17:35 Changeset [6439] by bdezonia
Added comboConcatSplitTest(). Other small edits.
17:23 Changeset [6438] by curtis
Fix ijview's Importer package.
17:22 Changeset [6437] by curtis
Add scaleFactor option to FakeReader for scaling gradient pixel values.
17:03 Changeset [6436] by melissa
Merged r6435 to 4.2 branch.
17:02 Changeset [6435] by melissa
Updated metadata support documentation.
14:48 Changeset [6434] by curtis
Throw IllegalArgumentException for invalid Z/C/T step.
14:11 Changeset [6433] by curtis
Fix intensity scaling issue with signed and float pixel types.
14:10 Changeset [6432] by curtis
Fix problem with step size of 0.
13:25 Changeset [6431] by bdezonia
Clarified TODOs at top of file
12:06 Changeset [6430] by melissa
* Updated OMEXMLMetadataImpl based on  ome-xml:r618. * Fixed a bunch of …
10:35 Changeset [6429] by callan
Added missing "continue". (See  omero:#2467 and r6424)
10:34 Changeset [6428] by callan
Reverting r6427.
10:33 Changeset [6427] by callan
Added missing "continue". (See  omero:#2467 and r6424)
10:21 Changeset [6426] by melissa
Fixed various metadata population bugs in the FV1000 reader. See …
10:18 Changeset [6425] by callan
Update of stylesheets ( ome-xml:r617).
09:32 Changeset [6424] by callan
Handle very nasty null reference sources and remove System.err logging in …


19:32 Changeset [6423] by curtis
Merge ChannelFiller bugfixes to 4.2.
19:32 Changeset [6422] by curtis
Fix more problems with ChannelFiller (some self-inflicted). Seems to work …
16:58 Changeset [6421] by bdezonia
further work on testColorComposite
15:24 Changeset [6420] by curtis
Merge ChannelFiller and FakeReader bugfixes to 4.2.
15:20 Changeset [6419] by curtis
Fix bugs in FakeReader with indexed color.
15:20 Changeset [6418] by curtis
Fix problems with ChannelFiller when lookup table color component count != …
15:19 Changeset [6417] by curtis
Flesh out the IFormatReader javadoc a bit.
10:32 Changeset [6416] by melissa
Fixed physical size Z scaling.
09:28 Changeset [6415] by callan
Merging r6413,r6414 from Trunk
07:48 Changeset [6414] by callan
Fixed some further NPEs when reading OME-TIFF files with no UUID objects.
07:38 Changeset [6413] by callan
General cleanup for metadata classes. Moved and overhauled ome.xml test …


18:25 Changeset [6412] by curtis
More tweaks to the conflicts list.
18:19 Changeset [6411] by curtis
Update conflicts list for latest bf-cpp with WiscScan.
15:39 Changeset [6410] by bdezonia
some refactoring, some composite test code
15:03 Changeset [6409] by melissa
Several fixes to Leica LEI, ND2, and Perkin Elmer readers.
11:59 Changeset [6408] by curtis
Fix image calibration bug.
11:44 Changeset [6407] by curtis
Temporary(?) hack to speed up text file reading.
11:40 Changeset [6406] by melissa
Updated several TIFF-based readers to populate Image.Description more …
10:46 Changeset [6405] by melissa
Fixed Detector/DetectorSettings population to correspond to what the …
10:03 Changeset [6404] by melissa
Trim the image name before placing it in the original metadata hashtable. …
09:55 Changeset [6403] by bdezonia
Minor edits
09:22 Changeset [6402] by callan
Merging r6401 from Trunk.
09:21 Changeset [6401] by callan
slf4j usage. Re-run of code generation ( ome-xml:r612)
06:16 Changeset [6400] by callan
Merging r6398,r6399 from Trunk
06:14 Changeset [6399] by callan
Initializing filenames and roiFilenames on close() in FV1000Reader.
03:45 Changeset [6398] by callan
Ensure that Image names are populated for Leica LEI when …


20:24 Changeset [6397] by curtis
Add reader for tabular text data.
20:24 Changeset [6396] by curtis
Fix bug where readLine and readCString returned "" instead of null at EOF.
20:05 Changeset [6395] by melissa
Read tags into a byte array, so that non-String tags are preserved. See …
17:24 Changeset [6394] by bdezonia
More work on color tests
15:58 Changeset [6393] by bdezonia
Some work on color tests
11:09 Changeset [6392] by melissa
Fixed LUT ordering bug. See  omero:2438.
10:49 Changeset [6391] by callan
Merging r6382,r6390 from Trunk
10:34 Changeset [6390] by callan
Re-run of code generation. ( ome-xml:r607)


