find contours miss some objects

edit

I use the following code to read through all objects that I segmented from my image which should be ordered in row and columns as semi-circle (because of segmentation and morphological processing for reducing noise):

    Imgproc.Canny(srcImg, srcImg, 50, 150);
    Imgcodecs.imwrite("/mnt/sdcard/DCIM/cannyImg.jpg", srcImg);//check

    List<MatOfPoint> contours = new ArrayList<MatOfPoint>();
    Mat hierarchy = new Mat();
    Imgproc.findContours(srcImg, contours, hierarchy, Imgproc.RETR_EXTERNAL, Imgproc.CHAIN_APPROX_SIMPLE, new Point(0,0));

    //int index = 0;
    //double maximc = Imgproc.contourArea(contours.get(0));
    for (int contourIdx = 1; contourIdx < contours.size(); contourIdx++) {
        double temp;
        temp = Imgproc.contourArea(contours.get(contourIdx));
        if (temp > 100) { 
                           // condition to differentiate between noise and objects
            Mat drawing = Mat.zeros(srcImg.size(), CvType.CV_8UC1);
            Imgproc.drawContours(drawing, contours, contourIdx, new Scalar(255), -1);

            Mat resultMat = new Mat();
            maskImg.copyTo(resultMat, drawing);
            Imgcodecs.imwrite("/mnt/sdcard/DCIM/resultImg" + contourIdx + ".jpg", resultMat);//check
         }   
    }

however, the loop can not read important objects in my image even canny image is correct and can identify all the objects. My questions are: in which order find contours read objects? and also is there another way in Opencv to read through all objects in the image other than find contours? last question i used the size of contours to differentiate between the objects and the noise, so is this Ok or you can suggest other methods.

Attached is the result image and the one with red circles correctly identified while the others which I need not being identified.

Any help is appreciated