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Crash writing history.json from dials.refine #1923

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dagewa opened this issue Nov 12, 2021 · 0 comments · Fixed by #1924
Closed

Crash writing history.json from dials.refine #1923

dagewa opened this issue Nov 12, 2021 · 0 comments · Fixed by #1924

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@dagewa
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dagewa commented Nov 12, 2021 

$ dials.refine ../refined.{expt,refl} correlation_plot.filename=corrgram.pdf track_condition_number=True history=history.json scan_varying=False

ended with

Traceback (most recent call last):
  File "/home/fcx32934/sw/cctbx/build/../modules/dials/command_line/refine.py", line 477, in <module>
    run()
  File "/home/fcx32934/sw/cctbx/conda_base/lib/python3.8/contextlib.py", line 75, in inner
    return func(*args, **kwds)
  File "/home/fcx32934/sw/cctbx/build/../modules/dials/command_line/refine.py", line 473, in run
    history.to_json_file(params.output.history)
  File "/home/fcx32934/sw/cctbx/modules/dials/algorithms/refinement/engine.py", line 134, in to_json_file
    json.dump(d, f)
  File "/home/fcx32934/sw/cctbx/conda_base/lib/python3.8/json/__init__.py", line 179, in dump
    for chunk in iterable:
  File "/home/fcx32934/sw/cctbx/conda_base/lib/python3.8/json/encoder.py", line 431, in _iterencode
    yield from _iterencode_dict(o, _current_indent_level)
  File "/home/fcx32934/sw/cctbx/conda_base/lib/python3.8/json/encoder.py", line 405, in _iterencode_dict
    yield from chunks
  File "/home/fcx32934/sw/cctbx/conda_base/lib/python3.8/json/encoder.py", line 405, in _iterencode_dict
    yield from chunks
  File "/home/fcx32934/sw/cctbx/conda_base/lib/python3.8/json/encoder.py", line 325, in _iterencode_list
    yield from chunks
  File "/home/fcx32934/sw/cctbx/conda_base/lib/python3.8/json/encoder.py", line 405, in _iterencode_dict
    yield from chunks
  File "/home/fcx32934/sw/cctbx/conda_base/lib/python3.8/json/encoder.py", line 438, in _iterencode
    o = _default(o)
  File "/home/fcx32934/sw/cctbx/conda_base/lib/python3.8/json/encoder.py", line 179, in default
    raise TypeError(f'Object of type {o.__class__.__name__} '
TypeError: Please report this error to dials-support@lists.sourceforge.net: Object of type double is not JSON serializable

The issue is that the parameter_correlation is kept in the journal as flex.double, which was fine when history was output as pickle, but breaks now it is JSON. The fix is easy, but should add a test as well.
dagewa added a commit that referenced this issue Nov 12, 2021
@dagewa
Avoid attempt to write flex.double to JSON
1c51c3d 
There is no performance advantage here, so use Python types from
the start and return a list not flex.double. Fixes #1923.
@dagewa dagewa mentioned this issue Nov 12, 2021
Merged
ndevenish added a commit that referenced this issue Jan 17, 2022
@dagewa @ndevenish
dials.refine: fix track_parameter_correlation crash bug (#1924)
22e933c 
Avoid attempt to write flex.double to JSON - use Python types from
the start and return a list not flex.double. Fixes #1923.

Additionally, add some typing from _packed_corr_mat backwards.

Co-authored-by: Nicholas Devenish <ndevenish@gmail.com>
ndevenish added a commit that referenced this issue Jan 25, 2022
@dagewa @ndevenish
dials.refine: fix track_parameter_correlation crash bug (#1924)
641fd62 
Avoid attempt to write flex.double to JSON - use Python types from
the start and return a list not flex.double. Fixes #1923.

Additionally, add some typing from _packed_corr_mat backwards.

Co-authored-by: Nicholas Devenish <ndevenish@gmail.com>
DiamondLightSource-build-server added a commit that referenced this issue Jan 25, 2022
@DiamondLightSource-build-server
DIALS 3.8.1
0a6683e 
Features
--------

- It is now possible to explicitly bootstrap all supported python versions. (#1988)

Bugfixes
--------

- ``dials.refine``: Fix crash from recording of parameter correlations in ``history.json``. (#1923)
- Correct reporting of phi angle in scan-varying model plots. (#1929)
- ``dials.sequence_to_stills``: correct error in the crystal model for scans that do not start from image 1. (#1933)
- `dials.show`: only show format class if meaningful (i.e. not Format or FormatMultiImage) (#1981)

Improved Documentation
----------------------

- Update some Cosym and resolution-related PHIL descriptions. (#1969)
Merged
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dials.refine: fix track_parameter_correlation bug dials/dials
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@dagewa