add input argument for z-scan file and function for computing muD from that file

Author: yucongalicechen

src/diffpy/labpdfproc/labpdfprocapp.py

@@ -124,6 +124,12 @@ def get_args(override_cli_inputs=None):
         ),
         default=None,
     )
+    p.add_argument(
+        "-z",
+        "--z-scan-file",
+        help="Path to the z-scan file to be loaded to overload the mu*D value.",
+        default=None,
+    )
     args = p.parse_args(override_cli_inputs)
     return args
 

src/diffpy/labpdfproc/tools.py

@@ -1,6 +1,7 @@
 import copy
 from pathlib import Path
 
+from diffpy.labpdfproc.mud_calculator import compute_mud
 from diffpy.utils.tools import get_package_info, get_user_info
 
 WAVELENGTHS = {"Mo": 0.71, "Ag": 0.59, "Cu": 1.54}
@@ -134,6 +135,28 @@ def set_wavelength(args):
     return args
 
 
+def set_mud(args):
+    """
+    Set the mud based on the given input arguments
+
+    Parameters
+    ----------
+    args argparse.Namespace
+        the arguments from the parser
+
+    Returns
+    -------
+    args argparse.Namespace
+    """
+    if args.z_scan_file:
+        filepath = Path(args.z_scan_file).resolve()
+        if not filepath.is_file():
+            raise FileNotFoundError(f"Cannot find {args.z_scan_file}. Please specify a valid file path.")
+        args.z_scan_file = filepath
+        args.mud = compute_mud(filepath)
+    return args
+
+
 def _load_key_value_pair(s):
     items = s.split("=")
     key = items[0].strip()
@@ -234,6 +257,7 @@ def preprocessing_args(args):
     args = set_input_lists(args)
     args.output_directory = set_output_directory(args)
     args = set_wavelength(args)
+    args = set_mud(args)
     args = load_user_metadata(args)
     return args