// 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);
}
}
}
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;
}
/** 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);
}
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;
}
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();
}
// 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;
}
void addImage() {
ImagePlus imp = IJ.getImage();
int[] wList = WindowManager.getIDList();
if (wList == null || wList.length < 2) {
IJ.error("Add Image...", "The command requires at least two open images.");
return;
}
String[] titles = new String[wList.length];
for (int i = 0; i < wList.length; i++) {
ImagePlus imp2 = WindowManager.getImage(wList[i]);
titles[i] = imp2 != null ? imp2.getTitle() : "";
}
int x = 0, y = 0;
Roi roi = imp.getRoi();
if (roi != null && roi.isArea()) {
Rectangle r = roi.getBounds();
x = r.x;
y = r.y;
}
int index = 0;
if (wList.length == 2) {
ImagePlus i1 = WindowManager.getImage(wList[0]);
ImagePlus i2 = WindowManager.getImage(wList[1]);
if (i2.getWidth() < i1.getWidth() && i2.getHeight() < i1.getHeight()) index = 1;
} else if (imp.getID() == wList[0]) index = 1;
GenericDialog gd = new GenericDialog("Add Image...");
gd.addChoice("Image to add:", titles, titles[index]);
gd.addNumericField("X location:", x, 0);
gd.addNumericField("Y location:", y, 0);
gd.addNumericField("Opacity (0-100%):", 100, 0);
gd.addCheckbox("Create image selection", createImageRoi);
gd.showDialog();
if (gd.wasCanceled()) return;
index = gd.getNextChoiceIndex();
x = (int) gd.getNextNumber();
y = (int) gd.getNextNumber();
double opacity = gd.getNextNumber() / 100.0;
createImageRoi = gd.getNextBoolean();
ImagePlus overlay = WindowManager.getImage(wList[index]);
if (wList.length == 2) {
ImagePlus i1 = WindowManager.getImage(wList[0]);
ImagePlus i2 = WindowManager.getImage(wList[1]);
if (i2.getWidth() < i1.getWidth() && i2.getHeight() < i1.getHeight()) {
imp = i1;
overlay = i2;
}
}
if (overlay == imp) {
IJ.error(
"Add Image...", "Image to be added cannot be the same as\n\"" + imp.getTitle() + "\".");
return;
}
if (overlay.getWidth() > imp.getWidth() && overlay.getHeight() > imp.getHeight()) {
IJ.error(
"Add Image...", "Image to be added cannnot be larger than\n\"" + imp.getTitle() + "\".");
return;
}
if (createImageRoi && x == 0 && y == 0) {
x = imp.getWidth() / 2 - overlay.getWidth() / 2;
y = imp.getHeight() / 2 - overlay.getHeight() / 2;
}
roi = new ImageRoi(x, y, overlay.getProcessor());
roi.setName(overlay.getShortTitle());
if (opacity != 1.0) ((ImageRoi) roi).setOpacity(opacity);
if (createImageRoi) imp.setRoi(roi);
else {
Overlay overlayList = imp.getOverlay();
if (overlayList == null) overlayList = new Overlay();
overlayList.add(roi);
imp.setOverlay(overlayList);
overlay2 = overlayList;
Undo.setup(Undo.OVERLAY_ADDITION, imp);
}
}
/** @deprecated replaced by ImagePlus.setOverlay(Roi, Color, int, Color) */
public void setDisplayList(Roi roi, Color color) {
roi.setStrokeColor(color);
Overlay list = new Overlay();
list.add(roi);
setOverlay(list);
}