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

[Vladimir Morozov]

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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