labpdfprocapp.py

import sys
from argparse import ArgumentParser

from gooey import Gooey, GooeyParser

from diffpy.labpdfproc.functions import CVE_METHODS, apply_corr, compute_cve
from diffpy.labpdfproc.tools import known_sources, load_metadata, preprocessing_args
from diffpy.utils.diffraction_objects import XQUANTITIES, DiffractionObject
from diffpy.utils.parsers.loaddata import loadData


def define_arguments():
    args = [
        {
            "name": ["mud"],
            "help": "Value of mu*D for your sample. Required.",
            "type": float,
        },
        {
            "name": ["input"],
            "help": (
                "The filename(s) or folder(s) of the datafile(s) to load. "
                "Required.\nSupply a space-separated list of files or directories. "
                "Long lists can be supplied, one per line, in a file with name "
                "file_list.txt. If one or more directory is provided, all valid "
                "data-files in that directory will be processed. Examples of valid "
                "inputs are 'file.xy', 'data/file.xy', 'file.xy, data/file.xy', "
                "'.' (load everything in the current directory), 'data' (load "
                "everything in the folder ./data), 'data/file_list.txt' (load "
                "the list of files contained in the text-file called "
                "file_list.txt that can be found in the folder ./data), "
                "'./*.chi', 'data/*.chi' (load all files with extension .chi in the "
                "folder ./data)."
            ),
            "nargs": "+",
            "widget": "MultiFileChooser",
        },
        {
            "name": ["-a", "--anode-type"],
            "help": (
                f"The type of the x-ray source. Allowed values are "
                f"{*[known_sources], }. Either specify a known x-ray source or specify wavelength."
            ),
            "default": "Mo",
        },
        {
            "name": ["-w", "--wavelength"],
            "help": (
                "X-ray source wavelength in angstroms. Not needed if the anode-type "
                "is specified. This wavelength will override the anode wavelength if both are specified."
            ),
            "type": float,
        },
        {
            "name": ["-o", "--output-directory"],
            "help": (
                "The name of the output directory. If not specified "
                "then corrected files will be written to the current directory. "
                "If the specified directory doesn't exist it will be created."
            ),
            "default": None,
        },
        {
            "name": ["-x", "--xtype"],
            "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."
            ),
            "default": "tth",
        },
        {
            "name": ["-c", "--output-correction"],
            "help": (
                "The absorption correction will be output to a file if this "
                "flag is set. Default is that it is not output."
            ),
            "action": "store_true",
        },
        {
            "name": ["-f", "--force-overwrite"],
            "help": "Outputs will not overwrite existing file unless --force is specified.",
            "action": "store_true",
        },
        {
            "name": ["-m", "--method"],
            "help": (
                f"The method for computing absorption correction. Allowed methods: {*CVE_METHODS, }. "
                f"Default method is polynomial interpolation if not specified. "
            ),
            "default": "polynomial_interpolation",
        },
        {
            "name": ["-u", "--user-metadata"],
            "help": (
                "Specify key-value pairs to be loaded into metadata using the format key=value. "
                "Separate pairs with whitespace, and ensure no whitespaces before or after the = sign. "
                "Avoid using = in keys. If multiple = signs are present, "
                "only the first separates the key and value. "
                "If a key or value contains whitespace, enclose it in quotes. "
                "For example, facility='NSLS II', 'facility=NSLS II', beamline=28ID-2, "
                "'beamline'='28ID-2', 'favorite color'=blue, are all valid key=value items. "
            ),
            "nargs": "+",
            "metavar": "KEY=VALUE",
        },
        {
            "name": ["-n", "--username"],
            "help": (
                "Username will be loaded from config files. Specify here "
                "only if you want to override that behavior at runtime. "
            ),
            "default": None,
        },
        {
            "name": ["-e", "--email"],
            "help": (
                "Email will be loaded from config files. Specify here "
                "only if you want to override that behavior at runtime. "
            ),
            "default": None,
        },
        {
            "name": ["-z", "--z-scan-file"],
            "help": "Path to the z-scan file to be loaded to determine the mu*D value",
            "default": None,
            "widget": "FileChooser",
        },
    ]
    return args


def get_args(override_cli_inputs=None):
    p = ArgumentParser()
    for arg in define_arguments():
        kwargs = {key: value for key, value in arg.items() if key != "name" and key != "widget"}
        p.add_argument(*arg["name"], **kwargs)
    args = p.parse_args(override_cli_inputs)
    return args


@Gooey(required_cols=1, optional_cols=1, program_name="Labpdfproc GUI")
def gooey_parser():
    p = GooeyParser()
    for arg in define_arguments():
        kwargs = {key: value for key, value in arg.items() if key != "name"}
        p.add_argument(*arg["name"], **kwargs)
    args = p.parse_args()
    return args


def main():
    args = gooey_parser() if len(sys.argv) == 1 or "--gui" in sys.argv else get_args()
    args = preprocessing_args(args)

    for filepath in args.input_paths:
        outfilestem = filepath.stem + "_corrected"
        corrfilestem = filepath.stem + "_cve"
        outfile = args.output_directory / (outfilestem + ".chi")
        corrfile = args.output_directory / (corrfilestem + ".chi")

        if outfile.exists() and not args.force_overwrite:
            sys.exit(
                f"Output file {str(outfile)} already exists. Please rerun "
                f"specifying -f if you want to overwrite it."
            )
        if corrfile.exists() and args.output_correction and not args.force_overwrite:
            sys.exit(
                f"Corrections file {str(corrfile)} was requested and already "
                f"exists. Please rerun specifying -f if you want to overwrite it."
            )

        xarray, yarray = loadData(filepath, unpack=True)
        input_pattern = DiffractionObject(
            xarray=xarray,
            yarray=yarray,
            xtype=args.xtype,
            wavelength=args.wavelength,
            scat_quantity="x-ray",
            name=filepath.stem,
            metadata=load_metadata(args, filepath),
        )

        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=args.xtype)

        if args.output_correction:
            absorption_correction.dump(f"{corrfile}", xtype=args.xtype)


if __name__ == "__main__":
    main()