[ome-devel] Woolz reader/writer

[Bill Hill]

Melissa,

I think I've merged and fixed conflicts OK. It seems
to build (using both ant & mvn) and run OK again for me now

I know you can find this stuff from git, but the following
notes on what I did might be useful:

add dir components/bio-formats/src/loci/formats/out

add components/bio-formats/src/loci/formats/in/WlzReader.java
add components/bio-formats/src/loci/formats/out/WlzWriter.java
add components/bio-formats/src/loci/formats/services/WlzService.java
add components/bio-formats/src/loci/formats/services/WlzServiceImpl.java

mod components/scifio/src/loci/formats/readers.txt
mod components/bio-formats/build.properties
mod components/bio-formats/pom.xml b/components/bio-formats/pom.xml
mod components/loci-legacy/src/loci/common/services/services.properties
mod components/scifio/src/loci/formats/writers.txt

Obviously to run something like:

./tools/showinf fruit.wlz

you need your LD_LIBRAY_PATH environment variable set, eg (for
t/csh):

setenv BFHOME   /home/bill/Build/src/bioformats
setenv LD_LIBRARY_PATH $BFHOME/lib:$LD_LIBRARY_PATH

Cheers,
Bill

> Hi Bill,
>
>> Does anyone know the status of the Woolz reader/writer in
>> bioformats. Is this incorporated into the OMERO5 build now?
>> If not can anyone tell if the system is waiting on me to do
>> something?
>>
>> https://github.com/openmicroscopy/bioformats/pull/663
>
> Sorry, this just needs some final review and testing from us - we were
> just a bit distracted by the 4.4.9 release.
>
> The only thing you need to do with that PR at the moment is to merge the
> latest 'develop' branch from the openmicroscopy/bioformats repository
> into your 'develop' branch, resolve any conflicts, and then push the
> branch back to Github.  If you would rather not have to deal with that,
> then I can close PR #663 and open a new one with the same commits, so
> that I own the PR and can take care of any conflict resolution.
>
> Regards,
> -Melissa
>
> On Fri, Oct 18, 2013 at 03:28:55PM +0100, Bill Hill wrote:
>> Does anyone know the status of the Woolz reader/writer in
>> bioformats. Is this incorporated into the OMERO5 build now?
>> If not can anyone tell if the system is waiting on me to do
>> something?
>>
>> https://github.com/openmicroscopy/bioformats/pull/663
>>
>>
>> I see:
>>
>>
>> Build
>>      1078
>> State
>>      Passed
>> Finished
>>      about a month ago
>> Duration
>>      1 hr 20 min 44 sec
>> Commit
>>      69ffe88 (develop)
>> Pull Request
>>      #663 woolz add bioformats
>> Author
>>      Bill Hill
>> Committer
>>      Bill Hill
>> Message
>>      Fixed JWlz.jar dependency path.
>>
>> 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.
>>
>> _______________________________________________
>> ome-devel mailing list
>> ome-devel at lists.openmicroscopy.org.uk
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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.