dials/dials issues and pull requests

#2535 - Ellipsoid profile model scale factor in mask calculation

Pull Request - State: closed - Opened by dagewa 11 months ago - 3 comments

#2534 - Handle shared models in dials.index with known orientations

Pull Request - State: closed - Opened by jbeilstenedmands 11 months ago - 1 comment

#2533 - repredict_only mode breaks stills_process

Issue - State: open - Opened by dermen 11 months ago

#2532 - Developer bootstrap.py install fails on MacOS Sonoma

Issue - State: closed - Opened by alyubimov 12 months ago - 24 comments

#2531 - dials.integrate, dials.export_best have problems with EIGER 16M data

Issue - State: closed - Opened by dmszebenyi 12 months ago - 1 comment

#2530 - `dials.cosym` does not change space group to the requested one (small molecule case)

Issue - State: open - Opened by dagewa 12 months ago - 2 comments

#2529 - codespell

Issue - State: closed - Opened by dagewa 12 months ago - 4 comments

#2528 - Sourceforge really is no more

Pull Request - State: open - Opened by graeme-winter 12 months ago - 3 comments

#2527 - dials.import_xds is useless

Issue - State: closed - Opened by graeme-winter 12 months ago - 2 comments

#2526 - Add check for compatible cells in cosym output

Pull Request - State: open - Opened by jbeilstenedmands 12 months ago - 2 comments
Labels: PR: merge conflicts

#2525 - Add include_datasets as an alias for use_datasets in dials.scale

Pull Request - State: closed - Opened by jbeilstenedmands 12 months ago - 1 comment

#2524 - Exit dials.cosym if single dataset input, with recommendation to run dials.symmetry

Pull Request - State: closed - Opened by jbeilstenedmands 12 months ago - 1 comment

#2523 - Fix log output line in dials.symmetry.

Pull Request - State: closed - Opened by jbeilstenedmands 12 months ago - 1 comment

#2522 - Build fail with bootstrap.py for Mac OSX Ventura 13.6

Issue - State: closed - Opened by toastisme 12 months ago - 7 comments

#2521 - dials.ssx_integrate: Add max_cell_volume_change_fraction parameter to catch highly divergent cell refinements

Pull Request - State: closed - Opened by jbeilstenedmands 12 months ago - 1 comment

#2520 - `dials_sequence_to_stills` trimmed scan fix

Pull Request - State: closed - Opened by dagewa 12 months ago - 1 comment

#2519 - `dials.sequence_to_stills` crashes with sequence that does not start from image 1

Issue - State: closed - Opened by dagewa 12 months ago

#2518 - Add mosaicity_max_limit option to dials.ssx_integrate

Pull Request - State: closed - Opened by jbeilstenedmands 12 months ago

#2517 - `dials.sequence_to_stills` improvements

Pull Request - State: closed - Opened by dagewa 12 months ago - 1 comment

#2516 - `dials.sequence_to_stills` without a scan-varying model fails

Issue - State: closed - Opened by dagewa 12 months ago

#2515 - Overriding geometry on import resets beam Probe

Issue - State: closed - Opened by dagewa 12 months ago - 3 comments

#2514 - Fix `exclude_images_multiple` for trimmed scans

Pull Request - State: closed - Opened by dagewa 12 months ago

#2511 - Shorthand to exclude regular calibration images

Pull Request - State: closed - Opened by dagewa 12 months ago - 2 comments

#2505 - MTZ export with an unsupported space group setting

Issue - State: closed - Opened by dagewa about 1 year ago - 8 comments

#2503 - Cosym: don't fill wij matrix where the overlap is less than min_pairs

Pull Request - State: closed - Opened by dwpaley about 1 year ago - 2 comments

#2502 - dials.import error for h5 image files

Issue - State: closed - Opened by DHekstra about 1 year ago - 5 comments

#2501 - Add r-free flags generation to merging function

Pull Request - State: closed - Opened by jbeilstenedmands about 1 year ago

#2500 - dials.cosym and dials.symmetry resolution estimates vary considerably

Issue - State: closed - Opened by huwjenkins about 1 year ago - 10 comments

#2499 - Improve cc1/2 fit for resolution estimation on noisy data

Pull Request - State: closed - Opened by jbeilstenedmands about 1 year ago - 4 comments

#2498 - Issue with reading in MarCCD images

Issue - State: closed - Opened by DHekstra about 1 year ago - 3 comments

#2497 - Possible bug fix for 2486

Pull Request - State: open - Opened by graeme-winter about 1 year ago - 2 comments

#2496 - dials.image_viewer fails to show a full CBF example in CBFlib

Issue - State: closed - Opened by biochem-fan about 1 year ago - 1 comment
Labels: dials.image_viewer

#2495 - DIALS 3.16.1

Pull Request - State: closed - Opened by DiamondLightSource-build-server about 1 year ago - 1 comment
Labels: upcoming release

#2494 - Turn off cxi.merge integration pickles

Pull Request - State: closed - Opened by phyy-nx about 1 year ago - 1 comment

#2493 - Reduce randomness of free flags generation test

Pull Request - State: closed - Opened by jbeilstenedmands about 1 year ago - 1 comment

