added new refine_ub route (#188)

Author: rosesyrett

src/diffcalc_api/models/ub.py

@@ -53,6 +53,14 @@ class AddReflectionParams(BaseModel):
     energy: float
 
 
+class RefineUbParams(BaseModel):
+    """Request body definition to refine the UB matrix."""
+
+    hkl: HklModel
+    position: PositionModel
+    wavelength: float
+
+
 class AddOrientationParams(BaseModel):
     """Request body definition to add an orientation of the UB calculation."""
 

src/diffcalc_api/routes/ub.py

@@ -30,6 +30,7 @@
     HklModel,
     MiscutModel,
     PositionModel,
+    RefineUbParams,
     SetLatticeParams,
     SphericalCoordinates,
     XyzModel,
@@ -597,6 +598,35 @@ async def get_u(
     return ArrayResponse(payload=content)
 
 
+@router.patch("/{name}/refine", response_model=InfoResponse)
+async def refine_ub(
+    name: str,
+    params: RefineUbParams = Body(...),
+    refine_lattice: bool = Query(default=False),
+    refine_u_matrix: bool = Query(default=False),
+    store: HklCalcStore = Depends(get_store),
+    collection: Optional[str] = Query(default=None, example="B07"),
+):
+    """Refine the UB matrix to match the diffractometer position to a given reflection.
+
+    Args:
+        name: the name of the hkl object to access within the store
+        params: the parameters to use to refine the UB matrix
+        store: accessor to the hkl object
+        collection: collection within which the hkl object resides
+
+    """
+    await service.refine_ub(
+        name, params, refine_lattice, refine_u_matrix, store, collection
+    )
+    return InfoResponse(
+        message=(
+            f"lattice has been set for UB calculation of crystal {name} in "
+            + f"collection {collection}"
+        )
+    )
+
+
 #######################################################################################
 #                            Surface and Reference Vectors                            #
 #######################################################################################

src/diffcalc_api/services/ub.py

@@ -20,6 +20,7 @@
     EditReflectionParams,
     HklModel,
     PositionModel,
+    RefineUbParams,
     SetLatticeParams,
     XyzModel,
 )
@@ -614,6 +615,38 @@ async def set_ub(
     await store.save(name, hklcalc, collection)
 
 
+async def refine_ub(
+    name: str,
+    params: RefineUbParams,
+    refine_lat: bool,
+    refine_u: bool,
+    store: HklCalcStore,
+    collection: Optional[str],
+) -> None:
+    """Refine the UB matrix to match the reflection given in the parameters.
+
+    Args:
+        name: the name of the hkl object to access within the store
+        params: parameters for refining the UB matrix.
+        store: accessor to the hkl object
+        collection: collection within which the hkl object resides
+    """
+    hklcalc = await store.load(name, collection)
+
+    ubcalc: UBCalculation = hklcalc.ubcalc
+    hkl: Tuple[float, float, float] = params.hkl.h, params.hkl.k, params.hkl.l
+
+    ubcalc.refine_ub(
+        hkl,
+        Position(**params.position.dict()),
+        params.wavelength,
+        refine_lattice=refine_lat,
+        refine_umatrix=refine_u,
+    )
+
+    await store.save(name, hklcalc, collection)
+
+
 #######################################################################################
 #                            Surface and Reference Vectors                            #
 #######################################################################################

tests/test_ubcalc.py

@@ -1,6 +1,7 @@
 import ast
 import math
 from ast import literal_eval
+from math import radians
 from typing import Dict
 
 import numpy as np
@@ -573,6 +574,43 @@ def test_set_ub():
     )
 
 
+def test_refine_ub():
+    ubcalc = UBCalculation()
+    hkl = HklCalculation(ubcalc, Constraints())
+    client = Client(hkl).client
+
+    ubcalc.set_lattice("LSMO_327", 3.78, 3.78, 20.1, 90, 90, 90)
+    ubcalc.add_orientation([0, 0, 1], [1, 0, 0])
+    ubcalc.add_orientation([0, 1, 0], [0, 1, 0])
+
+    ubcalc.calc_ub()
+
+    ubcalc.n_phi = [0.0, 1.0, 0.0]
+
+    ubcalc.set_miscut([1.0, 0.0, 0.0], radians(3))
+
+    ub_after_miscut = ubcalc.UB
+
+    client.patch(
+        "/ub/test/refine?collection=B07",
+        json={
+            "hkl": {"h": 0, "k": 0, "l": 2},
+            "position": {
+                "mu": 100.0,
+                "delta": 0.0,
+                "nu": 82.9408,
+                "eta": 0.0,
+                "chi": 30.31,
+                "phi": 0.0,
+            },
+            "wavelength": 13.3109,
+        },
+        params={"refine_lattice": 1, "refine_u_matrix": 1},
+    )
+
+    assert np.any(ubcalc.UB != ub_after_miscut)
+
+
 @pytest.mark.parametrize(
     ["url", "body", "property"],
     [