feat: affine

feat: `affine2d` class feat: `affine2d` initialize - converts inputs to anchor slot to extent numeric vectors (xmin, xmax, ymin, ymax) - regenerates rotate, shear, scale, translate values for the affine after every call feat: helpful internals for objects with `ext()` - `.get_centroid_xy()` internal for getting numeric centroid xy values of any object that responds to `ext()` - `.bound_poly()` internal for generating a dummy polygon from the extent of any object that responds to `ext()` feat: define `affine()` generic feat: `shear()` feat: `affine()` - change `decomp_affine()` to an internal that runs when `affine()` is called on a `matrix` - `.aff_shift_2d()`, `.aff_shift_2d<-()`, `.aff_linear_2d`, `.aff_linear_2d()` internals for accessing and manipulating affine matrices feat: extract methods for `affine2d` feat: `plot()` for `affine2d` - plots the affine transform described by an `affine2d` class. blue is start, red is end feat: `rescale()` for `affine2d` feat: `show()` for `affine2d` feat: `spatShift()` for `affine2d` chore: update news chore: document
jiajic · Jun 18, 2024 · b316ae1 · b316ae1
1 parent a0bae74
commit b316ae1
Show file tree

Hide file tree

Showing 25 changed files with 505 additions and 201 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(.DollarNames,affine2d)
 S3method(.DollarNames,dimObj)
 S3method(.DollarNames,metaData)
 S3method(.DollarNames,spatEnrObj)
@@ -8,8 +9,6 @@ S3method(.DollarNames,terraVectData)
 S3method(as.data.table,SpatVector)
 S3method(as.data.table,giottoPoints)
 S3method(as.data.table,giottoPolygon)
-S3method(print,affine_decomp)
-S3method(solve,affine_decomp)
 S3method(t,spatLocsObj)
 S3method(t,spatialNetworkObj)
 export(addCellMetadata)
@@ -102,7 +101,6 @@ export(create_spat_grid_obj)
 export(create_spat_locs_obj)
 export(create_spat_net_obj)
 export(cropGiottoLargeImage)
-export(decomp_affine)
 export(distGiottoImage)
 export(edge_distances)
 export(estimateImageBg)
@@ -361,6 +359,7 @@ exportMethods(reconnect)
 exportMethods(rescale)
 exportMethods(rownames)
 exportMethods(setGiotto)
+exportMethods(shear)
 exportMethods(spatIDs)
 exportMethods(spatShift)
 exportMethods(spatUnit)

diff --git a/NEWS.md b/NEWS.md
@@ -12,9 +12,13 @@
 
 ## new
 - `affine()` for `giottoPolygon`, `giottoPoints`, `spatLocsObj`
-- `decomp_affine()` for decomposing affine matrix to simple transforms
-- `shear()` for `spatLocsObj`
-- `solve()` method for `affine_decomp`
+- `shear()` for `giottoPoints`, `giottoPolygon`, `spatLocsObj`, `affine2d`
+- `affine2d` class for accumulating linear transforms to be used with `affine()`
+- `spin()`, `rescale`, `spatShift()` methods for `affine2d`
+- `initialize()`, `[`, `$`, `show()`, `plot()` methods for `affine2d`
+- `.get_centroid_xy()` internal for getting numeric centroid xy values of any object that responds to `ext()`
+- `.bound_poly()` internal for generating a dummy polygon from the extent of any object that responds to `ext()`
+- `.aff_shift_2d()`, `.aff_shift_2d<-()`, `.aff_linear_2d`, `.aff_linear_2d()` internals for accessing and manipulating affine matrices
 
 
 # GiottoClass 0.3.1 (2024/05/21)

diff --git a/R/classes.R b/R/classes.R
@@ -1630,6 +1630,34 @@ giottoLargeImage <- setClass(
     )
 )
 
