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Ticket #2000 (closed defect: fixed)

Opened 2013-09-03T13:55:45-05:00

Last modified 2014-05-01T12:34:51-05:00

Support nonlinear calibration functions

Reported by: bdezonia Owned by: bdezonia
Priority: major Milestone: imagej2-b8-analysis
Component: ImgLib2 Version:
Severity: serious Keywords:
Cc: Blocked By:
Blocking: #1923


The recent changes made to incorporate img-metadata are a good start for supporting calibration. However currently it is limited to linear scale with origin 0,0. We need to expand the img-metadata hierarchy such that we can support a number of axis types that scale in a nonlinear fashion. The initial set of nonlinear axes to support could mirror IJ1's fitting functions as present in CurveFitter (and also its Calibration class).

Change History

comment:1 Changed 2013-09-03T13:58:41-05:00 by bdezonia

CTR and BDZ discussed. The plan going forward is to define a subclass of CalibratedSpace called LinearSpace. It is based on LinearAxis's. A CalibratedAxis no longer will have calibration()/setCalibration(). It instead will support two methods that return doubles: getRawValue(double calibratedValue) and getCalibratedValue(double rawValue). So make these changes and propagate throughout Imglib and IJ2.

comment:2 Changed 2013-09-05T13:00:36-05:00 by bdezonia

I have done this for Imglib on the nonlinear-goodies branch. It is ready to be merged. I also have the changes necessary in IJ2 on my local machine. I am testing them. I will merge both of these after ctrueden releases an IJ2 beta subrelease here in the next day or so.

comment:3 Changed 2013-09-05T15:16:02-05:00 by bdezonia

I have also pushed a nonlinear-goodies branch for IJ2.

comment:4 Changed 2013-09-11T10:32:52-05:00 by bdezonia

I have written an email to fiji-devel soliciting feedback. Hopefully it can be merged soon.

comment:5 Changed 2014-05-01T12:34:51-05:00 by curtis

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

Barry and I  completed this work last fall.