Timeline


and

08/17/09:

16:25 Changeset [5394] by melissa
Parse metadata from Nugenesistemplate.txt files.
14:31 Changeset [5393] by melissa
* Fixed a few validation issues. * Added new marker to TillVision reader.
13:51 Changeset [5392] by curtis
Add get/setGroupID methods to metadata API, and regenerate.
13:49 Changeset [5391] by curtis
Add "-nosymbols" argument for generating alphanumeric passwords.

08/14/09:

11:56 Changeset [5390] by melissa
Fixed well row/column population to match up with WellSample.Index.
11:13 Changeset [5389] by melissa
Fixed a couple of file grouping and tag length bugs.
10:40 Changeset [5388] by melissa
Added support for alternate directory structure.
08:40 Changeset [5387] by melissa
* Added MetadataTools.populatePixels signature to toggle Image.Name …
04:12 Changeset [5386] by melissa
Fixed file separator replacement.

08/13/09:

10:53 Changeset [5385] by melissa
* Only populate PlaneTiming if the plane index is less than the total …
10:01 Changeset [5384] by melissa
Parse metadata from reusable TIFF tags.
08:47 Changeset [5383] by melissa
Fixed DetectorSettings population, so that DetectorSettings.Binning is not …
05:10 Changeset [5382] by melissa
Throw a more meaningful exception (HandleException) if an I/O error …

08/12/09:

11:14 Changeset [5381] by melissa
Added hack for datasets whose plate dimensions are not specified …
05:36 Changeset [5380] by melissa
Reverted DicomReader to r5378, as r5379 was largely untested.
05:32 Changeset [5379] by melissa
Better checks to ensure that DetectorSettings.Detector is valid.

08/11/09:

09:43 Changeset [5378] by melissa
* Removed unnecessary setId(String) implementation from ChannelFiller. * …
06:39 Changeset [5377] by melissa
Check for lookup tables after reading each plane, and print a warning for …
04:28 Changeset [5376] by melissa
Ensure that Detector and Objective IDs are unique.

08/10/09:

18:42 Changeset [5375] by curtis
Show progress bar while downloading loci_tools.jar upgrade.
15:39 Changeset [5374] by mike
Added the names of the 4 other conflicting methods in WiscScan
14:59 Changeset [5373] by curtis
* Rename native library from bfjace to bfcpp. * Escape conflicting …
13:48 Changeset [5372] by curtis
Remove debugging statement.
13:47 Changeset [5371] by curtis
Parse time base from file rather than hard coding.
13:47 Changeset [5370] by curtis
Record time base in nanoseconds to global metadata.
10:26 Changeset [5369] by melissa
Parse space-separated wavelength strings, and fixed LightSource IDs.
08:09 Changeset [5368] by melissa
Better physical size parsing.
06:49 Changeset [5367] by melissa
Don't call the Colorizer plugin if the ImagePlus object is not visible.
06:46 Changeset [5366] by melissa
Only set Image.Name if files are actually stitched.
06:01 Changeset [5365] by melissa
Fixed ImageTools.bgrToRgb to work with channel counts other than 3.
05:45 Changeset [5364] by melissa
Only populate DetectorSettings.Detector if other DetectorSettings …
05:38 Changeset [5363] by melissa
Make sure that Detector.ID and DetectorSettings.Detector are set …

08/07/09:

14:54 Changeset [5362] by melissa
Catch NumberFormatException when parsing channel metadata.
09:00 Changeset [5361] by curtis
Fix stupid export bug with first/last.

08/06/09:

15:12 Changeset [5360] by curtis
Fix problems with reader state preservation when duplicating reader …
12:26 Changeset [5359] by melissa
* Fixed DateTools.MICROSOFT constant. * Fixed two LSM metadata population …

08/05/09:

15:35 Changeset [5358] by melissa
* Added "sane XML" test to check for common OME-XML errors that are not …
15:13 Changeset [5357] by callan
Math.pow() is incredibly expensive, moving it outside the loop.
14:30 Changeset [5356] by melissa
Use ImageTools.bgrToRgb utility method when possible.
14:12 Changeset [5355] by callan
*sigh* Reverting erroneous changes to Eclipse preferences again.
14:09 Changeset [5354] by callan
Optimize the reading of single channel, 8 or 16 bit greyscale TIFFs and …
14:08 Changeset [5353] by melissa
* Fixed problems with QuickTime files that are not flattened. * Better …
11:16 Changeset [5352] by melissa
Fixed endianness and extended header size calculations.
08:53 Changeset [5351] by melissa
Fixed scaling problems with 16 bit data.

