How to eliminate small contours in a binary image?

edit

I will write some other methods to find the largest contour the first method use flooFill to eliminate small regions the second method uses connected componet parameter ( RETR_CCOMP) in findcontours then pass the biggest contour to drawContours with hierarchy

Mat gray = imread(".\\temp\\Image.jpg", IMREAD_GRAYSCALE);
gray = (gray > 200) * 255;          
Mat binarayImage = (gray > 200) * 255;  
vector<vector<Point> >contours;
vector<Vec4i>hierarchy;
int savedContour = -1;
double maxArea = 0.0;   
Mat result1 = binarayImage.clone();
// Find the largest contour
// findContours will "eat" the input image, so clone the binary Mat, we need it later:  
Rect rect;
findContours(binarayImage.clone(), contours, hierarchy, RETR_CCOMP, CHAIN_APPROX_NONE, Point());
for (int i = 0; i < contours.size(); i++)
{
    //ignore holes the following condition for  
    if (hierarchy[i][3] > -1)
        continue;
    double area = contourArea(contours[i]);
    if (area > maxArea)
    {
        if (savedContour >= 0)
            floodFill(result1, contours[savedContour][0], Scalar(0), &rect, 0, 0, 8);
        maxArea = area;
        savedContour = i;
    }
    else
        floodFill(result1, contours[i][0], Scalar(0), &rect, 0, 0, 8);
}

imwrite("c:\\temp\\biggest1.png", result1);//save method 1  
Mat result2 = Mat::zeros(binarayImage.size(), CV_8U);
drawContours(result2, contours, savedContour, Scalar(255), FILLED, 8,hierarchy);
imwrite("c:\\temp\\biggest2.png", result2);//save method 2

you're almost there ! all it needs is to actually apply the mask from drawContours !

(bitwise_and it with your binary image)

Mat result;
vector<vector<Point> >contours;
vector<Vec4i>hierarchy;
int savedContour = -1;
double maxArea = 0.0;
// Find the largest contour
//
//// findContours will "eat" the input image, so clone the binary Mat, we need it later:
//
findContours(binarayImage.clone(), contours, hierarchy, CV_RETR_EXTERNAL, CV_CHAIN_APPROX_SIMPLE, Point());
for (int i = 0; i< contours.size(); i++)
{
    double area = contourArea(contours[i]);
    if (area > maxArea)
    {
        maxArea = area;
        savedContour = i;
    }
}
// Create mask
drawContours(result, contours, savedContour, Scalar(255), CV_FILLED, 8);

// apply the mask:
binarayImage &= result;

When you find contours, you only find the boundaries, and each boundary is a separate contour. So when you eliminate the small ones, you eliminate the small contours inside the large one. You either need to explicitly keep all contours that are inside the large one (use the hierarchy output variable), or use connected components instead.

Connected Components might be closer to what you want. It finds all the blobs of white pixels. You simply filter the ones that have too small an area, and it keeps both the inner and outer boundaries.

Which one is best depends on what exactly you're doing with them, but both should work.