strkvis-mri/code/perimetry_helpers.R

# redmont data helper functions
#
# ds 2019-07-05
# ds 2021-03-01, tidied up.

require(tidyverse)
require(jsonlite)

#' get_s_name
#'
#' get the name from the dataframe
get_s_name <- function(d) {
  # theDate <- d$MedmontStudioExportFile$M600ThresholdExam$EntryDate[1]
  n <- tolower(
    paste0(
      d$MedmontStudioExportFile$Patient$LastName, "_",
      d$MedmontStudioExportFile$Patient$FirstName
    )
  )
}

#' convert medmont JSON to data frame
#'
#' returns
#' list(result, the_points, d)
#'
read_medmont <- function(fname) {
  
  # get data
  j <- jsonlite::read_json(fname)
  d <- fromJSON(fname)
  
  # unpack what’s in JSON structure -----------------------------------------
  exam <- d$MedmontStudioExportFile[4]
  test <- exam$M600ThresholdExam$ThresholdTest$Test
  
  # e.g.
  # test$BlindSpot
  
  
  # Now look for the experiment data ----------------------------------------
  
  # test points are inside here
  n_points <- parse_integer(test$TestPoints$elements)
  the_points <- test$TestPoints$ThresholdTestPoint
  
  # exporting to CSV (tidy) style format --------------------------------------
  # this is how two write out a subset to CSV file...
  
  # make sure to take last set of measurements (if it's a list)
  # also length less than 5 (which is the right order of mag for ATTEMPTS, rather than points)
  # if there is only 1 test, a previous version of the check didn't seem to do the right thing/
  if (is_list(the_points) && length(the_points) < 5) {
    the_points <- the_points[[length(the_points)]]
  }
  
  result <- the_points %>%
    mutate(
      ecc = parse_double(Position$Ring),
      pa = parse_double(Position$Meridian),
      pa_rad = pi* pa / 180,
      Value = parse_double(Value)
    ) 
  
}

# plotting function -------------------------------------------------------

plot_medmont <- function(the_points) {
  
  # NB-- the coord_polar step requires setting the starting point for 0 radians / 0 degrees...
  # to be offset from 12 o'clock
  
  the_points %>%
    mutate(
      xcoord = ecc * cos(pa_rad),
      ycoord = ecc * sin(pa_rad)
    ) %>%
    filter(State != "TS_UNTESTED") %>%
    ggplot(aes(x = xcoord, y = ycoord, size = Value, colour=State)) +
    geom_point(alpha = 0.9) +
    coord_fixed() +
    scale_colour_manual(values = c("red", "black", "gray")) + # "TS_SEEN"     "TS_UNTESTED" "TS_NOT_SEEN"
    # coord_polar is kind of broken...
    # https://community.rstudio.com/t/making-coord-polar-behave-like-standard-polar-coordinate-plotting/3762/6
    # coord_polar(theta = "x", start = -pi/4, direction = -1) +
    theme_minimal()
}



# convert - combined function ---------------------------------------------

#' read, make filename, write
#'
convert_medmont <- function(fname) {
  # read the data file
  data_list <- read_medmont(fname)
  # list(result, the_points, d)
  
  # filename from within?
  new_fname <- file.path(dirname(fname), paste0(get_s_name(data_list[[3]]), "-visualField", ".csv"))
  write_csv(data_list[[1]], new_fname)
  print(paste("wrote file:", new_fname))
}