initial commit

Author: yucongalicechen

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 +133,26 @@ 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, energy, density=None):
+    """
+    compute mu using the XrayDB database
+
+    Reference: https://xraypy.github.io/XrayDB/python.html#xraydb.material_mu
+
+    Parameters
+    ----------
+    sample str
+        the chemical formula or the name of the material
+    energy float
+        the energy in eV
+    density float or None
+        material density in gr/cm^3
+
+    Returns
+    -------
+    the attenuation coefficient mu in mm^{-1}
+    """
+    mu = material_mu(sample, energy, density=density, kind="total") / 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 +189,9 @@ def test_get_package_info(monkeypatch, inputs, expected):
     )
     actual_metadata = get_package_info(inputs[0], metadata=inputs[1])
     assert actual_metadata == expected
+
+
+def test_compute_mu_using_xraydb():
+    sample, energy, density = "ZrO2", 17445.362740959618, 1.009
+    actual_mu = compute_mu_using_xraydb(sample, energy, density=density)
+    assert actual_mu == pytest.approx(1.252, rel=1e-4, abs=0.1)