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2017-09-15Perform peak alignment check if requestedThomas White
2017-09-15Add restraints to prediction refinementThomas White
2017-09-15Remove debugging statementThomas White
2017-09-15Better way of displaying cell check optionThomas White
2017-09-15Record indices in write_pairs() (debugging function)Thomas 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.
2017-09-15Fix uninitialised peak counts (for info in stream only)Thomas White
2017-09-07Use compare_cells() for multi-lattice indexingThomas White
2017-09-07remove_flagged_crystals(): Return the number of crystals removedThomas White
2017-09-07Add compare_cells() (and use it in whirligig)Thomas White
2017-08-31Set first argument when running external indexing programsThomas White
This makes sure they have names in process displays.
2017-08-31setup_indexing(): Honour no_refineThomas White
Fixes a regression caused by 61565336125, which broke indexamajig --no-refine.
2017-07-24Update docsThomas White
2017-07-24Make struct taketwo_options constThomas White
2017-07-24Ensure TakeTwo arrays get freedThomas White
2017-07-24TakeTwo options againThomas White
2017-07-24Formatting/copyright datesThomas White
2017-07-21Add a warning about mask_file when mask is not setThomas White
2017-07-20Change units for TakeTwo parametersThomas White
2017-07-18Crashy for unknown reason, but have added the code for using custom params.cppxfel
2017-07-06indexamajig: Add TakeTwo-specific optionsThomas White
2017-07-06Fix typoThomas White
2017-07-06Merge branch 'master' into taketwoThomas White
2017-07-06Indexing engine private pointers should be void *Thomas White
2017-07-06Remove unnecessary headers and move an includeThomas White
2017-07-06Use void pointers for indexing engine private stuffThomas White
2017-07-06Update to peakfinder8, with bug fixed and new functionality. Code synced ↵Valerio Mariani
with OnDA and Oleksandr's programs
2017-07-05Update docsThomas White
2017-07-05Rearrange quaternion declarations so that gtk-doc can copeThomas White
The utils file contains two gtk-doc sections, "utils" and "quaternion", with a change of section halfway through. It seems that gtk-doc doesn't like it if the declarations are all mixed together.
2017-07-05Shoved a bunch of the stuff being passed from function to function into ↵cppxfel
TakeTwoCell, and shoved gsl_vector allocation into it as well to reduce alloc events
2017-07-01Adding a cutoff for maximum allowed vectors (100,000) to stop Tom's computer ↵cppxfel
(and others) falling apart again.
2017-06-30Ridiculous ASCII art to increase prominance of citationcppxfel
2017-06-30Removed unnecessary returns and set functions to void, and removed ↵cppxfel
superfluous integer declaration
2017-06-30Didn't use C99 code, fixingcppxfel
2017-06-30Yet more speed fiddlescppxfel
2017-06-30Removed some code, fixed some code, and so on and so forthcppxfel
2017-06-29WARNING - profanity - uploading to my server so I can gvalgrindcppxfel
2017-06-29Disable a check which wasn't acted upon to measure impact on speedcppxfel
2017-06-29Should not limit to proceeding vectors only when a new spot may have been ↵cppxfel
included\!
2017-06-29Relaxation of tolerancescppxfel
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.
2017-06-23Accept either cbf/cbf.h or cbflib/cbf.hThomas White
You get cbflib/cbf.h if you install CBFlib from source, and cbf/cbf.h if using the package manager in Fedora, probably other systems as well. We definitely don't want to include the cbf or cbflib folder in the include path, because CBFlib may bring its own HDF5 headers, which we don't want to touch with a bargepole.
2017-06-21Close more leftover HDF5 handlesThomas White
2017-06-21Don't compile CBF stuff without CBFlibThomas White
2017-06-21Close leftover HDF5 handlesThomas White
2017-06-21hdf5_read2(): Fix exit pathThomas White
Bad pixel map is not allocated at this point.
2017-06-19Reduced amount of gsl_matrix reallocationcppxfel
2017-06-19Changing cosine of angle to be most sensitive to 0.5 degreescppxfel