Merge pull request #288 from jiajic/patch_raster_loading

fix: terra rast() noflip

Author: jiajic

DESCRIPTION

@@ -41,7 +41,7 @@ Imports:
     methods,
     reticulate (>= 1.25),
     stats,
-    terra (>= 1.7-41)
+    terra (>= 1.8-21)
 Suggests: 
     Biobase,
     chihaya,

NEWS.md

@@ -14,9 +14,11 @@
 - replace internal usage of deprecated create_spat_net_obj -> createSpatNetObj and set_spatialNetwork -> setSpatialNetwork when calculating spatial networks.
 - fix `createGiottoPolygon()` not preserving attributes from `data.table` inputs
 - fix `loadGiotto()` error when a non-expected reticulate environment is already activated in the session
+- fix `createGiottoLargeImage()` and `createGiottoPolygonsFromMask()` to align with {terra} `v1.8-21` `rast(noflip = TRUE)` [#1102](https://github.com/drieslab/Giotto/issues/1102) by StevenWijnen and rbutleriii
 
 ## changes
 - move {magick} from imports to suggests
+- {terra} `>=v1.8-21`
 
 ## enhancements
 - `[[` can now be used to select channels in `giottoLargeImage`-inheriting objects

R/create.R

@@ -2363,7 +2363,7 @@ setMethod(
         # try failure means it should be vector file
         try_rast <- tryCatch(
             {
-                terra::rast(x)
+                .create_terra_spatraster(x)
             },
             error = function(e) {
                 return(invisible(NULL))
@@ -2426,10 +2426,10 @@ setMethod(
     fill_holes = TRUE,
     poly_IDs = NULL,
     ID_fmt = "cell_",
-    flip_vertical = TRUE,
-    shift_vertical_step = TRUE,
-    flip_horizontal = TRUE,
-    shift_horizontal_step = TRUE,
+    flip_vertical = FALSE,
+    shift_vertical_step = FALSE,
+    flip_horizontal = FALSE,
+    shift_horizontal_step = FALSE,
     remove_unvalid_polygons = TRUE,
     calc_centroids = FALSE,
     verbose = TRUE) {
@@ -2493,10 +2493,12 @@ setMethod(
 #' each polygon in the mask file.
 #' @param ID_fmt character. Only applied if `poly_IDs = NULL`. Naming scheme for
 #' poly_IDs. Default = "cell_". See *ID_fmt* section.
-#' @param flip_vertical flip mask figure in a vertical manner
-#' @param shift_vertical_step shift vertical (boolean or numerical)
-#' @param flip_horizontal flip mask figure in a horizontal manner
-#' @param shift_horizontal_step shift horizontal (boolean or numerical)
+#' @param flip_vertical,flip_horizontal logical. Flip output polygons across y
+#' (vertical) or x (horizontal) axis.
+#' @param shift_vertical_step,shift_horizontal_step logical or numeric. When
+#' `FALSE`, no shift is performed. When numeric, a shift of
+#' \eqn{image height \times step} (vertical) or \eqn{image width \times step}
+#' (horizontal) is performed.
 #' @param remove_unvalid_polygons remove unvalid polygons (default: TRUE)
 #' @concept mask polygon
 #' @section mask_method:
@@ -2532,10 +2534,10 @@ createGiottoPolygonsFromMask <- function(
         fill_holes = TRUE,
         poly_IDs = NULL,
         ID_fmt = "cell_",
-        flip_vertical = TRUE,
-        shift_vertical_step = TRUE,
-        flip_horizontal = TRUE,
-        shift_horizontal_step = TRUE,
+        flip_vertical = FALSE,
+        shift_vertical_step = FALSE,
+        flip_horizontal = FALSE,
+        shift_horizontal_step = FALSE,
         calc_centroids = FALSE,
         remove_unvalid_polygons = TRUE,
         verbose = FALSE) {
@@ -2593,10 +2595,12 @@ createGiottoPolygonsFromMask <- function(
 
     ## flip across axes ##
     if (isTRUE(flip_vertical)) {
-        terra_polygon <- .flip_spatvect(terra_polygon)
+        terra_polygon <- .flip_spatvect(terra_polygon,
+            direction = "vertical")
     }
     if (isTRUE(flip_horizontal)) {
-        terra_polygon <- .flip_spatvect(terra_polygon)
+        terra_polygon <- .flip_spatvect(terra_polygon,
+            direction = "horizontal")
     }
 
     # convert to DT format since we want to be able to compare number of geoms

R/images.R

@@ -682,7 +682,7 @@ reconnect_giottoImage_MG <- function(
 #' @keywords internal
 #' @returns spatRaster object
 .create_terra_spatraster <- function(image_path) {
-    raster_object <- try(handle_warnings(terra::rast(x = image_path))$result)
+    raster_object <- try(terra::rast(x = image_path, noflip = TRUE))
     if (inherits(raster_object, "try-error")) {
         stop(raster_object, " can not be read by terra::rast() \n")
     }

R/interoperability.R

@@ -2509,7 +2509,7 @@ seuratToGiottoV5 <- function(sobject,
 
 
 
-    # Find SueratImages, extract them, and pass to create image
+    # Find SeuratImages, extract them, and pass to create image
     image_list <- list()
     for (i in names(sobject@images)) {
         simg <- sobject[[i]]

R/methods-flip.R

@@ -163,15 +163,6 @@ setMethod(
     }
 )
 
-#' @rdname flip
-#' @export
-setMethod("flip", signature("giottoLargeImage"), function(x, direction = "vertical", x0 = 0, y0 = 0) {
-    a <- get_args_list()
-    a$x <- as(x, "giottoAffineImage") # convert to giottoAffineImage
-    res <- do.call(flip, args = a)
-    return(res)
-})
-
 #' @rdname flip
 #' @export
 setMethod("flip", signature("giottoAffineImage"), function(x, direction = "vertical", x0 = 0, y0 = 0) {
@@ -367,9 +358,6 @@ setMethod("flip", signature("affine2d"), function(x, direction = "vertical", x0
 
 #' @name .flip_large_image
 #' @title Flip a giottoLargeImage object
-#' @description Flip a giottoPoints over a designated x or y value depending on
-#' direction param input. Note that this behavior is different from terra's
-#' implementation of flip for SpatVectors where flips happen over the extent
 #' @param image giottoLargeImage
 #' @param direction character. Direction to flip. Should be either partial
 #' match to 'vertical' or 'horizontal'