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A renal stone cannot be missed by x-ray and sonography
both. There is a possibility that a small stone has passed down by now, renal stone causes maximum pain when they pass down the urinary passage. If there is no stone, & no symptoms , medicine is not required.
Why do you think you have calcium deficieny? And even if there is some, milk, youghurt, leafy vege's in plenty can compensate for it.