Releases · dials/dials

2025-04-29:

Features

dials.index: Separately report unindexed reflection counts for reflections away from ice regions. (#2827)
dials.cosym: Add the option output.excluded=True to set aside the data sets that cosym rejected, so that these can more easily be investigated separately. (#2854)
dials.image_viewer: Support iso-resolution lines (circles, ellipses, hyperbola) on non-coplanar and/or two_theta != 0 detectors. (#2867)
dials.correlation_matrix: Hierarchical clustering now defaults to Ward linkages. (#2876)
dials.cluster_unit_cell: Add option to use Ward linkage, rather than single linkage. (#2884)
dials.correlation_matrix: Perform principal component analysis on optimised cosym coordinates. Add a new matrix-style plot for displaying all projections at once. (#2885)
dxtbx: FormatROD_Arc: Support for Rigaku HyPix-Arc 100° and 150° curved detectors. (cctbx/dxtbx#787)
dxtbx: FormatBrukerELA: Add support for the DECTRIS-ELA detector images in Bruker SFRM format. (cctbx/dxtbx#802)
dxtbx.any2nexus: Add sensor_material= and sensor_thickness= options. (cctbx/dxtbx#803)
dxtbx: FormatXTC: New features for managing wavelength calibration and an adjustment to the minimum trusted range for the ePix. (cctbx/dxtbx#804)
xia2.multiplex: Addition of new PCA style plot to visualise cosine-angle clustering. (xia2/xia2#841)

Bugfixes

dials.find_spots: Prevent masked pixels from causing a "halo" of excluded pixels around them when using threashold.algorithm=extended_dispersion. (#2790)
dials.ssx_index: Fix crash when processing stills with no scan objects. (#2841)
dials.export format=mosflm: Do not write a DIRECTORY line if the image files do not exist (#2845)
dials.refine: Warn, don't crash, if trying to fix individual scan-varying parameters. (#2856)
dials.cluster_unit_cell: Clusters are given a cluster_id in order of decreasing size, and the output filenames match the cluster_id. (#2859)
dials.find_bad_pixels: Use dispersion algorithm for filtering, instead of extended dispersion. This is more sensitive for lone pixels. (#2881)
dials.scale: Fix potential bad scaling against a reference if resolution limit is greater than 2 Angstroms. (#2883)
dials.reciprocal_lattice_viewer: Fix translate function for Python 3.12. (#2888)
dxtbx: Fix issue where attempting to group experiments could fail. (cctbx/dxtbx#772)
dxtbx: dials.import: Reduce excessive memory usage when importing many (>100s) FormatNXMX files. (cctbx/dxtbx#789)
dxtbx: FormatNXmxEigerFilewriter: Improve heuristics when deciding whether to swap image dimensions. (cctbx/dxtbx#793)
dxtbx: FormatROD: Use the weighted average of K-alpha1 and K-alpha2 as the monochromatic wavelength for the beam model. (cctbx/dxtbx#800)
dxtbx: FormatRAXIS: Allow the possibility of reading compressed files. (cctbx/dxtbx#801)
xia2: Rename STRONG_PIXEL to SIGNAL_PIXEL following changes in XDS. (xia2/xia2#829)
xia2.ssx: Correctly handle incorrectly specified filepaths with a useful error message. (xia2/xia2#833)

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

Features

Python 3.10 is now the minimum python supported. (#2792)
Added initial support for a H5-based reflection table. This is turned off by default, but can be activated by setting the DIALS_USE_H5 environment variable. (#2677)
dials.index and dials.ssx_index: Add the CUDA-accelerated fast-feedback-indexer to DIALS as a lattice search algorithm. See https://github.com/paulscherrerinstitute/fast-feedback-indexer for more details. (#2717)
dials.estimate_resolution: Add resolution estimate based on limit of CC½ significance. (#2580)
dials.refine_error_model: Allow grouped and individual error model refinements. (#2685)
dials.symmetry: Enable oversampling in systematic_absences.method=fourier, for screw-axis detection. (#2701)
dials.correlation_matrix: Include reachability plot for visualisation of coordinate-clustering. (#2778)
dials.image_viewer: Add a line tool that gives start, end, and midpoints, plus a line profile graph. (#2798)
dials.search_beam_position: Include three new projection methods. (#2809)
dials.import: Add syntax for splitting a long scan into chunks. (#2816)
dxtbx: Nexus support: Handle reading new scale_factor fields (used for detector gain). (cctbx/dxtbx#756)
dxtbx: Add FormatSMVADSCCetaD to allow easier processing of 3DED images from the Ceta-D detector, which have been converted to SMV. (cctbx/dxtbx#770)
xia2.multiplex: Improvements to clustering output, and addition of cluster identification algorithm for comparisons. (xia2/xia2#783)

