/**
* Creates a dialog box, allowing the user to enter the requested width, height, x & y
* coordinates, slice number for a Region Of Interest, option for oval, and option for whether x &
* y coordinates to be centered.
*/
void showDialog() {
Calibration cal = imp.getCalibration();
int digits = 0;
if (scaledUnits && cal.scaled()) digits = 2;
Roi roi = imp.getRoi();
if (roi == null) drawRoi();
GenericDialog gd = new GenericDialog("Specify");
gd.addNumericField("Width:", width, digits);
gd.addNumericField("Height:", height, digits);
gd.addNumericField("X coordinate:", xRoi, digits);
gd.addNumericField("Y coordinate:", yRoi, digits);
if (stackSize > 1) gd.addNumericField("Slice:", iSlice, 0);
gd.addCheckbox("Oval", oval);
gd.addCheckbox("Constrain square/circle", square);
gd.addCheckbox("Centered", centered);
if (cal.scaled()) {
boolean unitsMatch = cal.getXUnit().equals(cal.getYUnit());
String units = unitsMatch ? cal.getUnits() : cal.getXUnit() + " x " + cal.getYUnit();
gd.addCheckbox("Scaled units (" + units + ")", scaledUnits);
}
fields = gd.getNumericFields();
gd.addDialogListener(this);
gd.showDialog();
if (gd.wasCanceled()) {
if (roi == null) imp.deleteRoi();
else // *ALWAYS* restore initial ROI when cancelled
imp.setRoi(roi);
}
}
public void run(String arg) {
imp = WindowManager.getCurrentImage();
if (arg.equals("add")) {
addToRoiManager(imp);
return;
}
if (imp == null) {
IJ.noImage();
return;
}
if (arg.equals("all")) imp.setRoi(0, 0, imp.getWidth(), imp.getHeight());
else if (arg.equals("none")) imp.killRoi();
else if (arg.equals("restore")) imp.restoreRoi();
else if (arg.equals("spline")) fitSpline();
else if (arg.equals("circle")) fitCircle(imp);
else if (arg.equals("ellipse")) createEllipse(imp);
else if (arg.equals("hull")) convexHull(imp);
else if (arg.equals("mask")) createMask(imp);
else if (arg.equals("from")) createSelectionFromMask(imp);
else if (arg.equals("inverse")) invert(imp);
else if (arg.equals("toarea")) lineToArea(imp);
else if (arg.equals("toline")) areaToLine(imp);
else if (arg.equals("properties")) {
setProperties("Properties ", imp.getRoi());
imp.draw();
} else if (arg.equals("band")) makeBand(imp);
else if (arg.equals("tobox")) toBoundingBox(imp);
else runMacro(arg);
}
void createEllipse(ImagePlus imp) {
IJ.showStatus("Fitting ellipse");
Roi roi = imp.getRoi();
if (roi == null) {
noRoi("Fit Ellipse");
return;
}
if (roi.isLine()) {
IJ.error("Fit Ellipse", "\"Fit Ellipse\" does not work with line selections");
return;
}
ImageProcessor ip = imp.getProcessor();
ip.setRoi(roi);
int options = Measurements.CENTROID + Measurements.ELLIPSE;
ImageStatistics stats = ImageStatistics.getStatistics(ip, options, null);
double dx = stats.major * Math.cos(stats.angle / 180.0 * Math.PI) / 2.0;
double dy = -stats.major * Math.sin(stats.angle / 180.0 * Math.PI) / 2.0;
double x1 = stats.xCentroid - dx;
double x2 = stats.xCentroid + dx;
double y1 = stats.yCentroid - dy;
double y2 = stats.yCentroid + dy;
double aspectRatio = stats.minor / stats.major;
imp.killRoi();
imp.setRoi(new EllipseRoi(x1, y1, x2, y2, aspectRatio));
}
void interpolate() {
Roi roi = imp.getRoi();
if (roi == null) {
noRoi("Interpolate");
return;
}
if (roi.getType() == Roi.POINT) return;
if (IJ.isMacro() && Macro.getOptions() == null) Macro.setOptions("interval=1");
