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GridTopology = function(cellcentre.offset, cellsize, cells.dim) {
new("GridTopology",
cellcentre.offset = cellcentre.offset,
cellsize = cellsize,
cells.dim = as.integer(cells.dim))
}
# setMethod("show", "GridTopology", function(object) summary(object))
as.data.frame.GridTopology = function(x, row.names, optional, ...) data.frame(
cellcentre.offset = x@cellcentre.offset,
cellsize = x@cellsize,
cells.dim = x@cells.dim
)
setAs("GridTopology", "data.frame", function(from) as.data.frame.GridTopology(from))
setMethod("coordinates", "GridTopology", function(obj) {
cc = do.call("expand.grid", coordinatevalues(obj))
# as.matrix(sapply(cc, as.numeric))
# dropping dimension for single cell grid
do.call("cbind", lapply(cc, as.numeric))
})
coordnamesGT = function(x, value) {
names(x@cellcentre.offset) = value
names(x@cellsize) = value
names(x@cells.dim) = value
x
}
setReplaceMethod("coordnames",
signature(x = "GridTopology", value = "character"), coordnamesGT)
coordinatevalues = function(obj) {
if (!is(obj, "GridTopology"))
stop("function only works for objects of class or extending GridTopology")
ret = list()
for (i in seq(along=obj@cells.dim)) {
if (i == 2) # y-axis is the exception--starting at top of map, and decreasing:
ret[[i]] = obj@cellcentre.offset[i] +
obj@cellsize[i] * ((obj@cells.dim[i] - 1):0)
else
ret[[i]] = obj@cellcentre.offset[i] +
obj@cellsize[i] * (0:(obj@cells.dim[i] - 1))
}
ns = names(obj@cellcentre.offset)
if (is.null(ns))
ns = paste("s", 1:length(ret), sep = "") #dimnames(obj@bbox)[[1]]
names(ret) = ns
ret
}
points2grid = function(points, tolerance=sqrt(.Machine$double.eps), round=NULL, fuzz.tol=3) {
# work out grid topology from points
n = dimensions(points)
ret = new("GridTopology",
cellcentre.offset = numeric(n),
cellsize = numeric(n),
cells.dim = as.integer(rep(1,n)))
cc = coordinates(points)
nr <- nrow(cc)
for (i in 1:n) { # loop over x, y, and possibly z
x = cc[, i]
sux = sort(unique(x))
fuzz <- nr/length(sux) < fuzz.tol
difx = diff(sux)
if (length(difx) == 0)
stop(paste("cannot determine cell size from constant coordinate", i))
#ru.difx = range(unique(difx))
ru.difx = range(unique(difx)) # min to max x coord leaps
err1 = diff(ru.difx) #?? /max(range(abs(sux))) # (max-min)/max(abs(x))
if (err1 > tolerance) {
xx = ru.difx / min(ru.difx)
err2 = max(abs(floor(xx) - xx)) # is it an integer multiple?
if (err2 > tolerance) {
cat(paste("suggested tolerance minimum:", err2, "\n"))
stop(paste("dimension", i,": coordinate intervals are not constant"))
} else if (fuzz) {
o <- kmeans(difx, 2)
mdx <- which.max(o$centers)
difx_in <- difx[o$cluster == mdx]
dxsd <- sd(difx_in)
if (dxsd > tolerance) {
warning(paste("grid has empty column/rows in dimension", i))
hh <- hist(difx_in, plot=FALSE)
hh1 <- which.max(hh$counts)
if (hh$counts[hh1] < sum(hh$counts)/2)
stop(paste("dimension", i,
": coordinate intervals are not constant",
"after allowing for numeric fuzz"))
hh1a <- difx_in >= hh$breaks[hh1]
hh1b <- difx_in <= hh$breaks[(hh1+1)]
difx <- mean(difx_in[hh1a & hh1b])
} else difx <- max(o$centers)
if (!is.null(round))
difx <- round(difx, digits=round)
} else {
difx = difx[difx < ru.difx[1] + tolerance]
warning(paste("grid has empty column/rows in dimension", i))
}
}
ret@cellsize[i] = mean(difx)
ret@cellcentre.offset[i] = min(sux)
ret@cells.dim[i] = as.integer(round(diff(range(sux))/ret@cellsize[i]) + 1)
#was: length(sux), but this will not cope with empty rows.
if (ret@cells.dim[i] > nr/2)
warning(paste("grid topology may be corrupt in dimension", i))
}
nm = dimnames(cc)[[2]]
names(ret@cellsize) = nm
names(ret@cellcentre.offset) = nm
names(ret@cells.dim) = nm
ret
}
.NumberOfCells = function(x) {
if (!is(x, "GridTopology"))
stop(".NumberOfCells only works on objects of class GridTopology")
prod(x@cells.dim)
}
print.GridTopology = function(x, ...) {
res = data.frame(rbind(x@cellcentre.offset, x@cellsize, as.numeric(x@cells.dim)))
rownames(res) = c("cellcentre.offset", "cellsize", "cells.dim")
if (!is.null(names(x@cellcentre.offset)))
names(res) = names(x@cellcentre.offset)
print(res)
invisible(res)
}
setMethod("show", "GridTopology", function(object) print.GridTopology(object))
summ.GridTopology = function(object, ...) {
ret = list()
ret[["values"]] = gridparameters(object)
class(ret) = "summary.GridTopology"
ret
}
setMethod("summary", "GridTopology", summ.GridTopology)
print.summary.GridTopology = function(x, ...) {
cat("Grid topology:\n")
print(x$values)
invisible(x)
}
# make a SpatialPolygons from a GridTopology - NERSC query
as.SpatialPolygons.GridTopology <- function(grd, proj4string=CRS(as.character(NA)))
{
grd_crds <- coordinates(grd)
IDs <- IDvaluesGridTopology(grd)
nPolygons <- nrow(grd_crds)
cS <- grd@cellsize
cS2 <- cS/2
cS2x <- cS2[1]
cS2y <- cS2[2]
Srl <- vector(mode="list", length=nPolygons)
for (i in 1:nPolygons) {
xi <- grd_crds[i,1]
yi <- grd_crds[i,2]
x <- c(xi-cS2x, xi-cS2x, xi+cS2x, xi+cS2x, xi-cS2x)
y <- c(yi-cS2y, yi+cS2y, yi+cS2y, yi-cS2y, yi-cS2y)
Srl[[i]] <- Polygons(list(Polygon(coords=cbind(x, y)
#, proj4string=proj4string
)), ID=IDs[i])
}
res <- SpatialPolygons(Srl, proj4string=proj4string)
res
}
setAs("GridTopology", "SpatialPolygons", function(from)
as.SpatialPolygons.GridTopology(from))
# mostly copied from coordinates() for GridTopology,
# makes IDs "c(i)r(j)" matching the coordinates
# used with SpatialRing-ed grids for the data frame rowname()
IDvaluesGridTopology <- function(obj) {
if (!is(obj, "GridTopology"))
stop("function only works for objects of class or extending GridTopology")
cc <- getGridIndex(coordinates(obj), obj)
res <- as.matrix(sapply(cc, as.integer))
paste("g", res, sep="")
}
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