public void drawPixels(ImageProcessor ip) {
int saveWidth = ip.getLineWidth();
if (getStrokeWidth() > 1f) ip.setLineWidth((int) Math.round(getStrokeWidth()));
double offset = getOffset(0.5);
if (xSpline != null) {
ip.moveTo(
x + (int) (Math.round(xSpline[0]) + offset), y + (int) Math.round(ySpline[0] + offset));
for (int i = 1; i < splinePoints; i++)
ip.lineTo(
x + (int) (Math.round(xSpline[i]) + offset), y + (int) Math.round(ySpline[i] + offset));
if (type == POLYGON || type == FREEROI || type == TRACED_ROI)
ip.lineTo(
x + (int) (Math.round(xSpline[0]) + offset), y + (int) Math.round(ySpline[0] + offset));
} else if (xpf != null) {
ip.moveTo(x + (int) (Math.round(xpf[0]) + offset), y + (int) Math.round(ypf[0] + offset));
for (int i = 1; i < nPoints; i++)
ip.lineTo(x + (int) (Math.round(xpf[i]) + offset), y + (int) Math.round(ypf[i] + offset));
if (type == POLYGON || type == FREEROI || type == TRACED_ROI)
ip.lineTo(x + (int) (Math.round(xpf[0]) + offset), y + (int) Math.round(ypf[0] + offset));
} else {
ip.moveTo(x + xp[0], y + yp[0]);
for (int i = 1; i < nPoints; i++) ip.lineTo(x + xp[i], y + yp[i]);
if (type == POLYGON || type == FREEROI || type == TRACED_ROI) ip.lineTo(x + xp[0], y + yp[0]);
}
ip.setLineWidth(saveWidth);
updateFullWindow = true;
}
/** Draws an outline of this OvalRoi on the image. */
public void drawPixels(ImageProcessor ip) {
Polygon p = getPolygon();
if (p.npoints > 0) {
int saveWidth = ip.getLineWidth();
if (getStrokeWidth() > 1f) ip.setLineWidth((int) Math.round(getStrokeWidth()));
ip.drawPolygon(p);
ip.setLineWidth(saveWidth);
}
if (Line.getWidth() > 1 || getStrokeWidth() > 1) updateFullWindow = true;
}
void lineWidth() {
int width = (int) IJ.getNumber("Line Width:", Line.getWidth());
if (width == IJ.CANCELED) return;
Line.setWidth(width);
LineWidthAdjuster.update();
ImagePlus imp = WindowManager.getCurrentImage();
if (imp != null && imp.isProcessor()) {
ImageProcessor ip = imp.getProcessor();
ip.setLineWidth(Line.getWidth());
Roi roi = imp.getRoi();
if (roi != null && roi.isLine()) imp.draw();
}
}
public void mousePressed(MouseEvent e) {
// super.mousePressed(e);
ImageProcessor ip = imp.getProcessor();
ip.setLineWidth(1);
if (Toolbar.getToolId() == Toolbar.DROPPER) IJ.setTool(Toolbar.RECTANGLE);
Rectangle flipperRect = new Rectangle(86, 268, 18, 18);
Rectangle resetRect = new Rectangle(86, 294, 18, 18);
Rectangle foreground1Rect = new Rectangle(9, 266, 45, 10);
Rectangle foreground2Rect = new Rectangle(9, 276, 23, 25);
Rectangle background1Rect = new Rectangle(33, 302, 45, 10);
Rectangle background2Rect = new Rectangle(56, 277, 23, 25);
int x = offScreenX(e.getX());
int y = offScreenY(e.getY());
long difference = System.currentTimeMillis() - mouseDownTime;
boolean doubleClick = (difference <= 250);
mouseDownTime = System.currentTimeMillis();
if (flipperRect.contains(x, y)) {
Color c = Toolbar.getBackgroundColor();
Toolbar.setBackgroundColor(Toolbar.getForegroundColor());
Toolbar.setForegroundColor(c);
} else if (resetRect.contains(x, y)) {
Toolbar.setForegroundColor(new Color(0x000000));
Toolbar.setBackgroundColor(new Color(0xffffff));
} else if ((background1Rect.contains(x, y)) || (background2Rect.contains(x, y))) {
