[BioC] EBImage Error in .Call("lib_readImages", as.character(files), as.integer(colormode),

Fri Apr 8 22:32:19 CEST 2011

Hi Greg.

On Fri, Apr 8, 2011 at 12:17 AM, Gregoire Pau <gregoire.pau at embl.de> wrote:
> This is right, Henrik.
>
> The image is 52703x20688: this is huge and I cannot display it on my
> computer. This image would take 52703x20688x8 bytes in memory, i.e. about 8
> GBytes. I am not sure if R (even the 64-bit version of R) can handle such
> big objects.

I don't think the image size in bytes matters, only the total number
of elements, i.e. prod(dim) where dim = c(height,width,depth) and
depth is number of layers (not bits).

May I suggest to add a test for too large dimensions to EBImage so a
more informative error message is generated rather than letting it
slip through and generate that confusing error message on negative
indices.  See my previous message on how to test.

Cheers,

Henrik

>
> Greg
> ---
> Gregoire Pau
> EMBL Research Officer
> http://www.embl.de/~gpau/
>
> On 07/04/11 18:50, Vladimir Morozov wrote:
>>
>> Henrik,
>>
>> I think you make the right guess.
>>
>> Anyway the tiff file is
>> 0500101820.0.tif -
>> https://docs.google.com/leaf?id=0B2NLCeM3RRN2ODIxYWVmZjItYzYwNS00YjJjLWE2YjQtYjQwZGUzZTJkOTBi&hl=en
>>
>> Thanks,
>>
>> Vlad
>>
>>
>> -----Original Message-----
>> From: henrik.bengtsson at gmail.com [mailto:henrik.bengtsson at gmail.com] On
>> Behalf Of Henrik Bengtsson
>> Sent: Thursday, April 07, 2011 12:46 PM
>> To: Vladimir Morozov
>> Cc: Gregoire Pau; bioconductor at stat.math.ethz.ch
>> Subject: Re: [BioC] EBImage Error in .Call("lib_readImages",
>> as.character(files), as.integer(colormode),
>>
>> A guess: Your image dimension might be too large.  In R, matrices/arrays
>> are stored as vectors with a dimension attribute meaning the number of
>> elements is limited by prod(dim(x)) for an array 'x', not max(dim(x)).
>>  Since indices are 32-bit integers in R, you may be hitting the maximum
>> limit:
>>
>>> .Machine$integer.max
>>
>> [1] 2147483647
>>
>> # For your small image that works
>>>
>>> dim<- c(26352,10344,3)
>>> prod(dim)
>>
>> [1] 817755264
>>>
>>> (prod(dim)<= .Machine$integer.max)
>>
>> [1] TRUE
>>
>> # For the 90/50=1.8 times larger one
>>>
>>> dim<- 1.8*c(26352,10344,3)
>>> prod(dim)
>>
>> [1] 4769148700
>>>
>>> (prod(dim)<= .Machine$integer.max)
>>
>> [1] FALSE
>>
>> /Henrik
>>
>>
>> On Thu, Apr 7, 2011 at 9:23 AM, Vladimir Morozov<vmorozov at als.net>  wrote:
>>>
>>> Hi Gregory,
>>>
>>> It dosen't seem to be multiple version problem:
>>>
>>> [rstats:ImageAnal] ldd
>>> /usr/local/lib64/R/library/EBImage/libs/EBImage.so|grep -i magic
>>>        libMagickCore.so.3 =>  /usr/lib64/libMagickCore.so.3
>>> (0x00007f264092f000)
>>>        libMagickWand.so.3 =>  /usr/lib64/libMagickWand.so.3
>>> (0x00007f263e62c000) [rstats:ImageAnal] which convert /usr/bin/convert
>>> [rstats:ImageAnal] ldd /usr/bin/convert
>>>        linux-vdso.so.1 =>   (0x00007fff09bff000)
>>>        libMagickCore.so.3 =>  /usr/lib64/libMagickCore.so.3
>>> (0x00007fdad3f45000)
>>>        libMagickWand.so.3 =>  /usr/lib64/libMagickWand.so.3
>>> (0x00007fdad3c26000)
>>>  ....
>>>
>>>
>>> I can resize the tiff image with ImageMagic:
>>> convert -channel B -resize '50%'
>>> /data/projects/ImageAnal/tiff/0500101820.0.tif
>>> /data/projects/ImageAnal/tiff/0500101820.05.png
>>> And then get it into R :
>>>>
>>>> x<- readImage('/data/projects/ImageAnal/tiff/0500101820.05.png')
>>>> dim(x)
>>>
>>> [1] 26352 10344     3
>>>
>>> However bigger resolution images fail:
>>> convert -channel B -resize '90%'
>>> /data/projects/ImageAnal/tiff/0500101820.0.tif
