Timeline


and

04/24/07:

18:10 Changeset [2667] by sorber
Moved getSelectionGrid() methods to OverlayUtil. Removed …
18:08 Changeset [2666] by sorber
Added utility class OverlayUtil.
15:20 Changeset [2665] by curtis
Whitespace.
14:54 Changeset [2664] by curtis
Eliminate obsolete classes.
14:04 Ticket #119 (Make sure Polyline and Freeform tools are in good working order) created by sorber
Make sure that Polyline and Freeform tools work well by Friday 4/27. This …
13:58 Ticket #89 (Update Polyline length as mouse is dragged) closed by sorber
fixed
13:47 Ticket #10 (Export overlay statistics to .xls) closed by sorber
fixed
13:39 Changeset [2663] by curtis
Tweak "2D with overlays" option text.
13:19 Changeset [2662] by curtis
* Fix bug in bins-to-nm conversion logic * Fix up full width half max …
10:48 Ticket #20 (Use QTObject.dispose() in QTJava-related code to avoid potential crashes ...) closed by melissa
fixed: Fixed in r2661.
10:48 Changeset [2661] by melissa
Added dispose() calls to avoid JVM crashes.
10:21 Ticket #117 (Eliminate invalid characters in generated OME-XML) closed by melissa
fixed

04/23/07:

13:32 Changeset [2660] by curtis
Eliminate use of term "stitch" in favor of terms "group" and …
13:15 Changeset [2659] by melissa
Updated 'save' method to include new template features.
13:11 Changeset [2658] by curtis
Tweak Javadoc comments.
13:09 Ticket #105 (Add rotation buttons to DisplayControls for 2D displays) closed by curtis
fixed: Added in r2657. Used 15 degrees instead, as it seems to work well (can be …
13:07 Changeset [2657] by curtis
Add clockwise and counterclockwise rotation buttons.
13:01 Changeset [2656] by melissa
Fixed several bugs and added a few new features to the template format.
12:25 Changeset [2655] by curtis
Merge FormatReader and FormatWriter debug logic into FormatHandler.
12:16 Ticket #33 (16-bit images do not display properly) closed by curtis
fixed: Fixed in r2654. The problem was that grabBytes really is inappropriate …
12:00 Changeset [2654] by curtis
Fix problem with ImageFlatField and 16-bit image data.
08:56 Ticket #118 (Support for MetaMorph .ND files) created by melissa
MetaMorph STK files can have a companion metadata file with the .ND …

04/20/07:

17:39 Changeset [2653] by sorber
Invisible overlay objects aren't rendered. Invisible overlay objects …
13:18 Ticket #117 (Eliminate invalid characters in generated OME-XML) created by melissa
The OME-XML generated by Bio-Formats sometimes contains invalid …
12:55 Changeset [2652] by melissa
Changed 'windows' to 'planes' in new merging logic, since we don't open …
12:52 Changeset [2651] by melissa
Provide additional merging options for files with more than 3 channels.
12:05 Ticket #116 (Add Dr. Inman's smoothing procedure to FreeformTool) created by sorber
In a 1981 paper, Littlewood and Inman describe the algorithm used to …
12:04 Changeset [2650] by curtis
Add preliminary support for rendering FWHMs as green lines; needs more …
11:38 Changeset [2649] by melissa
Improved template editor - can now define groups, remove …
09:20 Ticket #115 (Arbitrary slicing can throw NullPointerException) created by curtis
When visualizing the sdub dataset with an arbitrary slice, moving the Time …

04/19/07:

14:43 Changeset [2648] by curtis
Fix javadoc generation warnings.
13:55 Changeset [2647] by curtis
Add full width max peak calculation.
13:04 Changeset [2646] by melissa
Removed unnecessary import.
13:02 Changeset [2645] by melissa
- Load default template from an InputStream, not a File. - Don't switch …
12:46 Changeset [2644] by curtis
Update build scripts to include targets for both new 'OME Notebook' …
12:07 Changeset [2643] by melissa
Fixed bug with reading 2.4 GB file.
09:52 Changeset [2642] by melissa
Added test to check for valid OME-XML.
09:03 Changeset [2641] by melissa
Fixed a few more readers to support >2GB files.
08:46 Changeset [2640] by melissa
Use long variable to store plane offset.
08:41 Changeset [2639] by melissa
Updated to reflect changes in loci.formats and loci.ome.notebook package …
08:11 Ticket #41 (QuickTime reader colors for mjpb-encoded data differ from QTJava results) closed by melissa
fixed: Fixed in r2638.
08:10 Changeset [2638] by melissa
Fixed native mjpb.

