From d3f3161a26fbfbafd26c7b0792df7c65a4754e9a Mon Sep 17 00:00:00 2001 From: yucongalicechen Date: Wed, 30 Oct 2024 12:59:36 -0400 Subject: [PATCH 1/6] change name from abdo to more readable name cvedo --- src/diffpy/labpdfproc/functions.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/diffpy/labpdfproc/functions.py b/src/diffpy/labpdfproc/functions.py index d423468..e6f6819 100644 --- a/src/diffpy/labpdfproc/functions.py +++ b/src/diffpy/labpdfproc/functions.py @@ -264,9 +264,9 @@ 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] + cve_do_on_global_tth = cve_function(diffraction_data, mud) + global_tth = cve_do_on_global_tth.on_tth[0] + cve_on_global_tth = cve_do_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 = Diffraction_object(wavelength=diffraction_data.wavelength) From ddcc758bbaebac098532910f7c112af083827c2b Mon Sep 17 00:00:00 2001 From: yucongalicechen Date: Wed, 30 Oct 2024 22:00:59 -0400 Subject: [PATCH 2/6] add functionality to support xtype=q --- src/diffpy/labpdfproc/functions.py | 63 ++++++++++++++++++++++++------ tests/test_functions.py | 59 +++++++++++++++++++++++++--- 2 files changed, 106 insertions(+), 16 deletions(-) diff --git a/src/diffpy/labpdfproc/functions.py b/src/diffpy/labpdfproc/functions.py index e6f6819..aa15553 100644 --- a/src/diffpy/labpdfproc/functions.py +++ b/src/diffpy/labpdfproc/functions.py @@ -5,7 +5,12 @@ 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 ( + ANGLEQUANTITIES, + DQUANTITIES, + XQUANTITIES, + Diffraction_object, +) RADIUS_MM = 1 N_POINTS_ON_DIAMETER = 300 @@ -198,7 +203,6 @@ 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 +231,6 @@ 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 +249,54 @@ def _cve_method(method): return methods[method] -def compute_cve(diffraction_data, mud, method="polynomial_interpolation"): +def interpolate_to_xtype_grid(cve_do, xtype): + f""" + interpolates the cve grid to the xtype user specifies, raise an error if xtype is invalid + + Parameters + ---------- + cve_do Diffraction_object + the diffraction object that contains the cve to be applied + xtype str + the quantity on the independent variable axis, allowed values are {*XQUANTITIES, } + + Returns + ------- + the new diffraction object with interpolated cve curves + """ + + if xtype.lower() not in XQUANTITIES: + raise ValueError(f"Unknown xtype: {xtype}. Allowed xtypes are {*XQUANTITIES, }.") + if xtype.lower() in ANGLEQUANTITIES or xtype.lower() in DQUANTITIES: + return cve_do + + orig_grid, orig_cve = cve_do.on_tth[0], cve_do.on_tth[1] + new_grid = cve_do.tth_to_q() + new_cve = np.interp(new_grid, orig_grid, orig_cve) + new_cve_do = Diffraction_object(wavelength=cve_do.wavelength) + new_cve_do.insert_scattering_quantity( + new_grid, + new_cve, + xtype, + metadata=cve_do.metadata, + name=cve_do.name, + scat_quantity="cve", + ) + return new_cve_do + + +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, } @@ -265,21 +307,20 @@ def compute_cve(diffraction_data, mud, method="polynomial_interpolation"): cve_function = _cve_method(method) cve_do_on_global_tth = cve_function(diffraction_data, mud) - global_tth = cve_do_on_global_tth.on_tth[0] - cve_on_global_tth = cve_do_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_xtype = interpolate_to_xtype_grid(cve_do_on_global_tth, xtype) + orig_grid = diffraction_data.on_xtype(xtype)[0] + global_xtype = cve_do_on_global_xtype.on_xtype(xtype)[0] + cve_on_global_xtype = cve_do_on_global_xtype.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/tests/test_functions.py b/tests/test_functions.py index ac086a5..59e49f1 100644 --- a/tests/test_functions.py +++ b/tests/test_functions.py @@ -3,8 +3,14 @@ import numpy as np import pytest -from diffpy.labpdfproc.functions import CVE_METHODS, Gridded_circle, apply_corr, compute_cve -from diffpy.utils.scattering_objects.diffraction_objects import Diffraction_object +from diffpy.labpdfproc.functions import ( + CVE_METHODS, + Gridded_circle, + apply_corr, + compute_cve, + interpolate_to_xtype_grid, +) +from diffpy.utils.scattering_objects.diffraction_objects import XQUANTITIES, Diffraction_object params1 = [ ([0.5, 3, 1], {(0.0, -0.5), (0.0, 0.0), (0.5, 0.0), (-0.5, 0.0), (0.0, 0.5)}), @@ -58,12 +64,12 @@ 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"}, @@ -71,6 +77,49 @@ def _instantiate_test_do(xarray, yarray, name="test", scat_quantity="x-ray"): return test_do +params4 = [ + ([np.array([30, 60, 90]), np.array([1, 2, 3]), "tth"], [np.array([30, 60, 90]), np.array([1, 2, 3]), "tth"]), + ( + [np.array([30, 60, 90]), np.array([1, 2, 3]), "q"], + [np.array([2.11195, 4.07999, 5.76998]), np.array([1, 1, 1]), "q"], + ), +] + + +@pytest.mark.parametrize("inputs, expected", params4) +def test_interpolate_xtype(inputs, expected, mocker): + expected_cve_do = _instantiate_test_do( + expected[0], + expected[1], + xtype=expected[2], + name="absorption correction, cve, for test", + scat_quantity="cve", + ) + input_cve_do = _instantiate_test_do( + inputs[0], + inputs[1], + xtype="tth", + name="absorption correction, cve, for test", + scat_quantity="cve", + ) + actual_cve_do = interpolate_to_xtype_grid(input_cve_do, xtype=inputs[2]) + assert actual_cve_do == expected_cve_do + + +def test_interpolate_xtype_bad(): + input_cve_do = _instantiate_test_do( + np.array([30, 60, 90]), + np.array([1, 2, 3]), + xtype="tth", + name="absorption correction, cve, for test", + scat_quantity="cve", + ) + with pytest.raises( + ValueError, match=re.escape(f"Unknown xtype: invalid. Allowed xtypes are {*XQUANTITIES, }.") + ): + interpolate_to_xtype_grid(input_cve_do, xtype="invalid") + + 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]) @@ -92,7 +141,7 @@ 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, }."]), From 1811fe80931adfe15ff914fd332eca96221639a7 Mon Sep 17 00:00:00 2001 From: yucongalicechen Date: Wed, 30 Oct 2024 22:02:57 -0400 Subject: [PATCH 3/6] edit main module to match the edited function --- src/diffpy/labpdfproc/labpdfprocapp.py | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) 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__": From 45039e3f2869b6a24f7b0f781140711171c1c6fa Mon Sep 17 00:00:00 2001 From: yucongalicechen Date: Wed, 30 Oct 2024 22:35:09 -0400 Subject: [PATCH 4/6] add function in tools to set xtype to tth or q --- src/diffpy/labpdfproc/functions.py | 14 +++----------- src/diffpy/labpdfproc/tools.py | 21 +++++++++++++++++++++ tests/test_functions.py | 16 +--------------- tests/test_tools.py | 27 +++++++++++++++++++++++++++ 4 files changed, 52 insertions(+), 26 deletions(-) diff --git a/src/diffpy/labpdfproc/functions.py b/src/diffpy/labpdfproc/functions.py index aa15553..18e198b 100644 --- a/src/diffpy/labpdfproc/functions.py +++ b/src/diffpy/labpdfproc/functions.py @@ -5,12 +5,7 @@ import pandas as pd from scipy.interpolate import interp1d -from diffpy.utils.scattering_objects.diffraction_objects import ( - ANGLEQUANTITIES, - DQUANTITIES, - XQUANTITIES, - Diffraction_object, -) +from diffpy.utils.scattering_objects.diffraction_objects import XQUANTITIES, Diffraction_object RADIUS_MM = 1 N_POINTS_ON_DIAMETER = 300 @@ -251,7 +246,7 @@ def _cve_method(method): def interpolate_to_xtype_grid(cve_do, xtype): f""" - interpolates the cve grid to the xtype user specifies, raise an error if xtype is invalid + interpolates the cve grid to the xtype user specified Parameters ---------- @@ -264,10 +259,7 @@ def interpolate_to_xtype_grid(cve_do, xtype): ------- the new diffraction object with interpolated cve curves """ - - if xtype.lower() not in XQUANTITIES: - raise ValueError(f"Unknown xtype: {xtype}. Allowed xtypes are {*XQUANTITIES, }.") - if xtype.lower() in ANGLEQUANTITIES or xtype.lower() in DQUANTITIES: + if xtype == "tth": return cve_do orig_grid, orig_cve = cve_do.on_tth[0], cve_do.on_tth[1] 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 59e49f1..222be8c 100644 --- a/tests/test_functions.py +++ b/tests/test_functions.py @@ -10,7 +10,7 @@ compute_cve, interpolate_to_xtype_grid, ) -from diffpy.utils.scattering_objects.diffraction_objects import XQUANTITIES, Diffraction_object +from diffpy.utils.scattering_objects.diffraction_objects import Diffraction_object params1 = [ ([0.5, 3, 1], {(0.0, -0.5), (0.0, 0.0), (0.5, 0.0), (-0.5, 0.0), (0.0, 0.5)}), @@ -106,20 +106,6 @@ def test_interpolate_xtype(inputs, expected, mocker): assert actual_cve_do == expected_cve_do -def test_interpolate_xtype_bad(): - input_cve_do = _instantiate_test_do( - np.array([30, 60, 90]), - np.array([1, 2, 3]), - xtype="tth", - name="absorption correction, cve, for test", - scat_quantity="cve", - ) - with pytest.raises( - ValueError, match=re.escape(f"Unknown