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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.
2017-09-07Add compare_cells() (and use it in whirligig)Thomas White
2017-09-05cell_explorer: Display number of matching cells (on terminal)Thomas White
2017-09-04pattern_sim: Add crystal orientation and basis vectorsThomas White
2017-08-09partial_sim: Add missing bracket in parameter listThomas White
2017-07-24TakeTwo options againThomas White
2017-07-21Tidy up some warningsThomas 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
2017-07-06Temporary fix for the geomptimiser not being able to optimize whole quadrantsValerio Mariani
2017-07-04Add a missing newlineThomas White
2017-07-04pattern_sim: Try all OpenCL platforms to find one with a GPU deviceThomas White
2017-06-27indexamajig: Add --no-non-hits-in-streamThomas White
2017-06-21indexamajig: Add --min-peaks (basic hitfinder functionality)Thomas White
2017-06-21Merge branch 'tom/cbf'Thomas White
2017-05-16check_hkl: Calculate resolution of reflection with asymmetric indices for ↵Thomas White
both possible and measured reflections Previously, it used whichever indices it found first. This made the resolutions different enough to fall into different bins, and screwed up the completeness (fortunately, rarely).
2017-05-03hdfsee: Use new imagefile APIThomas White
2017-05-03HDF5 reading under new APIThomas White
2017-05-02Skeleton image file APIThomas White
2017-05-02Initial CBF stuffThomas White
2017-03-31geoptimiser: Show peak information when there is a problemThomas White
2017-03-31geoptimiser: Fix rounding of peak coordinatesThomas White
Peak locations in CrystFEL are considered to be distances (in pixel units) from the corner of the detector panel. Therefore, simple truncation is needed here, not rounding.
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
2017-03-13Added saturated peak management to peakfinder8Valerio Mariani
2017-03-13process_hkl: Add event IDs to "--stat" fileThomas White
2017-03-11Removed unused iargValerio Mariani
2017-03-10Fixed a couple of bugs reported by TomValerio Mariani
2017-03-10compare_hkl: Add --min-measurementsThomas White
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.
2017-03-08compare_hkl: Fix combination of sigma(I) values for d1sig and d2sigThomas White
2017-03-03cell_explorer: Better handling of dodgy cellsThomas White
2017-03-03partialator: Better handling of very small number of crystalsThomas White
2017-03-03geoptimiser: Call g_type_init() only if GLib is oldThomas White
2017-02-24get_hkl: Fix a segfault when there are no notesThomas White
2017-02-02Cannot use stamp_response() hereThomas White
We have a pipe index (0 to n_read), not a process index (0 to n_proc). These are two separate lists, with no correspondence between them. See 7dbbfa4 for another fix related to this issue.
2017-02-02indexamajig: Add ping mechanism to avoid timing out when trying lots of indexersThomas White
2017-02-02cell_explorer: Fix labels once and for allThomas White
2017-02-01partialator: Exit if point group is unrecognisedThomas White
2017-01-12indexamajig: Fix hanging on "Waiting for last patterns"Thomas White
2016-11-24partialator: Fix counting of imagesThomas White
2016-11-16partialator: Fix segfault when not using --custom-splitThomas White
Crash introduced by 775bbc2d. How silly of me. Thanks to Ken Beyerlein for fixing this.
2016-11-07render_hkl: Show max value, and improve documentation for --scale-topThomas White
2016-11-04Add (more) warnings about unique axesThomas White
2016-10-28partialator: Show some useful numbers about csplit datasetsThomas White
2016-10-28partialator: Don't write a dataset if it contains no crystalsThomas White
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