boolean setThresholdLevels(ImagePlus imp, ImageProcessor ip) {
double t1 = ip.getMinThreshold();
double t2 = ip.getMaxThreshold();
boolean invertedLut = imp.isInvertedLut();
boolean byteImage = ip instanceof ByteProcessor;
if (ip instanceof ShortProcessor) imageType = SHORT;
else if (ip instanceof FloatProcessor) imageType = FLOAT;
else imageType = BYTE;
if (t1 == ImageProcessor.NO_THRESHOLD) {
ImageStatistics stats = imp.getStatistics();
if (imageType != BYTE || (stats.histogram[0] + stats.histogram[255] != stats.pixelCount)) {
IJ.error(
"Particle Analyzer",
"A thresholded image or 8-bit binary image is\n"
+ "required. Threshold levels can be set using\n"
+ "the Image->Adjust->Threshold tool.");
canceled = true;
return false;
}
boolean threshold255 = invertedLut;
if (Prefs.blackBackground) threshold255 = !threshold255;
if (threshold255) {
level1 = 255;
level2 = 255;
fillColor = 64;
} else {
level1 = 0;
level2 = 0;
fillColor = 192;
}
} else {
level1 = t1;
level2 = t2;
if (imageType == BYTE) {
if (level1 > 0) fillColor = 0;
else if (level2 < 255) fillColor = 255;
} else if (imageType == SHORT) {
if (level1 > 0) fillColor = 0;
else if (level2 < 65535) fillColor = 65535;
} else if (imageType == FLOAT) fillColor = -Float.MAX_VALUE;
else return false;
}
imageType2 = imageType;
if (redirectIP != null) {
if (redirectIP instanceof ShortProcessor) imageType2 = SHORT;
else if (redirectIP instanceof FloatProcessor) imageType2 = FLOAT;
else if (redirectIP instanceof ColorProcessor) imageType2 = RGB;
else imageType2 = BYTE;
}
return true;
}
void drawOutline(ImageProcessor ip, Roi roi, int count) {
if (showChoice == OVERLAY_OUTLINES || showChoice == OVERLAY_MASKS) {
if (overlay == null) {
overlay = new Overlay();
overlay.drawLabels(true);
overlay.setLabelFont(new Font("SansSerif", Font.PLAIN, fontSize));
}
Roi roi2 = (Roi) roi.clone();
roi2.setStrokeColor(Color.cyan);
if (lineWidth != 1) roi2.setStrokeWidth(lineWidth);
if (showChoice == OVERLAY_MASKS) roi2.setFillColor(Color.cyan);
overlay.add(roi2);
} else {
Rectangle r = roi.getBounds();
int nPoints = ((PolygonRoi) roi).getNCoordinates();
int[] xp = ((PolygonRoi) roi).getXCoordinates();
int[] yp = ((PolygonRoi) roi).getYCoordinates();
int x = r.x, y = r.y;
if (!inSituShow) ip.setValue(0.0);
ip.moveTo(x + xp[0], y + yp[0]);
for (int i = 1; i < nPoints; i++) ip.lineTo(x + xp[i], y + yp[i]);
ip.lineTo(x + xp[0], y + yp[0]);
if (showChoice != BARE_OUTLINES) {
String s = ResultsTable.d2s(count, 0);
ip.moveTo(r.x + r.width / 2 - ip.getStringWidth(s) / 2, r.y + r.height / 2 + fontSize / 2);
if (!inSituShow) ip.setValue(1.0);
ip.drawString(s);
}
}
}
private String addMean(int column, String line, int start) {
if (start == -1) {
line += "\tNaN";
summaryHdr += "\t" + ResultsTable.getDefaultHeading(column);
} else {
float[] c = column >= 0 ? rt.getColumn(column) : null;
if (c != null) {
ImageProcessor ip = new FloatProcessor(c.length, 1, c, null);
if (ip == null) return line;
ip.setRoi(start, 0, ip.getWidth() - start, 1);
ip = ip.crop();
ImageStatistics stats = new FloatStatistics(ip);
if (stats == null) return line;
line += n(stats.mean);
} else line += "\tNaN";
summaryHdr += "\t" + rt.getColumnHeading(column);
}
return line;
}
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 drawRoiFilledParticle(ImageProcessor ip, Roi roi, ImageProcessor mask, int count) {
int grayLevel = (count < 65535) ? count : 65535;
ip.setValue((double) grayLevel);
ip.setRoi(roi.getBounds());
ip.fill(mask);
}
void drawFilledParticle(ImageProcessor ip, Roi roi, ImageProcessor mask) {
// IJ.write(roi.getBounds()+" "+mask.length);
ip.setRoi(roi.getBounds());
ip.fill(mask);
}
void analyzeParticle(int x, int y, ImagePlus imp, ImageProcessor ip) {
