diff --git a/news/xtype.rst b/news/xtype.rst
new file mode 100644
index 0000000..20ecef3
--- /dev/null
+++ b/news/xtype.rst
@@ -0,0 +1,23 @@
+**Added:**
+
+* Support for independent variables other than two-theta.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>
diff --git a/src/diffpy/labpdfproc/functions.py b/src/diffpy/labpdfproc/functions.py
index d423468..35d587c 100644
--- a/src/diffpy/labpdfproc/functions.py
+++ b/src/diffpy/labpdfproc/functions.py
@@ -5,7 +5,7 @@
import pandas as pd
from scipy.interpolate import interp1d
-from diffpy.utils.scattering_objects.diffraction_objects import Diffraction_object
+from diffpy.utils.scattering_objects.diffraction_objects import XQUANTITIES, Diffraction_object
RADIUS_MM = 1
N_POINTS_ON_DIAMETER = 300
@@ -198,7 +198,6 @@ def _cve_brute_force(diffraction_data, mud):
"tth",
metadata=diffraction_data.metadata,
name=f"absorption correction, cve, for {diffraction_data.name}",
- wavelength=diffraction_data.wavelength,
scat_quantity="cve",
)
return cve_do
@@ -227,7 +226,6 @@ def _cve_polynomial_interpolation(diffraction_data, mud):
"tth",
metadata=diffraction_data.metadata,
name=f"absorption correction, cve, for {diffraction_data.name}",
- wavelength=diffraction_data.wavelength,
scat_quantity="cve",
)
return cve_do
@@ -246,15 +244,18 @@ def _cve_method(method):
return methods[method]
-def compute_cve(diffraction_data, mud, method="polynomial_interpolation"):
+def compute_cve(diffraction_data, mud, method="polynomial_interpolation", xtype="tth"):
f"""
compute and interpolate the cve for the given diffraction data and mud using the selected method
+
Parameters
----------
diffraction_data Diffraction_object
the diffraction pattern
mud float
the mu*D of the diffraction object, where D is the diameter of the circle
+ xtype str
+ the quantity on the independent variable axis, allowed values are {*XQUANTITIES, }
method str
the method used to calculate cve, must be one of {* CVE_METHODS, }
@@ -264,22 +265,20 @@ def compute_cve(diffraction_data, mud, method="polynomial_interpolation"):
"""
cve_function = _cve_method(method)
- abdo_on_global_tth = cve_function(diffraction_data, mud)
- global_tth = abdo_on_global_tth.on_tth[0]
- cve_on_global_tth = abdo_on_global_tth.on_tth[1]
- orig_grid = diffraction_data.on_tth[0]
- newcve = np.interp(orig_grid, global_tth, cve_on_global_tth)
+ cve_do_on_global_grid = cve_function(diffraction_data, mud)
+ orig_grid = diffraction_data.on_xtype(xtype)[0]
+ global_xtype = cve_do_on_global_grid.on_xtype(xtype)[0]
+ cve_on_global_xtype = cve_do_on_global_grid.on_xtype(xtype)[1]
+ newcve = np.interp(orig_grid, global_xtype, cve_on_global_xtype)
cve_do = Diffraction_object(wavelength=diffraction_data.wavelength)
cve_do.insert_scattering_quantity(
orig_grid,
newcve,
- "tth",
+ xtype,
metadata=diffraction_data.metadata,
name=f"absorption correction, cve, for {diffraction_data.name}",
- wavelength=diffraction_data.wavelength,
scat_quantity="cve",
)
-
return cve_do
diff --git a/src/diffpy/labpdfproc/labpdfprocapp.py b/src/diffpy/labpdfproc/labpdfprocapp.py
index 1cbb78b..d63af8f 100644
--- a/src/diffpy/labpdfproc/labpdfprocapp.py
+++ b/src/diffpy/labpdfproc/labpdfprocapp.py
@@ -63,8 +63,7 @@ def get_args(override_cli_inputs=None):
help=(
f"The quantity on the independent variable axis. Allowed "
f"values: {*XQUANTITIES, }. If not specified then two-theta "
- f"is assumed for the independent variable. Only implemented for "
- f"tth currently."
+ f"is assumed for the independent variable."
),
default="tth",
)
@@ -160,19 +159,19 @@ def main():
input_pattern.insert_scattering_quantity(
xarray,
yarray,
- "tth",
+ args.xtype,
scat_quantity="x-ray",
name=filepath.stem,
metadata=load_metadata(args, filepath),
)
- absorption_correction = compute_cve(input_pattern, args.mud, args.method)
+ absorption_correction = compute_cve(input_pattern, args.mud, args.method, args.xtype)
corrected_data = apply_corr(input_pattern, absorption_correction)
corrected_data.name = f"Absorption corrected input_data: {input_pattern.name}"
- corrected_data.dump(f"{outfile}", xtype="tth")
+ corrected_data.dump(f"{outfile}", xtype=args.xtype)
if args.output_correction:
- absorption_correction.dump(f"{corrfile}", xtype="tth")
+ absorption_correction.dump(f"{corrfile}", xtype=args.xtype)
if __name__ == "__main__":
diff --git a/src/diffpy/labpdfproc/tools.py b/src/diffpy/labpdfproc/tools.py
index a4301ed..7bb3424 100644
--- a/src/diffpy/labpdfproc/tools.py
+++ b/src/diffpy/labpdfproc/tools.py
@@ -2,6 +2,7 @@
from pathlib import Path
from diffpy.labpdfproc.mud_calculator import compute_mud
+from diffpy.utils.scattering_objects.diffraction_objects import QQUANTITIES, XQUANTITIES
from diffpy.utils.tools import get_package_info, get_user_info
WAVELENGTHS = {"Mo": 0.71, "Ag": 0.59, "Cu": 1.54}
@@ -135,6 +136,25 @@ def set_wavelength(args):
return args
+def set_xtype(args):
+ f"""
+ Set the xtype based on the given input arguments, raise an error if xtype is not one of {*XQUANTITIES, }
+
+ Parameters
+ ----------
+ args argparse.Namespace
+ the arguments from the parser
+
+ Returns
+ -------
+ args argparse.Namespace
+ """
+ if args.xtype.lower() not in XQUANTITIES:
+ raise ValueError(f"Unknown xtype: {args.xtype}. Allowed xtypes are {*XQUANTITIES, }.")