background = true;
if (doubleClick) editColor();
((ColorGenerator) ip).refreshForeground();
((ColorGenerator) ip).refreshBackground();
} else if ((foreground1Rect.contains(x, y)) || (foreground2Rect.contains(x, y))) {
background = false;
if (doubleClick) editColor();
((ColorGenerator) ip).refreshBackground();
((ColorGenerator) ip).refreshForeground();
} else {
// IJ.log(" " + difference + " " + doubleClick);
if (doubleClick) editColor();
else {
setDrawingColor(offScreenX(e.getX()), offScreenY(e.getY()), background);
}
}
if (ip instanceof ColorGenerator) {
if (background) {
((ColorGenerator) ip).refreshForeground();
((ColorGenerator) ip).refreshBackground();
} else {
((ColorGenerator) ip).refreshBackground();
((ColorGenerator) ip).refreshForeground();
}
}
}
public void drawInto(ImageProcessor ip, int value, int linewidth, GeneralPath path) {
ip.setValue(value);
ip.setLineWidth(linewidth);
PathIterator it = path.getPathIterator(null);
float[] seg = new float[6];
int px = 0, py = 0;
while (!it.isDone()) {
int l = it.currentSegment(seg);
int x = Math.round(seg[0]);
int y = Math.round(seg[1]);
double d = Math.sqrt((px - x) * (px - x) + (py - y) * (py - y));
if (l == PathIterator.SEG_MOVETO || d > 15) ip.moveTo(x, y);
else ip.lineTo(x, y);
px = x;
py = y;
it.next();
}
}
/**
* Performs particle analysis on the specified ImagePlus and ImageProcessor. Returns false if
* there is an error.
*/
public boolean analyze(ImagePlus imp, ImageProcessor ip) {
if (this.imp == null) this.imp = imp;
showResults = (options & SHOW_RESULTS) != 0;
excludeEdgeParticles = (options & EXCLUDE_EDGE_PARTICLES) != 0;
resetCounter = (options & CLEAR_WORKSHEET) != 0;
showProgress = (options & SHOW_PROGRESS) != 0;
floodFill = (options & INCLUDE_HOLES) == 0;
recordStarts = (options & RECORD_STARTS) != 0;
addToManager = (options & ADD_TO_MANAGER) != 0;
displaySummary = (options & DISPLAY_SUMMARY) != 0;
inSituShow = (options & IN_SITU_SHOW) != 0;
outputImage = null;
ip.snapshot();
ip.setProgressBar(null);
if (Analyzer.isRedirectImage()) {
redirectImp = Analyzer.getRedirectImage(imp);
if (redirectImp == null) return false;
int depth = redirectImp.getStackSize();
if (depth > 1 && depth == imp.getStackSize()) {
ImageStack redirectStack = redirectImp.getStack();
redirectIP = redirectStack.getProcessor(imp.getCurrentSlice());
} else redirectIP = redirectImp.getProcessor();
} else if (imp.getType() == ImagePlus.COLOR_RGB) {
ImagePlus original = (ImagePlus) imp.getProperty("OriginalImage");
if (original != null
&& original.getWidth() == imp.getWidth()
&& original.getHeight() == imp.getHeight()) {
redirectImp = original;
redirectIP = original.getProcessor();
}
}
if (!setThresholdLevels(imp, ip)) return false;
width = ip.getWidth();
height = ip.getHeight();
if (!(showChoice == NOTHING || showChoice == OVERLAY_OUTLINES || showChoice == OVERLAY_MASKS)) {
blackBackground = Prefs.blackBackground && inSituShow;
if (slice == 1) outlines = new ImageStack(width, height);
if (showChoice == ROI_MASKS) drawIP = new ShortProcessor(width, height);
else drawIP = new ByteProcessor(width, height);
drawIP.setLineWidth(lineWidth);
if (showChoice == ROI_MASKS) {
} // Place holder for now...
