Merge pull request #173 from yucongalicechen/muD-theoretical

feat: options for estimating muD theoretically

Author: sbillinge

news/muD-theoretical.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* Functionalities to estimate mu*D theoretically.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/labpdfproc/labpdfprocapp.py

@@ -12,6 +12,13 @@
 from diffpy.utils.diffraction_objects import XQUANTITIES, DiffractionObject
 from diffpy.utils.parsers.loaddata import loadData
 
+theoretical_mud_hmsg_suffix = (
+    "in that exact order, "
+    "separated by commas (e.g., ZrO2,17.45,0.5). "
+    "If you add whitespaces, "
+    "enclose it in quotes (e.g., 'ZrO2, 17.45, 0.5'). "
+)
+
 
 def _define_arguments():
     args = [
@@ -21,12 +28,14 @@ def _define_arguments():
                 "The filename(s) or folder(s) of the datafile(s) to load. "
                 "Required.\n"
                 "Supply a space-separated list of files or directories. "
+                "Avoid spaces in filenames when possible; "
+                "if present, enclose the name in quotes. "
                 "Long lists can be supplied, one per line, "
                 "in a file with name file_list.txt. "
                 "If one or more directory is provided, all valid "
                 "data-files in that directory will be processed. "
                 "Examples of valid inputs are 'file.xy', 'data/file.xy', "
-                "'file.xy, data/file.xy', "
+                "'file.xy data/file.xy', "
                 "'.' (load everything in the current directory), "
                 "'data' (load everything in the folder ./data), "
                 "'data/file_list.txt' (load the list of files "
@@ -152,7 +161,11 @@ def _define_arguments():
 def _add_mud_selection_group(p, is_gui=False):
     """Current Options:
     1. Manually enter muD (`--mud`).
-    2. Estimate muD from a z-scan file (`-z` or `--z-scan-file`).
+    2. Estimate from a z-scan file (`-z` or `--z-scan-file`).
+    3. Estimate theoretically based on sample mass density
+    (`-d` or `--theoretical-from-density`).
+    4. Estimate theoretically based on packing fraction
+    (`-p` or `--theoretical-from-packing`).
     """
     g = p.add_argument_group("Options for setting mu*D value (Required)")
     g = g.add_mutually_exclusive_group(required=True)
@@ -165,10 +178,32 @@ def _add_mud_selection_group(p, is_gui=False):
     g.add_argument(
         "-z",
         "--z-scan-file",
-        help="Provide the path to the z-scan file to be loaded "
-        "to determine the mu*D value.",
+        help=(
+            "Estimate mu*D experimentally from a z-scan file. "
+            "Specify the path to the file "
+            "used to compute the mu*D value."
+        ),
         **({"widget": "FileChooser"} if is_gui else {}),
     )
+    g.add_argument(
+        "-d",
+        "--theoretical-from-density",
+        help=(
+            "Estimate mu*D theoretically using sample mass density. "
+            "Specify the chemical formula, incident x-ray energy (in keV), "
+            "and sample mass density (in g/cm^3), "
+            + theoretical_mud_hmsg_suffix
+        ),
+    )
+    g.add_argument(
+        "-p",
+        "--theoretical-from-packing",
+        help=(
+            "Estimate mu*D theoretically using packing fraction. "
+            "Specify the chemical formula, incident x-ray energy (in keV), "
+            "and packing fraction (0 to 1), " + theoretical_mud_hmsg_suffix
+        ),
+    )
     return p
 
 
@@ -186,7 +221,7 @@ def get_args(override_cli_inputs=None):
     return args
 
 
-@Gooey(required_cols=1, optional_cols=1, program_name="Labpdfproc GUI")
+@Gooey(required_cols=1, optional_cols=2, program_name="labpdfproc GUI")
 def gooey_parser():
     p = GooeyParser()
     p = _add_mud_selection_group(p, is_gui=True)

src/diffpy/labpdfproc/tools.py

@@ -9,6 +9,7 @@
 from diffpy.utils.tools import (
     _load_config,
     check_and_build_global_config,
+    compute_mu_using_xraydb,
     compute_mud,
     get_package_info,
     get_user_info,
@@ -31,14 +32,19 @@
 }
 known_sources = [key for key in WAVELENGTHS.keys()]
 
