Timeline


and

04/12/07:

14:48 Ticket #100 (Investigate ways to minimize VisAD's dependencies on Bio-Formats packages) closed by curtis
fixed: I have rearranged and tweaked things to eliminate all unnecessary …
14:39 Ticket #109 (OverlayArrow getData breaks for zero-length arrows) closed by sorber
fixed
14:39 Changeset [2615] by sorber
Set getData to return null for zero-length arrows.
14:36 Ticket #32 (Java2D support is broken) closed by curtis
wontfix: Fixed a bug setting the transparency mode for Java2D in r2614. But there …
14:33 Changeset [2614] by curtis
Avoid exception when setting transparency type for Java2D displays.
14:23 Changeset [2613] by melissa
Fixed white level/black level; only adds detectors if the appropriate …
14:18 Ticket #47 (Microns per pixel support is broken) closed by curtis
fixed: Fixed in r2612.
14:18 Changeset [2612] by curtis
Fix bug with micron width and height scaling.
14:06 Changeset [2611] by curtis
Remove call to setDefaultDisplaySettings that always fails (due to missing …
14:05 Ticket #111 (Better data transform changed events) created by sorber
Mouse events cause unnecessary updates to parts of the VisBio …
13:56 Ticket #110 (Make invisible overlay objects automatically delete themselves) created by sorber
Invisible (zero area, zero length, or fewer than two nodes) should be …
13:38 Changeset [2610] by curtis
Auto-detect calibration values from converted OME-XML.
13:37 Changeset [2609] by curtis
Temporarily comment out more undo/redo menu item code.
13:36 Ticket #109 (OverlayArrow getData breaks for zero-length arrows) created by sorber
When the tip and tail coordinates of an arrow are identical, a divide by …
13:17 Changeset [2608] by melissa
Temporarily commented out logic to disable metadata collection, because it …
13:13 Changeset [2607] by melissa
Fixed pixel size parsing.
12:50 Changeset [2606] by curtis
Pretty print XML output when using showinf's -omexml option.
12:05 Changeset [2605] by curtis
Temporarily comment out state save/restore/undo/redo logic.
11:55 Changeset [2604] by curtis
Style fixes.
11:03 Changeset [2603] by melissa
Improved Metamorph metadata parsing, courtesy of Sebastien Huart.
09:31 Ticket #108 (Investigate composite image stacks in ImageJ) created by melissa
As of ImageJ 1.38n, 16-bit RGB images can be displayed using …
09:23 Ticket #107 (QuickTime mjpb files no longer work) closed by melissa
fixed: Fixed in r2602.
09:23 Changeset [2602] by melissa
Fixed EOFException when reading QuickTime mjpb files.

04/11/07:

15:59 Ticket #107 (QuickTime mjpb files no longer work) created by curtis
As of r2584, attempting to read an mjpb-encoded QuickTime file results in …
15:49 Changeset [2601] by curtis
Style fixes.
15:21 Changeset [2600] by curtis
Allow public instance fields (struct-style).
15:18 Changeset [2599] by curtis
Eliminate deprecation warnings (how did I miss these before...).
15:12 Ticket #106 (make working with large data objects more efficient) created by curtis
VisBio can work with large (e.g., 4096x4096) images, but it is quite slow. …
09:15 Changeset [2598] by melissa
Create a composite image if "merge channels" is checked and we have a …
08:32 Changeset [2597] by melissa
Fixed how core.littleEndian is populated.

04/10/07:

17:38 Changeset [2596] by curtis
ImageJ v1.38n.
17:25 Changeset [2595] by curtis
Readd support for FITS and PGM using ImageJ, modeled after ImageIOReader.
16:41 Ticket #105 (Add rotation buttons to DisplayControls for 2D displays) created by sorber
Add two buttons to DisplayControls for 2D displays to permit clockwise and …
16:34 Ticket #104 (Polyline getData() sometimes breaks when filled box is checked) created by sorber
[…] I seem only able to produce this error when the polyline is …
16:14 Changeset [2594] by curtis
Pass TransformLink to getData method as optional first parameter. This can …
15:29 Changeset [2593] by sorber
Added X and Y column headers for noded lists to overlays spreadsheet.
14:54 Changeset [2592] by sorber
Switched radio button layout to vertical in "Would you like to …
14:44 Ticket #103 (Exception when removing display) created by sorber
[…] (just 3 lines) To generate this exception: * Add the sdub …
14:25 Changeset [2591] by sorber
Replaced hollow selection grid with filled.
13:26 Changeset [2590] by melissa
Multi-file readers now disable metadata collection for all but the first …
12:08 Changeset [2589] by melissa
Re-added Commons Codec acknowledgement.
11:40 Changeset [2588] by melissa
Updated documentation to reflect recent API changes.
11:16 Changeset [2587] by melissa
Eliminated remaining deprecation warnings; moved all deprecated methods to …
10:33 Changeset [2586] by melissa
* Added API to toggle metadata collection. * Fixed bugs in several …

