add getmud module with compute_diameter function, and CLI in main

Author: yucongalicechen

news/getmud.rst

@@ -0,0 +1,24 @@
+**Added:**
+
+* New ``getmuD`` module with the ``compute_diameter`` function to calculate capillary diameter.
+* CLI now supports ``compute_diameter`` function for target muD via a subcommand.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/labpdfproc/getmud.py

@@ -0,0 +1,39 @@
+from diffpy.utils.tools import compute_mu_using_xraydb
+
+
+def compute_diameter(
+    mud,
+    sample_composition,
+    xray_energy,
+    sample_mass_density=None,
+    packing_fraction=None,
+):
+    """
+    Compute capillary diameter (mm) from muD, sample composition, energy,
+    and either sample mass density or packing fraction.
+
+    Parameters
+    ----------
+    mud : float
+        The given muD of the sample.
+    sample_composition : str
+        The chemical formula of the material (e.g. "ZrO2").
+    xray_energy : float
+        The energy of the incident x-rays in keV.
+    sample_mass_density : float, optional
+        The mass density of the packed sample in g/cm^3.
+    packing_fraction : float, optional
+        The packing fraction of the sample (0–1).
+
+    Returns
+    -------
+    diameter : float
+        Computed capillary diameter in mm.
+    """
+    mu = compute_mu_using_xraydb(
+        sample_composition,
+        xray_energy,
+        sample_mass_density,
+        packing_fraction,
+    )
+    return mud / mu

src/diffpy/labpdfproc/labpdfprocapp.py

@@ -4,6 +4,7 @@
 from gooey import Gooey, GooeyParser
 
 from diffpy.labpdfproc.functions import CVE_METHODS, apply_corr, compute_cve
+from diffpy.labpdfproc.getmud import compute_diameter
 from diffpy.labpdfproc.tools import (
     known_sources,
     load_metadata,
@@ -207,7 +208,43 @@ def _add_mud_selection_group(p, is_gui=False):
     return p
 
 
+def _add_subparsers(p):
+    """Add subcommands for getmud module."""
+    subparsers = p.add_subparsers(dest="subcommand")
+    get_d_parser = subparsers.add_parser(
+        "get-diameter", help="Compute capillary diameter."
+    )
+    get_d_parser.add_argument(
+        "mud", type=float, help="The target muD of the sample."
+    )
+    get_d_parser.add_argument(
+        "composition",
+        help="The chemical formula of the material (e.g., ZrO2).",
+    )
+    get_d_parser.add_argument(
+        "energy", type=float, help="The X-ray energy in keV."
+    )
+    get_d_parser.add_argument(
+        "mass_density",
+        type=float,
+        help="The sample mass density in g/cm^3.",
+        default=None,
+    )
+    get_d_parser.set_defaults(func=compute_diameter)
+    return p
+
+
 def get_args(override_cli_inputs=None):
+    """Parse CLI arguments for main processing or subcommand mode."""
+    # User enters one of the subcommands
+    cli_args = override_cli_inputs or sys.argv[1:]
+    p = ArgumentParser()
+    p = _add_subparsers(p)
+    subcommands = ["get-diameter"]
+    if cli_args and cli_args[0] in subcommands:
+        return p.parse_args(override_cli_inputs)
+
+    # User does not enter subcommands
     p = ArgumentParser()
     p = _add_mud_selection_group(p, is_gui=False)
     for arg in _define_arguments():
@@ -238,6 +275,16 @@ def main():
         if len(sys.argv) == 1 or "--gui" in sys.argv
         else get_args()
     )
+    if getattr(args, "subcommand", None) == "get-diameter":
+        diameter = args.func(
+            mud=args.mud,
+            sample_composition=args.composition,
+            xray_energy=args.energy,
+            sample_mass_density=args.mass_density,
+        )
+        print(f"Capillary Diameter: {diameter:.2f} mm")
+        return
+
     args = preprocessing_args(args)
 
     for filepath in args.input_paths:

tests/test_getmud.py

@@ -0,0 +1,24 @@
+import pytest
+
+from diffpy.labpdfproc.getmud import compute_diameter
+
+
+@pytest.mark.parametrize(
+    "inputs, expected_diameter",
+    [
+        (
+            {
+                "mud": 2.0,
+                "sample_composition": "ZrO2",
+                "xray_energy": 17.45,
+                "sample_mass_density": 1.20,
+            },
+            1.3439,
+        ),
+    ],
+)
+def test_compute_diameter(inputs, expected_diameter):
+    actual_diameter = compute_diameter(**inputs)
+    assert actual_diameter == pytest.approx(
+        expected_diameter, rel=0.01, abs=0.1
+    )