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add gooey support #130

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merged 7 commits into from
Nov 26, 2024
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add gooey support #130

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add gui feature
yucongalicechen Nov 19, 2024
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add gooey package
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Merge branch 'main' into gui
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258 changes: 137 additions & 121 deletions src/diffpy/labpdfproc/labpdfprocapp.py
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Original file line number Diff line number Diff line change
@@ -1,140 +1,156 @@
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.parsers.loaddata import loadData
from diffpy.utils.scattering_objects.diffraction_objects import XQUANTITIES, Diffraction_object


def define_arguments():
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Since we need to redefine the input and zscan file arguments for gui, I think it's easier if we put all arguments in a separate function, so that later when we update the arguments we only need to update this.

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",
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When we have cli we support a mixture of multiple files, folders, and wildcards. In gui I think we can only choose one of multiple file or folder for one argument. I can maybe add another argument for selecting folders?

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yes, if that is the case in teh gui let's have them as separate inputs

},
{
"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()
p.add_argument("mud", help="Value of mu*D for your " "sample. Required.", type=float)
p.add_argument(
"input",
nargs="+",
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)."
),
)
p.add_argument(
"-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",
)
p.add_argument(
"-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."
),
default=None,
type=float,
)
p.add_argument(
"-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,
)
p.add_argument(
"-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",
)
p.add_argument(
"-c",
"--output-correction",
action="store_true",
help=(
"The absorption correction will be output to a file if this "
"flag is set. Default is that it is not output."
),
)
p.add_argument(
"-f",
"--force-overwrite",
action="store_true",
help="Outputs will not overwrite existing file unless --force is specified.",
)
p.add_argument(
"-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",
)
p.add_argument(
"-u",
"--user-metadata",
metavar="KEY=VALUE",
nargs="+",
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. "
),
)
p.add_argument(
"-n",
"--username",
help=(
"Username will be loaded from config files. Specify here "
"only if you want to override that behavior at runtime. "
),
default=None,
)
p.add_argument(
"-e",
"--email",
help=(
"Email will be loaded from config files. Specify here "
"only if you want to override that behavior at runtime. "
),
default=None,
)
p.add_argument(
"-z",
"--z-scan-file",
help="Path to the z-scan file to be loaded to determine the mu*D value",
default=None,
)
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 = get_args()
args = gooey_parser() if len(sys.argv) == 1 or "--gui" in sys.argv else get_args()
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args = preprocessing_args(args)

for filepath in args.input_paths:
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