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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.
2017-03-24indexamajig: 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
2017-03-08Add SLURM version of turbo-index scriptThomas White
2017-03-08Add example Eiger geometry fileThomas White
2017-03-03cell_explorer: Better handling of dodgy cellsThomas White
2017-03-03Return error code if cell can't be invertedThomas White
2017-03-03partialator: Better handling of very small number of crystalsThomas White
2017-03-03geoptimiser: Call g_type_init() only if GLib is oldThomas White
2017-02-24get_hkl: Fix a segfault when there are no notesThomas White
2017-02-17Update docs (add funding acknowledgements)Thomas White
2017-02-16Fix mask path placeholder checkThomas White
The mask paths for all panels have to have the same number of placeholders, but the masks do not have to have the same number of placeholders as the panel data blocks. This also tidies up a few excess strdup() calls, and removes partial_event_substitution() because retrieve_full_path() can now handle the number of placeholders being too small.
2017-02-02Cannot use stamp_response() hereThomas White
We have a pipe index (0 to n_read), not a process index (0 to n_proc). These are two separate lists, with no correspondence between them. See 7dbbfa4 for another fix related to this issue.
2017-02-02indexamajig: Add ping mechanism to avoid timing out when trying lots of indexersThomas White
2017-02-02cell_explorer: Fix labels once and for allThomas White
2017-02-01asdf.c: Divide volume constraints by number of lattice points per unit cell. ↵Alexandra Tolstikova
Add F centering
2017-02-01asdf.c: Divide volume constraints by number of lattice points per unit cell ↵Alexandra Tolstikova
since asdf always finds primitive cell
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