Merge pull request #155 from yucongalicechen/wavelength

fix: update wavelengths

Author: sbillinge

news/wavelength.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* Increased the number of significant figures for wavelength and separated values for Ka1 and Ka2.
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/labpdfproc/tools.py

@@ -13,7 +13,21 @@
     get_user_info,
 )
 
-WAVELENGTHS = {"Mo": 0.71073, "Ag": 0.59, "Cu": 1.5406}
+# Reference values are taken from
+# https://x-server.gmca.aps.anl.gov/cgi/www_dbli.exe?x0hdb=waves
+# Ka1Ka2 values are calculated as: (Ka1 * 2 + Ka2) / 3
+# For CuKa1Ka2: (1.54056 * 2 + 1.544398) / 3 = 1.54184
+WAVELENGTHS = {
+    "Mo": 0.71073,
+    "MoKa1": 0.70930,
+    "MoKa1Ka2": 0.71073,
+    "Ag": 0.56087,
+    "AgKa1": 0.55941,
+    "AgKa1Ka2": 0.56087,
+    "Cu": 1.54184,
+    "CuKa1": 1.54056,
+    "CuKa1Ka2": 1.54184,
+}
 known_sources = [key for key in WAVELENGTHS.keys()]
 
 # Exclude wavelength from metadata to prevent duplication,
@@ -166,28 +180,32 @@ def set_wavelength(args):
     args : argparse.Namespace
         The updated arguments with the wavelength.
     """
-    if args.wavelength is not None and args.wavelength <= 0:
-        raise ValueError(
-            "No valid wavelength. "
-            "Please rerun specifying a known anode_type "
-            "or a positive wavelength."
-        )
-    if (
-        not args.wavelength
-        and args.anode_type
-        and args.anode_type not in WAVELENGTHS
-    ):
-        raise ValueError(
-            f"Anode type not recognized. "
-            f"Please rerun specifying an anode_type from {*known_sources, }."
+    if args.wavelength is None:
+        matched_anode_type = next(
+            (
+                key
+                for key in WAVELENGTHS
+                if key.lower() == args.anode_type.lower()
+            ),
+            None,
         )
-
-    if args.wavelength:
-        delattr(args, "anode_type")
-    elif args.anode_type:
+        if matched_anode_type is None:
+            raise ValueError(
+                f"Anode type not recognized. "
+                f"Please rerun specifying an anode_type "
+                f"from {*known_sources, }."
+            )
+        args.anode_type = matched_anode_type
         args.wavelength = WAVELENGTHS[args.anode_type]
     else:
-        args.wavelength = WAVELENGTHS["Mo"]
+        if args.wavelength <= 0:
+            raise ValueError(
+                "No valid wavelength. "
+                "Please rerun specifying a known anode_type "
+                "or a positive wavelength."
+            )
+        else:
+            delattr(args, "anode_type")
     return args
 
 

tests/test_tools.py

@@ -198,9 +198,52 @@ def test_set_output_directory_bad(user_filesystem):
 @pytest.mark.parametrize(
     "inputs, expected",
     [
+        # C1: nothing passed in, expect default is Mo
         ([], {"wavelength": 0.71073, "anode_type": "Mo"}),
-        (["--anode-type", "Ag"], {"wavelength": 0.59, "anode_type": "Ag"}),
+        # C2: only a valid anode type was entered (case independent),
+        # expect to match the corresponding wavelength
+        # and preserve the correct case anode type
+        (["--anode-type", "Mo"], {"wavelength": 0.71073, "anode_type": "Mo"}),
+        (
+            ["--anode-type", "MoKa1"],
+            {"wavelength": 0.70930, "anode_type": "MoKa1"},
+        ),
+        (
+            ["--anode-type", "MoKa1Ka2"],
+            {"wavelength": 0.71073, "anode_type": "MoKa1Ka2"},
+        ),
+        (["--anode-type", "Ag"], {"wavelength": 0.56087, "anode_type": "Ag"}),
+        (
+            ["--anode-type", "AgKa1"],
+            {"wavelength": 0.55941, "anode_type": "AgKa1"},
+        ),
+        (
+            ["--anode-type", "AgKa1Ka2"],
+            {"wavelength": 0.56087, "anode_type": "AgKa1Ka2"},
+        ),
+        (["--anode-type", "Cu"], {"wavelength": 1.54184, "anode_type": "Cu"}),
+        (
+            ["--anode-type", "CuKa1"],
+            {"wavelength": 1.54056, "anode_type": "CuKa1"},
+        ),
+        (
+            ["--anode-type", "CuKa1Ka2"],
+            {"wavelength": 1.54184, "anode_type": "CuKa1Ka2"},
+        ),
+        (
+            ["--anode-type", "moKa1Ka2"],
+            {"wavelength": 0.71073, "anode_type": "MoKa1Ka2"},
+        ),
+        (["--anode-type", "ag"], {"wavelength": 0.56087, "anode_type": "Ag"}),
+        (
+            ["--anode-type", "cuka1"],
+            {"wavelength": 1.54056, "anode_type": "CuKa1"},
+        ),
+        # C3: only a valid wavelength was entered,
+        # expect to include the wavelength only and anode type is None
         (["--wavelength", "0.25"], {"wavelength": 0.25, "anode_type": None}),
+        # C4: both valid anode type and wavelength were entered,
+        # expect to remove the anode type and preserve wavelength only
         (
             ["--wavelength", "0.25", "--anode-type", "Ag"],
             {"wavelength": 0.25, "anode_type": None},