Timeline


and

05/25/07:

16:07 Changeset [2828] by sorber
Removed unnecessary import.
16:04 Changeset [2827] by sorber
Removed dependency on jgoodies.looks classes not in current looks jar.
15:23 Changeset [2826] by sorber
Added basic automatic spreadsheet launching.
15:03 Ticket #140 (Consolidate error message display methods in OverlayIO and OverlayWidget) created by sorber
There are methods in both classes to display JOptionPane errors. Could be …
13:44 Changeset [2825] by melissa
Check value of "bioformats.forceThumbnails" to determine whether or not to …
11:41 Changeset [2824] by sorber
(sorry) Removed left-over conflict marks.
11:34 Changeset [2823] by sorber
Replaced statistic name strings with constants. Added separate …
09:53 Changeset [2822] by melissa
Save the first image's CustomAttributes when setOriginalMetadata is …

05/24/07:

16:58 Ticket #139 (Clean up VisBio noded overlays code) created by sorber
Refactor: * FreeformTool * PolylineTool * OverlayNodedObject * …
12:38 Ticket #133 (StatsOptionsPane appears in "Load overlays..." file chooser) closed by sorber
fixed: Added extra JFileChooser object. There are now separate such …
09:53 Changeset [2821] by melissa
2007 May 24 release of LOCI Tools
09:53 Changeset [2820] by melissa
2007 May 24 release of LOCI Tools
09:53 Changeset [2819] by melissa
2007 May 24 release of LOCI Tools
09:53 Changeset [2818] by melissa
2007 May 24 release of LOCI Tools
09:53 Changeset [2817] by melissa
2007 May 24 release of LOCI Tools
09:53 Changeset [2816] by melissa
2007 May 24 release of LOCI Tools
09:53 Changeset [2815] by melissa
2007 May 24 release of LOCI Tools
09:53 Changeset [2814] by melissa
2007 May 24 release of LOCI Tools
09:52 Changeset [2813] by melissa
Deleting failed attempt at release.
09:43 Changeset [2812] by melissa
2007 May 24 release of LOCI Tools
09:34 Changeset [2811] by melissa
Reworked most of the logic in initFile to be more general.

05/23/07:

16:43 Ticket #138 (Document details of supported formats) created by melissa
It might be a good idea to document various things about each file format, …
15:59 Changeset [2810] by curtis
Add javadoc for helper class.
15:58 Changeset [2809] by curtis
Fix bug in ZCT coordinate conversions after image planes are done being …
15:56 Changeset [2808] by curtis
Fix bug in Micro Manager close(boolean) method.
14:38 Changeset [2807] by curtis
Fix bug in WiscScan OME-TIFF hack.
14:36 Changeset [2806] by curtis
Eliminate comment filter on long metadata fields (breaks OME-TIFF).
08:50 Changeset [2805] by melissa
Flip images vertically.
08:34 Ticket #137 (FITS and PGM do not work with compressed data) closed by melissa
fixed: Native support for FITS/PGM added in r2804.
08:33 Changeset [2804] by melissa
Eliminated dependency on ImageJ; updated what's new for next release.

05/22/07:

16:07 Ticket #137 (FITS and PGM do not work with compressed data) created by curtis
Both FitsReader and …
15:32 Changeset [2803] by curtis
Fix bug in ImageJ reader with relative path names.

05/21/07:

10:12 Changeset [2802] by melissa
Bug fixes.

05/20/07:

15:04 Changeset [2801] by curtis
Style.
14:51 Changeset [2800] by curtis
Whitespace.

05/18/07:

11:16 Changeset [2799] by curtis
More compact representation of sub-C dimensions.
11:16 Changeset [2798] by curtis
Eliminate no-longer-necessary override of getRGBChannelCount.
11:14 Changeset [2797] by curtis
Only allow setIntensity when no id is set; fix bugs in getSizeC.
10:27 Changeset [2796] by curtis
Move testRead and testConvert into separate ConsoleTools class; eliminate …

05/17/07:

11:41 Ticket #136 (Add pixel value check to testing framework) created by melissa
It would be a good idea to have a test that makes sure the pixel values …
11:34 Ticket #45 (Support for QuickTime rpza codec) closed by melissa
fixed: Finished in r2795.
11:33 Changeset [2795] by melissa
Finished rpza support.
09:05 Changeset [2794] by curtis
Remove Movie Stitcher targets.

