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Sprint3 bug fixes #124

Merged
merged 21 commits into from Aug 30, 2012

3 participants

@melissalinkert
Open Microscopy Environment member

First round of bug fixes for sprint 3. Labels in pink are the directories to test.

This also includes several sub-resolution fixes, so some manual testing of that might not be a bad idea.

melissalinkert added some commits Aug 15, 2012
@melissalinkert melissalinkert JPEG: correct for ImageIO not properly decoding YCbCr images 1eac2b9
@melissalinkert melissalinkert JPEG TIFF: only use YCbCr correction for subsampled images 0ef3c67
@melissalinkert melissalinkert Switch to the official 2012-06 OME-XML schema
...instead of the development version on GitHub.
0a25e87
@melissalinkert melissalinkert OME-TIFF: override the ZCT sizes if the image count is 1 e512493
@melissalinkert melissalinkert Refactor Prairie reader to be more readable
Closes #9454.
bd52ea4
@melissalinkert melissalinkert Zeiss: ensure that parseTimestamp returns consistent units
Previously, if the timestamp was stored as a String, the units were
milliseconds since the UNIX epoch (instead of ticks since the
ZVI-specific epoch).
262e0b3
@melissalinkert melissalinkert Perform lossless JPEG-2000 tests in memory
This prevents the creation of thousands of temporary files, which can be
very slow on Mac OS X.

See #9488.
df831f8
@melissalinkert melissalinkert ICS writer: make sure that the .ids file gets closed
Closes #9441.
1453785
@melissalinkert melissalinkert Make getCoreIndex() an IFormatReader method 19b23a8
@melissalinkert melissalinkert Add test to ensure that resolutions are read correctly 2143544
@melissalinkert melissalinkert Fix underlying usage of sub-resolution API 08c54ef
@melissalinkert melissalinkert Imaris HDF: fix usage of sub-resolution API 9adbaa1
@melissalinkert melissalinkert Add test for reading sub-resolution tiles 15d99d5
@melissalinkert melissalinkert SVS: fix usage of sub-resolution API a02d19c
@melissalinkert melissalinkert Zeiss ZVI: fix acquisition date parsing
Reported by Joe Padfield.
ea08582
@melissalinkert melissalinkert Update remaining readers to use sub-resolutions API correctly 8aaf216
@melissalinkert melissalinkert Fix a handful of lingering sub-resolution usage bugs d340ab1
@melissalinkert melissalinkert TIFF: remove cached tile buffer usage
We don't really need this any longer, and it can cause all sorts of
bizarre issues with sub-resolution support.
6ebb17e
@melissalinkert melissalinkert Revert "Zeiss ZVI: fix acquisition date parsing"
This reverts commit ea08582.

Not entirely convinced that this is correct; it certainly doesn't
correctly adjust for different time zones.
74a65cf
@melissalinkert melissalinkert Fix potential NPE 930b5c5
@rleigh-dundee
Open Microscopy Environment member

Sorry to sound stupid, but where are the "labels in pink" you mentioned, because I just see a plain list of commits?

@joshmoore
Open Microscopy Environment member

Roger, look under the "Issues" tab.

@rleigh-dundee
Open Microscopy Environment member

cellsens OK
imaris OK
jpeg2000 OK
leica-scn OK
ome-tiff OK
prairie OK
SVS FAIL
test_per_commit OK
tiff OK
zeiss-tiff FAIL
test_images_good (pending)

SVS:
Several different failures
(/ome/team/rleigh/pr124/svs.log)

Zeiss TIFF:
INFO [27-08-2012 14:36:15.875] testSaneOMEXML: FAILED (CreationDate)
(/ome/team/rleigh/pr124/zeiss-tiff.log)

@melissalinkert
Open Microscopy Environment member

zeiss-tiff failures fixed in the latest commit. SVS failures sadly expected at the moment given that the reordering was done on a different branch.

@rleigh-dundee
Open Microscopy Environment member

I've merged your latest change and set zeiss-tiff and zeiss-zvi going again (zeiss-zvi also failed, not really unexpected), and also test_images_good.

@rleigh-dundee
Open Microscopy Environment member

test_images_good passed with the exception of SVS.

@joshmoore joshmoore merged commit 44b2e8e into openmicroscopy:develop Aug 30, 2012
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