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

[Gregoire Pau]

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.

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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