04/09/07:

15:14 Ticket #92 (Notebook crashes when given a file from the command line) closed by melissa
fixed: Fixed in r2585.
15:14 Changeset [2585] by melissa
Better parsing of command-line arguments.
13:55 Changeset [2584] by melissa
Moved several variables out of the readers and into CoreMetadata.
10:23 Ticket #94 (Eliminate IFormatHandler's ubiquitous "String id" parameter) closed by melissa
fixed: Done in r2583. Old signatures have been deprecated for the time being; we …
10:19 Changeset [2583] by melissa
Deprecated all methods that take the 'id' parameter. The id should be st …

04/06/07:

16:36 Ticket #64 (Automatically create 2D display with overlays) closed by sorber
fixed
16:27 Changeset [2582] by sorber
Added 2D w/ overlays option to "Would you like to visualize" dialog.
16:22 Changeset [2581] by sorber
Added feature to update polyline curve length dynamically. Made slight …
15:28 Changeset [2580] by curtis
Updated VisAD JAR to work properly with latest Bio-Formats API.
15:26 Changeset [2579] by curtis
Eliminate deprecation warnings relating to save vs saveImage.
15:19 Changeset [2578] by curtis
Do not throw exception in close method if ome-java.jar is missing.
15:16 Changeset [2577] by curtis
Remove debugging statement.
15:07 Changeset [2576] by curtis
Eliminate deprecation warnings for save vs saveImage.
14:53 Changeset [2575] by curtis
Use @year@ tag instead of hardcoded year.
14:50 Changeset [2574] by curtis
Eliminate deprecation warnings related to save vs saveImage.
14:26 Changeset [2573] by curtis
Remove unnecessary import.
14:26 Changeset [2572] by curtis
Documentation tweaks.
13:53 Changeset [2571] by curtis
Change the way "allow open" stuff works, so that ComboFileFilter need not …
13:41 Ticket #95 (Rename IFormatWriter.save to IFormatWriter.saveImage) closed by melissa
fixed: Finished in r2569.
13:40 Changeset [2570] by melissa
Use FormatWriter.saveImage.
13:39 Changeset [2569] by melissa
Deprecated IFormatWriter.save(String, Image, boolean); replaced with …
13:26 Changeset [2568] by melissa
Updated docs to reflect recent changes.
13:18 Ticket #97 (Fix Leica color channel handling) closed by melissa
fixed: Fixed in r2567. Need to warn users that their data will look different.
13:17 Changeset [2567] by melissa
LeicaReader now properly handles color channels by parsing the channel …
12:41 Ticket #91 (IPLabReader fails to populate OME-XML metadata store) closed by melissa
fixed: Fixed in r2566. This was a bug in OMEXMLMetadataStore, not IPLabReader.
12:41 Changeset [2566] by melissa
Fixed bug that caused an ArrayIndexOutOfBoundsException when populating …
12:38 Changeset [2565] by sorber
Added static field and method to store and retrieve the VisBioFrame. …
12:28 Ticket #93 (Move IFormatReader.swapDimensions into separate DimensionSwapper delegate) closed by melissa
fixed: Done in r2564.
12:27 Changeset [2564] by melissa
Moved dimension swapping logic to ReaderWrapper subclass …
10:15 Ticket #99 (Remove "ignore color lookup table" option) closed by melissa
fixed: Removed all "ignore color table" logic in r2563.
10:14 Changeset [2563] by melissa
Removed "ignore color tables" logic.

04/05/07:

18:08 Changeset [2562] by sorber
Some cleanup to both files.
18:06 Ticket #102 (OverlayNodedObject getData() method sometimes makes invalid Gridded2DSets) created by sorber
Occasionally but rarely get a VisADSetException when drawing ONOs. 99% of …
15:52 Changeset [2561] by sorber
Tweaked OverlayLine selection layer to extend beyond end of line. Fixed …

04/04/07:

