\n"; String zOrigin = stackSize > 1 || cal.zOrigin != 0.0 ? "," + d2s(cal.zOrigin) : ""; s += "Coordinate origin: " + d2s(cal.xOrigin) + "," + d2s(cal.yOrigin) + zOrigin + "\n"; int type = imp.getType(); switch (type) { case ImagePlus.GRAY8: s += "Bits per pixel: 8 "; String lut = "LUT"; if (imp.getProcessor().isColorLut()) lut = "color " + lut; else lut = "grayscale " + lut; if (imp.isInvertedLut()) lut = "inverting " + lut; s += "(" + lut + ")\n"; if (imp.getNChannels() > 1) s += displayRanges(imp); else s += "Display range: " + (int) ip.getMin() + "-" + (int) ip.getMax() + "\n"; break; case ImagePlus.GRAY16: case ImagePlus.GRAY32: if (type == ImagePlus.GRAY16) { String sign = cal.isSigned16Bit() ? "signed" : "unsigned"; s += "Bits per pixel: 16 (" + sign + ")\n"; } else s += "Bits per pixel: 32 (float)\n"; if (imp.getNChannels() > 1) s += displayRanges(imp); else { s += "Display range: "; double min = ip.getMin(); double max = ip.getMax(); if (cal.calibrated()) { min = cal.getCValue((int) min); max = cal.getCValue((int) max); } s += IJ.d2s(min, digits) + " - " + IJ.d2s(max, digits) + "\n"; } break; case ImagePlus.COLOR_256: s += "Bits per pixel: 8 (color LUT)\n"; break; case ImagePlus.COLOR_RGB: s += "Bits per pixel: 32 (RGB)\n"; break; } double interval = cal.frameInterval; double fps = cal.fps; if (stackSize > 1) { ImageStack stack = imp.getStack(); int slice = imp.getCurrentSlice(); String number = slice + "/" + stackSize; String label = stack.getShortSliceLabel(slice); if (label != null && label.length() > 0) label = " (" + label + ")"; else label = ""; if (interval > 0.0 || fps != 0.0) { s += "Frame: " + number + label + "\n"; if (fps != 0.0) { String sRate = Math.abs(fps - Math.round(fps)) < 0.00001 ? IJ.d2s(fps, 0) : IJ.d2s(fps, 5); s += "Frame rate: " + sRate + " fps\n"; } if (interval != 0.0) s += "Frame interval: " + ((int) interval == interval ? IJ.d2s(interval, 0) : IJ.d2s(interval, 5)) + " " + cal.getTimeUnit() + "\n"; } else s += "Image: " + number + label + "\n"; if (imp.isHyperStack()) { if (channels > 1) s += " Channel: " + imp.getChannel() + "/" + channels + "\n"; if (slices > 1) s += " Slice: " + imp.getSlice() + "/" + slices + "\n"; if (frames > 1) s += " Frame: " + imp.getFrame() + "/" + frames + "\n"; } if (imp.isComposite()) { if (!imp.isHyperStack() && channels > 1) s += " Channels: " + channels + "\n"; String mode = ((CompositeImage) imp).getModeAsString(); s += " Composite mode: \"" + mode + "\"\n"; } } if (ip.getMinThreshold() == ImageProcessor.NO_THRESHOLD) s += "No Threshold\n"; else { double lower = ip.getMinThreshold(); double upper = ip.getMaxThreshold(); int dp = digits; if (cal.calibrated()) { lower = cal.getCValue((int) lower); upper = cal.getCValue((int) upper); dp = cal.isSigned16Bit() ? 