GenericDialog gd = new GenericDialog("Interpolate");
gd.addNumericField("Interval:", 1.0, 1, 4, "pixel");
gd.addCheckbox("Smooth", IJ.isMacro() ? false : smooth);
gd.showDialog();
if (gd.wasCanceled()) return;
double interval = gd.getNextNumber();
smooth = gd.getNextBoolean();
Undo.setup(Undo.ROI, imp);
FloatPolygon poly = roi.getInterpolatedPolygon(interval, smooth);
int t = roi.getType();
int type = roi.isLine() ? Roi.FREELINE : Roi.FREEROI;
if (t == Roi.POLYGON && interval > 1.0) type = Roi.POLYGON;
if ((t == Roi.RECTANGLE || t == Roi.OVAL || t == Roi.FREEROI) && interval >= 5.0)
type = Roi.POLYGON;
if ((t == Roi.LINE || t == Roi.FREELINE) && interval >= 5.0) type = Roi.POLYLINE;
if (t == Roi.POLYLINE && interval >= 1.0) type = Roi.POLYLINE;
ImageCanvas ic = imp.getCanvas();
if (poly.npoints <= 150 && ic != null && ic.getMagnification() >= 12.0)
type = roi.isLine() ? Roi.POLYLINE : Roi.POLYGON;
Roi p = new PolygonRoi(poly, type);
if (roi.getStroke() != null) p.setStrokeWidth(roi.getStrokeWidth());
p.setStrokeColor(roi.getStrokeColor());
p.setName(roi.getName());
transferProperties(roi, p);
imp.setRoi(p);
}
void lineToArea(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null || !roi.isLine()) {
IJ.error("Line to Area", "Line selection required");
return;
}
Undo.setup(Undo.ROI, imp);
Roi roi2 = null;
if (roi.getType() == Roi.LINE) {
double width = roi.getStrokeWidth();
if (width <= 1.0) roi.setStrokeWidth(1.0000001);
FloatPolygon p = roi.getFloatPolygon();
roi.setStrokeWidth(width);
roi2 = new PolygonRoi(p, Roi.POLYGON);
roi2.setDrawOffset(roi.getDrawOffset());
} else {
ImageProcessor ip2 = new ByteProcessor(imp.getWidth(), imp.getHeight());
ip2.setColor(255);
roi.drawPixels(ip2);
// new ImagePlus("ip2", ip2.duplicate()).show();
ip2.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
ThresholdToSelection tts = new ThresholdToSelection();
roi2 = tts.convert(ip2);
}
transferProperties(roi, roi2);
roi2.setStrokeWidth(0);
Color c = roi2.getStrokeColor();
if (c != null) // remove any transparency
roi2.setStrokeColor(new Color(c.getRed(), c.getGreen(), c.getBlue()));
imp.setRoi(roi2);
Roi.previousRoi = (Roi) roi.clone();
}
void lineToArea(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null || !roi.isLine()) {
IJ.error("Line to Area", "Line selection required");
return;
}
if (roi.getType() == Roi.LINE && roi.getStrokeWidth() == 1) {
IJ.error("Line to Area", "Straight line width must be > 1");
return;
}
ImageProcessor ip2 = new ByteProcessor(imp.getWidth(), imp.getHeight());
ip2.setColor(255);
if (roi.getType() == Roi.LINE) ip2.fillPolygon(roi.getPolygon());
else {
roi.drawPixels(ip2);
// BufferedImage bi = new BufferedImage(imp.getWidth(), imp.getHeight(),
// BufferedImage.TYPE_BYTE_GRAY);
// Graphics g = bi.getGraphics();
// Roi roi2 = (Roi)roi.clone();
// roi2.setStrokeColor(Color.white);
// roi2.drawOverlay(g);
// ip2 = new ByteProcessor(bi);
}
// new ImagePlus("ip2", ip2.duplicate()).show();
ip2.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
ThresholdToSelection tts = new ThresholdToSelection();
Roi roi2 = tts.convert(ip2);
imp.setRoi(roi2);
Roi.previousRoi = (Roi) roi.clone();
}
void toBoundingBox(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null) {
noRoi("To Bounding Box");
return;
}
Rectangle r = roi.getBounds();