19:01 Changeset [2560] by curtis
Fix compile error with IFormatWriter vs FormatWriter API change.
12:05 Changeset [2559] by sorber
Export stats to Excel.
10:24 Changeset [2558] by sorber
Added OverlayStat class.
07:55 Ticket #101 (Look into existing electronic notebooks) created by curtis
Various groups have attempted the electronic lab book concept in the past: …
07:38 Ticket #100 (Investigate ways to minimize VisAD's dependencies on Bio-Formats packages) created by curtis
Right now, VisAD uses several Bio-Formats utility classes, in particular …
07:30 Changeset [2557] by melissa
Moved core metadata variables to loci.formats.CoreMetadata.
07:28 Ticket #99 (Remove "ignore color lookup table" option) created by curtis
The "Ignore color lookup table" option in the Bio-Formats Importer plugin …
07:10 Ticket #98 (Add ability to toggle metadata collection) created by curtis
Right now, Bio-Formats always parses metadata during initialization and …
07:05 Ticket #97 (Fix Leica color channel handling) created by curtis
Leica LEI files have multiple image series, often with differing numbers …
07:01 Ticket #96 (Investigate TestNG data-driven testing) created by curtis
 TestNG supports a data driven testing model that …
07:00 Ticket #95 (Rename IFormatWriter.save to IFormatWriter.saveImage) created by curtis
IFormatReader has openImage; for symmetry IFormatWriter should have …
06:57 Ticket #94 (Eliminate IFormatHandler's ubiquitous "String id" parameter) created by curtis
Currently, an id parameter must be passed to nearly every method within …
06:53 Ticket #93 (Move IFormatReader.swapDimensions into separate DimensionSwapper delegate) created by curtis
The IFormatReader.swapDimensions(String, String) functionality is …
06:49 Ticket #92 (Notebook crashes when given a file from the command line) created by curtis
[…] It looks like the Notebook tries to parse command line arguments as …
06:43 Ticket #91 (IPLabReader fails to populate OME-XML metadata store) created by curtis
[…]
06:32 Changeset [2556] by curtis
Rearrange code a little.
06:12 Changeset [2555] by curtis
* Centralize all dependencies on ij.* into loci.visbio.util.ImageJUtil. …
05:57 Changeset [2554] by curtis
Remove loci.formats.ome dependencies from TiffReader.
05:46 Changeset [2553] by curtis
Remove unnecessary omexml instance field.
05:41 Changeset [2552] by curtis
Remove org.openmicroscopy.xml and loci.formats.ome dependencies from …
05:10 Changeset [2551] by curtis
Tweak documentation.
04:58 Changeset [2550] by curtis
Move configuration file logic out of ImageReader and ImageWriter into new …
04:47 Changeset [2549] by melissa
Re-added constructors.
04:40 Changeset [2548] by melissa
Add min/max values to MetadataStore once they have been computed.
04:03 Changeset [2547] by curtis
Use loci.formats.gui.

04/03/07:

17:45 Changeset [2546] by curtis
Remove note about rubber band box renderer (Abe solved it differently).
17:23 Changeset [2545] by curtis
Use new loci.formats.gui package for file chooser stuff.
17:22 Changeset [2544] by curtis
Use new loci.formats.gui package for file chooser stuff.
17:18 Changeset [2543] by curtis
Prettify some output in testRead.
17:10 Changeset [2542] by curtis
Tweak some comments.
17:08 Changeset [2541] by curtis
Remove some old commented out code.
17:04 Changeset [2540] by curtis
Switch bfview to use ImageViewer in new loci.formats.gui package.
17:03 Changeset [2539] by curtis
Remove ImageJReader from the list.
17:02 Changeset [2538] by curtis
* Move JFileChooser and FileFilter logic (Swing stuff) into separate …
14:17 Changeset [2537] by curtis
MinMaxCalculator wrapper class for channel min/max logic (from Melissa).
08:17 Changeset [2536] by melissa
Removed calls to updateMinMax.
08:14 Changeset [2535] by melissa
Moved channel min/max logic to ReaderWrapper subclass (MinMaxCalculator).

04/02/07:

18:38 Changeset [2534] by sorber
Began overlay statistics save/export feature. Made a small side-effect …
12:07 Changeset [2533] by melissa
Fixed compile error relating to DataTools modifications.
11:46 Changeset [2532] by curtis
Fix bug in IFD string parsing.
11:33 Changeset [2531] by curtis
Remove unnecessary small array allocations from IFD parsing logic.
11:22 Changeset [2530] by melissa
Populate objective magnification in MetadataStore.
11:14 Changeset [2529] by melissa
Reset variables related to sub-channel logic in multi-series readers.
11:03 Changeset [2528] by sorber
Improved OverlayMarker selection layer.
11:01 Changeset [2527] by melissa
Use a static int array to keep track of previous buffer sizes.
09:37 Changeset [2526] by curtis
Eliminate embedded small byte array allocations.
08:53 Changeset [2525] by curtis
Ignore *.class.

03/30/07:

16:29 Changeset [2524] by sorber
Added (preliminary) new, translucent selection layers to all overlays
10:42 Ticket #90 (Format and organize API methods in OverlayObject and subclasses) created by sorber
Check that JavaDoc comments, method order, and method categorization in …

03/29/07:

16:48 Ticket #18 (Support for additional dimensions (wrapped into channel)) closed by curtis
fixed: Completed in r2523.
16:47 Changeset [2523] by curtis
More work on support for multiple dimensions rasterized into C. * …
16:22 Changeset [2522] by curtis
Move old notebook to loci.ome.editor package.
16:21 Changeset [2521] by curtis
Remove unnecessary dependency on ij.IJ.
16:20 Changeset [2520] by curtis
Remove dependency on loci.ome.notebook package (use reflection).