// Wand wand = new Wand(ip);
ImageProcessor ip2 = redirectIP != null ? redirectIP : ip;
wand.autoOutline(x, y, level1, level2, wandMode);
if (wand.npoints == 0) {
IJ.log("wand error: " + x + " " + y);
return;
}
Roi roi = new PolygonRoi(wand.xpoints, wand.ypoints, wand.npoints, roiType);
Rectangle r = roi.getBounds();
if (r.width > 1 && r.height > 1) {
PolygonRoi proi = (PolygonRoi) roi;
pf.setPolygon(proi.getXCoordinates(), proi.getYCoordinates(), proi.getNCoordinates());
ip2.setMask(pf.getMask(r.width, r.height));
if (floodFill) ff.particleAnalyzerFill(x, y, level1, level2, ip2.getMask(), r);
}
ip2.setRoi(r);
ip.setValue(fillColor);
ImageStatistics stats = getStatistics(ip2, measurements, calibration);
boolean include = true;
if (excludeEdgeParticles) {
if (r.x == minX || r.y == minY || r.x + r.width == maxX || r.y + r.height == maxY)
include = false;
if (polygon != null) {
Rectangle bounds = roi.getBounds();
int x1 = bounds.x + wand.xpoints[wand.npoints - 1];
int y1 = bounds.y + wand.ypoints[wand.npoints - 1];
int x2, y2;
for (int i = 0; i < wand.npoints; i++) {
x2 = bounds.x + wand.xpoints[i];
y2 = bounds.y + wand.ypoints[i];
if (!polygon.contains(x2, y2)) {
include = false;
break;
}
if ((x1 == x2 && ip.getPixel(x1, y1 - 1) == fillColor)
|| (y1 == y2 && ip.getPixel(x1 - 1, y1) == fillColor)) {
include = false;
break;
}
x1 = x2;
y1 = y2;
}
}
}
ImageProcessor mask = ip2.getMask();
if (minCircularity > 0.0 || maxCircularity < 1.0) {
double perimeter = roi.getLength();
double circularity =
perimeter == 0.0 ? 0.0 : 4.0 * Math.PI * (stats.pixelCount / (perimeter * perimeter));
if (circularity > 1.0) circularity = 1.0;
// IJ.log(circularity+" "+perimeter+" "+stats.area);
if (circularity < minCircularity || circularity > maxCircularity) include = false;
}
if (stats.pixelCount >= minSize && stats.pixelCount <= maxSize && include) {
particleCount++;
if (roiNeedsImage) roi.setImage(imp);
stats.xstart = x;
stats.ystart = y;
saveResults(stats, roi);
if (showChoice != NOTHING) drawParticle(drawIP, roi, stats, mask);
}
if (redirectIP != null) ip.setRoi(r);
ip.fill(mask);
}
boolean eraseOutsideRoi(ImageProcessor ip, Rectangle r, ImageProcessor mask) {
int width = ip.getWidth();
int height = ip.getHeight();
ip.setRoi(r);
if (excludeEdgeParticles && polygon != null) {
ImageStatistics stats = ImageStatistics.getStatistics(ip, MIN_MAX, null);
if (fillColor >= stats.min && fillColor <= stats.max) {
double replaceColor = level1 - 1.0;
if (replaceColor < 0.0 || replaceColor == fillColor) {
replaceColor = level2 + 1.0;
int maxColor = imageType == BYTE ? 255 : 65535;
if (replaceColor > maxColor || replaceColor == fillColor) {
IJ.error("Particle Analyzer", "Unable to remove edge particles");
return false;
}
}
for (int y = minY; y < maxY; y++) {
for (int x = minX; x < maxX; x++) {
int v = ip.getPixel(x, y);
if (v == fillColor) ip.putPixel(x, y, (int) replaceColor);
}
}
}
}
ip.setValue(fillColor);
if (mask != null) {
mask = mask.duplicate();
mask.invert();
ip.fill(mask);
}
ip.setRoi(0, 0, r.x, height);
ip.fill();
ip.setRoi(r.x, 0, r.width, r.y);
ip.fill();
ip.setRoi(r.x, r.y + r.height, r.width, height - (r.y + r.height));
ip.fill();
ip.setRoi(r.x + r.width, 0, width - (r.x + r.width), height);
ip.fill();
ip.resetRoi();
// IJ.log("erase: "+fillColor+" "+level1+" "+level2+" "+excludeEdgeParticles);
// (new ImagePlus("ip2", ip.duplicate())).show();
return true;
}
/**
* 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;
}
private boolean isThresholdedRGB(ImagePlus imp) {
Object obj = imp.getProperty("Mask");
if (obj == null || !(obj instanceof ImageProcessor)) return false;
ImageProcessor mask = (ImageProcessor) obj;
return mask.getWidth() == imp.getWidth() && mask.getHeight() == imp.getHeight();
}