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DIALS 2.1 (2019-12-12)

Features

  • We now fully support Python 3 environments.
  • MessagePack is now the default reflection table file format. Temporarily, the environment variable DIALS_USE_PICKLE can be used to revert to the previous pickle-based format, however this will be removed in a future version. (#986)
  • new option for dials.show 'show_shared_models=True' displays which beam, crystal, and detector models are used across experiments (#996)
  • Import still image sequence as N experiments dereferencing into one image set rather than one experiment. (#1014)
  • Add reflection_table.get method for defaulted column access (#1031)

Bugfixes

  • Don't use -2 to indicate masked pixels, except for DECTRIS detectors where this is to be expected. (#536)
  • No longer show pixels that are above the trusted range upper bound as "saturated" on the "variance" image. (#846)
  • Correctly account for scan-varying crystals while providing a scan range to dials.integrate (#962)
  • Ensure that generated masks do not include pixels that are overloaded on a few images, but only pixels that are always outside the trusted range. (#978)
  • Rewritten parameter auto-reduction code for dials.refine provides finer-grained fixing of individual parameters rather than whole parameterisations and correctly takes constrained parameters into account (#990)
  • Fix output of predictions in dials.refine. A recently-introduced bug meant that the updated predictions weren't being copied to the output reflections file. (#991)
  • Allow scan-varying refinement where either the crystal cell or orientation is fixed. (#999)
  • Respect batch= option to dials.symmetry - can reduce time taken for finding the symmetry for large data sets. (#1000)
  • Scan-varying refinement no longer fails when the scan is wider than the observed reflections (e.g. when the crystal has died). Instead, the scan is first trimmed to match the range of the diffraction. (#1025)
  • If convert_sequences_to_stills then delete the goniometer and scan. (#1035)
  • Correctly account for scan-varying crystals in dials.slice_sequence (#1040)
  • Eliminate systematic absences before applying change of basis op to minimum cell in dials.symmetry. (#1064)

Improved Documentation

  • Add "Extending DIALS" page to developer documentation (#893)

Deprecations and Removals

  • The command dials.analyse_output was removed. Its replacement, dials.report, will give you more useful output. (#1009)

Misc

  • #983, #1004

DIALS 2.0 (2019-10-23)

Features

  • Support exporting multi-dataset and still experiments to XDS_ASCII (#637)
  • Replace default spotfinder with improved dispersion algorithm (#758)
  • dials.report now displays oscillation data with units and more significant figures (#896)
  • A new program, dials.sequence_to_stills to create split a sequence into a separate still Experiment for every scan point in the sequence, splitting reflections as necessary. (#917)
  • Moved dials.export format=best to dials.export_best as that one needed access to the format object, the rest do not, and having dials.export work in the general case seems like a better idea... (#921)
  • Unified logging output for dials programs - logs are no longer split into .log and .debug.log. Use -v to get debug output. (#923)
  • New command dials.resolutionizer (replaces xia2.resolutionizer). Add support for expt/refl in dials.resolutionizer. (#933)
  • Changed the selection of reflections used for determination of the reflection profile parameters in integration. Now uses reflections which were previously used in refinement rather than all reflections, resulting in a speed improvement for large data sets and a negligible difference in the quality of the integrated results. (#942)
  • dials.image_viewer now allows the choice between dispersion_extended (new default) and dispersion (old default) thresholding algorithms for investigating the effect of different spot-finding parameters. (#948)
  • dials.rs_mapper now respects masked regions of images (including the trusted range mask). (#955)

Bugfixes

  • Fix and reinstate normalisation option in dials.option (#919)

Misc

  • #795, #862, #895, #915, #924