From p.murrell at auckland.ac.nz  Wed Feb  2 02:16:58 2011
From: p.murrell at auckland.ac.nz (Paul Murrell)
Date: Wed, 02 Feb 2011 14:16:58 +1300
Subject: [Rd] [.raster bug {was "str() on raster objects fails .."}
In-Reply-To: <AANLkTimRBZbzgRfAkE2-VhnFmVRkWz1-cCqeD4VW7O42@mail.gmail.com>
References: <AANLkTimycPK-3_mj5OPd0eLauAh41r2-Wkrp7j2jo1sw@mail.gmail.com>	<19783.49835.494142.88222@stat.math.ethz.ch>	<4D48A96B.9020801@auckland.ac.nz>
	<AANLkTimRBZbzgRfAkE2-VhnFmVRkWz1-cCqeD4VW7O42@mail.gmail.com>
Message-ID: <4D48B08A.40302@auckland.ac.nz>

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.

Paul

>> 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
>>

-- 
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/



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