[ome-devel] adding woolz to bioformats

[Bill Hill]

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.