19:31 Changeset [6389] by melissa
Prevent each EmissionFilterRef from being populated multiple times.
16:21 Changeset [6388] by melissa
Fixed a bunch of Leica LIF metadata population bugs.
14:53 Changeset [6387] by bdezonia
Made testColorCustom work with corrected BF code
13:44 Changeset [6386] by curtis
Get Bio-Formats C++ bindings working again.
13:20 Changeset [6385] by curtis
Fix rounding error in LUT generation.
12:46 Changeset [6384] by curtis
Update header files for Bio-Formats C++ bindings.
11:54 Changeset [6383] by melissa
Make sure that references get resolved before dumping OME-XML; otherwise, …
11:11 Changeset [6382] by callan
Re-run of code generation. ( ome-xml:r604)
10:29 Changeset [6381] by melissa
Fixed bug in file renaming logic.
10:10 Changeset [6380] by callan
Merging r6379 from Trunk
10:09 Changeset [6379] by callan
Re-run of code generation; customizable enumeration mappings. …
09:51 Changeset [6378] by melissa
Tweaked MetamorphReader.isThisType so that Prairie TIFFs are not picked …
09:28 Changeset [6377] by melissa
Merged r6376 back to trunk.
09:22 Changeset [6376] by melissa
Updated remaining readers to use enumeration handlers.
09:05 Changeset [6375] by callan
Merging r6272,r6373,r6374 from Trunk
06:11 Changeset [6374] by callan
Re-run of code generation ( ome-xml:r602)
05:04 Changeset [6373] by callan
Removed another location of the same problem resolved with r6372.
03:54 Changeset [6372] by callan
Passing the metadata store down to planar TIFF reader causes metadata …


21:00 Changeset [6371] by melissa
Merged r6370 back to trunk.
20:56 Changeset [6370] by melissa
Updated Deltavision and Flex readers to use …
20:38 Changeset [6369] by melissa
Fixed a few SimplePCI dimension bugs.
16:56 Changeset [6368] by melissa
A few more LSM-related fixes.
11:57 Changeset [6367] by melissa
Prevent StringIndexOutOfBoundsException.
10:19 Changeset [6366] by callan
Merging r6365 from Trunk
10:18 Changeset [6365] by callan
Re-run of code generation. ( ome-xml:r601)
09:54 Changeset [6364] by callan
Merging r6359,r6360,r6362,r6263 from Trunk into 4.2 branch.
09:52 Changeset [6363] by callan
Fixing build. Removed unneeded EnumTest in favour of new infrastructure.
09:41 Changeset [6362] by callan
Re-run of code generation for enumeration handlers. Moved enumeration …
09:03 Changeset [6361] by melissa
Fixed several TIFF, Zeiss LSM and Zeiss ZVI bugs exposed during testing.
08:00 Changeset [6360] by callan
Fixing illumination parsing for FV1000 files.
05:50 Changeset [6359] by callan
Restoring LEI file to getUsedFiles().


09:25 Changeset [6358] by melissa
Added missing implementations of isSingleFile(String), …
09:12 Changeset [6357] by melissa
Ported r6356 to 4.2 branch.
06:14 Changeset [6356] by callan
Fixed broken instrument parsing for Leica LEI. (See  omero:#2410)


16:55 Changeset [6355] by melissa
Don't swap bits if the number of bits per pixel is less than or equal to …
15:51 Changeset [6354] by melissa
Prevent NumberFormatException from being thrown when parsing the number of …
14:04 Changeset [6353] by melissa
Call MetadataTools.populatePixels(...) after all of the CoreMetadata …
13:49 Changeset [6352] by melissa
Fixed Well -> WellSample linkage. See  omero:2406.
13:10 Changeset [6351] by melissa
Fixed endianness bug that occurred when expected series were missing.
12:25 Changeset [6350] by melissa
Skip over TIFF tiles/strips that have StripByteCounts == 0. See …
11:13 Changeset [6349] by melissa
Fixed various bugs exposed by test suite.
10:42 Ticket #494 (ImageJ importer plugin does not preserve pixel sizes) created by melissa
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 melissa
When opening data/fake/curtis/520series&series=520&sizeX=96&sizeY=48.fake, …


14:56 Changeset [6348] by bdezonia
minor edits
10:04 Changeset [6347] by bdezonia
minor edit in MemoryRecordTest
09:55 Changeset [6346] by bdezonia
simplified MemoryRecordTest


