| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2019-03-11 | Change horribly confusing names of unit cell comparison functions | Thomas White | |
| cells_are_similar -> compare_cell_parameters_and_orientation compare_cells -> compare_reindexed_cell_parameters_and_orientation cell_tool.c:cells_the_same -> cellutils.c:compare_cell_parameters All comparisons now done in real space, checking that centering is the same, and without uncentering anything. | |||
| 2019-01-22 | Fix some small memory leaks | Thomas White | |
| 2018-11-15 | indexamajig: Name and shame slow processing stages | Thomas White | |
| 2018-11-02 | Change a couple of important asserts to if statements | Thomas White | |
| 2018-07-11 | reduce minimum angle separation for similarity check of lattices | Yaroslav Gevorkov | |
| 2018-07-09 | Add number of indexing attempts to stream | Thomas White | |
| 2018-06-18 | Add interface to XGANDALF indexer | Yaroslav Gevorkov | |
| 2018-05-25 | Fix incorrect loop in cleanup_indexing | Thomas White | |
| 2018-04-20 | Restore peak alignment check and unset multi-lattice indexing as default | Thomas White | |
| Unfortunately, they seem to be severely reducing data quality. Partially reverts 60c48f3876b0d3c30bf729ce691dbd3f56665c4c | |||
| 2018-04-20 | Remove TakeTwo from default indexing method probes | Thomas White | |
| At least until it can be made faster. | |||
| 2018-02-27 | Read debug indexing from file | Thomas White | |
| 2017-11-28 | Fix check for cell parameters at start | Thomas White | |
| 2017-10-27 | Merge branch 'tom/simpler_felix' | Thomas White | |
| 2017-10-19 | Add probe for TakeTwo | Thomas White | |
| 2017-10-18 | indexamajig: Auto-detection of available indexing methods | Thomas White | |
| 2017-10-17 | Handle old indexing methods | Thomas White | |
| There are limits to how well they can be handled, but this avoids screwing users over too much. | |||
| 2017-10-12 | indexamajig: Simplify Felix options | Thomas White | |
| 2017-10-09 | indexer_str(): Don't return "none-nolatt-nocell" | Thomas White | |
| 2017-09-27 | Add an assertion | Thomas White | |
| 2017-09-27 | Don't reset user flag to zero | Thomas White | |
| Some indexing methods may set it to 1 already, in which case we should take the hint. | |||
| 2017-09-26 | Remove unnecessary counting | Thomas White | |
| 2017-09-22 | Don't send detector and tolerance to indexing methods | Thomas White | |
| The detector isn't used for anything, and the tolerance is none of their business. | |||
| 2017-09-22 | Fix silly mistake in friendly_indexer_name() | Thomas White | |
| 2017-09-22 | Set --no-check-cell if cell is given, but has no parameters | Thomas White | |
| 2017-09-22 | If no cell params or lattice type, set nocell/nolatt at top level | Thomas White | |
| Another thing that the indexing engines don't need to be repsonsible for. | |||
| 2017-09-22 | Stop if an indexing method can't be prepared | Thomas White | |
| 2017-09-21 | indexamajig: Friendlier display of indexing engines | Thomas White | |
| 2017-09-15 | Perform peak alignment check if requested | Thomas White | |
| 2017-09-15 | Remove debugging statement | Thomas White | |
| 2017-09-15 | Better way of displaying cell check option | Thomas White | |
| 2017-09-15 | Factorise cell parameter check | Thomas White | |
| 2017-09-15 | Simplify indexing options | Thomas 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. | |||
| 2017-09-07 | Use compare_cells() for multi-lattice indexing | Thomas White | |
| 2017-08-31 | setup_indexing(): Honour no_refine | Thomas White | |
| Fixes a regression caused by 61565336125, which broke indexamajig --no-refine. | |||
| 2017-07-06 | indexamajig: Add TakeTwo-specific options | Thomas White | |
| 2017-07-06 | Merge branch 'master' into taketwo | Thomas White | |
| 2017-06-27 | Dummy setup bits for INDEXING_NONE | Thomas White | |
| This doesn't do much except for preventing a possibly confusing warning message about "Failed to prepare indexing method none". You can actually do --indexing=none,asdf, but don't tell anyone... | |||
| 2017-06-27 | If prediction refinement fails, don't carry on and check the cell | Thomas White | |
| Doing so results in one crystal being counted as bad twice, which messes up the logic which follows. | |||
| 2017-03-24 | Propagate error if indexing method is unrecognised | Thomas White | |
| 2017-03-08 | Check unit cell parameters after prediction refinement | Thomas White | |
| 2017-03-08 | Allow indexing system to store its own data, independently of indexing methods | Thomas 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. | |||
| 2017-02-02 | Merge branch 'master' into taketwo | Thomas White | |
| 2017-02-02 | indexamajig: Add ping mechanism to avoid timing out when trying lots of indexers | Thomas White | |
| 2016-10-17 | Initial TakeTwo import | Thomas 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 | |||
| 2016-07-01 | No more slab-relative coordinates in libcrystfel | Thomas White | |
| 2016-02-03 | Set initial prediction parameters even when not doing prediction refinement | Thomas White | |
| Silly bug fix. Beamtime programming FTL. | |||
| 2016-01-30 | indexamajig: Restore --no-refine | Thomas White | |
| Adds yet another indexing option... | |||
| 2016-01-29 | Perform prediction refinement straight after indexing | Thomas 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. | |||
| 2016-01-29 | Use a fresh copy of the peak list for each new indexing method | Thomas White | |
| 2016-01-15 | Set indexing -nomulti as the default, and add a warning | Thomas White | |
 |
index : CrystFEL | |
| Data processing for serial crystallography | Thomas White |
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