[Rd] [.raster bug {was "str() on raster objects fails .."}
Paul Murrell
p.murrell at auckland.ac.nz
Tue Feb 8 21:59:29 CET 2011
Hi
On 7/02/2011 8:36 p.m., Martin Maechler wrote:
>>>>>> Simon Urbanek<simon.urbanek at r-project.org>
>>>>>> on Sun, 6 Feb 2011 20:53:01 -0500 writes:
>
> > On Feb 6, 2011, at 8:10 PM, Paul Murrell wrote:
>
> >> Hi
> >>
> >> On 3/02/2011 1:23 p.m., Simon Urbanek wrote:
> >>>
> >>> On Feb 2, 2011, at 7:00 PM, Paul Murrell wrote:
> >>>
> >>>> Hi
> >>>>
> >>>> Martin Maechler wrote:
> >>>>> On Wed, Feb 2, 2011 at 23:30, Simon
> >>>>> Urbanek<simon.urbanek at r-project.org> wrote:
>>>>>> On Feb 1, 2011, at 8:16 PM, Paul Murrell wrote:
>>>>>>
> >>>>>>> Hi
> >>>>>>>
> >>>>>>> On 2/02/2011 2:03 p.m., Henrik Bengtsson wrote:
> >>>>>>>> On Tue, Feb 1, 2011 at 4:46 PM, Paul
> >>>>>>>> Murrell<p.murrell at auckland.ac.nz> wrote:
> >>>>>>>>> Hi
> >>>>>>>>>
> >>>>>>>>> On 1/02/2011 9:22 p.m., Martin Maechler wrote:
> >>>>>>>>>>>>>>> Henrik Bengtsson<hb at biostat.ucsf.edu> on
> >>>>>>>>>>>>>>> Mon, 31 Jan 2011 11:16:59 -0800 writes:
> >>>>>>>>>>> Hi, str() on raster objects fails for certain
> >>>>>>>>>>> dimensions. For example:
> >>>>>>>>>>
> >>>>>>>>>>>> str(as.raster(0, nrow=1, ncol=100)) 'raster'
> >>>>>>>>>>>> chr [1, 1:100]
> >>>>>>>>>>> "#000000" "#000000" "#000000" "#000000" ...
> >>>>>>>>>>
> >>>>>>>>>>>> str(as.raster(0, nrow=1, ncol=101)) Error in
> >>>>>>>>>>>> `[.raster`(object,
> >>>>>>>>>>> seq_len(max.len)) : subscript out of bounds
> >>>>>>>>>>
> >>>>>>>>>>> This seems to do with how str() and "[.raster"()
> >>>>>>>>>>> is coded; when subsetting as a vector, which
> >>>>>>>>>>> str() relies on, "[.raster"() still returns a
> >>>>>>>>>>> matrix-like object, e.g.
> >>>>>>>>>>
> >>>>>>>>>>>> img<- as.raster(1:25, max=25, nrow=5, ncol=5);
> >>>>>>>>>>>> img[1:2]
> >>>>>>>>>>> [,1] [,2] [,3] [,4] [,5] [1,] "#0A0A0A"
> >>>>>>>>>>> "#3D3D3D" "#707070" "#A3A3A3" "#D6D6D6" [2,]
> >>>>>>>>>>> "#141414" "#474747" "#7A7A7A" "#ADADAD"
> >>>>>>>>>>> "#E0E0E0"
> >>>>>>>>>>
> >>>>>>>>>>> compare with:
> >>>>>>>>>>
> >>>>>>>>>>>> as.matrix(img)[1:2]
> >>>>>>>>>>> [1] "#0A0A0A" "#3D3D3D"
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>> The easy but incomplete fix is to do:
> >>>>>>>>>>
> >>>>>>>>>>> str.raster<- function(object, ...) {
> >>>>>>>>>>> str(as.matrix(object), ...); }
> >>>>>>>>>>
> >>>>>>>>>>> Other suggestions?
