Timeline


and

08/12/11:

13:22 Ticket #721 (Improve support for images where compositeChannelCount != numChannels) created by bdezonia
We have some images that would display well when composite channel count …

08/11/11:

13:32 Ticket #667 (Stack To Images problematic with RGB input) closed by bdezonia
fixed: Fixed in 97ba2789250130ab526723082e0e3b2bc82b968f.

08/10/11:

16:34 Ticket #720 (IJ2 Open command sets LUTs incorrectly) created by bdezonia
If you open the OME 4d series in IJ1 (via either File open command or BF …
16:31 Ticket #701 (LUTs getting out of sync) closed by bdezonia
fixed: This last issue with OME 4d has nothing to do with legacy layer as you …
14:43 Ticket #719 (Display painting bug) created by bdezonia
Sometimes IJ2 does not correctly paint images. This sequence can reliably …
14:40 Ticket #715 (Initial setup of selected region is wrong) closed by bdezonia
fixed: After discussions with Curtis have come to the conclusion that this is a …
12:51 Ticket #718 (ImageJ 1.45m added Image>Overlay>Overlay Options command) created by bdezonia
ImageJ 1.45m has an Overlay Options command. See if we need to write a new …
11:43 Ticket #665 (A Display can go from Composite to Color unexpectedly) closed by bdezonia
fixed

08/09/11:

09:45 Ticket #709 (Quit Plugin) closed by gharris
fixed
08:56 Ticket #717 (ProbeTool exception with Overlays outside of image area.) created by gharris
When an image is cropped using an overlay, the overlay remains defined and …

08/08/11:

15:44 Ticket #708 (Catch up on email) closed by curtis
fixed: Whew, down to 3 emails from 30.
15:01 Ticket #668 (Image :: Stack :: Stack to Images results in wrong colors and other issues) closed by bdezonia
fixed: After some discussion with Curtis decided my approach in …

08/04/11:

11:19 Ticket #716 (ProbeTool cursor is off) created by bdezonia
Now that the ProbeTool is always on its using a different cursor. The …

08/03/11:

15:15 Ticket #702 (Extraneous "There are no images open" popups) closed by bdezonia
fixed: fixed in 62472a6bbb0b4f7c08324eb4897295481cb55c7d
14:56 Ticket #714 (Image::Type::RGB Stack behaves unexpectedly) closed by bdezonia
fixed: Fixed in a524aeea69384bcc1fdb9f908d55de97f677965e.
11:15 Ticket #654 (Fix bf-cpp distribution bundle generation) closed by hinerm
fixed: Changes were made to the jar2lib templates and bio-formats supporting …
11:15 Ticket #298 (Make JVM creation method generic) closed by hinerm
fixed: jtools now automatically checks for a "jar" subdirectory, either in the …
11:14 Ticket #712 (Phase out Dataset::getSelection() code) closed by bdezonia
fixed: fixed. commits too numerous to mention. culminated in fix …

08/02/11:

15:58 Ticket #715 (Initial setup of selected region is wrong) created by bdezonia
Some plugins now work on the bounds of the currently selected region via …
15:55 Ticket #714 (Image::Type::RGB Stack behaves unexpectedly) created by bdezonia
Open Clown Choose Image::Type::RGB Stack Notice there are two images. One …
15:51 Ticket #713 (Zoom to selection is broken) created by bdezonia
I recently started using the bounds of the current selection for the Zoom …
15:48 Ticket #712 (Phase out Dataset::getSelection() code) created by bdezonia
Now that the OverlayService can return the currently selected bounds. Use …
15:09 Ticket #359 (Update "current status" page on ImageJDev.org) closed by curtis
fixed: Current status …
10:57 Ticket #46 (Integrate FARSIGHT with ImageJ) closed by curtis
wontfix: Leveraging ITK from ImageJ is a worthwhile goal, but pursuing …
10:55 Ticket #673 (Memory leak in LegacyOutputTracker) closed by bdezonia
fixed: My other fixes did not resurrect this bug. Closing.
10:52 Ticket #675 (Split Channels sometimes complains) closed by bdezonia
fixed: fixed in 736c97c545241fbd8189b087c2d218654d3e7bc1 and …
10:50 Ticket #674 (Stack to images no longer closes original image) closed by bdezonia
fixed: fixed in b72c24756c777ff866fe434ac0230107a0fc1fed

08/01/11:

