public boolean beadCalibration3d() { imp = IJ.getImage(); if (imp == null) { IJ.noImage(); return false; } else if (imp.getStackSize() == 1) { IJ.error("Stack required"); return false; } else if (imp.getType() != ImagePlus.GRAY8 && imp.getType() != ImagePlus.GRAY16) { // In order to support 32bit images, pict[] must be changed to float[], and getPixel(x, y); // requires a Float.intBitsToFloat() conversion IJ.error("8 or 16 bit greyscale image required"); return false; } width = imp.getWidth(); height = imp.getHeight(); nslices = imp.getStackSize(); imtitle = imp.getTitle(); models[0] = "*None*"; models[1] = "line"; models[2] = "2nd degree polynomial"; models[3] = "3rd degree polynomial"; models[4] = "4th degree polynomial"; GenericDialog gd = new GenericDialog("3D PALM calibration"); gd.addNumericField("Maximum FWHM (in px)", prefs.get("QuickPALM.3Dcal_fwhm", 20), 0); gd.addNumericField( "Particle local threshold (% maximum intensity)", prefs.get("QuickPALM.pthrsh", 20), 0); gd.addNumericField("Z-spacing (nm)", prefs.get("QuickPALM.z-step", 10), 2); gd.addNumericField("Calibration Z-smoothing (radius)", prefs.get("QuickPALM.window", 1), 0); gd.addChoice("Model", models, prefs.get("QuickPALM.model", models[3])); gd.addCheckbox( "Show divergence of bead positions against model", prefs.get("QuickPALM.3Dcal_showDivergence", false)); gd.addCheckbox("Show extra particle info", prefs.get("QuickPALM.3Dcal_showExtraInfo", false)); gd.addMessage("\n\nDon't forget to save the table in the end..."); gd.showDialog(); if (gd.wasCanceled()) return false; fwhm = gd.getNextNumber(); prefs.set("QuickPALM.QuickPALM.3Dcal_fwhm", fwhm); pthrsh = gd.getNextNumber() / 100; prefs.set("QuickPALM.pthrsh", pthrsh * 100); cal_z = gd.getNextNumber(); prefs.set("QuickPALM.z-step", cal_z); window = (int) gd.getNextNumber(); prefs.set("QuickPALM.window", window); model = gd.getNextChoice(); prefs.set("QuickPALM.model", model); part_divergence = gd.getNextBoolean(); prefs.set("QuickPALM.3Dcal_showDivergence", part_divergence); part_extrainfo = gd.getNextBoolean(); prefs.set("QuickPALM.3Dcal_showExtraInfo", part_extrainfo); return true; }
private boolean ignoreArrowKeys(ImagePlus imp) { Frame frame = WindowManager.getFrontWindow(); String title = frame.getTitle(); if (title != null && title.equals("ROI Manager")) return true; // Control Panel? if (frame != null && frame instanceof javax.swing.JFrame) return true; ImageWindow win = imp.getWindow(); // LOCI Data Browser window? if (imp.getStackSize() > 1 && win != null && win.getClass().getName().startsWith("loci")) return true; return false; }
public String getImageInfo(ImagePlus imp, ImageProcessor ip) { String infoProperty = null; if (imp.getStackSize() > 1) { ImageStack stack = imp.getStack(); String label = stack.getSliceLabel(imp.getCurrentSlice()); if (label != null && label.indexOf('\n') > 0) infoProperty = label; } if (infoProperty == null) { infoProperty = (String) imp.getProperty("Info"); if (infoProperty == null) infoProperty = getExifData(imp); } String info = getInfo(imp, ip); if (infoProperty != null) return infoProperty + "\n------------------------\n" + info; else return info; }
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; }
