dials.symmetry fails on multi-sweep centred data set due to instability of cctbx minimum-cell reduction routine

[graeme-winter]

DIALS (2018) Acta Cryst. D74, 85-97. https://doi.org/10.1107/S2059798317017235
DIALS 2.0.2-g25fc2fc43-release
The following parameters have been modified:

input {
  experiments = integrated.expt
  reflections = integrated.refl
}

Detected existence of a multi-dataset reflection table 
containing 4 datasets. 
...
Incompatible unit cell: (4.80801, 12.8219, 16.5573, 73.5157, 90.0253, 79.2275)
      median unit cell: (4.80765, 12.8188, 16.5583, 106.445, 90.0189, 100.786)

[graeme-winter]

Processed stepwise in /dls/tmp/gw56/i19-check/raw - integrated.(refl,expt) in there will reproduce issue.

Reproduce issue on master.

Input fine:

cs03r-sc-serv-16 raw :( $ dials.show integrated.expt |grep Unit
    Unit cell: (4.8052(4), 12.8081(10), 16.5449(12), 106.458(3), 90.007(2), 100.777(2))
    Unit cell: (4.8080(4), 12.8219(10), 16.5573(12), 106.484(3), 90.025(2), 100.773(2))
    Unit cell: (4.8097(4), 12.8156(10), 16.5593(12), 106.490(3), 90.017(2), 100.804(3))
    Unit cell: (4.8073(3), 12.8224(10), 16.5604(12), 106.432(2), 90.021(2), 100.795(2))

suspect issue is it maps one to mC lattice then finds others don't match, as mapping back is ambiguous.

[rjgildea]

Rather unhelpfully this works just fine on mac:

$ dials.symmetry integrated.*
$ dials.show symmetrized.expt | grep cell
    Unit cell: (25.164, 4.805, 16.545, 90.000, 106.764, 90.000)
    Unit cell: (25.192, 4.808, 16.557, 90.000, 106.794, 90.000)
    Unit cell: (25.177, 4.810, 16.559, 90.000, 106.800, 90.000)
    Unit cell: (25.191, 4.807, 16.560, 90.000, 106.741, 90.000)

[rjgildea]

And even more unhelpfully, I can't reproduce it with my linux sources:

$ dials.symmetry /dls/tmp/gw56/i19-check/raw/integrated.{refl,expt}
$ dials.show symmetrized.expt | grep cell
    Unit cell: (25.164, 4.805, 16.545, 90.000, 106.764, 90.000)
    Unit cell: (25.192, 4.808, 16.557, 90.000, 106.794, 90.000)
    Unit cell: (25.177, 4.810, 16.559, 90.000, 106.800, 90.000)
    Unit cell: (25.191, 4.807, 16.560, 90.000, 106.741, 90.000)

[rjgildea]

I don't think this is a general issue, but just a particular corner case with this specific dataset caused by the lack of robustness of the cctbx minimum-cell reduction routine. In fact this case only fails if the code is compiled on RHEL6, but works as expected on RHEL7 and mac.

[rjgildea]

See https://github.com/cctbx/cctbx_project/issues/419

[rjgildea]

Fixed by https://github.com/dials/dials/commit/6dacce377f10557624fca55a5fca06bb6cdfa87b

[graeme-winter]

Appears to be broken on Python 3.6.7

Grey-Area dials :) [master] $ pytest --regression test/command_line/test_symmetry.py::test_change_of_basis_ops_to_minimum_cell_1037
Test session starts (platform: darwin, Python 3.6.7, pytest 4.6.4, pytest-sugar 0.9.2)
rootdir: /Users/graeme/svn/cctbx/modules/dials, inifile: pytest.ini
plugins: sugar-0.9.2, mock-2.0.0, forked-1.1.2, xdist-1.31.0, dials-data-2.0.61
collecting ... 

―――――――――――――――― test_change_of_basis_ops_to_minimum_cell_1037 ―――――――――――――――――

mocker = <pytest_mock.plugin.MockFixture object at 0x1151f77b8>

    def test_change_of_basis_ops_to_minimum_cell_1037(mocker):
        # See https://github.com/dials/dials/issues/1037

        input_ucs = [
            (
                4.805202948916906,
                12.808064769657364,
                16.544899201125446,
                106.45808502003258,
                90.0065567098825,
                100.77735674275475,
            ),
            (
                4.808011343212577,
                12.821894835790472,
                16.557339561965573,
                106.48431244651402,
                90.0252848479048,
                100.77252933676507,
            ),
            (
                4.8096632137789985,
                12.815648858527567,
                16.55931712239122,
                106.48990701341536,
                90.01703141314147,
                100.80397887485773,
            ),
            (
                4.807294085194974,
                12.822386757910516,
                16.560411742466663,
                106.43185845358086,
                90.02067929544215,
                100.79522302759383,
            ),
        ]

        # Setup the input experiments and reflection tables
        expts = ExperimentList()
        for uc in input_ucs:
            uc = uctbx.unit_cell(uc)
            sg = sgtbx.space_group_info("P1").group()
            B = scitbx.matrix.sqr(uc.fractionalization_matrix()).transpose()
            expts.append(Experiment(crystal=Crystal(B, space_group=sg, reciprocal=True)))

