void showDialog() { int width = imp.getWidth(); int height = imp.getHeight(); Calibration cal = imp.getCalibration(); int places; if (cal.scaled()) { pixelWidth = cal.pixelWidth; pixelHeight = cal.pixelHeight; units = cal.getUnits(); places = 2; } else { pixelWidth = 1.0; pixelHeight = 1.0; units = "pixels"; places = 0; } if (areaPerPoint == 0.0) areaPerPoint = (width * cal.pixelWidth * height * cal.pixelHeight) / 81.0; // default to 9x9 grid ImageWindow win = imp.getWindow(); GenericDialog gd = new GenericDialog("Grid..."); gd.addChoice("Grid Type:", types, type); gd.addNumericField("Area per Point:", areaPerPoint, places, 6, units + "^2"); gd.addChoice("Color:", colors, color); gd.addCheckbox("Random Offset", randomOffset); gd.addDialogListener(this); gd.showDialog(); if (gd.wasCanceled()) showGrid(null); }
private void makeBand(ImagePlus imp) { Roi roi = imp.getRoi(); if (roi == null) { noRoi("Make Band"); return; } if (!roi.isArea()) { IJ.error("Make Band", "Area selection required"); return; } Calibration cal = imp.getCalibration(); double pixels = bandSize; double size = pixels * cal.pixelWidth; int decimalPlaces = 0; if ((int) size != size) decimalPlaces = 2; GenericDialog gd = new GenericDialog("Make Band"); gd.addNumericField("Band Size:", size, decimalPlaces, 4, cal.getUnits()); gd.showDialog(); if (gd.wasCanceled()) return; size = gd.getNextNumber(); if (Double.isNaN(size)) { IJ.error("Make Band", "invalid number"); return; } int n = (int) Math.round(size / cal.pixelWidth); if (n > 255) { IJ.error("Make Band", "Cannot make bands wider that 255 pixels"); return; } int width = imp.getWidth(); int height = imp.getHeight(); Rectangle r = roi.getBounds(); ImageProcessor ip = roi.getMask(); if (ip == null) { ip = new ByteProcessor(r.width, r.height); ip.invert(); } ImageProcessor mask = new ByteProcessor(width, height); mask.insert(ip, r.x, r.y); ImagePlus edm = new ImagePlus("mask", mask); boolean saveBlackBackground = Prefs.blackBackground; Prefs.blackBackground = false; IJ.run(edm, "Distance Map", ""); Prefs.blackBackground = saveBlackBackground; ip = edm.getProcessor(); ip.setThreshold(0, n, ImageProcessor.NO_LUT_UPDATE); int xx = -1, yy = -1; for (int x = r.x; x < r.x + r.width; x++) { for (int y = r.y; y < r.y + r.height; y++) { if (ip.getPixel(x, y) < n) { xx = x; yy = y; break; } } if (xx >= 0 || yy >= 0) break; } int count = IJ.doWand(edm, xx, yy, 0, null); if (count <= 0) { IJ.error("Make Band", "Unable to make band"); return; } ShapeRoi roi2 = new ShapeRoi(edm.getRoi()); if (!(roi instanceof ShapeRoi)) roi = new ShapeRoi(roi); ShapeRoi roi1 = (ShapeRoi) roi; roi2 = roi2.not(roi1); imp.setRoi(roi2); bandSize = n; }
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; }