imp.killRoi();
imp.setRoi(new Roi(r.x, r.y, r.width, r.height));
}
void invert(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null || !roi.isArea()) {
IJ.error("Inverse", "Area selection required");
return;
}
ShapeRoi s1, s2;
if (roi instanceof ShapeRoi) s1 = (ShapeRoi) roi;
else s1 = new ShapeRoi(roi);
s2 = new ShapeRoi(new Roi(0, 0, imp.getWidth(), imp.getHeight()));
imp.setRoi(s1.xor(s2));
}
void toBoundingBox(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null) {
noRoi("To Bounding Box");
return;
}
Undo.setup(Undo.ROI, imp);
Rectangle r = roi.getBounds();
imp.deleteRoi();
Roi roi2 = new Roi(r.x, r.y, r.width, r.height);
transferProperties(roi, roi2);
imp.setRoi(roi2);
}
public void run(ImageProcessor ip) {
if (canceled) return;
slice++;
if (imp.getStackSize() > 1 && processStack) imp.setSlice(slice);
if (imp.getType() == ImagePlus.COLOR_RGB) {
ip = (ImageProcessor) imp.getProperty("Mask");
ip.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
}
if (!analyze(imp, ip)) canceled = true;
if (slice == imp.getStackSize()) {
imp.updateAndDraw();
if (saveRoi != null) imp.setRoi(saveRoi);
}
}
void convexHull(ImagePlus imp) {
Roi roi = imp.getRoi();
int type = roi != null ? roi.getType() : -1;
if (!(type == Roi.FREEROI
|| type == Roi.TRACED_ROI
|| type == Roi.POLYGON
|| type == Roi.POINT)) {
IJ.error("Convex Hull", "Polygonal or point selection required");
return;
}
if (roi instanceof EllipseRoi) return;
Polygon p = roi.getConvexHull();
if (p != null) imp.setRoi(new PolygonRoi(p.xpoints, p.ypoints, p.npoints, roi.POLYGON));
}
void lineToArea(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null || !roi.isLine()) {
IJ.error("Line to Area", "Line selection required");
return;
}
ImageProcessor ip2 = new ByteProcessor(imp.getWidth(), imp.getHeight());
ip2.setColor(255);
if (roi.getType() == Roi.LINE && roi.getStrokeWidth() > 1) ip2.fillPolygon(roi.getPolygon());
else roi.drawPixels(ip2);
// new ImagePlus("ip2", ip2.duplicate()).show();
ip2.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
ThresholdToSelection tts = new ThresholdToSelection();
Roi roi2 = tts.convert(ip2);
imp.setRoi(roi2);
Roi.previousRoi = (Roi) roi.clone();
}
PolygonRoi trimPolygon(PolygonRoi roi, double length) {
int[] x = roi.getXCoordinates();
int[] y = roi.getYCoordinates();
int n = roi.getNCoordinates();
x = smooth(x, n);
y = smooth(y, n);
float[] curvature = getCurvature(x, y, n);
Rectangle r = roi.getBounds();
double threshold = rodbard(length);
// IJ.log("trim: "+length+" "+threshold);
double distance = Math.sqrt((x[1] - x[0]) * (x[1] - x[0]) + (y[1] - y[0]) * (y[1] - y[0]));
x[0] += r.x;
y[0] += r.y;
int i2 = 1;
int x1, y1, x2 = 0, y2 = 0;
for (int i = 1; i < n - 1; i++) {
x1 = x[i];
y1 = y[i];
x2 = x[i + 1];
y2 = y[i + 1];
distance += Math.sqrt((x2 - x1) * (x2 - x1) + (y2 - y1) * (y2 - y1)) + 1;
distance += curvature[i] * 2;
if (distance >= threshold) {
x[i2] = x2 + r.x;
y[i2] = y2 + r.y;
i2++;
distance = 0.0;
}
}
int type = roi.getType() == Roi.FREELINE ? Roi.POLYLINE : Roi.POLYGON;
if (type == Roi.POLYLINE && distance > 0.0) {
x[i2] = x2 + r.x;
y[i2] = y2 + r.y;
i2++;
}
PolygonRoi p = new PolygonRoi(x, y, i2, type);
if (roi.getStroke() != null) p.setStrokeWidth(roi.getStrokeWidth());
p.setStrokeColor(roi.getStrokeColor());
p.setName(roi.getName());
imp.setRoi(p);
