R/get_bscan.R

In barefootbiology/heyexr: Import, Transform and Visualize Optical Coherence Tomography Volumes in R

#' Parse the b-scan data from an OCT list object
#'
#' Parse the b-scan data from an OCT list object
#'
#' @param oct the OCT list object
#' @param n the ID of the requested b-scan
#'
#' @return a tbl_df containing the b-scan
#'
#' @export
#' @importFrom dplyr tbl_df mutate
#' @importFrom tidyr gather
#' @importFrom magrittr %>%
#' @importFrom reshape2 melt
#' @importFrom tibble as_tibble
#' @importFrom rlang set_names
get_bscan <- function(oct, n=1) {
    #matrix(data=oct$bscan_images[[n]], nrow=oct$header$size_z, byrow=TRUE) %>%
    oct$bscan_images[ , n, ] %>%
        melt() %>%
        as_tibble() %>%
        set_names(c("x", "z", "intensity")) # %>%
        # as.data.frame() %>%
        # cbind_rownames("z") %>%
        # mutate(z = as.numeric(as.character(z))) %>%
        # gather(x, intensity, -z) %>%
        # tbl_df %>%
        # mutate(x = as.numeric(gsub(as.character(x), pattern="V", replacement="")),
        # mutate(intensity = ifelse(intensity == 3.402823e+38, NA, intensity))
}