void checkForCalibrationConflict(ImagePlus imp, Calibration cal) { Calibration gcal = imp.getGlobalCalibration(); if (gcal == null || !showConflictMessage || IJ.isMacro()) return; if (cal.pixelWidth == gcal.pixelWidth && cal.getUnit().equals(gcal.getUnit())) return; GenericDialog gd = new GenericDialog(imp.getTitle()); gd.addMessage("The calibration of this image conflicts\nwith the current global calibration."); gd.addCheckbox("Disable_Global Calibration", true); gd.addCheckbox("Disable_these Messages", false); gd.showDialog(); if (gd.wasCanceled()) return; boolean disable = gd.getNextBoolean(); if (disable) { imp.setGlobalCalibration(null); imp.setCalibration(cal); WindowManager.repaintImageWindows(); } boolean dontShow = gd.getNextBoolean(); if (dontShow) showConflictMessage = false; }
private boolean showDialog() { String[] types = {"RAW", "JPEG", "ZLIB"}; GenericDialog gd = new GenericDialog("Generate Bricks"); gd.addChoice("FileType", types, filetype); gd.addNumericField("JPEG quality", jpeg_quality, 0); gd.addNumericField("Max file size (MB)", bdsizelimit, 0); int[] wlist = WindowManager.getIDList(); if (wlist == null) return false; String[] titles = new String[wlist.length]; for (int i = 0; i < wlist.length; i++) titles[i] = ""; int tnum = 0; for (int i = 0; i < wlist.length; i++) { ImagePlus imp = WindowManager.getImage(wlist[i]); if (imp != null) { titles[tnum] = imp.getTitle(); tnum++; } } gd.addChoice("Source image: ", titles, titles[0]); gd.showDialog(); if (gd.wasCanceled()) return false; filetype = types[gd.getNextChoiceIndex()]; jpeg_quality = (int) gd.getNextNumber(); if (jpeg_quality > 100) jpeg_quality = 100; if (jpeg_quality < 0) jpeg_quality = 0; bdsizelimit = (int) gd.getNextNumber(); int id = gd.getNextChoiceIndex(); lvImgTitle = new ArrayList<String>(); lvImgTitle.add(titles[id]); Prefs.set("filetype.string", filetype); Prefs.set("jpeg_quality.int", jpeg_quality); Prefs.set("bdsizelimit.int", bdsizelimit); return 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; }
void showInfo(String info, int width, int height) { new TextWindow("Info for " + imp.getTitle(), info, width, height); // Editor ed = new Editor(); // ed.setSize(width, height); // ed.create("Info for "+imp.getTitle(), info); }
boolean showDialog(ImageProcessor ip) { int bitDepth = imp.getBitDepth(); boolean isStack = imp.getStackSize() > 1; r = ip.getRoi(); int width = newWidth; if (width == 0) width = r.width; int height = (int) ((double) width * r.height / r.width); xscale = Tools.parseDouble(xstr, 0.0); yscale = Tools.parseDouble(ystr, 0.0); if (xscale != 0.0 && yscale != 0.0) { width = (int) (r.width * xscale); height = (int) (r.height * yscale); } else { xstr = "-"; ystr = "-"; } GenericDialog gd = new GenericDialog("Scale"); gd.addStringField("X Scale (0.05-25):", xstr); gd.addStringField("Y Scale (0.05-25):", ystr); gd.setInsets(5, 0, 5); gd.addStringField("Width (pixels):", "" + width); gd.addStringField("Height (pixels):", "" + height); fields = gd.getStringFields(); for (int i = 0; i < 3; i++) { ((TextField) fields.elementAt(i)).addTextListener(this); ((TextField) fields.elementAt(i)).addFocusListener(this); } xField = (TextField) fields.elementAt(0); yField = (TextField) fields.elementAt(1); widthField = (TextField) fields.elementAt(2); heightField = (TextField) fields.elementAt(3); fieldWithFocus = xField; gd.addCheckbox("Interpolate", interpolate); if (bitDepth == 8 || bitDepth == 24) gd.addCheckbox("Fill with Background Color", fillWithBackground); if (isStack) gd.addCheckbox("Process Entire Stack", processStack); gd.addCheckbox("Create New Window", newWindow); title = WindowManager.getUniqueName(imp.getTitle()); gd.setInsets(10, 0, 0); gd.addStringField("Title:", title, 12); gd.showDialog(); if (gd.wasCanceled()) return false; xstr = gd.getNextString(); ystr = gd.getNextString(); xscale = Tools.parseDouble(xstr, 0.0); yscale = Tools.parseDouble(ystr, 0.0); String wstr = gd.getNextString(); newWidth = (int) Tools.parseDouble(wstr, 0); newHeight = (int) Tools.parseDouble(gd.getNextString(), 0); if (newHeight != 0 && (wstr.equals("-") || wstr.equals("0"))) newWidth = (int) (newHeight * (double) r.width / r.height); if (newWidth == 0 || newHeight == 0) { IJ.error("Invalid width or height entered"); return false; } if (xscale > 25.0) xscale = 25.0; if (yscale > 25.0) yscale = 25.0; if (xscale > 0.0 && yscale > 0.0) { newWidth = (int) (r.width * xscale); newHeight = (int) (r.height * yscale); } interpolate = gd.getNextBoolean(); if (bitDepth == 8 || bitDepth == 24) fillWithBackground = gd.getNextBoolean(); if (isStack) processStack = gd.getNextBoolean(); newWindow = gd.getNextBoolean(); if (!newWindow && xscale == 0.0) { xscale = (double) newWidth / r.width; yscale = (double) newHeight / r.height; } title = gd.getNextString(); if (fillWithBackground) { Color bgc = Toolbar.getBackgroundColor(); if (bitDepth == 8) bgValue = ip.getBestIndex(bgc); else if (bitDepth == 24) bgValue = bgc.getRGB(); } else { if (bitDepth == 8) bgValue = ip.isInvertedLut() ? 0.0 : 255.0; // white else if (bitDepth == 24) bgValue = 0xffffffff; // white } return true; }
