Merge pull request #278 from yucongalicechen/mucalc

compute mu

Author: sbillinge

Diff for: 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>

Diff for: requirements/conda.txt

@@ -1,2 +1,3 @@
 numpy
+xraydb
 scipy

Diff for: requirements/pip.txt

@@ -1,2 +1,3 @@
 numpy
+xraydb
 scipy

Diff for: src/diffpy/utils/tools.py

@@ -6,6 +6,7 @@
 import numpy as np
 from scipy.optimize import dual_annealing
 from scipy.signal import convolve
+from xraydb import material_mu
 
 from diffpy.utils.parsers.loaddata import loadData
 
@@ -194,6 +195,57 @@ def get_package_info(package_names, metadata=None):
     return metadata
 
 
+def get_density_from_cloud(sample_composition, mp_token=""):
+    """Function to get material density from the MP or COD database.
+
+    It is not implemented yet.
+    """
+    raise NotImplementedError(
+        "So sorry, density computation from composition is not implemented right now. "
+        "We hope to have this implemented in the next release. "
+        "Please rerun specifying a sample mass density."
+    )
+
+
+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 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 of the material.
+    energy : float
+        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 g/cm*3.
+    packing_fraction : float, optional, Default is None
+        The fraction of sample in the capillary (between 0 and 1).
+        Specify either sample_mass_density or packing_fraction but not both.
+
+    Returns
+    -------
+    mu : float
+        The attenuation coefficient mu in mm^{-1}.
+    """
+    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 packing_fraction is not None:
+        sample_mass_density = get_density_from_cloud(sample_composition) * packing_fraction
+    energy_eV = energy * 1000
+    mu = material_mu(sample_composition, energy_eV, density=sample_mass_density, kind="total") / 10
+    return mu
+
+
 def _top_hat(z, half_slit_width):
     """Create a top-hat function, return 1.0 for values within the specified
     slit width and 0 otherwise."""

Diff for: tests/test_tools.py

@@ -9,6 +9,7 @@
 from diffpy.utils.tools import (
     _extend_z_and_convolve,
     check_and_build_global_config,
+    compute_mu_using_xraydb,
     compute_mud,
     get_package_info,
     get_user_info,
@@ -169,6 +170,35 @@ def test_get_package_info(monkeypatch, inputs, expected):
     assert actual_metadata == expected
 
 
+@pytest.mark.parametrize(
+    "inputs",
+    [
+        # Test when the function has invalid inputs
+        (  # C1: Both mass density and packing fraction are provided, expect ValueError exception
+            {
+                "sample_composition": "SiO2",
+                "energy": 10,
+                "sample_mass_density": 2.65,
+                "packing_fraction": 1,
+            }
+        ),
+        (  # C2: None of mass density or packing fraction are provided, expect ValueError exception
+            {
+                "sample_composition": "SiO2",
+                "energy": 10,
+            }
+        ),
+    ],
+)
+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)
+
+
 def test_compute_mud(tmp_path):
     diameter, slit_width, z0, I0, mud, slope = 1, 0.1, 0, 1e5, 3, 0
     z_data = np.linspace(-1, 1, 50)