03/27/07:

16:53 Ticket #89 (Update Polyline length as mouse is dragged) created by sorber
Display the approximate length of a Polyline while extending a segment. …
13:51 WikiFormatting edited by sorber
(diff)
13:45 Ticket #88 (Need system to scale selection areas to pixel coordinates) created by sorber
The dimensions of the selection grid or highlighting band should be scaled …

03/26/07:

17:31 Changeset [2519] by curtis
Channel min/max computation logic: * Clean up variable initialization in …
13:48 Changeset [2518] by curtis
Ignore *.class in loci.ome.notebook.editor package.
13:32 Ticket #87 (Exporter plugin doesn't preserve pixel type) closed by melissa
fixed: Fixed in r2517.
13:32 Changeset [2517] by melissa
Fixed exporter to preserve pixel type.
12:47 Ticket #87 (Exporter plugin doesn't preserve pixel type) created by melissa
The Bio-Formats Exporter for ImageJ always writes 8-bit images, even if …
12:35 Changeset [2516] by melissa
Added option to open the OME Notebook with metadata for the current file.
12:31 Changeset [2515] by melissa
Updated notebook scripts to reflect new class structure.
12:24 Changeset [2514] by melissa
Re-added OMEIS typedefs.
12:09 Changeset [2513] by melissa
New version of the OME notebook. Moved old version to old-notebook.
09:25 Changeset [2512] by melissa
Verify that CreationDate field is formatted correctly.
08:25 Ticket #76 (011B1_Morph_A01_s1_w1.TIF fails to import into OME using Bio-Formats) closed by melissa
fixed: As of r2511, the TIFF reader will always properly populate the …
08:23 Changeset [2511] by melissa
Always populate the CreationDate field, even if there isn't a valid date …

03/23/07:

14:30 Changeset [2510] by curtis
Eliminate needless warnings in setChannelGlobalMinMax.
13:48 Ticket #86 (Implement spectral projection feature) created by curtis
Long Yan devised a "spectral projection" technique that produces …
13:32 Ticket #85 (Look into other curve fitting algorithms) created by curtis
There are other potentially useful techniques for exponential curve …
13:29 Ticket #84 (Use system response file to calibrate data via deconvolution) created by curtis
We collect a system response file that represents the instrument's …
11:46 Changeset [2509] by curtis
Comment out support for 2-exponential fits, since it is still broken.
11:38 Ticket #22 (Data colorization is inconsistent) closed by curtis
fixed: Fixed in r2508.
11:37 Ticket #26 (Finish interactive color scale features) closed by curtis
fixed: Finished in r2508. Color scale only goes from red to blue (no violet), but …
11:32 Changeset [2508] by curtis
Add LUT buttons for color widget, add color range override, fix color …
10:21 Changeset [2507] by curtis
Simpler for Slim Plotter to depend on entire loci.formats.util package …
10:20 Changeset [2506] by curtis
Clean up dependencies for loci.visbio.util package.
10:02 Changeset [2505] by curtis
2007 Mar 23 build of VisAD.
09:43 Ticket #83 (ArrayIndexOutOfBoundsException in TIFF metadata parsing) closed by melissa
fixed: This is actually a bug in how WiscScan writes OME-TIFF files - it produces …
09:37 Changeset [2504] by melissa
Added hack to deal with incorrect OME-TIFF files produced by WiscScan.
08:29 Changeset [2503] by melissa
- Fixed NPE while checking for MetaMorph comment. - Fixed bug with TIFF …

03/22/07:

18:29 Ticket #25 (Log scale improvements) closed by curtis
fixed: All known relevant bugs with the log scale fixed in r2502.
18:28 Changeset [2502] by curtis
Fix bug in log scale causing fit results to be affected.
17:51 Changeset [2501] by curtis
Some improvements to the log scale.
14:57 Ticket #83 (ArrayIndexOutOfBoundsException in TIFF metadata parsing) created by curtis
[…]
13:29 Changeset [2500] by sorber
File chooser for export button.
13:05 Ticket #82 (Better support for writing OME-TIFF, including proposed modifications) created by curtis
Bio-Formats can write OME-TIFF by inserting the proper OME-XML string into …
12:56 Ticket #81 (More OME-TIFF code examples) created by curtis
We have several examples that use Bio-Formats to work with OME-TIFF files, …
12:48 Ticket #80 (Update OME-TIFF web site to reflect proposed modifications) created by curtis
I sent …
12:43 Changeset [2499] by curtis
Use Bio-Formats Status events instead of Task events.
12:33 Ticket #79 (Image window does not size down properly after being sized up) closed by curtis
fixed: Fixed in r2498. The problem was due to improper CacheIndicator
12:33 Changeset [2498] by curtis
Fix image window downsizing bug.
12:26 Changeset [2497] by curtis
Command line tool for launching OME Metadata Notebook.
12:25 Changeset [2496] by curtis
Make WiscScan view *not* the default.
12:20 Ticket #79 (Image window does not size down properly after being sized up) created by curtis
The GUI scales upwards properly when the image window is resized to be …
12:06 Ticket #77 (Some TIFF comment key/value pairs are parsed incorrectly) closed by melissa
fixed: Added logic to parse MetaMorph TIFF comments in r2495. Changed from …
12:02 Changeset [2495] by melissa
Parse MetaMorph TIFF comments.
10:25 Ticket #78 (Implement OMERO upload and download logic) created by curtis
Currently, OME I/O contains logic to communicate with an OME database. For …
10:12 Ticket #77 (Some TIFF comment key/value pairs are parsed incorrectly) created by curtis
Most of the key/value pairs found in the ImageDescription for (e.g.) …
10:01 Ticket #76 (011B1_Morph_A01_s1_w1.TIF fails to import into OME using Bio-Formats) created by curtis
Here is the stack trace: […] Examining the OME-XML that Bio-Formats …
09:41 Changeset [2494] by curtis
Eliminate deprecation warning from Java 6 compiler.
09:25 Ticket #40 (AVI writer produces incorrect video files) closed by curtis
fixed: Woo, it plays in Media Player, too.
08:56 Changeset [2493] by melissa
Fixed various LSM bugs.

