Timeline


and

09/06/09:

23:21 Changeset [5443] by curtis
Fix some Eclipse warnings.
23:03 Changeset [5442] by curtis
Fix Eclipse compile errors.

09/04/09:

14:32 Changeset [5441] by curtis
Initial version of LI-FLIM reader; openBytes is not yet implemented.
13:42 Changeset [5440] by curtis
INI parser improvements: * Add support for chapters. * Add …
11:44 Changeset [5439] by curtis
Add convenience method for reading entire file into a string.
11:29 Changeset [5438] by melissa
* Improved plate/well directory detection. * Throw more informative …
07:59 Changeset [5437] by melissa
Fixed NPE in getUsedFiles(boolean).

09/03/09:

19:04 Changeset [5436] by curtis
Fix seeking bug.
18:34 Changeset [5435] by curtis
Add RandomAccessInputStream.findString methods for efficiently searching …
12:17 Changeset [5434] by melissa
Override ImageProcessor.getStatistics(int, int, double, double) to prevent …
12:02 Ticket #413 (Very large images cannot be saved) created by melissa
The current writer API operates on full images. This causes problems when …

09/02/09:

14:49 Changeset [5433] by melissa
Print a warning if SamplesPerPixel is null (instead of throwing an …
14:28 Changeset [5432] by melissa
* Fixed endianness bug in TiffParser.planarUnpack. * Improved CellR …
12:02 Changeset [5431] by melissa
Don't assume that the dimension order is XYCZT.

09/01/09:

15:42 Changeset [5430] by melissa
Fix for (valid) element lengths between 0x8000 and 0xffff inclusive.
14:36 Changeset [5429] by melissa
Fixed FilterSet validation problems.
13:36 Changeset [5428] by melissa
Fix for reading datasets with more than 999 images in a single dimension. …
10:19 Changeset [5427] by melissa
Fix for datasets where the file names are listed before the directory …
09:34 Ticket #412 (Add support for scanning microscopy formats) created by melissa
We have source code from Image SXM for handling several scanning …

08/31/09:

16:22 Changeset [5426] by melissa
Only allow a series to be indexed if it is not RGB.
16:03 Changeset [5425] by melissa
Added FormatHandler.checkSuffix(String, String); fixes compile error.
15:43 Changeset [5424] by melissa
First version of multi-server/configuration logic.
13:07 Changeset [5423] by curtis
Fix for latest version of View5D plugin.
12:14 Changeset [5422] by curtis
Minor tweaks, for clarity.
08:06 Changeset [5421] by melissa
Respect isGroupFiles() when doing file grouping.

08/30/09:

13:17 Changeset [5420] by melissa
* Prevent NPE when constructing indexed color BufferedImages. * A handful …

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.
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