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2017-05-18Various fiddles to add symmetry operations but not functionalHelen Ginn
2017-05-18Update ChangeLogThomas White
2017-05-17Actually add scripts/sum-peaksThomas White
2017-05-16check_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).
2017-05-16Add scripts/sum-peaksThomas White
2017-05-12Make all Python scripts compatible with Python 2 and 3Thomas 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.
2017-05-09Allow reading CBF without geometry (only for simple viewing)Thomas White
2017-05-09Add missing checksThomas White
2017-05-05Show filename of CBF file if it can't be readThomas White
2017-05-05Fill in photon energy, clen and adu for CBFsThomas 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.
2017-05-05Allow location of photon energy (eg in HDF5 file) to start with any characterThomas White
2017-05-05Read CBF dataThomas White
2017-05-03hdfsee: Use new imagefile APIThomas White
2017-05-03Detect CBF files, interface bitsThomas White
2017-05-03hdfile_set_image(): Remove panel argumentThomas White
Seems to have been added in 2014 and is not used at the moment
2017-05-03autoconf bits for CBFlibThomas White
2017-05-03HDF5 reading under new APIThomas White
2017-05-02Skeleton image file APIThomas White
2017-05-02Initial CBF stuffThomas White
2017-04-13Add half-pixel offset for peakfinder8Thomas White
Like zaef, the pixel indices need to be converted to geometrical coordinates. This increases the indexing rate by about 5% in my test.
2017-04-13hdf5_read2(): Free buffers when read failsThomas White
2017-03-31geoptimiser: Show peak information when there is a problemThomas White
2017-03-31geoptimiser: Fix rounding of peak coordinatesThomas 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.
2017-03-31Offset peak locations from HDF5 or CXI files by 0.5,0.5Thomas 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.
2017-03-24Merge branch 'taketwo' of ssh://git.bitwiz.org.uk/crystfel into taketwoHelen Ginn
2017-03-24Now tries the shortest vectors first.Helen Ginn
2017-03-24indexamajig: Format --help and fix typosThomas White
2017-03-24Remove an old debugging messageThomas White
2017-03-24Propagate error if indexing method is unrecognisedThomas White
2017-03-24Merge branch 'valerio/peakfinder8'Thomas White
2017-03-24Mostly fussinessThomas White
2017-03-22Completely revamped implementation of peakfinder8Valerio Mariani
2017-03-15largest_q(): Handle NULL detectorThomas White
2017-03-13Added management of max_num_peaks per image instead of per panelValerio Mariani
2017-03-13Added information about max_num_peaks to documentationValerio Mariani
2017-03-13Added saturated peak management to peakfinder8Valerio Mariani
2017-03-13Ask for C99 in configure.ac, remove weird C99 declarationsThomas White
2017-03-13process_hkl: Add event IDs to "--stat" fileThomas White
2017-03-11Removed unused iargValerio Mariani
2017-03-11Fixed some more bugs reported by YaroslavValerio Mariani
2017-03-10Fixed a couple of bugs reported by TomValerio Mariani
2017-03-10Update ChangeLogThomas White
2017-03-10compare_hkl: Add --min-measurementsThomas White
2017-03-10Added peakfinder8 information to the indexamajig man pageValerio Mariani
2017-03-10cell_print(): Show reciprocal anglesThomas White
2017-03-10Peakfinder8 in CrystFEL. Same results as Anton's Cheetah implementationValerio Mariani
2017-03-08Check unit cell parameters after prediction refinementThomas White
2017-03-08Allow indexing system to store its own data, independently of indexing methodsThomas 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.
2017-03-08compare_hkl: Fix combination of sigma(I) values for d1sig and d2sigThomas White
2017-03-08compare_hkl: Fix documentationThomas White
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