Merge branch 'saveterrards' into devel

DESCRIPTION

@@ -54,6 +54,7 @@ Collate:
     'localResults.R'
     'read.R'
     'reexports.R'
+    'saveRDS.R'
     'spatialGraphs.R'
     'subset.R'
     'updateObject.R'

NAMESPACE

@@ -149,6 +149,7 @@ exportMethods(localResultNames)
 exportMethods(localResults)
 exportMethods(mirrorImg)
 exportMethods(rowGraphs)
+exportMethods(saveRDS)
 exportMethods(show)
 exportMethods(spatialGraph)
 exportMethods(spatialGraphNames)
@@ -206,6 +207,7 @@ importFrom(methods,is)
 importFrom(methods,new)
 importFrom(methods,setAs)
 importFrom(methods,setClass)
+importFrom(methods,setClassUnion)
 importFrom(methods,setGeneric)
 importFrom(methods,setMethod)
 importFrom(methods,setReplaceMethod)
@@ -261,7 +263,9 @@ importFrom(stats,setNames)
 importFrom(terra,"ext<-")
 importFrom(terra,ext)
 importFrom(terra,rast)
+importFrom(terra,unwrap)
 importFrom(terra,vect)
+importFrom(terra,wrap)
 importFrom(utils,getFromNamespace)
 importFrom(utils,packageVersion)
 importFrom(utils,read.csv)

R/AllGenerics.R

@@ -268,3 +268,4 @@ setGeneric("unit", function(x) standardGeneric("unit"))
 #' @export
 setGeneric("transposeImg", function(x, ...) standardGeneric("transposeImg"))
 
+if (!isGeneric("saveRDS")) {setGeneric("saveRDS", function (object, file="", ascii=FALSE, version=NULL, compress=TRUE, refhook=NULL) standardGeneric("saveRDS"))}

R/image.R

@@ -31,6 +31,7 @@
 #'   imgSource getImg
 #' @importFrom terra ext ext<-
 #' @importClassesFrom terra SpatRaster
+#' @importFrom methods setClassUnion
 #' @examples
 #' library(SFEData)
 #' sfe <- McKellarMuscleData("small")
@@ -48,10 +49,24 @@
 #' @aliases transposeImg
 NULL
 
+# Not exported by terra
+setClass("PackedSpatRaster",
+         representation (
+             definition = "character",
+             values = "matrix",
+             attributes = "list"
+         ),
+         prototype (
+             attributes = list()
+         )
+)
+
+setClassUnion("GeneralizedSpatRaster", members = c("SpatRaster", "PackedSpatRaster"))
+
 #' @rdname SFE-image
 #' @export
 setClass("SpatRasterImage", contains="VirtualSpatialImage",
-         slots=c(image="SpatRaster"))
+         slots=c(image="GeneralizedSpatRaster"))
 
 #' @rdname SFE-image
 #' @export

R/saveRDS.R

@@ -0,0 +1,42 @@
+#' Save SpatialFeatureExperiment as RDS file
+#'
+#' Saving SFE objects as RDS files is complicated by the \code{SpatRaster} class
+#' of the images. If present, the images need to be wrapped with the \code{\link{wrap}}
+#' function in \code{terra} before serializing the SFE object. Otherwise the
+#' images will be invalid pointers when the RDS is reloaded. If the image does
+#' not fit in memory and its file source is unknown, then it will be written to
+#' a temporary file, which is reloaded when the RDS file is loaded. When an SFE
+#' object with images is read from an RDS file, the images will not be unwrapped
+#' until necessary.
+#'
+#' @inheritParams base::saveRDS
+#' @param object A \code{SpatialFeatureExperiment} object.
+#' @return Invisibly \code{NULL}.
+#' @importFrom terra wrap unwrap
+#' @export
+#' @examples
+#' outdir <- system.file("extdata", package = "SpatialFeatureExperiment")
+#' samples <- file.path(outdir, paste0("sample0", 1:2))
+#' sfe <- read10xVisiumSFE(samples, type = "sparse", data = "filtered")
+#' saveRDS(sfe, "foo.rds")
+#'
+setMethod("saveRDS", "SpatialFeatureExperiment",
+          function(object, file = "", ascii = FALSE, version = NULL,
+                   compress = TRUE, refhook = NULL) {
+              if (is.null(imgData(object)))
+                  base::saveRDS(object, file = file, ascii = ascii,
+                                version = version, compress = compress,
+                                refhook = refhook)
+              else {
+                  for (i in seq_len(nrow(imgData(object)))) {
+                      img <- int_metadata(object)$imgData$data[[i]]
+                      if (is(imgRaster(img), "SpatRaster"))
+                          img@image <- wrap(img@image)
+                      int_metadata(object)$imgData$data[[i]] <- img
+                      # Then I need to add unwrap to functions that use the image
+                  }
+                  base::saveRDS(object, file = file, ascii = ascii,
+                                version = version, compress = compress,
+                                refhook = refhook)
+              }
+          })

tests/testthat/test-saveRDS.R

@@ -0,0 +1,21 @@
+outdir <- system.file("extdata", package = "SpatialFeatureExperiment")
+samples <- file.path(outdir, paste0("sample0", 1:2))
+sfe <- read10xVisiumSFE(samples, type = "sparse", data = "filtered")
+
+test_that("Save SFE with SpatRaster images as RDS", {
+    saveRDS(sfe, "foo.rds")
+    sfe2 <- readRDS("foo.rds")
+    imgs <- imgData(sfe2)$data
+    classes <- vapply(imgs, function(x) class(imgRaster(x)), FUN.VALUE = character(1))
+    expect_true(all(classes == "PackedSpatRaster"))
+    expect_s4_class(sfe2, "SpatialFeatureExperiment")
+    unlink("foo.rds")
+})
+
+test_that("Save SFE without images", {
+    imgData(sfe) <- NULL
+    saveRDS(sfe, "bar.rds")
+    sfe2 <- readRDS("bar.rds")
+    expect_equal(sfe, sfe2)
+    unlink("bar.rds")
+})