One irritating thing about OpenCV is that as a computer vision library it doesn’t actually offer a lot of routines for dealing with connected components easily and efficiently.

There’s cv::findContours and two versions of cv::connectedComponents — the regular one and one “WithStats”. The trouble is findContours returns polygons when what you often want is raster blob masks. connectedComponents returns a label image but OpenCV doesn’t offer a lot of routines for doing anything with a label images, and further connectedComponentsWithStats is pretty limited in what it will give you. For example, there is no option to be returned a pixel location contained by each connected component. The other issue is that even if you have a pixel location contained by each connected component of interest there is no version of floodFill that takes more than one seed. I really think this kind of floodFill function is something that should be added to OpenCV.

The following assumes single channel input and returns the results of the fills as a separate Mat rather than by modifying the input, but it could easily be extended to be polymorphic and support all the different variations that regular floodFill supports. Basically if we view the input as monochrome blobs, what it is doing is returning the union of all the connected components in the source bitmap that have a non-null intersection with the seed bitmap:

Mat FloodFillFromSeedMask(const Mat& image, const Mat& seeds, uchar src_val = 255, uchar target_val = 255, uchar connectivity = 4)
{
	auto sz = image.size();
	Mat output;
	copyMakeBorder(Mat::zeros(sz, CV_8U), output, 1, 1, 1, 1, BORDER_CONSTANT, target_val);
	for (int y = 0; y < seeds.rows; y++) {
		const uchar* img_ptr = image.ptr<uchar>(y);
		const uchar* seeds_ptr = seeds.ptr<uchar>(y);
		uchar* output_ptr = output.ptr<uchar>(y + 1) + 1;
		for (int x = 0; x < seeds.cols; x++) {
			if ( *img_ptr == src_val && *seeds_ptr > 0 && *output_ptr != target_val)
				floodFill(image, output, Point(x, y), target_val, nullptr, 0, 0, connectivity | (target_val << 8) | FLOODFILL_MASK_ONLY);
			img_ptr++;
			seeds_ptr++;
			output_ptr++;
		}
	}
	return Mat(output, Rect(Point(1, 1), sz));
}

and, yes, not using cv::Mat::at(y,x) is actually noticeably faster than using it and this function is substantially faster than calling findContours, iterating over the polygons returned, painting them, and testing for an intersection with the seed mask. It would be nice to get rid of that call to copyMakeBorder() but there doesn’t seem to be a way to create a bordered Mat directly. Didn’t feel like writing a function like that and then testing that mine is faster than the above…