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Ticket #1143 (closed feature: fixed)

Opened 2012-04-27T14:09:31-05:00

Last modified 2012-12-06T12:47:45-06:00

Improve support for ROIs, segmentation and labeling [headless]

Reported by: bdezonia Owned by: bdezonia
Priority: major Milestone: imagej2-b3-headless
Component: Data Model Version:
Severity: serious Keywords:
Cc: curtis Blocked By: #818, #922, #1195, #1201, #1205, #1215, #1217, #1224, #1229


Some notes about ROIs

SwingOverlayManager has a flatten command. In IJ1 this does a standard flatten but also includes the outline of the active roi on the flattened image. We need to be able to copy this behavior. If you take the current ARGBScreenImage it does not have the current roi rendering info. That is handled by JHotDraw. Somehow we have to tie these things together so that we can get a view of the dataset and roi composited on it as pixels/data points.

ROIs need to be pieces we can use to constrain operations. We might have a ROI (like an ellipse). And we want to fill the ellipse on it's correct slice. Or, like the fill command in IJ1, across all slices in the image if desired.

Also we have invert which inverts within the outline of the current roi. And all the math plugins should probably do the same. And we might want to take a ROI's outline and multiply all the pixels by 1.5 across all slices in the image. Using PointSets this can be easily accomplished. Using our current Overlays is trickier.

Change History

comment:1 Changed 1969-12-31T18:22:17-06:00 by curtis

  • Blocked By 1189 added

comment:1 Changed 2012-04-27T14:17:59-05:00 by bdezonia

  • Milestone set to imagej-2.0.0-beta3

comment:2 Changed 2012-05-04T13:19:28-05:00 by bdezonia

The last two paragraphs have been implemented recently. We should remember them for any redesign going forward.

comment:3 Changed 2012-05-14T13:10:11-05:00 by curtis

  • Summary changed from ROI needs to Improve support for ROIs, segmentation and labeling (beta3)

comment:4 Changed 2012-05-14T13:26:31-05:00 by curtis

  • Blocked By 818, 922, 984, 1103 added

comment:5 Changed 2012-05-14T13:27:23-05:00 by curtis

  • Blocked By 1131, 1152, 1165, 1166 added

comment:6 Changed 2012-05-14T14:17:43-05:00 by bdezonia

  • Blocking 1174 added

comment:7 Changed 2012-05-14T14:18:11-05:00 by bdezonia

  • Blocking 1174 removed
  • Blocked By 1174 added

comment:8 Changed 2012-05-14T14:23:12-05:00 by bdezonia

  • Blocked By 1175 added

comment:9 Changed 2012-05-15T10:34:49-05:00 by curtis

  • Blocked By 878 added

comment:10 Changed 2012-05-15T13:02:16-05:00 by curtis

  • Blocked By 536 added

comment:11 Changed 2012-05-15T13:13:04-05:00 by curtis

  • Blocked By 1048 added

comment:9 Changed 2012-05-15T13:13:38-05:00 by curtis

  • Summary changed from Improve support for ROIs, segmentation and labeling (beta3) to Improve support for ROIs, segmentation and labeling (2.0.0-beta3)

comment:10 Changed 2012-06-08T12:36:07-05:00 by bdezonia

  • Blocked By 1205 added

comment:11 Changed 2012-06-08T12:36:37-05:00 by bdezonia

  • Blocked By 1201 added

comment:12 Changed 2012-06-08T12:36:53-05:00 by bdezonia

  • Blocked By 1196 added

comment:13 Changed 2012-06-08T12:37:09-05:00 by bdezonia

  • Blocked By 1195 added

comment:14 Changed 2012-06-08T16:53:03-05:00 by curtis

  • Blocked By 1114 added

comment:15 Changed 2012-06-13T14:54:18-05:00 by bdezonia

  • Blocked By 1217 added

comment:16 Changed 2012-06-13T14:55:36-05:00 by bdezonia

  • Blocked By 1215 added

comment:17 Changed 2012-06-18T14:30:20-05:00 by bdezonia

  • Blocked By 1224 added

comment:18 Changed 2012-06-18T15:41:23-05:00 by bdezonia

  • Blocked By 1229 added

comment:19 Changed 2012-06-18T15:44:15-05:00 by bdezonia

In description paragraph one hatched as separate ticket #1229.

The remaining description has been handled by commits long ago.

comment:20 Changed 2012-06-18T15:49:43-05:00 by bdezonia

After the meeting in Barcelona some discussions were made about representing ROIs as probability maps inside Imglib2. This code needs to be written.

comment:21 Changed 2012-07-03T12:53:30-05:00 by curtis

  • Milestone changed from imagej-2.0.0-beta3 to imagej-2.0.0-beta4

comment:22 Changed 2012-07-03T12:58:25-05:00 by curtis

  • Milestone changed from imagej-2.0.0-beta4 to imagej-2.0.0-beta3

This feature ticket is, by definition, due for milestone:imagej-2.0.0-beta3. However, many of its constituent tickets need to migrate to #285.

comment:23 Changed 2012-07-03T13:28:24-05:00 by bdezonia

  • Blocked By 536, 878, 1048, 1103, 1114, 1131, 1152, 1165, 1166, 1174, 1175, 1189, 1196 removed

comment:24 Changed 2012-07-03T13:29:58-05:00 by bdezonia

  • Blocked By 984 removed

comment:25 Changed 2012-07-03T13:47:32-05:00 by bdezonia

  • Status changed from new to closed
  • Resolution set to fixed

comment:26 Changed 2012-07-12T11:03:12-05:00 by curtis

Note that remaining ROI issues were migrated to #285.

comment:27 Changed 2012-12-06T12:47:45-06:00 by curtis

  • Summary changed from Improve support for ROIs, segmentation and labeling (2.0.0-beta3) to Improve support for ROIs, segmentation and labeling [headless]