Bugfixes

Fix beam.get_s0() errors when trying to use image viewer with polychromatic data. (#2765)
Fix symmetry not being applied consistently post indexing, when multiple crystals and multiple orientations are present. (#2786)
dials.cosym: Fix weighting of cosym objective function, use count weights by default. (#2813)
dials.cosym: Use unbiased formula for standard error. (#2810)
dials.export: Fixes to work with gemmi v0.7. (#2834)
dials.generate_distortion_maps: Correct definitions for creating elliptical distortion correction maps. (#2787)
dials.image_viewer: Avoid error messages when quitting while one of the tools (ring, unit cell, etc.) is open. (#2836)
dials.image_viewer: Do not allow integer controls to take values outside of their bounds. (#2822)
dials.image_viewer: Fix display bug with the trusted range mask, when viewing stacked images. (#2830)
dials.image_viewer: Recover missing image scrollbar by increasing the panel height. (#2795)
dials.index: fix inconsistent experiment IDs after indexing with index_assignment.method=local (#2799)
dials.index: Fix minor bug in global index assignment. (#2800)
dials.integrate: Allow command line option d_min= without requiring full qualification as prediction.d_min=. (#2837)
dials.predict: Do not try to filter shadowed reflections, if no masker is provided. (#2805)
dials.predict: Now adds experiment identifiers to output reflections. (#2788)
dials.refine_bravais_settings: Select only the reflections used in refinement in the indexing step for the calculation, to reduce memory footprint with very high resolution data. (#2824)
xia2: Fix issue where command paths would fail to be resolved on Windows, with some configurations. (xia2/xia2#824)
xia2: Fix issue where multiple sweeps were not handled correctly on Windows. (xia2/xia2#825)
xia2.multiplex: Improve PHIL help for identifiers= option. (xia2/xia2#828)

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

2024-10-17:

Fix problem causing incorrect resolution values in viewers. (#2765)

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.

2024-10-15:

Features

Switched bootstrap.py to use CMake by default. You can pass --libtbx to get the previous behaviour, if you need to develop cctbx. (#2755)
Added scaling corrections for time-of-flight data. (#2704)
dials.correlation_matrix: Add dimension optimisation for intensity-based dataset clustering. (#2743)
dials.generate_distortion_maps: Much faster map generation for mode=ellipse. (#2745)
dials.generate_mask: Allow combining masks. (#2711)
dials.image_viewer: Added multi-panel polygon masking. (#2735)
dials.correlation_matrix: Add auto-selection and output of significant clusters and extended graphs in html output (#2770)
dxtbx: Add format class to read data from the NMX ESS detector. (cctbx/dxtbx#764)
xia2.ssx_reduce: Add option to apply a per-crystal I/sigma filter. (xia2/xia2#762)
xia2.multiplex: Include dimension optimsation for cos-angle clustering from dials.correlation_matrix. (xia2/xia2#814)

Bugfixes

dials.index: Ensure reflections associated with removed experiments are reset to unindexed. (#2653)
dials.find_spots: Enable threshold.algorithm=radial_profile for polychromatic data. (#2729)
dials.image_viewer: Fixed stacking of masks, and stacking of multiple experiments. (#2730)
dials.image_viewer: Fix UI glitches in masking tools. (#2731)
dials.resolution_analysis: Suppress output of potential scipy OptimizeWarning. (#2737)
dials.generate_distortion_maps: Fix bug with mode=ellipse for detectors with oblong panels. (#2740)
dials.cosym: Handle the case of very few reflections, leading to zero weights in weighted cosym analysis. (#2741)
dials.integrate: Ensure the polarization correction is only performed for X-ray data (not electron nor neutron). (#2754)
dials.image_viewer: Fix broken "Save As" PNG functionality. (#2759)
dials.index: When indexing multiple imagesets, ensure a failure to index one does not result in failure for all. (#2764)
dials.image_viewer: Fix errors when trying to view polychromatic data. (#2765)
dials.reciprocal_lattice_viewer: Fix errors when trying to view polychromatic data. (#2766)
dials.geometry_viewer: Fix errors when trying to view polychromatic experiments. (#2773)
dxtbx.dlsnxs2cbf: Add work around for issues with data recorded at 32-bit. (cctbx/dxtbx#759)
dxtbx: Auxiliary data processing files (mask, gain, pedestal, and dx and dy maps) will now always be loaded when available. (cctbx/dxtbx#760)
dxtbx: Refactor panel positions of FormatISISSXD to account for differences in panel positions, depending on the date of data collection. (cctbx/dxtbx#762)
dxtbx: Raise a more suitable error message when failing to load an experiment list. (cctbx/dxtbx#763)

