compute mu

news/mu.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* function to compute x-ray attenuation coefficient (mu) using XrayDB
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

requirements/conda.txt

@@ -1 +1,2 @@
 numpy
+xraydb

requirements/pip.txt

@@ -1 +1,2 @@
 numpy
+xraydb

src/diffpy/utils/tools.py

@@ -3,6 +3,8 @@
 from copy import copy
 from pathlib import Path
 
+from xraydb import material_mu
+
 
 def clean_dict(obj):
     """Remove keys from the dictionary where the corresponding value is None.
@@ -206,3 +208,31 @@ def get_package_info(package_names, metadata=None):
         pkg_info.update({package: importlib.metadata.version(package)})
     metadata["package_info"] = pkg_info
     return metadata
+
+
+def compute_mu_using_xraydb(sample_composition, energy, density=None, packing_fraction=1):
+    """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.
+    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 mass density of the packed powder/sample in gr/cm^3.
+    packing_fraction : float, optional, Default is 1
+        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
+    return mu

tests/test_tools.py

@@ -5,7 +5,12 @@
 
 import pytest
 
-from diffpy.utils.tools import check_and_build_global_config, get_package_info, get_user_info
+from diffpy.utils.tools import (
+    check_and_build_global_config,
+    compute_mu_using_xraydb,
+    get_package_info,
+    get_user_info,
+)
 
 
 @pytest.mark.parametrize(
@@ -160,3 +165,65 @@ def test_get_package_info(monkeypatch, inputs, expected):
     )
     actual_metadata = get_package_info(inputs[0], metadata=inputs[1])
     assert actual_metadata == expected
+
+
+@pytest.mark.parametrize(
+    "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
+            {
+                "sample_composition": "H2O",
+                "energy": 10,
+            },
+            0.5330,
+        ),
+        (  # C2: Packing fraction (=0.5) provided only (only for known material)
+            {
+                "sample_composition": "H2O",
+                "energy": 10,
+                "packing_fraction": 0.5,
+            },
+            0.2665,
+        ),
+        (  # C3: Density provided only, expect to compute mu based on it
+            # 1. Known material
+            {
+                "sample_composition": "H2O",
+                "energy": 10,
+                "density": 0.987,
+            },
+            0.5330,
+        ),
+        (  # 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
+            {
+                "sample_composition": "H2O",
+                "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)