public void keyPressed(KeyEvent e) { // if (e.isConsumed()) return; int keyCode = e.getKeyCode(); IJ.setKeyDown(keyCode); hotkey = false; if (keyCode == KeyEvent.VK_CONTROL || keyCode == KeyEvent.VK_SHIFT) return; char keyChar = e.getKeyChar(); int flags = e.getModifiers(); if (IJ.debugMode) IJ.log( "keyPressed: code=" + keyCode + " (" + KeyEvent.getKeyText(keyCode) + "), char=\"" + keyChar + "\" (" + (int) keyChar + "), flags=" + KeyEvent.getKeyModifiersText(flags)); boolean shift = (flags & KeyEvent.SHIFT_MASK) != 0; boolean control = (flags & KeyEvent.CTRL_MASK) != 0; boolean alt = (flags & KeyEvent.ALT_MASK) != 0; boolean meta = (flags & KeyEvent.META_MASK) != 0; String cmd = null; ImagePlus imp = WindowManager.getCurrentImage(); boolean isStack = (imp != null) && (imp.getStackSize() > 1); if (imp != null && !control && ((keyChar >= 32 && keyChar <= 255) || keyChar == '\b' || keyChar == '\n')) { Roi roi = imp.getRoi(); if (roi instanceof TextRoi) { if ((flags & KeyEvent.META_MASK) != 0 && IJ.isMacOSX()) return; if (alt) { switch (keyChar) { case 'u': case 'm': keyChar = IJ.micronSymbol; break; case 'A': keyChar = IJ.angstromSymbol; break; default: } } ((TextRoi) roi).addChar(keyChar); return; } } // Handle one character macro shortcuts if (!control && !meta) { Hashtable macroShortcuts = Menus.getMacroShortcuts(); if (macroShortcuts.size() > 0) { if (shift) cmd = (String) macroShortcuts.get(new Integer(keyCode + 200)); else cmd = (String) macroShortcuts.get(new Integer(keyCode)); if (cmd != null) { // MacroInstaller.runMacroCommand(cmd); commandName = cmd; MacroInstaller.runMacroShortcut(cmd); return; } } } if ((!Prefs.requireControlKey || control || meta) && keyChar != '+') { Hashtable shortcuts = Menus.getShortcuts(); if (shift) cmd = (String) shortcuts.get(new Integer(keyCode + 200)); else cmd = (String) shortcuts.get(new Integer(keyCode)); } if (cmd == null) { switch (keyChar) { case '<': case ',': if (isStack) cmd = "Previous Slice [<]"; break; case '>': case '.': case ';': if (isStack) cmd = "Next Slice [>]"; break; case '+': case '=': cmd = "In [+]"; break; case '-': cmd = "Out [-]"; break; case '/': cmd = "Reslice [/]..."; break; default: } } if (cmd == null) { switch (keyCode) { case KeyEvent.VK_TAB: WindowManager.putBehind(); return; case KeyEvent.VK_BACK_SPACE: // delete if (deleteOverlayRoi(imp)) return; cmd = "Clear"; hotkey = true; break; // case KeyEvent.VK_BACK_SLASH: cmd=IJ.altKeyDown()?"Animation Options...":"Start // Animation"; break; case KeyEvent.VK_EQUALS: cmd = "In [+]"; break; case KeyEvent.VK_MINUS: cmd = "Out [-]"; break; case KeyEvent.VK_SLASH: case 0xbf: cmd = "Reslice [/]..."; break; case KeyEvent.VK_COMMA: case 0xbc: if (isStack) cmd = "Previous Slice [<]"; break; case KeyEvent.VK_PERIOD: case 0xbe: if (isStack) cmd = "Next Slice [>]"; break; case KeyEvent.VK_LEFT: case KeyEvent.VK_RIGHT: case KeyEvent.VK_UP: case KeyEvent.VK_DOWN: // arrow keys if (imp == null) return; Roi roi = imp.getRoi(); if (IJ.shiftKeyDown() && imp == Orthogonal_Views.getImage()) return; boolean stackKey = imp.getStackSize() > 1 && (roi == null || IJ.shiftKeyDown()); boolean zoomKey = roi == null || IJ.shiftKeyDown() || IJ.controlKeyDown(); if (stackKey && keyCode == KeyEvent.VK_RIGHT) cmd = "Next Slice [>]"; else if (stackKey && keyCode == KeyEvent.VK_LEFT) cmd = "Previous Slice [<]"; else if (zoomKey && keyCode == KeyEvent.VK_DOWN && !ignoreArrowKeys(imp) && Toolbar.getToolId() < Toolbar.SPARE6) cmd = "Out [-]"; else if (zoomKey && keyCode == KeyEvent.VK_UP && !ignoreArrowKeys(imp) && Toolbar.getToolId() < Toolbar.SPARE6) cmd = "In [+]"; else if (roi != null) { if ((flags & KeyEvent.ALT_MASK) != 0) roi.nudgeCorner(keyCode); else roi.nudge(keyCode); return; } break; case KeyEvent.VK_ESCAPE: abortPluginOrMacro(imp); return; case KeyEvent.VK_ENTER: WindowManager.toFront(this); return; default: break; } } if (cmd != null && !cmd.equals("")) { commandName = cmd; if (cmd.equals("Fill") || cmd.equals("Draw")) hotkey = true; if (cmd.charAt(0) == MacroInstaller.commandPrefix) MacroInstaller.runMacroShortcut(cmd); else { doCommand(cmd); keyPressedTime = System.currentTimeMillis(); lastKeyCommand = cmd; } } }