/**
* Traces the boundary of the area with pixel values within 'tolerance' of the value of the pixel
* at the starting location. 'tolerance' is in uncalibrated units. 'mode' can be FOUR_CONNECTED or
* EIGHT_CONNECTED. Mode LEGACY_MODE is for compatibility with previous versions of ImageJ;
* ignored if tolerance > 0. Mode bit THRESHOLDED_MODE for internal use only; it is set by
* autoOutline with 'upper' and 'lower' arguments. When successful, npoints>0 and the boundary
* points can be accessed in the public xpoints and ypoints fields.
*/
public void autoOutline(int startX, int startY, double tolerance, int mode) {
if (startX < 0 || startX >= width || startY < 0 || startY >= height) return;
if (fpixels != null && Float.isNaN(getPixel(startX, startY))) return;
exactPixelValue = tolerance == 0;
boolean thresholdMode = (mode & THRESHOLDED_MODE) != 0;
boolean legacyMode = (mode & LEGACY_MODE) != 0 && tolerance == 0;
if (!thresholdMode) {
double startValue = getPixel(startX, startY);
lowerThreshold = (float) (startValue - tolerance);
upperThreshold = (float) (startValue + tolerance);
}
int x = startX;
int y = startY;
int seedX; // the first inside pixel
if (inside(x, y)) { // find a border when coming from inside
seedX = x; // (seedX, startY) is an inside pixel
do {
x++;
} while (inside(x, y));
} else { // find a border when coming from outside (thresholded only)
do {
x++;
if (x >= width) return; // no border found
} while (!inside(x, y));
seedX = x;
}
boolean fourConnected;
if (legacyMode) fourConnected = !thresholdMode && !(isLine(x, y));
else fourConnected = (mode & FOUR_CONNECTED) != 0;
// now, we have a border between (x-1, y) and (x,y)
boolean first = true;
while (true) { // loop until we have not traced an inner hole
boolean insideSelected = traceEdge(x, y, fourConnected);
if (legacyMode) return; // in legacy mode, don't care what we have got
if (insideSelected) { // not an inner hole
if (first) return; // started at seed, so we got it (sucessful)
if (xmin <= seedX) { // possibly the correct particle
Polygon poly = new Polygon(xpoints, ypoints, npoints);
if (poly.contains(seedX, startY)) return; // successful, particle contains seed
}
}
first = false;
// we have traced an inner hole or the wrong particle
if (!inside(x, y))
do {
x++; // traverse the hole
if (x > width) throw new RuntimeException("Wand Malfunction"); // should never happen
} while (!inside(x, y));
do {
x++;
} while (inside(x, y)); // retry here; maybe no inner hole any more
}
}
public boolean contains(int x, int y) {
if (!super.contains(x, y)) return false;
if (xSpline != null) {
FloatPolygon poly = new FloatPolygon(xSpline, ySpline, splinePoints);
return poly.contains(x - this.x, y - this.y);
} else if (xpf != null) {
FloatPolygon poly = new FloatPolygon(xpf, ypf, nPoints);
return poly.contains(x - this.x, y - this.y);
} else {
Polygon poly = new Polygon(xp, yp, nPoints);
return poly.contains(x - this.x, y - this.y);
}
}
void finishPolygon() {
if (xpf != null) {
FloatPolygon poly = new FloatPolygon(xpf, ypf, nPoints);
Rectangle r = poly.getBounds();
x = r.x;
y = r.y;
width = r.width;
height = r.height;
bounds = poly.getFloatBounds();
float xbase = (float) bounds.getX();
float ybase = (float) bounds.getY();
for (int i = 0; i < nPoints; i++) {
xpf[i] -= xbase;
ypf[i] -= ybase;
}
} else {
Polygon poly = new Polygon(xp, yp, nPoints);
Rectangle r = poly.getBounds();
x = r.x;
y = r.y;
width = r.width;
height = r.height;
for (int i = 0; i < nPoints; i++) {
xp[i] = xp[i] - x;
yp[i] = yp[i] - y;
}
bounds = null;
}
if (nPoints < 2
|| (!(type == FREELINE || type == POLYLINE || type == ANGLE)
&& (nPoints < 3 || width == 0 || height == 0))) {
if (imp != null) imp.deleteRoi();
if (type != POINT) return;
}
state = NORMAL;
if (imp != null && !(type == TRACED_ROI)) imp.draw(x - 5, y - 5, width + 10, height + 10);
oldX = x;
oldY = y;
oldWidth = width;
oldHeight = height;
if (Recorder.record
&& userCreated
&& (type == POLYGON
|| type == POLYLINE
|| type == ANGLE
|| (type == POINT && Recorder.scriptMode() && nPoints == 3)))
Recorder.recordRoi(getPolygon(), type);
if (type != POINT) modifyRoi();
LineWidthAdjuster.update();
}
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);
}