---
name: DIALS core meeting 2023-06-01
tags: core meeting
---

# 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](https://github.com/cctbx/dxtbx/pull/504)~~ [#570](https://github.com/cctbx/dxtbx/pull/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`](https://github.com/dials/dials/issues/2320)) ([prev](https://dials.github.io/kb/core/2023-03-09#dialscosym-applies-an-incompatible-reindexing-operator))
- [x] **ND**: Look at (CMake?) issues on [dials#2113](https://github.com/dials/dials/pull/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](https://github.com/cctbx/dxtbx/pull/612) is reasonable
- [ ] **DP**: Add msgpack "hot" path to include environment in cctbx ([prev](https://dials.github.io/kb/core/2023-05-04#msgpack-httpsgithubcomdialsdialspull2409))

## Agenda

### NX Writer! ([prev](https://dials.github.io/kb/core/2023-05-04#nx-writer-prev), [prev](https://dials.github.io/kb/core/2023-03-09#aob))

- https://github.com/cctbx/dxtbx/pull/615
- Dependent on [dxtbx#612 "Multidimensional Images"](https://github.com/cctbx/dxtbx/pull/612)
- 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](https://github.com/cctbx/dxtbx/issues/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)