Merge pull request #215 from drieslab/dev2

v0.3.3

Author: jiajic

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: GiottoClass
 Title: Giotto Suite object definitions and framework
-Version: 0.3.2
+Version: 0.3.3
 Authors@R: c(
 	person("Ruben", "Dries", email = "rubendries@gmail.com",
 		 role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")),

NEWS.md

@@ -1,4 +1,12 @@
 
+# GiottoClass 0.3.3
+
+## bug fixes
+- fix flipping issue with `giottoAffineImage` for certain affine transforms
+
+## enhancements
+- `missing` method for `affine()` instantiates an `affine2d` object
+
 # GiottoClass 0.3.2 (2024/07/26)
 
 ## breaking changes

R/giotto_structures.R

@@ -185,6 +185,14 @@
 .magick_image_corners <- function(x) {
     checkmate::assert_class(x, "magick-image")
     im_info <- magick::image_info(x)
+    
+    # generate spatLocsObj as a set of control points for magick distort. #
+    # ------------------------------------------------------------------- #
+    # - magick uses 0.5 to refer to the center of pixels
+    # - 3 points are needed for an affine distort
+    # pt1: bottom left
+    # pt2: top left
+    # pt3: bottom right
     spatLocsObj(
         name = "mg_ctrl_coords",
         coordinates = data.table::data.table(

R/methods-affine.R

@@ -150,8 +150,15 @@ setMethod(
     }
 )
 
+# * missing, missing ####
+#' @rdname affine
+#' @export
+setMethod("affine", signature(x = "missing", y = "missing"), function(x) {
+    new("affine2d", affine = diag(c(1, 1)))
+})
 
-# * ANY ####
+
+# * ANY, missing ####
 #' @rdname affine
 #' @export
 setMethod("affine", signature(x = "ANY", y = "missing"), function(x) {
@@ -337,12 +344,21 @@ setMethod("affine", signature(x = "affine2d", y = "matrix"), function(
 .gaffine_realize_magick <- function(x, size = 5e5, ...) {
     mg <- .spatraster_sample_values(x, output = "magick", size = size, ...)
     aff <- x@affine
+    
+    # create a dummy spatLocsObj to act as control points
+    # pt1: bottom left
+    # pt2: top left
+    # pt3: bottom right
     dummy_sl <- .magick_image_corners(mg)
-    aff_dummy_sl <- affine(dummy_sl, .aff_linear_2d(aff)) %>%
+    aff_dummy_sl <- dummy_sl %>%
+        affine(.aff_linear_2d(aff)) %>%
         flip() %>%
-        rescale(fx = 1 / aff$scale[["x"]], fy = 1 / aff$scale[["y"]])
-    # no rescaling should be performed at this step. Otherwise magick
+        rescale(fx = 1 / abs(aff$scale[["x"]]), #*see below
+                fy = 1 / abs(aff$scale[["y"]]))
+    # *no scaling should be performed at this step. Otherwise magick
     # will generate a differently sized image during distortion
+    # To prevent the scaling change, we use the decomposed scale values.
+    # However, flips ARE desired, so we make sure the use the abs() values.
 
     .sl_to_mat <- function(x) {
         x[][, c("sdimx", "sdimy")] %>% t()