boolean handleClickEvent(ClickEvent evt) {
boolean evtHandled = false;
if (state.isRadarVisible() && state.getLayer().xmlRadarAvailable) {
if (evt.x > radarX
&& evt.x < radarX + radarObjects.getWidth()
&& evt.y > radarY
&& evt.y < radarY + radarObjects.getHeight()) {
dialogState = RADAR_DIALOG;
evtHandled = true;
}
}
// Handle event
if (state.getNextLayerStatus() == ARXState.READY) {
// Loop through overlays
Iterator<Overlay> overlayIt = state.getLayer().getOverlays().iterator();
while (!evtHandled && overlayIt.hasNext()) {
Overlay ovl = overlayIt.next();
evtHandled = ovl.press(evt.x, evt.y, ctx, state);
}
// TODO:these should also be ordered according to distance.
Iterator<Placemark> placemarkIt = state.getLayer().getZOrderedPlacemarks().iterator();
while (!evtHandled && placemarkIt.hasNext()) {
Placemark pm = placemarkIt.next();
evtHandled = pm.press(evt.x, evt.y, ctx, state);
}
}
return evtHandled;
}
/* Wraps everything into a Cell Manager Class*/
private CellManager toCellManager(ImagePlus imp, ArrayList<PolygonRoi> rois, ImagePlus av_imp) {
CellManager cm = new CellManager(av_imp, imp, this.ovr);
Iterator itr = rois.iterator();
ArrayList<Double> av_sig = new ArrayList<>();
PolygonRoi roi;
while (itr.hasNext()) {
roi = (PolygonRoi) itr.next();
av_sig = Activity_Analysis.getAverageSignal(imp, roi);
CalciumSignal ca_sig = new CalciumSignal(av_sig, this.dt_r);
ovr.add(roi);
ca_sig.DeltaF();
cm.addCell(ca_sig, roi);
}
// catch(Exception e){
// IJ.showMessage(e.getMessage());
// }
// }
ovr.setLabelColor(Color.WHITE);
// ovr.setFillColor(Color.GREEN);
ovr.setStrokeColor(Color.getHSBColor(100, 30, 87));
av_imp.setOverlay(ovr);
av_imp.show();
IJ.run("In [+]", "");
IJ.run("In [+]", "");
return cm;
}
// Added by Marcel Boeglin 2013.09.22
private Overlay projectHyperStackRois(Overlay overlay) {
if (overlay == null) return null;
int t1 = imp.getFrame();
int channels = projImage.getNChannels();
int slices = 1;
int frames = projImage.getNFrames();
Overlay overlay2 = new Overlay();
Roi roi;
int c, z, t;
int size = channels * slices * frames;
for (Roi r : overlay.toArray()) {
c = r.getCPosition();
z = r.getZPosition();
t = r.getTPosition();
roi = (Roi) r.clone();
if (size == channels) { // current time frame
if (z >= startSlice && z <= stopSlice && t == t1 || c == 0) {
roi.setPosition(c);
overlay2.add(roi);
}
} else if (size == frames * channels) { // all time frames
if (z >= startSlice && z <= stopSlice) roi.setPosition(c, 1, t);
else if (z == 0) roi.setPosition(c, 0, t);
else continue;
overlay2.add(roi);
}
}
return overlay2;
}
void drawOutline(ImageProcessor ip, Roi roi, int count) {
if (showChoice == OVERLAY_OUTLINES || showChoice == OVERLAY_MASKS) {
if (overlay == null) {
overlay = new Overlay();
overlay.drawLabels(true);
overlay.setLabelFont(new Font("SansSerif", Font.PLAIN, fontSize));
}
Roi roi2 = (Roi) roi.clone();
roi2.setStrokeColor(Color.cyan);
if (lineWidth != 1) roi2.setStrokeWidth(lineWidth);
if (showChoice == OVERLAY_MASKS) roi2.setFillColor(Color.cyan);
overlay.add(roi2);
} else {
Rectangle r = roi.getBounds();
int nPoints = ((PolygonRoi) roi).getNCoordinates();
