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Resolve "Pre-processing: Adding CTF based single-distance phase-retrieval"

Nicola Vigano requested to merge 213-pre-processing-ctf-single-distance into master

About

Some of the ESRF beamlines (e.g. ID16A) often use different filters other than the Paganin filter for phase-retrieval. This MR track the development of the support for the contrast transfer function (CTF) single-distance phase-retrieval.

Closes #213 (closed), #44 (closed)

To do

  • CTF single-distance class
  • Local correction of the sample induced distortion
  • docstring and key comments for crucial / involved parts
  • Unit tests
  • Break down DetectionCorrector into single-purposed classes
  • Rebase on latest master and update PaganinPhaseRetrieval tests if needed (news API use meters !)
  • Remove commented code and last test case in test_ctf.py
  • Decouple distortion estimation from distortion correction in correct_flat_by_correlation

Notes

A comprehensive description of the CTF and it's derivation / usage can be found here: https://doi.org/10.1364/OE.26.011110 ( equation (8) for single distance; Equation (16) for multiple distances).

Corresponding reference code can be found here: https://gitlab.esrf.fr/ID16A/id16a_octave_beamline

Edited by Pierre Paleo

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