17:32 Changeset [6345] by curtis
Remove some obsolete code.
17:21 Changeset [6344] by bdezonia
more work on color tests. work on memoryRecord test too.
17:12 Changeset [6343] by curtis
Merge bugfixes for custom color mode.
17:11 Changeset [6342] by curtis
Initial implementation for custom color mode.
15:29 Changeset [6341] by curtis
Merge DataBrowser bugfixes to 4.2 branch.
15:29 Changeset [6340] by curtis
Tweak comments.
15:16 Changeset [6339] by melissa
Fixed IFD entry count calculation for BigTIFF files. See  omero:2390.
15:08 Changeset [6338] by curtis
Fix DataBrowser bugs with newer versions of ImageJ.
14:45 Changeset [6337] by melissa
Fixed LightPath and Image population to prevent AIOOB exceptions. See …
14:19 Changeset [6336] by melissa
Fixed Image -> ROI link. See  omero:2381.
14:11 Changeset [6335] by melissa
Moved SizeT population to prevent it from being 0. See  omero:2377.
14:04 Changeset [6334] by melissa
* Prevent PICT reader from reporting width or height less than 0. * Fixd …
13:07 Changeset [6333] by melissa
* Removed hopefully obsolete hack from RandomAccessInputStream.findString. …
12:00 Changeset [6332] by melissa
Fixed ROI transformation population, see  omero:2373.
09:47 Changeset [6331] by bdezonia
Stubbed out color tests


17:00 Changeset [6330] by melissa
Created 4.2 branch.
16:57 Changeset [6329] by melissa
Fixed a couple of bugs exposed by the test suite.
12:58 Ticket #486 (Generalize support for writing multiple files) closed by melissa
fixed: (In [6328]) Fixed a few multi-file export problems. Closes #486.
12:58 Changeset [6328] by melissa
Fixed a few multi-file export problems. Closes #486.
09:13 Changeset [6327] by melissa
Fixed NPE when closing NetCDF files. See  omero:#2378.
01:04 Changeset [6326] by curtis
Initial, naive implementation of color modes.
00:43 Changeset [6325] by curtis
Remove unfinished VisBio option.
00:40 Changeset [6324] by curtis
Add API for assigning custom colors programmatically.


15:08 Changeset [6323] by melissa
Fixed a couple of dimension calculation bugs.


17:49 Changeset [6322] by curtis
Initial version of color mode selector. Not yet working.
16:34 Changeset [6321] by bdezonia
Some generalization done. Got autoscale test to pass.
13:12 Ticket #492 (OME-TIFF reader does not support qualified namespaces) created by curtis
For the most part, the Bio-Formats OME-TIFF reader expects OME-XML …
12:55 Changeset [6320] by curtis
Use Double.isNaN for clarity instead of equality test (same performance …
12:43 Changeset [6319] by curtis
Change gradient to always start at smallest possible value for integer …
12:17 Changeset [6318] by curtis
Add utility method for extracting a stack trace string from an exception.
12:00 Export edited by melissa
11:21 Changeset [6317] by melissa
Fix for plates that do not have well labels, courtesy of Rubén Muñoz.
10:15 Changeset [6316] by melissa
Parse XY dimensions from IFD.PAGE_NAME entry, if present.


20:02 Changeset [6315] by melissa
Updated Filter population to use new LightPath model.
15:54 Changeset [6314] by bdezonia
Minor reorganization to simplify tracing a BF bug
15:30 Changeset [6313] by melissa
Fixed field count and image names, courtesy of Rubén Muñoz.
13:52 Changeset [6312] by bselinsky
Working version
13:32 Changeset [6311] by curtis
Unused import.
13:31 Changeset [6310] by curtis
13:09 Changeset [6309] by curtis
Fix bug with 8-bit indexed color when less than 3 channels.
13:04 Changeset [6308] by curtis
Add fake filename parameter checks.
12:55 Changeset [6307] by bdezonia
more work on autoscale so that its expected min is not always 0.
12:36 Export edited by melissa
12:35 Changeset [6306] by melissa
Exported OME-XML files can now be read.
12:29 Changeset [6305] by curtis
If indexed is set and pixel type is uint8 or uint16, generate LUTs.
12:28 Changeset [6304] by curtis
Minor tweaks.
10:53 Changeset [6303] by melissa
Fixed bug that caused get*BitLookupTable() to return null if openBytes had …
10:35 Changeset [6302] by bdezonia
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 melissa
fixed: There are now two ways to determine whether or not companion files are …
10:12 Changeset [6301] by melissa
Added 'boolean hasCompanionFiles()' to IFormatReader. See #438.
07:58 Changeset [6300] by melissa
Switched a few logging statements from 'debug' to 'trace'.


