[ome-devel] adding woolz to bioformats

[Melissa Linkert]

Hi Bill,

> *Q* At the meeting we talked about some way of encoding the
> origin (Woolz objects have an arbitrary, possibly -ve origin).
> I can't remember, did it involve stage coordinates meta-data?

The metadata I was referring to was:

http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2012-06/ome_xsd.html#StageLabel

...which is "setStageLabelX", "setStageLabelY", and "setStageLabelZ" in
the MetadataStore interface.

> Test run:
> 
> bill at bill-lt% setenv LD_LIBRARY_PATH \
>               /home/bill/src/Bioformats/bioformats/lib
> bill at bill-lt% ./tools/showinf ~/pics/artic_s4_02_06_06.wlz
> Checking file format [Woolz]
> Initializing reader
> WlzReader initializing /home/bill/pics/artic_s4_02_06_06.wlz
> Initialization took 0.038s

That all certainly looks like reasonable output; I would suggest
checking with the '-omexml' flag as well to make sure that the generated
OME-XML is valid.  Do you have a branch for this reader on Github?

Regards,
-Melissa

On Fri, Jun 28, 2013 at 05:00:58PM +0100, Bill Hill wrote:
> After speaking to Melissa at the Paris meeting I've written a
> Woolz reader for bioformats using the JNI. There are still a
> few bits to complete and I haven't started the writer, but
> the basics are there.
> 
> *Q* At the meeting we talked about some way of encoding the
> origin (Woolz objects have an arbitrary, possibly -ve origin).
> I can't remember, did it involve stage coordinates meta-data?
> 
> Test run:
> 
> bill at bill-lt% setenv LD_LIBRARY_PATH \
>               /home/bill/src/Bioformats/bioformats/lib
> bill at bill-lt% ./tools/showinf ~/pics/artic_s4_02_06_06.wlz
> Checking file format [Woolz]
> Initializing reader
> WlzReader initializing /home/bill/pics/artic_s4_02_06_06.wlz
> Initialization took 0.038s
> 
> Reading core metadata
> Filename = /home/bill/pics/artic_s4_02_06_06.wlz
> Series count = 1
> Series #0 :
>         Image count = 1
>         RGB = false (1)
>         Interleaved = false
>         Indexed = false (false color)
>         Width = 424
>         Height = 199
>         SizeZ = 1
>         SizeT = 1
>         SizeC = 1
>         Thumbnail size = 128 x 60
>         Endianness = motorola (big)
>         Dimension order = XYZCT (certain)
>         Pixel type = uint8
>         Valid bits per pixel = 8
>         Metadata complete = false
>         Thumbnail series = false
>         -----
>         Plane #0 <=> Z 0, C 0, T 0
> 
> 
> Reading pixel data (0-0)
>         Read 1/1 planes (100%)
> [done]
> 0.027s elapsed (27.0ms per plane)
> 
> Launching image viewer
> 
> Reading global metadata
> 
> Reading metadata
> 
> Cheers,
> Bill
> -- 
> Bill Hill                              : http://www.hgu.mrc.ac.uk
> MRC Human Genetics Unit                : http://www.emouseatlas.org
> MRC IGMM, University of Edinburgh      : Bill.Hill at igmm.ed.ac.uk
> Western General Hospital               : +44-131-3322471x2119
> Crewe Road, Edinburgh EH4 2XU, UK.     : +44-131-4678456
> 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> 
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