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2017-01-12indexamajig: Fix hanging on "Waiting for last patterns"Thomas White
2016-12-13Fix tests for new polarisation correctionThomas White
Actually, disable the polarisation correction in the tests.
2016-12-09New polarisation correctionThomas White
2016-11-25Display line numbers at which stream is corruptedThomas White
2016-11-24partialator: Fix counting of imagesThomas White
2016-11-16partialator: Fix segfault when not using --custom-splitThomas White
Crash introduced by 775bbc2d. How silly of me. Thanks to Ken Beyerlein for fixing this.
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.
2016-11-07render_hkl: Show max value, and improve documentation for --scale-topThomas White
2016-11-04Add (more) warnings about unique axesThomas White
2016-10-28partialator: Show some useful numbers about csplit datasetsThomas White
2016-10-28partialator: Don't write a dataset if it contains no crystalsThomas 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?
2016-10-14Add scripts/peakogram-streamThomas White
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
2016-10-10Fixed bug with positioning of secondary ASICsValerio Mariani
2016-10-10Geoptimiser now uses detector shift informationValerio Mariani
2016-10-10New default min peak distance for geoptimiserValerio Mariani
2016-10-10Added detector shift to crystal structure, wrote get and get functionsValerio Mariani
2016-10-10cell_explorer: Add "Save cell" functionThomas White
2016-10-07XDS: Clean up open filesThomas White
2016-10-06hdf5_write_image(): Write the correct dataThomas White
2016-10-06pattern_sim: Zero image array before each frameThomas White
2016-10-06hdf5_write_image(): Use correct dataspace for writingThomas White
2016-10-06pattern_sim: Free stuff at endThomas 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
2016-08-17Fix tests/ring_checkThomas White
2016-08-17Update tests to handle audit lines at end of reflection listsThomas White
2016-08-16indexamajig: Detect and kill hung worker processesThomas White
2016-08-16Remove unused memberThomas White
2016-08-16scripts/move-entire-detector: Use argparse instead of optparseThomas White
The main motivation for this was that argparse handles positional arguments which start with minus signs, which is the behaviour we prefer here.
2016-08-16scripts/create-mtz: Update to handle unknown number of lines after end markerThomas White
2016-08-16get_hkl: Preserve input file's notes in output fileThomas White
2016-08-16get_hkl, partialator, process_hkl: Add command line and version infoThomas 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
2016-08-09Update manualThomas White
2016-08-09Remove debugging outputThomas White
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