public void run(String arg) {
ImageJ ij = IJ.getInstance();
ij.setDropTarget(null);
new DropTarget(ij, this);
new DropTarget(Toolbar.getInstance(), this);
new DropTarget(ij.getStatusBar(), this);
}
private static Frame getParentFrame() {
Frame parent =
WindowManager.getCurrentImage() != null
? (Frame) WindowManager.getCurrentImage().getWindow()
: IJ.getInstance() != null ? IJ.getInstance() : new Frame();
if (IJ.isMacOSX() && IJ.isJava18()) {
ImageJ ij = IJ.getInstance();
if (ij != null && ij.isActive()) parent = ij;
else parent = null;
}
return parent;
}
public void runMacro(String name, Editor editor) {
if (anonymousName != null && name.equals(anonymousName)) {
ImageJ.setCommandName(name);
new MacroRunner(pgm, 0, anonymousName, editor);
return;
}
for (int i = 0; i < nMacros; i++)
if (name.equals(macroNames[i])) {
ImageJ.setCommandName(name);
new MacroRunner(pgm, macroStarts[i], name, editor);
return;
}
}
/** Remove both ours and the backed up event handlers. */
final void clearGui() {
for (final KeyListener l : canvasKeyListeners) canvas.removeKeyListener(l);
for (final KeyListener l : windowKeyListeners) window.removeKeyListener(l);
for (final KeyListener l : ijKeyListeners) ij.removeKeyListener(l);
for (final MouseListener l : canvasMouseListeners) canvas.removeMouseListener(l);
for (final MouseMotionListener l : canvasMouseMotionListeners)
canvas.removeMouseMotionListener(l);
for (final MouseWheelListener l : windowMouseWheelListeners)
window.removeMouseWheelListener(l);
canvas.removeKeyListener(Panorama_View.this);
window.removeKeyListener(Panorama_View.this);
ij.removeKeyListener(Panorama_View.this);
canvas.removeMouseListener(Panorama_View.this);
canvas.removeMouseMotionListener(Panorama_View.this);
window.removeMouseWheelListener(Panorama_View.this);
}
private void progress() {
if (display()) {
final ImageJ ij = IJ.getInstance();
if (ij != null) { // To avoid exceptions in ImageJ batch mode
final ProgressBar pb = ij.getProgressBar();
if (pb != null) {
final double lo = min();
final double hi = max();
pb.show(lo + percent * (hi - lo));
if (enforce()) {
final Graphics gx = pb.getGraphics();
if (gx != null) pb.paint(gx); // Enforces a refresh also when called from event stack
}
}
}
}
}
/** Restore the previously active Event handlers. */
final void restoreGui() {
clearGui();
for (final KeyListener l : canvasKeyListeners) canvas.addKeyListener(l);
for (final KeyListener l : windowKeyListeners) window.addKeyListener(l);
for (final KeyListener l : ijKeyListeners) ij.addKeyListener(l);
for (final MouseListener l : canvasMouseListeners) canvas.addMouseListener(l);
for (final MouseMotionListener l : canvasMouseMotionListeners)
canvas.addMouseMotionListener(l);
for (final MouseWheelListener l : windowMouseWheelListeners) window.addMouseWheelListener(l);
}
/** Creates a table mapping legacy ImageJ command labels to menu paths. */
private Map<String, MenuPath> parseMenus(final ij.ImageJ ij) {
final Map<String, MenuPath> menuTable = new HashMap<String, MenuPath>();
if (ij == null) return menuTable;
final MenuBar menubar = ij.getMenuBar();
final int menuCount = menubar.getMenuCount();
for (int i = 0; i < menuCount; i++) {
final Menu menu = menubar.getMenu(i);
parseMenu(menu, i, new MenuPath(), menuTable);
}
return menuTable;
}
public PlugInDialog(String title) {
super(IJ.isMacOSX() ? IJ.getInstance() : IJ.isJava16() ? null : new Frame(), title);
enableEvents(AWTEvent.WINDOW_EVENT_MASK);
this.title = title;
ImageJ ij = IJ.getInstance();
if (IJ.isMacOSX() && ij != null) {
