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 _stringify(obj):
     """
@@ -131,3 +133,31 @@ 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.
+
+    This function calculates mu based on the sample composition and energy.
+    If density is not provided, a standard reference density (e.g., 0.987 g/cm^3 for H2O) is used.
+    User can provide either a measured density or an estimated packing fraction (with a standard density).
+    It is recommended to specify the density, especially for materials like ZrO2, where it can vary.
+    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 eV
+    density: float, optional, Default is None
+        The mass density of the packed powder/sample in gr/cm^3. If None, a standard density from XrayDB is used.
+    packing_fraction: float, optional, Default is 1
+        The fraction of sample in the capillary (between 0 and 1)
+
+    Returns
+    -------
+    the attenuation coefficient mu in mm^{-1}
+    """
+    mu = material_mu(sample_composition, energy, density=density, kind="total") * packing_fraction / 10
+    return mu

tests/test_tools.py

@@ -5,7 +5,7 @@
 
 import pytest
 
-from diffpy.utils.tools import get_package_info, get_user_info
+from diffpy.utils.tools import compute_mu_using_xraydb, get_package_info, get_user_info
 
 # def _setup_dirs(monkeypatch, user_filesystem):
 #     home_dir, cwd_dir = user_filesystem.home_dir, user_filesystem.cwd_dir
@@ -189,3 +189,27 @@ def test_get_package_info(monkeypatch, inputs, expected):
     )
     actual_metadata = get_package_info(inputs[0], metadata=inputs[1])
     assert actual_metadata == expected
+
+
+params_mu = [
+    # C1: user didn't specify density or packing fraction
+    ({"sample_composition": "H2O", "energy": 10000, "density": None, "packing_fraction": 1}, 0.5330),
+    # C2: user specified packing fraction only
+    ({"sample_composition": "H2O", "energy": 10000, "density": None, "packing_fraction": 0.5}, 0.2665),
+    # C3: user specified density only
+    ({"sample_composition": "H2O", "energy": 10000, "density": 0.997, "packing_fraction": 1}, 0.5330),
+    ({"sample_composition": "H2O", "energy": 10000, "density": 0.4985, "packing_fraction": 1}, 0.2665),
+    # C4: user specified a standard density and a packing fraction
+    ({"sample_composition": "H2O", "energy": 10000, "density": 0.997, "packing_fraction": 0.5}, 0.2665),
+]
+
+
+@pytest.mark.parametrize("inputs, expected", params_mu)
+def test_compute_mu_using_xraydb(inputs, expected):
+    actual_mu = compute_mu_using_xraydb(
+        inputs["sample_composition"],
+        inputs["energy"],
+        density=inputs["density"],
+        packing_fraction=inputs["packing_fraction"],
+    )
+    assert actual_mu == pytest.approx(expected, rel=0.01, abs=0.1)