14:30 Milestone imagej-2.0-alpha4 completed
An alpha release demonstrating the new class hierarchy, plugin …
13:40 Ticket #690 (Rectangle overlay tool doesn't work after first rectangle is drawn) closed by leek
fixed: It turns out you need to get the selection tool from the toolbar. Luckily …
12:36 Ticket #19 (Efficient support for very large image planes) reopened by aivar
12:20 Ticket #672 (Delete Axis can throw a concurrent modification exception) reopened by bdezonia
Still an issue: Organ of Corti Delete Data: Z axis, pos 4, num slice 6 …
12:14 Ticket #90 (BaseTiffMock endianness) closed by leek
wontfix
11:44 Ticket #78 (CellProfiler-related bioformats tests) closed by leek
fixed
11:16 Ticket #19 (Efficient support for very large image planes) closed by aivar
fixed
11:11 Ticket #711 (Build TRI2 with SLIMCurve) created by aivar
Build a version of TRI2 locally that uses SLIMCurve for local testing.
10:58 Ticket #710 (Fix BioFormats ICSReader.java to handle Gray .ics files.) created by aivar
Rewrite ICSReader metadata handling. This already has a hack to handle …
10:57 Ticket #673 (Memory leak in LegacyOutputTracker) reopened by bdezonia
My hack causes other memory leaks. Reopening to make sure any change does …
10:56 Ticket #709 (Quit Plugin) created by gharris
Perhaps change from using message visibility to DialogPrompt
10:27 Ticket #708 (Catch up on email) created by curtis
Time for another email purge.
10:02 Ticket #20 (Efficient support for very large image data) closed by curtis
duplicate: We are working on new ImgLib2 container types for this. See ticket #216.
08:34 Ticket #707 (Non-Modal Plugin) created by gharris
Add ability to create a non-modal plugin frame which tracks the display …
08:04 Ticket #706 (Create ColorTable (LUT) Selector Plugin) created by gharris
Create a ColorTable (LUT) Selector Plugin for IJ2
08:03 Ticket #705 (Fix LookupTable (IJ1)) created by gharris
Set ColorTable (LUT) IJ1 Lookup Tables – shows next-to-last one selected.
07:20 Ticket #704 (Bug in AbstractRegionOfInterest) created by leek
Reported by Martin Horn: Stephan Preibisch gave me your E-Mail contact. We …

07/29/11:

23:00 Milestone biweekly-2011: Jul-18 to Jul-29 completed
18:03 Ticket #696 (Make math plugins only modify pixels within Roi extents) closed by bdezonia
fixed: fixed in 4b51896a2f6d7487bc4d7b54d80c6fb23f9728af
16:28 Ticket #703 (Race condition when repainting image canvas) created by curtis
[…] Threading issues can be difficult to replicate, but I can generally …
16:08 Ticket #702 (Extraneous "There are no images open" popups) created by curtis
ImageJ1 pops up an erroneous dialog reporting that "There are no images …
15:15 Ticket #672 (Delete Axis can throw a concurrent modification exception) closed by bdezonia
fixed: Fixed in 9baf85e833863fbbf8573ead3ae91803d77c330c Had to disable some …
13:27 Ticket #568 (Wrong LUTs getting set) closed by bdezonia
fixed: the repeated open/close bug is fixed. the other issue mentioned has been …
13:26 Ticket #701 (LUTs getting out of sync) created by bdezonia
Open multi-channel-4d-series.ome.tiff (or new Hyperstack 4 channels) Run …
12:37 Ticket #684 (Add data plugin can throw exception) closed by bdezonia
fixed: fixed in aca5f9a2e542eb17d633c081a430a365fe0d0882
11:27 Ticket #679 (Initialize IJ1 settings after IJ2 settings loaded) closed by bdezonia
fixed: Forewent event approach. Now just calling optionsSynchronizer.update() in …
11:27 Ticket #699 (Add discovery of Composite settings from IJ metadata) closed by curtis
fixed: I already did this yesterday. See: * …
11:24 Ticket #700 (Programmatic Plugin Invocation) created by gharris
Expand on InvokePluginTest to text/explore use of ModuleService and …
11:18 Ticket #699 (Add discovery of Composite settings from IJ metadata) created by gharris
Add discovery of Composite settings from IJ metadata so that IJ2 Opener …
11:17 Ticket #698 (Incorporate interface ColorTable<T>) created by gharris
Incorporate interface ColorTable<T> as appropriate where ColorTable8 is …

