Timeline


and

06/03/11:

23:00 Milestone biweekly-2011: May-23 to Jun-03 completed
Tasks from 2011-May-23 through 2011-Jun-03.
16:03 Ticket #566 (IJ2 Datasets are not always getting deleted) created by bdezonia
Datasets do not seem to go away always. A scenario that shows this: open …
15:06 Ticket #565 (Apply results of EditColors plugin to active Dataset) created by bdezonia
The EditColors dialog is not hooked to anything and does not update any …
12:41 Ticket #564 (Write pure IJ2 version of Image :: Show Info menu item) created by bdezonia
The Image :: Show Info command cannot show the correct info for all the …
09:52 Ticket #562 (Legacy layer can corrupt C/Z axis ordering) closed by bdezonia
fixed: Fixed in b2c057f7d9cf12855859d288f69e41e17b078d28
09:47 Ticket #384 (Display autoscaling) reopened by gharris
Actually, the ContrastBrightness plugin needs to be validated in terms of …
09:45 Ticket #384 (Display autoscaling) closed by gharris
fixed: Autoscaling is implemented in AbstractDatasetView by 1) using the min/max …

06/02/11:

17:22 Ticket #563 (Improve how legacy layer handles data that cannot be represented in IJ1) created by bdezonia
Right now if you pass a Dataset to the legacy layer that has some axis not …
17:14 Ticket #556 (Imported image reverses role of C & Z axis) closed by bdezonia
worksforme: Original issue cannot be duplicated with latest code. Assume fixed. …
17:12 Ticket #562 (Legacy layer can corrupt C/Z axis ordering) created by bdezonia
Use File :: Import :: BioFormats. Select the …
16:45 Ticket #561 (Test: can GrayscaleTranslator ever make a COLOR or GRAYSCALE ...) created by bdezonia
Code inspection leads me to believe that the legacy layer (via …
16:40 Ticket #560 (Performance improve Import BioFormats) created by bdezonia
If you open multichannel-4d-series.ome.tif from the ome-tiff directory on …
16:36 Ticket #559 (The legacy layer only supports 8-bit ColorTables) created by bdezonia
Currently the legacy layer only works with 8-bit ColorTables/LUTs. Put in …
16:29 Ticket #538 (Improve legacy data support) closed by bdezonia
fixed: Done
16:23 Ticket #525 (Update LUTs correctly in DatasetHarmonizer) closed by bdezonia
fixed: This code in place. Final touches added in …
16:16 Ticket #558 (To Binary Mask causes slider slowdown) created by bdezonia
I don't know much about the To Binary Mask command or how it should …
13:04 Ticket #144 (Set up logrotate on skynet) closed by curtis
fixed: Both skynet and dev now have logrotate rotating their web logs weekly. The …

06/01/11:

23:30 Milestone imagej-2.0-alpha3 completed
Third alpha release demonstrating the new class hierarchy, plugin …
20:13 Ticket #557 (Add permanent caching support to ImgIOUtils) created by curtis
The ImgIOUtils class currently caches HTTP downloads of images in a …
15:48 Ticket #556 (Imported image reverses role of C & Z axis) created by bdezonia
Use File :: Import :: BioFormats. Select the …
15:28 Ticket #555 (Convention for how a plugin handles no image/view selected) created by gharris
If the plugin relies on there being a view selected, it may do this in its …
14:57 Ticket #554 (File::New::Hyperstack results in duplicate images being created/displayed) created by bdezonia
Run File::New::Hyperstack. Choose c = 3, z = 1, t = 1. Choose Composite. …
14:52 Ticket #553 (Ij2 can get plugin confused) created by bdezonia
Do file :: import :: bioformats and feed it multichannel.ome.tiff from the …
12:34 Ticket #544 (Exception thrown on Dataset::delete()) closed by bdezonia
worksforme: Cannot duplicate with version 0a1002ec77ab2f2ee3da645b88791fcaed8305b7.
11:19 Ticket #538 (Improve legacy data support) reopened by bdezonia
11:18 Ticket #538 (Improve legacy data support) closed by bdezonia
fixed: The remaining issues on this ticket are encompassed in ticket #546. …

05/31/11:

