R/registerBand.R

In arsilva87/hyperbrick: Accessory Tools for Preprocessing Hyper-Spectral Images

#' Single Band-to-Band Registration (Translation)
#'
#' Hyperspectral image acquisition normaly causes spatial misalignment between
#' the spectral bands (layers) due to both equipment (such as band-to-band
#' recording delay) and external factors (e.g. sensor vibrations). In this case,
#' a geometric correction is necessary for remote sensing applications such
#' as combining/merging spectral bands. This function uses the HOG (Histogram
#' of Oriented Gradient) descriptor in order to find the optimal translation
#' (xy shift) on a 'slave' band to be spatially align with a 'master'
#' (reference) band.
#'
#' @param slave An object of class \code{RasterLayer} (from package
#' [raster]).
#'
#' @param master An object of class \code{RasterLayer} (from package
#' [raster]).
#'
#' @param ncells An integer giving the number of cells to compute the oriented
#' gradients of the HOG descriptor. Default is 24. See [OpenImageR::HOG()].
#'
#' @param orient An integer giving the number of orientations to compute the
#' oriented gradients of the HOG descriptor. Default is 8. See [OpenImageR::HOG()].
#'
#' @details The affine parameters are estimated using a general
#' optimization algorithm. This function only estimates translation parameters.
#' To register bands also with rotation fixes, please check [registerBand3()].
#' But this should be used carefully, as rotation affects the spatial dimensions.
#'
#' @return An object of the same classe as the input \code{slave}, with
#' the fixed extent. An additional attribute called \code{'affine_pars'} is
#' stored, containing the shift in x and y, in the same unit as the spatial
#' extent of the image.
#'
#' @seealso [OpenImageR::HOG()], [registerBrick()], [registerBand3()]
#'
#' @examples
#' # load an image
#' path <- system.file('exdata', 'obory.dat', package = 'hyperbrick')
#' dpath <- system.file('exdata', 'obory_dark.dat', package = 'hyperbrick')
#' im <- buildBrick(path, hFOV = 36.8, vFOV = 36.8, height = 45,
#'                 ref_layer = 35, spectral_feature = 'radiance',
#'                 dark_path = dpath)
#' print(im)
#'
#' # check bands 11 (550 nm) and 35 (670 nm)
#' plot(im[[35]], col = gray.colors(20), asp = 0)
#' plot(im[[11]], add = TRUE, legend = FALSE,
#'     col = adjustcolor(heat.colors(20), 0.3))
#'
#' # register band 11 to band 35
#' new11 <- registerBand(slave = im[[11]], master = im[[35]])
#' plot(im[[35]], col = gray.colors(20), asp = 0)
#' plot(new11, add = TRUE, legend = FALSE,
#'     col = adjustcolor(heat.colors(20), 0.3))
#'
#' # see the xy shift on band 11
#' attr(new11, "affine_pars")
#'
#' @importFrom OpenImageR HOG
#' @importFrom dfoptim nmk
#' @importFrom raster extent crop res shift
#'
#' @aliases registerBand
#'
#' @export
registerBand <- function(slave, master, ncells = 24, orient = 8)
{
   bx <- res(master)[1] * ncol(master)/10
   by <- res(master)[2] * nrow(master)/10
   ex <- extent(master)[]
   pol <- extent(c(ex[1]+bx, ex[2]-bx, ex[3]+by, ex[4]-by))
   r1c <- raster::as.matrix(crop(master, pol))
   hog1 <- HOG(r1c, cells = ncells, orientations = orient)
   fun_sxy <- function(par) {
      sx <- par[1]; sy <- par[2]
      pol2 <- extent(pol[] - c(sx, sx, sy, sy))
      r2c <- raster::as.matrix(crop(slave, pol2))
      hog2 <- HOG(r2c, cells = ncells, orientations = orient)
      dist(rbind(hog1, hog2))[1]
   }
   p <- nmk(c(0, 0), fun_sxy)
   sxy <- c(x = p$par[1], y = p$par[2])
   fixed <- shift(slave, dx = sxy[1], dy = sxy[2])
   attr(fixed, "affine_pars") <- sxy
   return(fixed)
}