#' Radiomic Calculation on Lung CTs

#'

#' Calculate individual radiomic features on the whole 3D lung, left and right lungs separately

#'

#' @param img CT scan in ANTs image file format

#' @param mask Mask of CT scan in ANTs image file format

#' @param sides Choose to calculate radiomic features on the right and/or left lungs. Note: Right lung = 1, left lung = 2, non-lung = 0

#' @param featuresFirst First level radiomic features to calculate

#' @param featuresSpatial Spatial radiomic features to calculate

#'

#' @return Values from selected features for both left and right lungs

#' @importFrom ANTsR maskImage

#' @export

radiomics_lung <- function(img,

                          mask,

                          sides = c("right", "left"),

                          featuresFirst = c('mean', 'sd', 'skew', 'kurtosis', 'min', 'q1', 'median', 'q3', 'max','energy', 'rms', 'uniformity', 'entropy'),

                          featuresSpatial = c('mi', 'gc', 'fd')){

  featuresMask <- lapply(sides, function(side){

    if(side == "right"){mv = 1}

    if(side == "left"){mv = 2}

    # Put image in array format and remove non-mask values

    img2 <- as.array(img)

    mask2 <- as.array(mask)

    img2[mask2 != mv] <- NA

    # Calculate features

    features1 <- radiomics_first(img2, featuresFirst)

    features2 <- radiomics_spatial(img2, featuresSpatial)

    return(c(features1, features2))

  })

  names(featuresMask) <- sides

  return(featuresMask)

}