@Override
public String commandExecuting(String command) {
if (command.equalsIgnoreCase("Quit") && frame_ != null) {
try {
if (!frame_.closeSequence(true)) {
return null;
}
} catch (Exception ex) {
// do nothing, just make sure to continue quitting
}
return command;
} else if (command.equals("Crop")) {
if (IJ.getImage().getStack() instanceof AcquisitionVirtualStack) {
new Duplicator().run(IJ.getImage()).show();
// abort further processing of the Crop command
return null;
}
} else if (command.equals("Add Noise")) {
// blanket method to make sure that ImageJ filters do not execute on disk-cached images
// this may backfire!
if (IJ.getImage().getStack() instanceof AcquisitionVirtualStack) {
AcquisitionVirtualStack avs = (AcquisitionVirtualStack) IJ.getImage().getStack();
if (avs.getVirtualAcquisitionDisplay().isDiskCached()) {
// duplicate the image and then run the ImageJ command on what is now the new image
new Duplicator().run(IJ.getImage()).show();
} else {
// Image is not disk chached. Warn that data will be lost
if (!IJ.showMessageWithCancel(
"Micro-Manager data not saved",
"Data are not saved and Undo is impossible. \n"
+ "Do you really want to execute the command?")) {
return null;
}
}
}
}
return command;
}
public void run(String arg) {
if (arg.equals("menus")) {
updateMenus();
return;
}
if (IJ.getApplet() != null) return;
// File file = new File(Prefs.getHomeDir() + File.separator + "ij.jar");
// if (isMac() && !file.exists())
// file = new File(Prefs.getHomeDir() + File.separator +
// "ImageJ.app/Contents/Resources/Java/ij.jar");
URL url = getClass().getResource("/ij/IJ.class");
String ij_jar = url == null ? null : url.toString().replaceAll("%20", " ");
if (ij_jar == null || !ij_jar.startsWith("jar:file:")) {
error("Could not determine location of ij.jar");
return;
}
int exclamation = ij_jar.indexOf('!');
ij_jar = ij_jar.substring(9, exclamation);
if (IJ.debugMode) IJ.log("Updater: " + ij_jar);
File file = new File(ij_jar);
if (!file.exists()) {
error("File not found: " + file.getPath());
return;
}
if (!file.canWrite()) {
String msg = "No write access: " + file.getPath();
if (IJ.isVista()) msg += Prefs.vistaHint;
error(msg);
return;
}
String[] list = openUrlAsList(IJ.URL + "/download/jars/list.txt");
int count = list.length + 2;
String[] versions = new String[count];
String[] urls = new String[count];
String uv = getUpgradeVersion();
if (uv == null) return;
versions[0] = "v" + uv;
urls[0] = IJ.URL + "/upgrade/ij.jar";
if (versions[0] == null) return;
for (int i = 1; i < count - 1; i++) {
String version = list[i - 1];
versions[i] = version.substring(0, version.length() - 1); // remove letter
urls[i] =
IJ.URL + "/download/jars/ij" + version.substring(1, 2) + version.substring(3, 6) + ".jar";
}
versions[count - 1] = "daily build";
urls[count - 1] = IJ.URL + "/ij.jar";
int choice = showDialog(versions);
if (choice == -1) return;
if (!versions[choice].startsWith("daily")
&& versions[choice].compareTo("v1.39") < 0
&& Menus.getCommands().get("ImageJ Updater") == null) {
String msg =
"This command is not available in versions of ImageJ prior\n"
+ "to 1.39 so you will need to install the plugin version at\n"
+ "<"
+ IJ.URL
+ "/plugins/imagej-updater.html>.";
if (!IJ.showMessageWithCancel("Update ImageJ", msg)) return;
}
byte[] jar = getJar(urls[choice]);
// file.renameTo(new File(file.getParent()+File.separator+"ij.bak"));
if (version().compareTo("1.37v") >= 0) Prefs.savePreferences();
// if (!renameJar(file)) return; // doesn't work on Vista
saveJar(file, jar);
if (choice < count - 1) // force macro Function Finder to download fresh list
new File(IJ.getDirectory("macros") + "functions.html").delete();
System.exit(0);
}
// 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) {
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;
}
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;
}