Ecosyste.ms: Issues

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GitHub / dials/dials issues and pull requests

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

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

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

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

#2476 - Add stereographic projection plots to dials.merge

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

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

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

#2474 - Support CMake environments in bootstrap.py

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

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

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

#2472 - Slice using batch offsets fix

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

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

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

#2470 - Log the experiment number when indexing multiple experiments

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

#2468 - DIALS 3.15.2

Pull Request - State: closed - Opened by DiamondLightSource-build-server over 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 over 1 year ago - 4 comments

#2466 - Update ssx_integrate test tolerance

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

#2465 - No datablocks

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

#2464 - dials.refine_bravais_lattice fails for multiple experiments

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

#2462 - Temporarily skip `test_model_background` on macos

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

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

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

#2459 - Revert "Remove force_2d option"

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

#2458 - Remove useless checkbox

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

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

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

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

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

#2454 - Remove as_grid_scan from dials.import

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

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

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

#2452 - Remove as_grid_scan from dials.import

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

#2448 - Inconsistent output from determine_reindex_operator_against_reference

Issue - State: open - Opened by graeme-winter over 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 over 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

#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

#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

#2426 - Fix obscure pickling bug affecting Python 3.11

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

#2422 - Remove force_2d option

Pull Request - State: closed - Opened by graeme-winter over 1 year ago - 5 comments

#2417 - Move core imageset_as_bitmaps out of cli

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

#2416 - dials.find_spots: force_2d does not

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

#2415 - masking ice rings

Issue - State: closed - Opened by ejfuentes over 1 year ago - 2 comments

#2413 - dials.import excessive output

Issue - State: closed - Opened by graeme-winter over 1 year ago - 3 comments

#2411 - Imageset slicing

Pull Request - State: closed - Opened by dagewa almost 2 years ago - 3 comments

#2409 - Handle no-conda environment, including msgpack

Pull Request - State: closed - Opened by phyy-nx almost 2 years ago - 3 comments

#2408 - Test changes for add_properties_table_to_scan dxtbx PR

Pull Request - State: closed - Opened by toastisme almost 2 years ago - 1 comment

#2407 - Make refinement working set more consistent

Pull Request - State: closed - Opened by toastisme almost 2 years ago - 1 comment

#2406 - `dials.model_background` only works with one experiment

Issue - State: open - Opened by dagewa almost 2 years ago - 1 comment

#2405 - `dials.model_background` fails for datasets that do not start at image 1

Issue - State: closed - Opened by dagewa almost 2 years ago - 1 comment

#2404 - Break the DIALS/xfel circular dependency

Pull Request - State: open - Opened by phyy-nx almost 2 years ago - 5 comments

#2403 - Avoid writing to dials_data in test_image_grouping.py

Pull Request - State: closed - Opened by jbeilstenedmands almost 2 years ago - 1 comment

#2402 - Update msgpack-c dependency to msgpack-cxx

Pull Request - State: closed - Opened by ndevenish almost 2 years ago

#2401 - dials.find_spots fails in 3.14.1

Issue - State: closed - Opened by KevinBattaile almost 2 years ago - 11 comments

#2400 - Silicon Mac installation issue

Issue - State: closed - Opened by lucajovine almost 2 years ago - 3 comments

#2399 - Incorrect definition for "inlier"

Issue - State: open - Opened by dagewa almost 2 years ago

#2397 - dials.export_bitmaps: display correct number of resolution rings

Pull Request - State: closed - Opened by rjgildea almost 2 years ago - 1 comment

#2396 - invert_rotation_axis option for dials.import does not work for > 1 scan

Issue - State: closed - Opened by graeme-winter almost 2 years ago - 2 comments

#2395 - dials 3.14.0 release error in reciprocal lattice viewer

Issue - State: closed - Opened by graeme-winter almost 2 years ago - 2 comments

#2394 - DIALS 3.14.1

Pull Request - State: closed - Opened by DiamondLightSource-build-server almost 2 years ago - 1 comment
Labels: upcoming release

#2393 - `dials.export_bitmaps`: optionally overlay ice rings

Pull Request - State: closed - Opened by rjgildea almost 2 years ago - 1 comment

#2392 - dials.export_bitmaps: scale resolution rings according to binning

Pull Request - State: closed - Opened by rjgildea almost 2 years ago - 1 comment
Labels: backported

#2390 - Remove cctbx.xfel dependency from dials.index

Pull Request - State: closed - Opened by jbeilstenedmands almost 2 years ago - 8 comments

#2389 - Remove cctbx.xfel dependency in dials.ssx_index

Issue - State: open - Opened by rjgildea almost 2 years ago - 1 comment

#2388 - include_images for dials scale

Issue - State: closed - Opened by cdavidowen almost 2 years ago

#2387 - DIALS tests seem to cause windows to appear but never render

Issue - State: closed - Opened by graeme-winter almost 2 years ago - 2 comments

#2385 - Hide system/cctbx_project warnings when building DIALS

Pull Request - State: closed - Opened by ndevenish almost 2 years ago - 1 comment

#2384 - DIALS 3.13.1

Pull Request - State: closed - Opened by DiamondLightSource-build-server almost 2 years ago - 1 comment
Labels: upcoming release, PR: merge conflicts

#2383 - Call `.astype(int)` on `.as_numpy_array()` result

Pull Request - State: closed - Opened by rjgildea almost 2 years ago - 2 comments

#2382 - test_match_by_hkle failure with pandas 2.0.0 on Windows

Issue - State: closed - Opened by rjgildea almost 2 years ago - 1 comment

#2381 - Increase tolerance to fix Jenkins test failure

Pull Request - State: closed - Opened by rjgildea almost 2 years ago - 2 comments

#2380 - Export MTZ with gemmi

Pull Request - State: closed - Opened by dagewa almost 2 years ago - 2 comments

#2379 - `dials.export` does not add `HKL_base` to MTZ

Issue - State: closed - Opened by dagewa almost 2 years ago - 2 comments

#2378 - Generate FreeR_flag column in merged mtz

Pull Request - State: closed - Opened by rjgildea almost 2 years ago - 1 comment

#2377 - Convert stills_process to use ImageSequence

Issue - State: open - Opened by dwpaley almost 2 years ago

#2376 - Document various different ways of excluding parts of datasets from processing

Issue - State: closed - Opened by dagewa almost 2 years ago - 1 comment

#2375 - Please can we kill stalebot?

Issue - State: closed - Opened by graeme-winter almost 2 years ago - 2 comments

#2374 - Use standard `exclude_images` syntax in `dials.find_spots` and `dials.integrate`

Pull Request - State: closed - Opened by dagewa almost 2 years ago - 15 comments

#2373 - Clarify coordinate system conventions

Pull Request - State: closed - Opened by dagewa almost 2 years ago - 1 comment

#2372 - Improve dials.ssx_index when unit cell values not known

Pull Request - State: closed - Opened by jbeilstenedmands almost 2 years ago - 2 comments

#2371 - Keep the experiment identifiers map when slicing a reflection table.

Pull Request - State: closed - Opened by jbeilstenedmands almost 2 years ago - 1 comment