public void run(String arg) { ImageCheck ic = new ImageCheck(); if (!ImageCheck.checkEnvironment()) return; ImagePlus imp = IJ.getImage(); if (!ic.isBinary(imp)) { IJ.error("8-bit binary (black and white only) image required."); return; } if (!ic.isVoxelIsotropic(imp, 1E-3)) { if (IJ.showMessageWithCancel( "Anisotropic voxels", "This image contains anisotropic voxels, which will\n" + "result in incorrect thickness calculation.\n\n" + "Consider rescaling your data so that voxels are isotropic\n" + "(Image > Scale...).\n\n" + "Continue anyway?")) { } else return; } GenericDialog gd = new GenericDialog("Options"); gd.addCheckbox("Thickness", true); gd.addCheckbox("Spacing", false); gd.addCheckbox("Graphic Result", true); gd.addCheckbox("Use_ROI_Manager", false); gd.addCheckbox("Mask thickness map", true); gd.addHelp("http://bonej.org/thickness"); gd.showDialog(); if (gd.wasCanceled()) { return; } boolean doThickness = gd.getNextBoolean(); boolean doSpacing = gd.getNextBoolean(); boolean doGraphic = gd.getNextBoolean(); boolean doRoi = gd.getNextBoolean(); boolean doMask = gd.getNextBoolean(); long startTime = System.currentTimeMillis(); String title = stripExtension(imp.getTitle()); RoiManager roiMan = RoiManager.getInstance(); // calculate trabecular thickness (Tb.Th) if (doThickness) { boolean inverse = false; ImagePlus impLTC = new ImagePlus(); if (doRoi && roiMan != null) { ImageStack stack = RoiMan.cropStack(roiMan, imp.getStack(), true, 0, 1); ImagePlus crop = new ImagePlus(imp.getTitle(), stack); crop.setCalibration(imp.getCalibration()); impLTC = getLocalThickness(crop, inverse, doMask); } else impLTC = getLocalThickness(imp, inverse, doMask); impLTC.setTitle(title + "_Tb.Th"); impLTC.setCalibration(imp.getCalibration()); double[] stats = StackStats.meanStdDev(impLTC); insertResults(imp, stats, inverse); if (doGraphic && !Interpreter.isBatchMode()) { impLTC.show(); impLTC.setSlice(1); impLTC.getProcessor().setMinAndMax(0, stats[2]); IJ.run("Fire"); } } if (doSpacing) { boolean inverse = true; ImagePlus impLTCi = new ImagePlus(); if (doRoi && roiMan != null) { ImageStack stack = RoiMan.cropStack(roiMan, imp.getStack(), true, 255, 1); ImagePlus crop = new ImagePlus(imp.getTitle(), stack); crop.setCalibration(imp.getCalibration()); impLTCi = getLocalThickness(crop, inverse, doMask); } else impLTCi = getLocalThickness(imp, inverse, doMask); // check marrow cavity size (i.e. trabcular separation, Tb.Sp) impLTCi.setTitle(title + "_Tb.Sp"); impLTCi.setCalibration(imp.getCalibration()); double[] stats = StackStats.meanStdDev(impLTCi); insertResults(imp, stats, inverse); if (doGraphic && !Interpreter.isBatchMode()) { impLTCi.show(); impLTCi.setSlice(1); impLTCi.getProcessor().setMinAndMax(0, stats[2]); IJ.run("Fire"); } } IJ.showProgress(1.0); IJ.showStatus("Done"); double duration = ((double) System.currentTimeMillis() - (double) startTime) / (double) 1000; IJ.log("Duration = " + IJ.d2s(duration, 3) + " s"); UsageReporter.reportEvent(this).send(); return; }
// Delete preferences file when ImageJ quits private void reset() { if (IJ.showMessageWithCancel( "Reset Preferences", "Preferences will be reset when ImageJ restarts.")) Prefs.resetPreferences(); }
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; }