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 (prev) (not urgent)
• ND or DW: Cannot view reciprocal lattice using dials.reciprocal_lattice_viewer #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
• ND: Update CI to use nightly on dials/dxtbx serialtbx merges, let AB know when ready
• ND: Test cosym Wij PR on diamond systems and merge

Agenda

SerialTBX status update (prev).

• cctbx#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
• 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
• 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)