Convergent beam crystallography project

This project consists of two packages - convergent beam simulation program (cbc) and experimental data processing package (cbc_dp)

1. Convergent beam simulation

Simulation for convergent beam diffration on a crystalline sample written in Python. Code is compatible with Python 2.X and 3.X.

For more information regarding the theory behind this see the article written by Prof. Henry Chapman.

Compilation

It’s a package called cbc, with which you can conduct a diffraction simulation. See usage examples: go to cbc package structure

Required dependencies:

• NumPy
• Numba
• SciPy
• matplotlib
• h5py

Features

The package can perform convergent beam diffraction simulation of crystalline samples based on first Born approximation theory.

Available incoming beam models:

• Gaussian beam
• Bessel beam
• Lens beam with rectangular or circular aperture

Samples could be composed of different compound unit cells deffined by array of atom coordinates within the unit cell and corresponding B-factors. These data can be imported via PDB format file. Unit cells are arranged in a rectangular grid.

cbc package structure

The library itself consists of two modules and an utility package:

• beam.py - a module with incoming beam classes
• lattice.py - a module with sample lattice classes
• wrapper.py - simulation calculation wrapper module
• utils - utility package:
  • utilfuncs.py - utility functions for convergent beam diffraction project
  • asf - atomic scattering factor calculation package:
    • load.py - a module, that loads atomic scattering factor fit coefficients
  • pdb - PDB data import package
    • readpdb.py - a module, that imports molecular structure .pdb files

Also there is a couple of usage examples:

• read.py - reading and ploting diffraction results
• diff_run.py - diffraction simulation example

Upcoming things to do

• consider different crystall space groups

2. Convergent crystallography data processing

Experimental convergent diffraction data processing package. Data is acquired from PETRA P06 beamtime on June 13, 2019.

Data correction:

- Flatfield correction
- Median filtering
- Non maximum supression

Line detection

- Progressive Probabilistic Hough line transform
- Line Segment Detector (LSD)

More information about Progressive Hough transform is written in this article and about Line Segment Detector in this article.

Indexing:

- Rotational diffraction pattern indexing
- Convergent beam indexer