+
+
+
+setClass(
+    Class = "affine2d",
+    slots = list(
+        anchor = "ANY",
+        affine = "matrix",
+        order = "character",
+        rotate = "numeric",
+        shear = "numeric",
+        scale = "numeric",
+        translate = "numeric"
+    ),
+    prototype = list(
+        anchor = c(-180, 180, -90, 90),
+        affine = diag(rep(1, 2L)),
+        order = c("rotate", "shear", "scale", "translate"),
+        rotate = 0,
+        shear = c(0, 0),
+        scale = c(1, 1),
+        translate = c(0, 0)
+    )
+)
+
+
+
+
 # function for updating image objects if structure definitions have changed
 .update_giotto_image <- function(x) {
     if (inherits(x, "giottoLargeImage")) {

diff --git a/R/generics.R b/R/generics.R
@@ -35,7 +35,7 @@ setGeneric(
 
 # Methods and documentations found in methods-spatShift.R
 setGeneric("spatShift", function(x, ...) standardGeneric("spatShift"))
-setGeneric("affine", function(x, ...) standardGeneric("affine"))
+setGeneric("affine", function(x, y, ...) standardGeneric("affine"))
 setGeneric("shear", function(x, ...) standardGeneric("shear"))
 
 # Methods and documentations found in methods-overlaps.R

diff --git a/R/giotto_structures.R b/R/giotto_structures.R
@@ -166,9 +166,19 @@
 }
 
 
+# from a spatvector, get the centroid xy values as a numeric vector
+.get_centroid_xy <- function(x) {
+    res <- centroids(x) %>% ext() %>% .ext_to_num_vec()
+    res[c(1L, 3L)]
+}
 
-
-
+# create a polygon of the extent.
+# useful for plotting and figuring out how the full data will behave spatially
+.bound_poly <- function(x) {
+    res <- ext(x) %>% as.polygons()
+    res$id <- "bound"
+    return(res)
+}
 
 
 

diff --git a/R/methods-affine.R b/R/methods-affine.R
@@ -2,7 +2,7 @@
 #' @include classes.R
 
 # docs ----------------------------------------------------------- #
-#' @title Apply an affine tranform
+#' @title Affine transformations
 #' @name affine
 #' @description Apply an affine transformation matrix to a spatial object.
 #' Currently only works for 2D transforms.
@@ -44,36 +44,55 @@ NULL
 
 #' @rdname affine
 #' @export
-setMethod("affine", signature("SpatVector"), function(x, m, inv = FALSE, ...) {
-    .affine_sv(x, m, inv, ...)
+setMethod("affine", signature(x = "ANY", y = "missing"), function(x) {
+    x <- as.matrix(x)
+    if (ncol(x) <= 3) {
+        res <- new("affine2d", affine = x)
+    }
+    return(res)
+})
+
+#' @rdname affine
+#' @export
+setMethod("affine", signature(x = "ANY", y = "affine2d"), function(x, y, ...) {
+    a <- get_args_list(...)
+    a$y <- y@affine
+    do.call(affine, args = a)
+})
+
+#' @rdname affine
+#' @export
+setMethod("affine", signature(x = "SpatVector", y = "matrix"), 
+          function(x, y, inv = FALSE, ...) {
+    .affine_sv(x, m = y, inv, ...)
 })
 
 #' @rdname affine
 #' @export
 setMethod(
-    "affine", signature("giottoPoints"),
-    function(x, m, inv = FALSE, ...) {
-        x[] <- .affine_sv(x = x[], m = m, inv = inv, ...)
+    "affine", signature(x = "giottoPoints", y = "matrix"),
+    function(x, y, inv = FALSE, ...) {
+        x[] <- .affine_sv(x = x[], m = y, inv = inv, ...)
         return(x)
     }
 )
 
