void scale(ImageProcessor ip) {
if (newWindow) {
Rectangle r = ip.getRoi();
ImagePlus imp2 = imp.createImagePlus();
imp2.setProcessor(title, ip.resize(newWidth, newHeight));
Calibration cal = imp2.getCalibration();
if (cal.scaled()) {
cal.pixelWidth *= 1.0 / xscale;
cal.pixelHeight *= 1.0 / yscale;
}
imp2.show();
imp.trimProcessor();
imp2.trimProcessor();
imp2.changes = true;
} else {
if (processStack && imp.getStackSize() > 1) {
Undo.reset();
StackProcessor sp = new StackProcessor(imp.getStack(), ip);
sp.scale(xscale, yscale, bgValue);
} else {
ip.snapshot();
Undo.setup(Undo.FILTER, imp);
ip.setSnapshotCopyMode(true);
ip.scale(xscale, yscale);
ip.setSnapshotCopyMode(false);
}
imp.killRoi();
imp.updateAndDraw();
imp.changes = true;
}
}
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 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 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;
Undo.setup(Undo.ROI, imp);
imp.deleteRoi();
Roi roi2 = new EllipseRoi(x1, y1, x2, y2, aspectRatio);
transferProperties(roi, roi2);
imp.setRoi(roi2);
}
void fitSpline() {
Roi roi = imp.getRoi();
if (roi == null) {
noRoi("Spline");
return;
}
int type = roi.getType();
boolean segmentedSelection = type == Roi.POLYGON || type == Roi.POLYLINE;
if (!(segmentedSelection
|| type == Roi.FREEROI
|| type == Roi.TRACED_ROI
|| type == Roi.FREELINE)) {
IJ.error("Spline", "Polygon or polyline selection required");
return;
}
if (roi instanceof EllipseRoi) return;
PolygonRoi p = (PolygonRoi) roi;
Undo.setup(Undo.ROI, imp);
if (!segmentedSelection && p.getNCoordinates() > 3) {
if (p.subPixelResolution()) p = trimFloatPolygon(p, p.getUncalibratedLength());
else p = trimPolygon(p, p.getUncalibratedLength());
}
String options = Macro.getOptions();
if (options != null && options.indexOf("straighten") != -1) p.fitSplineForStraightening();
else if (options != null && options.indexOf("remove") != -1) p.removeSplineFit();
else p.fitSpline();
imp.draw();
LineWidthAdjuster.update();
}
public void run(ImageProcessor ip) {
if (enlarge && gd.wasOKed())
synchronized (this) {
if (!isEnlarged) {
enlargeCanvas();
isEnlarged = true;
}
}
if (isEnlarged) { // enlarging may have made the ImageProcessor invalid, also for the parallel
// threads
int slice = pfr.getSliceNumber();
if (imp.getStackSize() == 1) ip = imp.getProcessor();
else ip = imp.getStack().getProcessor(slice);
}
ip.setInterpolationMethod(interpolationMethod);
if (fillWithBackground) {
Color bgc = Toolbar.getBackgroundColor();
if (bitDepth == 8) ip.setBackgroundValue(ip.getBestIndex(bgc));
else if (bitDepth == 24) ip.setBackgroundValue(bgc.getRGB());
} else ip.setBackgroundValue(0);
ip.rotate(angle);
if (!gd.wasOKed()) drawGridLines(gridLines);
if (isEnlarged && imp.getStackSize() == 1) {
imp.changes = true;
imp.updateAndDraw();
Undo.setup(Undo.COMPOUND_FILTER_DONE, imp);
}
}
void showResults() {
int count = rt.getCounter();
// if (count==0) return;
boolean lastSlice = !processStack || slice == imp.getStackSize();
if ((showChoice == OVERLAY_OUTLINES || showChoice == OVERLAY_MASKS) && slice == 1 && count > 0)
imp.setOverlay(overlay);
else if (outlines != null && lastSlice) {
String title = imp != null ? imp.getTitle() : "Outlines";
String prefix;
if (showChoice == MASKS) prefix = "Mask of ";
else if (showChoice == ROI_MASKS) prefix = "Count Masks of ";
else prefix = "Drawing of ";
outlines.update(drawIP);
outputImage = new ImagePlus(prefix + title, outlines);
if (inSituShow) {
if (imp.getStackSize() == 1) Undo.setup(Undo.TRANSFORM, imp);
imp.setStack(null, outputImage.getStack());
} else if (!hideOutputImage) outputImage.show();
}
if (showResults && !processStack) {
TextPanel tp = IJ.getTextPanel();
if (beginningCount > 0 && tp != null && tp.getLineCount() != count) rt.show("Results");
Analyzer.firstParticle = beginningCount;
Analyzer.lastParticle = Analyzer.getCounter() - 1;
} else Analyzer.firstParticle = Analyzer.lastParticle = 0;
}
private void enlarge(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi != null) {
Undo.setup(Undo.ROI, imp);
roi = (Roi) roi.clone();
(new RoiEnlarger()).run("");
} else noRoi("Enlarge");
}
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);
}
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()));
Undo.setup(Undo.ROI, imp);
imp.setRoi(s1.xor(s2));
}
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);
}
/**
* Execute the plugin functionality: duplicate and scale the given image.