03/21/07:

14:31 Changeset [2492] by melissa
Fixed bug causing corrupt files to be written.
11:34 Changeset [2491] by melissa
Fixed bug that caused skewing in Totem.
10:08 Ticket #40 (AVI writer produces incorrect video files) reopened by curtis
I tested with ImageJ's [ http://rsb.info.nih.gov/ij/plugins/avi.html AVI …
09:54 Changeset [2490] by curtis
Crappy binary diff utility.
08:57 Changeset [2489] by curtis
Use percentage of maximum for a parameters.
08:53 Ticket #75 (Improve robustness of OME Web Start launcher) created by curtis
To launch VisBio from the OME web interface via Java Web Start, OME …
08:40 Ticket #74 (Leverage the template engine across several distinct use cases) created by curtis
Because of the template engine described in ticket #72, Notes will be …
08:35 Ticket #73 (Graphical template editor) created by curtis
We need a graphical template editor to go along with the OME Notes …
08:28 Ticket #72 (More powerful template engine) created by curtis
While the OME Metadata Editor is a full-featured graphical OME-XML editor, …
08:02 Ticket #71 (Use OME Notes for metadata viewing and editing) created by curtis
VisBio currently has its own, out-of-date metadata viewer. As we develop …

03/20/07:

17:40 Ticket #70 (Additional OME-TIFF sample data) created by curtis
The [ http://www.loci.wisc.edu/ome/ome-tiff-data.html OME-TIFF sample data …
17:27 Ticket #69 (Adapt Data Converter into a Bio-Formats export GUI component) created by curtis
The Data Converter application is a good start on a general-purpose export …
14:49 Ticket #68 (Test all format readers with omebf) created by curtis
The omebf tool allows Bio-Formats to be used with an OME installation to …
14:17 Ticket #67 (Finish OME-TIFF and Bio-Formats section of FAQ web page) created by curtis
The [ http://www.loci.wisc.edu/ome/faq.html#formats OME-TIFF and …
14:14 Ticket #66 (Set default overlays filename) created by sorber
When overlays are exported or saved to text, no default filename is …
13:58 Ticket #65 (Cache indicators can report erroneous caching situation) created by curtis
If the dimensional scroll bars are clicked through too quickly on some …
13:50 Ticket #64 (Automatically create 2D display with overlays) created by sorber
Automatically create a 2D display with overlays after adding dataset. For …
13:48 Ticket #63 (Gray out File>Save and QuickSave when appropriate) created by curtis
For third party formats, the OME Metadata Editor should not be allowed to …
13:42 Changeset [2488] by sorber
Overlays help update: polyline tool.
13:33 Changeset [2487] by sorber
Commenting.
13:31 Ticket #62 (Record proprietary metadata under Image>CustomAttributes in OME-XML) created by curtis
Many third-party formats contain "proprietary" metadata -- information of …
13:27 Ticket #15 (Base TransientSelectBox resizing on pixel and not domain coordinates) closed by sorber
fixed
13:15 Ticket #61 (Integrate Slim Plotter features into VisBio) created by curtis
One of the major original goals of VisBio was to work with data of any …
13:06 Ticket #60 (Quality of exponential curve fit is questionable) created by curtis
The single exponential curve fits look good, but the raw chi-squared error …
12:58 Changeset [2486] by curtis
Limit number of exponential components to 1 or 2, for now.
12:57 Changeset [2485] by curtis
Reenable multi-exponential fitting. Switch multi-exponential fit to have …
11:21 Ticket #59 (Create OME Notes web page) created by curtis
There is a  stub in place for the …
11:19 Ticket #58 (Update OME plugin for ImageJ web site) created by curtis
The OME plugin for ImageJ has undergone many changes, and is no longer in …
09:50 Ticket #57 (Execute ImageJ macros on virtual stacks) created by curtis
Currently, when working with an ImageJ virtual stack, performing any …
08:26 Ticket #43 (Some QuickTime movies erroneously report missing resource fork) closed by melissa
fixed: Fixed in r2484. keck3.mov now throws the following exception: […]
08:25 Ticket #56 (Support for compressed QuickTime headers) created by melissa
Some QuickTime files (e.g. …
08:17 Changeset [2484] by melissa
Explicitly throw an exception if the QuickTime file has a compressed …

