Timeline
05/24/10:
- 21:00 Changeset [6371] by
- Merged r6370 back to trunk.
- 20:56 Changeset [6370] by
- Updated Deltavision and Flex readers to use …
- 20:38 Changeset [6369] by
- Fixed a few SimplePCI dimension bugs.
- 16:56 Changeset [6368] by
- A few more LSM-related fixes.
- 11:57 Changeset [6367] by
- Prevent StringIndexOutOfBoundsException.
- 10:19 Changeset [6366] by
- Merging r6365 from Trunk
- 10:18 Changeset [6365] by
- Re-run of code generation. ( ome-xml:r601)
- 09:54 Changeset [6364] by
- Merging r6359,r6360,r6362,r6263 from Trunk into 4.2 branch.
- 09:52 Changeset [6363] by
- Fixing build. Removed unneeded EnumTest in favour of new infrastructure.
- 09:41 Changeset [6362] by
- Re-run of code generation for enumeration handlers. Moved enumeration …
- 09:03 Changeset [6361] by
- Fixed several TIFF, Zeiss LSM and Zeiss ZVI bugs exposed during testing.
- 08:00 Changeset [6360] by
- Fixing illumination parsing for FV1000 files.
- 05:50 Changeset [6359] by
- Restoring LEI file to getUsedFiles().
05/21/10:
- 09:25 Changeset [6358] by
- Added missing implementations of isSingleFile(String), …
- 09:12 Changeset [6357] by
- Ported r6356 to 4.2 branch.
- 06:14 Changeset [6356] by
- Fixed broken instrument parsing for Leica LEI. (See omero:#2410)
05/20/10:
- 16:55 Changeset [6355] by
- Don't swap bits if the number of bits per pixel is less than or equal to …
- 15:51 Changeset [6354] by
- Prevent NumberFormatException from being thrown when parsing the number of …
- 14:04 Changeset [6353] by
- Call MetadataTools.populatePixels(...) after all of the CoreMetadata …
- 13:49 Changeset [6352] by
- Fixed Well -> WellSample linkage. See omero:2406.
- 13:10 Changeset [6351] by
- Fixed endianness bug that occurred when expected series were missing.
- 12:25 Changeset [6350] by
- Skip over TIFF tiles/strips that have StripByteCounts == 0. See …
- 11:13 Changeset [6349] by
- Fixed various bugs exposed by test suite.
- 10:42 Ticket #494 (ImageJ importer plugin does not preserve pixel sizes) created by
- Opening data/fv1000/glen/singlesimul.oib in ImageJ with the "Hyperstack" …
- 10:28 Ticket #493 (Series beyond 456 do not appear in ImageJ plugin) created by
- When opening data/fake/curtis/520series&series=520&sizeX=96&sizeY=48.fake, …
05/19/10:
- 14:56 Changeset [6348] by
- minor edits
- 10:04 Changeset [6347] by
- minor edit in MemoryRecordTest
- 09:55 Changeset [6346] by
- simplified MemoryRecordTest
05/18/10:
- 17:32 Changeset [6345] by
- Remove some obsolete code.
- 17:21 Changeset [6344] by
- more work on color tests. work on memoryRecord test too.
- 17:12 Changeset [6343] by
- Merge bugfixes for custom color mode.
- 17:11 Changeset [6342] by
- Initial implementation for custom color mode.
- 15:29 Changeset [6341] by
- Merge DataBrowser bugfixes to 4.2 branch.
- 15:29 Changeset [6340] by
- Tweak comments.
- 15:16 Changeset [6339] by
- Fixed IFD entry count calculation for BigTIFF files. See omero:2390.
- 15:08 Changeset [6338] by
- Fix DataBrowser bugs with newer versions of ImageJ.
- 14:45 Changeset [6337] by
- Fixed LightPath and Image population to prevent AIOOB exceptions. See …
- 14:19 Changeset [6336] by
- Fixed Image -> ROI link. See omero:2381.
