[BioC] EBImage: alpha plane in grey scale

Mon Feb 28 14:55:57 CET 2011

Hello Samuel,

Running the following code on my system:
 > library("EBImage")
 > a = matrix(runif(20*20), 20, 20)
 > writeImage(a, "a.tiff")
 > system("tiffinfo a.tiff")

Gives me:
Image Width: 20 Image Length: 20
   Resolution: 72, 72 pixels/inch
   Bits/Sample: 16
   Compression Scheme: None
   Photometric Interpretation: min-is-black
   FillOrder: msb-to-lsb
   Orientation: row 0 top, col 0 lhs
   Samples/Pixel: 1
   Rows/Strip: 204
   Planar Configuration: single image plane
   Page Number: 0-1
   DocumentName: a.tiff
   Software: ImageMagick 6.5.7-8 2010-12-02 Q16

Only one sample per pixel is present here. I am using EBImage 3.7.1 and 
ImageMagick 6.5.7. It seems that your version of ImageMagick is very old 
and is likely the cause of the extra alpha layer. I guess updating it 
will solve your problem.

Hope this helps,

Best,

Greg
---
Gregoire Pau
EMBL Research Officer
http://www.embl.de/~gpau/

On 28/02/11 14:35, Samuel GRANJEAUD - IR/ICIM wrote:
> Hello,
>
> Sometimes we build examples that do not reflect our minds. Sorry I was
> wrong in putting the same value in the matrix. Nevertheless, the runif
> matrix leads to the same result in respect to my point. As tiffinfo
> enlights it, there is an extra plane (aka ExtraSamples) in the tiff,
> that leads to a SamplePerPixel value of 2. Now BitsPerSample are 16 of
> course.
>
> Best regards.
>
>  > library(EBImage)
> Loading required package: abind
>  > a = matrix(runif(20*20), 20, 20)
>  > writeImage(a, "a.tiff")
>  > system("tiffinfo a.tiff")
> TIFF Directory at offset 0x648 (1608)
> Image Width: 20 Image Length: 20
> Resolution: 72, 72 pixels/inch
> Bits/Sample: 16
> Compression Scheme: None
> Photometric Interpretation: min-is-black
> Extra Samples: 1<unassoc-alpha>
> FillOrder: msb-to-lsb
> Orientation: row 0 top, col 0 lhs
> Samples/Pixel: 2
> Rows/Strip: 102
> Planar Configuration: single image plane
> DocumentName: a.tiff
> Software: ImageMagick 6.3.7 12/02/10 Q16 http://www.imagemagick.org
>
>
> Gregoire Pau wrote:
>> Hello Samuel,
>>
>> EBImage uses ImageMagick's WriteImage() to write images and doesn't do
>> anything more. Image format is guessed by ImageMagick from the file
>> name and the dynamic range of the image. As an example, the following
>> code creates a random uniform 16-bit grayscale TIFF 20x20 image:
>> > library("EBImage")
>> > a = matrix(runif(20*20), 20, 20)
>> > display(a)
>> > writeImage(a, "a.tiff")
>>
>> Your example uses an image with only one color and ImageMagick (and
>> therefore EBImage) uses the 1-bit mode of the TIFF image format to
>> write it. The bug you are facing seems to come from the fact that
>> ImageJ does not support the 1-bit TIFF image format.
>>
>> In the future, it would be nice to have more control in the output
>> image format. But, in the meanwhile, just use more colors to force
>> EBImage to use the 16-bit format.
>>
>> Hope this helps,
>> Best regards,
>>
>> Greg
>> ---
>> Gregoire Pau
>> EMBL Research officer
>> http://www.embl.de/~gpau/
>>
>> On 25/02/2011 19:37, Samuel GRANJEAUD - IR/ICIM wrote:
>>> Hello,
>>>
>>> I am using EBImage to convert matrix to tiff grey scale. And I would
>>> like to read them directly in ImageJ. Unfortunately such image contains
