ij.plugin.OverlayCommands Maven / Gradle / Ivy
package ij.plugin;
import ij.*;
import ij.process.*;
import ij.gui.*;
import ij.plugin.frame.RoiManager;
import ij.plugin.frame.Recorder;
import ij.macro.Interpreter;
import ij.io.RoiDecoder;
import ij.plugin.filter.PlugInFilter;
import ij.text.TextWindow;
import ij.measure.ResultsTable;
import java.awt.*;
import java.util.ArrayList;
/** This plugin implements the commands in the Image/Overlay menu. */
public class OverlayCommands implements PlugIn {
private static int opacity = 100;
private static Roi defaultRoi;
private static boolean zeroTransparent;
static {
defaultRoi = new Roi(0, 0, 1, 1);
defaultRoi.setPosition(1); // set stacks positions by default
}
public void run(String arg) {
if (arg.equals("add"))
addSelection();
else if (arg.equals("image"))
addImage(false);
else if (arg.equals("image-roi"))
addImage(true);
else if (arg.equals("flatten"))
flatten();
else if (arg.equals("hide"))
hide();
else if (arg.equals("show"))
show();
else if (arg.equals("remove"))
remove();
else if (arg.equals("from"))
fromRoiManager();
else if (arg.equals("to"))
toRoiManager();
else if (arg.equals("list"))
list();
else if (arg.equals("options"))
options();
}
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();
Overlay overlay = imp.getOverlay();
if (!roi.isDrawingTool()) {
if (roi.getStroke()==null)
roi.setStrokeWidth(defaultRoi.getStrokeWidth());
if (roi.getStrokeColor()==null || Line.getWidth()>1&&defaultRoi.getStrokeColor()!=null)
roi.setStrokeColor(defaultRoi.getStrokeColor());
if (roi.getFillColor()==null)
roi.setFillColor(defaultRoi.getFillColor());
}
boolean setPos = defaultRoi.getPosition()!=0;
int stackSize = imp.getStackSize();
if (setPos && stackSize>1) {
if (imp.isHyperStack()||imp.isComposite()) {
boolean compositeMode = imp.isComposite() && ((CompositeImage)imp).getMode()==IJ.COMPOSITE;
int channel = !compositeMode||imp.getNChannels()==stackSize?imp.getChannel():0;
if (imp.getNSlices()>1)
roi.setPosition(channel, imp.getSlice(), 0);
else if (imp.getNFrames()>1)
roi.setPosition(channel, 0, imp.getFrame());
} else
roi.setPosition(imp.getCurrentSlice());
}
boolean points = roi instanceof PointRoi && ((PolygonRoi)roi).getNCoordinates()>1;
if (IJ.altKeyDown() || (IJ.macroRunning() && Macro.getOptions()!=null)) {
RoiProperties rp = new RoiProperties("Add to Overlay", roi);
if (!rp.showDialog()) return;
defaultRoi.setStrokeColor(roi.getStrokeColor());
defaultRoi.setStrokeWidth(roi.getStrokeWidth());
defaultRoi.setFillColor(roi.getFillColor());
}
String name = roi.getName();
boolean newOverlay = name!=null && name.equals("new-overlay");
Roi roiClone = (Roi)roi.clone();
if (roi.getStrokeColor()==null)
roi.setStrokeColor(Roi.getColor());
if (overlay==null || newOverlay)
overlay = OverlayLabels.createOverlay();
overlay.add(roi);
defaultRoi.setPosition(setPos?1:0);
imp.setOverlay(overlay);
boolean brushRoi = roi.getType()==Roi.COMPOSITE && Toolbar.getToolId()==Toolbar.OVAL && Toolbar.getBrushSize()>0;
if (points || (roi instanceof ImageRoi) || (roi instanceof Arrow&&!Prefs.keepArrowSelections) || brushRoi)
imp.deleteRoi();
Undo.setup(Undo.OVERLAY_ADDITION, imp);
}
void addImage(boolean createImageRoi) {
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; iimp.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!=100)
((ImageRoi)roi).setOpacity(opacity/100.0);
((ImageRoi)roi).setZeroTransparent(zeroTransparent);
if (createImageRoi)
imp.setRoi(roi);
else {
Overlay overlayList = imp.getOverlay();