ij.toFront(); // needed for keyboard shortcuts to work
IJ.wait(250);
}
addWindowListener(this);
addFocusListener(this);
if (IJ.isLinux()) setBackground(ImageJ.backgroundColor);
if (ij != null && !IJ.isMacOSX() && IJ.isJava16()) {
Image img = ij.getIconImage();
if (img != null)
try {
setIconImage(img);
} catch (Exception e) {
}
}
}
/** Add new event handlers. */
final void takeOverGui() {
canvas.addKeyListener(Panorama_View.this);
window.addKeyListener(Panorama_View.this);
canvas.addMouseMotionListener(Panorama_View.this);
canvas.addMouseListener(Panorama_View.this);
ij.addKeyListener(Panorama_View.this);
window.addMouseWheelListener(Panorama_View.this);
}
public void actionPerformed(ActionEvent evt) {
String cmd = evt.getActionCommand();
ImageJ.setCommandName(cmd);
MenuItem item = (MenuItem) evt.getSource();
MenuContainer parent = item.getParent();
if (parent instanceof PopupMenu) {
for (int i = 0; i < nMacros; i++) {
if (macroNames[i].equals("Popup Menu")) {
new MacroRunner(pgm, macroStarts[i], "Popup Menu", cmd);
return;
}
}
}
runMacro(cmd);
}
public static void main(final String args[]) {
final File file =
new File(AppUtils.getBaseDirectory(TrackMate.class), "samples/FakeTracks.xml");
// 1 - Load test spots
System.out.println("Opening file: " + file.getAbsolutePath());
final TmXmlReader reader = new TmXmlReader(file);
final Model model = reader.getModel();
final Settings gs = new Settings();
reader.readSettings(gs, null, null, null, null, null);
System.out.println("Spots: " + model.getSpots());
System.out.println("Found " + model.getTrackModel().nTracks(false) + " tracks in the file:");
System.out.println("Track features: ");
System.out.println();
// 2 - Track the test spots
final long start = System.currentTimeMillis();
final Map<String, Object> settings = new HashMap<String, Object>();
settings.put(KEY_LINKING_MAX_DISTANCE, 15d);
final NearestNeighborTracker tracker = new NearestNeighborTracker(model.getSpots(), settings);
tracker.setLogger(Logger.DEFAULT_LOGGER);
if (!tracker.checkInput())
System.err.println("Error checking input: " + tracker.getErrorMessage());
if (!tracker.process()) System.err.println("Error in process: " + tracker.getErrorMessage());
final long end = System.currentTimeMillis();
model.setTracks(tracker.getResult(), true);
// 3 - Print out results for testing
System.out.println();
System.out.println();
System.out.println();
System.out.println("Found " + model.getTrackModel().nTracks(false) + " final tracks.");
System.out.println("Whole tracking done in " + (end - start) + " ms.");
System.out.println();
// 5 - Display tracks
// Load Image
ij.ImageJ.main(args);
final ImagePlus imp = gs.imp;
final TrackMateModelView sd2d = new HyperStackDisplayer(model, new SelectionModel(model), imp);
sd2d.render();
sd2d.setDisplaySettings(
TrackMateModelView.KEY_TRACK_DISPLAY_MODE, TrackMateModelView.TRACK_DISPLAY_MODE_WHOLE);
}
public static void main(String[] args) {
ij.ImageJ.main(args);
IJ.open("/Users/tinevez/Desktop/Data/FakeTracks.tif");
TrackMate_ model = new TrackMate_();
model.run(null);
}
public static void main(final String[] args) {
// TEST 2D case
// Parameters
final int size_x = 200;
final int size_y = 200;
final long a = 10;
final long b = 5;
final double phi_r = Math.toRadians(30);
final long max_radius = Math.max(a, b);
final double[] calibration = new double[] {1, 1};
// Create blank image
final Img<UnsignedByteType> img =
new ArrayImgFactory<UnsignedByteType>()
.create(new int[] {200, 200}, new UnsignedByteType());
final ImgPlus<UnsignedByteType> imgplus = new ImgPlus<UnsignedByteType>(img);