0 : 4; } s += "Threshold: " + IJ.d2s(lower, dp) + "-" + IJ.d2s(upper, dp) + "\n"; } ImageCanvas ic = imp.getCanvas(); double mag = ic != null ? ic.getMagnification() : 1.0; if (mag != 1.0) s += "Magnification: " + IJ.d2s(mag, 2) + "\n"; if (cal.calibrated()) { s += " \n"; int curveFit = cal.getFunction(); s += "Calibration Function: "; if (curveFit == Calibration.UNCALIBRATED_OD) s += "Uncalibrated OD\n"; else if (curveFit == Calibration.CUSTOM) s += "Custom lookup table\n"; else s += CurveFitter.fList[curveFit] + "\n"; double[] c = cal.getCoefficients(); if (c != null) { s += " a: " + IJ.d2s(c[0], 6) + "\n"; s += " b: " + IJ.d2s(c[1], 6) + "\n"; if (c.length >= 3) s += " c: " + IJ.d2s(c[2], 6) + "\n"; if (c.length >= 4) s += " c: " + IJ.d2s(c[3], 6) + "\n"; if (c.length >= 5) s += " c: " + IJ.d2s(c[4], 6) + "\n"; } s += " Unit: \"" + cal.getValueUnit() + "\"\n"; } else s += "Uncalibrated\n"; FileInfo fi = imp.getOriginalFileInfo(); if (fi != null) { if (fi.url != null && !fi.url.equals("")) s += "URL: " + fi.url + "\n"; else if (fi.directory != null && fi.fileName != null) s += "Path: " + fi.directory + fi.fileName + "\n"; } ImageWindow win = imp.getWindow(); if (win != null) { Point loc = win.getLocation(); Dimension screen = IJ.getScreenSize(); s += "Screen location: " + loc.x + "," + loc.y + " (" + screen.width + "x" + screen.height + ")\n"; } Overlay overlay = imp.getOverlay(); if (overlay != null) { String hidden = imp.getHideOverlay() ? " (hidden)" : " "; int n = overlay.size(); String elements = n == 1 ? " element" : " elements"; s += "Overlay: " + n + elements + (imp.getHideOverlay() ? " (hidden)" : "") + "\n"; } else s += "No Overlay\n"; Roi roi = imp.getRoi(); if (roi == null) { if (cal.calibrated()) s += " \n"; s += "No Selection\n"; } else if (roi instanceof EllipseRoi) { s += "\nElliptical Selection\n"; double[] p = ((EllipseRoi) roi).getParams(); double dx = p[2] - p[0]; double dy = p[3] - p[1]; double major = Math.sqrt(dx * dx + dy * dy); s += " Major: " + IJ.d2s(major, 2) + "\n"; s += " Minor: " + IJ.d2s(major * p[4], 2) + "\n"; s += " X1: " + IJ.d2s(p[0], 2) + "\n"; s += " Y1: " + IJ.d2s(p[1], 2) + "\n"; s += " X2: " + IJ.d2s(p[2], 2) + "\n"; s += " Y2: " + IJ.d2s(p[3], 2) + "\n"; s += " Aspect ratio: " + IJ.d2s(p[4], 2) + "\n"; } else { s += " \n"; s += roi.getTypeAsString() + " Selection"; String points = null; if (roi instanceof PointRoi) { int npoints = ((PolygonRoi) roi).getNCoordinates(); String suffix = npoints > 1 ? "s)" : ")"; points = " (" + npoints + " point" + suffix; } String name = roi.getName(); if (name != null) { s += " (\"" + name + "\")"; if (points != null) s += "\n " + points; } else if (points != null) s += points; s += "\n"; Rectangle r = roi.getBounds(); if (roi instanceof Line) { Line line = (Line) roi; s += " X1: " + IJ.d2s(line.x1d * cal.pixelWidth) + "\n"; s += " Y1: " + IJ.d2s(yy(line.y1d, imp) * cal.pixelHeight) + "\n"; s += " X2: " + IJ.d2s(line.x2d * cal.pixelWidth) + "\n"; s += " Y2: " + IJ.d2s(yy(line.y2d, imp) * cal.pixelHeight) + "\n"; } else if (cal.scaled()) { s += " X: " + IJ.d2s(cal.getX(r.x)) + " (" + r.x + ")\n"; s += " Y: " + IJ.d2s(cal.getY(r.y, imp.getHeight())) + " (" + r.y + ")\n"; s += " Width: " + IJ.d2s(r.width * cal.pixelWidth) + " (" + r.width + ")\n"; s += " Height: " + IJ.d2s(r.height * cal.pixelHeight) + " (" + r.height + ")\n"; } else { s += " X: " + r.x + "\n"; s += " Y: " + yy(r.y, imp) + "\n"; s += " Width: " + r.width + "\n"; s += " Height: " + r.height + "\n"; } } return s; }