From simon.urbanek at r-project.org  Thu Feb  3 01:23:28 2011
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Wed, 2 Feb 2011 19:23:28 -0500
Subject: [Rd] [.raster bug {was "str() on raster objects fails .."}
In-Reply-To: <4D49F024.6090906@stat.auckland.ac.nz>
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	<AANLkTikgSiucEMzfSa2s9YTypkqzYLCab9gJvkGyr0Pz@mail.gmail.com>
	<4D49F024.6090906@stat.auckland.ac.nz>
Message-ID: <74150327-8264-43FF-A4AC-1D3A2C469B4F@r-project.org>


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?

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/
> 
> 



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