From hb at biostat.ucsf.edu  Wed Feb  2 02:03:18 2011
From: hb at biostat.ucsf.edu (Henrik Bengtsson)
Date: Tue, 1 Feb 2011 17:03:18 -0800
Subject: [Rd] [.raster bug {was "str() on raster objects fails .."}
In-Reply-To: <4D48A96B.9020801@auckland.ac.nz>
References: <AANLkTimycPK-3_mj5OPd0eLauAh41r2-Wkrp7j2jo1sw@mail.gmail.com>
	<19783.49835.494142.88222@stat.math.ethz.ch>
	<4D48A96B.9020801@auckland.ac.nz>
Message-ID: <AANLkTimRBZbzgRfAkE2-VhnFmVRkWz1-cCqeD4VW7O42@mail.gmail.com>

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.

> 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"

> r[1:5,drop=TRUE]
     [,1]
[1,] "#202020"
[2,] "#404040"
[3,] "#606060"
[4,] "#808080"
[5,] "#9F9F9F"
Warning message:
In `[.raster`(r, 1:5, drop = TRUE) :
  'drop' is always implicitly FALSE in '[.raster'

Also,

> r[1:5] <- "white"
> r
     [,1]    [,2]    [,3]      [,4]
[1,] "white" "white" "white"   "#DFDFDF"
[2,] "white" "white" "#BFBFBF" "#FFFFFF"

/Henrik

>
> Paul
>
>> Thank you, Henrik, for the bug report.
>> Martin
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
> --
> 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/
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>



[Rd] [.raster bug {was "str() on raster objects fails .."}
Henrik Bengtsson