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I made a simple function that is equivalent to matlab's imfill('holes'). I've not tested it for many cases, but it has worked so far. I'm using it on edge images but it accepts any kind of binary image, like from a thresholding operation.

A hole is no more than a set of pixels that cannot be "reached" when background is filled, so,

void fillEdgeImage(cv::Mat edgesIn, cv::Mat& filledEdgesOut) const
{
    cv::Mat edgesNeg = edgesIn.clone();

    cv::floodFill(edgesNeg, cv::Point(0,0), CV_RGB(255,255,255));
    bitwise_not(edgesNeg, edgesNeg);
    filledEdgesOut = (edgesNeg | edgesIn);

    return;
}

Here is an example result

Regards