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;
}
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);
}