return p;
}
PolygonRoi trimFloatPolygon(PolygonRoi roi, double length) {
FloatPolygon poly = roi.getFloatPolygon();
float[] x = poly.xpoints;
float[] y = poly.ypoints;
int n = poly.npoints;
x = smooth(x, n);
y = smooth(y, n);
float[] curvature = getCurvature(x, y, n);
double threshold = rodbard(length);
// IJ.log("trim: "+length+" "+threshold);
double distance = Math.sqrt((x[1] - x[0]) * (x[1] - x[0]) + (y[1] - y[0]) * (y[1] - y[0]));
int i2 = 1;
double x1, y1, x2 = 0, y2 = 0;
for (int i = 1; i < n - 1; i++) {
x1 = x[i];
y1 = y[i];
x2 = x[i + 1];
y2 = y[i + 1];
distance += Math.sqrt((x2 - x1) * (x2 - x1) + (y2 - y1) * (y2 - y1)) + 1;
distance += curvature[i] * 2;
if (distance >= threshold) {
x[i2] = (float) x2;
y[i2] = (float) y2;
i2++;
distance = 0.0;
}
}
int type = roi.getType() == Roi.FREELINE ? Roi.POLYLINE : Roi.POLYGON;
if (type == Roi.POLYLINE && distance > 0.0) {
x[i2] = (float) x2;
y[i2] = (float) y2;
i2++;
}
PolygonRoi p = new PolygonRoi(x, y, i2, type);
if (roi.getStroke() != null) p.setStrokeWidth(roi.getStrokeWidth());
p.setStrokeColor(roi.getStrokeColor());
p.setDrawOffset(roi.getDrawOffset());
p.setName(roi.getName());
imp.setRoi(p);
return p;
}
void areaToLine(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null || !roi.isArea()) {
IJ.error("Area to Line", "Area selection required");
return;
}
Polygon p = roi.getPolygon();
if (p == null) return;
int type1 = roi.getType();
if (type1 == Roi.COMPOSITE) {
IJ.error("Area to Line", "Composite selections cannot be converted to lines.");
return;
}
int type2 = Roi.POLYLINE;
if (type1 == Roi.OVAL
|| type1 == Roi.FREEROI
|| type1 == Roi.TRACED_ROI
|| ((roi instanceof PolygonRoi) && ((PolygonRoi) roi).isSplineFit())) type2 = Roi.FREELINE;
Roi roi2 = new PolygonRoi(p.xpoints, p.ypoints, p.npoints, type2);
imp.setRoi(roi2);
}
void runMacro(String arg, ImagePlus imp) {
boolean rotate = arg.equals("rotate");
Roi roi = imp.getRoi();
if (rotate && IJ.macroRunning()) {
String options = Macro.getOptions();
if (options != null
&& (options.indexOf("grid=") != -1 || options.indexOf("interpolat") != -1)) {
IJ.run("Rotate... ", options); // run Image>Transform>Rotate
return;
}
}
if (roi == null) {
noRoi(rotate ? "Rotate" : "Enlarge");
return;
}
double dangle = Tools.parseDouble(angle);
if (Double.isNaN(dangle)) {
dangle = 15;
angle = "" + dangle;
}
if (rotate && (roi instanceof ImageRoi)) {
dangle = IJ.getNumber("Angle (degrees):", dangle);
((ImageRoi) roi).rotate(dangle);
imp.draw();
angle = "" + dangle;
return;
}
Undo.setup(Undo.ROI, imp);
roi = (Roi) roi.clone();
if (rotate) {
String value = IJ.runMacroFile("ij.jar:RotateSelection", angle);
Roi roi2 = imp.getRoi();
transferProperties(roi, roi2);
imp.setRoi(roi2);
if (value != null) angle = value;
} else if (arg.equals("enlarge")) (new RoiEnlarger()).run("");
}
void drawRoi() {
double xPxl = xRoi;
double yPxl = yRoi;
if (centered) {
xPxl -= width / 2;
yPxl -= height / 2;
}
double widthPxl = width;
double heightPxl = height;
Calibration cal = imp.getCalibration();
if (scaledUnits && cal.scaled()) {
xPxl /= cal.pixelWidth;
yPxl /= cal.pixelHeight;
widthPxl /= cal.pixelWidth;
heightPxl /= cal.pixelHeight;
prevPixelWidth = cal.pixelWidth;
}
Roi roi;
if (oval) roi = new OvalRoi(xPxl, yPxl, widthPxl, heightPxl);
else roi = new Roi(xPxl, yPxl, widthPxl, heightPxl);