- 14:11 Changeset [6335] by
- Moved SizeT population to prevent it from being 0. See omero:2377.
- 14:04 Changeset [6334] by
- * Prevent PICT reader from reporting width or height less than 0. * Fixd …
- 13:07 Changeset [6333] by
- * Removed hopefully obsolete hack from RandomAccessInputStream.findString. …
- 12:00 Changeset [6332] by
- Fixed ROI transformation population, see omero:2373.
- 09:47 Changeset [6331] by
- Stubbed out color tests
05/17/10:
- 17:00 Changeset [6330] by
- Created 4.2 branch.
- 16:57 Changeset [6329] by
- Fixed a couple of bugs exposed by the test suite.
- 12:58 Ticket #486 (Generalize support for writing multiple files) closed by
- fixed: (In [6328]) Fixed a few multi-file export problems. Closes #486.
- 12:58 Changeset [6328] by
- Fixed a few multi-file export problems. Closes #486.
- 09:13 Changeset [6327] by
- Fixed NPE when closing NetCDF files. See omero:#2378.
- 01:04 Changeset [6326] by
- Initial, naive implementation of color modes.
- 00:43 Changeset [6325] by
- Remove unfinished VisBio option.
- 00:40 Changeset [6324] by
- Add API for assigning custom colors programmatically.
05/15/10:
- 15:08 Changeset [6323] by
- Fixed a couple of dimension calculation bugs.
05/14/10:
- 17:49 Changeset [6322] by
- Initial version of color mode selector. Not yet working.
- 16:34 Changeset [6321] by
- Some generalization done. Got autoscale test to pass.
- 13:12 Ticket #492 (OME-TIFF reader does not support qualified namespaces) created by
- For the most part, the Bio-Formats OME-TIFF reader expects OME-XML …
- 12:55 Changeset [6320] by
- Use Double.isNaN for clarity instead of equality test (same performance …
- 12:43 Changeset [6319] by
- Change gradient to always start at smallest possible value for integer …
- 12:17 Changeset [6318] by
- Add utility method for extracting a stack trace string from an exception.
- 12:00 Export edited by
- (diff)
- 11:21 Changeset [6317] by
- Fix for plates that do not have well labels, courtesy of Rubén Muñoz.
- 10:15 Changeset [6316] by
- Parse XY dimensions from IFD.PAGE_NAME entry, if present.
05/13/10:
- 20:02 Changeset [6315] by
- Updated Filter population to use new LightPath model.
- 15:54 Changeset [6314] by
- Minor reorganization to simplify tracing a BF bug
- 15:30 Changeset [6313] by
- Fixed field count and image names, courtesy of Rubén Muñoz.
- 13:52 Changeset [6312] by
- Working version
- 13:32 Changeset [6311] by
- Unused import.
- 13:31 Changeset [6310] by
- Whitespace.
- 13:09 Changeset [6309] by
- Fix bug with 8-bit indexed color when less than 3 channels.
- 13:04 Changeset [6308] by
- Add fake filename parameter checks.
- 12:55 Changeset [6307] by
- more work on autoscale so that its expected min is not always 0.
- 12:36 Export edited by
- (diff)
- 12:35 Changeset [6306] by
- Exported OME-XML files can now be read.
- 12:29 Changeset [6305] by
- If indexed is set and pixel type is uint8 or uint16, generate LUTs.
- 12:28 Changeset [6304] by
- Minor tweaks.
- 10:53 Changeset [6303] by
- Fixed bug that caused get*BitLookupTable() to return null if openBytes had …
- 10:35 Changeset [6302] by
- minor modification to autoscale testing. refactored memoryRecord test.
- 10:13 Ticket #438 (Allow readers to report whether or not companion files can be expected) closed by
- fixed: There are now two ways to determine whether or not companion files are …
- 10:12 Changeset [6301] by
- Added 'boolean hasCompanionFiles()' to IFormatReader. See #438.