04/18/07:

14:18 Changeset [2637] by melissa
Place SemanticType node under SemanticTypeDefinitions.
12:10 Ticket #114 (Bio-Formats cannot handle files larger than 2GB) closed by melissa
fixed: Fixed in r2636. Support for files that are >2GB has been tested in …
12:02 Changeset [2636] by melissa
Fixed RandomAccessStream to allow files >2GB; tweaked readers to …

04/17/07:

18:01 Ticket #114 (Bio-Formats cannot handle files larger than 2GB) created by melissa
RandomAccessStream uses ints in several places, causing Bio-Formats to …
17:18 Changeset [2635] by curtis
2007 Apr 17 VisAD jar with CursorUtil class.
17:16 Changeset [2634] by curtis
Take advantage of new visad.util.CursorUtil.evaluate method.
17:16 Changeset [2633] by curtis
Filter out mappings inappropriate to the display.
17:11 Changeset [2632] by curtis
Add note about AppleJavaExtensions.jar being part of the SVN repository.
15:02 Ticket #3 (Support for Volocity databases) closed by melissa
duplicate: This is a duplicate of ticket #55.
13:31 Ticket #62 (Record proprietary metadata under Image>CustomAttributes in OME-XML) closed by melissa
fixed: Completed in r2631.
13:31 Changeset [2631] by melissa
Record values from the metadata hashtable in OME-XML using a custom ST …
12:14 Changeset [2630] by melissa
Save custom fields to the NotebookField ST under CustomAttributes.
11:17 Changeset [2629] by melissa
Updated to use FormLayout.
09:18 Changeset [2628] by curtis
Change private signatures to protected.
09:08 Changeset [2627] by melissa
Added close() method.

04/16/07:

15:25 Changeset [2626] by melissa
Updated to reflect recent API modifications.
11:39 Ticket #98 (Add ability to toggle metadata collection) closed by melissa
fixed
11:33 Ticket #112 (Support for NRRD format) closed by melissa
fixed: Added basic support in r2625. Some features of this format are not yet …
11:31 Changeset [2625] by melissa
Added basic support for the NRRD format.
10:02 Ticket #113 (Min/max calculation is incorrect for byte arrays) closed by melissa
fixed: Fixed in r2624.
10:02 Changeset [2624] by melissa
Fixed bug with how updateMinMax(byte[], int) converts bytes to doubles. …
09:04 Ticket #113 (Min/max calculation is incorrect for byte arrays) created by melissa
MinMaxCalculator.updateMinMax(byte[], int) produces incorrect min/max …

04/13/07:

15:26 Ticket #112 (Support for NRRD format) created by melissa
NRRD (Nearly Raw Raster Data):  http://teem.sourceforge.net/nrrd/
15:10 Changeset [2623] by curtis
Migrate pixelToDomain and related functions into visad.util.CursorUtil …
14:51 Changeset [2622] by curtis
Add temporary hack to suppress options of "Overlays" type.
14:45 Changeset [2621] by curtis
Add note about problem with setId call.
11:32 Changeset [2620] by curtis
Add comment about integer-based images.
11:25 Changeset [2619] by curtis
Add necessary import statement.
11:25 Changeset [2618] by curtis
Update ImageTester package.
11:09 Changeset [2617] by curtis
Add convenience method for overwriting TIFF comment.
11:03 Changeset [2616] by melissa
Uncommented metadata collection toggle; fixed readers that broke as a …

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 …
Note: See TracTimeline for information about the timeline view.