public void run(String arg) { ImagePlus imp = WindowManager.getCurrentImage(); if (imp == null) { IJ.noImage(); return; } ImageStack stack1 = imp.getStack(); String fileName = imp.getTitle(); int endslice = stack1.getSize(); ImagePlus imp2 = duplicateStack(imp); imp2.show(); String duplicateName = imp2.getTitle(); // IJ.showMessage("Box",fileName); ImageStack stack2 = imp2.getStack(); stack1.deleteSlice(1); stack2.deleteSlice(endslice); String calculatorstring = ("image1='" + fileName + "' operation=Subtract image2=" + imp2.getTitle() + " create stack"); IJ.run("Image Calculator...", calculatorstring); ImagePlus imp3 = WindowManager.getCurrentImage(); imp3.setTitle(fileName + " DeltaF up"); imp2.getWindow().close(); imp.getWindow().close(); }
public void run(String arg) { imp = WindowManager.getCurrentImage(); if (arg.equals("add")) { addToRoiManager(imp); return; } if (imp == null) { IJ.noImage(); return; } if (arg.equals("all")) imp.setRoi(0, 0, imp.getWidth(), imp.getHeight()); else if (arg.equals("none")) imp.killRoi(); else if (arg.equals("restore")) imp.restoreRoi(); else if (arg.equals("spline")) fitSpline(); else if (arg.equals("circle")) fitCircle(imp); else if (arg.equals("ellipse")) createEllipse(imp); else if (arg.equals("hull")) convexHull(imp); else if (arg.equals("mask")) createMask(imp); else if (arg.equals("from")) createSelectionFromMask(imp); else if (arg.equals("inverse")) invert(imp); else if (arg.equals("toarea")) lineToArea(imp); else if (arg.equals("toline")) areaToLine(imp); else if (arg.equals("properties")) { setProperties("Properties ", imp.getRoi()); imp.draw(); } else if (arg.equals("band")) makeBand(imp); else if (arg.equals("tobox")) toBoundingBox(imp); else runMacro(arg); }
public int setup(String arg, ImagePlus imp) { this.arg = arg; this.imp = imp; IJ.register(ParticleAnalyzer.class); if (imp == null) { IJ.noImage(); return DONE; } if (imp.getBitDepth() == 24 && !isThresholdedRGB(imp)) { IJ.error( "Particle Analyzer", "RGB images must be thresholded using\n" + "Image>Adjust>Color Threshold."); return DONE; } if (!showDialog()) return DONE; int baseFlags = DOES_ALL + NO_CHANGES + NO_UNDO; int flags = IJ.setupDialog(imp, baseFlags); processStack = (flags & DOES_STACKS) != 0; slice = 0; saveRoi = imp.getRoi(); if (saveRoi != null && saveRoi.getType() != Roi.RECTANGLE && saveRoi.isArea()) polygon = saveRoi.getPolygon(); imp.startTiming(); nextFontSize = defaultFontSize; nextLineWidth = 1; return flags; }
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; }
public void run(String arg) { imp = WindowManager.getCurrentImage(); if (imp == null) { IJ.noImage(); return; } ImageStack stack = imp.getStack(); int size = stack.getSize(); if (size == 1 || (imp.getNChannels() == size && imp.isComposite())) { IJ.error("Stack or hyperstack required"); return; } if (!showDialog(stack)) return; if (hyperstack) reduceHyperstack(imp, factor, reduceSlices); else reduceStack(imp, factor); }