- 07:58 Changeset [6300] by
- Switched a few logging statements from 'debug' to 'trace'.
05/12/10:
- 18:14 Changeset [6299] by
- Add bounds checking for laser wavelength.
- 17:52 Changeset [6298] by
- Fix compile error in TIFF pixels test.
- 17:36 Changeset [6297] by
- partial impl of autoscale
- 17:18 Changeset [6296] by
- Remove "standard ImageJ" display option.
- 17:17 Changeset [6295] by
- Fix autoscaling.
- 17:02 Changeset [6294] by
- Added API for tiled image and multi-file export (see #413 and #486). …
- 17:01 Export created by
- 16:09 Changeset [6293] by
- Remove non-working OMERO importer logic.
- 16:08 Changeset [6292] by
- Put information panel on right instead of bottom.
- 15:52 Changeset [6291] by
- Fix testDatasetConcatenate.
- 15:10 Changeset [6290] by
- Fixed NPE in FileStitcher.setGroupFiles.
- 14:54 Changeset [6289] by
- Fix showinf documentation for -nogroup option.
- 14:06 Changeset [6288] by
- fixed split tests. partial implementation of color tests. minor edits.
- 13:41 Changeset [6287] by
- Fix testSplitChannels.
- 13:00 Changeset [6286] by
- Fix bugs in splitZ/C/T tests.
- 11:48 Changeset [6285] by
- Added memoryRecord test. Also some code cleanup. Added tests in …
05/11/10:
- 17:37 Changeset [6284] by
- Progress on Z/C/T splitting. Works with Importer plugin, but test still …
- 17:25 Changeset [6283] by
- minor changes. some more code in color tests.
- 17:07 Changeset [6282] by
- Fixed swapdims test to handle all pixel formats.
- 16:34 Changeset [6281] by
- Incorporated merge changes. Put in test for out of bounds in range test.
- 16:33 Changeset [6280] by
- Remove obsolete(?) hack -- seems to work without it, at least.
- 16:28 Changeset [6279] by
- Fix a bunch of warnings.
- 15:58 Changeset [6278] by
- Progress on Bio-Formats Importer refactoring.
- 15:58 Changeset [6277] by
- Fix range test indices.
- 15:28 Changeset [6276] by
- Make ZCT index extraction methods smarter about FloatProcessor. Still …
- 14:57 Changeset [6275] by
- added an additional test for swapDims
- 14:48 Changeset [6274] by
- various impls and improvements. updated swapDimsTest to check order of …
- 14:07 Changeset [6273] by
- Progress on Bio-Formats Importer refactoring: * Fix problem with …
- 13:46 Changeset [6272] by
- Transforming from old OME-XML versions to 2010-04 *finally* works.
- 13:45 Changeset [6271] by
- Cleaner import preparation process (ImportProcess & ImportStep).
- 12:32 Changeset [6270] by
- fixed bug in splits tests
- 11:56 Changeset [6269] by
- Fixed expected values for split tests
- 10:16 Changeset [6268] by
- Merged changes from repository. Improved coverage of test code for …
- 08:29 Changeset [6267] by
- Fixed calls to IMinMaxStore.setChannelGlobalMinMax(...).
- 08:11 Ticket #491 (Check that Leica LIF physical dimensions are correct) created by
- For some Leica LIF files, the interval between timepoints (TimeIncrement) …
05/10/10:
- 21:41 Changeset [6266] by
- Re-added AggregateMetadata, DummyMetadata, and FilterMetadata.
- 18:55 Changeset [6265] by
- Progress on Bio-Formats Importer refactoring and tests.
- 18:48 Changeset [6264] by
- Allow toggling of patternIds flag in existing FileStitcher.
- 18:47 Changeset [6263] by
- Use List/ArrayList instead of Vector.