16:45 Ticket #248 (Bio-Formats ITK plug-in - populate physical pixel sizes) closed by hinerm
fixed: Issue resolved in …
15:31 Ticket #552 (Make it possible to pass a ImgFactory to ImageTranslator::createDataset()) created by bdezonia
RIght now ImageTranslator::createDataset() always makes a PlanarAccess …
15:25 Ticket #551 (Improve legacy layer) created by bdezonia
The legacy layer is now well fleshed out. Write more comprehensive tests …
15:06 Ticket #550 (Convert RGB to 8-bit color displays as grey) created by bdezonia
If you convert Clown to 8-bit color it still displays as grey. The LUT …
14:36 Ticket #549 (Improve legacy support of bit typed data) created by bdezonia
IJ1 treats bit masks as unsigned byte images with two values (0 & 255). If …
14:26 Ticket #548 (Type changer not working with color data correctly) created by bdezonia
Open Clown. Change Image :: Type to 12-bit. Display does not change. …

05/27/11:

09:20 Ticket #498 (Speed up RGBImageTranslator?) closed by bdezonia
wontfix: After further thought I think it does not make sense to change this. At …
08:58 Ticket #547 (Make pure IJ2 Revert plugin) created by bdezonia
Due to limitations laid out in bug #531 and bug #528 we need a pure IJ2 …
08:40 Ticket #247 (Add Write functionality to the Bio-Formats ITK plug-in) closed by hinerm
fixed: The write method has been implemented for the Jace and Pipes BFITK plug-in …

05/26/11:

16:06 Ticket #378 (Fix buggy Number parameter widgets) closed by curtis
fixed: In 63fe2c383daa27575ee2fef46f7db10a901e4e9f the Swing number widget code …
15:39 Ticket #546 (Minimize time spent harmonizing Datasets/ImagePluses) created by bdezonia
Right now, in LegacyPlugin, prePluginHarmonization() code is run that …
14:21 Ticket #532 (Make legacy layer smarter about handling new IJ2 data types) closed by bdezonia
fixed: Fixed (revision unknown but shortly before …
14:18 Ticket #545 (Enhance Contrast doesn't) created by bdezonia
Running legacy plugin Process :: Enhance Contrast does not work unless you …
13:46 Ticket #544 (Exception thrown on Dataset::delete()) created by bdezonia
Open Blobs sample Image. Choose Image :: Rename. Now close image window. …

05/25/11:

13:49 Ticket #543 (Add check for final @Parameter field) closed by curtis
fixed: Fixed in cecdd1ae4071a7339a7085e369a95c37653b0fad, using resolved as …
10:11 Ticket #543 (Add check for final @Parameter field) created by gharris
If a @Parameter annotated field is final, an input widget is presented and …

05/24/11:

15:45 Ticket #542 (Change legacy layer so that it maintains Display<-->ImagePlus mappings) created by bdezonia
Unlike IJ1, IJ2 allows one to view the same set of data in two different …
13:19 Ticket #528 (Have LegacyImageMap track Dataset events) closed by bdezonia
fixed: closing and tracking in ticket #531
10:26 Ticket #533 (DisplayPostProcessor should not generate DatasetChangedEvents) closed by bdezonia
fixed: made sure dataset events getting triggered in all places they need to in …
09:49 Ticket #539 (For given file probe reports different pixels values between IJ1 & IJ2.) closed by bdezonia
fixed: fixed in 7cadcce428524a961cebf8761f93af945100b73c
09:21 Ticket #541 (Invert image in IJ2 not always same as IJ1 invert) closed by bdezonia
fixed

05/23/11:

