Timeline


and

08/27/09:

17:18 Changeset [5419] by curtis
Add a program for testing RandomAccessInputStream performance.
16:36 Ticket #411 (Add support for Olympus ScanR) created by melissa
ScanR is a multi-file TIFF/XML format for high-content screening. See …
15:11 Changeset [5418] by curtis
* Rename bio-formats-auto package to autogen. * Clean up IniParser a …

08/25/09:

16:56 Changeset [5417] by melissa
Added document describing pre-release testing procedures. Still needs …
12:07 Changeset [5416] by melissa
Added new methods for retrieving used files: * getSeriesUsedFiles() * …

08/24/09:

16:41 Changeset [5415] by curtis
Add dist-flow target to main build file.
16:40 Changeset [5414] by curtis
Add dist target for WiscScan Flow Cytometry application.
12:18 Changeset [5413] by melissa
* Better marker checking. * Added some debugging statements to aid in …
10:24 Changeset [5412] by melissa
Fixed an axis size calculation bug and slightly reduced initialization …

08/21/09:

15:37 Changeset [5411] by curtis
Remove superfluous Image Objective entry.
15:31 Changeset [5410] by melissa
Various validation fixes.
10:35 Changeset [5409] by melissa
Plane elements are needed if StagePosition attributes are going to be …
09:30 Changeset [5408] by melissa
Create a DataInputStream even if the data is not compressed.

08/20/09:

14:33 Changeset [5407] by curtis
Do not populate unused Plane elements.
12:21 Changeset [5406] by melissa
Added missing LUT definitions.
11:19 Changeset [5405] by curtis
Fix whitespace on LUT warning.
10:09 Changeset [5404] by melissa
Fixed how deconvolution log files are parsed, so that EOFExceptions do not …

08/19/09:

15:55 Changeset [5403] by melissa
Cleaned up close()/close(boolean) implementations. close() now delegates …
13:44 Changeset [5402] by curtis
Fix indentation on usage instructions.
13:41 Changeset [5401] by curtis
Fix showinf NullPointerException with no args.
12:21 Changeset [5400] by melissa
Don't assume that '/' is the file separator.
09:22 Changeset [5399] by melissa
Removed debugging statement.
09:14 Changeset [5398] by melissa
Smarter magic bytes and dimension order checking.

08/18/09:

15:04 Changeset [5397] by melissa
Removed unnecessary calls to setObjectiveID and …
14:51 Changeset [5396] by melissa
Fix for datasets where the absolute path to TIFF is incorrect, but the …
11:55 Changeset [5395] by melissa
Fixed log file line parsing.

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.
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