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@Anthchirp Anthchirp released this Mar 18, 2019 · 131 commits to master since this release

Release notes

What happened to DIALS 1.13
We decided to use the release number 13 as a reference marker for developers to help migrating code changes to the upcoming DIALS 2.0 release.

DIALS 1.14.0 (2019-03-18):

  • dials.image_viewer can stack images without having to restart the viewer.
  • dev.dials.generate_shadow_mask is a new (unsupported) tool to create HDF5 shadow masks from the DIALS model of the goniometer shadow
  • dials.apply_mask now works with experiments (#673)
  • dials.scale general improvements to algorithm stability, speed and memory performance improvements
  • DIALS 1.14 is the final DIALS 1 release, and will be supported for a longer period than usual.

xia2 0.5.871:

  • This is the final xia2 0.5 release, and will be supported for a longer period than usual.
Assets 14
Mar 1, 2019
DIALS 2.0
To celebrate the many achievements since the 1.0 release.

To make a release you need to
 - make a new release branch (git checkout -b dials-2.0)
 - make any change on that branch (this is important),
   recommend changing the default version number in util/version.py
 - commit this change, preferably with a useful release message
 - tag this commit (git tag -a v2.0.0), again preferably with a useful message
Mar 1, 2019
DIALS 1.13 branch point
This does not mark the start of a release branch.
It serves as a reserved branch point in case someone needs to refer
back to, or build on, the codebase before the DIALS 2.0 commits but
outside of the supported DIALS 1.14 release branch.

@Anthchirp Anthchirp released this Nov 2, 2018 · 420 commits to master since this release

Release notes

DIALS 1.12.0 (2018-11-02):

  • dials.compute_delta_cchalf: new utility to implement a delta-cc12 analysis for removing scaled data sets with poor agreement.
  • dials.export can now export MTZs of single-image data sets.
  • dials.frame_orientations: new utility to output a table and plot of crystal orientations for each image expressed as a zone axis direction.
  • dials.reindex: allow reindexing against a reference file to give a common indexing between data sets.
  • dials.scale: Addition of weak B-restraint for physical model to improve refinement stability. General bug fixes and stability improvements. Addition of cross validation options for scaling.
  • dials.search_beam_position now works for multiple-sweep data sets.
  • dials.symmetry: add a round of outlier rejection before symmetry analysis.

xia2 0.5.744:

  • you can now run xia2 with pipeline=dials-full which uses DIALS scaling and analysis tools in place of POINTLESS and AIMLESS

DIALS 1.12.1 (2018-11-19) includes xia2 0.5.757:

  • dials.detect_blanks is now less conservative
  • dials.scale fixes
  • Updates to support Eiger stream data
  • Updates to support Fast DP v1.1
  • xia2: Added command line options dials.integrate.d_max and .d_min to set resolution limits for integration
  • xia2: Fixes for dials-full pipeline
  • xia2: Reduce size of xia2.report HTML output
  • xia2: Improve the experimental remove_blanks mechanism

DIALS 1.12.2 (2018-12-03) includes xia2 0.5.764:

  • DIALS image viewer: show hdf5-derived file extensions in file load dialogue
  • cosym: maintain experiment order as given in the input
  • cosym: only export relevant experiments when using a subset of the data for analysis
  • dials.reindex: sanity check space group before using a given reference
  • dials.scale: speed up outlier rejection
  • xia2: handle I2/C2 ambiguity in the dials-full pipeline (xia2/xia2#260)
  • xia2: general improvements to the dials-full pipeline

DIALS 1.12.3 (2019-01-07) includes xia2 0.5.767:

  • EIGER detector support fixes
  • dials.export_bitmaps: allow combining output_file with imageset_index
  • xia2: fix character encoding in HTML log
  • xia2: restore previously removed xia2.to_shelx command

DIALS 1.12.4 (2019-01-22) includes xia2 0.5.769:

  • dials.predict: switch index generation method for >50 images (#585)
  • xia2: bug fix for .h5 files where data files don't have 'data_' in file name (xia2/xia2#272)
  • Nexus file format support:
    • add workaround if scan is None
    • correctly interpret offset units