05/16/07:

12:46 Ticket #131 (Additional constructors) closed by melissa
fixed: Finished in r2793.
12:46 Changeset [2793] by melissa
Added additional constructors that take an OMENode instead of a file name.
12:35 Changeset [2792] by melissa
Fixed bug with files that have metadata interleaved with pixel data.
12:15 Changeset [2791] by melissa
Added main method to OMEWriter; updated omeul to use OMEWriter.
11:50 Changeset [2790] by curtis
Move Movie Stitcher into Bio-Formats GUI package as "Data Converter."
11:28 Changeset [2789] by curtis
Eliminate some no-longer-necessary exception handling.
11:25 Changeset [2788] by curtis
Simplify some exception handling, and eliminate catch-alls.
11:25 Changeset [2787] by curtis
Fix copyright.
11:16 Changeset [2786] by curtis
Make getZCTCoords and getIndex throw IllegalArgumentException rather than …
10:24 Changeset [2785] by curtis
Split promptId into a separate method for each type of location.

05/15/07:

15:19 Changeset [2784] by curtis
More cleanup and modularization of Bio-Formats Importer plugin.
14:19 Changeset [2783] by melissa
Fixed compile error.
14:09 Changeset [2782] by curtis
* Move bzip2-related code to loci.formats.codec package. * No need for …
14:03 Changeset [2781] by curtis
Add LICENSE_PROPERTY constant.
13:12 Changeset [2780] by melissa
First stab at a more usable template editor. Note that there are still a …
12:58 Changeset [2779] by curtis
More work on cleaning up importer code. Not done yet.

05/14/07:

17:19 Ticket #135 (Support for spectral calibration) created by curtis
Slim Plotter assumes that the lifetime histograms are relatively correct …
17:08 Ticket #134 (Align peaks needs to be more configurable) created by curtis
The align peaks is sometimes wrong due to background noise. There need to …

05/11/07:

18:48 Ticket #133 (StatsOptionsPane appears in "Load overlays..." file chooser) created by sorber
To remove, create a new JFileChooser object specifically for opening …
14:38 Changeset [2778] by curtis
Rearrange methods.
14:21 Ticket #132 (Write a tutorial for making measurements in VisBio) created by sorber
The tutorial should describe the steps required to make and record …
10:34 Changeset [2777] by curtis
* Add LuraWave license code prompt as needed * Clean up harvesting of …
08:35 Changeset [2776] by curtis
Small bugfix.

05/10/07:

11:01 Changeset [2775] by melissa
Improved XML parsing.

05/09/07:

10:25 Changeset [2774] by curtis
Add string constant for invalid license code error.
10:25 Changeset [2773] by curtis
Only wrap exception in FormatException if it is not already a …
09:10 Ticket #128 (Support for BioRad companion files) closed by melissa
fixed: Done in r2772.
09:10 Changeset [2772] by melissa
Added support for data.raw and lse.xml companion files.
08:53 Ticket #121 (Support for externally compressed files) closed by melissa
fixed: BZip2 support added in r2771.
08:52 Changeset [2771] by melissa
Added support for bz2-compressed files.
08:09 Changeset [2770] by curtis
Fix jikes warnings.

05/08/07:

18:36 Changeset [2769] by curtis
Explode pixel values according to scale factors.
18:34 Changeset [2768] by curtis
Tweaks.
18:34 Changeset [2767] by curtis
Look for license code every time a plane is extracted instead of …
17:30 Ticket #131 (Additional constructors) created by curtis
The existing constructor requires a template file and an OME-XML source …
16:51 Ticket #63 (Gray out File>Save and QuickSave when appropriate) closed by curtis
wontfix: Development on OME Metadata Editor has ceased in favor of OME Notes …
16:37 Changeset [2766] by curtis
More OME Notebook renaming.
16:19 Changeset [2765] by curtis
Fix compile errors and deprecation warnings.
16:16 Changeset [2764] by curtis
Rename OME Notebook to OME Notes.
16:07 Changeset [2763] by curtis
Rename OME Notebook to OME Notes; rename MetadataNotebook to …
15:25 Ticket #130 (Colorize data in intensity pane according to lifetime values) created by curtis
One of SPCImage's major features is the ability to view an image with …
13:39 Changeset [2762] by melissa
- Fixed used files list for NRRD files - Fixed multi-series issue with …
12:36 Changeset [2761] by curtis
Rename and clarify purpose of readerClasses and writerClasses static …
12:21 Changeset [2760] by curtis
Revert custom readers.txt bugfix. The readerClasses field is a static …
08:55 Changeset [2759] by melissa
Fixed bug with loading custom readers.txt (fix sent by Brian).

