R/read_center_xml.R

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

#' Read "grid center" XML file generated by the Iowa Reference Algorithms
#'
#' Reads the coordinates of the grid center as output by the Iowa Reference
#' Algorithms (XML format).
#'
#' @param center_file path to the XML file containing the grid center coordinates
#'
#' @return a list containing the x and y coordinates of the grid center
#'
#' @export
#' @importFrom magrittr %>%
#' @importFrom xml2 read_xml as_list
#' @importFrom purrr modify_depth map as_vector
#' @importFrom tibble as_tibble tibble
#' @importFrom readr type_convert col_date col_integer col_double col_time cols
#' @importFrom rlang .data
read_center_xml <- function(center_file) {
    # TASK: Add documentation above

    # oct_center_xml = xmlParse(center_file)
    oct_center_xml <- read_xml(center_file)

    parsed_center <-  as_list(oct_center_xml)[[1L]]

    #-------------------------------------------------------------------------------
    update_cols <-
        cols("executable_date" = col_date(format = "%m/%d/%Y"),
             "modification_date" = col_date(format = "%m/%d/%Y"),
             "modification_time" = col_time(format = "%H:%M:%S"),
             "scan_characteristics_size_x" = col_integer(),
             "scan_characteristics_size_y" = col_integer(),
             "scan_characteristics_size_z" = col_integer(),
             "scan_characteristics_voxel_size_x" = col_double(),
             "scan_characteristics_voxel_size_y" = col_double(),
             "scan_characteristics_voxel_size_z" = col_double(),
             "center_x" = col_integer(),
             "center_z" = col_integer()
        )

    header <-
        parsed_center %>%
        delist_singletons() %>%
        list_to_onerow() %>%
        map(as_vector) %>%
        as_tibble() %>%
        type_convert(update_cols) %>%
        mutate(center_x = .data$center_x + 1) %>% # To handle R's 1-based vectors.
        # Rescale the center B-scan coordinate to align with Heidelberg coordinates.
        # (Using the subtracting from size$x automatically adjusts for 1-based coordinates)
        mutate(center_z = .data$scan_characteristics_size_z - .data$center_z)

    header$center_file <- center_file

    #--------------------------------------------------------------------------------

    # Convert from characters to appropriate data types
    parsed_center$center <- parsed_center$center %>%
        modify_depth(2, ~as.integer(.x))

    parsed_center$scan_characteristics$voxel_size[c("x", "y", "z")] <- parsed_center$scan_characteristics$voxel_size[c("x", "y", "z")] %>%
        modify_depth(2, ~as.numeric(.x))

    parsed_center$scan_characteristics$size[c("x", "y", "z")] <- parsed_center$scan_characteristics$size[c("x", "y", "z")] %>%
        modify_depth(2, ~as.numeric(.x))

    # parsed_center[["center"]][["x"]] <-
    #     xmlRoot(oct_center_xml)[["center"]][["x"]] %>%
    #     xmlValue %>% as.numeric()
    # parsed_center[["center"]][["z"]] <-
    #     xmlRoot(oct_center_xml)[["center"]][["z"]] %>%
    #     xmlValue %>% as.numeric()

    # TASK: Parse the rest of the values in the XML file

    parsed_center$center$x <-  parsed_center$center$x[[1]] + 1

    # Rescale the center B-scan coordinate to align with Heidelberg coordinates.
    # (Using the subtracting from size$x automatically adjusts for 1-based coordinates)
    parsed_center$center$z <- parsed_center$scan_characteristics$size$z[[1]] - parsed_center$center$z[[1]]
    #parsed_center$center$z <-  parsed_center$center$z[[1]] + 1

    # NOTE: For the time being, I'm simply adding in the cleanly parsed header tibble to
    # the original output. However, I need to revisit this code in the future and ONLY
    # return the parsed output. That will entail revising a LOT of code that needs the
    # fovea center information.
    parsed_center$header <- header

    return(parsed_center)
}