else if (showChoice == MASKS && !blackBackground) drawIP.invertLut();
else if (showChoice == OUTLINES) {
if (!inSituShow) {
if (customLut == null) makeCustomLut();
drawIP.setColorModel(customLut);
}
drawIP.setFont(new Font("SansSerif", Font.PLAIN, fontSize));
if (fontSize > 12 && inSituShow) drawIP.setAntialiasedText(true);
}
outlines.addSlice(null, drawIP);
if (showChoice == ROI_MASKS || blackBackground) {
drawIP.setColor(Color.black);
drawIP.fill();
drawIP.setColor(Color.white);
} else {
drawIP.setColor(Color.white);
drawIP.fill();
drawIP.setColor(Color.black);
}
}
calibration = redirectImp != null ? redirectImp.getCalibration() : imp.getCalibration();
if (rt == null) {
rt = Analyzer.getResultsTable();
analyzer = new Analyzer(imp);
} else analyzer = new Analyzer(imp, measurements, rt);
if (resetCounter && slice == 1) {
if (!Analyzer.resetCounter()) return false;
}
beginningCount = Analyzer.getCounter();
byte[] pixels = null;
if (ip instanceof ByteProcessor) pixels = (byte[]) ip.getPixels();
if (r == null) {
r = ip.getRoi();
mask = ip.getMask();
if (displaySummary) {
if (mask != null) totalArea = ImageStatistics.getStatistics(ip, AREA, calibration).area;
else totalArea = r.width * calibration.pixelWidth * r.height * calibration.pixelHeight;
}
}
minX = r.x;
maxX = r.x + r.width;
minY = r.y;
maxY = r.y + r.height;
if (r.width < width || r.height < height || mask != null) {
if (!eraseOutsideRoi(ip, r, mask)) return false;
}
int offset;
double value;
int inc = Math.max(r.height / 25, 1);
int mi = 0;
ImageWindow win = imp.getWindow();
if (win != null) win.running = true;
if (measurements == 0) measurements = Analyzer.getMeasurements();
if (showChoice == ELLIPSES) measurements |= ELLIPSE;
measurements &= ~LIMIT; // ignore "Limit to Threshold"
roiNeedsImage =
(measurements & PERIMETER) != 0
|| (measurements & SHAPE_DESCRIPTORS) != 0
|| (measurements & FERET) != 0;
particleCount = 0;
wand = new Wand(ip);
pf = new PolygonFiller();
if (floodFill) {
ImageProcessor ipf = ip.duplicate();
ipf.setValue(fillColor);
ff = new FloodFiller(ipf);
}
roiType = Wand.allPoints() ? Roi.FREEROI : Roi.TRACED_ROI;
for (int y = r.y; y < (r.y + r.height); y++) {
offset = y * width;
for (int x = r.x; x < (r.x + r.width); x++) {
if (pixels != null) value = pixels[offset + x] & 255;
else if (imageType == SHORT) value = ip.getPixel(x, y);
else value = ip.getPixelValue(x, y);
if (value >= level1 && value <= level2) analyzeParticle(x, y, imp, ip);
}
if (showProgress && ((y % inc) == 0)) IJ.showProgress((double) (y - r.y) / r.height);
if (win != null) canceled = !win.running;
if (canceled) {
Macro.abort();
break;
}
}
if (showProgress) IJ.showProgress(1.0);
if (showResults) rt.updateResults();
imp.killRoi();
ip.resetRoi();
ip.reset();
if (displaySummary && IJ.getInstance() != null) updateSliceSummary();
if (addToManager && roiManager != null) roiManager.setEditMode(imp, true);
maxParticleCount = (particleCount > maxParticleCount) ? particleCount : maxParticleCount;
totalCount += particleCount;
if (!canceled) showResults();
return true;
}