#' Calculate Jacobian Determinant Image for the Lungs

#'

#' This function calculates the Jacobian determinant image for the left and right lungs separately.

#'

#' @param right_transformation Transformations for the right lung

#' @param left_transformation Transformations for the left lung

#' @param mask Fixed mask (or standard lung template mask)

#' @param doLog Return the log Jacobian

#' @param geom Use the geometric Jacobian calculation

#' @param relative Returen the relative Jacobian (Jacobian divided by mean Jacobian)

#'

#' @return Jacobian Image

#' @importFrom ANTsR createJacobianDeterminantImage maskImage

#'

#' @export

jacobian_lung = function(

  right_transformation,

  left_transformation,

  mask,

  doLog = TRUE,

  geom = FALSE,

  relative = TRUE

) {

  # Create separate left and right masks

  right = mask == 1

  left = mask == 2

  # Create Jacobian Determinant Image

  jacob_right <- createJacobianDeterminantImage(domainImg = mask,

                                          tx = right_transformation,

                                          doLog = doLog,

                                          geom = FALSE)

  jacob_right <- maskImage(jacob_right, right)

  jacob_left <- createJacobianDeterminantImage(domainImg = mask,

                                                tx = left_transformation,

                                                doLog = doLog,

                                                geom = FALSE)

  jacob_left <- maskImage(jacob_left, left)

  # Put images together

  jacob = jacob_right + jacob_left

  if(relative){

    jacob_right_relative <- jacob_right/mean(jacob_right)

    jacob_left_relative <- jacob_left/mean(jacob_left)

    jacob_relative <- jacob_right_relative + jacob_left_relative

    mylist = list(jacob = jacob,

                  jacob_relative = jacob_relative)

  }else{

    mylist = jacob

  }

  return(mylist)

}