07/28/11:

18:00 Ticket #427 (Make some Process > Math plugins have preview ability) closed by bdezonia
fixed: Last issue fixed in e8af5ec592cdd743dd11d8797a07bf16b9bbe783. We could …
14:07 Ticket #697 (Check Performance of CompositeXYProjector) created by gharris
Check performance of CompositeXYProjector, now that it applies a ceiling …
13:22 Ticket #514 (Increase the quality of IJ2's color display results) closed by curtis
fixed: (In [3527]) Update references to CompositeXYProjector. Fixes #514, due to …
12:33 Ticket #696 (Make math plugins only modify pixels within Roi extents) created by bdezonia
This ticket cannot be addressed until the IJ2 data structures and API are …
10:34 Ticket #691 (Exception thrown for char parameters) closed by curtis
fixed: (In [3521]) Fix widget bug with character inputs. Closes #691.

07/27/11:

15:52 Ticket #694 (Add invoke methods with explicit parameter values) closed by curtis
fixed: Fixed in a339895e78474dfc160e7acec08fd5f6ad94aab8. As of …
13:21 Ticket #695 (invert broken) created by afraser
Invert via the legacy layer AND via the new plugin exhibit the same …
10:04 Ticket #694 (Add invoke methods with explicit parameter values) created by curtis
Grant wrote an InvokePluginTest plugin that attempts to invoke …
09:54 Ticket #693 (ij.gui.Overlay not tracked in legacy layer) created by leek
ImageJ 1 overlays are not tracked in the legacy layer. An overlay appears …

07/26/11:

16:43 Ticket #685 (The input harvester can throw exceptions) closed by curtis
fixed: Fixed in 34e48b71f589a4c09ebcdfd58293bd1582b8908c.
16:31 Ticket #692 (Exception thrown for BigInteger parameters) created by curtis
Uncomment the BigInteger field's @Parameter annotation in ParameterTester …
16:30 Ticket #691 (Exception thrown for char parameters) created by curtis
Uncomment the char field's @Parameter annotation in ParameterTester and …
14:37 Ticket #686 (All DynamicPlugin implementations suffer from poor titles) closed by curtis
fixed: Fixed in ae10b0995b118365b73a347f60e0b963c438f8d1.
13:31 Ticket #690 (Rectangle overlay tool doesn't work after first rectangle is drawn) created by leek
The old behavior: press rectangle tool, draw rectangle, rectangle tool …
12:00 Ticket #681 (Fix old code that gets Datasets from Displays) closed by bdezonia
fixed: Done with numerous commits between …
11:01 Ticket #689 (Plugins > New > Macro throws an exception) created by afraser
from the menu: Plugins > New > Macro throws an exception when there is no …
10:58 Ticket #688 (Macros that open images do not display them) created by afraser
Note: this bug makes it difficult to write macros that easily reproduce a …
10:52 Ticket #687 (Hold spacebar to pan) created by afraser
Holding the spacebar should temporarily enable the pan tool as is done in …
10:25 Ticket #558 (To Binary Mask causes slider slowdown) closed by leek
fixed
10:24 Ticket #374 (Multi-channel .tif files in CellProfiler) closed by leek
duplicate: I'll take care of this in CellProfiler's tracking system

07/25/11:

16:43 Ticket #686 (All DynamicPlugin implementations suffer from poor titles) created by bdezonia
The DynamicPlugin implementations (axispos and restructure packages) have …
16:33 Ticket #685 (The input harvester can throw exceptions) created by bdezonia
Open Organ Of Corti Open the Delete Axis plugin An exception is thrown …
16:28 Ticket #684 (Add data plugin can throw exception) created by bdezonia
Open Organ Of Corti Run Add Data plugin Choose Channel as the axis to add …
16:07 Ticket #683 (Allow parameters to be contextually activated) created by curtis
Some modules may have differing inputs depending on the values of other …
16:04 Ticket #682 (Allow parameter attribute changes besides value during callback methods) created by curtis
A DynamicPlugin has the capability to update an input's attributes, such …
14:57 Ticket #606 (Improve restructure plugins to use runtime data) closed by bdezonia
fixed: Plugins updated in commits ranging from …
14:55 Ticket #636 (Populate parameters of axis plugins at runtime) closed by bdezonia
fixed: These plugins have been updated. Relevant commits range from …
11:11 Ticket #681 (Fix old code that gets Datasets from Displays) created by bdezonia
There are places in the code that do things like this: dataset = …

