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AgeCommit message (Collapse)Author
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
2016-10-10Add missing newlineThomas White
2016-10-10Fussiness / boilerplateThomas White
2016-10-10Added detector shift to crystal structure, wrote get and get functionsValerio Mariani
2016-10-07XDS: Clean up open filesThomas White
2016-10-06hdf5_write_image(): Write the correct dataThomas White
2016-10-06hdf5_write_image(): Use correct dataspace for writingThomas White
2016-10-06pattern_sim: Fix loop bounds in record_image()Thomas White
2016-09-12Add newline at end of geometry file in stream, if not already presentThomas White
2016-09-12Restore loading of saturation mapThomas White
2016-09-12Restore loading of bad pixel mapThomas White
2016-09-07XDS: Create fake coordinates taking detector z into accountThomas White
2016-09-07Mosflm: Create fake coordinates taking detector z into accountThomas White
2016-08-16Add reflist_add_command_and_version()Thomas White
2016-08-16Read and write RefList notes to reflection list filesThomas White
2016-08-16Add notes to RefListThomas White
2016-08-11Take rail direction as a vector rather than individual x,y,z valuesThomas White
Just to make it more consistent with fs/ss directions
2016-08-11Use whole of 'value' field when parsing top-level geometry optionsThomas White
This is a long-standing bug, which we got away with up to now because top-level options with more than just a single number or location were rare or possibly never used at all.
2016-08-10Ensure z component is set in dir_conv()Thomas White
2016-08-10Set default clen_for_centeringThomas White
If the rail vector is +z (the default), then the value doesn't matter. However, it still mustn't be NaN.
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