16:41 Ticket #541 (Invert image in IJ2 not always same as IJ1 invert) created by bdezonia
In IJ1 inversion of an image is relative to 0/255. In IJ2, for generality, …
16:39 Ticket #540 (Convolution oriented plugins wrong in 8-bit case) created by bdezonia
IJ1 has special case code for convolve3x3() on a ByteProcessor. IJ2 code …
15:31 Ticket #539 (For given file probe reports different pixels values between IJ1 & IJ2.) created by bdezonia
The attached file displays differently in IJ1 & IJ2. At first I thought it …
15:01 Ticket #248 (Bio-Formats ITK plug-in - populate physical pixel sizes) reopened by hinerm
In the Jace implementation there is a NullPointerException at the first …
14:59 Ticket #538 (Improve legacy data support) created by bdezonia
The DatasetHarmonizer and the LegacyImageMap have evolved. They are …
14:44 Ticket #529 (IJ2 not setting current ImagePlus at correct time) closed by bdezonia
fixed: Fixed in 1a3c034a8d2f4436ab57f3e9b00aa9022cdc3ac1. …
14:42 Ticket #530 (Make legacy harmonization bidirectional) closed by bdezonia
fixed
14:42 Ticket #530 (Make legacy harmonization bidirectional) reopened by bdezonia
14:42 Ticket #530 (Make legacy harmonization bidirectional) closed by bdezonia
fixed: Initial implementation in 1a3c034a8d2f4436ab57f3e9b00aa9022cdc3ac1. Some …
11:52 Ticket #537 (Update ROIs correctly in DatasetHarmonizer) created by curtis
The legacy layer needs to translate ROIs back and forth between IJ1 and …
11:26 Ticket #172 (Improve jar2lib's CMake build file to assemble final resources post-build) closed by hinerm
fixed: Fixed with svn revision 7709 * updated cmake velocity template to …
11:21 Ticket #536 (Decide on ROI Persistence Mechanism) created by gharris
We need to decide on the persistence mechanism for ROIs. JHotDraw SVG …
10:56 Ticket #423 (Z Project can fail with an exception) closed by gharris
fixed

05/20/11:

23:00 Milestone biweekly-2011: May-09 to May-20 completed
Tasks from 2011-May-09 through 2011-May-20.
17:38 Ticket #481 (Refresh Display on DatasetChanged Event) closed by curtis
fixed: Both DatasetView and SwingDisplayWindow listen for DatasetUpdatedEvents …
17:16 Ticket #494 (Bugs displaying gradient images) closed by curtis
duplicate: Duplicate of #384.
17:06 Ticket #479 (Should Window, Key and Mouse Events extend DisplayEvent) closed by curtis
invalid: No comment in two weeks—closing ticket. If it comes up again we can …
17:04 Ticket #521 (Post JHotDraw incorporation none of the Tools work) closed by curtis
fixed: The tools are ostensibly working again. Zoom and probe still have some …
16:45 Ticket #534 (Image::Rename does not work) closed by bdezonia
fixed: Fixed in 9aafd7ecfc0a85f4bea25d6d37514304fc532c6f. Harmonization takes …
16:35 Ticket #379 (Add support for plugin previews) closed by curtis
fixed: Initial preview feature added in 37c47161459c98b3bdfbe77d1ae375668054e1e8. …
15:57 Ticket #535 (Add dirty bit tracking to Dataset) closed by bdezonia
fixed: Added in 40be2ad269d824182a2ef35b8ff8881dbadb25b4. Tracking in Dataset …
15:53 Ticket #535 (Add dirty bit tracking to Dataset) created by bdezonia
Create a dirty bit facility for Dataset. Update flag when data changes …
14:54 Ticket #534 (Image::Rename does not work) created by bdezonia
Open any sample. Choose Image :: Rename and enter a new name. The window …
14:47 Ticket #533 (DisplayPostProcessor should not generate DatasetChangedEvents) created by bdezonia
We bootstrapped the display architecture on the idea that the …
14:11 Ticket #532 (Make legacy layer smarter about handling new IJ2 data types) created by bdezonia
Freshly start IJ2. Create a gradient image that is 12-bit. Run the Image …
14:06 Ticket #531 (Legacy layer has limitations in regard to plugins that change data types) created by bdezonia
Open Bridge sample. Change type to 12-bit. Find Edges. File Revert. Data …
14:03 Ticket #530 (Make legacy harmonization bidirectional) created by bdezonia
From previous instantiations of IJ1 plugins there may be a remembered …
13:56 Ticket #529 (IJ2 not setting current ImagePlus at correct time) created by bdezonia
Open Bridge sample. Then create a Gradient image. Choose IJ1 plugin Rotate …
13:52 Ticket #528 (Have LegacyImageMap track Dataset events) created by bdezonia
The LegacyImageMap needs to track at least some of the Dataset events …
13:46 Ticket #527 (Exceptions thrown with 12-bit revert) closed by bdezonia
fixed: Closing this ticket and opening a series of related tickets
13:15 Ticket #377 (Support for color parameters) closed by curtis
fixed: Added in 4c2a819d5a11904148756c09a61c8379ef453b8d, and fully working as of …
10:08 Ticket #527 (Exceptions thrown with 12-bit revert) created by bdezonia
Open Bridge sample. Convert type to 12-bit. Do File::Revert. Multiple …
09:45 Ticket #519 (Image :: Type menu does unnecessary work) closed by bdezonia
fixed: fixed in 34584b1b27aff24a6183d31d87316862b1f552c1

