DIALS 3.4.2

2021-04-12:

• Log messages from spot finding and integration no longer ignore logging level when using nproc > 1. This mainly affects usage of dials from outside contexts. (#1645)
• xia2: Fix reading of split HKL files output from XSCALE (xia2/xia2#579)

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

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

DIALS 3.4.1

2021-04-01:

• dials.cosym: Significantly faster via improved computation of functional, gradients and curvatures (#1639)
• dials.integrate: Added parameter valid_foreground_threshold=, to require a minimum fraction of valid pixels before profile fitting is attempted (#1640)
• dials.cosym: Cache cases where Rij is undefined, rather than recalculating each time. This can have significant performance benefits when handling large numbers of sparse data sets. (#1634)
• dials.cosym: Fix factor of 2 error when calculating target weights (#1635)
• dials.cosym: Fix broken engine=scipy option (#1636)
• dials.integrate: Reject reflections with a high number of invalid pixels, which were being integrated since 3.4.0. This restores better merging statistics, and prevents many reflections being incorrect profiled as zero-intensity. (#1640)
• Fix rare crash in symmetry calculations when no resolution limit could be calculated (#1641)
• xia2.multiplex: Use resolution cutoff determined during scaling for cluster analysis (xia2/xia2#576)
• xia2.multiplex: Fix cos-angle clustering varying between runs (xia2/xia2#576)
• dxtbx: Nexus: Diamond Light Source beamlines are now properly identified (cctbx/dxtbx#339)

For a more complete list of changes and fixed bugs check the dials, dxtbx and xia2 changelogs.

There are no changes to cctbx in this release.

DIALS 3.4.0

2021-03-15:

Major Features

• dials.integrate: In some cases, many more reflections now qualify for profile fitting, by allowing reflections with masked pixels or are near the edge of the panel. This can drastically increase the number of profile-integrated reflections on multi-panel detectors. (#1297)
• dials.scale:
  • An additional outlier rejection based on normalised intensities has been added (#1627)
  • Fix issue of error model not always being carried through after the profile/summation intensity combination step. (#1566)
• dials.image_viewer:
  • New parameter basis_vector_scale= to adjust the length of the basis vector overlay (#1598)
  • Fix various display issues relating to viewing still images (#1463)
• dials.reciprocal_lattice_viewer: Added an option to label the reciprocal lattice point nearest the centre (#1614)
• dials.background:
  • Add option output.plot= to save an image to disk instead of showing interactively. Image files can now also be used directly. (#1537)
  • dials.background: Fix crash when writing output plot with bad display configuration (#1550)
• dials.estimate_resolution: Reject Wilson outliers to minimise effect of spurious observations, like ice rings, on the resulting resolution estimates (#1580)
• dials.import: Individual components of a reference model can be selected with use_beam_reference=, use_gonio_reference= and use_detector_reference=. (#1371)
• dials.merge: add option to set wavelength_tolerance for MAD datasets (#1609)
• dxtbx: Improved support for Timepix 2M (cctbx/dxtbx#298), SwissFEL Jungfrau 16M (cctbx/dxtbx#303) and Eiger 16M XE at Diamond (cctbx/dxtbx#323) detectors.

Removals/Deprecations

• The previously deprecated masking parameter use_trusted_range= has been removed (#1156)
• dials.background: The plot= parameter to interactively display the background plot has been removed. Use output.plot= to save to file instead. (#1554)
• dials.util.masking.MaskGenerator is deprecated in favour of dials.util.masking.generate_mask (#1569)
• dxtbx: DataBlock is now deprecated. Please use ExperimentList instead. (cctbx/dxtbx#288)
• dxtbx: ExperimentListTemplateImporter is now deprecated. Please use ExperimentList.from_templates. (cctbx/dxtbx#333)

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

DIALS 3.3.4

2021-03-05:

• dials.import: Selecting a subset of images with image_range= now works on stills (#1592)
• dials.search_beam_centre: Dramatically improved execution time for large data sets (#1612)
• dials.reindex: Write .refl files in a better format for compatibility with downstream programs (#1616)
• dials.scale: Fix rare memory crash from infinite loop, that could occur with very bad quality datasets (#1622)
• dials.refine: More informative error message when reflections have weights of zero (#1584)
• xia2: Fix type object has no attribute 'ignore' error (xia2/xia2#570)
• dxtbx: Fix error sometimes corrupting data when writing CBF files with dxtbx.dlsnxs2cbf and dials.merge_cbf (cctbx/dxtbx#314)

