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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
2017-02-01Fix malloc fail due to integer overflow in N_tripletsAlexandra Tolstikova
2017-02-01Change volume_min, volume_max and d_max when indexing=asdf-combAlexandra Tolstikova
2017-02-01Change d_max according to the provided cellAlexandra Tolstikova
2017-02-01partialator: Exit if point group is unrecognisedThomas White
2017-01-12indexamajig: Fix hanging on "Waiting for last patterns"Thomas White
2016-12-13Fix tests for new polarisation correctionThomas White
Actually, disable the polarisation correction in the tests.
2016-12-09New polarisation correctionThomas White
2016-11-25Display line numbers at which stream is corruptedThomas White
2016-11-24partialator: Fix counting of imagesThomas White
2016-11-16partialator: Fix segfault when not using --custom-splitThomas White
Crash introduced by 775bbc2d. How silly of me. Thanks to Ken Beyerlein for fixing this.
2016-11-10Fix 2theta calculation in locate_peak_on_panel()Thomas White
The "improved" version of this, added by 9b1374999 along with the new spot position calculation for out-of-plane panels, actually assumes that the reflection is at the exact Bragg condition. This is not a valid assumption here. The difference is small (<0.5 px), but made the prediction refinement gradients completely wrong.
2016-11-07render_hkl: Show max value, and improve documentation for --scale-topThomas White
2016-11-04Add (more) warnings about unique axesThomas White
2016-10-28partialator: Show some useful numbers about csplit datasetsThomas White
2016-10-28partialator: Don't write a dataset if it contains no crystalsThomas White
2016-10-14validate_peaks(): Remove drifting and proximity checks, and use original ↵Thomas White
coordinates We trust the HDF5 peaks, even if we can't see a peak there. That means we can't reliably take a centroid and "improve" the coordinates. In some cases, the centroiding procedure seems to be making the peak coordinates worse than they were originally. Now, the only remaining checks are: 1. Is the peak in a bad region of the detector? 2. Is it saturated? (but --use-saturated is the default) 3. If --check-hdf5-snr, is it above the minimum SNR?
2016-10-14Add scripts/peakogram-streamThomas White
2016-10-10Fix bad regionsThomas White
Previously, this was broken when not using a mask
2016-10-10Add missing newlineThomas White
2016-10-10Fussiness / boilerplateThomas White
2016-10-10Fixed bug with positioning of secondary ASICsValerio Mariani
2016-10-10Geoptimiser now uses detector shift informationValerio Mariani
2016-10-10New default min peak distance for geoptimiserValerio Mariani
2016-10-10Added detector shift to crystal structure, wrote get and get functionsValerio Mariani
2016-10-10cell_explorer: Add "Save cell" functionThomas White
2016-10-07XDS: Clean up open filesThomas White
2016-10-06hdf5_write_image(): Write the correct dataThomas White
2016-10-06pattern_sim: Zero image array before each frameThomas White
2016-10-06hdf5_write_image(): Use correct dataspace for writingThomas White
2016-10-06pattern_sim: Free stuff at endThomas White
2016-10-06pattern_sim: Fix loop bounds in record_image()Thomas White
2016-09-12Add newline at end of geometry file in stream, if not already presentThomas White
2016-09-12Restore loading of saturation mapThomas White
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