Merge branch 'main' into metadata3

Author: yucongalicechen

src/diffpy/labpdfproc/functions.py

@@ -197,7 +197,7 @@ def compute_cve(diffraction_data, mud, wavelength):
     """
 
     mu_sample_invmm = mud / 2
-    abs_correction = Gridded_circle(n_points_on_diameter=N_POINTS_ON_DIAMETER, mu=mu_sample_invmm)
+    abs_correction = Gridded_circle(mu=mu_sample_invmm)
     distances, muls = [], []
     for angle in TTH_GRID:
         abs_correction.set_distances_at_angle(angle)

src/diffpy/labpdfproc/labpdfprocapp.py

@@ -117,7 +117,7 @@ def main():
     args = load_user_info(args)
     args = set_input_lists(args)
     args.output_directory = set_output_directory(args)
-    args.wavelength = set_wavelength(args)
+    args = set_wavelength(args)
     args = load_user_metadata(args)
 
     for filepath in args.input_paths:

src/diffpy/labpdfproc/tests/test_functions.py

@@ -1,7 +1,7 @@
 import numpy as np
 import pytest
 
-from diffpy.labpdfproc.functions import Gridded_circle, compute_cve
+from diffpy.labpdfproc.functions import Gridded_circle, apply_corr, compute_cve
 from diffpy.utils.scattering_objects.diffraction_objects import Diffraction_object
 
 params1 = [
@@ -56,27 +56,47 @@ def test_set_muls_at_angle(inputs, expected):
     assert actual_muls_sorted == pytest.approx(expected_muls_sorted, rel=1e-4, abs=1e-6)
 
 
-def test_compute_cve(mocker):
-    mocker.patch("diffpy.labpdfproc.functions.N_POINTS_ON_DIAMETER", 4)
-    mocker.patch("diffpy.labpdfproc.functions.TTH_GRID", np.array([45, 60, 90]))
-    input_pattern = Diffraction_object(wavelength=1.54)
-    input_pattern.insert_scattering_quantity(
-        np.array([45, 60, 90]),
-        np.array([2.2, 3, 4]),
+def _instantiate_test_do(xarray, yarray, name="test", scat_quantity="x-ray"):
+    test_do = Diffraction_object(wavelength=1.54)
+    test_do.insert_scattering_quantity(
+        xarray,
+        yarray,
         "tth",
-        scat_quantity="x-ray",
-        name="test",
+        scat_quantity=scat_quantity,
+        name=name,
         metadata={"thing1": 1, "thing2": "thing2"},
     )
+    return test_do
+
+
+def test_compute_cve(mocker):
+    xarray, yarray = np.array([90, 90.1, 90.2]), np.array([2, 2, 2])
+    expected_cve = np.array([0.5, 0.5, 0.5])
+    mocker.patch("diffpy.labpdfproc.functions.TTH_GRID", xarray)
+    mocker.patch("numpy.interp", return_value=expected_cve)
+    input_pattern = _instantiate_test_do(xarray, yarray)
     actual_abdo = compute_cve(input_pattern, mud=1, wavelength=1.54)
-    expected_abdo = Diffraction_object()
-    expected_abdo.insert_scattering_quantity(
-        np.array([45, 60, 90]),
-        np.array([2.54253, 2.52852, 2.49717]),
-        "tth",
-        metadata={"thing1": 1, "thing2": "thing2"},
+    expected_abdo = _instantiate_test_do(
+        xarray,
+        expected_cve,
         name="absorption correction, cve, for test",
-        wavelength=1.54,
         scat_quantity="cve",
     )
     assert actual_abdo == expected_abdo
+
+
+def test_apply_corr(mocker):
+    xarray, yarray = np.array([90, 90.1, 90.2]), np.array([2, 2, 2])
+    expected_cve = np.array([0.5, 0.5, 0.5])
+    mocker.patch("diffpy.labpdfproc.functions.TTH_GRID", xarray)
+    mocker.patch("numpy.interp", return_value=expected_cve)
+    input_pattern = _instantiate_test_do(xarray, yarray)
+    absorption_correction = _instantiate_test_do(
+        xarray,
+        expected_cve,
+        name="absorption correction, cve, for test",
+        scat_quantity="cve",
+    )
+    actual_corr = apply_corr(input_pattern, absorption_correction)
+    expected_corr = _instantiate_test_do(xarray, np.array([1, 1, 1]))
+    assert actual_corr == expected_corr

src/diffpy/labpdfproc/tests/test_tools.py

@@ -146,20 +146,21 @@ def test_set_output_directory_bad(user_filesystem):
 
 
 params2 = [
-    ([], [0.71]),
-    (["--anode-type", "Ag"], [0.59]),
-    (["--wavelength", "0.25"], [0.25]),
-    (["--wavelength", "0.25", "--anode-type", "Ag"], [0.25]),
+    ([], [0.71, "Mo"]),
+    (["--anode-type", "Ag"], [0.59, "Ag"]),
+    (["--wavelength", "0.25"], [0.25, None]),
+    (["--wavelength", "0.25", "--anode-type", "Ag"], [0.25, None]),
 ]
 
 
 @pytest.mark.parametrize("inputs, expected", params2)
 def test_set_wavelength(inputs, expected):
-    expected_wavelength = expected[0]
+    expected_wavelength, expected_anode_type = expected[0], expected[1]
     cli_inputs = ["2.5", "data.xy"] + inputs
     actual_args = get_args(cli_inputs)
-    actual_args.wavelength = set_wavelength(actual_args)
+    actual_args = set_wavelength(actual_args)
     assert actual_args.wavelength == expected_wavelength
+    assert getattr(actual_args, "anode_type", None) == expected_anode_type
 
 
 params3 = [
@@ -183,7 +184,7 @@ def test_set_wavelength_bad(inputs, msg):
     cli_inputs = ["2.5", "data.xy"] + inputs
     actual_args = get_args(cli_inputs)
     with pytest.raises(ValueError, match=re.escape(msg[0])):
-        actual_args.wavelength = set_wavelength(actual_args)
+        actual_args = set_wavelength(actual_args)
 
 
 params5 = [

src/diffpy/labpdfproc/tools.py

@@ -127,11 +127,12 @@ def set_wavelength(args):
         )
 
     if args.wavelength:
-        return args.wavelength
+        delattr(args, "anode_type")
     elif args.anode_type:
-        return WAVELENGTHS[args.anode_type]
+        args.wavelength = WAVELENGTHS[args.anode_type]
     else:
-        return WAVELENGTHS["Mo"]
+        args.wavelength = WAVELENGTHS["Mo"]
+    return args
 
 
 def _load_key_value_pair(s):