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2017-10-27Merge branch 'tom/simpler_felix'Thomas White
2017-10-18indexamajig: Auto-detection of available indexing methodsThomas White
2017-10-17Handle old indexing methodsThomas White
There are limits to how well they can be handled, but this avoids screwing users over too much.
2017-10-12indexamajig: Simplify Felix optionsThomas White
2017-09-22Remove "latt" from asdfThomas White
For consistency with other algorithms, let's standardise on an interpretation where just using the centering information in combination with the cell parameters, which is always necessary, doesn't qualify as "cell-latt", only "cell-nolatt". "Using lattice type as prior information" implies that asdf would behave differently with cell-nolatt, if it were allowed, than with cell-latt. It wouldn't. It just needs the centering to calculate the cell volume correctly. Note that TakeTwo, by contrast, would behave differently in this hypothetical case, because it uses the lattice type to exclude certain solutions by symmetry. Mosflm allows all four combinations of no/cell and no/latt, and does indeed behave differently between them.
2017-09-22asdf uses prior information for its volume constraint, so add "cell" to the ↵Thomas White
method
2017-09-15Simplify indexing optionsThomas White
mosflm-cell-nolatt-multi-refine-bad-retry.... it's all getting a bit too much. This commit removes all the options from the indexing methods except for the prior information flags (cell/nocell and latt/nolatt). All the other options are now given at the top level with new indexamajig options, e.g. --no-multi and --no-retry. They are applied to all the methods, with no option to (say) use retry for one method and not for another. This also makes the "peak alignment test" default to OFF, and multi-lattice indexing ON. I think that the prediction refinement does a good enough job of checking the validity of indexing solutions, allowing us to turn off the alignment check which filters out most multi-lattice solutions.
2017-07-06indexamajig: Add TakeTwo-specific optionsThomas White
2017-07-06Merge branch 'master' into taketwoThomas White
2017-07-05Update docsThomas 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
2016-10-19Default/required/optional flags for TakeTwoThomas 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
2016-01-30indexamajig: Restore --no-refineThomas White
Adds yet another indexing option...
2016-01-15Set indexing -nomulti as the default, and add a warningThomas White
2016-01-08Make indexing "retry" and "multi" optionalThomas White
2015-09-15Implement Felix IndexerKenneth Beyerlein
2015-07-21Update API docsThomas White
2015-06-25Set MOSFLM default flags to include cell parameters, and add some checksThomas 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
2015-04-20Add INDEXING_DEBUGThomas White
2015-02-11'asdf' indexing method addedAlexandra Tolstikova
2014-09-22Beam file removal, part IThomas White
2014-06-13Add extern "C" for C++ compatibilityChuck
2014-05-21Tidy up headersThomas White
2014-05-08Strip out the "prepare_filename" rubbishThomas White
2013-12-03Update docsThomas White
2013-10-29Change XDS default behaviour, and add warning about axis permutationThomas White
2013-09-13Add INDEXING_SIMULATION for streams made by partial_simThomas White
2013-03-01Update docs (and shake out buglets revealed along the way)Thomas White
2013-02-22Move processing pipeline to separate fileThomas 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
2013-02-12Improve handling of indexing methodsThomas White
2013-02-09Clarify lattice type informationThomas White
2013-02-05Indexing pipeline - "done"!Thomas White
2013-02-04Indexing stuffThomas White
2013-02-01WIP on new indexing pipeline logicThomas White
2013-01-28Tried to fix errors in xds.cCornelius Gati
2013-01-28Changed index.c/.hCornelius Gati
2013-01-08Skeleton indexing method for GrainSpotterThomas White
2013-01-04Tidy up documentationThomas White
2012-05-25WIP on tidy-upThomas White
2012-03-12Update copyright notices to show actual contribution yearsThomas White
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