[ome-devel] adding woolz to bioformats

[Bill Hill]

Melissa & Roger,

Thanks for the quick replies. I'll look to getting the
stage labels into the Reader and starting on the writer
next week. *Q* Will these work outside OME, eg in imagej?

I'm not sure how you want to handle the packaging? You'll
probably want to avoid any dependence on Woolz in bioformats.
I've a few Woolz plugins, eg gimp, Amira, etc and my thoughts
were to pushing this out to a new Woolz associated repository
but I'm happy with any way of getting it out there. I've
cloned but not forked in git, seems overkill yet as it's only
a single file modification and two new source files. Some
time ago (before swig existed!) I built a java wrapper
generator for Woolz. This makes most of the higher level stuff
of Woolz available to Java. It's probably only us that would
be interested, but it may be of interest? It's the volume of
stuff that's pulled in that makes me think you might want to
keep it separate, eg 500+ Woolz Java files and 8 Woolz libs.

Cheers,
Bill


> 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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>

-- 
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.