int[] xp = ((PolygonRoi) roi).getXCoordinates();
int[] yp = ((PolygonRoi) roi).getYCoordinates();
int x = r.x, y = r.y;
if (!inSituShow) ip.setValue(0.0);
ip.moveTo(x + xp[0], y + yp[0]);
for (int i = 1; i < nPoints; i++) ip.lineTo(x + xp[i], y + yp[i]);
ip.lineTo(x + xp[0], y + yp[0]);
if (showChoice != BARE_OUTLINES) {
String s = ResultsTable.d2s(count, 0);
ip.moveTo(r.x + r.width / 2 - ip.getStringWidth(s) / 2, r.y + r.height / 2 + fontSize / 2);
if (!inSituShow) ip.setValue(1.0);
ip.drawString(s);
}
}
}
public static void setOverlay(Overlay s) {
if (current != null) {
current.dispose();
}
last = current;
current = s;
current.create();
}
public boolean onDoubleTapEvent(final MotionEvent e, final MapView pMapView) {
for (final Overlay overlay : this.overlaysReversed()) {
if (overlay.onDoubleTapEvent(e, pMapView)) {
return true;
}
}
return false;
}
public boolean onTrackballEvent(final MotionEvent event, final MapView pMapView) {
for (final Overlay overlay : this.overlaysReversed()) {
if (overlay.onTrackballEvent(event, pMapView)) {
return true;
}
}
return false;
}
public boolean onKeyUp(final int keyCode, final KeyEvent event, final MapView pMapView) {
for (final Overlay overlay : this.overlaysReversed()) {
if (overlay.onKeyUp(keyCode, event, pMapView)) {
return true;
}
}
return false;
}
public void onDetach(final MapView pMapView) {
if (mTilesOverlay != null) {
mTilesOverlay.onDetach(pMapView);
}
for (final Overlay overlay : this.overlaysReversed()) {
overlay.onDetach(pMapView);
}
}
public boolean onSingleTapUp(final MotionEvent pEvent, final MapView pMapView) {
for (final Overlay overlay : this.overlaysReversed()) {
if (overlay.onSingleTapUp(pEvent, pMapView)) {
return true;
}
}
return false;
}
public void redrawAll() {
resetBackground(); // Reset the background to the original at the correct size.:
for (Overlay overlay : overlays) {
for (List<Annotation> annotations : overlay.getAnnotationSets()) {
for (Annotation annotation : annotations) {
annotation.drawOnCanvas(backingCanvas, resizeRatio);
}
}
}
}
/** @deprecated replaced by ImagePlus.setOverlay(ij.gui.Overlay) */
public void setDisplayList(Vector list) {
if (list != null) {
Overlay list2 = new Overlay();
list2.setVector(list);
setOverlay(list2);
} else setOverlay(null);
if (overlay != null)
overlay.drawLabels(overlay.size() > 0 && overlay.get(0).getStrokeColor() == null);
else customRoi = false;
repaint();
}
/** Return the ROI Manager "Show All" list as an overlay. */
public Overlay getShowAllList() {
if (!showAllROIs) return null;
if (showAllList != null) return showAllList;
RoiManager rm = RoiManager.getInstance();
if (rm == null) return null;
Roi[] rois = rm.getRoisAsArray();
if (rois.length == 0) return null;
Overlay overlay = new Overlay();
for (int i = 0; i < rois.length; i++) overlay.add((Roi) rois[i].clone());
return overlay;
}
/** @deprecated replaced by ImagePlus.setOverlay(Shape, Color, BasicStroke) */
public void setDisplayList(Shape shape, Color color, BasicStroke stroke) {
if (shape == null) {
setOverlay(null);
return;
}
Roi roi = new ShapeRoi(shape);
roi.setStrokeColor(color);
roi.setStroke(stroke);
Overlay list = new Overlay();