/*------------------------------------------------------------------*/ public void run(String arg) { ImagePlus imp = WindowManager.getCurrentImage(); this.imp = imp; if (imp == null) { IJ.noImage(); return; } if ((1 < imp.getStackSize()) && (imp.getType() == imp.COLOR_256)) { IJ.error("Stack of color images not supported (use grayscale)"); return; } if (1 < imp.getStackSize()) { if (imp.getStack().isRGB()) { IJ.error("RGB color images not supported (use grayscale)"); return; } } if (1 < imp.getStackSize()) { if (imp.getStack().isHSB()) { IJ.error("HSB color images not supported (use grayscale)"); return; } } if (imp.getType() == imp.COLOR_256) { IJ.error("Indexed color images not supported (use grayscale)"); return; } if (imp.getType() == imp.COLOR_RGB) { IJ.error("Color images not supported (use grayscale)"); return; } differentialsDialog dialog = new differentialsDialog(IJ.getInstance(), "Differentials", true, operation); GUI.center(dialog); dialog.setVisible(true); cancel = dialog.getCancel(); operation = dialog.getOperation(); dialog.dispose(); if (cancel) { return; } imp.startTiming(); if (1 < imp.getStackSize()) { if (!(imp.getProcessor().getPixels() instanceof float[])) { new StackConverter(imp).convertToGray32(); } } else { if (!(imp.getProcessor().getPixels() instanceof float[])) { new ImageConverter(imp).convertToGray32(); } } ImageStack stack = imp.getStack(); stackSize = stack.getSize(); Undo.reset(); setupProgressBar(); resetProgressBar(); for (int i = 1; (i <= stackSize); i++) { ImageProcessor ip = stack.getProcessor(i); doIt(ip); imp.getProcessor().resetMinAndMax(); imp.setSlice(i); imp.updateAndRepaintWindow(); } imp.getProcessor().resetMinAndMax(); imp.setSlice(1); imp.updateAndRepaintWindow(); cleanUpProgressBar(); IJ.showTime(imp, imp.getStartTime(), "Differentials: "); ImageWindow win = imp.getWindow(); if (win != null) { win.running = false; } } /* end run */
public void run(String arg) { imp = IJ.getImage(); int stackSize = imp.getStackSize(); if (imp == null) { IJ.noImage(); return; } // Make sure input image is a stack. if (stackSize == 1) { IJ.error("Z Project", "Stack required"); return; } // Check for inverting LUT. if (imp.getProcessor().isInvertedLut()) { if (!IJ.showMessageWithCancel("ZProjection", lutMessage)) return; } // Set default bounds. int channels = imp.getNChannels(); int frames = imp.getNFrames(); int slices = imp.getNSlices(); isHyperstack = imp.isHyperStack() || (ij.macro.Interpreter.isBatchMode() && ((frames > 1 && frames < stackSize) || (slices > 1 && slices < stackSize))); boolean simpleComposite = channels == stackSize; if (simpleComposite) isHyperstack = false; startSlice = 1; if (isHyperstack) { int nSlices = imp.getNSlices(); if (nSlices > 1) stopSlice = nSlices; else stopSlice = imp.getNFrames(); } else stopSlice = stackSize; // Build control dialog GenericDialog gd = buildControlDialog(startSlice, stopSlice); gd.showDialog(); if (gd.wasCanceled()) return; if (!imp.lock()) return; // exit if in use long tstart = System.currentTimeMillis(); setStartSlice((int) gd.getNextNumber()); setStopSlice((int) gd.getNextNumber()); method = gd.getNextChoiceIndex(); Prefs.set(METHOD_KEY, method); if (isHyperstack) { allTimeFrames = imp.getNFrames() > 1 && imp.getNSlices() > 1 ? gd.getNextBoolean() : false; doHyperStackProjection(allTimeFrames); } else if (imp.getType() == ImagePlus.COLOR_RGB) doRGBProjection(true); else doProjection(true); if (arg.equals("") && projImage != null) { long tstop = System.currentTimeMillis(); projImage.setCalibration(imp.getCalibration()); if (simpleComposite) IJ.run(projImage, "Grays", ""); projImage.show("ZProjector: " + IJ.d2s((tstop - tstart) / 1000.0, 2) + " seconds"); } imp.unlock(); IJ.register(ZProjector.class); return; }