Unwrap SpatRaster images in imgRaster

R/geometry_operation.R

@@ -479,7 +479,7 @@ setMethod("bbox", "SpatialFeatureExperiment", function(sfe, sample_id = NULL) {
     if (nrow(imgData(sfe))) {
         inds <- imgData(sfe)$sample_id == sample_id
         new_imgs <- lapply(imgData(sfe)$data[inds], function(img) {
-            img_new <- img_fun(img@image, ...)
+            img_new <- img_fun(imgRaster(img), ...)
             if (shift_img)
                 img_new <- terra::shift(img_new, dx = add[1], dy = add[2])
             new("SpatRasterImage", image = img_new)
@@ -536,7 +536,7 @@ transpose <- function(sfe, sample_id = "all") {
         m <- matrix(c(0,-1,-1,0), ncol = 2)
         bboxes <- lapply(sample_id, function(s) {
             # Assume that all images of the same sample have the same extent
-            img <- imgData(sfe)$data[[which(imgData(sfe)$sample_id == s)[1]]]@image
+            img <- imgRaster(imgData(sfe)$data[[which(imgData(sfe)$sample_id == s)[1]]])
             as.vector(ext(img))
         })
         bboxes <- do.call(cbind, bboxes)
@@ -571,7 +571,7 @@ mirror <- function(sfe, sample_id = "all",
     if (nrow(imgData(sfe))) {
         bboxes <- lapply(sample_id, function(s) {
             # Assume that all images of the same sample have the same extent
-            img <- imgData(sfe)$data[[which(imgData(sfe)$sample_id == s)[1]]]@image
+            img <- imgRaster(imgData(sfe)$data[[which(imgData(sfe)$sample_id == s)[1]]])
             as.vector(ext(img))
         })
         bboxes <- do.call(cbind, bboxes)

R/image.R

@@ -133,15 +133,15 @@ setMethod("addImg", "SpatialFeatureExperiment",
 #' @export
 setMethod("transposeImg", "SpatRasterImage",
           function(x) {
-              x@image <- terra::trans(x@image)
+              x@image <- terra::trans(imgRaster(x))
               x
           })
 
 #' @rdname SFE-image
 #' @export
 setMethod("mirrorImg", "SpatRasterImage",
           function(x, direction = "vertical") {
-              x@image <- terra::flip(x@image, direction = direction)
+              x@image <- terra::flip(imgRaster(x), direction = direction)
               x
           })
 
@@ -175,14 +175,18 @@ setMethod("mirrorImg", "SpatialFeatureExperiment",
 
 #' @rdname SFE-image
 #' @export
-setMethod("imgRaster", "SpatRasterImage", function(x) x@image)
+setMethod("imgRaster", "SpatRasterImage", function(x) {
+    if (is(x@image, "PackedSpatRaster")) unwrap(x@image)
+    else x@image
+})
 
 #' @rdname SFE-image
 #' @export
+#' @importFrom terra sources
 setMethod("imgSource",
           "SpatRasterImage",
           function(x) {
-              NA_character_
+              sources(imgRaster(x))
           })
 
 .crop_imgs <- function(x, bboxes) {
@@ -197,7 +201,7 @@ setMethod("imgSource",
             img_data <- imgData(x)$data[imgData(x)$sample_id == s]
             bbox_use <- ext(bboxes[c("xmin", "xmax", "ymin", "ymax"),s])
             lapply(img_data, function(img) {
-                new("SpatRasterImage", image = terra::crop(img@image, bbox_use, snap = "out"))
+                new("SpatRasterImage", image = terra::crop(imgRaster(img), bbox_use, snap = "out"))
             })
         })
         new_imgs <- unlist(new_imgs, recursive = FALSE)

R/saveRDS.R

@@ -30,10 +30,9 @@ setMethod("saveRDS", "SpatialFeatureExperiment",
               else {
                   for (i in seq_len(nrow(imgData(object)))) {
                       img <- int_metadata(object)$imgData$data[[i]]
-                      if (is(imgRaster(img), "SpatRaster"))
+                      if (is(img@image, "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,

tests/testthat/test-coerce.R

@@ -44,7 +44,7 @@ test_that("Convert SPE to SFE, loaded images", {
     expect_equal(v1, v2)
 
     bbox <- st_bbox(centroids(sfe))
-    bbox_img <- as.vector(ext(img2@image)) # That the image is properly scaled
+    bbox_img <- as.vector(ext(imgRaster(img2))) # That the image is properly scaled
     diffs1 <- bbox[3:4] - bbox[1:2]
     diffs2 <- bbox_img[c(2,4)] - bbox_img[c(1,3)]
     expect_true(all(diffs1 / diffs2 > (1-1/min(dim(img1)))))
@@ -64,7 +64,7 @@ test_that("Convert SPE to SFE, stored images", {
     expect_equal(v1, v2)
 
