Performance and position count fixes for ND2

[melissalinkert]

Fixes https://trac.openmicroscopy.org.uk/ome/ticket/12477 and https://trac.openmicroscopy.org.uk/ome/ticket/12508. I am intentionally leaving 12477 open though, as I think more investigation at the formats-common level is in order (but likely not appropriate for 5.0.x).

To test, verify that jobs are green, and that QA 9438 (corresponding to ticket 12508) has 4 positions and 4 channels. Physical size X and Y should be present, as should exposure times. Initialization times of large .nd2 files (e.g. nd2/richard, nd2/guillaume) should be slightly smaller with this PR included.

[bramalingam]

Everything looks good. Please merge.

Imported the following files,

%ND2 jobs
nd2_job={10939,'/Volumes/ome/team/rleigh/samples/nd2/nowell/CamND2.nd2';...
11998,'/Volumes/ome/apache_repo/7906';11305,...
'/Volumes/ome/apache_repo/7534';11305,...
'/Volumes/ome/apache_repo/7535';11873,...
'/Volumes/ome/apache_repo/7799';11997,...
'/Volumes/ome/apache_repo/7908';12205,...
'/Volumes/ome/apache_repo/9183';10773,...
'/Volumes/ome/apache_repo/5042';11387,...
'/Volumes/ome/apache_repo/7571';'All_ND2',...
'/Volumes/ome/data_repo/from_skyking/nd2’};

and QA 9438.

Performance on Aug4th :
OMERO Version: 5.0.3-rc3-46-e7a742d-ice35-b94
Bioformats version: 5.0.3-DEV revision: b67297a date: 4 August 2014
Server: 5.0.3
Client: 5.0.3-rc3-46-e7a742d-ice35-b94
Java Version: 1.7.0_11
OS Name: Mac OS X
OS Arch: x86_64
OS Version: 10.9.4

Time take for 224 file sets : 6.5 hours

Performance on August 21st :
OMERO Version: 5.0.3-11-42b1483-ice35-b108
Bioformats version: 5.0.3-DEV revision: d5302f5 date: 21 August 2014
Attempting initial SSL connection to localhost:14064
Server: 5.0.3
Client: 5.0.3-11-42b1483-ice35-b108
Java Version: 1.7.0_11
OS Name: Mac OS X
OS Arch: x86_64
OS Version: 10.9.4

Time taken for 224 file sets : 5.80 hours.

[ghost]

Last commit looks fine and wavelength looks correct in OME-XML.

[melissalinkert]

--rebased-to #1311