Per-tilt CTF and dose weighting, spectrum whitening, and rotational symmetry

Version 0.3.0 is out!

Functionality updates to pytom_match_template.py:

• The --per-tilt-weighting option has been expanded so it can now model a 3D CTF with tilt and dose weighting (as previously described in methods like Relion subtomo averaging, Warp, and EmClarity). To enable the full weighting 3 files need to be provided: a .rawtlt/.tlt file with tilt angle info, a .defocus/.txt file with per tilt defocus (in nm), and a file with accumulated dose per tilt (in e-/A2). The defocus file and dose file are assumed to have the same ordering as the tlt file. PR #53
• Spectrum whitening is now available (similar to Rickgauer et al., (2017) for 2DTM). The power spectrum radial average is estimated for the full tomogram, and the whitening filter is calculated from it and applied to tomogram and template. It sharpens the correlation peaks! PR #53
• There is now a rotational-symmetry option to reduce the angular search for templates with rotational symmetry. PR #55
• It is now possible to provide a custom angular search file. PR #56

Fixes:

• pytom_create_template.py has a more specific warning message for the low pass filter. PR #51

Docs will be updated soon and we are working on a tutorial!

Thanks @rdrighetto for some very useful discussion on the CTF model.