> >>>>>>>>>>
> >>>>>>>>>> The informal "raster" class is behaving
> >>>>>>>>>> ``illogical'' in the following sense:
> >>>>>>>>>>
> >>>>>>>>>>> r<- as.raster(0, nrow=1, ncol=11)
> >>>>>>>>>>> r[seq_along(r)]
> >>>>>>>>>> Error in `[.raster`(r, seq_along(r)) : subscript
> >>>>>>>>>> out of bounds
> >>>>>>>>>>
> >>>>>>>>>> or, here equivalently,
> >>>>>>>>>>> r[1:length(r)]
> >>>>>>>>>> Error in `[.raster`(r, 1:length(r)) : subscript
> >>>>>>>>>> out of bounds
> >>>>>>>>>>
> >>>>>>>>>> When classes do behave in such a way, they
> >>>>>>>>>> definitely need their own str() method.
> >>>>>>>>>>
> >>>>>>>>>> However, the bug really is in "[.raster":
> >>>>>>>>>> Currently, r[i] is equivalent to r[i,] which is
> >>>>>>>>>> not at all matrix-like and its help clearly says
> >>>>>>>>>> that subsetting should work as for matrices. A
> >>>>>>>>>> recent thread on R-help/R-devel has mentioned the
> >>>>>>>>>> fact that "[" methods for matrix-like methods
> >>>>>>>>>> need to use both nargs() and missing() and that
> >>>>>>>>>> "[.dataframe" has been the example to follow
> >>>>>>>>>> "forever", IIRC already in S and S-plus as of 20
> >>>>>>>>>> years ago.
> >>>>>>>>> The main motivation for non-standard behaviour
> >>>>>>>>> here is to make sure that a subset of a raster
> >>>>>>>>> object NEVER produces a vector (because the
> >>>>>>>>> conversion back to a raster object then produces a
> >>>>>>>>> single-column raster and that may be a
> >>>>>>>>> "surprise"). Thanks for making the code more
> >>>>>>>>> standard and robust.
> >>>>>>>>>
> >>>>>>>>> The r[i] case is still tricky. The following
> >>>>>>>>> behaviour is quite convenient ...
> >>>>>>>>>
> >>>>>>>>> r[r == "black"]<- "white"
> >>>>>>>>>
> >>>>>>>>> ... but the next behaviour is quite jarring (at
> >>>>>>>>> least in terms of the raster image that results
> >>>>>>>>> from it) ...
> >>>>>>>>>
> >>>>>>>>> r2<- r[1:(nrow(r) + 1)]
> >>>>>>>>>
> >>>>>>>>> So I think there is some justification for further
> >>>>>>>>> non-standardness to try to ensure that the subset
> >>>>>>>>> of a raster image always produces a sensible
> >>>>>>>>> image. A simple solution would be just to outlaw
> >>>>>>>>> r[i] for raster objects and force the user to
> >>>>>>>>> write r[i, ] or r[, j], depending on what they
> >>>>>>>>> want.
> >>>>>>>> FYI, I've tried out Martin's updated version at it
> >>>>>>>> seems like a one-column raster matrix is now
> >>>>>>>> returned for r[i], e.g.
> >>>>>>> Yes, that's what I've been looking at ...
> >>>>>>>
> >>>>>>>>> r<- as.raster(1:8, max=8, nrow=2, ncol=4); r
> >>>>>>>> [,1] [,2] [,3] [,4] [1,] "#202020" "#606060"
> >>>>>>>> "#9F9F9F" "#DFDFDF" [2,] "#404040" "#808080"
> >>>>>>>> "#BFBFBF" "#FFFFFF"
> >>>>>>>>
> >>>>>>>>> r[1:length(r)]
> >>>>>>>> [,1] [1,] "#202020" [2,] "#404040" [3,] "#606060"
> >>>>>>>> [4,] "#808080" [5,] "#9F9F9F" [6,] "#BFBFBF" [7,]
> >>>>>>>> "#DFDFDF" [8,] "#FFFFFF"
> >>>>>>> ... and the above is exactly the sort of thing that
> >>>>>>> will fry your mind if the image that you are
> >>>>>>> subsetting is, for example, a photo.
