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2017-03-24Propagate error if indexing method is unrecognisedThomas White
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.
2017-02-02Merge branch 'master' into taketwoThomas White
2017-02-02indexamajig: Add ping mechanism to avoid timing out when trying lots of indexersThomas White
2016-10-17Initial TakeTwo importThomas White
Only changes from Helen's code so far: 1. Stripping trailing spaces 2. Tweaking includes (<> -> "") 3. Adding initial CrystFEL hooks at the bottom of taketwo.c 4. Moving definition of struct SpotVec to taketwo.c 5. Removing prototype for run_taketwo from taketwo.h (comment moved to .c) 6. Authorship/copyright boilerplate
2016-07-01No more slab-relative coordinates in libcrystfelThomas White
2016-02-03Set initial prediction parameters even when not doing prediction refinementThomas White
Silly bug fix. Beamtime programming FTL.
2016-01-30indexamajig: Restore --no-refineThomas White
Adds yet another indexing option...
2016-01-29Perform prediction refinement straight after indexingThomas White
This allows indexing to be attempted again (either a new method or with "retry") if the prediction refinement fails, increasing overall indexing rate. Side-effect: there are some hoops which would need to be jumped through to store the profile radius before refinement and hence enable scripts/plot-predict-refine to work. For now, we'll ignore this as it's clear that the prediction refinement is working.
2016-01-29Use a fresh copy of the peak list for each new indexing methodThomas White
2016-01-15Set indexing -nomulti as the default, and add a warningThomas White
2016-01-13Fix logic for -retry and -multiThomas White
2016-01-08Make indexing "retry" and "multi" optionalThomas White
2015-12-18"Retry" mechanism for indexingThomas White
This increases the indexing rate a bit in situations where there are lots of weak peaks which, although they may be real, don't help indexing. The weakest 10% of peaks get cut out and the indexing re-run. This also allows multiple hits to be indexed, using the "inelegant peak subtraction method", by retrying indexing in the same way after deleting peaks which are accounted for by the lattice just found.
2015-09-15Formatting / fussinessThomas White
2015-09-15Update boilerplate commentsThomas White
2015-09-15Remove unnecessary breaksThomas White
2015-09-15Implement Felix IndexerKenneth Beyerlein
2015-06-25Set MOSFLM default flags to include cell parameters, and add some checksThomas White
2015-06-25Tidy up some small leaks and memory bugsThomas White
2015-06-19Remove ReAx and GrainSpotterThomas White
Neither of these ever really worked, and better algorithms exist now.
2015-06-18Merge branch 'tolstikova/dirax'Thomas White
Conflicts: libcrystfel/src/index.h
2015-04-20Improve error messageThomas White
2015-04-20Add INDEXING_DEBUGThomas White
2015-02-11'asdf' indexing method addedAlexandra Tolstikova
2014-11-25Add warning if the number of peaks is hugeThomas White
2014-09-22Beam file removal, part IThomas White
2014-09-05Multi-event modeValerio Mariani
2014-05-08Strip out the "prepare_filename" rubbishThomas White
2014-02-23build_indexed_list(): Recognise "simulation"Thomas White
Because we also need it to work when reading a stream.
2013-09-13Add INDEXING_SIMULATION for streams made by partial_simThomas White
2013-05-27Fix ReAx stack corruptionThomas White
2013-03-01Update docs (and shake out buglets revealed along the way)Thomas White
2013-02-19Add -cell and -nocell to indexing methodsThomas White
2013-02-18Update XDS for new indexing subsystemThomas White
2013-02-18Merge branch 'cornelius/xds' into tom/multicrystalThomas White
Conflicts: libcrystfel/Makefile.am libcrystfel/src/index.c libcrystfel/src/index.h
2013-02-18Read GrainSpotter's output properlyThomas White
2013-02-18Merge branch 'tom/grainspotter' into tom/multicrystalThomas White
Conflicts: libcrystfel/Makefile.am libcrystfel/src/index.c libcrystfel/src/index.h
2013-02-15FussinessThomas White
2013-02-12Improve handling of indexing methodsThomas White
2013-02-09Add cleanup functions for DirAx and MOSFLMThomas White
2013-02-09Complain if a unit cell is needed and not providedThomas White
2013-02-09Clarify lattice type informationThomas White
2013-02-08Allow --indexing=noneThomas White
2013-02-05WIP on updating partialatorThomas White
2013-02-05Fixes for indexing pipelineThomas White
2013-02-05Indexing pipeline - "done"!Thomas White
2013-02-04Indexing stuffThomas White
2013-02-01WIP on new indexing pipeline logicThomas White
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