03/19/07:

15:25 Ticket #40 (AVI writer produces incorrect video files) closed by melissa
fixed: This was a bug in the AVI reader (not the writer); see r2483. Totem (xine …
15:23 Ticket #55 (Support for Volocity format) created by curtis
There are several file types involved in the Volocity database structure, …
14:57 Ticket #54 (Screencasts for LOCI software tools) created by curtis
It would be really great to create screencasts (see the …
14:49 Changeset [2483] by melissa
Fixed AVI reader bug; simplified some logic in the AVI writer.
13:37 Ticket #53 (OME download feature should use ImageFlatField) created by curtis
VisBio's ability to download from OME uses the Bio-Formats OMEReader
13:33 Ticket #52 (Revamp GUI for next major release) created by curtis
The VisBio GUI is powerful, but quite cumbersome for common tasks. It …
13:29 Ticket #51 (Support for multi-series data) created by curtis
Bio-Formats introduces the concept of a multi-series dataset to deal with …
13:27 Ticket #50 (TIFF export should write in OME-TIFF format) created by curtis
VisBio currently exports TIFF without OME-XML in the header. It should be …
13:25 Ticket #49 (More flexible cache manager) created by curtis
The VisBio cache manager currently keeps exactly one image plane in memory …
13:13 Ticket #48 (Eliminate "range component" concept from VisBio) created by curtis
With the next major revision of VisBio, the idea of "range components" …
13:09 Ticket #47 (Microns per pixel support is broken) created by curtis
With the latest version, checking the "Use microns instead of pixels" …
13:05 Ticket #46 (Thumbnailing support should use Bio-Formats) created by curtis
Going along with the idea that VisBio should lean on Bio-Formats more …
12:46 Ticket #45 (Support for QuickTime rpza codec) created by curtis
We have at least one QuickTime movie that uses the rpza codec in …
12:41 Ticket #44 (Support for AVI msrle codec) created by curtis
Adding support to AVIReader for many different AVI codecs is outside the …
12:36 Ticket #43 (Some QuickTime movies erroneously report missing resource fork) created by curtis
Some movies with unsupported codecs (at least svq3, and maybe others) …
12:33 Ticket #42 (Support for QuickTime Sorenson 3 codec) created by curtis
Some of the [ http://www.loci.wisc.edu/visbio/movies.html videos on from …
12:22 Ticket #41 (QuickTime reader colors for mjpb-encoded data differ from QTJava results) created by curtis
The native QuickTime reader handles the mjpb codec (Motion JPEG-B) but the …
12:12 Ticket #40 (AVI writer produces incorrect video files) created by curtis
The AVI writer sometimes produces videos that are skewed or scrambled. The …
12:02 Ticket #39 (Dimension labels cannot be overridden) created by curtis
VisBio used to allow the user to manually specify the label for each …
11:57 Ticket #38 (Arbitrary slicing does not work for large data) created by curtis
The arbitrary slicing logic in VisBio was recently rewritten to be more …
11:46 Changeset [2482] by curtis
Fix possible configuration skew problems between constituent readers, and …
11:36 Ticket #37 (Resampling should not call unpackFloats) created by curtis
The point of using ImageFlatField within VisBio is for efficiency. There …
11:23 Ticket #36 (4-channel data does not import correctly) created by curtis
Files with 4 channels (and potentially more) throw an exception during …
11:18 Ticket #35 (More intelligent usage of Bio-Formats) created by curtis
VisBio was migrated from its own importer code from the pre-Bio-Formats …
11:01 Ticket #34 (Better ImageFlatField support within VisAD) created by curtis
VisBio is using VisAD's ImageFlatField class, which was added to support …
10:45 Ticket #33 (16-bit images do not display properly) created by curtis
Since switching VisBio over to the ImageFlatField logic, 16-bit images do …
10:43 Ticket #29 (Zeiss LSM/MDB bug: "No such method: mdb_open") closed by melissa
fixed: Fixed in r2481.
10:42 Ticket #32 (Java2D support is broken) created by curtis
VisBio is supposed to support Java2D displays, but currently makes several …
10:42 Changeset [2481] by melissa
Use absolute path to MDB file.
10:31 Changeset [2480] by melissa
Open the MDB file using a mdbtools.jdbc2.File object, *not* a java.io.File …
10:20 Ticket #31 (Save/restore state feature is broken) created by curtis
In theory, VisBio allows the state to be saved to an XML file which can …
10:19 Ticket #30 (State logic needs support for invertible operations) created by curtis
The undo/redo logic currently functions by saving a snapshot of the …
10:02 Ticket #29 (Zeiss LSM/MDB bug: "No such method: mdb_open") created by curtis
VisBio throws an exception when attempting to open …
09:53 Changeset [2479] by curtis
Add unit to tau range label.
09:40 Ticket #28 (Ability to bin channels together and export to SDT) created by curtis
It would be useful for Slim Plotter to be able to bin together several …
09:39 Ticket #27 (Write to SDT format) created by curtis
Certain features of Slim Plotter require the ability to export to SDT …
09:28 Ticket #26 (Finish interactive color scale features) created by curtis
The interactive color scale is a good start toward more fine-grained color …
09:21 Ticket #25 (Log scale improvements) created by curtis
The log scale has some inadequacies. It would be nice if it had proper z …
09:18 Ticket #14 (Format handler subclasses should send status update events) closed by melissa
fixed: Status events added in r2478.
09:16 Ticket #24 (Multiple exponential curve fitting) created by curtis
Preliminary support for multi-exponential curve fitting was added to Slim …
09:15 Changeset [2478] by melissa
Added status events to readers.
09:15 Ticket #23 (Minimum and maximum color value sliders do not work as expected) created by curtis
The min/max color sliders for adjusting the intensity pane's black level …
09:11 Ticket #22 (Data colorization is inconsistent) created by curtis
When toggling between "counts" and "lifetimes" colorization modes, the …
09:06 Ticket #21 (Residuals colorization is inconsistent) created by curtis
When recomputing color ranges is required, such as when toggling linear …