05/19/11:

17:30 Ticket #526 (Handle loading of images that cannot come in at 1:1 scale) created by bdezonia
Since the adoption of JHotDraw the code that handled the loading and …
17:28 Ticket #518 (NullPtrExcep thrown when changing type of image) closed by bdezonia
fixed: Found that scale initialized to 0 in CanvasHelper. Now defaulting to 1 and …
15:43 Ticket #511 (Image window sometimes does not resize upon dimension change) closed by bdezonia
fixed: As of 4db5647609829d3e9bad8bee379a36ce582e1a00 (sometime after replacement …
13:50 Ticket #235 (Propagate change to ImageStack::getImageArray() throughout IJ) closed by bdezonia
fixed: Recently made the DatasetHarmonizer reset plane references in a Dataset …
13:10 Ticket #513 (Image::Type::HSB Stack plugin results display poorly) closed by bdezonia
fixed: Curtis found sliders not updating issue by …
13:05 Ticket #524 (DatasetView:setPosition() called more often than expected) closed by curtis
fixed: Fixed in 267a33831ffeddb55ce12b6d172325010c50e508.
13:01 Ticket #525 (Update LUTs correctly in DatasetHarmonizer) created by bdezonia
DatasetHarmonizer does nothing about bringing LUTs across from IJ1. So if …
12:37 Ticket #524 (DatasetView:setPosition() called more often than expected) created by bdezonia
When you scroll within a slider of a 3 or more dimensional image …
12:03 Ticket #523 (Improve Jar2Lib to proxy a set of core Java classes) closed by hinerm
fixed: This feature was implemented in revision 7707 through a "-core …

05/18/11:

12:10 Ticket #523 (Improve Jar2Lib to proxy a set of core Java classes) created by hinerm
Currently it's not entirely clear how Jace chooses which core Java classes …
10:46 Ticket #522 (Determine how to approach HSB support) created by bdezonia
IJ1 has some support for HSB images. You can take a RGB image, use …
10:09 Ticket #521 (Post JHotDraw incorporation none of the Tools work) created by bdezonia
The tools no longer work. You can select them but can't do anything with …
10:04 Ticket #520 (Running data changing plugins seems to have no effect) closed by bdezonia
fixed: Nobody was reacting to DatasetUpdatedEvents. Made DatasetView call …
10:03 Ticket #520 (Running data changing plugins seems to have no effect) created by bdezonia
Post JHotDraw support: Choose a Process menu entry like find edges. …

05/17/11:

12:47 Ticket #519 (Image :: Type menu does unnecessary work) created by bdezonia
If you choose an Image :: Type submenu item that matches your current type …
12:45 Ticket #517 (TypeChanger only supports planar Imgs) reopened by bdezonia
Actually this is the case as it is written for changeType(). Make …
12:41 Ticket #517 (TypeChanger only supports planar Imgs) closed by bdezonia
invalid: After investigation I see that TypeCHanger supports user specified …
12:26 Ticket #518 (NullPtrExcep thrown when changing type of image) created by bdezonia
If you change the type of an image via Image :: Type submenu the image …
11:48 Ticket #517 (TypeChanger only supports planar Imgs) created by bdezonia
Looking at TypeChanger it is apparent that it creates a new Img of planar …
09:09 Ticket #516 (Add arbitrary properties to Metadata) created by gharris
Wondering if we want to add something like properties to the ImgPlus …

05/12/11:

16:24 Ticket #515 (Performance improve OPS) created by bdezonia
IJ2 relies on the performance of OPS' AssignOperation. That class works on …
12:26 Ticket #500 (Rename RegionCursor) closed by bdezonia
fixed

05/11/11:

15:24 Ticket #514 (Increase the quality of IJ2's color display results) created by bdezonia
IJ2's display of color data needs improvement. The easiest way to see this …
15:21 Ticket #513 (Image::Type::HSB Stack plugin results display poorly) created by bdezonia
If you load clown and run the Image::Type:HSB Stack plugin the results are …
15:14 Ticket #512 (IJ1's Image::Type::HSB menu command is not working) closed by bdezonia
fixed: fixed issue in LegacyImageMap. returned data looks correct though IJ2's …
14:47 Ticket #512 (IJ1's Image::Type::HSB menu command is not working) created by bdezonia
Open clown. Run Image::Type::HSB Stack on it. Notice that data is changed. …
10:19 Ticket #495 (Tool cursors can get out of synch) closed by bdezonia
fixed

05/10/11:

17:33 Ticket #511 (Image window sometimes does not resize upon dimension change) created by bdezonia
Code to repack the image window is now in place. And if you run crop or …
17:08 Ticket #496 (Resize image panel at appropriate times) closed by bdezonia
fixed: mostly fixed the problem where the display window would not resize when …
15:21 Ticket #510 (Menu entry File::Revert does not work) closed by bdezonia
fixed: It turns out IJ1's revert was not working because the underlying plane …
15:08 Ticket #392 (Handle IJ1's in place manipulations of ImagePluses) closed by bdezonia
fixed: Fixed delete slice. Also fixed LegacyImageMap to correctly sync when …
15:05 Ticket #504 (Legacy layer gotchas) closed by bdezonia
fixed: improve the ability of IJ1 changes to be mirrored in IJ2 data structures …
09:54 Ticket #510 (Menu entry File::Revert does not work) created by bdezonia
The file revert menu command does not work. Create an IJ2 plugin to …
09:46 Ticket #25 (Improve Bio-Formats ITK plugin class structure and build system) closed by hinerm
wontfix: As each of these pieces serves a necessary purpose, and the overall …

05/09/11:

16:57 Ticket #509 (Determine how to approach legacy Image::Type menu plugins) created by bdezonia
The RGB Stack and HSB Stack plugins seem to work when fed 3 channel color …
16:48 Ticket #508 (Preserve IJ1 metadata) created by bdezonia
In IJ1 an ImageStack can have a label for each slice. IJ2 does not …
16:25 Ticket #507 (opening Clown image results in out of memory in heap) closed by bdezonia
fixed: Fixed bug in RgbImageTranslator that caused infinite recursive loop inside …
15:57 Ticket #507 (opening Clown image results in out of memory in heap) created by bdezonia
Can no longer open the clown image without a runtime exception (out of …
14:47 Ticket #506 (Fix fill plugin when color selection code in place) created by bdezonia
Currently the Fill plugin prompts the user for a value to fill the Dataset …
14:46 Ticket #505 (Fix Crop plugin when region selection code in place) created by bdezonia
The Crop plugin currently asks for the extents of the region to crop. When …
13:36 Ticket #499 (Image math tries to run even if given no input Datasets) closed by bdezonia
fixed

05/06/11:

23:00 Milestone biweekly-2011: Apr-25 to May-06 completed
Tasks from 2011-Apr-25 through 2011-May-06.
17:24 Ticket #504 (Legacy layer gotchas) created by bdezonia
If an IJ1 plugin modifies the ImageStack of an ImagePlus that is …
17:16 Ticket #472 (Test and improve legacy layer) closed by bdezonia
fixed: unit tests done. ticket complete.
16:58 Ticket #482 (Delete Dataset on final Display Closed) closed by curtis
duplicate: Duplicate of #413, already fixed. When a view goes away, …
12:28 Ticket #503 (Improve Bio-Formats Hudson builds) created by curtis
Currently, there are several different Bio-Formats Hudson jobs on both the …
11:54 Ticket #472 (Test and improve legacy layer) reopened by bdezonia
11:20 Ticket #472 (Test and improve legacy layer) closed by bdezonia
fixed: 2) pretty sure I understand what needed to be done here. completed Ticket …
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