for (int d = 0; d < imgplus.numDimensions(); d++) {
imgplus.setAxis(new DefaultLinearAxis(imgplus.axis(d).type(), calibration[d]), d);
}
final byte on = (byte) 255;
// Create an ellipse
long start = System.currentTimeMillis();
System.out.println(String.format("Creating an ellipse with a = %d, b = %d", a, b));
System.out.println(String.format("phi = %.1f", Math.toDegrees(phi_r)));
final long[] center = new long[] {size_x / 2, size_y / 2};
final long[] radiuses = new long[] {max_radius, max_radius};
final EllipseNeighborhood<UnsignedByteType> disc =
new EllipseNeighborhood<UnsignedByteType>(img, center, radiuses);
final EllipseCursor<UnsignedByteType> sc = disc.cursor();
double r2, phi, term;
double cosphi, sinphi;
while (sc.hasNext()) {
sc.fwd();
r2 = sc.getDistanceSquared();
phi = sc.getPhi();
cosphi = Math.cos(phi - phi_r);
sinphi = Math.sin(phi - phi_r);
term = r2 * cosphi * cosphi / a / a + r2 * sinphi * sinphi / b / b;
if (term <= 1) sc.get().set(on);
}
final long end = System.currentTimeMillis();
System.out.println("Ellipse creation done in " + (end - start) + " ms.");
System.out.println();
ij.ImageJ.main(args);
ImageJFunctions.show(imgplus);
start = System.currentTimeMillis();
final Spot spot = new Spot(center[0], center[1], 0d, max_radius, -1d);
final SpotMorphologyAnalyzer<UnsignedByteType> bm =
new SpotMorphologyAnalyzer<UnsignedByteType>(imgplus, null);
bm.process(spot);
System.out.println("Blob morphology analyzed in " + (end - start) + " ms.");
double phiv, thetav, lv;
for (int j = 0; j < 2; j++) {
lv = spot.getFeature(featurelist_sa[j]);
phiv = spot.getFeature(featurelist_phi[j]);
thetav = spot.getFeature(featurelist_theta[j]);
System.out.println(
String.format(
"For axis of semi-length %.1f, orientation is phi = %.1f°, theta = %.1f°",
lv, Math.toDegrees(phiv), Math.toDegrees(thetav)));
}
System.out.println(spot.echo());
// TEST 3D case
/*
*
* // Parameters int size_x = 200; int size_y = 200; int size_z = 200;
*
* double a = 5.5f; double b = 4.9f; double c = 5; double theta_r =
* (double) Math.toRadians(0); // I am unable to have it working for
* theta_r != 0 double phi_r = (double) Math.toRadians(45);
*
* double max_radius = Math.max(a, Math.max(b, c)); double[] calibration
* = new double[] {1, 1, 1};
*
* // Create blank image Image<UnsignedByteType> img = new
* ImageFactory<UnsignedByteType>( new UnsignedByteType(), new
* ArrayContainerFactory() ).createImage(new int[] {200, 200, 200});
* final byte on = (byte) 255;
*
* // Create an ellipse long start = System.currentTimeMillis();
* System.out.println(String.format(
* "Creating an ellipse with a = %.1f, b = %.1f, c = %.1f", a, b, c));
* System.out.println(String.format("phi = %.1f and theta = %.1f",
* Math.toDegrees(phi_r), Math.toDegrees(theta_r))); double[] center =
* new double[] { size_x/2, size_y/2, size_z/2 };
* SphereCursor<UnsignedByteType> sc = new
* SphereCursor<UnsignedByteType>(img, center, max_radius, calibration);
* double r2, theta, phi, term; double cosphi, sinphi, costheta,
* sintheta; while (sc.hasNext()) { sc.fwd(); r2 =
* sc.getDistanceSquared(); phi = sc.getPhi(); theta = sc.getTheta();
* cosphi = Math.cos(phi-phi_r); sinphi = Math.sin(phi-phi_r); costheta
* = Math.cos(theta-theta_r); sintheta = Math.sin(theta-theta_r); term =
* r2*cosphi*cosphi*sintheta*sintheta/a/a +
* r2*sinphi*sinphi*sintheta*sintheta/b/b + r2*costheta*costheta/c/c; if
* (term <= 1) sc.getType().set(on); } sc.close(); long end =
* System.currentTimeMillis();
* System.out.println("Ellipse creation done in " + (end-start) +