03/16/07:

18:54 Changeset [2477] by sorber
TransientSelectBox now based on pixel coordinates, no longer rotates with …
16:32 Ticket #20 (Use QTObject.dispose() in QTJava-related code to avoid potential crashes ...) created by curtis
A [ http://lists.apple.com/archives/quicktime-java/2006/Jul/msg00039.html
16:22 Ticket #19 (File pattern detection sometimes depends on the file chosen as the basis) created by curtis
Some file groups are not always properly detected due to variations in …
14:33 Changeset [2476] by curtis
2007 Mar 16 release of LOCI Tools
14:33 Changeset [2475] by curtis
2007 Mar 16 release of LOCI Tools
14:33 Changeset [2474] by curtis
2007 Mar 16 release of LOCI Tools
14:33 Changeset [2473] by curtis
2007 Mar 16 release of LOCI Tools
14:33 Changeset [2472] by curtis
2007 Mar 16 release of LOCI Tools
14:33 Changeset [2471] by curtis
2007 Mar 16 release of LOCI Tools
14:33 Changeset [2470] by curtis
2007 Mar 16 release of LOCI Tools
14:33 Changeset [2469] by curtis
2007 Mar 16 release of LOCI Tools
14:32 Changeset [2468] by curtis
Remove Leica Converter targets from build script.
14:23 Changeset [2467] by curtis
Update what's new list with most recent changes.
14:21 Changeset [2466] by curtis
Populate calibration and file info in Image5D.
14:15 Changeset [2465] by melissa
If needed, swap endianness in ZeissLSMReader.openBytes.
13:48 Changeset [2464] by curtis
buildFileChooser moved from FormatHandler to FormatTools.
13:43 Ticket #18 (Support for additional dimensions (wrapped into channel)) created by curtis
Bio-Formats strongly supports OME's 5D model (XYZCT), but LOCI collects …
13:28 Ticket #17 (Bio-Formats importer does not set calibration information for alternate ...) created by curtis
When importing data with the Bio-Formats Importer plugin, if "Standard …
13:26 Changeset [2463] by curtis
Insert Thread.sleep call in MacroManager thread to avoid 100% CPU usage. …
13:05 Ticket #16 (OME Uploader API should be merged with format writer logic) created by curtis
Bio-Formats includes tools for downloading from an OME database …
13:04 Ticket #15 (Base TransientSelectBox resizing on pixel and not domain coordinates) created by sorber
When you stretch the TransientSelectBox, the coordinates of the box …
13:02 Ticket #14 (Format handler subclasses should send status update events) created by curtis
It is now possible for classes that extend FormatHandler to fire status …
12:58 Ticket #13 (Behavior of overlay tools when no data object present) created by sorber
Using overlay tools on a display with no data object causes the overlays …
11:54 Ticket #12 (Override createSubtitle() properly) created by curtis
As [ https://list.nih.gov/cgi-bin/wa?A2=ind0703&L=imagej&H=1&P=11874
11:34 Ticket #11 (Improve behavior on multi-head configurations) created by curtis
I briefly tested VisBio on an nVidia system with TwinView on Linux, and it …

