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Oct 21, 2025
Merged

Flake8 changes #23

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16 changes: 11 additions & 5 deletions aemworkflow/aemworkflow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,11 +6,13 @@
from .interpretation import main as interpretation
from .exports import main as exports


@click.group()
def cli():
"""AEM Interpretation Conversion CLI."""
pass


@cli.command()
@click.option("--i", "input_directory", type=click.Path(exists=True), required=True)
@click.option("--o", "output_directory", type=click.Path(), required=True)
Expand All @@ -21,11 +23,12 @@ def cli():
def pre_interpret(input_directory, output_directory, crs, gis="esri_arcmap_0.5", lines=10, lines_increment=30):
try:
pre_interpretation(input_directory, output_directory, crs, gis, lines, lines_increment)
click.echo(f"Completed pre-interpretation")
click.echo("Completed pre-interpretation")
except Exception as e:
click.echo(f"Error: {e}", err=True)
sys.exit(1)


@cli.command()
@click.option("--i", "input_directory", type=click.Path(exists=True), required=True)
@click.option("--o", "output_directory", type=click.Path(), required=True)
Expand All @@ -36,35 +39,38 @@ def pre_interpret(input_directory, output_directory, crs, gis="esri_arcmap_0.5",
def interpret(input_directory, output_directory, crs="28349", gis="esri_arcmap_0.5", lines=10, lines_increment=30):
try:
interpretation(input_directory, output_directory, crs, gis, lines, lines_increment)
click.echo(f"Completed interpretation")
click.echo("Completed interpretation")
except Exception as e:
click.echo(f"Error: {e}", err=True)
sys.exit(1)


@cli.command()
@click.option("--i", "input_directory", type=click.Path(exists=True), required=True)
@click.option("--o", "output_directory", type=click.Path(), required=True)
@click.option("--a", "asud_filename", type=click.Path(exists=True), required=True)
def validate(input_directory, output_directory, asud_filename):
try:
validation(input_directory, output_directory, asud_filename)
click.echo(f"Completed validation")
click.echo("Completed validation")
except Exception as e:
click.echo(f"Error: {e}", err=True)
sys.exit(1)


@cli.command()
@click.option("--i", "input_directory", type=click.Path(exists=True), required=True)
@click.option("--o", "output_directory", type=click.Path(), required=True)
@click.option("--crs", default="28349", help="Coordinate Reference System (default: EPSG:28349)")
def convert(input_directory, output_directory, crs):
try:
conversion(input_directory, output_directory, crs)
click.echo(f"Completed conversion")
click.echo("Completed conversion")
except Exception as e:
click.echo(f"Error: {e}", err=True)
sys.exit(1)


@cli.command()
@click.option("--i", "input_directory", type=click.Path(exists=True), required=True)
@click.option("--o", "output_directory", type=click.Path(), required=True)
Expand All @@ -76,7 +82,7 @@ def convert(input_directory, output_directory, crs):
def export(input_directory, output_directory, boundary_filename, split_filename, mdc, mdch, egs):
try:
exports(input_directory, output_directory, boundary_filename, split_filename, mdc, mdch, egs)
click.echo(f"Completed export")
click.echo("Completed export")
except Exception as e:
click.echo(f"Error: {e}", err=True)
sys.exit(1)
2 changes: 1 addition & 1 deletion aemworkflow/conversion.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ def conversion_zedfix_gmt_to_srt(wrk_dir: str, path_dir: str, ext_file: str, log
fidd = 0
row = exdf.query("nm == @nm")
y_scale = (row['t_bot'].iloc[0] - row['t_top'].iloc[0]) /\
(row['frame_bot'].iloc[0] - row['frame_top'].iloc[0])
(row['frame_bot'].iloc[0] - row['frame_top'].iloc[0])
p_file = Path(path_dir) / f"{nm}.path.txt"
tdf = pd.read_csv(p_file, sep=r'\s+', names=pcols, header=None, index_col=False)
# pdf_list.append(tdf)
Expand Down
116 changes: 58 additions & 58 deletions aemworkflow/exports.py
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Original file line number Diff line number Diff line change
Expand Up @@ -200,8 +200,8 @@ def gmtsddd_to_mdch(wrk_dir: str, colors: str, nm_list: List[int]) -> None:
csvwriter.writerow([f"name:{filen[0]}_{segn}_{line[2]}"])
csvwriter.writerow(["*atoms:false"])
csvwriter.writerow(["*line*color: %f %f %f 1" % (r[line[2]] / 256,
g[line[2]] / 256,
b[line[2]] / 256)])
g[line[2]] / 256,
b[line[2]] / 256)])
csvwriter.writerow(["use_feature_color: false"])
csvwriter.writerow(["width: 5"])
csvwriter.writerow([f"*metadata*Line: {filen[0]}"])
Expand Down Expand Up @@ -284,14 +284,14 @@ def gmts_2_egs(wrk_dir: str, alt_colors: str, nm_lst: List[int]) -> None:
sys.exit(0)