list.add(roi);
setOverlay(list);
}
public boolean onFling(
final MotionEvent pEvent1,
final MotionEvent pEvent2,
final float pVelocityX,
final float pVelocityY,
final MapView pMapView) {
for (final Overlay overlay : this.overlaysReversed()) {
if (overlay.onFling(pEvent1, pEvent2, pVelocityX, pVelocityY, pMapView)) {
return true;
}
}
return false;
}
public boolean onScroll(
final MotionEvent pEvent1,
final MotionEvent pEvent2,
final float pDistanceX,
final float pDistanceY,
final MapView pMapView) {
for (final Overlay overlay : this.overlaysReversed()) {
if (overlay.onScroll(pEvent1, pEvent2, pDistanceX, pDistanceY, pMapView)) {
return true;
}
}
return false;
}
void addSelection() {
ImagePlus imp = IJ.getImage();
String macroOptions = Macro.getOptions();
if (macroOptions != null && IJ.macroRunning() && macroOptions.indexOf("remove") != -1) {
imp.setOverlay(null);
return;
}
Roi roi = imp.getRoi();
if (roi == null && imp.getOverlay() != null) {
GenericDialog gd = new GenericDialog("No Selection");
gd.addMessage("\"Overlay>Add\" requires a selection.");
gd.setInsets(15, 40, 0);
gd.addCheckbox("Remove existing overlay", false);
gd.showDialog();
if (gd.wasCanceled()) return;
if (gd.getNextBoolean()) imp.setOverlay(null);
return;
}
if (roi == null) {
IJ.error("This command requires a selection.");
return;
}
roi = (Roi) roi.clone();
if (roi.getStrokeColor() == null) roi.setStrokeColor(Toolbar.getForegroundColor());
int width = Line.getWidth();
Rectangle bounds = roi.getBounds();
boolean tooWide = width > Math.max(bounds.width, bounds.height) / 3.0;
if (roi.getStroke() == null && width > 1 && !tooWide) roi.setStrokeWidth(Line.getWidth());
Overlay overlay = imp.getOverlay();
if (overlay != null && overlay.size() > 0 && !roi.isDrawingTool()) {
Roi roi2 = overlay.get(overlay.size() - 1);
if (roi.getStroke() == null) roi.setStrokeWidth(roi2.getStrokeWidth());
if (roi.getFillColor() == null) roi.setFillColor(roi2.getFillColor());
}
boolean points = roi instanceof PointRoi && ((PolygonRoi) roi).getNCoordinates() > 1;
if (points) roi.setStrokeColor(Color.red);
if (!IJ.altKeyDown() && !(roi instanceof Arrow)) {
RoiProperties rp = new RoiProperties("Add to Overlay", roi);
if (!rp.showDialog()) return;
}
String name = roi.getName();
boolean newOverlay = name != null && name.equals("new-overlay");
if (overlay == null || newOverlay) overlay = new Overlay();
overlay.add(roi);
imp.setOverlay(overlay);
overlay2 = overlay;
if (points || (roi instanceof ImageRoi) || (roi instanceof Arrow)) imp.killRoi();
Undo.setup(Undo.OVERLAY_ADDITION, imp);
}
// Added by Marcel Boeglin 2013.09.23
private Overlay projectStackRois(Overlay overlay) {
if (overlay == null) return null;
Overlay overlay2 = new Overlay();
Roi roi;
int s;
for (Roi r : overlay.toArray()) {
s = r.getPosition();
roi = (Roi) r.clone();
if (s >= startSlice && s <= stopSlice || s == 0) {
roi.setPosition(s);
overlay2.add(roi);
}
}
return overlay2;
}
@Obvious
@Override
public PhotoOverlay withOverlayObjectExtension(
final List<AbstractObject> overlayObjectExtension) {
super.withOverlayObjectExtension(overlayObjectExtension);
return this;
}
@Override
