ssx_integrate: catch ValueError

[rjgildea]

A ValueError occasionally arise from rstbx parameter_reduction on setting the orientation

[codecov]

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  Files         593      593              
  Lines       68542    68548       +6     
  Branches     9213     9213              
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+ Partials     2132     2130       -2     

[jbeilstenedmands]

Do you know at which precise point the ValueError can be raised? I think my preference would be to catch at the precise call and reraise as a RuntimeError, to avoid hiding any other potential failures/bugs that may cause ValueErrors.

[rjgildea]

Do you know at which precise point the ValueError can be raised? I think my preference would be to catch at the precise call and reraise as a RuntimeError, to avoid hiding any other potential failures/bugs that may cause ValueErrors.

Running:

$ cat run.sh
module load dials/latest
xia2.ssx template=/path/to/images_#####.cbf \
  reference_geometry=/path/to/reference_geometry.expt \
  unit_cell=<unit_cell> \
  space_group=P222

gives the following traceback:

multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/conda_base/lib/python3.10/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/conda_base/lib/python3.10/multiprocessing/pool.py", line 48, in mapstar
    return list(map(*args))
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/build/../modules/dials/src/dials/command_line/ssx_integrate.py", line 251, in wrap_integrate_one
    expt, refls, collector = process_one_image(
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/build/../modules/dials/src/dials/command_line/ssx_integrate.py", line 174, in process_one_image
    experiment, table, collector = integrator.run(experiment, table)
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/modules/dials/src/dials/algorithms/integration/ssx/ellipsoid_integrate.py", line 110, in run
    experiment, table, refiner_output = self.refine(
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/modules/dials/src/dials/algorithms/integration/ssx/ellipsoid_integrate.py", line 184, in refine
    expts, refls, output_data = run_ellipsoid_refinement(
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/modules/dials/src/dials/algorithms/profile_model/ellipsoid/algorithm.py", line 461, in run_ellipsoid_refinement
    _ = refine_crystal(
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/modules/dials/src/dials/algorithms/profile_model/ellipsoid/algorithm.py", line 342, in refine_crystal
    refiner.refine()
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/modules/dials/src/dials/algorithms/profile_model/ellipsoid/refiner.py", line 899, in refine
    self.refine_fisher_scoring()
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/modules/dials/src/dials/algorithms/profile_model/ellipsoid/refiner.py", line 928, in refine_fisher_scoring
    self.ml.solve()
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/modules/dials/src/dials/algorithms/profile_model/ellipsoid/refiner.py", line 597, in solve
    x = self.gradient_search(x0)
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/modules/dials/src/dials/algorithms/profile_model/ellipsoid/refiner.py", line 660, in gradient_search
    return gradient_descent(f, df, x0, max_iter=1, tolerance=self.tolerance)
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/modules/dials/src/dials/algorithms/profile_model/ellipsoid/refiner.py", line 544, in gradient_descent
    p = -matrix.col(df(x0))
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/modules/dials/src/dials/algorithms/profile_model/ellipsoid/refiner.py", line 658, in df
    return -self.score(x)
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/modules/dials/src/dials/algorithms/profile_model/ellipsoid/refiner.py", line 733, in score
    self.model.active_parameters = x
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/modules/dials/src/dials/algorithms/profile_model/ellipsoid/parameterisation.py", line 560, in active_parameters
    self.B_params = temp
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/modules/dials/src/dials/algorithms/profile_model/ellipsoid/parameterisation.py", line 465, in B_params
    self._B_parameterisation.set_param_vals(tuple(float(i) for i in params))
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/modules/dials/src/dials/algorithms/refinement/parameterisation/model_parameters.py", line 255, in set_param_vals
    self.compose()
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/modules/dials/src/dials/algorithms/refinement/parameterisation/crystal_parameters.py", line 206, in compose
    newB, self._dstate_dp = self._compose_core([p.value for p in self._param])
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/modules/dials/src/dials/algorithms/refinement/parameterisation/crystal_parameters.py", line 135, in _compose_core
    S.set_orientation(orientation=self._model.get_B())
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/modules/cctbx_project/rstbx/symmetry/constraints/parameter_reduction.py", line 38, in set_orientation
    self.orientation = which_setting[select.index(True)]
ValueError: True is not in list
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/build/../modules/dials/src/dials/command_line/ssx_integrate.py", line 482, in <module>
    run()
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/conda_base/lib/python3.10/contextlib.py", line 79, in inner
    return func(*args, **kwds)
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/build/../modules/dials/src/dials/command_line/ssx_integrate.py", line 428, in run
    for i, (int_expt, int_refl, aggregator) in enumerate(
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/build/../modules/dials/src/dials/command_line/ssx_integrate.py", line 360, in run_integration
    integrated_experiments, integrated_reflections = process_batch(
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/build/../modules/dials/src/dials/command_line/ssx_integrate.py", line 309, in process_batch
    results: List[IntegrationResult] = pool.map(
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/conda_base/lib/python3.10/multiprocessing/pool.py", line 367, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
  File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20230224/conda_base/lib/python3.10/multiprocessing/pool.py", line 774, in get
    raise self._value
ValueError: Please report this error to dials-support@lists.sourceforge.net: True is not in list

[jbeilstenedmands]

Verified the above fix on the data in question