compute mu

src/diffpy/utils/tools.py

@@ -1,5 +1,6 @@
 import importlib.metadata
 import json
+import warnings
 from copy import copy
 from pathlib import Path
 
@@ -210,29 +211,45 @@ def get_package_info(package_names, metadata=None):
     return metadata
 
 
-def compute_mu_using_xraydb(sample_composition, energy, density=None, packing_fraction=1):
+def compute_mu_using_xraydb(sample_composition, energy, sample_mass_density=None, packing_fraction=None):
     """Compute the attenuation coefficient (mu) using the XrayDB database.
 
     Computes mu based on the sample composition and energy.
-    User can provide a measured density or an estimated packing fraction.
-    Specifying the density is recommended, though not required for some pure or standard materials.
+    User should provide a sample mass density or a packing fraction.
+    If neither density nor packing fraction is specified, or if both are specified, a ValueError will be raised.
     Reference: https://xraypy.github.io/XrayDB/python.html#xraydb.material_mu.
 
     Parameters
     ----------
     sample_composition : str
         The chemical formula or the name of the material.
     energy : float
-        The energy in keV.
-    density : float, optional, Default is None
+        The energy of the incident x-rays in keV.
+    sample_mass_density : float, optional, Default is None
         The mass density of the packed powder/sample in gr/cm^3.
-    packing_fraction : float, optional, Default is 1
+    packing_fraction : float, optional, Default is None
         The fraction of sample in the capillary (between 0 and 1).
 
     Returns
     -------
     mu : float
         The attenuation coefficient mu in mm^{-1}.
     """
-    mu = material_mu(sample_composition, energy * 1000, density=density, kind="total") * packing_fraction / 10
+    if (sample_mass_density is None and packing_fraction is None) or (
+        sample_mass_density is not None and packing_fraction is not None
+    ):
+        raise ValueError(
+            "You must specify either sample_mass_density or packing_fraction, but not both. "
+            "Please rerun specifying only one."
+        )
+    if sample_mass_density is not None:
+        mu = material_mu(sample_composition, energy * 1000, density=sample_mass_density, kind="total") / 10
+    else:
+        warnings.warn(
+            "Warning: Density is set to None if a packing fraction is specified, "
+            "which may cause errors for some materials. "
+            "We recommend specifying sample mass density for now. "
+            "Auto-density calculation is coming soon."
+        )
+        mu = material_mu(sample_composition, energy * 1000, density=None, kind="total") * packing_fraction / 10
     return mu

tests/test_tools.py

@@ -171,59 +171,61 @@ def test_get_package_info(monkeypatch, inputs, expected):
     "inputs, expected_mu",
     [
         # Test whether the function returns the correct mu
-        (  # C1: No density or packing fraction (only for known material), expect to get mu from database
+        (  # C1: Composition, energy, and mass density provided, expect to get mu based on mass density
+            # 1. Fully dense mass density
+            {"sample_composition": "quartz", "energy": 10, "sample_mass_density": 2.65},
+            5.0368,
+        ),
+        (  # 2. Measured mass density
             {
-                "sample_composition": "H2O",
-                "energy": 10,
+                "sample_composition": "ZrO2",
+                "energy": 17.445,
+                "sample_mass_density": 1.009,
             },
-            0.5330,
+            1.2522,
         ),
-        (  # C2: Packing fraction (=0.5) provided only (only for known material)
+        (  # C2: Composition, energy, and packing fraction provided, expect to get mu based on packing fraction
+            # Reuse pattern from C1.1 here
             {
-                "sample_composition": "H2O",
+                "sample_composition": "quartz",
                 "energy": 10,
                 "packing_fraction": 0.5,
             },
-            0.2665,
+            2.5184,
         ),
-        (  # C3: Density provided only, expect to compute mu based on it
-            # 1. Known material
+    ],
+)
+def test_compute_mu_using_xraydb(inputs, expected_mu):
+    actual_mu = compute_mu_using_xraydb(**inputs)
+    assert actual_mu == pytest.approx(expected_mu, rel=1e-6, abs=1e-4)
+
+
+@pytest.mark.parametrize(
+    "inputs",
+    [
+        # Test when the function raises ValueError
+        # C1: Both mass density and packing fraction are provided
+        (
             {
-                "sample_composition": "H2O",
+                "sample_composition": "quartz",
                 "energy": 10,
-                "density": 0.987,
-            },
-            0.5330,
+                "sample_mass_density": 2.65,
+                "packing_fraction": 1,
+            }
         ),
-        (  # 2. Unknown material
-            {
-                "sample_composition": "ZrO2",
-                "energy": 17,
-                "density": 1.009,
-            },
-            1.252,
-        ),
-        (  # C4: Both density and packing fraction are provided, expect to compute mu based on both
-            # 1. Known material
+        # C2: None of mass density or packing fraction are provided
+        (
             {
-                "sample_composition": "H2O",
+                "sample_composition": "quartz",
                 "energy": 10,
-                "density": 0.997,
-                "packing_fraction": 0.5,
-            },
-            0.2665,
-        ),
-        (  # 2. Unknown material
-            {
-                "sample_composition": "ZrO2",
-                "energy": 17,
-                "density": 1.009,
-                "packing_fraction": 0.5,
-            },
-            0.626,
+            }
         ),
     ],
 )
-def test_compute_mu_using_xraydb(inputs, expected_mu):
-    actual_mu = compute_mu_using_xraydb(**inputs)
-    assert actual_mu == pytest.approx(expected_mu, rel=0.01, abs=0.1)
+def test_compute_mu_using_xraydb_bad(inputs):
+    with pytest.raises(
+        ValueError,
+        match="You must specify either sample_mass_density or packing_fraction, but not both. "
+        "Please rerun specifying only one.",
+    ):
+        compute_mu_using_xraydb(**inputs)