Tools Example

This example will demonstrate how to use diffpy.labpdfproc.tools module to preprocess diffraction data using an argparse.Namespace called args. These functions help set up inputs, metadata, and parameters before applying absorption correction.

1. We begin by estimating the mu*D value used for absorption correction using set_mud(args). You can do this in one of the following four ways:

from argparse import Namespace
# Option 1: Manual value
args = Namespace(mud=2)
# Option 2: From a z-scan file
args = Namespace(z_scan_file="zscan.xy")
# Option 3: Using sample mass density
args = Namespace(sample_composition="ZrO2", sample_mass_density="17.45", diameter="1.2")
# Set and view the computed mu*D value
args = set_mud(args)
print(args.mud)

  1. Next, we load the input files for correction using set_input_lists(args):

args = Namespace(input="file1.xy file2.xy")
args = set_input_lists(args)
print(args.input_paths)

This function resolves the input filenames into full file paths. For details on supported input formats, check labpdfproc --help.

  1. We now set the output directory where the cve and corrected files will be saved:

args = Namespace(output_directory="output") # creates "output/" directory if it doesn't exist
args = set_output_directory(args)
print(args.output_directory)

If a filename is provided instead of a directory, an error will be raised. If no output directory is specified, it defaults to the current working directory.

  1. We then set wavelength and xtype, both of which are necessary for absorption correction:

# Option 1: Specify wavelength directly
args = Namespace(wavelength=0.7)
# Option 2: Use a valid anode type
args = Namespace(wavelength="Mo")
args = set_wavelength(args)

Note that you should specify either a wavelength or an anode type, not both, to avoid conflicts. If you provide an anode type, the corresponding wavelength will be retrieved from global parameters. You may use labpdfproc --help to view a list of valid anode types. If neither is given, it’s only acceptable if the input diffraction data is already on a two-theta grid.

To set the x-axis type (xtype) for your diffraction data:

args = Namespace(xtype="tth")
args = set_xtype(args)

This sets the xtype to tth. Other valid options including q and d spacing.

1. Finally, we load user metadata, user information, and package information into args. To load metadata, pass key-value pairs as a list:

args = Namespace(
    user_metadata=[
        "facility=NSLS II",
        "beamline=28ID-2",
])
args = load_user_metadata(args)

This ensures all key-value pairs are parsed and added as attributes.

To load your user information (username, email, and orcid), you can manually add it through args:

args = Namespace(username="Joe", email="joe@example.com", orcid="0000-0000-0000-0000")
args = load_user_info(args)
print(args.username, args.email, args.orcid)

Alternatively, this can be saved in a config file (see https://www.diffpy.org/diffpy.utils/examples/tools_example.html). If nothing is found, you will be prompted to create one. Note that it is not recommended to store personal information on a public or shared computer.

Furthermore, the function load_package_info(args) is used to attach package name and version info for reproducibility. This is typically run automatically but can be called explicitly:

args = load_package_info(args)
print(args.package_info) # Output example: {"diffpy.labpdfproc": "0.0.1", "diffpy.utils": "3.0.0"}

  1. We also provide a convenient function to run all steps above at once:

args = preprocessing_args(args)

7. The final step is converting your args to a metadata dictionary so that it can be attached to the diffraction object’s header during output writing. Using the function load_metadata(args, filepath) requires both the argument.Namespace and the current input file path. For more details about working with diffraction objects and how they are written to output files, see https://www.diffpy.org/diffpy.utils/examples/diffraction_objects_example.html.

Creating diffpyconfig.json file

To simplify workflows and avoid re-entering it every time, we recommend saving the wavelength or anode type to a diffpy config file. For example,

from pathlib import Path
import json
home_dir = Path.home()
wavelength_data = {"wavelength": 0.3}
with open(home_dir / "diffpyconfig.json", "w") as f:
    json.dump(wavelength_data, f)