>>> an extra plane that is not needed and not supported by ImageJ. This
>>> alpha plane seems to be automatically added at the creation of the image
>>> in the C code (I guess). In ImageMagick API, this is referred as "matte"
>>> http://www.imagemagick.org/api/magick-image.php#MagickSetImageMatte
>>>
>>> If I am not wrong, it would be nice if this alpha plane could be removed
>>> in next release.
>>>
>>> Regards,
>>> Samuel
>>>
>>> ~$ R --vanilla
>>>
>>> R version 2.12.1 (2010-12-16)
>>> Copyright (C) 2010 The R Foundation for Statistical Computing
>>> ISBN 3-900051-07-0
>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>>
>>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>>> You are welcome to redistribute it under certain conditions.
>>> Type 'license()' or 'licence()' for distribution details.
>>>
>>> Natural language support but running in an English locale
>>>
>>> R is a collaborative project with many contributors.
>>> Type 'contributors()' for more information and
>>> 'citation()' on how to cite R or R packages in publications.
>>>
>>> Type 'demo()' for some demos, 'help()' for on-line help, or
>>> 'help.start()' for an HTML browser interface to help.
>>> Type 'q()' to quit R.
>>>
>>> > library(EBImage)
>>> Loading required package: abind
>>> > a <- matrix(10,20,20)
>>> > b <- Image(a)
>>> > b
>>> Image
>>> colormode: Grayscale
>>> storage.mode: double
>>> dim: 20 20
>>> nb.total.frames: 1
>>> nb.render.frames: 1
>>>
>>> imageData(object)[1:5,1:6]:
>>> [,1] [,2] [,3] [,4] [,5] [,6]
>>> [1,] 10 10 10 10 10 10
>>> [2,] 10 10 10 10 10 10
>>> [3,] 10 10 10 10 10 10
>>> [4,] 10 10 10 10 10 10
>>> [5,] 10 10 10 10 10 10
>>>
>>> > writeImage(b,"b.tif")
>>> > system("tiffinfo b.tif")
>>> TIFF Directory at offset 0x6c (108)
>>> Image Width: 20 Image Length: 20
>>> Resolution: 72, 72 pixels/inch
>>> Bits/Sample: 1
>>> Compression Scheme: None
>>> Photometric Interpretation: min-is-black
>>> Extra Samples: 1<unassoc-alpha>
>>> FillOrder: msb-to-lsb
>>> Orientation: row 0 top, col 0 lhs
>>> Samples/Pixel: 2
>>> Rows/Strip: 1638
>>> Planar Configuration: single image plane
>>> DocumentName: b.tif
>>> Software: ImageMagick 6.3.7 12/02/10 Q16 http://www.imagemagick.org
>>> > system("convert b.tif +matte c.tif")
>>> > system("tiffinfo c.tif")
>>> TIFF Directory at offset 0x44 (68)
>>> Image Width: 20 Image Length: 20
>>> Resolution: 72, 72 pixels/inch
>>> Bits/Sample: 1
>>> Compression Scheme: None
>>> Photometric Interpretation: min-is-black
>>> FillOrder: msb-to-lsb
>>> Orientation: row 0 top, col 0 lhs
>>> Samples/Pixel: 1
>>> Rows/Strip: 2730
>>> Planar Configuration: single image plane
>>> DocumentName: c.tif
>>> Software: ImageMagick 6.3.7 12/02/10 Q16 http://www.imagemagick.org
>>> > sessionInfo()
>>> R version 2.12.1 (2010-12-16)
>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>>
>>> locale:
>>> [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.utf8
>>> LC_COLLATE=en_GB.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8 [7]
>>> LC_PAPER=en_GB.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11]
>>> LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets methods base
>>> other attached packages:
>>> [1] EBImage_3.6.0 abind_1.1-0
>>>
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>>
>