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# sp functions:
if (!isClass("ppp"))
setClass("ppp")
if (!isClass("psp"))
setClass("psp")
if (!isClass("owin"))
setClass("owin")
if (!isClass("im"))
setClass("im")
if (!isClass("tess"))
setClass("tess")
#if (!isClass("RasterLayer"))
# setClass("RasterLayer")
as.SpatialPoints.ppp = function(from) {
mult <- 1
if (!is.null(from$window$units) && !is.null(from$window$units$multiplier))
mult <- from$window$units$multiplier
mx <- mult*from$x
storage.mode(mx) <- "double"
my <- mult*from$y
storage.mode(my) <- "double"
crds <- cbind(mx, my)
if (from$window$type == "rectangle") {
ow <- from$window
bbox <- rbind(mult*as.double(ow$xrange), mult*as.double(ow$yrange))
colnames(bbox) <- c("min", "max")
} else bbox <- NULL
SpatialPoints(coords=crds, bbox=bbox)
}
setAs("ppp", "SpatialPoints", as.SpatialPoints.ppp)
as.SpatialPointsDataFrame.ppp = function(from) {
SP <- as(from, "SpatialPoints")
SpatialPointsDataFrame(SP, data.frame(marks = from$marks))
}
setAs("ppp", "SpatialPointsDataFrame", as.SpatialPointsDataFrame.ppp)
as.SpatialGridDataFrame.ppp = function(from) {
# require(spatstat)
#if (!requireNamespace("spatstat", quietly = TRUE))
# stop("package spatstat required for .SP2owin")
w = from$window
if (w$type != "mask")
stop("window is not of type mask")
offset = c(w$xrange[1] + 0.5 * w$xstep, w$yrange[1] + 0.5 * w$ystep)
cellsize = c(diff(w$xrange)/w$dim[2], diff(w$yrange)/w$dim[1])
dim = c(w$dim[2], w$dim[1])
gt = GridTopology(offset, cellsize, dim)
m = t(w$m[nrow(w$m):1,])
m[!m] = NA
data = data.frame(mask = as.vector(m))
SpatialGridDataFrame(gt, data)
}
setAs("ppp", "SpatialGridDataFrame", as.SpatialGridDataFrame.ppp)
as.SpatialGridDataFrame.im = function(from) {
# require(spatstat)
offset = c(from$xrange[1] + 0.5 * from$xstep, from$yrange[1] +
0.5 * from$ystep)
cellsize = c(diff(from$xrange)/from$dim[2], diff(from$yrange)/from$dim[1])
dim = c(from$dim[2], from$dim[1])
gt = GridTopology(offset, cellsize, dim)
m = t(from$v[nrow(from$v):1,])
data = data.frame(v = as.vector(m))
SpatialGridDataFrame(gt, data)
}
setAs("im", "SpatialGridDataFrame", as.SpatialGridDataFrame.im)
as.im.SpatialGridDataFrame = function(from) {
#require(spatstat)
if (!requireNamespace("spatstat", quietly = TRUE))
stop("package spatstat required for as.im.SpatialGridDataFrame")
xi <- as.image.SpatialGridDataFrame(from)
spatstat::im(t(xi$z), xcol=xi$x, yrow=xi$y)
}
setAs("SpatialGridDataFrame", "im", as.im.SpatialGridDataFrame)
#as.im.RasterLayer <- function(from)
#{
# if (!requireNamespace("spatstat", quietly = TRUE))
# stop("package spatstat required for coercion")
# if (!requireNamespace("raster", quietly = TRUE))
# stop("package raster required for coercion")
# if (!raster::hasValues(from)) stop("values required in RasterLayer object")
# if (raster::rotated(from)) {
# stop("\n Cannot coerce because the object is rotated.\n Either coerce to SpatialPoints* from\n or first use the \"rectify\" function")
# }
# rs <- raster::res(from)
# orig <- bbox(from)[, 1] + 0.5 * rs
# dm <- dim(from)[2:1]
# xx <- unname(orig[1] + cumsum(c(0, rep(rs[1], dm[1]-1))))
# yy <- unname(orig[2] + cumsum(c(0, rep(rs[2], dm[2]-1))))
# im <- spatstat::im(matrix(raster::values(from), ncol=dm[1], nrow=dm[2],
# byrow=TRUE)[dm[2]:1,], xcol=xx, yrow=yy)
# im
#}
# contributed by Matthew Lewis https://github.com/spatstat/spatstat/issues/132
as.im.RasterLayer <- function(from, factor.col.name = NULL)
{
if (!requireNamespace("spatstat", quietly = TRUE))
stop("package spatstat required for coercion")
if (!requireNamespace("raster", quietly = TRUE))
stop("package raster required for coercion")
if (!raster::hasValues(from)) stop("values required in RasterLayer object")
if (raster::rotated(from)) {
stop("\n Cannot coerce because the object is rotated.\n Either coerce to SpatialPoints* from\n or first use the \"rectify\" function")
}
rs <- raster::res(from)
orig <- bbox(from)[, 1] + 0.5 * rs
dm <- dim(from)[2:1]
xx <- unname(orig[1] + cumsum(c(0, rep(rs[1], dm[1]-1))))
yy <- unname(orig[2] + cumsum(c(0, rep(rs[2], dm[2]-1))))
## Use `from` to make a vector `val` with input values
val <- raster::values(from)
if(is.factor(from)){
lev <- levels(from)[[1]]
if(!is.null(factor.col.name)){
if(factor.col.name %in% colnames(lev)){
factor.col <- which(colnames(lev) == factor.col.name)
} else {
stop("'factor.col.name' is not a column name of the raster 'from'")
}
}else{
factor.col <- length(lev)
}
val <- factor(val, levels = lev$ID, labels = lev[[factor.col]])
}
## Assign dimensions to `val` as a matrix in raster layout:
dim(val) <- dm
## Transform to spatstat format
val <- spatstat::transmat(val, from = list(x="-i", y="j"), to = "spatstat")
im <- spatstat::im(val, xcol=xx, yrow=yy)
return(im)
}
#if (requireNamespace("spatstat", quietly = TRUE) && requireNamespace("raster", quietly = TRUE)) {
# setAs("RasterLayer", "im", as.im.RasterLayer)
#}
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