protected void paintComponent(Graphics g) {
BufferedImage image = theImage.getImage();
if (image != null) {
Graphics2D gg = (Graphics2D) g.create();
overlay.paint(gg, image, theImage.getImageTransform());
gg.dispose();
}
}
public void ctick(int dt) {
int dt2 = dt + initdelay;
initdelay = 0;
for (GAttrib a : attr.values()) {
if (a instanceof Drawable) a.ctick(dt2);
else a.ctick(dt);
}
for (Iterator<Overlay> i = ols.iterator(); i.hasNext(); ) {
Overlay ol = i.next();
if (ol.spr == null) {
if (((getattr(Drawable.class) == null) || (getneg() != null)) && (ol.res.get() != null))
ol.spr = Sprite.create(this, ol.res.get(), ol.sdt);
} else {
boolean done = ol.spr.tick(dt);
if ((!ol.delign || (ol.spr instanceof Overlay.CDel)) && done) i.remove();
}
}
}
void drawAllROIs(Graphics g) {
RoiManager rm = RoiManager.getInstance();
if (rm == null) {
rm = Interpreter.getBatchModeRoiManager();
if (rm != null && rm.getList().getItemCount() == 0) rm = null;
}
if (rm == null) {
// if (showAllList!=null)
// overlay = showAllList;
showAllROIs = false;
repaint();
return;
}
initGraphics(g, null, showAllColor);
Hashtable rois = rm.getROIs();
java.awt.List list = rm.getList();
boolean drawLabels = rm.getDrawLabels();
currentRoi = null;
int n = list.getItemCount();
if (IJ.debugMode) IJ.log("paint: drawing " + n + " \"Show All\" ROIs");
if (labelRects == null || labelRects.length != n) labelRects = new Rectangle[n];
if (!drawLabels) showAllList = new Overlay();
else showAllList = null;
if (imp == null) return;
int currentImage = imp.getCurrentSlice();
int channel = 0, slice = 0, frame = 0;
boolean hyperstack = imp.isHyperStack();
if (hyperstack) {
channel = imp.getChannel();
slice = imp.getSlice();
frame = imp.getFrame();
}
drawNames = Prefs.useNamesAsLabels;
for (int i = 0; i < n; i++) {
String label = list.getItem(i);
Roi roi = (Roi) rois.get(label);
if (roi == null) continue;
if (showAllList != null) showAllList.add(roi);
if (i < 200 && drawLabels && roi == imp.getRoi()) currentRoi = roi;
if (Prefs.showAllSliceOnly && imp.getStackSize() > 1) {
if (hyperstack && roi.getPosition() == 0) {
int c = roi.getCPosition();
int z = roi.getZPosition();
int t = roi.getTPosition();
if ((c == 0 || c == channel) && (z == 0 || z == slice) && (t == 0 || t == frame))
drawRoi(g, roi, drawLabels ? i : -1);
} else {
int position = roi.getPosition();
if (position == 0) position = getSliceNumber(roi.getName());
if (position == 0 || position == currentImage) drawRoi(g, roi, drawLabels ? i : -1);
}
} else drawRoi(g, roi, drawLabels ? i : -1);
}
((Graphics2D) g).setStroke(Roi.onePixelWide);
drawNames = false;
}
public boolean equals(Object other) {
if (other instanceof Overlay == false) {
return false;
}
Overlay otherOverlay = (Overlay) other;
if (m_addOrder.length != otherOverlay.getAddOrder().length) {
return false;
}
for (int i = 0; i < m_parents.length; i++) {
if (m_parents[i] != otherOverlay.getParents()[i]) {
return false;
}
}
return true;
}
@SuppressWarnings("unused")
private void toggle() {
QWidget current = panels.currentWidget();
QWidget next = panels.widget((panels.currentIndex() + 1) % 2);
// make sure the layout is up to date...