03/15/07:

15:27 Ticket #10 (Export overlay statistics to .xls) created by sorber
Statistics include position, dimensions, etc. of overlays. The overlays …
15:09 Ticket #9 (Improve selection of overlays) created by sorber
Come up with a way less obtrusive than the current yellow grid to indicate …
15:01 Ticket #8 (Improve Checkstyle configuration to enforce additional coding standards) created by curtis
There are several checks that would be nice to add to the checkstyle.xml …
14:53 Ticket #7 (Investigate source code auto-formatting tools) created by curtis
Style checkers are nice, but it would be useful to be able to run our …
14:45 Ticket #6 (Improve VisBio.exe Windows launcher) created by curtis
VisBio (and Slim Plotter) uses the Marner Java Launcher for deployment on …
14:22 Changeset [2462] by curtis
Add status events to Alicona initFile.
14:22 Changeset [2461] by curtis
Tweaks.
14:22 Changeset [2460] by curtis
Add output of status events to testRead.
13:33 Changeset [2459] by curtis
Simply canMerge test.
13:29 Ticket #5 (Better channel merging in Bio-Formats Importer) created by curtis
As mentioned in ticket #2, the method to use for merging more than three …
10:50 Ticket #4 (Bio-Formats native solution) created by curtis
Many developers, especially those working on applications for acquisition …
10:42 Ticket #2 (Bio-Formats Importer plugin loses some channels when merging) closed by melissa
fixed: Fixed in r2458. The solution was to only allow merging if there are 2 or …
10:41 Changeset [2458] by melissa
Only allow merging if there are 2 or 3 channels; otherwise display a …
10:15 Ticket #3 (Support for Volocity databases) created by curtis
Several people, including Michael Schell, Jeremy Sanderson, Kurt De Vos …
10:06 Ticket #2 (Bio-Formats Importer plugin loses some channels when merging) created by curtis
When using "Merge to RGB" with the Bio-Formats Importer plugin, datasets …
09:36 Changeset [2457] by curtis
Add status reporting to OME uploader. But uploader is broken right now.
08:06 Changeset [2456] by melissa
Calculate plane size based on the RGB channel count, not sizeC.

03/14/07:

17:06 Changeset [2455] by curtis
Clean up comments, style and whitespace.
16:22 Changeset [2454] by curtis
Add status update hooks to loci.formats.ome.Uploader logic.
16:11 Changeset [2453] by curtis
Add event for listening to status updates from format readers and writers. …
14:58 Changeset [2452] by curtis
Remove note about obsolete bad-files.txt.
14:55 Changeset [2451] by curtis
Package description for loci.formats.codec package.
14:54 Changeset [2450] by curtis
Move compression/decompression logic into new loci.formats.codec package.
13:46 Changeset [2449] by curtis
Ignore *.class.
13:45 Changeset [2448] by curtis
Move MultiLUT into loci.apps package.
13:44 Changeset [2447] by curtis
No need to keep maintaining this package.
11:38 Changeset [2446] by curtis
Only upload data once per dataset.
11:33 Changeset [2445] by curtis
Whitespace.
11:31 Changeset [2444] by curtis
Tweak comments.
11:25 Changeset [2443] by curtis
Tweak javadoc.
11:24 Changeset [2442] by curtis
Move rasterToPosition, positionToRaster
11:23 Changeset [2441] by curtis
OMEUploader should work, though events still aren't worked out.
11:17 Changeset [2440] by curtis
Remove old batch file.
11:15 Changeset [2439] by curtis
Remove old batch files.
11:14 Changeset [2438] by curtis
Move Bits.swap utility methods into DataTools.
07:51 Ticket #1 (Leica Reader openBytes() Exception) closed by melissa
fixed
07:40 Changeset [2437] by melissa
Implemented openBytes(String, int, byte[]) in LeicaReader.
05:42 Ticket #1 (Leica Reader openBytes() Exception) created by callan
The Leica reader currently throws and exception when the …

03/13/07:

18:26 Changeset [2436] by curtis
Tweak.
18:25 Changeset [2435] by curtis
Add Windows batch file versions of command line tools.
18:03 Changeset [2434] by curtis
Remove omeul from VisBio distribution.
18:01 Changeset [2433] by curtis
Remove old scripts.
17:56 Changeset [2432] by curtis
Add LOCI command line tools.
17:47 Changeset [2431] by sorber
Polyline last node highlights on mouse-over.
17:03 Changeset [2430] by curtis
Move static FormatReader methods to new FormatTools class. The rationale …
16:32 Changeset [2429] by sorber
Replaced instances of deprecated HSSF.setCellValue(String) method.
16:19 Changeset [2428] by sorber
Basic export overlays to .xls format.
10:39 Changeset [2427] by melissa
Improved macro propagation logic.
Note: See TracTimeline for information about the timeline view.