05/07/07:

19:20 Changeset [2758] by melissa
Fixed bug in custom semantic type definition.
12:13 Changeset [2757] by melissa
Removed the "mustGroupFiles(String)" method, and replaced it with "int …
08:19 Ticket #129 (Fix how data browser handles OME images) closed by melissa
fixed: Fixed in r2756.
08:18 Changeset [2756] by melissa
Fixed bug with OME images.

05/06/07:

14:16 Changeset [2755] by melissa
Added new methods to IFormatReader to allow more flexible file grouping: …

05/04/07:

15:55 Changeset [2754] by curtis
Load the default readers.txt and/or writers.txt the first time the default …
15:53 Changeset [2753] by curtis
Remove unnecessary import.
11:43 Ticket #129 (Fix how data browser handles OME images) created by melissa
There are several problems with downloading from OME into the data …

05/03/07:

16:50 Changeset [2752] by curtis
2007 May 03 release of LOCI Tools
16:50 Changeset [2751] by curtis
2007 May 03 release of LOCI Tools
16:50 Changeset [2750] by curtis
2007 May 03 release of LOCI Tools
16:50 Changeset [2749] by curtis
2007 May 03 release of LOCI Tools
16:50 Changeset [2748] by curtis
2007 May 03 release of LOCI Tools
16:50 Changeset [2747] by curtis
2007 May 03 release of LOCI Tools
16:50 Changeset [2746] by curtis
2007 May 03 release of LOCI Tools
16:50 Changeset [2745] by curtis
2007 May 03 release of LOCI Tools
16:42 Changeset [2744] by curtis
Use reflection to construct CompositeImage -- otherwise class loader dies …
16:39 Changeset [2743] by melissa
Temporarily commented out stitching logic.
16:37 Changeset [2742] by melissa
Fixed compile error.
16:34 Changeset [2741] by melissa
Fixed interleaving issue.
16:14 Ticket #128 (Support for BioRad companion files) created by melissa
BioRad PIC files can have a companion file with the .raw extension. We …
16:09 Ticket #127 (Upload to OME plugin does not respect Cancel button) closed by melissa
fixed: Fixed in r2740.
16:09 Changeset [2740] by melissa
Fixed possible NPE in OMEWriter; fixed OME upload plugin to respect …
15:58 Ticket #127 (Upload to OME plugin does not respect Cancel button) created by curtis
If the Upload to OME plugin is launched, and Cancel is then pressed on the …
15:19 Changeset [2739] by melissa
Don't throw an exception if there is no companion file.
14:59 Changeset [2738] by melissa
Added support for zip-compressed files.
14:55 Ticket #118 (Support for MetaMorph .ND files) closed by melissa
fixed: Completed in r2737.
14:55 Changeset [2737] by melissa
Preliminary support for .nd companion files.

05/02/07:

15:30 Changeset [2736] by curtis
2007 May 02 release of LOCI Tools
15:30 Changeset [2735] by curtis
2007 May 02 release of LOCI Tools
15:30 Changeset [2734] by curtis
2007 May 02 release of LOCI Tools
15:30 Changeset [2733] by curtis
2007 May 02 release of LOCI Tools
15:30 Changeset [2732] by curtis
2007 May 02 release of LOCI Tools
15:30 Changeset [2731] by curtis
2007 May 02 release of LOCI Tools
15:30 Changeset [2730] by curtis
2007 May 02 release of LOCI Tools
15:30 Changeset [2729] by curtis
2007 May 02 release of LOCI Tools
14:51 Ticket #126 (Investigate leveraging existing ontology/terminology solutions) created by curtis
The graphical template editor (described in ticket #73) needs to provide a …
14:15 Changeset [2728] by curtis
Tweak what's new in preparation for 2007 May 2 release.
14:10 Changeset [2727] by melissa
Added gzip support to whats-new.
14:07 Changeset [2726] by curtis
Whitespace.
14:05 Changeset [2725] by curtis
Whitespace.
14:04 Changeset [2724] by melissa
Fixed several trivial bugs.
13:55 Changeset [2723] by curtis
Only write current slice for output formats that cannot do stacks.
11:26 Ticket #125 (Automatically launch spreadsheet application when exporting overlays) created by sorber
Use system calls to automatically launch Excel, OpenOffice, etc. when …
11:20 Ticket #124 (Use more powerful erasing algorithm in FreeformTool) created by sorber
Erasing currently only works on one freeform at a time. Use an algorithm …
11:16 Ticket #123 (Enable erasing of freeform just drawn) created by sorber
FreeformTool: Eraser tool will not work on freeforms just drawn.
11:05 Changeset [2722] by curtis
Generalize the way the library checking methods work.
10:57 Ticket #122 (OverlayMarker size should scale with zoom) created by sorber
OverlayMarker width should use pixel coordinates and not domain …
10:53 Ticket #88 (Need system to scale selection areas to pixel coordinates) closed by sorber
fixed: Completed scaling of arrow width, polyine proximity circles. Most …
10:50 Ticket #119 (Make sure Polyline and Freeform tools are in good working order) closed by sorber
fixed
10:48 Ticket #102 (OverlayNodedObject getData() method sometimes makes invalid Gridded2DSets) closed by sorber
fixed
10:05 Changeset [2721] by melissa
Added support for reading gzip-compressed files.
08:32 Changeset [2720] by melissa
Fixed Z/T size bug.

05/01/07:

19:19 Ticket #116 (Add Dr. Inman's smoothing procedure to FreeformTool) closed by sorber
fixed: Implemented in FreeformTool.
18:52 Changeset [2719] by sorber
Added Dr. Inman's smoothing algorithm (ticket #116) for OverlayFreeforms. …
18:19 Changeset [2718] by curtis
Remove old OverlayUtil from loci.visbio.util package.
17:53 Changeset [2717] by sorber
Return null if no valid sets in noded object selection layer.
17:50 Changeset [2716] by sorber
Added missing support for negative node coordinates in loadOverlays …
17:39 Changeset [2715] by sorber
Removed unnecessary import of OverlayUtil
17:37 Changeset [2714] by sorber
Fixed bug #104 (bad array length FieldException when filling some …
16:25 Ticket #104 (Polyline getData() sometimes breaks when filled box is checked) closed by sorber
fixed
12:45 Changeset [2713] by curtis
Update implementation notes, and what's new list.
12:17 Changeset [2712] by curtis
Remove unnecessary deprecated method (old method was added since last …
11:23 Changeset [2711] by curtis
Flex reader, using LuraWave decoding library.
10:44 Ticket #121 (Support for externally compressed files) created by melissa
We should be able to read files that have been compressed using gzip (and …
10:27 Changeset [2710] by melissa
Bugfixes.

04/30/07:

14:09 Changeset [2709] by curtis
Fix problem with C sub-dimensions not populated if sizeC is 1.
14:04 Changeset [2708] by curtis
Add warning for mismatch between C sub-dimensions.
14:01 Changeset [2707] by curtis
To handle files with differing numbers of images, check ZCT coordinate …
11:31 Changeset [2706] by curtis
Fix bugs in sub-C dimensions; simplify deprecated method implementations.
09:35 Changeset [2705] by curtis
Fix inverted transmitted channel bug.
09:27 Ticket #44 (Support for AVI msrle codec) closed by melissa
fixed: Finished in r2704.
09:27 Changeset [2704] by melissa
Finished msrle support for AVI; fixed NPE in DICOM reader.
09:26 Changeset [2703] by melissa
Fixed to handle files with different image counts.
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