CrystFEL - Data processing for serial crystallography

Age	Commit message (Collapse)	Author
2013-10-08	Read scalar values from HDF5 files as 0d arrays	Thomas White
	Historically, scalar values have been represented in our data files as 1d arrays with size=1. Now they are (more correctly) written as 0d arrays. This change allows CrystFEL to read both.
2013-09-20	partial_sim: Fix racy locking	Thomas White

2013-09-19	hdfsee: Use beam parameters file (--beam option)	Thomas White

2013-09-13	Stop PR when mean change in partiality is small	Thomas White

2013-09-13	Debugging/verbosity tweaks	Thomas White

2013-09-13	partialator: Debugging stuff	Thomas White

2013-09-13	partialator: Use read/write lock	Thomas White

2013-09-13	partial_sim: Use read/write lock	Thomas White

2013-09-13	Add INDEXING_SIMULATION for streams made by partial_sim	Thomas White

2013-09-04	hdfsee: Add accelerators for "Show features" and "Resolution rings"	Thomas White

2013-08-26	Fix previous commit	Thomas White

2013-08-26	Display indexing yield as a percentage	Thomas White

2013-08-20	process_hkl: Fix --histogram	Thomas White
	List of values now expands as necessary Values are no longer double counted when using --scale
2013-08-20	get_hkl: Add --cutoff-angstroms	Thomas White

2013-08-12	Improve show_matrix_eqn()	Thomas White

2013-08-08	render_hkl: Fix it once and for all	Thomas White

2013-08-01	Count filtered eigenvalues	Thomas White

2013-08-01	Use a struct to contain information for scaling report	Thomas White

2013-08-01	Count filtered eigenvalues	Thomas White

2013-08-01	Fix Lorentz gradient	Thomas White

2013-08-01	Add test for gradient of Lorentz factor (as well as partiality)	Thomas White

2013-08-01	Fix previous commit	Thomas White

2013-07-31	Flag crystals as "not refined" if SVD fails	Thomas White

2013-07-31	Refine divergence as well	Thomas White

2013-07-31	Rescale the normal equations before attempting to solve	Thomas White
	This makes the equations insensitive to the units of the parameters being refined, e.g. divergence is measured in radians whereas cell parameters are measured in m^-1, so their magnitudes are very different.
2013-07-31	Use the correct reference list for selection	Thomas White

2013-07-31	Tweak rejection criteria	Thomas White

2013-07-31	Count reflections gained and lost during initial partiality calculation	Thomas White

2013-07-31	Count number of "dud" crystals each iteration, not just at the end	Thomas White

2013-07-31	Tweak error path	Thomas White

2013-07-31	Require scaling convergence to 5%, not 1%	Thomas White

2013-07-31	Revert refinement step if too many reflections are lost	Thomas White

2013-07-31	partialator: New convergence criterion for scaling	Thomas White
	Instead of stopping iteration when the absolute value of any scaling factor changes by more than a certain (small) amount, calculate the ratios of the scaling factors to their previous values, and stop when no scaling factor changes by more than 1% compared to the mean ratio. This method is robust against "drifting" of the scale factors when the partiality estimates are poor.
2013-07-31	hdfsee: Show simple rings even if not using detector geometry	Thomas White

2013-07-26	partialator: Use Lorentz factor in partiality histograms	Thomas White

2013-07-25	Tweak comments	Thomas White

2013-07-25	partialator: Account for Lorentz factor	Thomas White

2013-07-25	partialator: Simplify scaling	Thomas White

2013-07-22	compare_hkl: Fix typo	Thomas White

2013-07-04	Tidy up unused variables	Thomas White

2013-07-04	process_hkl: Fix sigma calculation (again)	Thomas White
	Bessel's correction isn't needed here. Or, at least it hasn't been used in the past.
2013-06-30	compare_hkl: Tidy up and fix CRDano	Thomas White

2013-06-29	compare_hkl: For 'CRDano', use known mean of zero	Thomas White

2013-06-29	Added rms correlation ratio to compare_hkl (CRDano)	Lorenzo Galli

2013-06-29	partialator: Initialise mosaicity	Thomas White

2013-06-28	partial_sim: Initialise crystal mosaicity, num peaks and num saturated peaks	Thomas White

2013-06-20	compare_hkl: Fix quoted number of rejected reflections	Thomas White

2013-06-10	indexamajig: Fix default integration method	Thomas White

2013-06-06	Set default integration method to "rings-nocen"	Thomas White
	Applying the Principle of Least Surprise before merging to master. Previously, it was rings-cen.
2013-06-02	hdfsee: Fix crash when clicking a found peak with numbers window open	Thomas White