initial imp. for delayed transformations

.Rbuildignore

@@ -3,3 +3,5 @@
 LICENSE.md
 .github
 .git
+^\.positai$
+^\.claude$

.gitignore

@@ -4,3 +4,4 @@
 .Ruserdata
 inst/.DS_Store
 *.Rproj
+.positai

DESCRIPTION

@@ -27,7 +27,8 @@ Imports:
   Rarr,
   ZarrArray,
   magick,
-  tools
+  tools,
+  BiocGenerics
 Suggests: 
   testthat (>= 3.0.0),
   knitr,

NAMESPACE

@@ -12,10 +12,12 @@ exportMethods("[")
 exportMethods("[[")
 exportMethods("[[<-")
 exportMethods("path<-")
+exportMethods(affine)
 exportMethods(aperm)
 exportMethods(axes)
 exportMethods(crop)
 exportMethods(dim)
+exportMethods(extent)
 exportMethods(flip)
 exportMethods(flop)
 exportMethods(length)
@@ -25,8 +27,11 @@ exportMethods(negate)
 exportMethods(path)
 exportMethods(realize)
 exportMethods(rotate)
+exportMethods(scale)
+exportMethods(translation)
 exportMethods(type)
 import(DelayedArray)
+importFrom(BiocGenerics,scale)
 importFrom(DelayedArray,DelayedArray)
 importFrom(DelayedArray,path)
 importFrom(EBImage,flip)

R/ImageArray.R

@@ -14,7 +14,6 @@
 #'  }
 #' }
 #' @param drop ignored
-#' @param angle value between 0 and 360 for degrees to rotate
 #' @param brightness the brightness of the new image in percentage, e.g. 120
 #' @param perm perm
 #' @param index a named or unnamed list of indices for cropping/subsetting the
@@ -30,14 +29,8 @@
 #' @aliases
 #' [[,ImageArray,numeric-method
 #' [[<-,ImageArray,numeric-method
-#' rotate
-#' rotate,ImageArray-method
 #' crop
 #' crop,ImageArray-method
-#' flip
-#' flip,ImageArray-method
-#' flop
-#' flop,ImageArray-method
 #' negate
 #' negate,ImageArray-method
 #' modulate
@@ -52,6 +45,8 @@
 #' as.raster,ImageArray-method
 #' path
 #' path,ImageArray-method
+#' extent
+#' extent,ImageArray-method
 #'
 #' @examples
 #' # get image
@@ -89,6 +84,9 @@
 #'
 #' # realize
 #' imgarray <- realize(imgarray)
+#' 
+#' # extent
+#' extent(imgarray)
 NULL
 
 #' @describeIn ImageArray-methods subset and crop
@@ -99,12 +97,6 @@ setMethod(
   f = "[",
   signature = c("ImageArray"),
   function(x, i, j, ..., drop = FALSE) {
-    if (missing(x)) {
-      stop("'x' is missing")
-    }
-    if (!.isTRUEorFALSE(drop)) {
-      stop("'drop' must be TRUE or FALSE")
-    }
     Nindex <- S4Arrays:::extract_Nindex_from_syscall(sys.call(), parent.frame())
     crop(x, index = Nindex)
   }
@@ -580,17 +572,10 @@ writeImageArray <- function(
     if(format == "hdf5") format <- "h5"
     if(fileext != format && format != "in-memory") {
       warning(
-        sprintf(
-          paste(
-            "The file extension of the output path%s does", 
-            "not match the specified format (%s),", 
-            "The object will be written as (%s).", 
-            sep = " "
-          ),
-          if (fileext == "") "" else paste0(" (", fileext, ")"),
-          format,
-          format
-        )
+        "The file extension of the output path", 
+        if (fileext == "") "" else sprintf(" '%s'", fileext),
+        " does not match the specified format (", format, "). ", 
+        "The object will be saved as ", format, " format. "
       )
     }
   }

R/allgenerics.R

@@ -1,11 +1,20 @@
+#' @importFrom BiocGenerics scale
+
 # generics of ImageArray
 setGeneric("crop", function(object, ...) standardGeneric("crop"))
 setGeneric("negate", function(object, ...) standardGeneric("negate"))
 setGeneric("modulate", function(object, ...) standardGeneric("modulate"))
 setGeneric("meta", function(object, ...) standardGeneric("meta"))
 setGeneric("axes", function(object, ...) standardGeneric("axes"))
+setGeneric("extent", \(x, ...) standardGeneric("extent"))
 
 # generics from EBImage
 setGeneric("rotate")
 setGeneric("flip")
 setGeneric("flop")
+
+# transformations
+setGeneric("affine", \(x, ...) standardGeneric("affine"))
+setGeneric("translation", \(x, ...) standardGeneric("translation"))
+setGeneric("rotate_transform",
+           \(x, ...) standardGeneric("rotate_transform"))

R/manipulation.R

@@ -1,43 +1,3 @@
-#' @importFrom EBImage rotate flip flop
-NULL
-
-#' @describeIn ImageArray-methods rotate image array to 90, 180, 270 degrees
-#' @export
-setMethod("rotate", signature = "ImageArray", function(x, angle) {
-  # validate rotation
-  if (!angle %in% c(0, 90, 180, 270, 360)) {
-    stop("Only rotations of 0,90,180,270,360 degrees are supported!")
-  }
-
-  # check dimensions
-  .check_dim(x)
-  dim_img <- dim(x[[1]])
-  ax <- axes(x)
-
-  # array perm.
-  if (angle %in% c(90, 270)) {
-    cur_perm <- .swap(
-      seq_along(dim_img),
-      which(ax == "x"),
-      which(ax == "y")
-    )
-    x <- aperm(x, perm = cur_perm)
-  }
-
-  # flop
-  if (angle %in% c(90, 180)) {
-    x <- flop(x)
-  }
-
-  # flip
-  if (angle %in% c(180, 270)) {
-    x <- flip(x)
-  }
-
-  # return
-  x
-})
-
 #' @describeIn ImageArray-methods permute image
 #' @exportMethod aperm
 setMethod("aperm", signature = "ImageArray", function(a, perm) {
@@ -74,37 +34,6 @@ setMethod("modulate", signature = "ImageArray", function(object, brightness) {
   object
 })
 
-#' @importFrom stats setNames
-#' @noRd
-.flipflop <- function(object, direction = "x") {
-  ax <- axes(object)
-
-  # check dim
-  .check_dim(object)
-
-  # flip all
-  for (i in seq_along(object@levels)) {
-    img <- object[[i]]
-    dim_img <- stats::setNames(dim(img), ax)
-    cur_ind <- stats::setNames(lapply(dim_img, seq_len), ax)
-    cur_ind[[direction]] <- rev(cur_ind[[direction]])
-    object[[i]] <- .subset_array(object[[i]], cur_ind, drop = FALSE)
-  }
-  object
-}
-
-#' @describeIn ImageArray-methods vertical flipping image
-#' @export
-setMethod("flip", signature = "ImageArray", function(x) {
-  .flipflop(x, direction = "y")
-})
-
-#' @describeIn ImageArray-methods horizontal flipping image
-#' @export
-setMethod("flop", signature = "ImageArray", function(x) {
-  .flipflop(x, direction = "x")
-})
-
 #' @describeIn ImageArray-methods cropping image
 #' @importFrom utils head tail
 #' @importFrom stats setNames