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Ticket #489 (closed enhancement: fixed)

Opened 2011-05-03T14:22:47-05:00

Last modified 2011-06-16T12:32:05-05:00

Add/Delete "Slice" in ImageJ2

Reported by: gharris Owned by: bdezonia
Priority: major Milestone: biweekly-2011: Jun-06 to Jun-17
Component: Data Model Version:
Severity: major Keywords:
Cc: Blocked By:


Decide what a "slice" is and how to designate how to apply an add or delete operation sensibly.

Change History

comment:1 Changed 2011-05-03T14:23:12-05:00 by gharris

  • Milestone set to imagej-2.0-beta2

comment:2 Changed 2011-05-09T17:04:40-05:00 by bdezonia

Note that in the legacy layer we are supporting what IJ1 does. Thus if you have a 2x3x4 CZT stack of XY planes and you call a plugin that deletes a slice you get back a 1x23x1 CZT image of XY planes.

comment:3 Changed 2011-05-10T11:22:03-05:00 by bdezonia

Last comment not entirely accurate. Delete slice is sort of working now. IJ2 takes a 4x15 CZ stack and when deleting a slice turns it into a 4x14 stack (thus deleting 4 planes). This is likely just by accident.

Add slice is not working right now.

Probably best if we define our own plugins to replace a number of them in Image::Stacks menu (such as add slice, delete slice, next slice, prev slice, set slice).

comment:4 Changed 2011-05-10T11:27:51-05:00 by bdezonia

Add slice sort of works at the moment:

  • add slice to T1 Head (3D) -> new slice added at position 2 of stack
  • add slice to Organ of Corti (4D) any number of times 0> no changes

comment:5 Changed 2011-06-10T12:16:04-05:00 by bdezonia

  • Milestone changed from imagej-2.0-beta2 to biweekly-2011: Jun-06 to Jun-17

Wrote pure IJ2 Add Data and Delete Data plugins

comment:6 Changed 2011-06-10T15:10:31-05:00 by bdezonia

Wrote pure IJ2 Add Axis and Delete Axis plugins

comment:7 Changed 2011-06-10T17:01:57-05:00 by bdezonia

Wrote pure IJ2 Reorder Axes plugin. Needs testing. Some TODOs listed in

Some things that could be done to completely replace IJ1's functionality:

  • setPosition (needs to be multidimensional and updates slider positions of UI)
  • next slice and previous slice (needs to cycle thru current dimension and wrap other dims at boundaries) Maybe we need to specify the current dim to cycle within.

comment:8 Changed 2011-06-16T12:32:05-05:00 by bdezonia

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

Implemented all plugins to replace add slice, delete slice, next slice, prev slice, and set slice. Finished with c7876a41c96570e82a483472b737f7ca71680d4b and 581bfaabb4c1c38a332707ca94deaa3d4a155e8f.