[BioC] EBImage: alpha plane in grey scale

Mon Feb 28 14:35:56 CET 2011

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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>