bbox 4-dimensional objects - suitable method?

Hi Edzer

Thanks for a good answer. I did read the asdar-book, and especially the
section on time grids. I guess the book (together with the sp source) is a
must when dealing with the sp-classes.

As far as I understand this means that in SpatialTimeGridDataFrame
 coordinates and time has to be stored several times. That is my main
 motivation to define a new class. Let's take one example where one has a
 structure similar to SpatialPointsDataFrame, while the other has a
 structure of Spatial3dArray.

## SpatialPointsDataFrame ##
# (since it takes a long time to convert it to a sppdf, this is omitted)

# Create coordinates
long2 <- seq(35, 48, length.out = 146)
lat2 <- seq(2, 15, length.out = 188)
long <- matrix(long2, length(long2), length(lat2), byrow = FALSE)
lat <- matrix(lat2, length(long2), length(lat2), byrow = TRUE)
long3 <- rep(c(long), 504)
lat3 <- rep(c(lat), 504)
ptc.coord <- cbind(x = long3, y=lat3)

# Create data variable
z <- seq(1, 10000, length.out = dim(ptc.coord)[1])

# Create time
tm <- rep(seq(as.POSIXct("2002-01-01 06:00:00"),
	  as.POSIXct("2002-01-22 06:00:00"),
	  length.out = 504), each = dim(long)[1]*dim(long)[2])

# make data.frame
dummy <- as.data.frame(cbind(ptc.coord, z, tm))
# do not run:
# system.time(coordinates(dummy)=~x+y+tm)

# What is the object size?
objs <- object.size(dummy)
print(objs, quote = FALSE, units = "Mb")
## end spatial points ##

## Spatial3dArray ##

# arrange z as an array
array.data <- array(z, c(length(long2), length(lat2), 504))
# create a time vector
tm2 <- seq(as.POSIXct("2002-01-01 06:00:00"),
	  as.POSIXct("2002-01-22 06:00:00"),
	  length.out = 504)

x <- new("Spatial3dArray",
	  data = array.data,
	  coords = list(long=long, lat=lat),
	  bbox = matrix(c(min(long),
			  min(lat),
			  max(long),
			  max(lat)), 2, 2,
	  dimnames = list(c("long", "lat"), c("min","max"))),
	  time = as.character(tm2),
	  btime = c("2002-01-01 06:00:00",
			   "2002-01-22 06:00:00"))

dimnames(slot(x, "data"))=list(NULL,
				NULL,
				slot(x, "time"))


objs2 <- object.size(x)
print(objs2, quote = FALSE, units = "Mb")

## end Spatial3dArray ##

So, I think it makes sense to have other classes when dealing with time
 data with a certain dimension. Agree?

I have already rewritten overlay, summary, and added spmean, spmax, and
 spmin (with options on which dimensions the method should be applied
 over). In addition binding methods (sp3dAbind equal to cbind for
 data.frames. Will also introduce timeBind, or similar) has been
 introduced.

Best wishes
Torleif

On Monday 23 November 2009 14:45:16 Edzer Pebesma wrote:

Torleif,

sp classes SpatialPoints* SpatialPixels* and SpatialGrid* already allow

3- and higher dimensional data; providing an example with nonsense data:

library(sp)
data(meuse)
meuse$z = rnorm(155)
coordinates(meuse)=~x+y+z
summary(as(meuse, "SpatialPoints"))

Object of class SpatialPoints
Coordinates:
            min          max
x 178605.000000 1.813900e+05
y 329714.000000 3.336110e+05
z     -2.168683 3.006463e+00
Is projected: NA
proj4string : [NA]
Number of points: 155

It can be used this way to do 3D interpolation (package gstat), and
several of the sp methods work; obviously, several do ignore everything
beyond x and y.

If you store your time as double, you can even think about adding that
as one of the coordinates.

Chapter 6 of http://www.asdar-book.org/ gives code examples of this
approach, where a third dimension represents (posix) time, and methods
are given to select a certain spatial grid from a
SpatialTimeGridDataFrame based on its posix time (range).

The motivation for your approach becomes stronger when time cannot be
stored as double (numeric); I find it harder to see the motivation to
store z differently from the x and y coordinates, create a separate
bounding box for it and rewrite all methods.
--
Edzer

Torleif Markussen Lunde wrote:

Hi

As previously mentioned I am working on 3D and 4D spatial classes. To
get things compatible with the other sp-classes I would like to ask for
your opinion what would be the most suitable bbox methods for
Spatial3dArrays and Spatial4dArrays.

My first thought was that bbox should return the 2D geographical extent
of the object. This to comply with other spatial methods. For the 3D
case an additional slot, btime is added to show the temporal extent of
the object. As writing the 4D case, I started wondering whether it
would be wise to stick to this (my conclusion at the moment is yes). In
that case a new slot called zextent could be added.

To retrieve the extent of the different dimensions one would have three
functions; bbox(), btime(), and zextent()

The other option is to make a bbox slot as a list. bbox() would still
return x-y extent, while bbox.full() could return a list of the full
extent:

list(bbox = matrix(c(1,1,4,4), 2,2,
     			dimnames = list(c("long", "lat"),
		     	c("min", "max"))),
    btime = matrix(c("2002-01-01 06:00:00", "2002-01-01 06:00:00"), 1,
2, dimnames = list(c("time"),
		     	c("min", "max"))),
    zextent = matrix(c(512, 1024), 1,2,
     			dimnames = list(c("masl"),
		     	c("min", "max"))))

Since bbox is defined as a matrix in Spatial, this would be a bad idea.
So, at best bbox could be a matrix of min/max of x, y, and z (since
they all are numeric). bbox() would then return a x, y subset of
bbox(), while bbox.full() could return a list(xyz, time).

Any comments on what would be best suitable to be compatible with the
other Spatial classes?

Best wishes
Torleif
PhD candidate
Centre for International Health
Bjerknes Centre for Climate Research
University of Bergen
Norway