* " ms."); System.out.println();
*
* ij.ImageJ.main(args); img.getDisplay().setMinMax();
* ImageJFunctions.copyToImagePlus(img).show();
*
* start = System.currentTimeMillis(); BlobMorphology<UnsignedByteType>
* bm = new BlobMorphology<UnsignedByteType>(img, calibration); SpotImp
* spot = new SpotImp(center); spot.putFeature(Feature.RADIUS,
* max_radius); bm.process(spot); end = System.currentTimeMillis();
* System.out.println("Blob morphology analyzed in " + (end-start) +
* " ms."); double phiv, thetav, lv; for (int j = 0; j < 3; j++) { lv =
* spot.getFeature(featurelist_sa[j]); phiv =
* spot.getFeature(featurelist_phi[j]); thetav =
* spot.getFeature(featurelist_theta[j]);
* System.out.println(String.format(
* "For axis of semi-length %.1f, orientation is phi = %.1f°, theta = %.1f°"
* , lv, Math.toDegrees(phiv), Math.toDegrees(thetav))); }
* System.out.println(spot.echo());
*/
}
public static void main(String args[]) {
if (System.getProperty("java.version").substring(0, 3).compareTo("1.5") < 0) {
javax.swing.JOptionPane.showMessageDialog(
null, "ImageJ " + VERSION + " requires Java 1.5 or later.");
System.exit(0);
}
boolean noGUI = false;
int mode = STANDALONE;
arguments = args;
// System.setProperty("file.encoding", "UTF-8");
int nArgs = args != null ? args.length : 0;
boolean commandLine = false;
for (int i = 0; i < nArgs; i++) {
String arg = args[i];
if (arg == null) continue;
if (args[i].startsWith("-")) {
if (args[i].startsWith("-batch")) noGUI = true;
else if (args[i].startsWith("-debug")) IJ.setDebugMode(true);
else if (args[i].startsWith("-ijpath") && i + 1 < nArgs) {
if (IJ.debugMode) IJ.log("-ijpath: " + args[i + 1]);
Prefs.setHomeDir(args[i + 1]);
commandLine = true;
args[i + 1] = null;
} else if (args[i].startsWith("-port")) {
int delta = (int) Tools.parseDouble(args[i].substring(5, args[i].length()), 0.0);
commandLine = true;
if (delta == 0) mode = EMBEDDED;
else if (delta > 0 && DEFAULT_PORT + delta < 65536) port = DEFAULT_PORT + delta;
}
}
}
// If existing ImageJ instance, pass arguments to it and quit.
boolean passArgs = mode == STANDALONE && !noGUI;
if (IJ.isMacOSX() && !commandLine) passArgs = false;
if (passArgs && isRunning(args)) return;
ImageJ ij = IJ.getInstance();
if (!noGUI && (ij == null || (ij != null && !ij.isShowing()))) {
ij = new ImageJ(null, mode);
ij.exitWhenQuitting = true;
}
int macros = 0;
for (int i = 0; i < nArgs; i++) {
String arg = args[i];
if (arg == null) continue;
if (arg.startsWith("-")) {
if ((arg.startsWith("-macro") || arg.startsWith("-batch")) && i + 1 < nArgs) {
String arg2 = i + 2 < nArgs ? args[i + 2] : null;
Prefs.commandLineMacro = true;
if (noGUI && args[i + 1].endsWith(".js")) Interpreter.batchMode = true;
IJ.runMacroFile(args[i + 1], arg2);
break;
} else if (arg.startsWith("-eval") && i + 1 < nArgs) {
String rtn = IJ.runMacro(args[i + 1]);
if (rtn != null) System.out.print(rtn);
args[i + 1] = null;
} else if (arg.startsWith("-run") && i + 1 < nArgs) {
IJ.run(args[i + 1]);
args[i + 1] = null;
}
} else if (macros == 0 && (arg.endsWith(".ijm") || arg.endsWith(".txt"))) {
IJ.runMacroFile(arg);
macros++;
} else if (arg.length() > 0 && arg.indexOf("ij.ImageJ") == -1) {
File file = new File(arg);
IJ.open(file.getAbsolutePath());
}
}
if (IJ.debugMode && IJ.getInstance() == null) new JavaProperties().run("");
if (noGUI) System.exit(0);
}
public void windowActivated(WindowEvent e) {
ImageJ ij = IJ.getInstance();
if (IJ.isMacOSX() && ij != null && !ij.isActive() && !(this instanceof ThresholdAdjuster))
ij.toFront();
WindowManager.setWindow(this);
}