From p.murrell at auckland.ac.nz  Mon Feb  7 02:10:20 2011
From: p.murrell at auckland.ac.nz (Paul Murrell)
Date: Mon, 07 Feb 2011 14:10:20 +1300
Subject: [Rd] [.raster bug {was "str() on raster objects fails .."}
In-Reply-To: <74150327-8264-43FF-A4AC-1D3A2C469B4F@r-project.org>
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	<AANLkTikgSiucEMzfSa2s9YTypkqzYLCab9gJvkGyr0Pz@mail.gmail.com>
	<4D49F024.6090906@stat.auckland.ac.nz>
	<74150327-8264-43FF-A4AC-1D3A2C469B4F@r-project.org>
Message-ID: <4D4F467C.8040201@auckland.ac.nz>

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.

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


> Cheers, Simon
>
>
>
>
>
>> Paul
>>
>>> Martin
>>>>> 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
>>>>>>>>
>>>>>>>> ______________________________________________
>>
>> -- 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/
>>
>>
>

-- 
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