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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
2018-02-27indexamajig: Add --overpredictThomas White
2018-02-08FormattingThomas White
2018-02-08Fix indexamajig help formatting.Kenneth R. Beyerlein
2018-02-08Changed the naming of felix options and variables to make them more obvious.Kenneth R. Beyerlein
2018-02-08Change Felix min-uniqueness paramter name to max-uniqueness.Kenneth R. Beyerlein
2018-02-08Add Felix option felix-max-inter-angleKenneth R. Beyerlein
2018-02-08Make felix-domega optionKenneth R. Beyerlein
2017-12-12indexamajig: Actually rename serial-offset to serial-startThomas White
2017-12-12indexamajig: Rename --serial-offset to --serial-startThomas White
Because "offset" sounds like it will add the argument to the serial numbers, i.e. --serial-offset=500 would start at 501. Actually, you just give the first serial number you'd like.
2017-12-12indexamajig: Add --serial-offsetThomas White
2017-10-27Fix Felix tth options typo.Kenneth R. Beyerlein
2017-10-27Merge branch 'tom/simpler_felix'Thomas White
2017-10-18indexamajig: Auto-detection of available indexing methodsThomas White
2017-10-12indexamajig: Simplify Felix optionsThomas White
2017-10-02indexamajig: Tidy up --helpThomas White
2017-10-02indexamajig: Add missing documentation for --check-peaksThomas White
2017-09-22indexamajig: Avoid segfault when no unit cell givenThomas White
2017-09-21indexamajig: Hide indexing setup messages if we are not indexing anythingThomas White
2017-09-17Fix logic for new indexing optionsThomas White
2017-09-17indexamajig: --help documentation for new indexing optionsThomas 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.
2017-07-24TakeTwo options againThomas White
2017-07-21Fix option names for TakeTwo parametersThomas White
2017-07-20Change units for TakeTwo parametersThomas White
2017-07-07Convert angle_tol to radiansThomas White
2017-07-06indexamajig: Add TakeTwo-specific optionsThomas White
2017-06-27indexamajig: Add --no-non-hits-in-streamThomas White
2017-06-21indexamajig: Add --min-peaks (basic hitfinder functionality)Thomas White
2017-05-02Skeleton image file APIThomas White
2017-03-31Offset peak locations from HDF5 or CXI files by 0.5,0.5Thomas White
CrystFEL considers all peak locations to be distances from the corner of the detector panel, in pixel units, consistent with its description of detector geometry. In contrast, Cheetah considers the peak locations to be pixel indices in the data array. Therefore, a half-pixel offset is needed when importing the peak lists. For users who need the old behaviour, this commit adds a new option indexamajig --no-half-pixel-shift to deactivate this offset.
2017-03-24indexamajig: Format --help and fix typosThomas White
2017-03-24Merge branch 'valerio/peakfinder8'Thomas White
2017-03-10Fixed a couple of bugs reported by TomValerio Mariani
2017-03-10Peakfinder8 in CrystFEL. Same results as Anton's Cheetah implementationValerio Mariani
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.
2016-08-10Allow peak table location to be given in geometry fileThomas White
2016-03-01indexamajig: Wall clock profilingThomas White
2016-01-30indexamajig: Restore --no-refineThomas White
Adds yet another indexing option...
2015-11-27indexamajig: Write target unit cell into streamThomas White
2015-11-17Make integration WITHOUT gradient background the defaultThomas White
2015-11-17Make gradient background fitting optionalThomas White
2015-09-15Implement Felix IndexerKenneth Beyerlein
2015-08-27indexamajig: Update docsThomas White
2015-07-23indexamajig: Peak detection method must be parsed before checking peak pathThomas White
2015-07-21indexamajig: Tidy up option handlingThomas White
2015-07-13Slow down the status updatesThomas White
2015-06-25Tidy up some small leaks and memory bugsThomas White
2015-06-17Use a POSIX semaphore for synchronising terminal access during indexingThomas White
Nice side-effect: indexamajig -j and --int-diag can now be used together
2015-04-20indexamajig: Add --no-refineThomas White
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