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;
}
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;
}
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);
}