#2492 - Fix test failures caused by dxtbx@831061f

Pull Request - State: closed - Opened by ndevenish about 1 year ago

#2491 - dials.merge: Fix potential for crash with r_free_flags.extend=True if there are no new flags to extend

Pull Request - State: closed - Opened by jbeilstenedmands about 1 year ago - 1 comment
Labels: backported

#2490 - dials.import, convert_stills_to_sequences=True + image_range=x,y

Pull Request - State: closed - Opened by jbeilstenedmands about 1 year ago - 1 comment

#2489 - Remove xfel-test-skipping for tests that no longer need xfel

Pull Request - State: closed - Opened by ndevenish about 1 year ago - 1 comment

#2488 - DIALS fails to import cbf from Pilatus3 1M at BL02B1, SPRING-8

Issue - State: open - Opened by ndevenish about 1 year ago - 19 comments

#2487 - dials.symmetry should also print the unit cell

Issue - State: closed - Opened by graeme-winter about 1 year ago

#2486 - dials.cosym finds the right operator but puts it wrongly

Issue - State: closed - Opened by biochem-fan about 1 year ago - 31 comments
Labels: bug

#2485 - Selection on `id` in `AssignIndicesStrategy` classes leads to surprising behaviour

Issue - State: open - Opened by dagewa about 1 year ago

#2484 - `dials.image_viewer`: remove basis vector display

Pull Request - State: closed - Opened by dagewa about 1 year ago - 1 comment

#2483 - `dials.rlv` - handle cases where the beam centre cannot be set

Pull Request - State: closed - Opened by dagewa about 1 year ago - 1 comment

#2482 - Beam model probe changes in `dials.show` tests.

Pull Request - State: closed - Opened by dagewa about 1 year ago - 2 comments

#2481 - Cannot change settings in dials.recprocal_lattice_viewer when the detector swing angle is larger than 90

Issue - State: closed - Opened by biochem-fan about 1 year ago - 8 comments
Labels: bug, dials.reciprocal_lattice_viewer

#2480 - `dials.image_viewer` basis vector display is problematic

Issue - State: closed - Opened by dagewa about 1 year ago - 2 comments

#2479 - Fix `dials.image_viewer` crash when the detector swing angle is larger than 90°

Pull Request - State: closed - Opened by dagewa about 1 year ago - 8 comments

#2478 - dials.image_viewer crashes when the detector swing angle is larger than 90

Issue - State: closed - Opened by biochem-fan about 1 year ago
Labels: bug, dials.image_viewer

#2477 - Add a `small_cell` indexer to `dials.index`

Pull Request - State: open - Opened by dagewa about 1 year ago - 37 comments
Labels: PR: merge conflicts

#2476 - Add stereographic projection plots to dials.merge

Pull Request - State: closed - Opened by jbeilstenedmands about 1 year ago - 1 comment

#2475 - Subclasses should give a hit that they subclass a parent class

Issue - State: closed - Opened by graeme-winter about 1 year ago - 1 comment

#2474 - Support CMake environments in bootstrap.py

Pull Request - State: closed - Opened by ndevenish about 1 year ago - 4 comments

#2473 - DIALS does not handle the `four_circle_eiger` test data set

Issue - State: closed - Opened by dagewa about 1 year ago - 1 comment

#2472 - Slice using batch offsets fix

Pull Request - State: closed - Opened by jbeilstenedmands about 1 year ago - 1 comment

#2471 - Allow setting of wavelength tolerance in dials.export

Pull Request - State: closed - Opened by jbeilstenedmands about 1 year ago - 1 comment

#2470 - Log the experiment number when indexing multiple experiments

Pull Request - State: closed - Opened by dagewa about 1 year ago - 8 comments

#2469 - Ensure `invert_rotation_axis=True` is only applied once to each goniometer model

Pull Request - State: closed - Opened by dagewa about 1 year ago - 2 comments

#2468 - DIALS 3.15.2

Pull Request - State: closed - Opened by DiamondLightSource-build-server about 1 year ago - 1 comment
Labels: upcoming release, PR: merge conflicts

#2467 - dials.import invert_rotation_axis=true fails for even numbers of imagesets

Issue - State: closed - Opened by dagewa about 1 year ago - 4 comments

#2466 - Update ssx_integrate test tolerance

Pull Request - State: closed - Opened by jbeilstenedmands about 1 year ago - 1 comment

#2465 - No datablocks

Pull Request - State: closed - Opened by dagewa about 1 year ago - 5 comments

#2464 - dials.refine_bravais_lattice fails for multiple experiments

Issue - State: closed - Opened by dmszebenyi about 1 year ago - 2 comments

#2463 - Correct angular-dependent ellipsoid mosaicity models for dials.ssx_integrate