boolean showDialog(ImageProcessor ip) { String macroOptions = Macro.getOptions(); if (macroOptions != null) { if (macroOptions.indexOf(" interpolate") != -1) macroOptions.replaceAll(" interpolate", " interpolation=Bilinear"); else if (macroOptions.indexOf(" interpolation=") == -1) macroOptions = macroOptions + " interpolation=None"; Macro.setOptions(macroOptions); } int bitDepth = imp.getBitDepth(); int stackSize = imp.getStackSize(); boolean isStack = stackSize > 1; oldDepth = stackSize; if (isStack) { xstr = "1.0"; ystr = "1.0"; zstr = "1.0"; } r = ip.getRoi(); int width = newWidth; if (width == 0) width = r.width; int height = (int) ((double) width * r.height / r.width); xscale = Tools.parseDouble(xstr, 0.0); yscale = Tools.parseDouble(ystr, 0.0); zscale = 1.0; if (xscale != 0.0 && yscale != 0.0) { width = (int) (r.width * xscale); height = (int) (r.height * yscale); } else { xstr = "-"; ystr = "-"; } GenericDialog gd = new GenericDialog("Scale"); gd.addStringField("X Scale:", xstr); gd.addStringField("Y Scale:", ystr); if (isStack) gd.addStringField("Z Scale:", zstr); gd.setInsets(5, 0, 5); gd.addStringField("Width (pixels):", "" + width); gd.addStringField("Height (pixels):", "" + height); if (isStack) { String label = "Depth (images):"; if (imp.isHyperStack()) { int slices = imp.getNSlices(); int frames = imp.getNFrames(); if (slices == 1 && frames > 1) { label = "Depth (frames):"; oldDepth = frames; } else { label = "Depth (slices):"; oldDepth = slices; } } gd.addStringField(label, "" + oldDepth); } fields = gd.getStringFields(); for (int i = 0; i < fields.size(); i++) { ((TextField) fields.elementAt(i)).addTextListener(this); ((TextField) fields.elementAt(i)).addFocusListener(this); } xField = (TextField) fields.elementAt(0); yField = (TextField) fields.elementAt(1); if (isStack) { zField = (TextField) fields.elementAt(2); widthField = (TextField) fields.elementAt(3); heightField = (TextField) fields.elementAt(4); depthField = (TextField) fields.elementAt(5); } else { widthField = (TextField) fields.elementAt(2); heightField = (TextField) fields.elementAt(3); } fieldWithFocus = xField; gd.addChoice("Interpolation:", methods, methods[interpolationMethod]); if (bitDepth == 8 || bitDepth == 24) gd.addCheckbox("Fill with background color", fillWithBackground); gd.addCheckbox("Average when downsizing", averageWhenDownsizing); boolean hyperstack = imp.isHyperStack() || imp.isComposite(); if (isStack && !hyperstack) gd.addCheckbox("Process entire stack", processStack); gd.addCheckbox("Create new window", newWindow); title = WindowManager.getUniqueName(imp.getTitle()); gd.setInsets(10, 0, 0); gd.addStringField("Title:", title, 12); gd.showDialog(); if (gd.wasCanceled()) return false; xstr = gd.getNextString(); ystr = gd.getNextString(); xscale = Tools.parseDouble(xstr, 0.0); yscale = Tools.parseDouble(ystr, 0.0); if (isStack) { zstr = gd.getNextString(); zscale = Tools.parseDouble(ystr, 0.0); } String wstr = gd.getNextString(); newWidth = (int) Tools.parseDouble(wstr, 0); newHeight = (int) Tools.parseDouble(gd.getNextString(), 0); if (newHeight != 0 && (wstr.equals("-") || wstr.equals("0"))) newWidth = (int) (newHeight * (double) r.width / r.height); if (newWidth == 0 || newHeight == 0) { IJ.error("Scaler", "Width or height is 0"); return false; } if (xscale > 0.0 && yscale > 0.0) { newWidth = (int) (r.width * xscale); newHeight = (int) (r.height * yscale); } if (isStack) newDepth = (int) Tools.parseDouble(gd.getNextString(), 0); interpolationMethod = gd.getNextChoiceIndex(); if (bitDepth == 8 || bitDepth == 24) fillWithBackground = gd.getNextBoolean(); averageWhenDownsizing = gd.getNextBoolean(); if (isStack && !hyperstack) processStack = gd.getNextBoolean(); if (hyperstack) processStack = true; newWindow = gd.getNextBoolean(); if (xscale == 0.0) { xscale = (double) newWidth / r.width; yscale = (double) newHeight / r.height; } title = gd.getNextString(); if (fillWithBackground) { Color bgc = Toolbar.getBackgroundColor(); if (bitDepth == 8) bgValue = ip.getBestIndex(bgc); else if (bitDepth == 24) bgValue = bgc.getRGB(); } else bgValue = 0.0; return true; }
void setMagnification2(double magnification) { if (magnification > 32.0) magnification = 32.0; if (magnification < 0.03125) magnification = 0.03125; this.magnification = magnification; imp.setTitle(imp.getTitle()); }