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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
2016-10-14validate_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.
2016-08-10Allow peak table location to be given in geometry fileThomas White
2016-08-09Remove debugging outputThomas White
2016-08-09Add rail direction to geometryThomas White
2016-07-29Use z components in predictionThomas White
2016-07-29Add z direction to panel directions and update get_q_for_panel()Thomas White
2016-07-29Set image->dp in hdf5_read()Thomas White
2016-07-28Check return values when writing to Mosflm or DirAxThomas White
2016-07-01Provide dataspace when reading data, mask and satmapThomas White
2016-07-01Remove slab-relative coordinates from geoptimiserThomas White
2016-07-01Store all "=" fields from stream, not just HDF5 onesThomas White
2016-07-01No more slab-relative coordinates in libcrystfelThomas White
2016-05-20Fixed problem with parsing of geometry fileValerio Mariani
2016-05-19integrate_peak(): Trap if pk_total=0Thomas White
2016-04-21Use correct dataspace when reading HDF5 stringsThomas White
2016-04-13Fix event enumerationThomas White
I broke it. Sorry about that.
2016-04-13FormattingThomas White
2016-04-12Merge branch 'tom/testing'Thomas White
2016-04-01Add adu_per_photon (distinct from adu_per_eV)Thomas White
2016-04-01Remove "Too few paired peaks" warningsThomas White
We know that the prediction refinement is working. These "warnings" are really just synonyms for "indexing failed for this pattern". No big deal.
2016-04-01Fix silly bugs and tidy upThomas White
2016-03-31Handle placeholders in --hdf5-peaksThomas White
2016-03-24Fussiness/formattingThomas White
2016-03-24Simplify event enumeration a bitThomas White
2016-03-24event_path_placeholder_subst(): Simplify a bitThomas White
2016-03-24Don't use %C conversionThomas White
2016-03-21This is CrystFEL 0.6.20.6.2Thomas White
2016-03-15write_detector_geometry_2(): Clean upThomas White
Fixes CRYS-138: hdfsee wipes geometry if new file is saved over old one
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