imp.setRoi(roi);
prevRoi = roi.getBounds();
// prevPixelWidth = cal.pixelWidth;
}
void convexHull(ImagePlus imp) {
Roi roi = imp.getRoi();
int type = roi != null ? roi.getType() : -1;
if (!(type == Roi.FREEROI
|| type == Roi.TRACED_ROI
|| type == Roi.POLYGON
|| type == Roi.POINT)) {
IJ.error("Convex Hull", "Polygonal or point selection required");
return;
}
if (roi instanceof EllipseRoi) return;
// if (roi.subPixelResolution() && roi instanceof PolygonRoi) {
// FloatPolygon p = ((PolygonRoi)roi).getFloatConvexHull();
// if (p!=null)
// imp.setRoi(new PolygonRoi(p.xpoints, p.ypoints, p.npoints, roi.POLYGON));
// } else {
Polygon p = roi.getConvexHull();
if (p != null) {
Undo.setup(Undo.ROI, imp);
Roi roi2 = new PolygonRoi(p.xpoints, p.ypoints, p.npoints, roi.POLYGON);
transferProperties(roi, roi2);
imp.setRoi(roi2);
}
}
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);
}
}
public void run(ImageProcessor ip) {
String[] imageNames = getOpenImageNames();
if (imageNames[0] == "None") {
IJ.error("need at least 2 binary open images");
return;
}
double previousMinOverlap = Prefs.get("BVTB.BinaryFeatureExtractor.minOverlap", 0);
boolean previousCombine = Prefs.get("BVTB.BinaryFeatureExtractor.combine", false);
GenericDialog gd = new GenericDialog("Binary Feature Extractor");
gd.addChoice("Objects image", imageNames, imageNames[0]);
gd.addChoice("Selector image", imageNames, imageNames[1]);
gd.addNumericField("Object_overlap in % (0=off)", previousMinOverlap, 0, 9, "");
gd.addCheckbox("Combine objects and selectors", previousCombine);
gd.addCheckbox("Count output", true);
gd.addCheckbox("Analysis tables", false);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
String objectsImgTitle = gd.getNextChoice();
String selectorsImgTitle = gd.getNextChoice();
double minOverlap = gd.getNextNumber();
boolean combineImages = gd.getNextBoolean();
boolean showCountOutput = gd.getNextBoolean();
boolean showAnalysis = gd.getNextBoolean();
if (gd.invalidNumber() || minOverlap < 0 || minOverlap > 100) {
IJ.error("invalid number");
return;
}
Prefs.set("BVTB.BinaryFeatureExtractor.minOverlap", minOverlap);
Prefs.set("BVTB.BinaryFeatureExtractor.combine", combineImages);
if (objectsImgTitle.equals(selectorsImgTitle)) {
IJ.error("images need to be different");
return;
}
ImagePlus objectsImp = WindowManager.getImage(objectsImgTitle);
ImageProcessor objectsIP = objectsImp.getProcessor();
ImagePlus selectorsImp = WindowManager.getImage(selectorsImgTitle);
ImageProcessor selectorsIP = selectorsImp.getProcessor();
if (!objectsIP.isBinary() || !selectorsIP.isBinary()) {
IJ.error("works with 8-bit binary images only");
return;
}
if ((objectsImp.getWidth() != selectorsImp.getWidth())
|| objectsImp.getHeight() != selectorsImp.getHeight()) {
IJ.error("images need to be of the same size");
return;
}
// close any existing RoiManager before instantiating a new one for this analysis
RoiManager oldRM = RoiManager.getInstance2();
if (oldRM != null) {
oldRM.close();
}
RoiManager objectsRM = new RoiManager(true);
ResultsTable objectsRT = new ResultsTable();
ParticleAnalyzer analyzeObjects =
new ParticleAnalyzer(analyzerOptions, measurementFlags, objectsRT, 0.0, 999999999.9);
analyzeObjects.setRoiManager(objectsRM);
analyzeObjects.analyze(objectsImp);