> >>>>>>>
>>>>>> Why doesn't raster behave consistently like any matrix
> >>>>>>> object?
>>>>>> I would expect simply
>>>>>>
> >>>>>>> r[1:length(r)]
>>>>>> [1] "#202020" "#404040" "#606060" "#808080" "#9F9F9F"
> >>>>>>> "#BFBFBF"
>>>>>> "#DFDFDF" [8] "#FFFFFF"
>>>>>>
>>>>>> Where it's obvious what happened. I saw the comment about
> >>>>>>> the
>>>>>> vector but I'm not sure I get it - why don't you want a
> >>>>>>> vector?
>>>>>> The raster is no different than matrices - you still need
> >>>>>>> to
>>>>>> define the dimensions when going back anyway, moreover
> >>>>>>> what you
>>>>>> get now is not consistent at all since there raster never
> >>>>>>> had
>>>>>> that dimension anyway ...
>>>>>>
>>>>>> Cheers, Simon
> >>>>> I agree that this would be the most "logical" and
> >>>>> notably least surprising behavior, which I find the
> >>>>> most important argument (I'm sorry my last message was
> >>>>> cut off as it was sent accidentally before being
> >>>>> finished completely).
> >>>>
> >>>> I think this behaviour might surprise some ...
> >>>>
> >>>> download.file("http://cran.r-project.org/Rlogo.jpg",
> >>>> "Rlogo.jpg") library(ReadImages) logo<-
> >>>> read.jpeg("Rlogo.jpg")
> >>>>
> >>>> rLogo<- as.raster(logo) rLogoBit<- rLogo[50:60, 50:60]
> >>>>
> >>>> library(grid) # Original image grid.raster(rLogoBit)
> >>>> grid.newpage() # Subset produces a vector
> >>>> grid.raster(rLogoBit[1:length(rLogoBit)])
> >>>>
> >>>
>>> But this should fail IMHO since you're supplying a vector but
> >>> grid.raster (assuming it's the same as rasterImage)
> >>> requires a matrix - exactly as you would expect in the
> >>> matrix case - if a function requires a matrix and you
> >>> pass a vector, it will bark. I think you are explaining
> >>> why going to vector *is* desirable ;). In the current
> >>> case it simply generates the wrong dimensions instead of
> >>> resulting in a vector, right?
> >>
> >> The raster subsetting always produces a raster, but
> >> grid.raster() works with vectors anyway because
> >> as.raster() has a vector method.
> >>
>
> > Well, isn't that the actual problem? ;) It could make sense but it
> > should fail if dimensions are not specified for exactly the reason you
> > mentioned - it is fatal if what you have is really an image ...
>
> > Cheers, Simon
>
>
> >> Anyway, I'm happy to go with things as they now are. I
> >> think at worst it will encourage people to specify two
> >> indices when subsetting a raster object, and that's not a
> >> bad thing.
> >>
> >> Paul
>
> I and (maybe others) are getting a bit lost..
>
> AFAIK:
>
> - Simon proposes that r[i] should return a simple character vector
> such that raster images behave more naturally like matrices.
>
> - Paul seems happy with r[i] returning a (k x 1) raster object
> -- where k almost completely unrelated to the original
> dim(r) -- with the argument that raster subsetting must always
> return a "raster".
Actually, I'd prefer it to return something more sensible, or just fail
(I don't see why raster images should behave in all ways like matrices) ...
> My vote would be for Simon's proposal, hence raster subsetting
> should return a raster only when [i,j] or [i,] or [,j] syntax
> is used.
... but I can also live with (Martin's interpretation of) Simon's proposal.
Paul
> Martin
--
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
paul at stat.auckland.ac.nz
http://www.stat.auckland.ac.nz/~paul/
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