*
* @return an Object[] array with the name and the scaled ImagePlus. Does NOT show the new, image;
* just returns it.
*/
public Object[] exec(
ImagePlus imp, String myMethod, int radius, double par1, double par2, boolean doIwhite) {
// 0 - Check validity of parameters
if (null == imp) return null;
ImageProcessor ip = imp.getProcessor();
int xe = ip.getWidth();
int ye = ip.getHeight();
// int [] data = (ip.getHistogram());
IJ.showStatus("Thresholding...");
long startTime = System.currentTimeMillis();
// 1 Do it
if (imp.getStackSize() == 1) {
ip.snapshot();
Undo.setup(Undo.FILTER, imp);
}
// Apply the selected algorithm
if (myMethod.equals("Bernsen")) {
Bernsen(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("Contrast")) {
Contrast(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("Mean")) {
Mean(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("Median")) {
Median(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("MidGrey")) {
MidGrey(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("Niblack")) {
Niblack(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("Otsu")) {
Otsu(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("Phansalkar")) {
Phansalkar(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("Sauvola")) {
Sauvola(imp, radius, par1, par2, doIwhite);
}
// IJ.showProgress((double)(255-i)/255);
imp.updateAndDraw();
imp.getProcessor().setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
// 2 - Return the threshold and the image
IJ.showStatus("\nDone " + (System.currentTimeMillis() - startTime) / 1000.0);
return new Object[] {imp};
}
void enlargeCanvas() {
imp.unlock();
if (imp.getStackSize() == 1) Undo.setup(Undo.COMPOUND_FILTER, imp);
IJ.run("Select All");
IJ.run("Rotate...", "angle=" + angle);
Roi roi = imp.getRoi();
Rectangle r = roi.getBounds();
if (r.width < imp.getWidth()) r.width = imp.getWidth();
if (r.height < imp.getHeight()) r.height = imp.getHeight();
IJ.showStatus("Rotate: Enlarging...");
IJ.run(
"Canvas Size...",
"width="
+ r.width
+ " height="
+ r.height
+ " position=Center "
+ (fillWithBackground ? "" : "zero"));
IJ.showStatus("Rotating...");
}
void areaToLine(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null || !roi.isArea()) {
IJ.error("Area to Line", "Area selection required");
return;
}
Undo.setup(Undo.ROI, imp);
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);
transferProperties(roi, roi2);
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 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);
}
}
private void makeBand(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null) {
noRoi("Make Band");
return;
}
Roi roiOrig = roi;
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;
int saveType = EDM.getOutputType();
EDM.setOutputType(EDM.BYTE_OVERWRITE);
IJ.run(edm, "Distance Map", "");
EDM.setOutputType(saveType);
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);
Undo.setup(Undo.ROI, imp);
transferProperties(roiOrig, roi2);
imp.setRoi(roi2);
bandSize = n;
}
public void mousePressed(MouseEvent e) {
Undo.reset();
if (!Prefs.noClickToGC) System.gc();
IJ.showStatus(version() + IJ.freeMemory());
if (IJ.debugMode) IJ.log("Windows: " + WindowManager.getWindowCount());
}
/*
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));
}
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(String arg) {
ImagePlus imp = WindowManager.getCurrentImage();
this.imp = imp;
if (imp == null) {
IJ.noImage();
return;
}
if ((1 < imp.getStackSize()) && (imp.getType() == imp.COLOR_256)) {
IJ.error("Stack of color images not supported (use grayscale)");
return;
}
if (1 < imp.getStackSize()) {
if (imp.getStack().isRGB()) {
IJ.error("RGB color images not supported (use grayscale)");
return;
}
}
if (1 < imp.getStackSize()) {
if (imp.getStack().isHSB()) {
IJ.error("HSB color images not supported (use grayscale)");
return;
}
}
if (imp.getType() == imp.COLOR_256) {
IJ.error("Indexed color images not supported (use grayscale)");
return;
}
if (imp.getType() == imp.COLOR_RGB) {
IJ.error("Color images not supported (use grayscale)");
return;
}
differentialsDialog dialog =
new differentialsDialog(IJ.getInstance(), "Differentials", true, operation);
GUI.center(dialog);
dialog.setVisible(true);
cancel = dialog.getCancel();
operation = dialog.getOperation();
dialog.dispose();
if (cancel) {
return;
}
imp.startTiming();
if (1 < imp.getStackSize()) {
if (!(imp.getProcessor().getPixels() instanceof float[])) {
new StackConverter(imp).convertToGray32();
}
} else {
if (!(imp.getProcessor().getPixels() instanceof float[])) {
new ImageConverter(imp).convertToGray32();
}
}
ImageStack stack = imp.getStack();
stackSize = stack.getSize();
Undo.reset();
setupProgressBar();
resetProgressBar();
for (int i = 1; (i <= stackSize); i++) {
ImageProcessor ip = stack.getProcessor(i);
doIt(ip);
imp.getProcessor().resetMinAndMax();
imp.setSlice(i);
imp.updateAndRepaintWindow();
}
imp.getProcessor().resetMinAndMax();
imp.setSlice(1);
imp.updateAndRepaintWindow();
cleanUpProgressBar();
IJ.showTime(imp, imp.getStartTime(), "Differentials: ");
ImageWindow win = imp.getWindow();
if (win != null) {
win.running = false;
}
} /* end run */