diff --git a/aemworkflow/aemworkflow.py b/aemworkflow/aemworkflow.py index 16deff2..d4bbb91 100644 --- a/aemworkflow/aemworkflow.py +++ b/aemworkflow/aemworkflow.py @@ -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) @@ -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) @@ -36,11 +39,12 @@ 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) @@ -48,11 +52,12 @@ def interpret(input_directory, output_directory, crs="28349", gis="esri_arcmap_0 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) @@ -60,11 +65,12 @@ def validate(input_directory, output_directory, asud_filename): 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) @@ -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) diff --git a/aemworkflow/conversion.py b/aemworkflow/conversion.py index 688e424..4895444 100644 --- a/aemworkflow/conversion.py +++ b/aemworkflow/conversion.py @@ -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) diff --git a/aemworkflow/exports.py b/aemworkflow/exports.py index ecf7a70..6ceef53 100644 --- a/aemworkflow/exports.py +++ b/aemworkflow/exports.py @@ -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]}"]) @@ -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]+') @@ -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 @@ -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" @@ -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())] diff --git a/aemworkflow/pre_interpretation.py b/aemworkflow/pre_interpretation.py index bf94a98..b0eb268 100644 --- a/aemworkflow/pre_interpretation.py +++ b/aemworkflow/pre_interpretation.py @@ -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 diff --git a/pyproject.toml b/pyproject.toml index f33821f..52a33ab 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -55,4 +55,4 @@ addopts = [ [tool.flake8] max-line-length = 120 -ignore = ["E402"] +ignore = ["E402", "F401", "F841"]