     bbox <- st_bbox(centroids(sfe))
-    bbox_img <- as.vector(ext(img2@image))
+    bbox_img <- as.vector(ext(imgRaster(img2)))
     diffs1 <- bbox[3:4] - bbox[1:2]
     diffs2 <- bbox_img[c(2,4)] - bbox_img[c(1,3)]
     expect_true(all(diffs1 / diffs2 > (1-1/min(dim(img1)))))

tests/testthat/test-geometry_operation.R

@@ -288,7 +288,7 @@ sfe <- read10xVisiumSFE("ob")
 test_that("Image is shifted after removing empty space", {
     sfe2 <- removeEmptySpace(sfe)
     cg <- df2sf(spatialCoords(sfe2), spatialCoordsNames(sfe2))
-    img <- getImg(sfe2)@image
+    img <- imgRaster(getImg(sfe2))
     v <- terra::extract(terra::mean(img), cg)
     nCounts <- Matrix::colSums(counts(sfe2))
     expect_true(abs(cor(nCounts, v$mean)) > 0.4)
@@ -306,7 +306,7 @@ test_that("Image is cropped after cropping SFE object", {
         st_bbox() |> st_as_sfc()
     sfe2 <- SpatialFeatureExperiment::crop(sfe, bbox_use)
     cg <- df2sf(spatialCoords(sfe2), spatialCoordsNames(sfe2))
-    img <- getImg(sfe2)@image
+    img <- imgRaster(getImg(sfe2))
     v <- terra::extract(terra::mean(img), cg)
     nCounts <- Matrix::colSums(counts(sfe2))
     expect_true(abs(cor(nCounts, v$mean, use = "complete.obs")) > 0.4)
@@ -319,7 +319,7 @@ test_that("Image is cropped after cropping SFE object", {
 test_that("Transpose SFE object with image", {
     sfe2 <- transpose(sfe)
     cg <- df2sf(spatialCoords(sfe2), spatialCoordsNames(sfe2))
-    img <- getImg(sfe2)@image
+    img <- imgRaster(getImg(sfe2))
     v <- terra::extract(terra::mean(img), cg)
     nCounts <- Matrix::colSums(counts(sfe2))
     expect_true(abs(cor(nCounts, v$mean)) > 0.4)
@@ -332,7 +332,7 @@ test_that("Transpose SFE object with image, after cropping image", {
     sfe <- sfe[,sfe$in_tissue]
     sfe2 <- transpose(sfe)
     cg <- df2sf(spatialCoords(sfe2), spatialCoordsNames(sfe2))
-    img <- getImg(sfe2)@image
+    img <- imgRaster(getImg(sfe2))
     v <- terra::extract(terra::mean(img), cg)
     nCounts <- Matrix::colSums(counts(sfe2))
     expect_true(abs(cor(nCounts, v$mean)) > 0.4)
@@ -344,7 +344,7 @@ test_that("Transpose SFE object with image, after cropping image", {
 test_that("Mirror SFE object with image, vertical", {
     sfe2 <- mirror(sfe, direction = "vertical")
     cg <- df2sf(spatialCoords(sfe2), spatialCoordsNames(sfe2))
-    img <- getImg(sfe2)@image
+    img <- imgRaster(getImg(sfe2))
     v <- terra::extract(terra::mean(img), cg)
     nCounts <- Matrix::colSums(counts(sfe2))
     expect_true(abs(cor(nCounts, v$mean)) > 0.4)
@@ -356,7 +356,7 @@ test_that("Mirror SFE object with image, vertical", {
 test_that("Mirror SFE object with image, horizontal", {
     sfe2 <- mirror(sfe, direction = "horizontal")
     cg <- df2sf(spatialCoords(sfe2), spatialCoordsNames(sfe2))
-    img <- getImg(sfe2)@image
+    img <- imgRaster(getImg(sfe2))
     v <- terra::extract(terra::mean(img), cg)
     nCounts <- Matrix::colSums(counts(sfe2))
     expect_true(abs(cor(nCounts, v$mean)) > 0.4)

