Add API to support sub-resolutions

[melissalinkert]

With this branch, each series can now have a pyramid of sub-resolution series associated with it.

The new methods in IFormatReader are:

• setFlattenedResolutions(boolean) (controls whether or not the resolution hierarchy is respected)
• hasFlattenedResolutions() (true by default; whether or not the resolution hierarchy is respected)
• int getResolutionCount() (the number of sub-resolutions for the current series)
• setResolution(int) (sets the current sub-resolution for the current series)
• int getResolution() (gets the current sub-resolution for the current series)

Affected readers have data in the following directories:

• cellsens
• imaris
• jpeg2000
• ome-tiff
• tiff
• svs
• test_images_good

There is also a new test (loci.tests.testng.SubResolutionTest) which will be added to Jenkins once this PR is merged.

[ghost]

Testing with test_images_good, there were 23 commit test failures:

/ome/data_repo/test_images_good/Cell Sens/anda/Image_01_V76 K2 11_lung.vsi:
SizeX: FAILED (Series 0)
/SizeY: FAILED (Series 0)

/ome/data_repo/test_images_good/cellworx/hms/plate1/plate1.HTD:
testPixelsHashes: FAILED (series 0)
testSubimagePixelsHashes: FAILED (series 0)
/ome/data_repo/test_images_good/dv/CFPNEAT01_R3D.dv:
testPixelsHashes: FAILED (series 0)
testSubimagePixelsHashes: FAILED (series 0)
/ome/data_repo/test_images_good/dv/IAGFP-Noc01_R3D.dv:
testPixelsHashes: FAILED (series 0)
testSubimagePixelsHashes: FAILED (series 0)
/ome/data_repo/test_images_good/dv/SMN10ul03_R3D_D3D.dv:
testPixelsHashes: FAILED (series 0)
testSubimagePixelsHashes: FAILED (series 0)
/ome/data_repo/test_images_good/dv/lung-lentiCMtriple-4_R3D.dv:
testPixelsHashes: FAILED (series 0)
testSubimagePixelsHashes: FAILED (series 0)
/ome/data_repo/test_images_good/dv/mt1_R3D_D3D.dv:
testPixelsHashes: FAILED (series 0)
testSubimagePixelsHashes: FAILED (series 0)
/ome/data_repo/test_images_good/dv/off_by_1_a.dv:
testPixelsHashes: FAILED (series 0)
testSubimagePixelsHashes: FAILED (series 0)
/ome/data_repo/test_images_good/dv/test11_R3D.dv:
testPixelsHashes: FAILED (series 0)
testSubimagePixelsHashes: FAILED (series 0)
/ome/data_repo/test_images_good/dv/very_small.d3d.dv:
testPixelsHashes: FAILED (series 0)
testSubimagePixelsHashes: FAILED (series 0)
/ome/data_repo/test_images_good/dv_single/test11_R3D.dv:
testPixelsHashes: FAILED (series 0)
testSubimagePixelsHashes: FAILED (series 0)

Initializing /ome/data_repo/test_images_good/pyramid/101_pyramid:
testValidXML: FAILED ()

Just repo configuration issues for most of these?

[melissalinkert]

The testValidXML failure is fixed on a different branch. Everything else should be working if you're testing against the latest origin/develop with sub-resolutions merged in.

[ghost]

Merged into current develop, all tests pass with zero failures.