Add as.raster methods for NeuroSlice and NeuroVol

DESCRIPTION

@@ -58,6 +58,7 @@ Collate:
     'searchlight.R'
     'sparse_neurovec.R'
     'spat_filter.R'
+    'as_raster.R'
     'zzz.R'
 RoxygenNote: 7.3.2.9000
 Imports: 

NAMESPACE

@@ -45,6 +45,7 @@ export(as.dense)
 export(as.mask)
 export(as.matrix)
 export(as.sparse)
+export(as.raster)
 export(as_nifti_header)
 export(axes)
 export(bilateral_filter)
@@ -198,6 +199,7 @@ exportMethods(as.mask)
 exportMethods(as.matrix)
 exportMethods(as.numeric)
 exportMethods(as.sparse)
+exportMethods(as.raster)
 exportMethods(axes)
 exportMethods(bounds)
 exportMethods(centroid)

R/all_generic.R

@@ -1450,6 +1450,7 @@ if (!isGeneric("image"))
 #' @param x An object to be converted.
 #' @param ... Additional arguments passed to the conversion methods.
 #' @return A \code{raster} object representing \code{x}.
+#' @export
 #' @rdname as.raster
 if (!isGeneric("as.raster"))
   setGeneric("as.raster", function(x, ...) standardGeneric("as.raster"))

R/as_raster.R

@@ -0,0 +1,32 @@
+#' Convert neuroimaging objects to raster images
+#'
+#' These methods convert \code{NeuroSlice} and \code{NeuroVol} objects
+#' into \code{raster} images that can be displayed with
+#' \code{grid::grid.raster} or base \code{plot}.
+#'
+#' @inheritParams plot,NeuroSlice-method
+#' @param x object to convert.
+#' @param zlevel slice index for \code{NeuroVol} objects. Defaults to the middle slice.
+#' @param ... additional arguments passed to methods
+#' @return A \code{raster} object
+#' @seealso \code{\link{plot,NeuroSlice-method}}, \code{\link{plot,NeuroVol-method}}
+#' @rdname as.raster-methods
+#' @export
+setMethod("as.raster", "NeuroSlice",
+          function(x,
+                   cmap=gray(seq(0,1,length.out=255)),
+                   irange=range(x, na.rm=TRUE), ...){
+            cols <- mapToColors(x, col=cmap, alpha=1,
+                                irange=irange, zero_col="#00000000")
+            grDevices::as.raster(cols)
+          })
+
+#' @rdname as.raster-methods
+#' @export
+setMethod("as.raster", "NeuroVol",
+          function(x, zlevel=ceiling(dim(x)[3]/2),
+                   cmap=gray(seq(0,1,length.out=255)),
+                   irange=range(x, na.rm=TRUE), ...){
+            sl <- slice(x, zlevel=zlevel, along=3)
+            as.raster(sl, cmap=cmap, irange=irange, ...)
+          })

R/neuroslice.R

@@ -178,6 +178,8 @@ setMethod(f="index_to_grid",
 #' @details when `x` is a NeuroSlice object, the plot method returns a \code{ggplot2} object containing the raster visualization of the slice data.
 #'         The plot can be further customized using standard ggplot2 functions.
 #'
+#' @seealso \code{\link{as.raster}}
+#'
 #' @examples
 #' # Create example slice
 #' slice_space <- NeuroSpace(c(100, 100))

R/neurovol.R

@@ -1083,6 +1083,7 @@ setMethod(f="[", signature=signature(x = "SparseNeuroVol", i = "numeric", j = "n
 #' @param alpha the level of alpha transparency
 #' @param bgvol a background volume that serves as an image underlay (currently ignored).
 #' @param bgcmap a color map for backround layer consisting of a vector of colors in hex format (e.g. \code{gray(n=255)})
+#' @seealso \code{\link{as.raster}}
 #' @export
 #' @importFrom graphics plot
 #' @import colorplane

tests/testthat/test-as-raster.R

@@ -0,0 +1,17 @@
+test_that("as.raster works for NeuroSlice", {
+  space <- NeuroSpace(c(10, 10))
+  dat <- matrix(rnorm(100), 10, 10)
+  sl <- NeuroSlice(dat, space)
+  r <- as.raster(sl)
+  expect_s3_class(r, "raster")
+  expect_equal(dim(r), dim(dat))
+})
+
+test_that("as.raster works for NeuroVol", {
+  space <- NeuroSpace(c(10,10,5))
+  dat <- array(rnorm(10*10*5), c(10,10,5))
+  vol <- NeuroVol(dat, space)
+  r <- as.raster(vol, zlevel=1)
+  expect_s3_class(r, "raster")
+  expect_equal(dim(r), dim(dat)[1:2])
+})