tests/testthat/test-image.R

@@ -31,11 +31,11 @@ test_that("transposeImg", {
     # SpatRasterImage method
     img_t <- transposeImg(img)
     expect_s4_class(img_t, "SpatRasterImage")
-    expect_equal(dim(img@image)[1:2], dim(img_t@image)[2:1])
+    expect_equal(dim(imgRaster(img))[1:2], dim(imgRaster(img_t))[2:1])
     # SFE method
     sfe <- transposeImg(sfe, sample_id = "Vis5A", image_id = "lowres")
     img_t2 <- getImg(sfe, sample_id = "Vis5A", image_id = "lowres")
-    expect_equal(dim(img@image)[1:2], dim(img_t2@image)[2:1])
+    expect_equal(dim(imgRaster(img))[1:2], dim(imgRaster(img_t2))[2:1])
 })
 
 test_that("mirrorImg", {
@@ -44,14 +44,14 @@ test_that("mirrorImg", {
     img <- getImg(sfe)
     # SpatRasterImage method
     img_m <- mirrorImg(img)
-    mat1 <- terra::as.array(terra::mean(img@image))[,,1]
-    mat2 <- terra::as.array(terra::mean(img_m@image))[,,1]
+    mat1 <- terra::as.array(terra::mean(imgRaster(img)))[,,1]
+    mat2 <- terra::as.array(terra::mean(imgRaster(img_m)))[,,1]
     mat2_rev <- apply(mat2, 2, rev)
     expect_equal(mat1, mat2_rev)
     # SFE method
     sfe <- mirrorImg(sfe, sample_id = "Vis5A", image_id = "lowres")
     img_m2 <- getImg(sfe)
-    mat3 <- terra::as.array(terra::mean(img_m2@image))[,,1]
+    mat3 <- terra::as.array(terra::mean(imgRaster(img_m2)))[,,1]
     mat3_rev <- apply(mat3, 2, rev)
     expect_equal(mat1, mat3_rev)
 })
@@ -63,6 +63,14 @@ test_that("imgRaster, trivial", {
     expect_s4_class(img, "SpatRaster")
 })
 
+test_that("imgRaster, loaded from RDS", {
+    saveRDS(sfe, "baz.rds")
+    sfe_read <- readRDS("baz.rds")
+    img <- imgRaster(getImg(sfe))
+    expect_s4_class(img, "SpatRaster")
+    unlink("baz.rds")
+})
+
 test_that("imgSource, trivial", {
-    expect_true(is.na(imgSource(getImg(sfe))))
+    expect_type(imgSource(getImg(sfe)), "character")
 })