08/04/09:

16:15 Changeset [5350] by curtis
Add support for Paul Barber's time resolved lifetime ICS data.
15:47 Changeset [5349] by curtis
Add DelegateReader.isLegacy() method, and make class abstract.
15:46 Changeset [5348] by curtis
Add support for pixel types beyond uint16 and int16.
15:45 Changeset [5347] by melissa
Be less strict about checking file sizes, to account for differences in …
15:17 Changeset [5346] by melissa
Updated metadata support documentation for HCS formats.
12:35 Changeset [5345] by curtis
Add "-format" command line flag for forcing use of a specific format.
10:29 Changeset [5344] by melissa
* Added min/max arguments to ImageTools.make24Bits methods. * Added …
09:04 Changeset [5343] by melissa
Use a custom DataBuffer for signed short data. This prevents an …

08/03/09:

15:25 Changeset [5342] by melissa
A bunch of improvements to Leica LIF/TCS metadata parsing - still needs …
10:47 Changeset [5341] by melissa
* Fixed COBOL epoch constant. * POITools uses generics when possible. * …

08/01/09:

11:28 Changeset [5340] by curtis
In debug mode, print no exception if header file is missing during type …

07/31/09:

13:16 Ticket #410 (showinf's -fast flag adjusts data too naively) closed by melissa
fixed: (In [5339]) * Fixed scaling problems in make24Bits methods. Closes #410. …
13:16 Changeset [5339] by melissa
* Fixed scaling problems in make24Bits methods. Closes #410. * Added …

07/30/09:

12:30 Changeset [5338] by curtis
Update to latest TIFF API; fix problem with missing methods in …
12:23 Changeset [5337] by melissa
* Eliminated .pty filename length checks. * Use generics in FV1000Reader …

07/29/09:

18:07 Changeset [5336] by curtis
Update to latest TIFF API.
17:55 Changeset [5335] by curtis
Update to latest TIFF API.
17:55 Changeset [5334] by curtis
Finish TiffTools migration; clean up import statements.
16:58 Changeset [5333] by curtis
Fix linker error on Windows (avoid using JInt directly with cout).
14:40 Changeset [5332] by curtis
Tweak text.
14:39 Changeset [5331] by curtis
More reflection testing.
13:11 Changeset [5330] by curtis
Benchmark utility for testing reflection performance.
09:10 Changeset [5329] by melissa
* Style fixes. * Added CodecOptions constructor that takes a CodecOptions …

07/28/09:

21:19 Changeset [5328] by melissa
Ensure that the number of DetectorSettings is less than or equal to the …
19:58 Changeset [5327] by gbonamy
Fixing compilation error. See if importing the …
19:08 Changeset [5326] by gbonamy
Added support for JPEG2000 Lossy compression. Please make sure that the …
16:53 Changeset [5325] by melissa
Updated examples to work with recent revisions. Moved component-specific …
16:11 Ticket #410 (showinf's -fast flag adjusts data too naively) created by curtis
When using the -fast flag with the showinf command line utility, 16-bit …
15:08 Changeset [5324] by curtis
Add MetadataTools.keys(Hashtable) method for easily obtaining sorted keys.
15:07 Changeset [5323] by curtis
Add code for metadata output.
13:55 Changeset [5322] by melissa
Automatically group together .pic files that belong to the same dataset, …
12:50 Changeset [5321] by curtis
Include stdio/stdlib for atoi on Linux; miscellaneous tweaks.
12:06 Changeset [5320] by melissa
getCurrentFile() now returns 'currentId' directly. This prevents an …
11:49 Changeset [5319] by melissa
Fix for file names that contain 'pty', but do not have the '.pty' …
10:40 Changeset [5318] by gbonamy
Fixed improper formating in package.html files.