        # We want to spy on the return value of this function
        mocker.spy(symmetry, "unit_cells_are_similar_to")

        # Actually run the method we are testing
        cb_ops = change_of_basis_ops_to_minimum_cell(
            expts, max_delta=5, relative_length_tolerance=0.05, absolute_angle_tolerance=2
        )
>       assert symmetry.unit_cells_are_similar_to.return_value is True
E       AssertionError: assert <MagicMock name='unit_cells_are_similar_to()' id='4652289720'> is True
E        +  where <MagicMock name='unit_cells_are_similar_to()' id='4652289720'> = <function unit_cells_are_similar_to at 0x115503488>.return_value
E        +    where <function unit_cells_are_similar_to at 0x115503488> = symmetry.unit_cells_are_similar_to

test/command_line/test_symmetry.py:301: AssertionError

 test/command_line/test_symmetry.py ⨯                            100% ██████████

Results (1.49s):
       1 failed
         - test/command_line/test_symmetry.py:248 test_change_of_basis_ops_to_minimum_cell_1037

[graeme-winter]

Joy - this test proves to be unstable - hooray for numerical stability

Today it works - on the same machine, same build:

Grey-Area dials :) [master] $ pytest --regression test/command_line/test_symmetry.py::test_change_of_basis_ops_to_minimum_cell_1037
Test session starts (platform: darwin, Python 3.6.7, pytest 4.6.4, pytest-sugar 0.9.2)
rootdir: /Users/graeme/svn/cctbx/modules/dials, inifile: pytest.ini
plugins: sugar-0.9.2, mock-2.0.0, forked-1.1.2, xdist-1.31.0, dials-data-2.0.61
collecting ... 
 test/command_line/test_symmetry.py ✓                            100% ██████████

Results (1.42s):
       1 passed

[picca]

I can confirm that I have this bug on Debian unstable

$ LIBTBX_BUILD=/usr/lib/python3/dist-packages/ pytest-3 test/command_line/test_symmetry.py::test_change_of_basis_ops_to_minimum_cell_1037
================================================================================== test session starts ==================================================================================
platform linux -- Python 3.8.3rc1, pytest-4.6.9, py-1.8.1, pluggy-0.13.0
rootdir: /usr/lib/python3/dist-packages/dials, inifile: pytest.ini
plugins: requests-mock-1.7.0, mock-1.10.4
collected 1 item                                                                                                                                                                        

test/command_line/test_symmetry.py F                                                                                                                                              [100%]

======================================================================================= FAILURES ========================================================================================
_____________________________________________________________________ test_change_of_basis_ops_to_minimum_cell_1037 _____________________________________________________________________

mocker = <pytest_mock.MockFixture object at 0x7f014701de80>

    def test_change_of_basis_ops_to_minimum_cell_1037(mocker):
        # See https://github.com/dials/dials/issues/1037

        input_ucs = [
            (
                4.805202948916906,
                12.808064769657364,
                16.544899201125446,
                106.45808502003258,
                90.0065567098825,
                100.77735674275475,
            ),
            (
                4.808011343212577,
                12.821894835790472,
                16.557339561965573,
                106.48431244651402,
                90.0252848479048,
                100.77252933676507,
            ),
            (
                4.8096632137789985,
                12.815648858527567,
                16.55931712239122,
                106.48990701341536,
                90.01703141314147,
                100.80397887485773,
            ),
            (
                4.807294085194974,
                12.822386757910516,
                16.560411742466663,
                106.43185845358086,
                90.02067929544215,
                100.79522302759383,
            ),
        ]

        # Setup the input experiments and reflection tables
        expts = ExperimentList()
        for uc in input_ucs:
            uc = uctbx.unit_cell(uc)
            sg = sgtbx.space_group_info("P1").group()
            B = scitbx.matrix.sqr(uc.fractionalization_matrix()).transpose()
            expts.append(Experiment(crystal=Crystal(B, space_group=sg, reciprocal=True)))

        # We want to spy on the return value of this function
        mocker.spy(symmetry, "unit_cells_are_similar_to")

        # Actually run the method we are testing
        cb_ops = change_of_basis_ops_to_minimum_cell(
            expts, max_delta=5, relative_length_tolerance=0.05, absolute_angle_tolerance=2
        )
        import pytest_mock

        if pytest_mock.version.startswith("1."):
>           assert symmetry.unit_cells_are_similar_to.return_value is True
E           AssertionError: assert <MagicMock name='unit_cells_are_similar_to()' id='139643462811408'> is True
E            +  where <MagicMock name='unit_cells_are_similar_to()' id='139643462811408'> = <function unit_cells_are_similar_to at 0x7f0146fdb8b0>.return_value
E            +    where <function unit_cells_are_similar_to at 0x7f0146fdb8b0> = symmetry.unit_cells_are_similar_to

test/command_line/test_symmetry.py:369: AssertionError

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. The label will be removed automatically if any activity occurs. Thank you for your contributions.

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. The label will be removed automatically if any activity occurs. Thank you for your contributions.