CrystFEL - Crystallography with a FEL
-------------------------------------

Thomas White <taw@physics.org>, CFEL, DESY

CrystFEL is a suite of programs for simulating and processing crystallographic
(Bragg diffraction) data acquired with a free electron laser.  The particular
characteristics of such data which call for a specialised software suite are

- The sliced, rather than integrated, measurement of intensity data.  Many, if
   not all reflections are partially integrated.  Unique correction factors are
   needed.

- The crystals are small, leading to significant Fourier truncation effects on
   the detector.

- Many patterns (>10,000) are required - high throughput is needed.


The main programs are:

	- pattern_sim, for simulating patterns.

	- indexamajig, for finding hits, locating peaks, indexing patterns
	               and constructing lists of h,k,l,I,sigma(I) for each
	               pattern.

	- process_hkl, for merging per-pattern lists of intensities into a
	               single reflection list.

	- hdfsee, a simple HDF5 image viewer.

In addition, there is also:

	- get_hkl, for generating a list of squared structure factors for
	           comparison to simulated or experimental data.

	- powder_plot, for turning an image into a list of reciprocal space
	               vector moduli and intensities (i.e. a powder diffraction
	               trace).

	- compare_hkl, for working out the differences (e.g. a q-dependent
	               scaling factor) between two lists of reflections.