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path: root/libcrystfel/src/index.c
AgeCommit message (Collapse)Author
2019-09-12WhitespaceThomas White
2019-09-12Add pinkIndexer interfaceYaroslav Gevorkov
2019-09-06Use new peak check only when doing multi-lattice indexingThomas White
2019-09-03Fix memory leaks in cell comparisonThomas White
2019-08-29Use compare_cell_parameters for after-refinement cell checkThomas White
No need to do all the cell reduction stuff again.
2019-08-29indexamajig: Remove --no-cell-combinationsThomas White
Also remove all the related API stuff. We now have a much better way of checking indexing results.
2019-08-22Tidy up comparison function definitionsThomas White
Especially, remove the last ltl/atl tolerance values.
2019-08-22Framework for new unit cell comparison functionThomas White
2019-08-16Clarify cell vs reference in comparison functions. Also reindexed vs permutedThomas White
2019-08-16Use new cell comparison functions for indexingThomas White
2019-08-16indexamajig: Accept six values for unit cell toleranceThomas White
2019-05-07Update all source code comments to Doxygen formatThomas White
2019-03-11Change horribly confusing names of unit cell comparison functionsThomas 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.
2019-01-22Fix some small memory leaksThomas White
2018-11-15indexamajig: Name and shame slow processing stagesThomas White
2018-11-02Change a couple of important asserts to if statementsThomas White
2018-07-11reduce minimum angle separation for similarity check of latticesYaroslav Gevorkov
2018-07-09Add number of indexing attempts to streamThomas White
2018-06-18Add interface to XGANDALF indexerYaroslav Gevorkov
2018-05-25Fix incorrect loop in cleanup_indexingThomas White
2018-04-20Restore peak alignment check and unset multi-lattice indexing as defaultThomas White
Unfortunately, they seem to be severely reducing data quality. Partially reverts 60c48f3876b0d3c30bf729ce691dbd3f56665c4c
2018-04-20Remove TakeTwo from default indexing method probesThomas White
At least until it can be made faster.
2018-02-27Read debug indexing from fileThomas White
2017-11-28Fix check for cell parameters at startThomas White
2017-10-27Merge branch 'tom/simpler_felix'Thomas White
2017-10-19Add probe for TakeTwoThomas 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
2017-10-09indexer_str(): Don't return "none-nolatt-nocell"Thomas White
2017-09-27Add an assertionThomas White
2017-09-27Don't reset user flag to zeroThomas White
Some indexing methods may set it to 1 already, in which case we should take the hint.
2017-09-26Remove unnecessary countingThomas White
2017-09-22Don't send detector and tolerance to indexing methodsThomas White
The detector isn't used for anything, and the tolerance is none of their business.
2017-09-22Fix silly mistake in friendly_indexer_name()Thomas White
2017-09-22Set --no-check-cell if cell is given, but has no parametersThomas White
2017-09-22If no cell params or lattice type, set nocell/nolatt at top levelThomas White
Another thing that the indexing engines don't need to be repsonsible for.
2017-09-22Stop if an indexing method can't be preparedThomas White
2017-09-21indexamajig: Friendlier display of indexing enginesThomas White
2017-09-15Perform peak alignment check if requestedThomas White
2017-09-15Remove debugging statementThomas White
2017-09-15Better way of displaying cell check optionThomas White
2017-09-15Factorise cell parameter checkThomas White
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.
2017-09-07Use compare_cells() for multi-lattice indexingThomas White
2017-08-31setup_indexing(): Honour no_refineThomas White
Fixes a regression caused by 61565336125, which broke indexamajig --no-refine.
2017-07-06indexamajig: Add TakeTwo-specific optionsThomas White
2017-07-06Merge branch 'master' into taketwoThomas White
2017-06-27Dummy setup bits for INDEXING_NONEThomas 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...
2017-06-27If prediction refinement fails, don't carry on and check the cellThomas White
Doing so results in one crystal being counted as bad twice, which messes up the logic which follows.
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