header = "Vertex,SegmentID,X,Y,ELEVATION,PixelX," \
"PixelY,AusAEM_DEM,DEPTH,Type,OverAge,UnderAge," \
"BoundConf,ContactTyp,BasisOfInt,OvrStrtUnt," \
"OvrStratNo,OvrConf,UndStrtUnt,UndStratNo," \
"UndConf,WithinStrt,WithinStNo,WithinConf," \
"HydStrtType,HydStrConf,BOMNAFUnt,BOMNAFNo," \
"InterpRef,Comment,Annotation,NewObs,Operator," \
"" \
"Date,SURVEY_LINE\n"
"PixelY,AusAEM_DEM,DEPTH,Type,OverAge,UnderAge," \
"BoundConf,ContactTyp,BasisOfInt,OvrStrtUnt," \
"OvrStratNo,OvrConf,UndStrtUnt,UndStratNo," \
"UndConf,WithinStrt,WithinStNo,WithinConf," \
"HydStrtType,HydStrConf,BOMNAFUnt,BOMNAFNo," \
"InterpRef,Comment,Annotation,NewObs,Operator," \
"" \
"Date,SURVEY_LINE\n"

regex2 = re.compile('[+-]?([0-9]*[.])?[0-9]+')

Expand Down Expand Up @@ -327,9 +327,9 @@ def gmts_2_egs(wrk_dir: str, alt_colors: str, nm_lst: List[int]) -> None:
while regex2.match(line.split()[0]):
los = line.split()
fou.write(f"{los[9]},{los[8]},{los[2]},"
f"{los[3]},{los[4]},{los[0]},"
f"{los[1]},{los[5]},{los[6]},"
f"{met},{nm}\n")
f"{los[3]},{los[4]},{los[0]},"
f"{los[1]},{los[5]},{los[6]},"
f"{met},{nm}\n")
line = lines.pop(0)
except IndexError:
pass
Expand All @@ -355,46 +355,46 @@ def gmts_2_mdc(wrk_dir: str, colors: str, nm_lst: List[int]) -> None:

