Merge pull request #33 from jiajic/dev

Next steps:
Consider `across_spat_units` and `across_feat_types` params for finer control over subsets.
Could have a special ':all:' input that will then tell it to apply the subset to all spat_units/feat_types

How should hierarchical subsetting be done?

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: GiottoClass
 Title: Giotto Suite object definitions and framework
-Version: 0.0.0.9004
+Version: 0.0.0.9005
 Authors@R: c(
 	person("Ruben", "Dries", email = "rubendries@gmail.com",
 		 role = c("aut", "cre")),

NEWS.md

@@ -3,6 +3,8 @@
 ## Breaking Changes
 
 ## Added
+- Added `ext<-()` method for `giottoPolygon`, `giottoPoints`
+- Added `crop()` method for `giottoLargeImage`, `giottoPoints`
 
 ## Changes
 - Improved performance of gefToGiotto()

R/methods-coerce.R

@@ -56,8 +56,9 @@ as.data.table.giottoPoints <- function(x, ...) {
 
 
 # DT -> SpatVector ####
-
 # TODO
+# as.points / as.polygon generics from terra are an option, but terra deals with
+# this kind of conversion using vect() usually
 
 
 

R/methods_crop.R

@@ -1,15 +1,23 @@
 
+# documentation ####
 
 #' @name crop-generic
 #' @title Crop to a spatial subset
 #' @description see [terra::crop]. Object x will be cropped using object y.
 #' @param x object
 #' @param y any object that has a SpatExtent or returns a SpatExtent
-#' @param ... additional params to pass to terra::crop
+#' @param \dots additional params to pass to terra::crop
 NULL
 
 
 
+
+
+
+# methods ####
+
+
+
 #' @describeIn crop-generic Crop a giottoLargeImage
 #' @export
 setMethod('crop', signature('giottoLargeImage'), function(x, y, ...) {
@@ -21,3 +29,74 @@ setMethod('crop', signature('giottoLargeImage'), function(x, y, ...) {
 
   x
 })
+
+
+#' @describeIn crop-generic Crop a giottoPoints
+#' @param DT logical. Use alternative DT subsetting for crop operation
+#' @param xmin,xmax,ymin,ymax only used if DT = TRUE. Set extent bounds
+#' independently
+#' @export
+setMethod('crop', signature('giottoPoints'), function(
+    x, y, DT = TRUE, xmin = NULL, xmax = NULL, ymin = NULL, ymax = NULL, ...
+) {
+  checkmate::assert_logical(DT)
+  if(DT) {
+    # converting to DT, subsetting, then regeneration of SpatVector with vect()
+    # is currently faster than using terra::crop() as of 9/21/23
+    missing_y = missing(y)
+    n_single_bounds = 4 - sum(sapply(list(xmin, xmax, ymin, ymax), is.null))
+
+    # check cropping params
+    # ONLY y OR the single spat bounds can be used at any one time
+    if((missing_y && n_single_bounds == 0) ||
+       (!missing_y && n_single_bounds > 0)) {
+      stop(wrap_txt('Crop bounds must be supplied through either a SpatExtent passed to \'y\'
+                    or single numerical bounds passed to one or more of \'xmin\',\'xmax\', \'ymin\', \'ymax\''))
+    }
+
+    # 1. Get full set of cropping bounds
+    if(!missing_y) {
+      # if y is available, use y values directly.
+      # only the extent of y is usable for the DT method
+      if(!inherits(y, 'SpatExtent')) {
+        warning(wrap_txt('Only the extent of y is used when cropping with DT = TRUE'))
+        y = ext(y)
+      }
+
+      xmin = terra::xmin(y)
+      xmax = terra::xmax(y)
+      ymin = terra::ymin(y)
+      ymax = terra::ymax(y)
+
+    } else {
+      # otherwise, fill in any spatial subset bounds that may not have been
+      # supplied with the current extent value(s)
+      current_ext = ext(x)
+      if(is.null(xmin)) xmin = terra::xmin(current_ext)
+      if(is.null(xmax)) xmax = terra::xmax(current_ext)
+      if(is.null(ymin)) ymin = terra::ymin(current_ext)
+      if(is.null(ymax)) ymax = terra::ymax(current_ext)
+    }
+
+    # 2. convert to DT
+    sv = x@spatVector
+    spatDT = as.data.table(sv, geom = 'XY')
+
+    # 3. spatial subset then vect() to SpatVector again
+    spatDT_subset = spatDT[x >= xmin & x <= xmax & y >= ymin & y <= ymax]
+    sv_subset = terra::vect(spatDT_subset, c('x', 'y'))
+
+    # 4. update x
+    x@spatVector = sv_subset
+
+  } else {
+    x@spatVector = terra::crop(x@spatVector, y, ...)
+  }
+
+  # update ID cache and return
+  x@unique_ID_cache = unique(terra::values(x@spatVector)$feat_ID)
+  x
+})
+
+
+