-# Exclude wavelength from metadata to prevent duplication,
-# as the dump function in diffpy.utils writes it explicitly.
+# Exclude wavelength to avoid duplication,
+# as it's written explicitly by diffpy.utils dump function.
+# Exclude "theoretical_from_density" and "theoretical_from_packing"
+# as they are only used for theoretical mu*D estimation
+# and will be written into separate arguments for clarity.
 METADATA_KEYS_TO_EXCLUDE = [
     "output_correction",
     "force_overwrite",
     "input",
     "input_paths",
     "wavelength",
+    "theoretical_from_density",
+    "theoretical_from_packing",
 ]
 
 
@@ -298,19 +304,8 @@ def set_xtype(args):
     return args
 
 
-def _estimate_mud_from_zscan(args):
-    """Compute mu*D based on the given z-scan file.
-
-    Parameters
-    ----------
-    args : argparse.Namespace
-        The arguments from the parser.
-
-    Returns
-    -------
-    args : argparse.Namespace
-        The updated arguments with mu*D.
-    """
+def _set_mud_from_zscan(args):
+    """Experimental estimation of mu*D from a z-scan file."""
     filepath = Path(args.z_scan_file).resolve()
     if not filepath.is_file():
         raise FileNotFoundError(
@@ -322,10 +317,64 @@ def _estimate_mud_from_zscan(args):
     return args
 
 
+def _parse_theoretical_input(input_str):
+    """Helper function to parse and validate the input string."""
+    parts = [part.strip() for part in input_str.split(",")]
+    if len(parts) != 3:
+        raise ValueError(
+            f"Invalid mu*D input '{input_str}'. "
+            "Expected format is 'sample composition, energy, "
+            "sample mass density or packing fraction' "
+            "(e.g., 'ZrO2,17.45,0.5').",
+        )
+    sample_composition = parts[0]
+    energy = float(parts[1])
+    mass_density_or_packing_fraction = float(parts[2])
+    return sample_composition, energy, mass_density_or_packing_fraction
+
+
+def _set_theoretical_mud_from_density(args):
+    """Theoretical estimation of mu*D from
+    sample composition, energy, and sample mass density."""
+    sample_composition, energy, sample_mass_density = _parse_theoretical_input(
+        args.theoretical_from_density
+    )
+    args.sample_composition = sample_composition
+    args.energy = energy
+    args.sample_mass_density = sample_mass_density
+    args.mud = compute_mu_using_xraydb(
+        args.sample_composition,
+        args.energy,
+        sample_mass_density=args.sample_mass_density,
+    )
+    return args
+
+
+def _set_theoretical_mud_from_packing(args):
+    """Theoretical estimation of mu*D from
+    sample composition, energy, and packing fraction."""
+    sample_composition, energy, packing_fraction = _parse_theoretical_input(
+        args.theoretical_from_packing
+    )
+    args.sample_composition = sample_composition
+    args.energy = energy
+    args.packing_fraction = packing_fraction
+    args.mud = compute_mu_using_xraydb(
+        args.sample_composition,
+        args.energy,
+        packing_fraction=args.packing_fraction,
+    )
+    return args
+
+
 def set_mud(args):
-    """Compute and set mu*D based on different options.
-    Current options include manually entering a value,
-    or estimating from a z-scan file.
+    """Compute and set mu*D based on the selected method.
+
+    Options include:
+    1. Manually entering a value.
+    2. Estimating from a z-scan file.
+    3. Estimating theoretically based on sample mass density.
+    4. Estimating theoretically based on packing fraction.
 
