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;
}