objectsRM.runCommand("Show None");
int objectNumber = objectsRT.getCounter();
Roi[] objectRoi = objectsRM.getRoisAsArray();
ResultsTable measureSelectorsRT = new ResultsTable();
Analyzer overlapAnalyzer = new Analyzer(selectorsImp, measurementFlags, measureSelectorsRT);
ImagePlus outputImp =
IJ.createImage("output", "8-bit black", objectsImp.getWidth(), objectsImp.getHeight(), 1);
ImageProcessor outputIP = outputImp.getProcessor();
double[] measuredOverlap = new double[objectNumber];
outputIP.setValue(255.0);
for (int o = 0; o < objectNumber; o++) {
selectorsImp.killRoi();
selectorsImp.setRoi(objectRoi[o]);
overlapAnalyzer.measure();
measuredOverlap[o] = measureSelectorsRT.getValue("%Area", o);
if (minOverlap != 0.0 && measuredOverlap[o] >= minOverlap) {
outputIP.fill(objectRoi[o]);
finalCount++;
} else if (minOverlap == 0.0 && measuredOverlap[o] > 0.0) {
outputIP.fill(objectRoi[o]);
finalCount++;
}
}
// measureSelectorsRT.show("Objects");
selectorsImp.killRoi();
RoiManager selectorRM = new RoiManager(true);
ResultsTable selectorRT = new ResultsTable();
ParticleAnalyzer.setRoiManager(selectorRM);
ParticleAnalyzer analyzeSelectors =
new ParticleAnalyzer(analyzerOptions, measurementFlags, selectorRT, 0.0, 999999999.9);
analyzeSelectors.analyze(selectorsImp);
selectorRM.runCommand("Show None");
int selectorNumber = selectorRT.getCounter();
if (combineImages) {
outputImp.updateAndDraw();
Roi[] selectorRoi = selectorRM.getRoisAsArray();
ResultsTable measureObjectsRT = new ResultsTable();
Analyzer selectorAnalyzer = new Analyzer(outputImp, measurementFlags, measureObjectsRT);
double[] selectorOverlap = new double[selectorNumber];
outputIP.setValue(255.0);
for (int s = 0; s < selectorNumber; s++) {
outputImp.killRoi();
outputImp.setRoi(selectorRoi[s]);
selectorAnalyzer.measure();
selectorOverlap[s] = measureObjectsRT.getValue("%Area", s);
if (selectorOverlap[s] > 0.0d) {
outputIP.fill(selectorRoi[s]);
}
}
selectorRoi = null;
selectorAnalyzer = null;
measureObjectsRT = null;
}
// selectorRT.show("Selectors");
outputImp.killRoi();
String outputImageTitle = WindowManager.getUniqueName("Extracted_" + objectsImgTitle);
outputImp.setTitle(outputImageTitle);
outputImp.show();
outputImp.changes = true;
if (showCountOutput) {
String[] openTextWindows = WindowManager.getNonImageTitles();
boolean makeNewTable = true;
for (int w = 0; w < openTextWindows.length; w++) {
if (openTextWindows[w].equals("BFE_Results")) {
makeNewTable = false;
}
}
TextWindow existingCountTable = ResultsTable.getResultsWindow();
if (makeNewTable) {
countTable = new ResultsTable();
countTable.setPrecision(0);
countTable.setValue("Image", 0, outputImageTitle);
countTable.setValue("Objects", 0, objectNumber);
countTable.setValue("Selectors", 0, selectorNumber);
countTable.setValue("Extracted", 0, finalCount);
countTable.show("BFE_Results");
} else {
IJ.renameResults("BFE_Results", "Results");
countTable = ResultsTable.getResultsTable();
countTable.setPrecision(0);
countTable.incrementCounter();
countTable.addValue("Image", outputImageTitle);
countTable.addValue("Objects", objectNumber);
countTable.addValue("Selectors", selectorNumber);
countTable.addValue("Extracted", finalCount);
IJ.renameResults("Results", "BFE_Results");
countTable.show("BFE_Results");
}
}
if (showAnalysis) {
ResultsTable extractedRT = new ResultsTable();
