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Merge pull request #130 from yucongalicechen/gui
add gooey support
2 parents a1dba3c + f09bd49 commit a2572da

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-121
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‎news/gui.rst

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**Added:**
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* Gooey support so that the app can be run with GUI
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**Changed:**
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* <news item>
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**Deprecated:**
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* <news item>
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**Removed:**
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* <news item>
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**Fixed:**
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* <news item>
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**Security:**
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* <news item>

‎requirements/conda.txt

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@@ -2,3 +2,4 @@ numpy
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diffpy.utils
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pandas
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scipy
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gooey

‎requirements/pip.txt

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@@ -2,3 +2,4 @@ numpy
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diffpy.utils
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pandas
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scipy
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gooey

‎src/diffpy/labpdfproc/labpdfprocapp.py

+137-121
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@@ -1,140 +1,156 @@
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import sys
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from argparse import ArgumentParser
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from gooey import Gooey, GooeyParser
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from diffpy.labpdfproc.functions import CVE_METHODS, apply_corr, compute_cve
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from diffpy.labpdfproc.tools import known_sources, load_metadata, preprocessing_args
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from diffpy.utils.parsers.loaddata import loadData
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from diffpy.utils.scattering_objects.diffraction_objects import XQUANTITIES, Diffraction_object
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911