try:
fsctn = ("GOCAD PLine 1\n"
"HEADER {{\n"
"name:{}_{}_{}\n"
"*atoms:false\n"
"*line*color:{:.6f} {:.6f} {:.6f} 1\n"
"use_feature_color: false\n"
"width:5\n"
"*metadata*Line: {}\n"
"*metadata*Type: {}\n"
"*metadata*BoundaryNm: {}\n"
"*metadata*BoundConf: {}\n"
"*metadata*BasisOfInt: {}\n"
"*metadata*OvrStrtUnt: {}\n"
"*metadata*OvrStrtCod: {}\n"
"*metadata*OvrConf: {}\n"
"*metadata*UndStrtUnt: {}\n"
"*metadata*UndStrtCod: {}\n"
"*metadata*UndConf: {}\n"
"*metadata*WithinType: {}\n"
"*metadata*WithinStrt: {}\n"
"*metadata*WithinStNo: {}\n"
"*metadata*WithinConf: {}\n"
"*metadata*InterpRef: {}\n"
"*metadata*Comment: {}\n"
"*metadata*Annotation: {}\n"
"*metadata*NewObs: {}\n"
"*metadata*Operator: {}\n"
"*metadata*Organization: Geoscience Australia\n"
"}}\n"
"PROPERTIES px py gl depth\n"
"GOCAD_ORIGINAL_COORDINATE_SYSTEM\n"
'NAME " gocad Local"\n'
'PROJECTION " GDA94 / MGA zone 53"\n'
'DATUM " Mean Sea Level"\n'
"AXIS_NAME X Y Z\n"
"AXIS_UNIT m m m\n"
"ZPOSITIVE Elevation\n"
"END_ORIGINAL_COORDINATE_SYSTEM\n"
"GEOLOGICAL_FEATURE {}\n"
"ILINE\n"
)
"HEADER {{\n"
"name:{}_{}_{}\n"
"*atoms:false\n"
"*line*color:{:.6f} {:.6f} {:.6f} 1\n"
"use_feature_color: false\n"
"width:5\n"
"*metadata*Line: {}\n"
"*metadata*Type: {}\n"
"*metadata*BoundaryNm: {}\n"
"*metadata*BoundConf: {}\n"
"*metadata*BasisOfInt: {}\n"
"*metadata*OvrStrtUnt: {}\n"
"*metadata*OvrStrtCod: {}\n"
"*metadata*OvrConf: {}\n"
"*metadata*UndStrtUnt: {}\n"
"*metadata*UndStrtCod: {}\n"
"*metadata*UndConf: {}\n"
"*metadata*WithinType: {}\n"
"*metadata*WithinStrt: {}\n"
"*metadata*WithinStNo: {}\n"
"*metadata*WithinConf: {}\n"
"*metadata*InterpRef: {}\n"
"*metadata*Comment: {}\n"
"*metadata*Annotation: {}\n"
"*metadata*NewObs: {}\n"
"*metadata*Operator: {}\n"
"*metadata*Organization: Geoscience Australia\n"
"}}\n"
"PROPERTIES px py gl depth\n"
"GOCAD_ORIGINAL_COORDINATE_SYSTEM\n"
'NAME " gocad Local"\n'
'PROJECTION " GDA94 / MGA zone 53"\n'
'DATUM " Mean Sea Level"\n'
"AXIS_NAME X Y Z\n"
"AXIS_UNIT m m m\n"
"ZPOSITIVE Elevation\n"
"END_ORIGINAL_COORDINATE_SYSTEM\n"
"GEOLOGICAL_FEATURE {}\n"
"ILINE\n"
)
fmt = "PVRTX {:0.0f} {:6.1f} {:7.1f} {:.1f} {:.6f} {:.6f} {:.1f} {:.1f}\n"

srt_dir = Path(wrk_dir) / "SORT"
Expand Down Expand Up @@ -429,11 +429,11 @@ def gmts_2_mdc(wrk_dir: str, colors: str, nm_lst: List[int]) -> None:
frst = int(frst)
# segn = int(segn)
fou.write(fsctn.format(nm, segn, met[2],
row['Red'].iloc[0], row['Green'].iloc[0], row['Blue'].iloc[0],
nm,
*met[2:21],
nm
))
row['Red'].iloc[0], row['Green'].iloc[0], row['Blue'].iloc[0],
nm,
*met[2:21],
nm
))
try:
while regex2.match(line.split()[0]):
los = [int(_l) if i == 7 else float(_l) for i, _l in enumerate(line.split())]
Expand Down
2 changes: 1 addition & 1 deletion aemworkflow/pre_interpretation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -121,7 +121,7 @@ def box_elevation(extent_file_path, path_file_path, output_file_path, depth_line
ppt = int(path_fields[1])
py = (y_of - float(path_fields[8])) / y_fact
out_file.write(f"{int(path_fields[1]) - 1} "
f"{round(decimal.Decimal((-py + ypo) - (2 / y_fact)), 4).normalize()}\n")
f"{round(decimal.Decimal((-py + ypo) - (2 / y_fact)), 4).normalize()}\n")
yy.insert(ppt - 1, py * -1)
last = ppt

Expand Down
2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -55,4 +55,4 @@ addopts = [

[tool.flake8]
max-line-length = 120
ignore = ["E402"]
ignore = ["E402", "F401", "F841"]
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