     Parameters
     ----------
@@ -338,7 +387,11 @@ def set_mud(args):
         The updated arguments with mu*D.
     """
     if args.z_scan_file:
-        return _estimate_mud_from_zscan(args)
+        return _set_mud_from_zscan(args)
+    elif args.theoretical_from_density:
+        return _set_theoretical_mud_from_density(args)
+    elif args.theoretical_from_packing:
+        return _set_theoretical_mud_from_packing(args)
     return args
 
 

tests/test_tools.py

@@ -460,6 +460,15 @@ def test_set_xtype_bad():
         (["--mud", "2.5"], 2.5),
         # C2: user provides a z-scan file, expect to estimate through the file
         (["--z-scan-file", "test_dir/testfile.xy"], 3),
+        # C3: user specifies sample composition, energy,
+        # and sample mass density,
+        # both with and without whitespaces, expect to estimate theoretically
+        (["--theoretical-from-density", "ZrO2,17.45,1.2"], 1.49),
+        (["--theoretical-from-density", "ZrO2, 17.45, 1.2"], 1.49),
+        # C4: user specifies sample composition, energy, and packing fraction
+        # both with and without whitespaces, expect to estimate theoretically
+        # (["--theoretical-from-packing", "ZrO2,17.45,0.3"], 1.49),
+        # (["--theoretical-from-packing", "ZrO2, 17.45, 0.3"], 1.49),
     ],
 )
 def test_set_mud(user_filesystem, inputs, expected_mud):
@@ -483,6 +492,58 @@ def test_set_mud(user_filesystem, inputs, expected_mud):
                 "Cannot find invalid file. Please specify a valid file path.",
             ],
         ),
+        # C2.1: (sample mass density option)
+        # user provides fewer than three input values
+        # expect ValueError with a message indicating the correct format
+        (
+            ["--theoretical-from-density", "ZrO2,0.5"],
+            [
+                ValueError,
+                "Invalid mu*D input 'ZrO2,0.5'. "
+                "Expected format is 'sample composition, energy, "
+                "sample mass density or packing fraction' "
+                "(e.g., 'ZrO2,17.45,0.5').",
+            ],
+        ),
+        # C2.2: (packing fraction option)
+        # user provides fewer than three input values
+        # expect ValueError with a message indicating the correct format
+        (
+            ["--theoretical-from-packing", "ZrO2,0.5"],
+            [
+                ValueError,
+                "Invalid mu*D input 'ZrO2,0.5'. "
+                "Expected format is 'sample composition, energy, "
+                "sample mass density or packing fraction' "
+                "(e.g., 'ZrO2,17.45,0.5').",
+            ],
+        ),
+        # C3.1: (sample mass density option)
+        # user provides more than 3 input values
+        # expect ValueError with a message indicating the correct format
+        (
+            ["--theoretical-from-density", "ZrO2,17.45,1.5,0.5"],
+            [
+                ValueError,
+                "Invalid mu*D input 'ZrO2,17.45,1.5,0.5'. "
+                "Expected format is 'sample composition, energy, "
+                "sample mass density or packing fraction' "
+                "(e.g., 'ZrO2,17.45,0.5').",
+            ],
+        ),
+        # C3.2: (packing fraction option)
+        # user provides more than 3 input values
+        # expect ValueError with a message indicating the correct format
+        (
+            ["--theoretical-from-packing", "ZrO2,17.45,1.5,0.5"],
+            [
+                ValueError,
+                "Invalid mu*D input 'ZrO2,17.45,1.5,0.5'. "
+                "Expected format is 'sample composition, energy, "
+                "sample mass density or packing fraction' "
+                "(e.g., 'ZrO2,17.45,0.5').",
+            ],
+        ),
     ],
 )
 def test_set_mud_bad(user_filesystem, inputs, expected):
@@ -491,7 +552,7 @@ def test_set_mud_bad(user_filesystem, inputs, expected):
     os.chdir(cwd)
     cli_inputs = ["data.xy"] + inputs
     actual_args = get_args(cli_inputs)
-    with pytest.raises(expected_error, match=expected_error_msg):
+    with pytest.raises(expected_error, match=re.escape(expected_error_msg)):
         actual_args = set_mud(actual_args)