CrystFEL - Data processing for serial crystallography

Age	Commit message (Collapse)	Author
2017-10-19	partial_sim: Write the symmetry to the reflection list	Thomas White

2017-10-19	partial_sim: Show the symmetry of the reflection list	Thomas White

2017-10-19	partial_sim: Use symmetry from file	Thomas White

2017-10-19	pattern_sim: Show the symmetry of the reflection list	Thomas White

2017-10-19	pattern_sim: Use symmetry from file	Thomas White

2017-10-19	get_hkl: Use symmetry from file	Thomas White

2017-10-19	compare_hkl: Use symmetry from file	Thomas White

2017-10-19	check_hkl: Use symmetry from file	Thomas White

2017-10-19	render_hkl: Use symmetry from file	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	hdfsee: Add "peaks", "preds" or "rings" to export filename, as applicable	Thomas White

2017-10-12	hdfsee: Add event ID to exported image filename	Thomas White

2017-10-02	indexamajig: Tidy up --help	Thomas White

2017-10-02	indexamajig: Add missing documentation for --check-peaks	Thomas White

2017-09-27	Fix check for CBF files in event enumeration	Thomas White
	-1 means the check failed.
2017-09-22	cell_explorer: Also count cells excluded by the choice of indexing method	Thomas White

2017-09-22	indexamajig: Avoid segfault when no unit cell given	Thomas White

2017-09-21	hdfsee: Increase ring thickness	Thomas White

2017-09-21	indexamajig: Hide indexing setup messages if we are not indexing anything	Thomas White

2017-09-21	Improve error message when using CBF files and a multi-event geometry	Thomas White

2017-09-19	geoptimiser: Remove deprecated option from --help	Thomas White

2017-09-17	Fix logic for new indexing options	Thomas White

2017-09-17	indexamajig: --help documentation for new indexing options	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	Add compare_cells() (and use it in whirligig)	Thomas White

2017-09-05	cell_explorer: Display number of matching cells (on terminal)	Thomas White

2017-09-04	pattern_sim: Add crystal orientation and basis vectors	Thomas White

2017-08-09	partial_sim: Add missing bracket in parameter list	Thomas White

2017-07-24	TakeTwo options again	Thomas White

2017-07-21	Tidy up some warnings	Thomas White

2017-07-21	Fix option names for TakeTwo parameters	Thomas White

2017-07-20	Change units for TakeTwo parameters	Thomas White

2017-07-07	Convert angle_tol to radians	Thomas White

2017-07-06	indexamajig: Add TakeTwo-specific options	Thomas White

2017-07-06	Temporary fix for the geomptimiser not being able to optimize whole quadrants	Valerio Mariani

2017-07-04	Add a missing newline	Thomas White

2017-07-04	pattern_sim: Try all OpenCL platforms to find one with a GPU device	Thomas White

2017-06-27	indexamajig: Add --no-non-hits-in-stream	Thomas White

2017-06-21	indexamajig: Add --min-peaks (basic hitfinder functionality)	Thomas White

2017-06-21	Merge branch 'tom/cbf'	Thomas White

2017-05-16	check_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).
2017-05-03	hdfsee: Use new imagefile API	Thomas White

2017-05-03	HDF5 reading under new API	Thomas White

2017-05-02	Skeleton image file API	Thomas White

2017-05-02	Initial CBF stuff	Thomas White

2017-03-31	geoptimiser: Show peak information when there is a problem	Thomas White

2017-03-31	geoptimiser: Fix rounding of peak coordinates	Thomas 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.
2017-03-31	Offset peak locations from HDF5 or CXI files by 0.5,0.5	Thomas 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.
2017-03-24	indexamajig: Format --help and fix typos	Thomas White