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

DIALS 3.3.3

2020-02-15:

• Fix for missing SENSOR_THICKNESS= in XDS.INP generated for EIGER datasets introduced in 3.3.1 (xia2/xia2#564, cctbx/dxtbx#296)

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

DIALS 3.3.2

2021-02-01:

• dials.export: Allow data with either summation or profile fitted intensities to be exported. Previously, both were (erroneously) required to be present (#1556).
• dials.scale: Fix crash if only summation intensities present and intensity_choice=combine (#1557).
• Fix unicode logging errors on Windows (#1565).
• Improve performance with internal mask generation. This speeds up spotfinding (#1449).
• dxtbx: Don't interpret windows paths as URIs, causing failure to import images (cctbx/dxtbx#284).
• dxtbx: Fix miscounting of images in VDS nexus files (cctbx/dxtbx#285).
• dxtbx: Fix cacheing bug with live per-image analysis of HDF5/SWMR files that prevented seeing new images after opening a file once (cctbx/dxtbx#289).
• dxtbx: Don't write DETECTOR=PILATUS for Eiger detectors generating XDS.INP (cctbx/dxtbx#292).
• xia2: Fix unicode logging errors on Windows (xia2/xia2#558).
• cctbx: Update as_cif_block() method to match updated definitions of the pdbx mmcif v5 dictionary (cctbx/cctbx_project#582).

For a complete list of changes and fixed bugs check the DIALS, dxtbx, and xia changelogs.

DIALS 3.3.1

2021-01-18:

• dials.index: More verbose debug logs when rejecting crystal models (#1538)
• dials.stills_process: Fix spotfinding error "Failed to remap experiment IDs" (#1180)
• Improved spot-finding performance for HDF5 when using a single processor (#1539)
• dxtbx: NeXus files are now opened in SWMR mode (cctbx/dxtbx#270)

For a 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 3.3.0

DIALS 3.3.0 (2021-01-04):

• dials.estimate_resolution: Use only cc_half for the default resolution analysis. (#1492)
• dials.export: Allow on-the-fly bzip2 or gzip compression for mmCIF output, because unmerged mmCIF reflection files are large. (#1480)
• dials.find_spots and dials.integrate both now have nproc=Auto by default, which uses the number of allowed/available cores detected. (#1441)
• dials.merge: Report <dF/s(dF)>, if anomalous=True. An html report is also generated to plot this statistic. (#1483)
• dials.scale: Apply a more realistic initial error model, or load the existing error model, if rescaling. (#1526)
• dials.stills_process: Allow using different saturation cutoffs for indexing and integration. (#1473)
• dxtbx: Read detector distance from the XTC streams for LCLS Jungfrau data (cctbx/dxtbx#246)
• dxtbx: Set the per-shot gain for the ePix and Jungfrau detectors at LCLS. (cctbx/dxtbx#250)
• dxtbx: Format classes can now be marked as @abstract. (cctbx/dxtbx#255)
• Various deprecated interfaces have been removed across dials and dxtbx
• for a more complete list of changes and fixed bugs check the DIALS and dxtbx changelogs

xia2 3.3.0:

• Updates to xia2.mmcif output to conform to the latest pdb dictionaries (v5) (xia2/xia2#537)
• xia2.html: Add <dF/s(dF)>-by-resolution plot if running xia with anomalous=True (xia2/xia2#551)
• xia2.multiplex: fix occasional error generating stereographic projections. (xia2/xia2#546)
• for a more complete list of changes check the xia2 changelog

DIALS 3.2.3

2020-12-07:

• dials.slice_sequence: Fix crash using block_size= option (#1502)
• dials.scale: Fix broken exclude_images= option (#1509)

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

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

DIALS 3.2.2

2020-11-23:

• Fix case where dials.stills_process could swallow error messages
• dials.cosym: Fix non-determinism. Repeat runs will now give identical results. (#1490)
• Developers: Fix precommit installation failure on MacOS (#1489)

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

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