- 18:47 Changeset [6262] by
- Fix some warnings.
- 17:24 Changeset [6261] by
- more work on splitting tests
- 17:06 Changeset [6260] by
- initial impl of the split routines
- 16:34 Changeset [6259] by
- further work: group files, open indiv files
- 14:41 Changeset [6258] by
- Fix bug with dimensional extents.
- 14:17 Changeset [6257] by
- Log transformation warnings using SLF4J instead of printing to System.err.
- 14:09 Changeset [6256] by
- Added command line flag to disable file grouping.
- 13:52 Changeset [6255] by
- Ported r6254 to 4.1 branch.
- 13:51 Changeset [6254] by
- Adjust the dimensions if the dimensions stored in the file do not match …
- 13:34 Changeset [6253] by
- added reflection code for testing private vars of ImagePlus
- 13:02 Changeset [6252] by
- Skip file existence check for fake files in FileStitcher.
- 12:58 Changeset [6251] by
- Further test implementation
05/07/10:
- 16:53 Changeset [6250] by
- Further implementation
- 14:54 Changeset [6249] by
- Update the way View5D is invoked.
- 14:33 Changeset [6248] by
- partial implementation
- 14:17 Changeset [6247] by
- Progress on Bio-Formats Importer refactoring.
05/06/10:
- 16:42 Changeset [6246] by
- Add API to ImporterOptions for setting series, range and crop values.
- 14:48 Changeset [6245] by
- Example demonstrating how to parse physical dimensions.
- 14:00 Changeset [6244] by
- Add brief javadoc justifying Region's existence.
- 12:33 Ticket #489 (Andor TIFF timestamps are missing or incorrect) closed by
- fixed: (In [6243]) * Fixed timestamp parsing bugs in Andor/Fluoview TIFF reader. …
- 12:33 Changeset [6243] by
- * Fixed timestamp parsing bugs in Andor/Fluoview TIFF reader. Closes …
05/05/10:
- 17:18 Changeset [6242] by
- Specify a pixel type for the importer tests.
- 16:40 Changeset [6241] by
- Updated Bio-Formats utils to use new MetadataStore/MetadataRetrieve.
- 16:10 Changeset [6240] by
- Initial version of some simple tests for Bio-Formats Importer.
- 16:10 Changeset [6239] by
- Minor progress on Bio-Formats Importer refactoring.
- 16:09 Changeset [6238] by
- Add toplevel utility method for obtaining ImagePlus from path string.
- 16:08 Changeset [6237] by
- Temporarily disable bf-ice and ome-notes components in dependency checker.
- 16:07 Changeset [6236] by
- Add a hack to skip file existence check for .fake files.
- 16:07 Changeset [6235] by
- Add ome-xml.jar to Eclipse classpath, hopefully as a temporary workaround.
- 14:28 Changeset [6234] by
- * Fixed compile errors introduced in r6230. * Added transformations from …
- 13:24 Ticket #490 (Add support for PDS files) created by
- See files in data/pds/.
- 11:34 Changeset [6233] by
- Populate original metadata using StructuredAnnotations.
- 10:30 Changeset [6232] by
- OME-XML generation should work now.
05/04/10:
- 20:41 Changeset [6231] by
- Added loci.formats.ome.OMEXMLMetadataImpl, which should have been in …
- 20:26 Changeset [6230] by
- Updated to new MetadataStore/MetadataRetrieve APIs. This may temporarily …
- 17:23 Changeset [6229] by
- Minor progress on Bio-Formats plugins refactoring. * Reorganize some …
- 17:03 Changeset [6228] by
- Change certain logger warnings to debug instead, to avoid extraneous …
- 16:58 Changeset [6227] by
- Fix problems with available() and readString(int). Fixes an indirect bug …
- 12:22 Changeset [6226] by
- Re-run of code generation ( ome-xml:r585).
- 05:09 Changeset [6225] by
- Adding code for Metadata Store test cases in Instrument, Plate and ROI.