next.setGeometry(current.geometry());
QPixmap startpm = QPixmap.grabWidget(current);
QPixmap endpm = QPixmap.grabWidget(next);
Overlay overlay = new Overlay(startpm, endpm);
overlay.setTransition(transition);
overlay.setParent(this);
overlay.setGeometry(panels.geometry());
overlay.show();
panels.setCurrentIndex((panels.currentIndex() + 1) % 2);
}
void fromRoiManager() {
ImagePlus imp = IJ.getImage();
RoiManager rm = RoiManager.getInstance();
if (rm == null) {
IJ.error("ROI Manager is not open");
return;
}
Roi[] rois = rm.getRoisAsArray();
if (rois.length == 0) {
IJ.error("ROI Manager is empty");
return;
}
Overlay overlay = new Overlay();
for (int i = 0; i < rois.length; i++) overlay.add((Roi) rois[i].clone());
imp.setOverlay(overlay);
ImageCanvas ic = imp.getCanvas();
if (ic != null) ic.setShowAllROIs(false);
rm.setEditMode(imp, false);
imp.killRoi();
}
private boolean deleteOverlayRoi(ImagePlus imp) {
if (imp == null) return false;
Overlay overlay = null;
ImageCanvas ic = imp.getCanvas();
if (ic != null) overlay = ic.getShowAllList();
if (overlay == null) overlay = imp.getOverlay();
if (overlay == null) return false;
Roi roi = imp.getRoi();
for (int i = 0; i < overlay.size(); i++) {
Roi roi2 = overlay.get(i);
if (roi2 == roi) {
overlay.remove(i);
imp.deleteRoi();
ic = imp.getCanvas();
if (ic != null) ic.roiManagerSelect(roi, true);
return true;
}
}
return false;
}
public void paint(Graphics g) {
if (backBufferWidth != getSize().width
|| backBufferHeight != getSize().height
|| backBufferImage == null
|| backBufferGraphics == null) resetBackBuffer();
final Rectangle src = getSrcRect();
synchronized (this) {
super.paint(backBufferGraphics);
for (Overlay overlay : overlays)
overlay.paint(backBufferGraphics, src.x, src.y, magnification);
final Roi roi = super.imp.getRoi();
if (roi != null) roi.draw(backBufferGraphics);
}
g.drawImage(backBufferImage, 0, 0, this);
}
// Added by Marcel Boeglin 2013.09.22
private Overlay projectRGBHyperStackRois(Overlay overlay) {
if (overlay == null) return null;
int frames = projImage.getNFrames();
int t1 = imp.getFrame();
Overlay overlay2 = new Overlay();
Roi roi;
int c, z, t;
for (Roi r : overlay.toArray()) {
c = r.getCPosition();
z = r.getZPosition();
t = r.getTPosition();
roi = (Roi) r.clone();
if (z >= startSlice && z <= stopSlice || z == 0 || c == 0 || t == 0) {
if (frames == 1 && t != t1 && t != 0) // current time frame
continue;
roi.setPosition(t);
overlay2.add(roi);
}
}
return overlay2;
}
public void draw(Canvas canvas, MapView mapview, boolean flag) {
Projection projection = mapview.getProjection();
Paint paint = new Paint();
Point point = new Point();
projection.toPixels(gp1, point);
paint.setColor(color);
Point point1 = new Point();
projection.toPixels(gp2, point1);
paint.setStrokeWidth(5F);
paint.setAlpha(120);
canvas.drawLine(point.x, point.y, point1.x, point1.y, paint);
super.draw(canvas, mapview, flag);
}
public static void main(String[] args) {
if (args.length > 0) {
String command = args[0];
String[] arguments = new String[args.length - 1];
System.arraycopy(args, 1, arguments, 0, arguments.length);
boolean exitAfterCallingMain = true;
try {
if (command.equals("ConvertColorspace")) {
ConvertColorspace.main(arguments);
} else if (command.equals("Decrypt")) {
Decrypt.main(arguments);
} else if (command.equals("Encrypt")) {
Encrypt.main(arguments);
} else if (command.equals("ExtractText")) {
ExtractText.main(arguments);
} else if (command.equals("Overlay")) {
Overlay.main(arguments);
} else if (command.equals("PrintPDF")) {
PrintPDF.main(arguments);
} else if (command.equals("PDFDebugger")) {
PDFDebugger.main(arguments);
exitAfterCallingMain = false;
} else if (command.equals("PDFMerger")) {
PDFMerger.main(arguments);
} else if (command.equals("PDFReader")) {
PDFReader.main(arguments);
exitAfterCallingMain = false;
} else if (command.equals("PDFSplit")) {
PDFSplit.main(arguments);
} else if (command.equals("PDFToImage")) {
PDFToImage.main(arguments);
} else if (command.equals("TextToPDF")) {
TextToPDF.main(arguments);
} else if (command.equals("WriteDecodedDoc")) {
WriteDecodedDoc.main(arguments);
} else {
showMessageAndExit();
}
if (exitAfterCallingMain) {
System.exit(0);
}
} catch (Exception e) {
System.err.println(command + " failed with the following exception:");
e.printStackTrace();
System.exit(1);
}
} else {
showMessageAndExit();
}
}