CrystFEL - Data processing for serial crystallography

Age	Commit message (Collapse)	Author
2017-10-19	peakogram-stream: Fix list indices for beta and gamma angles	Thomas White
	Whoops!
2017-10-19	peakogram-stream: Fix included peaks	Thomas White
	The min and max values are specified inclusively.
2017-10-19	peakogram-stream: Show the line and cell parameters when the maths goes wrong	Thomas White

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

2017-10-19	Add read_reflections_2() to API	Thomas White
	New version for reading the symmetry as well
2017-10-19	Remove read_reflections_from_file() from API	Thomas White
	See c0ce8fb4 for the rationale behind this.
2017-10-19	Add probe for TakeTwo	Thomas White

2017-10-18	move-entire-detector: Fix output filename	Thomas White

2017-10-18	New version of sum-peaks	Thomas White
	This version gets the array dimensions automatically. However, it still assumes the data is "slabby".
2017-10-18	Check that dirax,felix,mosflm or xds are available at the start	Thomas White
	Avoids a confusing error message later.
2017-10-18	indexamajig: Auto-detection of available indexing methods	Thomas White

2017-10-18	Add probe functions to 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.
2017-10-17	felix: Set nsigmas=1	Thomas White

2017-10-12	indexamajig: Simplify Felix options	Thomas White

2017-10-12	Remove write_reflections_to_file() from API	Thomas White
	It's there because it used to be used to write the reflections into the stream. Therefore there was a need for a function to write a bare list of reflections to a file, with no headers. Since then, the stream and merged reflection file formats have diverged, so there's no use for this other than to confuse people.
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

2017-10-09	indexer_str(): Don't return "none-nolatt-nocell"	Thomas White

2017-10-09	configure.ac: Fix CBFlib path variable name	Thomas White
	Whoops.
2017-10-02	indexamajig: Tidy up --help	Thomas White

2017-10-02	indexamajig(1): Add --temp-dir	Thomas White

2017-10-02	Formatting fussiness	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.
2017-09-27	remove_flagged_crystals(): Remove multiple bad crystals	Thomas White
	A silly bug
2017-09-27	Add an assertion	Thomas White

2017-09-27	Don't reset user flag to zero	Thomas White
	Some indexing methods may set it to 1 already, in which case we should take the hint.
2017-09-26	Remove unnecessary counting	Thomas White

2017-09-22	Don't send detector and tolerance to indexing methods	Thomas White
	The detector isn't used for anything, and the tolerance is none of their business.
2017-09-22	Fix silly mistake in friendly_indexer_name()	Thomas White

2017-09-22	Remove "latt" from asdf	Thomas White
	For consistency with other algorithms, let's standardise on an interpretation where just using the centering information in combination with the cell parameters, which is always necessary, doesn't qualify as "cell-latt", only "cell-nolatt". "Using lattice type as prior information" implies that asdf would behave differently with cell-nolatt, if it were allowed, than with cell-latt. It wouldn't. It just needs the centering to calculate the cell volume correctly. Note that TakeTwo, by contrast, would behave differently in this hypothetical case, because it uses the lattice type to exclude certain solutions by symmetry. Mosflm allows all four combinations of no/cell and no/latt, and does indeed behave differently between them.
2017-09-22	asdf uses prior information for its volume constraint, so add "cell" to the ↵	Thomas White
	method
2017-09-22	cell_explorer: Also count cells excluded by the choice of indexing method	Thomas White

2017-09-22	Set --no-check-cell if cell is given, but has no parameters	Thomas White

2017-09-22	cell_new_from_cell(): Don't try to duplicate non-existent parameters	Thomas White

2017-09-22	Mosflm: Recognise P3 as hexagonal P lattice	Thomas White

2017-09-22	Don't write cell parameters to the stream if we don't have them	Thomas White

2017-09-22	If no cell params or lattice type, set nocell/nolatt at top level	Thomas White
	Another thing that the indexing engines don't need to be repsonsible for.
2017-09-22	Stop if an indexing method can't be prepared	Thomas White

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

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