05/03/10:
- 18:09 Changeset [6224] by
- Better error output for scan-deps.
- 17:43 Changeset [6223] by
- Temporary fix for compile errors.
- 17:27 Changeset [6222] by
- Ported r6221 to 4.1 branch.
- 17:27 Changeset [6221] by
- Fixed Nikon type, compression, and image count detection bugs.
- 17:26 Changeset [6220] by
- Open sliced images as hyperstacks by default.
- 17:25 Changeset [6219] by
- Fix Slicer plugin.
- 13:47 Changeset [6218] by
- * Cache previously opened LSM plane if channels are being split. * …
- 12:10 Changeset [6217] by
- Reduced Zeiss LSM IFD parsing time.
- 12:05 Changeset [6216] by
- Enabling check of abstract-proprietary type counts. (At the moment only …
- 12:04 Changeset [6215] by
- Re-run of code generation ( ome-xml:r584).
- 11:00 Changeset [6214] by
- Updated test cases from Andrew and a couple more passing with some changes …
- 10:32 Changeset [6213] by
- IMetadata getter test cases.
- 09:44 Changeset [6212] by
- Test case updates from Andrew.
- 09:09 Changeset [6211] by
- Initial commit of IMetadata mock. Passes initial Image test cases.
- 09:03 Changeset [6210] by
- Re-run of code generation ( ome-xml:r583).
- 05:34 Changeset [6209] by
- Moved test cases to a mock based foundation.
04/30/10:
- 18:33 Changeset [6208] by
- Minor fix to showinf output.
- 15:09 Ticket #489 (Andor TIFF timestamps are missing or incorrect) created by
- […] See files in data/andor/pariksheet.
- 14:06 Ticket #488 (Add support for OpenEXR files) created by
- See data in data/openexr/ and http://www.openexr.com/.
- 13:58 Changeset [6207] by
- Fixed parsing of ND filter from log file.
- 10:54 Changeset [6206] by
- OME XML metadata implementation. Re-run of code generation ( ome-xml:r582).
04/29/10:
- 12:54 Changeset [6205] by
- Prevent NPE if ROI file is missing.
- 11:59 Changeset [6204] by
- Initial version of OME XML metadata and updated metadata store and …
- 10:57 Changeset [6203] by
- Removed SPA-LEED reader, which hasn't yet been committed.
- 10:41 Changeset [6202] by
- Re-run of code generation ( ome-xml:r579).
- 03:53 Changeset [6201] by
- Reverting changes to Eclipse settings.
- 03:52 Changeset [6200] by
- Removed erroneous classes from the OMERO schema.
04/28/10:
- 10:16 Changeset [6199] by
- Metadata store and retrieve interfaces for examination and testing. Re-run …
04/27/10:
- 14:01 Changeset [6198] by
- Tweaked matching priorities so that reordering works again.
- 13:16 Changeset [6197] by
- * Added Molecular Imaging and JPK readers. See #412. * Minor cleanup in …
- 04:37 Changeset [6196] by
- Move to use primitives for NonNegativeInteger, PositiveInteger and …
- 03:16 Changeset [6195] by
- All tests passing. Re-run of code generation ( ome-xml:r554).
04/26/10:
- 16:03 Changeset [6194] by
- Re-run of code generation ( ome-xml:r552).
- 13:51 Changeset [6193] by
- Added RHK Technologies reader. See #412.
- 12:45 Changeset [6192] by
- Fix classpath problem with Windows batch files.
- 12:11 Changeset [6191] by
- Added SBIG reader and fixed a NIfTI type detection bug. See #412.
04/25/10:
- 13:46 Changeset [6190] by
- * Updated remaining readers to respect MetadataOptions. * Added bounds …
04/24/10:
- 19:25 Changeset [6189] by
- Fix for NullPointerException, courtesy of Lee Kamentsky.
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