R/calc_zenith_colrow.R

In rcaiman: CAnopy IMage ANalysis

#' Calculate zenith raster coordinates
#'
#' Calculate zenith raster coordinates from points digitized with the
#' open-source software package ‘ImageJ’. The zenith is the point on the image
#' that represents the zenith when upward-looking photographs are taken with the
#' optical axis vertically aligned.
#'
#' The technique described under the headline ‘Optical center characterization’
#' of the [user manual of the software
#' Can-Eye](https://www6.paca.inrae.fr/can-eye/content/download/3052/30819/version/4/file/CAN_EYE_User_Manual.pdf)
#' can be used to acquire the data for determining the zenith coordinates. This
#' technique was used by \insertCite{Pekin2009;textual}{rcaiman}, among others.
#' Briefly, it consists in drilling a small hole in the cap of the fisheye lens
#' (it must be away from the center of the cap), and taking about ten
#' photographs without removing the cap. The cap must be rotated about 30º
#' before taking each photograph.(**NOTE:**
#' The method implemented here does not support multiple holes).
#'
#' The [point selection tool of ‘ImageJ’
#' software](https://imagej.net/ij/docs/guide/146-19.html#sec:Multi-point-Tool)
#' should be used to manually digitize the white dots and create a CSV file to
#' feed this function. After digitizing the points on the image, use the
#' dropdown menu Analyze>Measure to open the Results window. To obtain the CSV
#' file, use File>Save As...
#'
#' Another method--only valid when enough of the circle perimeter is depicted in
#' the image-- is taking a very bright picture (for example, a picture of the
#' corner of a room with walls painted in light colors) with the lens completely
#' free (do not use any mount). Then, digitize points over the circle perimeter.
#' This was the method used for producing the example file (see Examples). It is
#' worth noting that the perimeter of the circle depicted in a circular
#' hemispherical photograph is not necessarily the horizon.
#'
#' @inheritParams calibrate_lens
#'
#' @references \insertAllCited{}
#'
#' @family Lens Functions
#'
#' @export
#'
#' @return Numeric vector of length two. Raster coordinates of the zenith,
#'   assuming a lens facing up with its optical axis parallel to the vertical
#'   line. It is important to note the difference between the raster coordinates
#'   and the Cartesian coordinates. In the latter,  the vertical axis value
#'   decreases downward, but the opposite is true for the raster coordinates,
#'   which works like a spreadsheet.
#'
#' @examples
#' \dontrun{
#' path <- system.file("external/points_over_perimeter.csv",
#'                     package = "rcaiman")
#' calc_zenith_colrow(path)
#' }
calc_zenith_colrow <- function(path_to_csv) {
  .this_requires_conicfit()
  x <- utils::read.csv(path_to_csv)
  x <- cbind(x$X, x$Y)
  circle <- as.matrix(x) %>%
      conicfit::CircleFitByKasa() %>%
      .[-3]
  names(circle) <- c("col", "row")
  circle
}