if (overlayList==null) overlayList = new Overlay();
overlayList.add(roi);
imp.setOverlay(overlayList);
Undo.setup(Undo.OVERLAY_ADDITION, imp);
}
}
void hide() {
ImagePlus imp = IJ.getImage();
imp.setHideOverlay(true);
RoiManager rm = RoiManager.getInstance();
if (rm!=null) rm.runCommand("show none");
}
void show() {
ImagePlus imp = IJ.getImage();
imp.setHideOverlay(false);
if (imp.getOverlay()==null) {
RoiManager rm = RoiManager.getInstance();
if (rm!=null && rm.getCount()>1) {
if (!IJ.isMacro()) rm.toFront();
rm.runCommand("show all with labels");
}
}
}
void remove() {
ImagePlus imp = WindowManager.getCurrentImage();
if (imp!=null) {
ImageCanvas ic = imp.getCanvas();
if (ic!=null)
ic.setShowAllList(null);
imp.setOverlay(null);
}
}
void flatten() {
ImagePlus imp = IJ.getImage();
if (imp.getStackSize()>1 || imp.getBitDepth()==24) {
Overlay overlay = imp.getOverlay();
Overlay roiManagerOverlay = null;
ImageCanvas ic = imp.getCanvas();
if (ic!=null)
roiManagerOverlay = ic.getShowAllList();
if (overlay==null && roiManagerOverlay==null && !imp.isComposite() && !(IJ.macroRunning()&&imp.getStackSize()==1)) {
IJ.error("Flatten", "Overlay or multi-channel image required");
return;
}
}
int flags = IJ.setupDialog(imp, 0);
if (flags==PlugInFilter.DONE)
return;
else if (flags==PlugInFilter.DOES_STACKS) {
//Added by Marcel Boeglin 2014.01.24
if (!IJ.isJava16()) {
IJ.error("Flatten Stack", "Java 1.6 required to flatten a stack");
return;
}
flattenStack(imp);
if (Recorder.record)
Recorder.recordCall("imp.flattenStack();");
} else {
ImagePlus imp2 = imp.flatten();
imp2.setTitle(WindowManager.getUniqueName(imp.getTitle()));
imp2.show();
if (Recorder.record) // Added by Marcel Boeglin 2014.01.12
Recorder.recordCall("imp2 = imp.flatten();");
}
}
//Marcel Boeglin 2014.01.25
void flattenStack(ImagePlus imp) {
imp.flattenStack();
}
void fromRoiManager() {
ImagePlus imp = IJ.getImage();
RoiManager rm = RoiManager.getInstance2();
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;
}
rm.moveRoisToOverlay(imp);
imp.deleteRoi();
}
void toRoiManager() {
ImagePlus imp = IJ.getImage();
Overlay overlay = imp.getOverlay();
if (overlay==null) {
IJ.error("Overlay required");
return;
}
RoiManager rm = RoiManager.getInstance();
if (rm==null) {
if (Macro.getOptions()!=null && Interpreter.isBatchMode())
rm = Interpreter.getBatchModeRoiManager();
if (rm==null) {
Frame frame = WindowManager.getFrame("ROI Manager");
if (frame==null)
IJ.run("ROI Manager...");
frame = WindowManager.getFrame("ROI Manager");
if (frame==null || !(frame instanceof RoiManager))
return;
rm = (RoiManager)frame;
}
}
if (overlay.size()>=4 && overlay.get(3).getPosition()!=0)
Prefs.showAllSliceOnly = true;
rm.runCommand("reset");
rm.setEditMode(imp, false);
for (int i=0; i1&&defaultRoi.getStrokeColor()!=null)
roi.setStrokeColor(defaultRoi.getStrokeColor());
if (roi.getFillColor()==null)
roi.setFillColor(defaultRoi.getFillColor());
}
boolean points = roi instanceof PointRoi && ((PolygonRoi)roi).getNCoordinates()>1;
if (points) roi.setStrokeColor(Color.red);
roi.setPosition(defaultRoi.getPosition());
RoiProperties rp = new RoiProperties("Overlay Options", roi);
if (!rp.showDialog()) return;
defaultRoi = roi;
}
void list() {
ImagePlus imp = IJ.getImage();
Overlay overlay = imp.getOverlay();
if (overlay!=null)
listRois(overlay.toArray());
}
public static void listRois(Roi[] rois) {
ArrayList list = new ArrayList();
for (int i=0; i © 2015 - 2025 Weber Informatics LLC | Privacy Policy