Pull Request - State: closed - Opened by jbeilstenedmands about 1 year ago

#2462 - Temporarily skip `test_model_background` on macos

Pull Request - State: closed - Opened by dagewa about 1 year ago - 1 comment

#2461 - Export bitmaps with resolution rings at specific d-spacings

Pull Request - State: closed - Opened by dagewa about 1 year ago - 1 comment

#2460 - dials.ssx_integrate can use a lot of memory when handling many images

Issue - State: open - Opened by JunAishima about 1 year ago - 3 comments

#2459 - Revert "Remove force_2d option"

Pull Request - State: closed - Opened by ndevenish about 1 year ago
Labels: backported

#2458 - Remove useless checkbox

Pull Request - State: closed - Opened by dagewa about 1 year ago - 2 comments

#2457 - Gently fail when too few spots for NN analysis

Pull Request - State: closed - Opened by dagewa about 1 year ago - 1 comment

#2456 - indexing.refinement_protocol.mode=None for more than just stills

Pull Request - State: closed - Opened by dagewa about 1 year ago - 1 comment

#2455 - dials.scale: switch off absorption correction when all scattering angles are small

Pull Request - State: closed - Opened by dagewa about 1 year ago - 8 comments

#2454 - Remove as_grid_scan from dials.import

Pull Request - State: closed - Opened by graeme-winter about 1 year ago - 3 comments

#2453 - Image viewer: Opening h5 data files throws UnicodeDecodeError

Issue - State: open - Opened by ndevenish about 1 year ago - 5 comments

#2452 - Remove as_grid_scan from dials.import

Issue - State: closed - Opened by graeme-winter about 1 year ago - 4 comments

#2451 - determine_reindex_operator_against_reference: identity operation when tested gives misleading results

Issue - State: open - Opened by graeme-winter about 1 year ago - 5 comments

#2450 - dials.index: if iterating through many experiments please give hint of experiment number

Issue - State: closed - Opened by graeme-winter about 1 year ago - 6 comments

#2449 - determine_reindex_operator_against_reference does not consider the identity

Issue - State: closed - Opened by graeme-winter about 1 year ago - 2 comments

#2448 - Inconsistent output from determine_reindex_operator_against_reference

Issue - State: open - Opened by graeme-winter about 1 year ago - 2 comments

#2447 - SSX (grid scan) spot finding not parallelized and using a lot of memory

Issue - State: open - Opened by JunAishima about 1 year ago - 7 comments

#2446 - Cmake build for CI

Pull Request - State: closed - Opened by ndevenish over 1 year ago

#2445 - Drop Python 3.8 support

Pull Request - State: closed - Opened by rjgildea over 1 year ago - 4 comments

#2444 - Update data_files.rst

Pull Request - State: closed - Opened by dagewa over 1 year ago - 2 comments

#2443 - reciprocal_lattice_viewer not working on Windows

Issue - State: closed - Opened by xjxrjx over 1 year ago - 13 comments
Labels: dials.reciprocal_lattice_viewer, windows

#2442 - DIALS 3.15.1

Pull Request - State: closed - Opened by DiamondLightSource-build-server over 1 year ago - 1 comment
Labels: upcoming release

#2441 - Ensure the `resolution_rings.fontsize` option of `dials.export_bitmaps` works on Macs

Pull Request - State: closed - Opened by dagewa over 1 year ago - 5 comments
Labels: backported

#2440 - dials.export_bitmaps fontsize doesn't work on Mac due to name of Arial.tff

Issue - State: closed - Opened by huwjenkins over 1 year ago - 5 comments

#2439 - Fix typo in name of method call in dials.reindex

Pull Request - State: closed - Opened by jbeilstenedmands over 1 year ago - 1 comment

#2438 - Mark xfel dependency on image grouping test

Pull Request - State: closed - Opened by rjgildea over 1 year ago - 1 comment

#2437 - Fix import template tests on windows

Pull Request - State: closed - Opened by rjgildea over 1 year ago - 1 comment

#2436 - DIALS logging does not output to root logger by default with no way to override

Issue - State: open - Opened by PrinceWalnut over 1 year ago

#2435 - Use pathlib for dials_regression tests

Pull Request - State: closed - Opened by ndevenish over 1 year ago

#2434 - Testing: Prevent dials_regression having trailing slash

Pull Request - State: closed - Opened by ndevenish over 1 year ago - 1 comment

#2433 - Replace use of procrunner with subprocess

Pull Request - State: closed - Opened by rjgildea over 1 year ago - 1 comment

#2432 - Don't print template for every image of a grid scan

Pull Request - State: closed - Opened by rjgildea over 1 year ago

#2431 - Switch off parameter auto-reduction for refinement special cases

Pull Request - State: closed - Opened by dagewa over 1 year ago - 1 comment

#2430 - dials.refine being able to turn off auto_reduce would be useful in certain cases

Issue - State: closed - Opened by PrinceWalnut over 1 year ago

#2429 - Improve ellipsoid partiality estimation in ssx_integrate

Pull Request - State: closed - Opened by jbeilstenedmands over 1 year ago

#2428 - Adjust test tolerance for dials.ssx_integrate take2

Pull Request - State: closed - Opened by jbeilstenedmands over 1 year ago

GitHub / dials/dials issues and pull requests