Ticket #445 (closed task: fixed)

Opened 9 years ago

Last modified 6 years ago

Add unit support to IJ2 as needed

Reported by: bdezonia Owned by: curtis
Priority: major Milestone: imagej2-b8-analysis
Component: Core Version:
Severity: serious Keywords:
Cc: Blocked By: #1999
Blocking:

Description (last modified by bdezonia) (diff)

Add the capability to tag axes with units. Curtis had planned to use an existing Java library for this support. I'm not sure if this should be done at the imglib level or the imagej2 level.

Change History

comment:1 Changed 9 years ago by bdezonia

  • Description modified (diff)

comment:2 Changed 9 years ago by bdezonia

  • Summary changed from Add unit support to as needed to Add unit support to IJ2 as needed

comment:3 Changed 8 years ago by bdezonia

  • Milestone changed from imagej-2.0-beta1 to imagej-2.0-beta2

comment:4 Changed 8 years ago by bdezonia

  • Owner changed from bdezonia to curtis
  • Status changed from new to assigned

Curtis, this could be part of the project to meld dimensions and axes and calibration values. I'm assigning to you for now and you can modify that ticket as you see fit or assign this back.

comment:5 Changed 8 years ago by bdezonia

  • Blocking 564 added

comment:6 Changed 8 years ago by bdezonia

  • Blocking 490 added

comment:5 Changed 8 years ago by curtis

  • Blocking 490, 564 removed
  • Milestone changed from imagej-2.0.0-beta3 to imagej-2.0.0-beta4

We should consider using the  Units of Measurement API, probably the  JScience implementation thereof. See  this thread on imagej-devel for details.

Last edited 8 years ago by curtis (previous) (diff)

comment:6 Changed 7 years ago by dscho

  • Blocking 1333 added

comment:7 Changed 7 years ago by bdezonia

  • Blocking 564 added

(In #564) Don't know why blocked by 445 was removed. The implementation of this feature requires one to display units in the info window.

comment:8 Changed 7 years ago by curtis

  • Blocking 9 added; 1333 removed
  • Milestone changed from imagej-2.0.0-beta4 to imagej-2.0.0-beta5

comment:9 Changed 7 years ago by bdezonia

  • Blocking 1222 added

comment:10 Changed 7 years ago by bdezonia

Note that Roger Leigh is working on the roi-model through the SciJava group and he has mentioned in his notes the usefulness of physical units at the SciJava level.

comment:11 Changed 7 years ago by curtis

As discussed in #imagejdev today, the other possibility we had been considering is  UCAR Units. But from what I have read so far, I like JScience better right now. Requires further investigation as part of this ticket, of course.

comment:12 Changed 7 years ago by aivar

Other possibilities that might work:

Units of Measurement API
 http://code.google.com/p/unitsofmeasure/

Frink Interpreter
 http://futureboy.us/frinkdocs/
 http://futureboy.us/frinkdocs/#EmbeddingFrink

comment:13 Changed 7 years ago by dscho

How well researched are unitsofmeasure and frink? Curtis spent a considerable amount of time to investigate the strengths and weaknesses of ucar-units and JScience. Before considering to use alternatives, those alternatives should be equally well investigated.

comment:14 Changed 7 years ago by curtis

The Units of Measurement API is a specification, not an implementation. The JScience code implements that specification, and is BSD licensed.

Frink looks very cool in that it targets the Android platform, but it is not open source. The license is not clear, but the binary JAR is obfuscated to make decompilation more difficult, so it is highly unlikely the author would be amenable to changing the license.

Please at least verify the license of a package before suggesting it for use with ImageJ2.

comment:15 Changed 7 years ago by dscho

Thanks, Curtis, for clarifying. You are correct, of course, in your implicit assumption that I should do the research myself in the future, rather than letting you do my homework.

comment:16 Changed 7 years ago by bdezonia

  • Blocking 1620 added; 9 removed

comment:17 Changed 7 years ago by bdezonia

  • Blocking 1620 removed

(In #1620) See also #445

comment:18 Changed 7 years ago by curtis

  • Milestone changed from imagej2-b7-ndim-data to imagej2-b8-analysis

This work is pending on the img-metadata branches of imagej.git and imglib.git. But will not make it into beta7.

comment:19 Changed 6 years ago by bdezonia

The img-metadata package was merged to master recently. Soon we can set units. But actual unit conversion still requires us to choose a unit library and use it.

comment:20 Changed 6 years ago by bdezonia

  • Blocked By 1999 added

comment:21 Changed 6 years ago by bdezonia

  • Blocking 1222 removed

comment:22 Changed 6 years ago by bdezonia

  • Blocking 564 removed

(In #564) Fixed with commit 8d63e7ef9cbe902a0ad316c118b9b30a09c6f1d6

comment:23 Changed 6 years ago by bdezonia

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

Unit library chosen (UCAR UDUNITS).

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