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Various fixes (API break !)

Pierre Paleo requested to merge ci_fix2 into master

About

This MR does the following:

  • Make all the CoR estimator use the same convention, where zero is the left-most pixel (more on that below) - close #486 (closed)
  • Fix some CoR tests along the way
  • Remove unused helical code - Close #548 (closed)

To do

  • Fix TestCtf.test_ctf_id16_class
  • Remove unused helical tests
  • Fix CoR tests

Notes

CoR results convention (API break !)

By default, all CoR estimators in nabu.estimation now return a value relative to the left.

  • Zero is the index of left-most pixel in the image (technically, -0.5 is the coordinate of the left border of the leftmost pixel).
  • (width - 1)/2 corresponds to the middle of the image

This is to have a hopefully consistent convention for all CoR estimators. The API is modified in the sense that some CoR previously returned offsets relative to the middle of the image. This can still be recovered by using return_relative_to_middle=True in the CoR estimators.

Now we only use values relative to the left-most pixel. For the record, this convention is also used by tomopy and algotom.

In my opinion, the "relative CoR" (i.e offset relative to the middle of the image) shoud only be used for display to the user, not for internal calculations.

There might be still some width / 2 (instead of (width - 1)/2) leftovers, to be sorted out.

Remove obsolete (?) helical pipeline code:

  • Remove helical/tests/test_accumulator.py
  • Rmove helical/tests/test_pipeline_elements_full.py
  • Remove helical/teets/test_strategy.py
Edited by Pierre Paleo

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