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AgeCommit message (Collapse)Author
2017-01-17Fiddle with parameter - temporaryHelen Ginn
2017-01-17Remove flip required for cppxfel coordinate systemHelen Ginn
2017-01-17Add rlp retrieval from peak list and tidy up the output to the screen a tadHelen Ginn
2017-01-17Committing all newest antics which DOES produce a decent solution for a ↵Helen Ginn
decent peak list...
2016-12-09New polarisation correctionThomas White
2016-11-25Display line numbers at which stream is corruptedThomas White
2016-11-11FussinessHelen Ginn
2016-11-11Send all possible seeds through the seed-starterHelen Ginn
2016-11-11Find potential matches between observed and simulated vectors now returns a ↵Helen Ginn
list, not a single match, in preparation for being more thorough searching
2016-11-10Fix 2theta calculation in locate_peak_on_panel()Thomas White
The "improved" version of this, added by 9b1374999 along with the new spot position calculation for out-of-plane panels, actually assumes that the reflection is at the exact Bragg condition. This is not a valid assumption here. The difference is small (<0.5 px), but made the prediction refinement gradients completely wrong.
2016-11-04Add (more) warnings about unique axesThomas White
2016-11-04Fixes the bug I discovered in Hamburg - closest_rot_mat needs to check whetherHelen Ginn
the theta angle is the minimum or maximum angle or whether to add Pi.
2016-10-25TEMPORARY horrible debugging stuffThomas White
2016-10-25j_idxThomas White
2016-10-25Sort the vectors according to distance, and use a larger toleranceThomas White
2016-10-24Separate tolerance for matrix traceThomas White
2016-10-24D'ohThomas White
2016-10-20FussinessThomas White
2016-10-20Set toleranceThomas White
2016-10-20Vector fixesThomas White
2016-10-20Add tracking of cell match numbers to taketwo.ccppxfel
2016-10-20Add the central beamThomas White
2016-10-20Fix indicesThomas White
2016-10-20FormattingThomas White
2016-10-19Minor cleanupsThomas White
2016-10-19Normalise the rotation axisThomas White
2016-10-19Default/required/optional flags for TakeTwoThomas White
2016-10-19D'ohThomas White
2016-10-19Fix weird pointersThomas White
2016-10-19Fix maximum index determinationThomas White
2016-10-19Fix units in constantsThomas White
2016-10-19FormattingThomas White
2016-10-19Fix iteration boundsThomas White
2016-10-19Final hooky bitsThomas White
2016-10-19Generate the resulting cellThomas White
2016-10-19Add transform_cell_gsl()Thomas White
2016-10-19gen_theoretical_vecsThomas White
2016-10-19rot_mats_are_similarThomas White
2016-10-19Fussiness (extreme)Thomas White
2016-10-18Fix up last commitThomas White
2016-10-18secondTwizzleMatrixThomas White
2016-10-18Implmement closest_rot_matThomas White
2016-10-18Fixup last commitThomas White
2016-10-18Rotate obs2Thomas White
2016-10-18rotation_between_vectorsThomas White
2016-10-18ANGLE_TOLERANCEThomas White
2016-10-18Stuff to make it compileThomas White
2016-10-17Initial TakeTwo importThomas White
Only changes from Helen's code so far: 1. Stripping trailing spaces 2. Tweaking includes (<> -> "") 3. Adding initial CrystFEL hooks at the bottom of taketwo.c 4. Moving definition of struct SpotVec to taketwo.c 5. Removing prototype for run_taketwo from taketwo.h (comment moved to .c) 6. Authorship/copyright boilerplate
2016-10-14validate_peaks(): Remove drifting and proximity checks, and use original ↵Thomas White
coordinates We trust the HDF5 peaks, even if we can't see a peak there. That means we can't reliably take a centroid and "improve" the coordinates. In some cases, the centroiding procedure seems to be making the peak coordinates worse than they were originally. Now, the only remaining checks are: 1. Is the peak in a bad region of the detector? 2. Is it saturated? (but --use-saturated is the default) 3. If --check-hdf5-snr, is it above the minimum SNR?
2016-10-10Fix bad regionsThomas White
Previously, this was broken when not using a mask
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