DIALS core meeting 2023-06-01

Previous Actions

• ND: PR to remove std::string support for messagepack from dials code
• ND Investigate getting psana tests running on the DIALS xfel-regression testing
• Dropping Data Blocks (#504 #570)
  • ND: Look at DIALS failures and work out what needs to be migrated
• RG: Investigate dials.cosym applies an incompatible reindexing operator (dials/2320) (prev)
• ND: Look at (CMake?) issues on dials#2113
  • Was issue relating to unguarded header files in scitbx. Deployed same fix applied to dials previously.
  • Merged
• AB: Check test case on Multidimensional Images dxtbx#612 is reasonable
• DP: Add msgpack “hot” path to include environment in cctbx (prev)

Agenda

NX Writer! (prev, prev)

• https://github.com/cctbx/dxtbx/pull/615
• Dependent on dxtbx#612 “Multidimensional Images”
  • Richard added basic test case -> Aaron is ok?

Removing circular xfel dependencies with serialtbx

• Set of PRs to implement
  • CCTBX: https://github.com/cctbx/cctbx_project/pull/872 - contains descriptions of all changes made
  • dxtbx: https://github.com/cctbx/dxtbx/pull/627
  • dials: https://github.com/dials/dials/pull/2404
  • iota: https://github.com/ssrl-px/iota/pull/5
  • xfel_regression https://gitlab.com/cctbx/xfel_regression/-/merge_requests/10
• We all need to look at things
  • Schedule some time next week at DLS to look over these PRs
• ND reviewed, looks OK, please can we hold off from merging until the dust settles from scan and polybeam changes.
• ASB happy for this to hold off a couple weeks for non-technical reasons

Polychromatic Beam

• https://github.com/cctbx/dxtbx/pull/621
• Discuss in DLS meeting to look over circular dependencies
• Merge next meeting if not looked over
• DGW to look at next week
• People have looked over it, looks good to them, changes made as suggested
• Action ND to merge
• Addressing internally, push this off Agenda for now

• Scans

• https://github.com/cctbx/dxtbx/pull/620
• Same as above. ND: Get people to look at it
• Made suggested changes, some unresolved conversations
• after open questions resolved, merge
• Addressing internally, push this off Agenda for now

NXMX

• Discussion about dynamic masking in NXmx.
• Defer until DP back, recollection on this discussion is fuzzy
• Possibly:
  • https://github.com/dials/nxmx/pull/17
  • https://github.com/cctbx/dxtbx/pull/629
• Action: RG to have look at

xia2.multiplex fails because “Duplicate batch offsets detected”

• Longstanding (>3 years) issue: https://github.com/xia2/xia2/issues/430
• Now getting reports from real user data
• Potential solution suggested to never share Scan objects cctbx/dxtbx#152
• implement non-sharing of Scan objects - no logic for doing so, since readonly?
• JBE: Do this

Imageset slicing broken

• https://github.com/cctbx/dxtbx/issues/633
• Fix now ready at https://github.com/cctbx/dxtbx/pull/634 and https://github.com/dials/dials/pull/2411
• Anyone else want to look?
• When merged, will require reversion of changes to azure-pipelines YML files to checkout specific dxtbx branch
• DGW thinks this one can be merged without contention - needs sync’d repo merge
• rebase this branch on top of Scans branch & run tests
• Tie off loose ends and merge internally

bit_depth_imageset

• Forthcoming NIAC meeting, GW proposal to add should pass
• Pragmatism!

AOB?

Note that interesting workshop at CHESS coming up -> https://indico.classe.cornell.edu/event/2248/overview

Congratulations to RG on new position

Negativity

• Treatment of negative data / pixel values in Jungfrau data: what is best practice?
• DGW: Need to select simple background subtraction in integration
• AB: Have used lots of CSPAD data with negatives, simple background is useful
  • Precedent for adding a pedestal that is subtracted (ADSC)

Next meeting

Thursday, June 15th, 4pm (BST), 8am (PDT)