Merge pull request #273 from bluesky/215-restore_reflections

restore_reflections() use renamed motor axes if so defined

RELEASE_NOTES.rst

@@ -11,11 +11,21 @@ Release History
     Deprecations
     Contributors
 
-v1.1 (expected 2024)
+v1.2 (expected 2024)
 ======================================
 
 User-requested changes
 
+v1.1 (expected 2023-12)
+======================================
+
+Add new geometries from upstream *libhkl*.
+
+Fixes
+-----
+
+* ``util.restore_reflections()`` use renamed motor axes if so defined.
+
 v1.0.4 (released 2023-10-06)
 ======================================
 

hkl/tests/test_util.py

@@ -6,6 +6,75 @@
 NO_SUCH_PACKAGE_NAME = "no-such-package"
 
 
+@pytest.fixture(scope="function")
+def cat():
+    import databroker
+
+    yield databroker.temp().v2
+
+
+@pytest.fixture(scope="function")
+def RE(cat):
+    import bluesky
+
+    engine = bluesky.RunEngine()
+    engine.subscribe(cat.v1.insert)
+    yield engine
+
+
+@pytest.fixture(scope="function")
+def fourc():
+    """4-circle with renamed axes and oriented sample."""
+    from hkl import E4CV, SimMixin
+    from ophyd import Component
+    from ophyd import SoftPositioner
+
+    class FourCircle(SimMixin, E4CV):
+        theta = Component(SoftPositioner, kind="hinted", init_pos=0)
+        chi = Component(SoftPositioner, kind="hinted", init_pos=0)
+        phi = Component(SoftPositioner, kind="hinted", init_pos=0)
+        ttheta = Component(SoftPositioner, kind="hinted", init_pos=0)
+
+    fourc = FourCircle("", name="fourc")
+    # rename the physical axes
+    fourc.calc.physical_axis_names = {
+        # E4CV: local
+        "omega": "theta",
+        "chi": "chi",
+        "phi": "phi",
+        "tth": "ttheta",
+    }
+
+    # fourc.wait_for_connection()
+    fourc._update_calc_energy()
+    crystal_setup(fourc)
+
+    yield fourc
+
+
+def crystal_setup(diffractometer):
+    from hkl import Lattice
+
+    diffractometer.calc.wavelength = 1.0
+    a0 = 5.4321
+    # fmt: off
+    diffractometer.calc.new_sample(
+        "vibranium",
+        lattice=Lattice(a=a0, b=a0, c=a0, alpha=90, beta=90, gamma=90)
+    )
+
+    diffractometer.calc.sample.add_reflection(
+        1, 2, 3,
+        position=diffractometer.calc.Position(
+            ttheta=60,
+            theta=40,
+            chi=0,
+            phi=0,
+        ),
+    )
+    # fmt: on
+
+
 def test__package_info_states():
     assert hkl.util._package_info is None
     hkl.util.get_package_info("hkl")
@@ -74,3 +143,53 @@ def test_software_versions_items(package_name, minimum_version):
         assert v_package >= version.parse(minimum_version)
     else:
         assert package_name in ("hklpy", NO_SUCH_PACKAGE_NAME)
+
+
+def test_issue215(cat, RE, fourc):
+    """restore_reflections(orientation, fourc) cannot find renamed positioner."""
+    from bluesky import plans as bp
+
+    canonical_names = "omega chi phi tth".split()
+    our_names = "theta chi phi ttheta".split()
+    assert our_names != canonical_names
+    assert fourc.calc.physical_axis_names != canonical_names
+    assert fourc.calc.physical_axis_names == our_names
+
+    problem_reflection_dict = {
+        "reflection": {"h": 1.0, "k": -3.0, "l": -1.0},
+        "flag": 1,
+        "wavelength": 1.1169734383241103,
+        "position": {
+            "omega": -8.208399999999983,
+            "chi": -47.47651999999994,
+            "phi": -5.684341886080802e-14,
+            "tth": 25.09473789610388,
+        },
+        "orientation_reflection": False,
+    }
+    problem_positioner_names = list(problem_reflection_dict["position"].keys())
+    assert problem_positioner_names == canonical_names
+
+    assert len(cat) == 0
+    uids = RE(bp.count([fourc]))
+    assert len(uids) == 1
+    assert len(cat) == 1
+
+    orientation = hkl.util.run_orientation_info(cat[-1])
+    assert isinstance(orientation, dict)
+    assert fourc.name in orientation
+    # assert list(orientation.keys()) == []
+
+    orient = orientation[fourc.name]
+    assert orient["_reals"] != canonical_names
+    assert orient["_reals"] == our_names
+    for reflection in orient["reflections_details"]:
+        assert list(reflection["position"].keys()) == canonical_names
+
+    success = False
+    try:
+        # since it is just a problem of motor names in reflections ...
+        hkl.util.restore_reflections(orient, fourc)
+        success = True
+    finally:
+        assert success, "Could not restore orientation reflections."

hkl/util.py

@@ -423,6 +423,10 @@ def restore_reflections(orientation, diffractometer):
     pseudos = orientation["_pseudos"]
     reals = orientation["_reals"]
     orientation_reflections = []
+    # might be renamed axes
+    renaming = diffractometer.calc._axis_name_to_original
+    if len(renaming) > 0:
+        reals = [renaming[k] for k in reals]
 
     for ref_base in orientation["reflections_details"]:
         # every reflection has its own wavelength