07/24/09:

11:50 Changeset [5317] by melissa
Smarter .mdb/.lsm file grouping.
11:40 Changeset [5316] by curtis
Read pixels (but do not display) in C++ version of showinf.
11:29 Ticket #409 (int8 BufferedImages are displayed incorrectly) closed by melissa
fixed: (In [5315]) Fixed scaling problems with signed byte data. Closes #409.
11:29 Changeset [5315] by melissa
Fixed scaling problems with signed byte data. Closes #409.
11:21 Changeset [5314] by curtis
* Include LOCI Common library in bf-cpp build. * Progress on C++ version …
10:29 Changeset [5313] by curtis
Avoid bf-cpp compile error with loci.formats.tiff.IFD.IFD constant.
09:54 Changeset [5312] by curtis
Add FilePattern.findPattern(String path) convenience method.
09:11 Changeset [5311] by curtis
Consolidate ImageReader's assertId checks into getReader() method.
08:54 Ticket #409 (int8 BufferedImages are displayed incorrectly) created by melissa
Can be reproduced using data/ics/melissa/signed-8-bit.ics or: […]

07/23/09:

17:00 Changeset [5310] by curtis
Better series macro labels (series_1, series_2, series_3, etc., instead of …
16:59 Changeset [5309] by curtis
Fix potential NullPointerException?
16:58 Changeset [5308] by curtis
Better series names.
16:43 Changeset [5307] by curtis
Add hack to support testing with fake datasets.
16:15 Changeset [5306] by curtis
Fix typos.
16:14 Changeset [5305] by curtis
Add examples of usage to Javadoc.
15:56 Changeset [5304] by curtis
Add "fake" reader for simulating data of various types.
15:04 Changeset [5303] by curtis
Remove mysterious unnecessary constructor.
14:58 Changeset [5302] by curtis
QuickTime should have suffixNecessary = false, not suffixSufficient = …
14:47 Changeset [5301] by curtis
Clean up isThisType implementations.
13:20 Changeset [5300] by curtis
Clean up DataTools byte translation methods: * Deprecate superfluous …
11:11 Changeset [5299] by melissa
If the DV file is a deconvolved file, attempt to parse metadata from the …
10:40 Changeset [5298] by melissa
Populate Detector.Zoom, fixed Image.Name, and swapped …

07/22/09:

16:33 Changeset [5297] by curtis
Fix Windows-specific hacks.
16:11 Changeset [5296] by curtis
Update path to problematic CMYK and RGB constants.
15:13 Ticket #408 (Exception when opening files with > 512 series in ImageJ) created by melissa
Opening data/incell/brian/2008.03.16.13.04.12/2008.03.16.13.04.12.xdce …
14:32 Changeset [5295] by melissa
Fixed transposed row/column dimensions.
14:02 Changeset [5294] by melissa
Use DateTools utility methods to do date/time parsing.
13:25 Changeset [5293] by melissa
Fixed several NPEs and ArrayList usage problems.
08:16 Ticket #407 (Add support for Slidebook spool (.spl) files) created by melissa
Slidebook .sld files are supported, but .spl files are not - a brief …
06:32 Changeset [5292] by callan
Reverting erroneous changes to Eclipse settings.
06:29 Changeset [5291] by callan
* Fixed parsing of different date-time formats. * Fixed issues with IFD …

07/21/09:

17:43 Changeset [5290] by melissa
Fixed macro options to work with 4.0.1 and trunk versions of the importer …
17:32 Changeset [5289] by curtis
Include typedefs for common primitive array types.
17:17 Changeset [5288] by curtis
Eliminate unused variables with potential for NullPointerException.
16:19 Changeset [5287] by curtis
Add MetadataTools.asStore and MetadataTools.asRetrieve convenience …
16:06 Changeset [5286] by melissa
Fixed physical size and objective population.
14:36 Changeset [5285] by melissa
Make sure that minimum metadata is populated, even if OME-XML is …
14:07 Changeset [5284] by melissa
Updated plugin arguments to work with 4.0.1 and trunk versions of …
13:49 Changeset [5283] by melissa
Various MIAS speed improvements. May need a little more work, but a 384 …
08:58 Changeset [5282] by melissa
* Fixed RandomAccessInputStream.readCString() implementation. * Fixed …

07/20/09:

13:23 Changeset [5281] by curtis
Update documentation on Jace to indicate revision 23 or later is needed.
13:17 Changeset [5280] by curtis
Remove JACE_PROXY_API hack (fixed in recent Jace revisions).
13:16 Changeset [5279] by curtis
Remove debugging statements.
12:22 Changeset [5278] by curtis
Only require CMake 2.6.4 on Windows; otherwise require only CMake 2.6.
12:20 Changeset [5277] by curtis
Update to latest Bio-Formats and Jace. Works out of the box now.
10:53 Changeset [5276] by melissa
* FV1000 reader now closes all of its' files. * Removed duplicate …
09:44 Changeset [5275] by melissa
* Set Image.Name to the current file name by default. * TIFF companion …
09:00 Changeset [5274] by melissa
Imaris HDF files now initialize much more quickly. A slightly more …
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