CrystFEL - Data processing for serial crystallography

Age	Commit message (Collapse)	Author
2017-06-21	Don't compile CBF stuff without CBFlib	Thomas White

2017-06-21	Close leftover HDF5 handles	Thomas White

2017-06-21	hdf5_read2(): Fix exit path	Thomas White
	Bad pixel map is not allocated at this point.
2017-06-21	indexamajig: Add --min-peaks (basic hitfinder functionality)	Thomas White

2017-06-21	Merge branch 'tom/cbf'	Thomas White

2017-05-18	Update ChangeLog	Thomas White

2017-05-17	Actually add scripts/sum-peaks	Thomas White

2017-05-16	check_hkl: Calculate resolution of reflection with asymmetric indices for ↵	Thomas White
	both possible and measured reflections Previously, it used whichever indices it found first. This made the resolutions different enough to fall into different bins, and screwed up the completeness (fortunately, rarely).
2017-05-16	Add scripts/sum-peaks	Thomas White

2017-05-12	Make all Python scripts compatible with Python 2 and 3	Thomas White
	It would be nice to upgrade completely to Python 3, but this may create problems at SLAC because psana only supports Python 2 (Python 3 is available, but means that users have to jump through hoops to run a simple CrystFEL script). None of our scripts do anything complicated, so they can all be compatible with both so far. If anyone adds a script which requires a particular version, make sure to specify the version in the first line, consistent with PEP 394.
2017-05-09	Allow reading CBF without geometry (only for simple viewing)	Thomas White

2017-05-09	Add missing checks	Thomas White

2017-05-05	Show filename of CBF file if it can't be read	Thomas White

2017-05-05	Fill in photon energy, clen and adu for CBFs	Thomas White
	This needed a bit of reorganisation and clarification of who is repsonsible for loading what. The low-level file loaders, e.g. hdf5_read and hdf5_read2 in hdf5-file.c or cbf_read in image.c, are responsible. There is a helper function adjust_centering_for_rail in detector.h which they can use. It seems like this could be done more cleanly at the imagefile layer. However, we need to make sure that the "old" hdfile API still works on its own, even when not accessed via the new imagefile API.
2017-05-05	Allow location of photon energy (eg in HDF5 file) to start with any character	Thomas White

2017-05-05	Read CBF data	Thomas White

2017-05-03	hdfsee: Use new imagefile API	Thomas White

2017-05-03	Detect CBF files, interface bits	Thomas White

2017-05-03	hdfile_set_image(): Remove panel argument	Thomas White
	Seems to have been added in 2014 and is not used at the moment
2017-05-03	autoconf bits for CBFlib	Thomas White

2017-05-03	HDF5 reading under new API	Thomas White

2017-05-02	Skeleton image file API	Thomas White

2017-05-02	Initial CBF stuff	Thomas White

2017-04-13	Add half-pixel offset for peakfinder8	Thomas White
	Like zaef, the pixel indices need to be converted to geometrical coordinates. This increases the indexing rate by about 5% in my test.
2017-04-13	hdf5_read2(): Free buffers when read fails	Thomas White

2017-03-31	geoptimiser: Show peak information when there is a problem	Thomas White

2017-03-31	geoptimiser: Fix rounding of peak coordinates	Thomas White
	Peak locations in CrystFEL are considered to be distances (in pixel units) from the corner of the detector panel. Therefore, simple truncation is needed here, not rounding.
2017-03-31	Offset peak locations from HDF5 or CXI files by 0.5,0.5	Thomas White
	CrystFEL considers all peak locations to be distances from the corner of the detector panel, in pixel units, consistent with its description of detector geometry. In contrast, Cheetah considers the peak locations to be pixel indices in the data array. Therefore, a half-pixel offset is needed when importing the peak lists. For users who need the old behaviour, this commit adds a new option indexamajig --no-half-pixel-shift to deactivate this offset.
2017-03-24	indexamajig: Format --help and fix typos	Thomas White

2017-03-24	Remove an old debugging message	Thomas White

2017-03-24	Propagate error if indexing method is unrecognised	Thomas White

2017-03-24	Merge branch 'valerio/peakfinder8'	Thomas White

2017-03-24	Mostly fussiness	Thomas White

2017-03-22	Completely revamped implementation of peakfinder8	Valerio Mariani

2017-03-15	largest_q(): Handle NULL detector	Thomas White

2017-03-13	Added management of max_num_peaks per image instead of per panel	Valerio Mariani

2017-03-13	Added information about max_num_peaks to documentation	Valerio Mariani

2017-03-13	Added saturated peak management to peakfinder8	Valerio Mariani

2017-03-13	Ask for C99 in configure.ac, remove weird C99 declarations	Thomas White

2017-03-13	process_hkl: Add event IDs to "--stat" file	Thomas White

2017-03-11	Removed unused iarg	Valerio Mariani

2017-03-11	Fixed some more bugs reported by Yaroslav	Valerio Mariani

2017-03-10	Fixed a couple of bugs reported by Tom	Valerio Mariani

2017-03-10	Update ChangeLog	Thomas White

2017-03-10	compare_hkl: Add --min-measurements	Thomas White

2017-03-10	Added peakfinder8 information to the indexamajig man page	Valerio Mariani

2017-03-10	cell_print(): Show reciprocal angles	Thomas White

2017-03-10	Peakfinder8 in CrystFEL. Same results as Anton's Cheetah implementation	Valerio Mariani

2017-03-08	Check unit cell parameters after prediction refinement	Thomas White

2017-03-08	Allow indexing system to store its own data, independently of indexing methods	Thomas White
	Previously, the indexing system passed all the information on to the indexing engines and then forgot about it. That made it difficult to do things like check the indexing solution after prediction refinement, because the target unit cell was unavailable. Now, the indexing system itself can keep some information. Of course, that information includes the private pointers for the indexing engines themselves. I took the opportunity to streamline things a little bit. The caller can now set up the indexing system in one step, without having to separately parse the names of the indexing methods. The caller no longer has to keep track of a separate array of methods, instead just one structure which contains everything.