ParticleAnalyzer analyzeExtracted =
new ParticleAnalyzer(
ParticleAnalyzer.CLEAR_WORKSHEET | ParticleAnalyzer.RECORD_STARTS,
measurementFlags,
extractedRT,
0.0,
999999999.9);
analyzeExtracted.analyze(outputImp);
objectsRT.show("Objects");
selectorRT.show("Selectors");
extractedRT.show("Extracted");
} else {
objectsRT = null;
selectorRT = null;
}
objectsRM = null;
measureSelectorsRT = null;
analyzeObjects = null;
overlapAnalyzer = null;
objectRoi = null;
selectorRM = null;
objectsImp.killRoi();
objectsImp.changes = false;
selectorsImp.changes = false;
}
void toBoundingBox(ImagePlus imp) {
Roi roi = imp.getRoi();
Rectangle r = roi.getBounds();
imp.killRoi();
imp.setRoi(new Roi(r.x, r.y, r.width, r.height));
}
private void makeBand(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null) {
noRoi("Make Band");
return;
}
if (!roi.isArea()) {
IJ.error("Make Band", "Area selection required");
return;
}
Calibration cal = imp.getCalibration();
double pixels = bandSize;
double size = pixels * cal.pixelWidth;
int decimalPlaces = 0;
if ((int) size != size) decimalPlaces = 2;
GenericDialog gd = new GenericDialog("Make Band");
gd.addNumericField("Band Size:", size, decimalPlaces, 4, cal.getUnits());
gd.showDialog();
if (gd.wasCanceled()) return;
size = gd.getNextNumber();
if (Double.isNaN(size)) {
IJ.error("Make Band", "invalid number");
return;
}
int n = (int) Math.round(size / cal.pixelWidth);
if (n > 255) {
IJ.error("Make Band", "Cannot make bands wider that 255 pixels");
return;
}
int width = imp.getWidth();
int height = imp.getHeight();
Rectangle r = roi.getBounds();
ImageProcessor ip = roi.getMask();
if (ip == null) {
ip = new ByteProcessor(r.width, r.height);
ip.invert();
}
ImageProcessor mask = new ByteProcessor(width, height);
mask.insert(ip, r.x, r.y);
ImagePlus edm = new ImagePlus("mask", mask);
boolean saveBlackBackground = Prefs.blackBackground;
Prefs.blackBackground = false;
IJ.run(edm, "Distance Map", "");
Prefs.blackBackground = saveBlackBackground;
ip = edm.getProcessor();
ip.setThreshold(0, n, ImageProcessor.NO_LUT_UPDATE);
int xx = -1, yy = -1;
for (int x = r.x; x < r.x + r.width; x++) {
for (int y = r.y; y < r.y + r.height; y++) {
if (ip.getPixel(x, y) < n) {
xx = x;
yy = y;
break;
}
}
if (xx >= 0 || yy >= 0) break;
}
int count = IJ.doWand(edm, xx, yy, 0, null);
if (count <= 0) {
IJ.error("Make Band", "Unable to make band");
return;
}
ShapeRoi roi2 = new ShapeRoi(edm.getRoi());
if (!(roi instanceof ShapeRoi)) roi = new ShapeRoi(roi);
ShapeRoi roi1 = (ShapeRoi) roi;
roi2 = roi2.not(roi1);
imp.setRoi(roi2);
bandSize = n;
}
/*
if selection is closed shape, create a circle with the same area and centroid, otherwise use<br>
the Pratt method to fit a circle to the points that define the line or multi-point selection.<br>
Reference: Pratt V., Direct least-squares fitting of algebraic surfaces", Computer Graphics, Vol. 21, pages 145-152 (1987).<br>
Original code: Nikolai Chernov's MATLAB script for Newton-based Pratt fit.<br>
(http://www.math.uab.edu/~chernov/cl/MATLABcircle.html)<br>
Java version: https://github.com/mdoube/BoneJ/blob/master/src/org/doube/geometry/FitCircle.java<br>
Authors: Nikolai Chernov, Michael Doube, Ved Sharma
*/
void fitCircle(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null) {
noRoi("Fit Circle");
