Skip to content

Sprint3 bug fixes #124

merged 21 commits into from Aug 30, 2012

3 participants

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.
@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.
@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).
@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.
@melissalinkert melissalinkert ICS writer: make sure that the .ids file gets closed
Closes #9441.
@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.
@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.
@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.
@melissalinkert melissalinkert Fix potential NPE 930b5c5
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?

Open Microscopy Environment member

Roger, look under the "Issues" tab.

Open Microscopy Environment member

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

Several different failures

Zeiss TIFF:
INFO [27-08-2012 14:36:15.875] testSaneOMEXML: FAILED (CreationDate)

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.

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.

Open Microscopy Environment member

test_images_good passed with the exception of SVS.

@joshmoore joshmoore merged commit 44b2e8e into openmicroscopy:develop Aug 30, 2012
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Something went wrong with that request. Please try again.