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gui.py
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from gooey import Gooey, GooeyParser
import mscl_aggregator as mst
import renamer
import xrf_aggregator as xrf
import xyz_aggregator as xyz
@Gooey(
program_name=f"Data Aggregator and Renamer {renamer.version}",
navigation="TABBED",
default_size=(600, 680),
)
def main():
parser = GooeyParser(
description="Aggregate and assign CoreID names to data from Geotek and Itrax machines."
)
subs = parser.add_subparsers(help="commands", dest="command")
mst_parser = subs.add_parser("MSCL-S", help="Combine whole-core data.")
input_output_mst = mst_parser.add_argument_group(gooey_options={"columns": 1})
input_output_mst.add_argument(
"input_directory",
metavar="Input Directory",
type=str,
widget="DirChooser",
help="Directory containing the MSCL-S folders.",
)
input_output_mst.add_argument(
"output_filename",
metavar="Output Filename",
type=str,
help="Name of the combined output file.",
)
input_output_mst.add_argument(
"separator",
metavar="Data Directory Naming Convention",
help="Text portion of data directory name preceding part number e.g. '-p' for -p1, -p2, -p3... or '_part' for _part1, _part2, _part3...",
type=str,
widget="Dropdown",
choices=["_p", "_part", "-p", "-part"],
default="_p"
)
options_mst = mst_parser.add_argument_group("Options", gooey_options={"columns": 1})
options_mst.add_argument(
"-e",
"--excel",
metavar="Export as Excel ",
action="store_true",
help="Export combined data as an Excel (xlsx) file.",
)
options_mst.add_argument(
"-v",
"--verbose",
metavar="Verbose ",
action="store_true",
help="Display troubleshooting info.",
)
xyz_parser = subs.add_parser("MSCL-XYZ", help="Combine split-core data.")
input_output_xyz = xyz_parser.add_argument_group(gooey_options={"columns": 1})
input_output_xyz.add_argument(
"input_directory",
metavar="Input Directory",
type=str,
widget="DirChooser",
help="Directory containing the MSCL-XYZ folders.",
)
input_output_xyz.add_argument(
"output_filename",
metavar="Output Filename",
type=str,
help="Name of the combined output file.",
)
input_output_xyz.add_argument(
"separator",
metavar="Data Directory Naming Convention",
help="Text portion of data directory name preceding part number e.g. '-p' for -p1, -p2, -p3... or '_part' for _part1, _part2, _part3...",
type=str,
widget="Dropdown",
choices=["-p", "-part", "_p", "_part"],
default="-part"
)
options_xyz = xyz_parser.add_argument_group("Options", gooey_options={"columns": 1})
options_xyz.add_argument(
"-f",
"--filter",
metavar="Filter bad MS values",
action="store_true",
help="Filter magnetic susceptibility values < -50 (machine error) ",
)
options_xyz.add_argument(
"-e",
"--excel",
metavar="Export as Excel ",
action="store_true",
help="Export combined data as an Excel (xlsx) file.",
)
options_xyz.add_argument(
"-v",
"--verbose",
metavar="Verbose ",
action="store_true",
help="Display troubleshooting info.",
)
xrf_parser = subs.add_parser("XRF", help="Combine XRF data.")
input_output_xrf = xrf_parser.add_argument_group(gooey_options={"columns": 1})
input_output_xrf.add_argument(
"input_directory",
metavar="Input Directory",
type=str,
widget="DirChooser",
help="Directory containing the XRF folders.",
)
input_output_xrf.add_argument(
"output_filename",
metavar="Output Filename",
type=str,
help="Name of the combined output file.",
)
options_xrf = xrf_parser.add_argument_group("Options", gooey_options={"columns": 1})
options_xrf.add_argument(
"-s",
"--sitehole",
metavar="Export by SiteHole ",
action="store_true",
help="Split aggregated
A2AD
data by SiteHole and export each file individually.",
)
options_xrf.add_argument(
"-e",
"--excel",
metavar="Export as Excel ",
action="store_true",
help="Export combined data as an Excel (xlsx) file.",
)
options_xrf.add_argument(
"-v",
"--verbose",
metavar="Verbose ",
action="store_true",
help="Display troubleshooting info.",
)
renamer_parser = subs.add_parser(
"Rename", help="Rename aggregated data with CoreIDs"
)
input_output_renamer = renamer_parser.add_argument_group(
gooey_options={"columns": 1}
)
input_output_renamer.add_argument(
"input_file",
widget="FileChooser",
metavar="Input file (without CoreIDs)",
help="Name of input file.",
)
input_output_renamer.add_argument(
"corelist",
widget="FileChooser",
metavar="Core list file",
help="CSV in the format coreID,sectionNumber",
)
options_renamer = renamer_parser.add_argument_group(
"Optional Parameters ",
"The program will try to make sensible choices if these are left blank.",
gooey_options={"columns": 2},
)
options_renamer.add_argument(
"-o",
"--output_filename",
metavar="Output filename",
type=str,
help="Name of the output file.",
)
options_renamer.add_argument(
"-v",
"--verbose",
metavar="Verbose ",
action="store_true",
help="Print troubleshooting information.",
)
options_renamer.add_argument(
"-s",
"--section_column",
type=int,
metavar="Section Number Column",
help="Column number the section numbers are in (count starts at 0).",
)
options_renamer.add_argument(
"-d",
"--depth_column",
type=int,
metavar="Section Depth Column",
help="Column number the section depths are in (count starts at 0).",
)
args = parser.parse_args()
if args.command == "MSCL-S":
mst.aggregate_mscl_data(
input_dir=args.input_directory,
out_filename=args.output_filename,
separator=args.separator,
excel=args.excel,
verbose=args.verbose,
)
elif args.command == "MSCL-XYZ":
print(args)
xyz.aggregate_xyz_data(
input_dir=args.input_directory,
out_filename=args.output_filename,
separator=args.separator,
filter=args.filter,
excel=args.excel,
verbose=args.verbose,
)
elif args.command == "XRF":
xrf.aggregate_xrf_data(
input_dir=args.input_directory,
out_filename=args.output_filename,
excel=args.excel,
sitehole=args.sitehole,
verbose=args.verbose,
)
elif args.command == "Rename":
renamer.apply_names(
args.input_file,
args.corelist,
section_column=args.section_column,
depth_column=args.depth_column,
output_filename=args.output_filename,
verbose=args.verbose,
)
else:
print(f"Something went wrong. Invalid data type: {args.data_type}")
if __name__ == "__main__":
main()