tests/testthat/test-read.R

@@ -79,12 +79,12 @@ test_that("Image is properly aligned in pixel space", {
     cg <- spotPoly(sfe)
     cg$nCounts <- Matrix::colSums(counts(sfe))
     cg$geometry <- st_centroid(cg$geometry)
-    img_lo <- getImg(sfe, image_id = "lowres")@image
+    img_lo <- getImg(sfe, image_id = "lowres") |> imgRaster()
     img_lo <- terra::mean(img_lo)
     v_lo <- terra::extract(img_lo, cg)
     # This test only works for this tissue for filtered data
     expect_true(abs(cor(cg$nCounts, v_lo$mean)) > 0.4)
-    img_hi <- getImg(sfe, image_id = "hires")@image
+    img_hi <- getImg(sfe, image_id = "hires") |> imgRaster()
     img_hi <- terra::mean(img_hi)
     v_hi <- terra::extract(img_hi, cg)
     expect_true(abs(cor(cg$nCounts, v_hi$mean)) > 0.4)
@@ -108,11 +108,11 @@ test_that("Image is properly aligned in micron space", {
     cg <- spotPoly(sfe)
     cg$nCounts <- Matrix::colSums(counts(sfe))
     cg$geometry <- st_centroid(cg$geometry)
-    img_lo <- getImg(sfe, image_id = "lowres")@image
+    img_lo <- getImg(sfe, image_id = "lowres") |> imgRaster()
     img_lo <- terra::mean(img_lo)
     v_lo <- terra::extract(img_lo, cg)
     expect_true(abs(cor(cg$nCounts, v_lo$mean)) > 0.4)
-    img_hi <- getImg(sfe, image_id = "hires")@image
+    img_hi <- getImg(sfe, image_id = "hires") |> imgRaster()
     img_hi <- terra::mean(img_hi)
     v_hi <- terra::extract(img_hi, cg)
     expect_true(abs(cor(cg$nCounts, v_hi$mean)) > 0.4)
@@ -142,7 +142,7 @@ test_that("readVizgen flip geometry, use cellpose", {
                       flip = "geometry", min_area = 15)
     expect_equal(unit(sfe), "micron")
     expect_equal(imgData(sfe)$image_id, "PolyT")
-    img <- getImg(sfe)@image
+    img <- imgRaster(getImg(sfe))
     cg <- SpatialFeatureExperiment::centroids(sfe)
     v <- terra::extract(img, cg)
     nCounts <- Matrix::colSums(counts(sfe))
@@ -162,7 +162,7 @@ test_that("readVizgen flip geometry, don't use cellpose", {
     sfe <- readVizgen(dir_use, z = 0L, use_cellpose = FALSE, image = "PolyT",
                       flip = "geometry")
     expect_equal(unit(sfe), "micron")
-    img <- getImg(sfe)@image
+    img <- imgRaster(getImg(sfe))
     cg <- SpatialFeatureExperiment::centroids(sfe)
     v <- terra::extract(img, cg)
     nCounts <- Matrix::colSums(counts(sfe))
@@ -177,7 +177,7 @@ test_that("readVizgen flip image", {
     sfe <- readVizgen(dir_use, z = 0L, use_cellpose = TRUE, image = "PolyT",
                       flip = "image")
     expect_equal(unit(sfe), "micron")
-    img <- getImg(sfe)@image
+    img <- imgRaster(getImg(sfe))
     cg <- SpatialFeatureExperiment::centroids(sfe)
     v <- terra::extract(img, cg)
     nCounts <- Matrix::colSums(counts(sfe))
@@ -191,7 +191,7 @@ test_that("readVizgen don't flip image when image is too large", {
     sfe <- readVizgen(dir_use, z = 0L, use_cellpose = TRUE, image = "PolyT",
                       flip = "image", max_flip = "0.02 MB")
     suppressWarnings(img_orig <- rast(file.path(dir_use, "images", "mosaic_PolyT_z0.tif")))
-    img <- getImg(sfe)@image
+    img <- imgRaster(getImg(sfe))
     # Make sure image was not flipped
     expect_equal(terra::values(img), terra::values(img_orig))
     cg <- SpatialFeatureExperiment::centroids(sfe)
@@ -203,12 +203,12 @@ test_that("readVizgen don't flip image when image is too large", {
 test_that("Don't flip image if it's GeoTIFF", {
     sfe <- readVizgen(dir_use, z = 0L, use_cellpose = TRUE, image = "PolyT",
                       flip = "image")
-    terra::writeRaster(getImg(sfe)@image,
+    terra::writeRaster(imgRaster(getImg(sfe)),
                        filename = file.path("vizgen", "images", "mosaic_DAPI_z0.tif"),
                        overwrite = TRUE)
     sfe2 <- readVizgen(dir_use, z = 0L, use_cellpose = TRUE, image = "DAPI",
                        flip = "image")
-    expect_equal(terra::values(getImg(sfe)@image), terra::values(getImg(sfe2)@image))
+    expect_equal(terra::values(imgRaster(getImg(sfe))), terra::values(imgRaster(getImg(sfe2))))
     file.remove(file.path("vizgen", "images", "mosaic_DAPI_z0.tif"))
 })
 

tests/testthat/test-saveRDS.R

@@ -6,7 +6,7 @@ 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))
+    classes <- vapply(imgs, function(x) class(x@image), FUN.VALUE = character(1))
     expect_true(all(classes == "PackedSpatRaster"))
     expect_s4_class(sfe2, "SpatialFeatureExperiment")
     unlink("foo.rds")

tests/testthat/test-subset.R

@@ -135,13 +135,13 @@ test_that("Images are cropped after subsetting, multiple samples", {
     cg <- st_centroid(spotPoly(sfe3, sample_id = "all"))
     nCounts <- Matrix::colSums(counts(sfe3))
     # For sample 1
-    img1 <- getImg(sfe3, sample_id = "ob")@image
+    img1 <- getImg(sfe3, sample_id = "ob") |> imgRaster()
     bbox_geom <- st_bbox(spotPoly(sfe3, "ob")) |> st_as_sfc()
     bbox_img <- as.vector(ext(img1)) |> st_bbox() |> st_as_sfc()
     expect_true(st_covered_by(bbox_geom, bbox_img, sparse = FALSE))
-    
+
     # For sample 2
-    img2 <- getImg(sfe3, sample_id = "kidney")@image
+    img2 <- getImg(sfe3, sample_id = "kidney") |> imgRaster()
     bbox_geom <- st_bbox(spotPoly(sfe3, "kidney")) |> st_as_sfc()
     bbox_img <- as.vector(ext(img2)) |> st_bbox() |> st_as_sfc()
     expect_true(st_covered_by(bbox_geom, bbox_img, sparse = FALSE))