DIALS 3.7.0

2021-11-01:

A short summary of features and fixes in this release:

Features

• Bootstrap support for MacOS M1 platforms. (#1841)
• New dials.find_rotation_axis program optimises the rotation axis from strong spot positions prior to indexing. (#1884)
• dials.image_viewer:
  • Draw resolution rings for curved detectors. (#1899)
  • Add the option to display the rotation axis (#1856)
  • Resolution Coordinates are now given in fast, slow order. (#1849)
• dials.import: Unhandled files (e.g. *.log files) are now by default ignored. (#1881)
• dials.import: New fast_slow_beam_centre= parameter for detector models. (cctbx/dxtbx#421)
• dials.scale: Allow fixing of a particular physical correction. (#1883)
• dials.stills_process: Performance improvements for highly mosaic crystals and Kapton absorption correction. (#1846)
• dxtbx: Support NeXus data from the Tristan event-mode detector on beamline I19 at Diamond Light Source. (cctbx/dxtbx#428)
• dxtbx: Better support for detector SMV ADSC SN442. (cctbx/dxtbx#445)
• xia2: New option general.check_for_saturated_pixels=True, to warn about saturated pixels found whilst performing spot finding. (xia2/xia2#624)

Bugfixes

• dials.compute_delta_cchalf: Fix crash when only using passing dataset/group. (#1892)
• dials.image_viewer: Crystal basis vectors are now shown in the same colour as their predictions. (#1855)
• dials.import: Allow importing templates with no template characters. (#1840)
• dxtbx: Allow importing experiment lists from single-file templates. (cctbx/dxtbx#425)
• xia2.compare_merging_statistics: If no input files provided, print help, and not empty plots. (xia2/xia2#629)

For a more complete list of changes please check the DIALS, dxtbx and xia2 changelogs.

DIALS 3.6.2

2021-09-21:

• dials.reciprocal_lattice_viewer: In cases with multiple lattices, "Crystal Frame" now aligns all crystal frames, rather than just the first. Unindexed reflections are no longer shown in this mode. (#1868)
• dxtbx: Fix broken dxtbx.install_format command. (cctbx/dxtbx#434)

For a more complete list of changes and fixed bugs check the dials and dxtbx changelogs.

There are no changes to cctbx or xia2 in this release.

DIALS 3.6.1

2021-09-06:

• xia2: Allow xia2 installation while offline (xia2/xia2#619)

For a more complete list of changes and fixed bugs check the xia2 changelog.

There are no changes to cctbx, dials or dxtbx in this release.

DIALS 3.6

2021-08-16:

A short summary of features and fixes in this release:

Features

• This is the last release to support Python 3.6. Future releases will require a minimum of Python 3.7.
• New program: dials.reference_profile_viewer for viewing reference profiles dumped by dials.integrate (#1759)
• dials.combine_experiments: Unindexed reflections are now included in the combined output (#1760)
• dials.image_viewer: Improvements to overlays, basis vector control and automatic colour choices (#1750, #1780, #1781)
• dials.reciprocal_lattice_viewer: The resolution of the "nearest point" will be shown, and default marker size scales based on intensity (#1770, #1773)
• dials.scale: Always enables absorption correction if the absorption_level= parameter is set (#1793)
• dials.scale: Allow a shared absorption correction between sweeps if using the physical model, with the option share.absorption=True (#1811)
• dxtbx: Added dxtbx.flumpy module for zero-copy conversions between numpy and scitbx.array_family.flex arrays (cctbx/dxtbx#377)

Bugfixes

• dials.integrate: Change default configuration so that unintegrated reflections are not retained. This helps reduce memory usage of downstream tools. (#1753)
• dials.combine_experiments: Correctly preserve mapping to images. This affects dials.image_viewer and dial.reciprocal_lattice_viewer. (#1093)
• dials.reciprocal_lattice_viewer: More robust beam centre control that works for multiple panel detectors (#1842)
• dials.refine_bravais_settings: correctly report mI Bravais settings (#1825)
• dxtbx: Fix support of older FormatSMVADSCSN442 images (cctbx/dxtbx#369)
• dxtbx: Fix error reading BioMAX data with H5py 3.3 (cctbx/dxtbx#389)
• dxtbx: Check for empty beams in XTC streams (cctbx/dxtbx#419)
• xia2: Fix crash with xia2.compare_merging_stats when setting anomalous=True (xia2/xia2#613)

For a more complete list of changes please check the DIALS, dxtbx and xia2 changelogs.

