---
# System prepended metadata

title: DIALS core meeting 2023-10-05
tags: [core meeting]

---

---
name: DIALS core meeting 2023-10-05
tags: core meeting
---

# DIALS core meeting 2023-10-05

## 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
- [ ] **JBE:** Solve  "multiplex: Duplicate Batch offsets detected" [xia2#430](https://github.com/xia2/xia2/issues/430) ([prev](https://dials.github.io/kb/core/2023-06-15#xia2multiplex-fails-because-duplicate-batch-offsets-detected)) (not urgent)
- [ ] **ND** or **DW**: Cannot view reciprocal lattice using dials.reciprocal_lattice_viewer [#2443](https://github.com/dials/dials/issues/2443)
    - Probably needs someone to dig into windows gltbx behaviour, or at least work out where issue lies
    - Reports from CCP4 workshop that people are having issue on latest ubuntu
- **ND**: Investigate using stable-nightly conda builds of cctbx (e.g. cctbx tests) longer term
- [x] **ND**: Update CI to use nightly on dials/dxtbx serialtbx merges, let AB know when ready
- [x] ~~**ND**: Test cosym Wij PR on diamond systems and merge~~

## Agenda


### SerialTBX status update ([prev](https://dials.github.io/kb/core/2023-06-15#removing-circular-xfel-dependencies-with-serialtbx)).
- [cctbx#872](https://github.com/cctbx/cctbx_project/pull/872) now marked ready for review
    - Awaiting NKS approval
- dxtbx will break when changes applied, until next cctbx release
    - Planning to switch to cctbx nightly for dxtbx/dials tests
- All went through successfully, after a couple of days of nightly tweaks

### small cell serialtbx
https://github.com/dials/dials/pull/2477 - small cell code did not make it into serialtbx yet.

- AB: Did small cell xfel recently. Had sequences indexer success over stills.
    - Ran sweeps indexer. Many bad indexing solutions, suspect differences down to index assignment tolerance at 0.3 hkl by default
    - Can still move code into serial toolbox, but don't think best end solution is obvious yet
 
### DIALS-support "Error importing .cbf files using DIALS"
- [dials#2488](https://github.com/dials/dials/issues/2488)
-  Pilatus3 1M at BL02B1, SPRING-8 appears to be transposed!!??!?
- Graeme got some info from Kunio, Takanori seems to be looking at
- Seems to be no explanation for the very odd inverted-detector behaviour
    - Done for Crysalis convention
    - Takanori appears to have Format class in hand
    - Okay to ignore the exceptionally different files as no timestamp and no longer generated
- Take a look at state of things in a couple of weeks



### dials.cosym finds the right operator but puts it wrongly
- [dials#2486](https://github.com/dials/dials/issues/2486)
- Draft PR at https://github.com/dials/dials/pull/2497
- Pulled in other problems that need to be worked through
- Potential fix opened a large box of problems
- GW believes needs a rethink and a rewrite and patching is essentially impossible
- GW and DP to discuss on 27th
    - Met! DP has made some progress but had other obligations


### Add properties table to scan
- https://github.com/cctbx/dxtbx/pull/620
- Outstanding review request from GW
    - Approve. **ND to sort out merges.**

## AOB?

### Add support for Pilatus 4
- GW has data, has promised to ensure works - apropos to this the current issue is 

```
--------------------------------------------------------------------------------
Finding strong spots in imageset 0
--------------------------------------------------------------------------------

Finding spots in image 1 to 240...
Setting chunksize=20
Extracting strong pixels from images
 Using multiprocessing with 1 parallel job(s)

Traceback (most recent call last):
  File "/Users/graeme/git/dials/build/../modules/dials/src/dials/command_line/find_spots.py", line 242, in <module>
    run()
  File "/Users/graeme/git/dials/conda_base/lib/python3.10/contextlib.py", line 79, in inner
    return func(*args, **kwds)
  File "/Users/graeme/git/dials/build/../modules/dials/src/dials/command_line/find_spots.py", line 236, in run
    results = do_spotfinding(experiments, params)
  File "/Users/graeme/git/dials/build/../modules/dials/src/dials/command_line/find_spots.py", line 127, in do_spotfinding
    reflections = flex.reflection_table.from_observations(experiments, params)
  File "/Users/graeme/git/dials/modules/dials/src/dials/array_family/flex_ext.py", line 183, in from_observations
    return spotfinder.find_spots(experiments)
  File "/Users/graeme/git/dials/modules/dials/src/dials/algorithms/spot_finding/finder.py", line 704, in find_spots
    table, hot_mask = self._find_spots_in_imageset(imageset)
  File "/Users/graeme/git/dials/modules/dials/src/dials/algorithms/spot_finding/finder.py", line 820, in _find_spots_in_imageset
    r, h = extract_spots(imageset[j0:j1])
  File "/Users/graeme/git/dials/modules/dials/src/dials/algorithms/spot_finding/finder.py", line 417, in __call__
    return self._find_spots(imageset)
  File "/Users/graeme/git/dials/modules/dials/src/dials/algorithms/spot_finding/finder.py", line 519, in _find_spots
    result = function(task)
  File "/Users/graeme/git/dials/modules/dials/src/dials/algorithms/spot_finding/finder.py", line 79, in __call__
    mask = self.imageset.get_mask(index)
RuntimeError: Please report this error to dials-support@lists.sourceforge.net: dxtbx Internal Error: /Users/graeme/git/dials/modules/dxtbx/src/dxtbx/model/panel.h(397): DXTBX_ASSERT(data.accessor()[1] == image_size_[0]) failure.
```

### Conda-forge renaming of boost packages

- https://github.com/conda-forge/cctbx-base-feedstock/pull/74/files
- Will need applying to downstream dials, dxtbx
- conda envs


### Next meeting

Thursday, October 19th, 4pm (BST), 8am (PDT)