DIALS 1.12.5 (2019-02-05) includes xia2 0.5.769:

DIALS 1.12.6 (2019-02-19) includes xia2:

  • improved electron diffraction data support (ADSC-electron-57)
Assets 45

@Anthchirp Anthchirp released this Sep 3, 2018 · 610 commits to master since this release

Release notes

DIALS 1.11.0 (2018-08-24):

  • dials.background: now allows masking prior to background calculation. Improved plots.
  • dials.filter_reflections: create subsets of a reflection file based on user-specified criteria
  • dials.export: command line interface change. Intensity choice for export given by option intensity, and exporting of partials now determined by options partiality_threshold and combine_partials.
  • dials.scale: (for testing / evaluation) new program for scaling data from DIALS integration
  • Behaviour change: DIALS commands will no longer read STDIN for parameters by default - you must specify that you want this behaviour e.g. cat some_params.phil | dials.import --phil=-. You may also pass filenames directly into the argument to get the identical behaviour e.g. --phil=some_params.phil (#466)

xia2 0.5.649:

  • Add support for dials.scale

DIALS 1.11.1 (2018-09-03) includes xia2 0.5.651:

  • dials.export: Rename prf to profile for export and scaling options
  • dials.analyse_output: Fix grid_size parameter handling (#611)

DIALS 1.11.2 (2018-09-18) includes xia2 0.5.653:

  • cosym/dials.symmetry: fix profile errors
  • xia2.strategy: Fix crash at dials.export step
  • xia2.strategy: Do not require profiles on export
  • make merging statistics generation code more fault tolerant

DIALS 1.11.3 (2018-10-02) includes xia2 0.5.655:

  • Remove debug output from image viewer
  • Fix rare dials.index crash (#620)

DIALS 1.11.4 (2018-10-16) includes xia2 0.5.655:

  • Improves support for Eiger2
  • dials.cosym: fix math error
  • dials.index: if indexing from known orientation then use provided space group setting unless specified
  • Fix dials.background crash when run without parameters
  • Fix dials.symmetry crash (#619)
Assets 33

@Anthchirp Anthchirp released this May 21, 2018 · 23 commits to dials-1.10 since this release

Release notes

DIALS 1.10.0 (2018-05-21):

  • Faster refinement for hierarchical multiple panel detectors by moving calculations to C++
  • Scan-varying refinement of the goniometer setting matrix is now possible
  • dials.plot_scan_varying_crystal changed to dials.plot_scan_varying_model. Now plots beam centre drift and error bars on scan-varying unit cell, if these have been recorded (#414)
  • Improvements to profile fitting in the presence of negative-valued pixels (#537)
  • 'DQE' renamed to 'QE' in across function names and in output data (#544)
  • Improved support for Bruker Photon II detectors
  • New program dials.cosym: implementation of algorithms described in Gildea, R.J. & Winter, G. (2018). Acta Cryst. D74, https://doi.org/10.1107/S2059798318002978
  • dials.reindex: bug fix when dealing with multi-sweep datasets (4027299)
  • dials.refine_bravais_settings: bug fix for multi-sweep datasets if experimental models differ between experiments (#554)

xia2 0.5.577:

  • pipeline=2d has been marked as deprecated and will be removed at some point in the future

DIALS 1.10.1 (2018-06-16) includes xia2 0.5.580:

  • Format fixes for Bruker Photon II images
  • dials.show compatibility fixes
  • xia2: gracefully handle invalid ranges with image=image_0001.cbf:start:end syntax
  • xia2: disable currently unreliable check_indexing_symmetry feature

DIALS 1.10.2 (2018-06-26) includes xia2 0.5.580:

  • dials.export_bitmaps: Fix for still images, add output_file parameter
  • Remove problematic format class from dxtbx
  • Fix installation on newer Ubuntu versions

DIALS 1.10.3 (2018-07-10) includes xia2 0.5.580:

  • xia2: fix missing CIF information

DIALS 1.10.4 (2018-07-24) includes xia2 0.5.582:

  • dials.report: Fix incorrect y-axis labels in plots
  • xia2: Allow image= without range on Windows
Assets 33

