[ome-devel] adding woolz to bioformats
Bill Hill
Bill.Hill at igmm.ed.ac.uk
Fri Jul 12 15:11:36 BST 2013
Melissa,
Thanks again! That's it building without any nasty hacks
Writer next, when I get some time.
Cheers,
Bill
> Hi Bill,
>
>> I've pulled a fresh development (the default) branch of
>> bioformats from github and added (reduced git status output):
>>
>>
>> # new file:
>> components/bio-formats/src/loci/formats/in/WlzReader.java
>>
>> # modified: components/scifio/src/loci/formats/readers.txt
>> # modified: scan-deps.pl
>> #
>> # Untracked files:
>> # (use "git add <file>..." to include in what will be committed)
>> #
>> # 00-bills-notes.txt
>> # jar/JWlz.jar
>> # lib/libJWlz-1.3.2.so
>> # lib/libJWlz.so
>>
>> *Q* How do I get the build system to see/use my JWlz jar file?
>
> To have your reader build with jar/JWlz.jar, you
> will need to update the component.classpath property in
> components/bio-formats/build.properties to include ${lib.dir}/JWlz.jar.
> You will also need to add a block similar to this in the "dependencies"
> section of components/bio-formats/pom.xml:
>
> <dependency>
> <groupId>woolz</groupId>
> <artifactId>JWlz</artifactId>
> <version>1.3.2</version>
> <scope>system</scope>
> <systemPath>${basedir}/jar/JWlz.jar</systemPath>
> </dependency>
>
> The JWlz.jar and any of the *.so files that it needs should be committed
> on the same branch as WlzReader.java.
>
>> I modified scan-deps.pl:
>>
>> +my %woolz = (
>> + NAME => "woolz",
>> + TITLE => "Woolz",
>> + JAR => "JWlz.jar",
>> + PACKAGE => "uk.ac.mrc.hgu.Wlz",
>> + LICENSE => "GPL",
>> + URL => "https://github.com/ma-tech/Woolz",
>> + NOTES => <<ZZ,
>> +used for reading/writing Woolz objects
>> +ZZ
>> + VERSION => "1.3.2"
>> +);
>>
>> although I'm not sure if I needed to do this (*Q*)? Trying
>> to run scan-deps.pl just gives complaints about non-existant
>> jar files, eg
>>
>> Component bf-autogen.jar does not exist at ./scan-deps.pl line 623.
>>
>> *Q* Is this normal?
>
> Updating scan-deps.pl is not something you need to worry about; it won't
> affect building the reader. If needed, we can always update it later.
>
>> Previously I just hacked in a symbolic link to my java-woolz
>> sources.
>>
>> I know I've still to write the service that will isolate
>> bioformats from Woolz, but I'll write it once I've a sensible
>> build going with read/write of Woolz objects. That way I'll
>> know what's needed.
>
> Makes complete sense. If any of the above is unclear, just let us know.
>
> Regards,
> -Melissa
>
> On Fri, Jul 12, 2013 at 02:06:53PM +0100, Bill Hill wrote:
>> I'm revisiting the Woolz file reader. This now works for most
>> Woolz objects that would probably be considered images (2D,
>> 3D, 1/2 a dozen pixel/voxel types, no pixels/voxels give an
>> unsigned byte 0/255 image corresponding to the object domain.
>>
>> When I wrote the reader I just hacked the build system to get
>> it going - I now want to add it the right way.
>>
>> I've pulled a fresh development (the default) branch of
>> bioformats from github and added (reduced git status output):
>>
>>
>> # new file:
>> components/bio-formats/src/loci/formats/in/WlzReader.java
>>
>> # modified: components/scifio/src/loci/formats/readers.txt
>> # modified: scan-deps.pl
>> #
>> # Untracked files:
>> # (use "git add <file>..." to include in what will be committed)
>> #
>> # 00-bills-notes.txt
>> # jar/JWlz.jar
>> # lib/libJWlz-1.3.2.so
>> # lib/libJWlz.so
>>
>> *Q* How do I get the build system to see/use my JWlz jar file?
>>
>> I modified scan-deps.pl:
>>
>> +my %woolz = (
>> + NAME => "woolz",
>> + TITLE => "Woolz",
>> + JAR => "JWlz.jar",
>> + PACKAGE => "uk.ac.mrc.hgu.Wlz",
>> + LICENSE => "GPL",
>> + URL => "https://github.com/ma-tech/Woolz",
>> + NOTES => <<ZZ,
>> +used for reading/writing Woolz objects
>> +ZZ
>> + VERSION => "1.3.2"
>> +);
>>
>> although I'm not sure if I needed to do this (*Q*)? Trying
>> to run scan-deps.pl just gives complaints about non-existant
>> jar files, eg
>>
>> Component bf-autogen.jar does not exist at ./scan-deps.pl line 623.
>>
>> *Q* Is this normal?
>>
>> Previously I just hacked in a symbolic link to my java-woolz
>> sources.
>>
>> I know I've still to write the service that will isolate
>> bioformats from Woolz, but I'll write it once I've a sensible
>> build going with read/write of Woolz objects. That way I'll
>> know what's needed.
>>
>> Thanks for the help so far.
>>
>> Cheers,
>> Bill
>>
>>> 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.
>>
>> _______________________________________________
>> 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.
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