18:14 Changeset [6299] by curtis
Add bounds checking for laser wavelength.
17:52 Changeset [6298] by curtis
Fix compile error in TIFF pixels test.
17:36 Changeset [6297] by bdezonia
partial impl of autoscale
17:18 Changeset [6296] by curtis
Remove "standard ImageJ" display option.
17:17 Changeset [6295] by curtis
Fix autoscaling.
17:02 Changeset [6294] by melissa
Added API for tiled image and multi-file export (see #413 and #486). …
17:01 Export created by melissa
16:09 Changeset [6293] by curtis
Remove non-working OMERO importer logic.
16:08 Changeset [6292] by curtis
Put information panel on right instead of bottom.
15:52 Changeset [6291] by curtis
Fix testDatasetConcatenate.
15:10 Changeset [6290] by melissa
Fixed NPE in FileStitcher.setGroupFiles.
14:54 Changeset [6289] by curtis
Fix showinf documentation for -nogroup option.
14:06 Changeset [6288] by bdezonia
fixed split tests. partial implementation of color tests. minor edits.
13:41 Changeset [6287] by curtis
Fix testSplitChannels.
13:00 Changeset [6286] by curtis
Fix bugs in splitZ/C/T tests.
11:48 Changeset [6285] by bdezonia
Added memoryRecord test. Also some code cleanup. Added tests in …


17:37 Changeset [6284] by curtis
Progress on Z/C/T splitting. Works with Importer plugin, but test still …
17:25 Changeset [6283] by bdezonia
minor changes. some more code in color tests.
17:07 Changeset [6282] by bdezonia
Fixed swapdims test to handle all pixel formats.
16:34 Changeset [6281] by bdezonia
Incorporated merge changes. Put in test for out of bounds in range test.
16:33 Changeset [6280] by curtis
Remove obsolete(?) hack -- seems to work without it, at least.
16:28 Changeset [6279] by curtis
Fix a bunch of warnings.
15:58 Changeset [6278] by curtis
Progress on Bio-Formats Importer refactoring.
15:58 Changeset [6277] by curtis
Fix range test indices.
15:28 Changeset [6276] by curtis
Make ZCT index extraction methods smarter about FloatProcessor. Still …
14:57 Changeset [6275] by bdezonia
added an additional test for swapDims
14:48 Changeset [6274] by bdezonia
various impls and improvements. updated swapDimsTest to check order of …
14:07 Changeset [6273] by curtis
Progress on Bio-Formats Importer refactoring: * Fix problem with …
13:46 Changeset [6272] by melissa
Transforming from old OME-XML versions to 2010-04 *finally* works.
13:45 Changeset [6271] by curtis
Cleaner import preparation process (ImportProcess & ImportStep).
12:32 Changeset [6270] by bdezonia
fixed bug in splits tests
11:56 Changeset [6269] by bdezonia
Fixed expected values for split tests
10:16 Changeset [6268] by bdezonia
Merged changes from repository. Improved coverage of test code for …
08:29 Changeset [6267] by melissa
Fixed calls to IMinMaxStore.setChannelGlobalMinMax(...).
08:11 Ticket #491 (Check that Leica LIF physical dimensions are correct) created by melissa
For some Leica LIF files, the interval between timepoints (TimeIncrement) …


21:41 Changeset [6266] by melissa
Re-added AggregateMetadata, DummyMetadata, and FilterMetadata.
18:55 Changeset [6265] by curtis
Progress on Bio-Formats Importer refactoring and tests.
18:48 Changeset [6264] by curtis
Allow toggling of patternIds flag in existing FileStitcher.
18:47 Changeset [6263] by curtis
Use List/ArrayList instead of Vector.
18:47 Changeset [6262] by curtis
Fix some warnings.
17:24 Changeset [6261] by bdezonia
more work on splitting tests
17:06 Changeset [6260] by bdezonia
initial impl of the split routines
16:34 Changeset [6259] by bdezonia
further work: group files, open indiv files
14:41 Changeset [6258] by curtis
Fix bug with dimensional extents.
14:17 Changeset [6257] by melissa
Log transformation warnings using SLF4J instead of printing to System.err.
14:09 Changeset [6256] by melissa
Added command line flag to disable file grouping.
13:52 Changeset [6255] by melissa
Ported r6254 to 4.1 branch.
13:51 Changeset [6254] by melissa
Adjust the dimensions if the dimensions stored in the file do not match …
13:34 Changeset [6253] by bdezonia
added reflection code for testing private vars of ImagePlus
13:02 Changeset [6252] by curtis
Skip file existence check for fake files in FileStitcher.
12:58 Changeset [6251] by bdezonia
Further test implementation


16:53 Changeset [6250] by bdezonia
Further implementation
14:54 Changeset [6249] by curtis
Update the way View5D is invoked.
14:33 Changeset [6248] by bdezonia
partial implementation
14:17 Changeset [6247] by curtis
Progress on Bio-Formats Importer refactoring.


