Meaning of headers in output .csv from homogeneous refinment?

Tips
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Hi all,

Is there documentation about what the different columns in the refinement output .csv file mean? The ones starting with ctf_params and data_input make sense to me. I’m less sure about the data related to alignments. Can anyone help me fill in the gaps or suggest a resource? I read the paper and the supplement which answered some of my questions.

  • alignments.model.E - image alignment error E(r,t) ?
  • alignments.model.E_min_alpha - ?
  • alignments.model.alpha - ?
  • alignments.model.cross_cor - ?
  • alignments.model.dr - ?
  • alignments.model.dt - ?
  • alignments.model.image_pow - ?
  • alignments.model.phiC - related to pose variable?
  • alignments.model.r.0 - angle phi?
  • alignments.model.r.1 - angle theta?
  • alignments.model.r.2 - angle psi?
  • alignments.model.resid_pow - ?
  • alignments.model.slice_pow - ?
  • alignments.model.t.0 - translational parameter x?
  • alignments.model.t.1 - translational parameter y?

Thanks!
S

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If you are curious, I suggest you read the code for csparc2star.py. The most important model fields (particle poses and class membership probability) are documented (or are self-evident) in the code.

Your guesses are mostly right, except cryoSPARC uses the axis-angle representation and r.0-2 are the elements of the axis-angle vector.

Euler angles are so 18th century, the 1840s are really where it’s at when it comes to rotations! :wink:

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Oh right! Great point, @DanielAsarnow . I will check it out. :slight_smile: Thanks as always for your work.

PS: I’m disappointed that Euler angles are so 18th century, because I finally started pronouncing “Euler” correctly. UGH what a waste of time.

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Haha, fortunately, William Rowan Hamilton is pretty straightforward to say. Unfortunately, Olinde Rodrigues less so.

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