feat: initial commit on getmud module

Author: yucongalicechen

news/getmud.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* Functionalities to estimate sample mass density or capillary diameter from muD and related chemical info.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/labpdfproc/getmud.py

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+import numpy as np
+from scipy.optimize import newton
+
+from diffpy.utils.tools import compute_mu_using_xraydb
+
+
+def estimate_mass_density(mud, diameter, sample_composition, energy):
+    """Estimate sample mass density (g/cm^3) from mu*D
+    using capillary diameter, sample composition, and energy.
+
+    Parameters
+    ----------
+    mud : float
+        The given product of attenuation coefficient mu
+        in mm^{-1} and capillary diameter in mm.
+    diameter : float
+        The given diameter of the sample capillary in mm.
+    sample_composition : str
+        The chemical formula of the material.
+    energy : float
+        The energy of the incident x-rays in keV.
+
+    Returns
+    -------
+    estimated_density : float
+        The estimated mass density of the packed powder/sample in g/cm^3.
+    """
+    mu = mud / diameter
+
+    def residual_density(density):
+        return np.abs(
+            compute_mu_using_xraydb(
+                sample_composition, energy, sample_mass_density=density
+            )
+            - mu
+        )
+
+    estimated_density = newton(residual_density, x0=1.0, x1=10.0)
+    return estimated_density
+
+
+def estimate_diameter(
+    mud,
+    sample_composition,
+    energy,
+    sample_mass_density=None,
+    packing_fraction=None,
+):
+    """Estimate capillary diameter (mm) from mu*D and mu.
+
+    Parameters
+    ----------
+    mud : float
+        The given product of attenuation coefficient mu
+        in mm^{-1} and capillary diameter in mm.
+    sample_composition : str
+        The chemical formula of the material.
+    energy : float
+        The energy of the incident x-rays in keV.
+    sample_mass_density : float
+        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
+    -------
+    diameter : float
+        The given diameter of the sample capillary in mm.
+    """
+    mu = compute_mu_using_xraydb(
+        sample_composition, energy, sample_mass_density, packing_fraction
+    )
+    return mud / mu

tests/test_getmud.py

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+import pytest
+
+from diffpy.labpdfproc.getmud import estimate_diameter, estimate_mass_density
+
+
+@pytest.mark.parametrize(
+    "inputs, expected_mass_density",
+    [
+        (
+            {
+                "mud": 2.0,
+                "diameter": 1.5,
+                "sample_composition": "ZrO2",
+                "energy": 20,
+            },
+            0.25,
+        ),
+    ],
+)
+def test_estimate_mass_density(inputs, expected_mass_density):
+    actual_mass_density = estimate_mass_density(
+        inputs["mud"],
+        inputs["diameter"],
+        inputs["sample_composition"],
+        inputs["energy"],
+    )
+    assert actual_mass_density == pytest.approx(
+        expected_mass_density, rel=0.01, abs=0.1
+    )
+
+
+@pytest.mark.parametrize(
+    "inputs, expected_diameter",
+    [
+        (  # C1: user specifies a sample mass density
+            {
+                "mud": 2.0,
+                "sample_composition": "ZrO2",
+                "energy": 20,
+                "sample_mass_density": 0.25,
+            },
+            1.5,
+        ),
+        # (   # C2: user specifies a packing fraction
+        #     {
+        #         "mud": 2.0,
+        #         "sample_composition": "ZrO2",
+        #         "energy": 20,
+        #         "packing_fraction": 0.3
+        #     },
+        #     1.5
+        # ),
+    ],
+)
+def test_estimate_diameter(inputs, expected_diameter):
+    actual_diameter = estimate_diameter(**inputs)
+    assert actual_diameter == pytest.approx(
+        expected_diameter, rel=0.01, abs=0.1
+    )