Software for ptychography reconstruction and other quantitative interpretation of diffraction patterns

[uellue]

Since this doesn't quite fit individual methods, but rather a specific family of data analysis methods that requires similar data and metadata, I wasn't sure how to incorporate that in the existing lists.

Ptychography

• Adorym
• PtychoSTEM and pyPtychoSTEM
• Ptychography 4.0, see also Utility functions for iterative algorithms Ptychography-4-0/ptychography#60 for more details regarding ptychography metadata
• PtyPy
• DESY/HZDR ptychography code -- not public
• nfPhasing, c/o Nico Hoffmann at HZDR -- not public
• Near Field Ptychography by Andrew Maiden: https://www.nature.com/articles/srep01927
• Center of mass analysis in LiberTEM, see also Helper function to guess CoM parameters LiberTEM/LiberTEM#1111 for code to determine and validate correct alignment

Phase, orientation and strain mapping

• pyxem
• ASTAR and other Nanomegas software

Both ptychography and phase, orientation and strain mapping work with scanning diffraction data and require the following information or a subset of it:

• Physical coordinates of scan points in the specimen coordinate system
• Relation between detector coordinates and scattering coordinates:
  • Center, optical axis position on the detector
  • Diffraction angle per pixel (for example as camera length and physical detector pixel size, or radius of the incident beam in px combined with convergence semi-angle for STEM)
  • Rotation+handedness relative to scan coordinates -- problem area for scanning diffraction since easy to mix up in some way
• Incident wavelength
  • Photon energy, electron energy, wavelength are equivalent
• Incident illumination. Usually a convergence angle and possibly defocus are used for STEM since it often works with a convergent focused beam. Generally, a complex-valued function in the specimen plane describes the incident radiation.