DIALS 3.5.4

2021-07-27:

• dials.stills_process: Fix case where imagesets and experiment filenames could potentially disagree (#1814)
• dials.scale: Fix incorrect output files, for targeted scaling with more than one target dataset. (#1815)
• dials.image_viewer: Fix opening datasets with load_models=False (#1818)
• dxtbx: Allow reading of new SACLA hdf5 data (cctbx/dxtbx#408)

For a more complete list of changes and fixed bugs check the dials and dxtbx changelogs.

There are no changes to cctbx or xia2 in this release.

DIALS 3.5.3

2021-07-12:

• dials.image_viewer: Fix the basis_vector_scale= parameter. (#1769)

For a more complete list of changes and fixed bugs check the dials changelog.

There are no changes to cctbx, dxtbx or xia2 in this release.

DIALS 3.5.2

2021-06-28:

• dials.image_viewer: Fix display of spotfinding intermediates (threshold, dispersion, etc) when viewing multiple still experiments (#1734)
• dials.image_viewer: Stacking images no longer gives incorrect results for multi-sweep data beyond the first sweep (#1758)
• dxtbx: End the DLS I03 "bad mask" duration, since it is now masked at the file level. (cctbx/dxtbx#385)
• dxtbx.dlsnxs2cbf: Handle missing chi/phi axis entries. (cctbx/dxtbx#387)

For a more complete list of changes and fixed bugs check the dials and dxtbx changelogs.

There are no changes to cctbx or xia2 in this release.

DIALS 3.5.1

2021-06-14:

• dxtbx: Extend duration of bad module mask for Diamond I03 EIGER 2XE 16M detector indefinitely. This will be updated in a future release. (cctbx/dxtbx#370)
• dxtbx: Handle scan data which wraps through 0° instead of >=360° (cctbx/dxtbx#379)

For a more complete list of changes and fixed bugs check the dxtbx changelog.

There are no changes to cctbx, dials or xia2 in this release.

DIALS 3.5.0

2021-05-27:

A short summary of features and fixes in this release:

• New bootstrap options: --mamba to install with micromamba, and --clean to remove installation caches immediately after completion. (#1676)
• New command: dials.find_bad_pixels to identify pixels which are identified as signal in >= 50% of images (#1710)
• dials.integrate: Allow processing of data too large to fit in memory (#1392)
• dials.scale: Add option error_model.grouping= to control refinement of error models during scaling (#1684)
• dials.scale: Added physical.absorption_level=[low|medium|high] for bulk control of absorption correction (#1688)
• dials.cosym: Significantly faster calculation of Rij matrix of pairwise correlation coefficients (#1693)
• dials.image_viewer: Add selector to choose between a new default "image" and traditional "lab" coordinate frames (#1716)
• dials.export_bitmaps: Gained this same projection= option. (#1716)
• dials.find_spots and dials.integrate: nproc= now works with N > 1 on Windows. (#1724)
• dials.report: Add units of pixels / images to centroid difference histograms (#1677)
• dials.integrate: Improved background model variance calculation for integrating detectors. (#1692)
• xia2: Separate anomalous pairs when scaling with dials.scale if anomalous=True (xia2/xia2#539)
• xia2: Added absorption_level=[low|medium|high] to control of the absorption correction in dials.scale. (xia2/xia2#592)
• dxtbx: Add FormatMRC.py for electron diffraction images and image stacks recorded on Thermo Fisher microscopes (dxtbx/dxtbx#335)
• dxtbx: Add support for Python 3.9. (dxtbx/dxtbx#365)

For a more complete list of changes please check the DIALS, dxtbx and xia2 changelogs.

DIALS 3.4.3

2021-04-20:

• dials.scale: Fix crash when full-matrix minimisation is unsuccessful due to indeterminate normal equations. (#1653)
• dials.scale: Fix crash when no reflections remain after initial filtering. (#1654)
• dials.export: Fix error observed with format=mmcif for narrow sweeps with low symmetry (#1656)
• Fix image numbering inconsistency in ascii histogram of per-image spot counts (#1660)
• dials.find_spots_server: Significant performance improvement for HDF5 grid scans. (#1665)

For a more complete list of changes and fixed bugs check the dials changelog.

There are no changes to cctbx, dxtbx or xia2 in this release.