>>> /data/projects/ImageAnal/tiff/0500101820.09.png
>>>
>>>> x<- readImage('/data/projects/ImageAnal/tiff/0500101820.09.png')
>>>
>>> Error in .Call("lib_readImages", as.character(files),
>>> as.integer(colormode),  :
>>>  negative length vectors are not allowed
>>>
>>> So it doesn't look as ImageMagic problem. If you still want the tiff
>>> file, I can post it
>>>
>>> Best
>>> Vlad
>>>
>>>
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: Gregoire Pau [mailto:gregoire.pau at embl.de]
>>> Sent: Thursday, April 07, 2011 11:53 AM
>>> To: Vladimir Morozov
>>> Cc: 'bioconductor at stat.math.ethz.ch'
>>> Subject: Re: [BioC] EBImage Error in .Call("lib_readImages",
>>> as.character(files), as.integer(colormode),
>>>
>>> Hello Vladimir,
>>>
>>> If ImageMagick is able to read the image, EBImage should be able to do
>>> so. Do you have several installed versions of ImageMagick ? To which
>>> ImageMagick version EBImage is linked to (try otool or ldd on EBImage.so or
>>> EBImage.dll) ?
>>>
>>> TIFF is a not a file format but a file container which can contain exotic
>>> formats: could you please send me your image for inspection ?
>>>
>>> Cheers,
>>>
>>> Greg
>>> ---
>>> Gregoire Pau
>>> EMBL Research Officer
>>> http://www.embl.de/~gpau/
>>>
>>> On 07/04/11 16:48, Vladimir Morozov wrote:
>>>>
>>>> Hi,
>>>>
>>>> I get image reading error:
>>>>
>>>>> x<- readImage(
>>>>
>>>> "/data/projects/ImageAnal/tiff/0500101820.0.tif"
>>>>
>>>> )
>>>>
>>>> Error in .Call("lib_readImages", as.character(files),
>>>> as.integer(colormode), :
>>>>
>>>> negative length vectors are not allowed
>>>>
>>>>> packageVersion('EBImage')
>>>>
>>>> [1] '3.6.0'
>>>>
>>>>>
>>>>
>>>> ImageMagic can work with this image:
>>>>
>>>> convert -channel B -resize '70%'
>>>> /data/projects/ImageAnal/tiff/0500101820.0.tif
>>>> /data/projects/ImageAnal/tiff/0500101820.07.jpeg&
>>>>
>>>>
>>>>
>>>> Tthis image is the bigest image from SVS stack:
>>>>
>>>> convert /data/projects/ImageAnal/svs/0500101820.svs
>>>> /data/projects/ImageAnal/tiff/0500101820.%d.tif
>>>>
>>>> [rstats:ImageAnal] ll -h  /data/projects/ImageAnal/tiff/0500101820.*
>>>> -rw-r--r-- 1 vmorozov users  24K 2011-04-06 15:18
>>>> /data/projects/ImageAnal/tiff/0500101820.1.tif
>>>> -rw-r--r-- 1 vmorozov users  81M 2011-04-06 15:18
>>>> /data/projects/ImageAnal/tiff/0500101820.0.tif
>>>> -rw-r--r-- 1 vmorozov users 155K 2011-04-06 15:18
>>>> /data/projects/ImageAnal/tiff/0500101820.5.tif
>>>> -rw-r--r-- 1 vmorozov users  49K 2011-04-06 15:18
>>>> /data/projects/ImageAnal/tiff/0500101820.4.tif
>>>> -rw-r--r-- 1 vmorozov users 196K 2011-04-06 15:18
>>>> /data/projects/ImageAnal/tiff/0500101820.3.tif
>>>> -rw-r--r-- 1 vmorozov users 3.0M 2011-04-06 15:18
>>>> /data/projects/ImageAnal/tiff/0500101820.2.tif
>>>> [rstats:ImageAnal] convert -v
>>>> Version: ImageMagick 6.6.1-0 2010-07-29 Q16
>>>> http://www.imagemagick.org
>>>> Copyright: Copyright (C) 1999-2010 ImageMagick Studio LLC
>>>> Features: OpenMP
>>>> .....
>>>>
>>>>
>>>>
>>>> I have the same problem with other SVS stacks, i.e readImage fails to
>>>> read the most quality images. it works fine on smaller images
>>>>
>>>>
>>>>
>>>> Any suggestions would be apriciated
>>>>
>>>> Thanks
>>>>
>>>>
>>>>
>>>> Vladimir Morozov
>>>> Sr. Computational Biologist
>>>> ALS Therapy Development Institute
>>>> 215 First Street, Cambridge MA, 02142 www.als.net<http://www.als.net>
>>>> Help End ALS! Click Here<http://als.net/EndALS.aspx>   or Text "EndALS"
>>>> to 20222 to make a $5 donation towards research.
>>>>
>>>>
>>>>
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>>
>>
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