@Anthchirp Anthchirp released this Mar 11, 2018 · 1294 commits to master since this release

Release notes

DIALS 1.9.0 (2018-03-10):

  • support for scan-varying beam models
  • dials.discover_better_experimental_model has been renamed to dials.search_beam_position (#418)
  • fixed crash on Ubuntu 14.04 (#513)
  • dials.image_viewer will now work with large Nexus files
  • errors when reading files should be more informative

xia2 0.5.540:

  • make some processing error messages more informative

DIALS 1.9.1 (2018-04-03) includes xia2 0.5.542:

  • Correctly identify Timepix detector images
  • dials.image_viewer: Fix issues with mask display, #520
  • xia2: use correctly capitalized H5ToXds executable instead of H5ToXDS

DIALS 1.9.2 (2018-04-10) includes xia2 0.5.542:

DIALS 1.9.3 (2018-05-08) includes xia2 0.5.546:

  • Nexus format files: correctly determine number of images in dataset
  • Force scan_varying=False during indexing as indexing only uses static models
  • dials.spot_counts_per_image: generate joint .json result file unless told not to.
  • xia2: fix HDF5 template issue (xia2/xia2#219)
  • xia2: fix processing of .nxs files if a _master.h5 file is present for the same dataset
  • xia2: save integrated reflections to DataFiles directory
Assets 23

@Anthchirp Anthchirp released this Nov 15, 2017 · 1572 commits to master since this release

Release notes

DIALS 1.8.0 (2017-11-02):

  • Added option dials.show show_flags=true, for more information about how reflections were classified
  • dials.refine: new diagnostic for problematic refinement cases, using the condition number of the Jacobian
  • dials.refine: increase default max_iterations for problematic refinement cases
  • dials.refine: bug fix for setting smoother parameters for scan-varying refinement
  • dials: spot_counts_per_image fixes

xia2 0.5.469:

  • respect the number of allocated CPUs on SGE clusters.
  • sensible trusted range for Rayonix CCD images with XDS processing
  • basic support for Eiger data sets from BioMAX, requires correct goniometer axis to be specified on command line
  • can now "see" data with template prefix.nnnn.bz2 etc.
  • xia2 / dials / cctbx: correct interpretation of geometry for Rigaku lab source CCD detectors
  • xia2 / DIALS: support for Eiger data sets with >1000 sub-files via ulimit
  • xia2 / XDS: support for use of "neggia" plugin if in XDS binary directory & processing HDF5 / Eiger data

DIALS 1.8.1 includes xia2 0.5.474 (2017-11-16):

  • dials: fix build issue on macOS 10.13 (High Sierra), #77
  • dials: fix run issues on macOS <10.12
  • dials: fix DLS I23 image interpretation
  • xia2: Fix ImportError bug on Windows (xia2/xia2#194)
  • xia2 / XDS: Fix 'pixel value' issue with recent XDS versions (xia2/xia2#193)
  • xia2 / XDS: Refine detector position in second integration round (xia2/xia2#181)

DIALS 1.8.2 includes xia2 0.5.476 (2017-12-05):

  • dials: Fix indexing for small molecule data with unit cell <100A^3.
  • dials: Improve Eiger file support
  • dials: Smargon support for data from DLS I03
  • xia2: Fix indexing method fallback

DIALS 1.8.3 includes xia2 0.5.482 (2018-01-16):

  • dials.image_viewer: fix crash on Windows
  • dials.image_viewer: fix crash when using masks (cctbx/cctbx_project#107)
  • dials.stills_process: fix out of memory error when processing large files
  • xia2: pipeline=2d support for Rigaku RAXIS detectors (xia2/xia2#200)

DIALS 1.8.4 includes xia2 0.5.487 (2018-01-30):

  • dials.image_viewer: Fix crash with "dxtbx Internal Error" (#493)
  • dials.stills_process: Validate mask file exists at the start of the program
  • xia2: immediately stop when Aimless failed to process data
  • xia2: Warn when using XDS with HDF5 files and necessary libraries are missing (xia2/xia2#197)
  • Fixed support for DLS I03 full CBF images