 #' @rdname affine
 #' @export
 setMethod(
-    "affine", signature("giottoPolygon"),
-    function(x, m, inv = FALSE, ...) {
-        .do_gpoly(x, what = .affine_sv, args = list(m = m, inv = inv, ...))
+    "affine", signature(x = "giottoPolygon", y = "matrix"),
+    function(x, y, inv = FALSE, ...) {
+        .do_gpoly(x, what = .affine_sv, args = list(m = y, inv = inv, ...))
     }
 )
 
 #' @rdname affine
 #' @export
 setMethod(
-    "affine", signature("spatLocsObj"),
-    function(x, m, inv = FALSE, ...) {
+    "affine", signature("spatLocsObj", y = "matrix"),
+    function(x, y, inv = FALSE, ...) {
         x[] <- .affine_dt(
-            x = x[], m = m, xcol = "sdimx", ycol = "sdimy", inv = inv, ...
+            x = x[], m = y, xcol = "sdimx", ycol = "sdimy", inv = inv, ...
         )
         return(x)
     }
@@ -89,7 +108,6 @@ setMethod(
     m <- as.matrix(m)
     gtype <- terra::geomtype(x)
     xdt <- data.table::as.data.table(x, geom = "XY")
-
     xdt <- .affine_dt(
         x = xdt, m = m, xcol = "x", ycol = "y", inv = inv, ...
     )
@@ -165,13 +183,13 @@ setMethod(
 #'     100, 29, 1
 #' ), nrow = 3, byrow = TRUE)
 #' 
-#' # show decomps
+#' # create affine objects
 #' # values are shown in order of operations
-#' decomp_affine(m)
-#' decomp_affine(trans_m)
-#' decomp_affine(scale_m)
-#' s <- decomp_affine(shear_m)
-#' a <- decomp_affine(aff_m)
+#' affine(m)
+#' affine(trans_m)
+#' affine(scale_m)
+#' s <- affine(shear_m)
+#' a <- affine(aff_m)
 #' force(a)
 #' 
 #' # perform piecewise transforms with decomp
@@ -193,9 +211,7 @@ setMethod(
 #' plot(affine(sl, aff_m))
 #' plot(sl_aff_piecewise)
 #' 
-#' @export
-#' @seealso [solve.affine_decomp()]
-decomp_affine <- function(x) {
+.decomp_affine <- function(x) {
     # should be matrix or coercible to matrix
     x <- as.matrix(x)
 
@@ -219,12 +235,13 @@ decomp_affine <- function(x) {
     # apply xy translations
     if (ncol(x) == 3) {
         res$translate = res$translate + x[seq(2), 3]
+    } else {
+        # append translations
+        x <- cbind(x, rep(0, 2L)) %>%
+            rbind(c(0, 0, 1))
     }
 
-    res <- structure(
-        .Data = c(res, list(matrix = x)), class = "affine_decomp"
-    )
-
+    res$affine <- x
     return(res)
 }
 
@@ -280,68 +297,38 @@ decomp_affine <- function(x) {
     )
 }
 
-
-
-#' @name print.affine_decomp
-#' @title affine_decomp print method
-#' @param x object to print
-#' @param \dots additional params to pass (none implemented)
-#' @keywords internal
-#' @export
-print.affine_decomp <- function(x, ...) {
-    cat("<affine_decomp>\n")
-    # reorder in order of piecewise transforms
-    x <- x[x$order]
-    print_list(x)
+.aff_linear_2d <- function(x) {
+    if (inherits(x, "affine2d")) x <- x[]
+    x[][seq(2), seq(2)]
 }
 