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

2024-08-23:

xia2: Fix compatibility with XDS 20240723, which changed some output in INTEGRATE.LP. (xia2/xia2#805)
dxtbx: Stop dxtbx.image_average shuffling panel positions for segmented detectors. (cctbx/dxtbx#752)

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.

2024-08-20:

Features

Add functionality to support time-of-flight and Laue indexing and refinement. (#2662)
dials.symmetry: Allow free selection of significance_level in the range [0,1]. (#2696)
dials.export: Add support for exporting still data in mmcif format that GEMMI can read. (#2709)
dxtbx: Add Nonius KappaCCD format. (cctbx/dxtbx#741)

Bugfixes

dials.index: Fix a pink_indexer error that caused failures for images with electron diffraction geometry. (#2680)
dials.correlation_matrix: Correctly select datasets for output json after filtering, when used by multiplex. (#2681)
dials.index: Avoid mm to px conversion when the refinement_protocol is set to do no refinement, as the required data are not available. (#2687)
dials.image_viewer: Increase the maximum resolution for the ring tool radius. This was too small for new detectors. (#2697)
dials.index: Fix potential crash in max_cell estimation when all spots are at the resolution of ice rings. (#2699)
dials.merge: Use GEMMI to output merged MTZs, for consistency with dials.export. (#2700)
dials.reciprocal_lattice_viewer: Fix middle mouse drag to translate function. (#2707)
Performance improvement for selections from large reflection tables. (#2718)
dxtbx: FormatMRC: Relax restrictive check on the overloaded MZ header value, which caused failures to read files where MZ == 1. (cctbx/dxtbx#740)
dxtbx: FormatCBFMini: When parsing header lines for a timestamp, avoid clashes with Windows paths. (cctbx/dxtbx#742)
dxtbx: FormatPy: Add fix for pickle files. (cctbx/dxtbx#744)
dxtbx: FormatSMVRigakuSaturnNoTS: Fix a bug in reading the image pedestal from headers. (cctbx/dxtbx#746)
xia2.ssx_reduce: Make sure space group naming is correct after cosym batch reindexing. (xia2/xia2#798)
xia2: Convert merged MTZ output to use GEMMI, following #2700 (xia2/xia2#799)
xia2: Try to reduce number of resolution bins for report generation, for sparse data, to avoid crash. (xia2/xia2#801)

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

2024-06-19:

Features

DIALS is now compatible with Python 3.12. (#2651)
New tool: dials.correlation_matrix: A new command-line tool for correlation and cosine similarity clustering of multi-crystal datasets, independent of xia2.multiplex. (#2632)
New tool: dials.split_still_data for splitting dials-processed still data based on image number (e.g. dose series). (#2672)
dials.scale: Add filtering options to default basic error model to allow error modelling of stills data. (#2654)
dials.cosym: Add alternative weighting during cosym CC calculation with a new cc_weights= option. (#2666)
dxtbx: The template handling mechanism is extended. A template with a single # is expanded to match non-zero padded sequential numbers. (cctbx/dxtbx#705)
dxtbx: Add dxtbx.any2nexus program, to convert any file dxtbx can read to a NeXus file. (cctbx/dxtbx#735)
xia2.ssx_reduce: Optimise and apply an error model correction in scaling. (xia2/xia2#792)

Bugfixes

Fix dials.show beam checks for time of flight experiments. (#2660)
dials.find_rotation_axis: Correctly set the orientation of the rotation axis for a multi-axis goniometer. (#2658)
When masking, raise an error if d_min > d_max (where no spots would be found). (#2664)
dials.cosym: Make function return structure correctly, in the recently added cc_we 8000 ights= option. (#2668)
dials.find_rotation_axis: Add reflection selection criteria, to avoid runs that use a very large amount of memory. (#2670)
dials.cosym: Fix to give more accurate cc calculation when running with a space_group= set. (#2674)
Fix flex.reflection_table.concat, to not modify in-place. (#2679)
dxtbx: FormatROD: set the beam probe to "electron" for 3D ED experiments. (cctbx/dxtbx#728)
dxtbx: Raise an error if geometry.goniometer.axis= is set with a multi-axis goniometer. In that case, geometry.goniometer.axes= must be set instead. (cctbx/dxtbx#730)
dxtbx: Update goniometer for FormatISISSXD to allow for different ways the goniometer angle can be stored. (cctbx/dxtbx#731)
dxtbx: Fix Scan.get_property key type. (cctbx/dxtbx#734)
xia2.multiplex: Reset batches after filtering steps to prevent inconsistencies and duplications. (xia2/xia2#789)
xia2.ssx_reduce: Improve indexing ambiguity resolution with a reference by direct call to dials.reindex methods. (xia2/xia2#794)

