Utilities

Overview of utilities offered by diffpy.labpdfproc. Check the examples provided for how to use these.

labpdfprocapp Utility

The diffpy.labpdfproc.labpdfprocapp module provides both a command-line (CLI) and graphical user interface (GUI) for processing diffraction data, applying absorption correction, and saving the output files.

  • get_args(): This function parses all CLI arguments.

  • gooey_parser(): This function provides a GUI for argument input.

  • main(): This function validates all arguments, performs preprocessing, and saves the output files.

For a more in-depth tutorial for how to get started, click here.

Functions Utility

The diffpy.labpdfproc.functions module provides tools for computing and applying absorption correction (cve) to 1D diffraction patterns.

  • Gridded_circle: This class supports absorption correction by creating a uniform grid of points within a circle for a given radius and linear absorption coefficient mu, and computing the path length and effective volume for each grid point at a given angle.

  • compute_cve: This function computes the absorption correction curve for a given muD value (the product of mu and capillary diameter D). For brute-force computation, it averages the effective volume across all grid points and computes the cve values as the reciprocal of this average. Alternatively, for fast calculation, it uses polynomial interpolation with pre-computed coefficients to estimate cve values for a given muD. Polynomial interpolation is available for muD values between 0.5-7.

  • apply_corr: This function applies the computed absorption correction to the input diffraction pattern by multiplying it with the corresponding cve, resulting in a corrected diffraction pattern.

For a more in-depth tutorial for how to use these tools, click here.

Tools Utility

The diffpy.labpdfproc.tools module provides functions to manage user inputs, output directories, and diffraction information. These functions work mostly with an argparse.Namespace object and help prepare data for diffraction processing.

  • set_mud(): This function determines the muD value used to compute absorption correction. Users can either provide the value directly, upload a z-scan file, or specify relevant chemical information to get a theoretical estimation.

  • set_input_lists(): This function parses all specified input files. Users can provide a list of files or directories via command-line arguments or GUI selection. You can also specify a file_list.txt that contains file paths (one per line), including paths to entire directories. Wildcard patterns are also supported for matching multiple files.

  • set_output_directory(): This function ensures that an output directory is defined and exists. If it is not explicitly provided, it defaults to the current working directory. This directory is used to store all cve and corrected output files.

  • load_wavelength_from_config_file() and set_wavelength(): These two functions work together to determine the wavelength for processing. load_wavelength_from_config_file() reads the default wavelength or anode type from user input or a diffpy configuration file, and set_wavelength() finalizes the wavelength value. It is recommended to store the wavelength information in a diffpy configuration file to avoid re-entering it every time.

  • set_xtype(): This function sets the x-axis variable for intensity interpolation (e.g. two-theta, q, d-spacing) and should be the same of the input diffraction data. The default is two-theta.

  • load_user_metadata(): This function loads experimental metadata or any user-defined key-value pairs to be recorded in the output files.

  • load_user_info(): This function loads user identification (name, email, orcid). Users can provide the information directly through arguments or store it in a diffpy configuration file. If no information is found, the function will prompt the user to create a configuration file, which is then saved for use in output metadata and future uses.

  • load_package_info(): This functions stores the package name and version for record-keeping.

  • preprocessing_args(): This is a convenience function that runs all standard setup steps listed above. It ensures the input/output paths, wavelength, muD value, metadata, and user and package info are fully initialized before applying the correction.

  • load_metadata(): This function transfers all collected information from the argparse.Namespace object into a diffraction object, allowing it to be saved in the output file header for tracking purpose.

For a more in-depth tutorial for how to use these tools, click here.