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.

CrystFEL includes programs for simulating and processing patterns subject to the
above characteristics.  The main programs are:

	- pattern_sim, for simulating patterns.

	- indexamajig, a "batch indexer" and data reduction program.
	               It is used for finding hits, locating peaks, indexing
	               patterns and constructing lists of h,k,l,I,sigma(I) (or
	               similar) for each pattern.

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

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.

And, because I'm so nice, included at no extra cost is:

	- hdfsee, a simple viewer for images stored in HDF5 format.


CrystFEL mostly works with images stored in HDF5 format, unit cell and atomic
coordinate data in PDB format, and reflection lists in plain text format (i.e.
not MTZ).

For documentation on the individual programs and topics, see the files inside
the "doc" directory.


Installation
------------

See the "INSTALL" file for the generic instructions on how to use the build
system.  In short, it's

$ ./configure
$ make
$ sudo make install

You might want to substitute something based on one of the following for the
first step:

$ ./configure --enable-opencl
$ ./configure --with-hdf5=/some/strange/location
$ ./configure --with-libtiff=/some/strange/location
$ ./configure --with-gsl=/some/strange/location
$ ./configure --disable-gtk

If you're compiling on Mac OS X, where GTK, libPNG and libTIFF seem to be much
harder to come by, disable lots of things:

$ ./configure --disable-gtk --disable-png --disable-libtiff


A note on data orientation
--------------------------

CrystFEL defines "x" as the most quickly varying coordinate in the data, and "y"
as the second most quickly varying coordinate in the data.  It doesn't know what
to do with any extra dimensions beyond the second.

The origin, which is considered the lower left corner of the image, is defined
by CrystFEL as the first element in the image data.  Positive x points in a
direction to the right, and positive y points upwards.  When a right-handed
coordinate system is formed using these definitions, CrystFEL will consider the
positive z direction to point towards the source of the incident beam.

The detector surface is assumed to be perpendicular to the incident beam.


Program name
------------

There seems to be a tendency to capitalise the names of programs in
publications.  It's not 1970 any more, and programs can have capitalisation
any way we choose, not just all capitals.  I hope you can forgive me for being
fussy about how my work is referred to in publications and talks.

The name for the overall software suite is "CrystFEL", with this being the only
acceptable capitalisation.  The individual programs should always be referred to
with all letters in lower case, exactly as written earlier in this file.

In most cases, it will be more appropriate to refer to the overall suite than to
one of its constituent programs.

The following are NOT acceptable forms: "CRYSTFEL", "crystFEL", "Crystfel",
"Indexamajig", "INDEXAMAJIG", "PATTERN_SIM", "Pattern_Sim", "Pattern_sim".

In addition, CrystFEL is made up of "programs", not "routines" nor "procedures".
(The "programs" in turn are made up from "routines" and "procedures", but unless
you are exploring the source code, there's no need for you to know about that).