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

2024-05-23:

dxtbx: Fix case where old I03 Eiger nexus data (pre-2020) would fail to process. (cctbx/dxtbx#737)

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.

2024-04-17:

Features

dials.predict: Allow usage when image data are not available. (#2553)
dials.ssx_index: Allow use of sequences indexer, pink_indexer and low_res_spot_match indexing algorithms. (#2614)
dials.export: Add option composition= to specify of asymmetric unit composition for SHELX .ins file output. (#2623)
Add TOFSpotFinder to tailor default params to time of flight experiments and add additional reflection table data. (#2602)
dxtbx: Add format reader for Jungfrau4M serial images from beamline ID29 at ESRF. (cctbx/dxtbx#659)
dxtbx: Better handling for bad data in spectra calibration in XTC format. (cctbx/dxtbx#674)
dxtbx: Add Bruker and miniCBF format readers for the ELDICO ED-1 electron diffractometer with DECTRIS QUADRO detector. (cctbx/dxtbx#682)
dxtbx: FormatSMVTimePix_SU: Always mask out the central cross of virtual pixels. (cctbx/dxtbx#683)
dxtbx: Add format reader for ISIS SXD detector. (cctbx/dxtbx#687)
dxtbx: Detector distance can now be manually overridden for multi-panel detectors. (cctbx/dxtbx#698)
dxtbx: Add format reader to read time of flight Laue data fro 8B9E m MANDI. (cctbx/dxtbx#703)

Bugfixes

Fix building on RHEL8 and other more recent distributions. (#1465)
dials.index: Joint indexing is automatically set on for rotation data, off for still data. This can be overridden by explicit use of joint_indexing=. (#2605)
dials.export format=shelx: Increased precision of unit cell parameters and their estimated standard deviations written to .ins file. (#2624)
dials.ssx_index: Don't combine detector models if individually refined. (#2634)
dials.scale: Fix error in propagation of partiality variance, when scaling still data. (#2642)
dials.export: Fix crash when exporting scaled still-shot data. (#2646)
dxtbx: Fix scan comparison for scan properties changes (cctbx/dxtbx#669)
dxtbx: Eiger Support: Invert the module dimensions, only for older firmware versions. See https://media.dectris.com/230203-Release_Notes-DECTRIS_EIGER2.pdf for reference. (cctbx/dxtbx#676)
dxtbx: FormatMRC: Better handling of extended headers. (ccpem/mrcfile#50), and extended headers are ignored if they contain junk values. (cctbx/dxtbx#679)
dxtbx: Negative rotation angles are now allowed, the goniometer axis will be inverted if necessary. (cctbx/dxtbx#690)
dxtbx: dials.import now uses natural sorting on input data, instead of strict sorting. (cctbx/dxtbx#697)
dxtbx: Fix setting detector distance for single panel detectors that have a hierarchy. (cctbx/dxtbx#699)
dxtbx: Fix error introduced in FormatSMVJHSim causing test failures. (cctbx/dxtbx#710)
xia2.multiplex: Avoid space group analysis if given reference file. (xia2/xia2#770)
xia2.ssx: Allow use of stills.indexer=sequences in ssx_index routine. (xia2/xia2#779)
xia2.multiplex: Allow use of relative_length_tolerance= and absolute_angle_tolerance= (used by cosym) in multiplex. (xia2/xia2#786)

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

2024-03-26:

wxPython was inadvertently reverted to 4.1 instead of 4.2 for python 3.9 and 3.10 releases. (#2636)

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.

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Releases: dials/dials

DIALS 3.24.0

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DIALS 3.23.0

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DIALS 3.22.1

DIALS 3.22.0

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DIALS 3.21.1

DIALS 3.21.0

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DIALS 3.20.0

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DIALS 3.19.1

DIALS 3.19.0

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DIALS 3.18.1