return;
}
if (roi.isArea()) { // create circle with the same area and centroid
Undo.setup(Undo.ROI, imp);
ImageProcessor ip = imp.getProcessor();
ip.setRoi(roi);
ImageStatistics stats =
ImageStatistics.getStatistics(ip, Measurements.AREA + Measurements.CENTROID, null);
double r = Math.sqrt(stats.pixelCount / Math.PI);
imp.deleteRoi();
int d = (int) Math.round(2.0 * r);
Roi roi2 =
new OvalRoi(
(int) Math.round(stats.xCentroid - r), (int) Math.round(stats.yCentroid - r), d, d);
transferProperties(roi, roi2);
imp.setRoi(roi2);
return;
}
Polygon poly = roi.getPolygon();
int n = poly.npoints;
int[] x = poly.xpoints;
int[] y = poly.ypoints;
if (n < 3) {
IJ.error("Fit Circle", "At least 3 points are required to fit a circle.");
return;
}
// calculate point centroid
double sumx = 0, sumy = 0;
for (int i = 0; i < n; i++) {
sumx = sumx + poly.xpoints[i];
sumy = sumy + poly.ypoints[i];
}
double meanx = sumx / n;
double meany = sumy / n;
// calculate moments
double[] X = new double[n], Y = new double[n];
double Mxx = 0, Myy = 0, Mxy = 0, Mxz = 0, Myz = 0, Mzz = 0;
for (int i = 0; i < n; i++) {
X[i] = x[i] - meanx;
Y[i] = y[i] - meany;
double Zi = X[i] * X[i] + Y[i] * Y[i];
Mxy = Mxy + X[i] * Y[i];
Mxx = Mxx + X[i] * X[i];
Myy = Myy + Y[i] * Y[i];
Mxz = Mxz + X[i] * Zi;
Myz = Myz + Y[i] * Zi;
Mzz = Mzz + Zi * Zi;
}
Mxx = Mxx / n;
Myy = Myy / n;
Mxy = Mxy / n;
Mxz = Mxz / n;
Myz = Myz / n;
Mzz = Mzz / n;
// calculate the coefficients of the characteristic polynomial
double Mz = Mxx + Myy;
double Cov_xy = Mxx * Myy - Mxy * Mxy;
double Mxz2 = Mxz * Mxz;
double Myz2 = Myz * Myz;
double A2 = 4 * Cov_xy - 3 * Mz * Mz - Mzz;
double A1 = Mzz * Mz + 4 * Cov_xy * Mz - Mxz2 - Myz2 - Mz * Mz * Mz;
double A0 = Mxz2 * Myy + Myz2 * Mxx - Mzz * Cov_xy - 2 * Mxz * Myz * Mxy + Mz * Mz * Cov_xy;
double A22 = A2 + A2;
double epsilon = 1e-12;
double ynew = 1e+20;
int IterMax = 20;
double xnew = 0;
int iterations = 0;
// Newton's method starting at x=0
for (int iter = 1; iter <= IterMax; iter++) {
iterations = iter;
double yold = ynew;
ynew = A0 + xnew * (A1 + xnew * (A2 + 4. * xnew * xnew));
if (Math.abs(ynew) > Math.abs(yold)) {
if (IJ.debugMode) IJ.log("Fit Circle: wrong direction: |ynew| > |yold|");
xnew = 0;
break;
}
double Dy = A1 + xnew * (A22 + 16 * xnew * xnew);
double xold = xnew;
xnew = xold - ynew / Dy;
if (Math.abs((xnew - xold) / xnew) < epsilon) break;
if (iter >= IterMax) {
if (IJ.debugMode) IJ.log("Fit Circle: will not converge");
xnew = 0;
}
if (xnew < 0) {
if (IJ.debugMode) IJ.log("Fit Circle: negative root: x = " + xnew);
xnew = 0;
}
}
if (IJ.debugMode)
IJ.log("Fit Circle: n=" + n + ", xnew=" + IJ.d2s(xnew, 2) + ", iterations=" + iterations);
// calculate the circle parameters
double DET = xnew * xnew - xnew * Mz + Cov_xy;
double CenterX = (Mxz * (Myy - xnew) - Myz * Mxy) / (2 * DET);
double CenterY = (Myz * (Mxx - xnew) - Mxz * Mxy) / (2 * DET);
double radius = Math.sqrt(CenterX * CenterX + CenterY * CenterY + Mz + 2 * xnew);
if (Double.isNaN(radius)) {
IJ.error("Fit Circle", "Points are collinear.");
return;
}
CenterX = CenterX + meanx;
CenterY = CenterY + meany;
Undo.setup(Undo.ROI, imp);
imp.deleteRoi();
IJ.makeOval(
(int) Math.round(CenterX - radius),
(int) Math.round(CenterY - radius),
(int) Math.round(2 * radius),
(int) Math.round(2 * radius));
}