[ome-users] [LOCI] Incomplete colormap with getXBitLookupTable() method.

[Melissa Linkert]

Hi Stephane,

My apologies for the delay.

> Thanks for your reply. By alpha information i meant complete
> transparent color, in GIF you can define a specific color index to
> be transparent (defined in section 23.c.viii). I attached an example
> GIF file with a transparent background.
> I was expecting an alpha entry set to 0 for the transparent color
> index (and 255 for the others) but maybe there is an other way to
> retrieve this information from Bio-Formats ?

This change is under review for inclusion:

https://github.com/openmicroscopy/bioformats/pull/503

That would let you find the transparency color using the "Transparency
index" metadata value as an index into the array returned by
get8BitLookupTable().

Regards,
-Melissa

On Fri, Apr 12, 2013 at 11:08:53AM +0200, Stéphane Dallongeville wrote:
> Hi Melissa,
> 
> Thanks for your reply. By alpha information i meant complete
> transparent color, in GIF you can define a specific color index to
> be transparent (defined in section 23.c.viii). I attached an example
> GIF file with a transparent background.
> I was expecting an alpha entry set to 0 for the transparent color
> index (and 255 for the others) but maybe there is an other way to
> retrieve this information from Bio-Formats ?
> Thanks for the "ExtraSamples" metadata tip, i will try to use it :)
> 
> Best Regards,
> 
> - Stephane
> 
> 
> Le 11/04/2013 22:40, Melissa Linkert a écrit :
> >Hi Stéphane,
> >
> >[CC'ing the ome-users mailing list]
> >
> >>When i open a GIF file with transparent background i can't recover
> >>the alpha information from the colormap value with
> >>get8BitLookupTable() method as it returns only RGB colormap and not
> >>RGBA ones. Is there any plans of providing RGBA colormap information
> >>in future ?
> >The current behavior is correct.  GIF files do not contain alpha information;
> >see the color table definition (section 19) in:
> >
> >http://www.w3.org/Graphics/GIF/spec-gif89a.txt
> >
> >>Also i wanted to know if there some way to know if the 4th channel
> >>of a TIF image basically contains alpha data or color data ? Thanks.
> >The presence of a non-zero "ExtraSamples" entry in the metadata table
> >generally indicates that the last channel is an alpha channel.
> >Bio-Formats itself doesn't make any distinction between alpha and
> >non-alpha data.
> >
> >Regards,
> >-Melissa
> >
> >On Thu, Apr 11, 2013 at 12:09:19PM +0200, Stéphane Dallongeville wrote:
> >>Hi Melissa,
> >>
> >>When i open a GIF file with transparent background i can't recover
> >>the alpha information from the colormap value with
> >>get8BitLookupTable() method as it returns only RGB colormap and not
> >>RGBA ones. Is there any plans of providing RGBA colormap information
> >>in future ?
> >>Also i wanted to know if there some way to know if the 4th channel
> >>of a TIF image basically contains alpha data or color data ? Thanks.
> >>
> >>Best regards,
> >>
> >>-- 
> >>Stephane Dallongeville
> >>Unité d'Analyse d'Images Quantitative
> >>CNRS URA 2582
> >>Institut Pasteur
> >>25 rue du Dr Roux - 75015 Paris - France
> >>
> >>Tel: +33 (0)1 45 68 87 01
> >>Fax: +33 (0)1 40 61 33 30
> >>
> >>http://www.bioimageanalysis.org/
> >>
> 
> 
> -- 
> Stephane Dallongeville
> Unité d'Analyse d'Images Quantitative
> CNRS URA 2582
> Institut Pasteur
> 25 rue du Dr Roux - 75015 Paris - France
> 
> Tel: +33 (0)1 45 68 87 01
> Fax: +33 (0)1 40 61 33 30
> 
> http://www.bioimageanalysis.org/
> 


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