-#' @name solve.affine_decomp
-#' @title Solve for inverted 2D affine decomp
-#' @param a `affine_decomp` object
-#' @param b not used
-#' @param \dots additional params to pass (none implemented)
-#' @examples
-#' sl <- GiottoData::loadSubObjectMini("spatLocsObj")
-#' 
-#' m <- matrix(c(
-#'     2, 0.5, 1000, 
-#'     -0.3, 3, 20,
-#'     100, 29, 1
-#' ), nrow = 3, byrow = TRUE)
-#' 
-#' a <- decomp_affine(m)
-#' i <- solve(decomp) # inverted
-#' 
-#' aff_sl <- affine(sl, aff_m)
-#' inv_sl <- aff_sl %>%
-#'     spatShift(dx = i$translate[["x"]], dy = i$translate[["y"]]) %>%
-#'     spin(GiottoUtils::degrees(i$rotate), x0 = 0, y0 = 0) %>%
-#'     shear(fx = i$shear[["x"]], fy = i$shear[["y"]], x0 = 0, y0 = 0) %>%
-#'     rescale(fx = i$scale[["x"]], fy = i$scale[["y"]], x0 = 0, y0 = 0)
-#' 
-#' plot(aff_sl)
-#' plot(sl)
-#' plot(inv_sl) # same as original
-#' 
-#' @export
-solve.affine_decomp <- function(a, b, ...) {
-    m <- a$matrix[seq(2), seq(2)]
-    m <- solve(m)
-    # translations <- NULL
-    translation <- -a$translate
-
-    inv_m <- rbind(m, c(0,0)) %>%
-        cbind(c(translation, 1))
+`.aff_linear_2d<-` <- function(x, value) {
+    checkmate::assert_matrix(value, nrows = 2L, ncols = 2L)
+    if (inherits(x, "affine2d")) {
+        x[][seq(2), seq(2)] <- value
+        x <- initialize(x)
+    }
+    else x[seq(2), seq(2)] <- value
 
-    res <- decomp_affine(inv_m)
-    res$order <- c("translate", "rotate", "shear", "scale")
-    class(res) <- "affine_decomp"
-    return(res)
+    return(x)
 }
 
+.aff_shift_2d <- function(x) {
+    if (inherits(x, "affine2d")) x <- x[]
+    x[seq(2), 3]
+}
 
-
-
+`.aff_shift_2d<-` <- function(x, value) {
+    checkmate::assert_numeric(value, len = 2L)
+    if (inherits(x, "affine2d")) {
+        x[][seq(2), 3] <- value
+        x <- initialize(x)
+    } else {
+        x[seq(2), 3] <- value
+    }
+
+    return(x)
+}
 
 
 

diff --git a/R/methods-extract.R b/R/methods-extract.R
@@ -186,6 +186,24 @@ setMethod(
     names(x@spatVector)
 }
 
+#' @rdname extract-methods
+#' @section \code{`$`} methods:
+#'   Select piecewise transform values from `affine2d`
+#' @export
+setMethod("$", signature("affine2d"), function(x, name) {
+    accessible <- c("affine", "order", "rotate", "shear", "scale", "translate")
+    if (name %in% accessible) {
+        return(slot(x, name))
+    } else {
+        return(NULL)
+    }
+})
+
+#' @export
+.DollarNames.affine2d <- function(x, pattern) {
+    c("affine", "order", "rotate", "shear", "scale", "translate")
+}
+
 
 # [ S4 access generic ####
 
@@ -955,3 +973,31 @@ setMethod(
         x
     }
 )
+
+#' @rdname extract-methods
+#' @export
+setMethod(
+    "[",
+    signature(
+        x = "affine2d", i = "missing", j = "missing", drop = "missing"
+    ),
+    function(x) {
+        x@affine
+    }
+)
+
+#' @rdname extract-methods
+#' @aliases [<-,affine2d,missing,missing,
+#' ANY-method [<-,affine2d,missing,missing-method
+#' @docType methods
+#' @section \code{`[<-`} methods:
+#'   Assign to \code{affine} slot in affine2d
+#' @export
+setMethod(
+    "[<-",
+    signature(x = "affine2d", i = "missing", j = "missing", value = "ANY"),
+    function(x, value) {
+        x@affine <- value
+        return(initialize(x))
+    }
+)