/**
* Returns a ROI that contains the point.
*
* @param coordenadas point
* @return Roi that contains the point
*/
public int getRoi(Point coordenadas) {
Roi roi;
if (arrayRois != null) {
for (int i = 0; i < arrayRois.length; i++) {
roi = arrayRois[i];
if (roi.contains(coordenadas.x, coordenadas.y)) {
return i;
}
}
}
return -1;
}
/*
* Searches the x and y coordinate arrays in a wand object to see if they
* contain the values provided as parameters
*
* NOTE: does not account for if the given coordinates represent the same
* point only if each array contains the specified coordinate.
*
* returns true if both points are found in the arrays, otherwise returns
* false
*/
public boolean wandContains(Roi region, int x, int y) {
return region.contains(x, y);
}
void labelParticles(
ImageProcessor ipBinary,
ImageProcessor ipRaw,
int nFrame,
double dPixelSize_,
int nAreaCut,
double dPSFsigma_,
Overlay SpotsPositions__,
boolean bShow,
Roi RoiAct) {
int width = ipBinary.getWidth();
int height = ipBinary.getHeight();
int dBorder; // radius in pixels around center point to fit Gaussian
int nArea;
int i, j;
double dVal, dInt;
double dIMax, dIMin;
double xCentroid, yCentroid;
boolean bBorder;
boolean bInRoi;
int lab = 1;
int[] pos;
Stack<int[]> sstack = new Stack<int[]>();
int[][] label = new int[width][height];
OvalRoi spotROI;
dBorder = (int) (dPSFsigma_ * DOMConstants.FITRADIUS);
for (int r = 1; r < width - 1; r++)
for (int c = 1; c < height - 1; c++) {
if (ipBinary.getPixel(r, c) == 0.0) continue;
if (label[r][c] > 0.0) continue;
/* encountered unlabeled foreground pixel at position r, c */
/* it means it is a new spot! */
/* push the position in the stack and assign label */
sstack.push(new int[] {r, c});
label[r][c] = lab;
nArea = 0;
dIMax = -1000;
xCentroid = 0;
yCentroid = 0;
// xMax = 0; yMax = 0;
dInt = 0;
bBorder = false;
/* start the float fill */
while (!sstack.isEmpty()) {
pos = (int[]) sstack.pop();
i = pos[0];
j = pos[1];
// remove all spots at border
if (i == 0 || j == 0 || i == (width - 1) || j == (height - 1)) bBorder = true;
nArea++;
dVal = ipRaw.getPixel(i, j);
if (dVal > dIMax) dIMax = dVal;
dInt += dVal;
xCentroid += dVal * i;
yCentroid += dVal * j;
if (ipBinary.getPixel(i - 1, j - 1) > 0 && label[i - 1][j - 1] == 0) {
sstack.push(new int[] {i - 1, j - 1});
label[i - 1][j - 1] = lab;
}
if (ipBinary.getPixel(i - 1, j) > 0 && label[i - 1][j] == 0) {
sstack.push(new int[] {i - 1, j});
label[i - 1][j] = lab;
}
if (ipBinary.getPixel(i - 1, j + 1) > 0 && label[i - 1][j + 1] == 0) {
sstack.push(new int[] {i - 1, j + 1});
label[i - 1][j + 1] = lab;
}
if (ipBinary.getPixel(i, j - 1) > 0 && label[i][j - 1] == 0) {
sstack.push(new int[] {i, j - 1});
label[i][j - 1] = lab;
}
if (ipBinary.getPixel(i, j + 1) > 0 && label[i][j + 1] == 0) {
sstack.push(new int[] {i, j + 1});
label[i][j + 1] = lab;
}
if (ipBinary.getPixel(i + 1, j - 1) > 0 && label[i + 1][j - 1] == 0) {
sstack.push(new int[] {i + 1, j - 1});
label[i + 1][j - 1] = lab;
}
if (ipBinary.getPixel(i + 1, j) > 0 && label[i + 1][j] == 0) {
sstack.push(new int[] {i + 1, j});
label[i + 1][j] = lab;
}
if (ipBinary.getPixel(i + 1, j + 1) > 0 && label[i + 1][j + 1] == 0) {
sstack.push(new int[] {i + 1, j + 1});
label[i + 1][j + 1] = lab;
}
} /* end while */
if (!bBorder && nArea > nAreaCut) {
xCentroid /= dInt;
yCentroid /= dInt;
if ((xCentroid > dBorder)
&& (yCentroid > dBorder)
&& (xCentroid < (width - 1 - dBorder))
&& (yCentroid < (height - 1 - dBorder))) {
bInRoi = true;
if (RoiAct != null) {
if (!RoiAct.contains((int) xCentroid, (int) yCentroid)) bInRoi = false;
}
if (bInRoi) {
// find minimum value around peak position
dIMin = 1000000;
// nCount = 0;
for (i = (int) (Math.round(xCentroid) - dBorder);
i <= Math.round(xCentroid) + dBorder;
i++)
for (j = (int) (Math.round(yCentroid) - dBorder);
j <= Math.round(yCentroid) + dBorder;
j++) {
dVal = ipRaw.getPixel(i, j);
if (dVal < dIMin) dIMin = dVal;
}
ptable_lock.lock();
ptable.incrementCounter();
ptable.addValue("Frame Number", nFrame + 1);
ptable.addValue("X_centroid_(px)", xCentroid);
ptable.addValue("Y_centroid_(px)", yCentroid);
ptable.addValue("MaxInt", dIMax);
ptable.addValue("MinInt", dIMin);
ptable_lock.unlock();
if (bShow) {
spotROI =
new OvalRoi(
0.5 + xCentroid - 2 * dPSFsigma_,
0.5 + yCentroid - 2 * dPSFsigma_,
4.0 * dPSFsigma_,
4.0 * dPSFsigma_);
spotROI.setStrokeColor(Color.yellow);
spotROI.setPosition(nFrame + 1);
SpotsPositions__.add(spotROI);
}
}
}
}
lab++;
} // end for cycle
return; // label ;
}