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def define_arguments():
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args = [
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{
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"name": ["mud"],
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"help": "Value of mu*D for your sample. Required.",
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"type": float,
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},
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{
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"name": ["input"],
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"help": (
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"The filename(s) or folder(s) of the datafile(s) to load. "
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"Required.\nSupply a space-separated list of files or directories. "
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"Long lists can be supplied, one per line, in a file with name "
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"file_list.txt. If one or more directory is provided, all valid "
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"data-files in that directory will be processed. Examples of valid "
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"inputs are 'file.xy', 'data/file.xy', 'file.xy, data/file.xy', "
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"'.' (load everything in the current directory), 'data' (load "
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"everything in the folder ./data), 'data/file_list.txt' (load "
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"the list of files contained in the text-file called "
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"file_list.txt that can be found in the folder ./data), "
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"'./*.chi', 'data/*.chi' (load all files with extension .chi in the "
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"folder ./data)."
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),
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"nargs": "+",
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"widget": "MultiFileChooser",
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},
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{
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"name": ["-a", "--anode-type"],
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"help": (
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f"The type of the x-ray source. Allowed values are "
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f"{*[known_sources], }. Either specify a known x-ray source or specify wavelength."
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),
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"default": "Mo",
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},
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{
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"name": ["-w", "--wavelength"],
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"help": (
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"X-ray source wavelength in angstroms. Not needed if the anode-type "
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"is specified. This wavelength will override the anode wavelength if both are specified."
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),
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"type": float,
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},
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{
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"name": ["-o", "--output-directory"],
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"help": (
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"The name of the output directory. If not specified "
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"then corrected files will be written to the current directory. "
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"If the specified directory doesn't exist it will be created."
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),
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"default": None,
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},
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{
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"name": ["-x", "--xtype"],
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"help": (
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f"The quantity on the independent variable axis. Allowed "
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f"values: {*XQUANTITIES, }. If not specified then two-theta "
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f"is assumed for the independent variable."
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),
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"default": "tth",
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},
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{
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"name": ["-c", "--output-correction"],
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"help": (
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"The absorption correction will be output to a file if this "
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"flag is set. Default is that it is not output."
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),
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"action": "store_true",
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},
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{
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"name": ["-f", "--force-overwrite"],
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"help": "Outputs will not overwrite existing file unless --force is specified.",
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"action": "store_true",
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},
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{
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"name": ["-m", "--method"],
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"help": (
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f"The method for computing absorption correction. Allowed methods: {*CVE_METHODS, }. "
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f"Default method is polynomial interpolation if not specified. "
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),
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"default": "polynomial_interpolation",
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},
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{
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"name": ["-u", "--user-metadata"],
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"help": (
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"Specify key-value pairs to be loaded into metadata using the format key=value. "
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"Separate pairs with whitespace, and ensure no whitespaces before or after the = sign. "
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"Avoid using = in keys. If multiple = signs are present, "
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"only the first separates the key and value. "
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"If a key or value contains whitespace, enclose it in quotes. "
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"For example, facility='NSLS II', 'facility=NSLS II', beamline=28ID-2, "
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"'beamline'='28ID-2', 'favorite color'=blue, are all valid key=value items. "
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),
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"nargs": "+",
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"metavar": "KEY=VALUE",
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},
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{
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"name": ["-n", "--username"],
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"help": (
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"Username will be loaded from config files. Specify here "
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"only if you want to override that behavior at runtime. "
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),
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"default": None,
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},
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{
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"name": ["-e", "--email"],
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"help": (
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"Email will be loaded from config files. Specify here "
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"only if you want to override that behavior at runtime. "
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),
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"default": None,
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},
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{
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"name": ["-z", "--z-scan-file"],
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"help": "Path to the z-scan file to be loaded to determine the mu*D value",
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"default": None,
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"widget": "FileChooser",
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},
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]
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return args
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def get_args(override_cli_inputs=None):
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p = ArgumentParser()
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p.add_argument("mud", help="Value of mu*D for your " "sample. Required.", type=float)
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p.add_argument(
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"input",
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nargs="+",
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help=(
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"The filename(s) or folder(s) of the datafile(s) to load. "
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"Required.\nSupply a space-separated list of files or directories. "
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"Long lists can be supplied, one per line, in a file with name "
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"file_list.txt. If one or more directory is provided, all valid "
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"data-files in that directory will be processed. Examples of valid "
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"inputs are 'file.xy', 'data/file.xy', 'file.xy, data/file.xy', "
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"'.' (load everything in the current directory), 'data' (load "
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"everything in the folder ./data), 'data/file_list.txt' (load "
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"the list of files contained in the text-file called "
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"file_list.txt that can be found in the folder ./data), "
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"'./*.chi', 'data/*.chi' (load all files with extension .chi in the "
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"folder ./data)."
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),
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)
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p.add_argument(
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"-a",
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"--anode-type",
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help=(
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f"The type of the x-ray source. Allowed values are "
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f"{*[known_sources], }. Either specify a known x-ray source or specify wavelength."
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),
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default="Mo",
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)
40-
p.add_argument(
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"-w",
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"--wavelength",
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help=(
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"X-ray source wavelength in angstroms. Not needed if the anode-type "
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"is specified. This wavelength will override the anode wavelength if both are specified."
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),
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default=None,
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type=float,
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)
50-
p.add_argument(
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"-o",
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"--output-directory",
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help=(
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"The name of the output directory. If not specified "
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"then corrected files will be written to the current directory. "
56-
"If the specified directory doesn't exist it will be created."
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),
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default=None,
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)
60-
p.add_argument(
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"-x",
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"--xtype",
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help=(
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f"The quantity on the independent variable axis. Allowed "
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f"values: {*XQUANTITIES, }. If not specified then two-theta "
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f"is assumed for the independent variable."
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),
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default="tth",
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)
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p.add_argument(
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"-c",
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"--output-correction",
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action="store_true",
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help=(
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"The absorption correction will be output to a file if this "
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"flag is set. Default is that it is not output."
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),
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)
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p.add_argument(
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"-f",
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"--force-overwrite",
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action="store_true",
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help="Outputs will not overwrite existing file unless --force is specified.",
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)
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p.add_argument(
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"-m",
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"--method",
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help=(
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f"The method for computing absorption correction. Allowed methods: {*CVE_METHODS, }. "
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f"Default method is polynomial interpolation if not specified. "
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),
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default="polynomial_interpolation",
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)
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p.add_argument(
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"-u",
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"--user-metadata",
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metavar="KEY=VALUE",
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nargs="+",
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help=(
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"Specify key-value pairs to be loaded into metadata using the format key=value. "
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"Separate pairs with whitespace, and ensure no whitespaces before or after the = sign. "
102-
"Avoid using = in keys. If multiple = signs are present, only the first separates the key and value. "
103-
"If a key or value contains whitespace, enclose it in quotes. "
104-
"For example, facility='NSLS II', 'facility=NSLS II', beamline=28ID-2, "
105-
"'beamline'='28ID-2', 'favorite color'=blue, are all valid key=value items. "
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),
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)
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p.add_argument(
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"-n",
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"--username",
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help=(
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"Username will be loaded from config files. Specify here "
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"only if you want to override that behavior at runtime. "
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),
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default=None,
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)
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p.add_argument(
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"-e",
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"--email",
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help=(
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"Email will be loaded from config files. Specify here "
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"only if you want to override that behavior at runtime. "
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),
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default=None,
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)
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p.add_argument(
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"-z",
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"--z-scan-file",
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help="Path to the z-scan file to be loaded to determine the mu*D value",
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default=None,
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)
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for arg in define_arguments():
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kwargs = {key: value for key, value in arg.items() if key != "name" and key != "widget"}
137+
p.add_argument(*arg["name"], **kwargs)
132138
args = p.parse_args(override_cli_inputs)
133139
return args
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135141

142+
@Gooey(required_cols=1, optional_cols=1, program_name="Labpdfproc GUI")
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def gooey_parser():
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p = GooeyParser()
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for arg in define_arguments():
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kwargs = {key: value for key, value in arg.items() if key != "name"}
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p.add_argument(*arg["name"], **kwargs)
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args = p.parse_args()
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return args
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def main():
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args = get_args()
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args = gooey_parser() if len(sys.argv) == 1 or "--gui" in sys.argv else get_args()
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args = preprocessing_args(args)
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for filepath in args.input_paths:

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