07/22/11:

16:48 Ticket #608 (Dragging sliders does not update status readout) closed by bdezonia
fixed: Tested in 6a5d95f52fc099e1710677a0998ec65bc81edea2 and this is no longer a …
16:43 Ticket #680 (PlanePosition bug) closed by bdezonia
fixed: fixed in 6a5d95f52fc099e1710677a0998ec65bc81edea2
16:07 Ticket #623 (Make plugin parameters modifiable at runtime) closed by curtis
fixed: Dynamic plugins are now possible with …
15:24 Ticket #680 (PlanePosition bug) created by bdezonia
If you load Neuron sample image you can see channel label might be off by …
14:50 Ticket #637 (Eliminate static class variables from AxisUtils) closed by bdezonia
fixed: Placed active axis code in the Display hierarchy. Fixed in …
14:38 Ticket #679 (Initialize IJ1 settings after IJ2 settings loaded) created by bdezonia
There is incorrect placeholder code in Main.java for setting IJ1's options …
14:04 Ticket #640 (Make DisplayView position functions consistent) closed by bdezonia
fixed: This ticket is no longer valid. With the refactoring of getPlanePosition() …
14:02 Ticket #678 (Improve design of AbstractDisplayView) closed by bdezonia
fixed
14:02 Ticket #678 (Improve design of AbstractDisplayView) created by bdezonia
AbstractDisplayView has a few protected members that are initialized and …
13:32 Ticket #570 (Test: make sure that firing of SwingOverlayView::figureRemoved() removes ...) closed by bdezonia
fixed: I have not been able to find any bad ramifications. After looking at this …
12:39 Ticket #465 (Rename imagej.util.Index) closed by bdezonia
fixed: Replaced code in numerous places that could beneift from using Positions. …

07/21/11:

16:41 Ticket #677 (Generalized Dialog Box) closed by gharris
fixed
16:41 Ticket #677 (Generalized Dialog Box) created by gharris
Generalized Dialog Box Added an interface DialogPrompt. Added a …

07/20/11:

15:23 Ticket #676 (Update Edit::Options::Proxy) created by bdezonia
In 1.45l13 Wayne added a new option in the Proxy menu. Update IJ2 to …
15:01 Ticket #675 (Split Channels sometimes complains) created by bdezonia
Split Channels command sometimes runs and sometimes complains that it …
14:55 Ticket #674 (Stack to images no longer closes original image) created by bdezonia
My hack to catch memory leaks in LegacyImageMap is getting in the way of …

07/18/11:

13:50 Ticket #673 (Memory leak in LegacyOutputTracker) closed by bdezonia
fixed: fixed with a hack in e623f73300cca17a04846ce2191e687633d3f0c3
12:52 Ticket #673 (Memory leak in LegacyOutputTracker) created by bdezonia
It turns out that there is a memory leak in LegacyOutputTracker. To …

07/15/11:

23:00 Milestone biweekly-2011: Jul-05 to Jul-15 completed
22:41 Ticket #591 (First steps for OverlayManager) closed by afraser
fixed
17:41 Ticket #672 (Delete Axis can throw a concurrent modification exception) created by bdezonia
Open Organ of Corti Use Image :: Stacks :: Delete Axis plugin and delete …
13:19 Ticket #641 (Move some core plugins to their own project) closed by bdezonia
fixed: Fixed in 01ed7a3a37609beb13903100bd93f7411f3bebf5. Added as ij-io. …
12:33 Ticket #320 (WorkFlowPipes static IJ1/2 plugin generation & menu integration) closed by curtis
duplicate: Essentially a duplicate of #318.
12:31 Ticket #317 (Create an ImageJ plugin from WorkFlowPipes) closed by curtis
wontfix: Any future WFP work will focus on IJ2 only.
12:28 Ticket #622 (Add more getters to InputWidget subinterfaces) closed by curtis
fixed: As of a9404d5a77e38b315f7c931841e4c1eaeb5e6ca0, these values can now be …

07/14/11:

14:43 Ticket #666 (Nitpick: zoom scale should not be displayed if 100%) closed by bdezonia
fixed: Fixed in 1440a93f5623c68496807bb6e85ace996847de51
14:27 Ticket #669 (IJ2 seems to be holding onto memory) closed by bdezonia
fixed: Fixed all known memory leaks in 93b146572a7afa2a109415c1669f60ada5743a40, …
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