xtype: invalid. Allowed xtypes are {*XQUANTITIES, }.") - ): - interpolate_to_xtype_grid(input_cve_do, xtype="invalid") - - 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]) 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) From 3bd24cdac741facb9d66c52f536263b7e90c9666 Mon Sep 17 00:00:00 2001 From: yucongalicechen Date: Thu, 31 Oct 2024 11:29:03 -0400 Subject: [PATCH 5/6] remove unnecessary interpolation function, edit test for compute_cve for different xtypes --- src/diffpy/labpdfproc/functions.py | 40 +++------------------------ tests/test_functions.py | 43 ++++++------------------------ 2 files changed, 11 insertions(+), 72 deletions(-) diff --git a/src/diffpy/labpdfproc/functions.py b/src/diffpy/labpdfproc/functions.py index 18e198b..35d587c 100644 --- a/src/diffpy/labpdfproc/functions.py +++ b/src/diffpy/labpdfproc/functions.py @@ -244,39 +244,6 @@ def _cve_method(method): return methods[method] -def interpolate_to_xtype_grid(cve_do, xtype): - f""" - interpolates the cve grid to the xtype user specified - - Parameters - ---------- - cve_do Diffraction_object - the diffraction object that contains the cve to be applied - xtype str - the quantity on the independent variable axis, allowed values are {*XQUANTITIES, } - - Returns - ------- - the new diffraction object with interpolated cve curves - """ - if xtype == "tth": - return cve_do - - orig_grid, orig_cve = cve_do.on_tth[0], cve_do.on_tth[1] - new_grid = cve_do.tth_to_q() - new_cve = np.interp(new_grid, orig_grid, orig_cve) - new_cve_do = Diffraction_object(wavelength=cve_do.wavelength) - new_cve_do.insert_scattering_quantity( - new_grid, - new_cve, - xtype, - metadata=cve_do.metadata, - name=cve_do.name, - scat_quantity="cve", - ) - return new_cve_do - - 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 @@ -298,11 +265,10 @@ def compute_cve(diffraction_data, mud, method="polynomial_interpolation", xtype= """ cve_function = _cve_method(method) - cve_do_on_global_tth = cve_function(diffraction_data, mud) - cve_do_on_global_xtype = interpolate_to_xtype_grid(cve_do_on_global_tth, xtype) + cve_do_on_global_grid = cve_function(diffraction_data, mud) orig_grid = diffraction_data.on_xtype(xtype)[0] - global_xtype = cve_do_on_global_xtype.on_xtype(xtype)[0] - cve_on_global_xtype = cve_do_on_global_xtype.on_xtype(xtype)[1] + 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( diff --git a/tests/test_functions.py b/tests/test_functions.py index 222be8c..f23c32d 100644 --- a/tests/test_functions.py +++ b/tests/test_functions.py @@ -3,13 +3,7 @@ import numpy as np import pytest -from diffpy.labpdfproc.functions import ( - CVE_METHODS, - Gridded_circle, - apply_corr, - compute_cve, - interpolate_to_xtype_grid, -) +from diffpy.labpdfproc.functions import CVE_METHODS, Gridded_circle, apply_corr, compute_cve from diffpy.utils.scattering_objects.diffraction_objects import Diffraction_object params1 = [ @@ -78,44 +72,23 @@ def _instantiate_test_do(xarray, yarray, xtype="tth", name="test", scat_quantity params4 = [ - ([np.array([30, 60, 90]), np.array([1, 2, 3]), "tth"], [np.array([30, 60, 90]), np.array([1, 2, 3]), "tth"]), - ( - [np.array([30, 60, 90]), np.array([1, 2, 3]), "q"], - [np.array([2.11195, 4.07999, 5.76998]), np.array([1, 1, 1]), "q"], - ), + (["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_interpolate_xtype(inputs, expected, mocker): - expected_cve_do = _instantiate_test_do( - expected[0], - expected[1], - xtype=expected[2], - name="absorption correction, cve, for test", - scat_quantity="cve", - ) - input_cve_do = _instantiate_test_do( - inputs[0], - inputs[1], - xtype="tth", - name="absorption correction, cve, for test", - scat_quantity="cve", - ) - actual_cve_do = interpolate_to_xtype_grid(input_cve_do, xtype=inputs[2]) - assert actual_cve_do == expected_cve_do - - -def test_compute_cve(mocker): +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", ) From b558f1801b061b3d937b087ff2d7ab14cdf24893 Mon Sep 17 00:00:00 2001 From: yucongalicechen Date: Thu, 31 Oct 2024 14:31:21 -0400 Subject: [PATCH 6/6] add news --- news/xtype.rst | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 news/xtype.rst 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:** + +* + +**Deprecated:** + +* + +**Removed:** + +* + +**Fixed:** + +* + +**Security:** + +*