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    //applying the transformation
    Imgproc.warpPerspective(inputMat,outputMat,perspectiveTransformation,new Size(dst_width,dst_height));

try this?

    //applying the transformation
    Imgproc.warpPerspective(inputMat,outputMat,perspectiveTransformation,new Size(dst_height,dst_width));

IIRC, android camera does something strange with the orientation.