16:42 Changeset [6246] by curtis
Add API to ImporterOptions for setting series, range and crop values.
14:48 Changeset [6245] by curtis
Example demonstrating how to parse physical dimensions.
14:00 Changeset [6244] by curtis
Add brief javadoc justifying Region's existence.
12:33 Ticket #489 (Andor TIFF timestamps are missing or incorrect) closed by melissa
fixed: (In [6243]) * Fixed timestamp parsing bugs in Andor/Fluoview TIFF reader. …
12:33 Changeset [6243] by melissa
* Fixed timestamp parsing bugs in Andor/Fluoview TIFF reader. Closes …


17:18 Changeset [6242] by curtis
Specify a pixel type for the importer tests.
16:40 Changeset [6241] by melissa
Updated Bio-Formats utils to use new MetadataStore/MetadataRetrieve.
16:10 Changeset [6240] by curtis
Initial version of some simple tests for Bio-Formats Importer.
16:10 Changeset [6239] by curtis
Minor progress on Bio-Formats Importer refactoring.
16:09 Changeset [6238] by curtis
Add toplevel utility method for obtaining ImagePlus from path string.
16:08 Changeset [6237] by curtis
Temporarily disable bf-ice and ome-notes components in dependency checker.
16:07 Changeset [6236] by curtis
Add a hack to skip file existence check for .fake files.
16:07 Changeset [6235] by curtis
Add ome-xml.jar to Eclipse classpath, hopefully as a temporary workaround.
14:28 Changeset [6234] by melissa
* Fixed compile errors introduced in r6230. * Added transformations from …
13:24 Ticket #490 (Add support for PDS files) created by melissa
See files in data/pds/.
11:34 Changeset [6233] by melissa
Populate original metadata using StructuredAnnotations.
10:30 Changeset [6232] by melissa
OME-XML generation should work now.


20:41 Changeset [6231] by melissa
Added loci.formats.ome.OMEXMLMetadataImpl, which should have been in …
20:26 Changeset [6230] by melissa
Updated to new MetadataStore/MetadataRetrieve APIs. This may temporarily …
17:23 Changeset [6229] by curtis
Minor progress on Bio-Formats plugins refactoring. * Reorganize some …
17:03 Changeset [6228] by curtis
Change certain logger warnings to debug instead, to avoid extraneous …
16:58 Changeset [6227] by curtis
Fix problems with available() and readString(int). Fixes an indirect bug …
12:22 Changeset [6226] by callan
Re-run of code generation ( ome-xml:r585).
05:09 Changeset [6225] by andrew
Adding code for Metadata Store test cases in Instrument, Plate and ROI.


18:09 Changeset [6224] by curtis
Better error output for scan-deps.
17:43 Changeset [6223] by curtis
Temporary fix for compile errors.
17:27 Changeset [6222] by melissa
Ported r6221 to 4.1 branch.
17:27 Changeset [6221] by melissa
Fixed Nikon type, compression, and image count detection bugs.
17:26 Changeset [6220] by curtis
Open sliced images as hyperstacks by default.
17:25 Changeset [6219] by curtis
Fix Slicer plugin.
13:47 Changeset [6218] by melissa
* Cache previously opened LSM plane if channels are being split. * …
12:10 Changeset [6217] by melissa
Reduced Zeiss LSM IFD parsing time.
12:05 Changeset [6216] by callan
Enabling check of abstract-proprietary type counts. (At the moment only …
12:04 Changeset [6215] by callan
Re-run of code generation ( ome-xml:r584).
11:00 Changeset [6214] by callan
Updated test cases from Andrew and a couple more passing with some changes …
10:32 Changeset [6213] by callan
IMetadata getter test cases.
09:44 Changeset [6212] by callan
Test case updates from Andrew.
09:09 Changeset [6211] by callan
Initial commit of IMetadata mock. Passes initial Image test cases.
09:03 Changeset [6210] by callan
Re-run of code generation ( ome-xml:r583).
05:34 Changeset [6209] by callan
Moved test cases to a mock based foundation.
Note: See TracTimeline for information about the timeline view.