+ args.xtype = "q" if args.xtype.lower() in QQUANTITIES else "tth"
+ return args
+
+
def set_mud(args):
"""
Set the mud based on the given input arguments
@@ -257,6 +277,7 @@ def preprocessing_args(args):
args = set_input_lists(args)
args.output_directory = set_output_directory(args)
args = set_wavelength(args)
+ args = set_xtype(args)
args = set_mud(args)
args = load_user_metadata(args)
return args
diff --git a/tests/test_functions.py b/tests/test_functions.py
index ac086a5..f23c32d 100644
--- a/tests/test_functions.py
+++ b/tests/test_functions.py
@@ -58,12 +58,12 @@ def test_set_muls_at_angle(inputs, expected):
assert actual_muls_sorted == pytest.approx(expected_muls_sorted, rel=1e-4, abs=1e-6)
-def _instantiate_test_do(xarray, yarray, name="test", scat_quantity="x-ray"):
+def _instantiate_test_do(xarray, yarray, xtype="tth", name="test", scat_quantity="x-ray"):
test_do = Diffraction_object(wavelength=1.54)
test_do.insert_scattering_quantity(
xarray,
yarray,
- "tth",
+ xtype,
scat_quantity=scat_quantity,
name=name,
metadata={"thing1": 1, "thing2": "thing2"},
@@ -71,16 +71,24 @@ def _instantiate_test_do(xarray, yarray, name="test", scat_quantity="x-ray"):
return test_do
-def test_compute_cve(mocker):
+params4 = [
+ (["tth"], [np.array([90, 90.1, 90.2]), np.array([0.5, 0.5, 0.5]), "tth"]),
+ (["q"], [np.array([5.76998, 5.77501, 5.78004]), np.array([0.5, 0.5, 0.5]), "q"]),
+]
+
+
+@pytest.mark.parametrize("inputs, expected", params4)
+def test_compute_cve(inputs, expected, 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_cve_do = compute_cve(input_pattern, mud=1)
+ actual_cve_do = compute_cve(input_pattern, mud=1, method="polynomial_interpolation", xtype=inputs[0])
expected_cve_do = _instantiate_test_do(
- xarray,
- expected_cve,
+ expected[0],
+ expected[1],
+ expected[2],
name="absorption correction, cve, for test",
scat_quantity="cve",
)
@@ -92,7 +100,7 @@ def test_compute_cve(mocker):
[7, "polynomial_interpolation"],
[
f"mu*D is out of the acceptable range (0.5 to 6) for polynomial interpolation. "
- f"Please rerun with a value within this range or specifying another method from {* CVE_METHODS, }."
+ f"Please rerun with a value within this range or specifying another method from {*CVE_METHODS, }."
],
),
([1, "invalid_method"], [f"Unknown method: invalid_method. Allowed methods are {*CVE_METHODS, }."]),
diff --git a/tests/test_tools.py b/tests/test_tools.py
index 67773e4..077a5ed 100644
--- a/tests/test_tools.py
+++ b/tests/test_tools.py
@@ -16,7 +16,9 @@
set_mud,
set_output_directory,
set_wavelength,
+ set_xtype,
)
+from diffpy.utils.scattering_objects.diffraction_objects import XQUANTITIES
# Use cases can be found here: https://github.com/diffpy/diffpy.labpdfproc/issues/48
@@ -189,6 +191,31 @@ def test_set_wavelength_bad(inputs, msg):
actual_args = set_wavelength(actual_args)
+params4 = [
+ ([], ["tth"]),
+ (["--xtype", "2theta"], ["tth"]),
+ (["--xtype", "d"], ["tth"]),
+ (["--xtype", "q"], ["q"]),
+]
+
+
+@pytest.mark.parametrize("inputs, expected", params4)
+def test_set_xtype(inputs, expected):
+ cli_inputs = ["2.5", "data.xy"] + inputs
+ actual_args = get_args(cli_inputs)
+ actual_args = set_xtype(actual_args)
+ assert actual_args.xtype == expected[0]
+
+
+def test_set_xtype_bad():
+ cli_inputs = ["2.5", "data.xy", "--xtype", "invalid"]
+ actual_args = get_args(cli_inputs)
+ with pytest.raises(
+ ValueError, match=re.escape(f"Unknown xtype: invalid. Allowed xtypes are {*XQUANTITIES, }.")
+ ):
+ actual_args = set_xtype(actual_args)
+
+
def test_set_mud(user_filesystem):
cli_inputs = ["2.5", "data.xy"]
actual_args = get_args(cli_inputs)