DIALS 1.8.5 includes xia2 0.5.492 (2018-02-20):

  • allow splitting output of dials.spot_counts_per_image per metric
  • xia2: fix crash with .xinfo non-native file line endings
  • xia2: add full DIALS paper reference
Assets 39

@Anthchirp Anthchirp released this Aug 18, 2017 · 1752 commits to master since this release

Release notes

DIALS 1.7.0 (2017-08-18):

  • dials.refine: performance improvements for scan-varying refinement
  • dials.refine: bug fix for I23's P12M detector
  • Better default gain for ADSC CCD detectors
  • dials.import: dynamic_shadowing now turned on by default where a goniometer shadow model is available

xia2 0.5.428:

  • xia2: dynamic_shadowing now turned on by default where a goniometer shadow model is available
  • xia2.html: ensure merging statistics consistent with those reported in text output

DIALS 1.7.1 includes xia2 0.5.432 (2017-09-04):

  • dials.show improvements and shoebox stats
  • Allow disabling of ice ring filtering in spot finding server
  • xia2: Fix dynamic shadowing for pipeline=3d
  • xia2.strategy: improve BEST integration

DIALS 1.7.2 includes xia2 0.5.436 (2017-09-19):

  • bug fix for DLS I23 images where MultiAxisGoniometer does not exist
  • fix map coordinates in dials.image_viewer (#442)
  • fix max_cell determination in indexing (#386)
  • fix for setting interval widths in scan-varying refinement
  • xia2.report: fix multiplicity p

DIALS 1.7.3 includes xia2 0.5.438 (2017-10-03):

  • dev.dials.csv: clean up command line help
  • xia2 ISPyB interface: use files in DataFiles directory in preference to other locations.
  • pytest 3 compatibility fix

DIALS 1.7.4 includes xia2 0.5.442 (2017-10-24):

  • fix HDF5 library download location
  • support for Smargon goniometer on Soleil PROXIMA-1
  • xia2: fix issue with XDS trusted ranges (xia2/xia2#182)
  • xia2: allow processing of images with .gz extension (xia2/xia2#184)
Assets 29

@Anthchirp Anthchirp released this Jun 5, 2017 · 1960 commits to master since this release

Release notes

DIALS 1.6.0 (2017-06-02):

  • dials/xia2: dynamic masking of diamond anvil cells for DLS I19-2 high pressure experiments
  • JMP improvements to mosaic spread estimate (#342, #119)

xia2 0.5.319:

  • xia2: new xia2.html
  • xia2 fixed for I23 data with distance != 0; xia2/xia2#124 & friends

DIALS 1.6.1 includes xia2 0.5.325 (2017-06-14):

  • dials.image_viewer: respect kernel_size parameter (#354)
  • Rayonix TIFF format fixes (#370)
  • xia2: XDS compatibility fixes (xia2/xia2#131)
  • xia2: Trap non-fatal fatal error (xia2/xia2#115)
  • xia2: respect batch_range parameter in resolution determination
  • xia2: silence xtriage output

DIALS 1.6.2 includes xia2 0.5.328 (2017-06-20):

DIALS 1.6.3 includes xia2 0.5.337 (2017-07-03):

  • Many dials.export fixes, including exports from single images (#388)
  • xia2: Make d_min= command line parameter work again (xia2/xia2#136)
  • xia2: Avoid crash when running xtriage on centric data (xia2/xia2#139)
  • xia2: Move extra multiplicity files away from main directory (xia2/xia2#140)
  • xia2: Remove '.bat' from output file names when run on Windows
  • xia2: Improvements in HTML report (xia2/xia2#133, xia2/xia2#141)
  • xia2: xia2.strategy fixes

DIALS 1.6.4 includes xia2 0.5.340 (2017-07-17):

  • dials.reciprocal_lattice_viewer: correctly handle multiple sweeps in single file (#407)
  • xia2: image= parameter did not work as expected when including multiple slices from the same dataset (xia2/xia2#138)
  • Recognize and drop NaN values in iotbx data plotting (xia2/xia2#142)
Assets 33
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