// 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;
}
/** @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);
}
// 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 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;
}
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;
}
// 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 drawOverlay(Graphics g) {
if (imp != null && imp.getHideOverlay()) return;
Color labelColor = overlay.getLabelColor();
if (labelColor == null) labelColor = Color.white;
initGraphics(g, labelColor, Roi.getColor());
int n = overlay.size();
if (IJ.debugMode) IJ.log("paint: drawing " + n + " ROI display list");
int currentImage = imp != null ? imp.getCurrentSlice() : -1;
if (imp.getStackSize() == 1) currentImage = -1;
int channel = 0, slice = 0, frame = 0;
boolean hyperstack = imp.isHyperStack();
if (hyperstack) {
channel = imp.getChannel();
slice = imp.getSlice();
frame = imp.getFrame();
}
drawNames = overlay.getDrawNames();
boolean drawLabels = drawNames || overlay.getDrawLabels();
for (int i = 0; i < n; i++) {
if (overlay == null) break;
Roi roi = overlay.get(i);
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 + LIST_OFFSET : -1);
} else {
int position = roi.getPosition();
if (position == 0 || position == currentImage)
drawRoi(g, roi, drawLabels ? i + LIST_OFFSET : -1);
}
}
((Graphics2D) g).setStroke(Roi.onePixelWide);
drawNames = false;
}
void initGraphics(Graphics g, Color textColor, Color defaultColor) {
if (smallFont == null) {
smallFont = new Font("SansSerif", Font.PLAIN, 9);
largeFont = new Font("SansSerif", Font.PLAIN, 12);
}
if (textColor != null) {
labelColor = textColor;
if (overlay != null && overlay.getDrawBackgrounds())
bgColor =
new Color(
255 - labelColor.getRed(), 255 - labelColor.getGreen(), 255 - labelColor.getBlue());
else bgColor = null;
} else {
int red = defaultColor.getRed();
int green = defaultColor.getGreen();
int blue = defaultColor.getBlue();
if ((red + green + blue) / 3 < 128) labelColor = Color.white;
else labelColor = Color.black;
bgColor = defaultColor;
}
this.defaultColor = defaultColor;
g.setColor(defaultColor);
}
/** @deprecated replaced by ImagePlus.getOverlay() */
public Vector getDisplayList() {
if (overlay == null) return null;
Vector displayList = new Vector();
for (int i = 0; i < overlay.size(); i++) displayList.add(overlay.get(i));
return displayList;
}
/** @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);
}
/** Use ImagePlus.setOverlay(ij.gui.Overlay). */
public void setOverlay(Overlay overlay) {
this.overlay = overlay;
if (overlay != null) font = overlay.getLabelsFont();
repaint();
}