Use yaml files for loading input parameters

las_manipulation.py

@@ -1,7 +1,9 @@
 import os
 import sys
+import yaml
 import argparse
 import subprocess
+from glob import glob
 from tqdm import tqdm
 import numpy as np
 from scipy import interpolate
@@ -337,43 +339,29 @@ def polygon_wave_runup(xyz_1m, direction, shp_name, set_check_value, distance_ch
 
     return None
 
+
 def remove_temp_files(directory):
     for f in os.listdir(directory):
         os.unlink(os.path.join(directory, f))
 
     return None
 
-def main():
-    parser = argparse.ArgumentParser()
-    parser.add_argument(
-        'input_file',
-        metavar='PARAMS_FILE',
-        help='name of parameter file',
-        default=None)
-
-    # Print usage if no arguments are provided
-    if len(sys.argv) == 1:
-        parser.print_help(sys.stderr)
-        sys.exit(1)
 
-    args = parser.parse_args()
+def process(yaml_file):
+    with open(yaml_file, 'r') as f:
+        params = yaml.safe_load(f)
 
-    # read the parameters file and scroll through it
+    print("Starting to process %s" % params['BEACH'])
-    input_file = args.input_file
+    input_las = params['INPUT LAS']
-    params_file=pd.read_excel(input_file, sheet_name="PARAMS")
+    initial_crop_poly = params['INITIAL CROP POLY']
-
+    lasground_step  = params['LASGROUND STEP']
-    for i, row in params_file.iterrows():
+    zone_MGA = params['ZONE MGA']
-        print("Starting to process %s" % row['BEACH'])
+    check_value = params['CHECK VALUE']
-        input_las = row['INPUT LAS']
+    direct = params['DIRECTION']
-        initial_crop_poly = row['INITIAL CROP POLY']
+    check_distance = params['CHECK DISTANCE']
-        lasground_step  = row['LASGROUND STEP']
+    las_dir  = params['LAS CLASSIFIED FOLDER']
-        zone_MGA = row['ZONE MGA']
+    shp_dir  = params['SHP SWASH FOLDER']
-        check_value = row['CHECK VALUE']
+    tmp_dir = params['TMP FOLDER']
-        direct = row['DIRECTION']
-        check_distance = row['CHECK DISTANCE']
-        las_dir  = row['LAS CLASSIFIED FOLDER']
-        shp_dir  = row['SHP SWASH FOLDER']
-        tmp_dir = row['TMP FOLDER']
 
     # Get base name of input las
     las_basename = os.path.splitext(os.path.basename(input_las))[0]
@@ -409,5 +397,38 @@ def main():
     remove_temp_files(tmp_dir)
 
 
+def main():
+    example_text = """examples:
+
+    # Process single survey at specific beach
+    python las_manipulation.py survey-1-avoca.yaml
+
+    # Process all surveys at specific beach
+    python las_manipulation.py *avoca.yaml
+
+    # Process all beaches for specific survey date
+    python las_manipulation.py survey-1*.yaml
+    """
+
+    # Set up command line arguments
+    parser = argparse.ArgumentParser(
+        epilog=example_text,
+        formatter_class=argparse.RawDescriptionHelpFormatter)
+    parser.add_argument('input', help='path to yaml file(s)', nargs='*')
+
+    # Print usage if no arguments are provided
+    if len(sys.argv) == 1:
+        parser.print_help(sys.stderr)
+        sys.exit(1)
+
+    # Parse arguments
+    args = parser.parse_args()
+    yaml_files = []
+    [yaml_files.extend(glob(f)) for f in args.input]
+
+    for yaml_file in yaml_files:
+        process(yaml_file)
+
+
 if __name__ == '__main__':
     main()

las_outputs.py

@@ -15,11 +15,13 @@ import io
 import re
 import sys
 import math
+import yaml
 import argparse
 import datetime
 import subprocess
 import numpy as np
 import pandas as pd
+from glob import glob
 from cycler import cycler
 import matplotlib.pyplot as plt
 from matplotlib.ticker import MultipleLocator
@@ -166,43 +168,27 @@ def calculate_volumes(profile_name, survey_date, csv_output_dir, ch_limits, volu
     return delta_vol
 
 
-def main():
+def process(yaml_file):
-    parser = argparse.ArgumentParser()
+    with open(yaml_file, 'r') as f:
-    parser.add_argument(
+        params = yaml.safe_load(f)
-        'input_file',
+
-        metavar='PARAMS_FILE',
+    print("Starting to process %s" % params['BEACH'])
-        help='name of parameter file',
+    beach = params['BEACH']
-        default=None)
+    survey_date = str(params['SURVEY DATE'])
-
+    original_las = params['INPUT LAS']
-    # Print usage if no arguments are provided
+    classified_las_dir = params['LAS CLASSIFIED FOLDER']
-    if len(sys.argv) == 1:
+    shp_swash_dir = params['SHP SWASH FOLDER']
-        parser.print_help(sys.stderr)
+    crop_heatmap_poly = params['HEATMAP CROP POLY']
-        sys.exit(1)
+    output_las_dir = params['LAS OUTPUT FOLDER']
-
+    zone_MGA = params['ZONE MGA']
-    args = parser.parse_args()
+    output_poly_dir = params['SHP RASTER FOLDER']
-
+    output_tif_dir = params['TIF OUTPUT FOLDER']
-    # read the parameters file and scroll through it
+    cp_csv = params['INPUT CSV']
-    input_file = args.input_file
+    profile_limit_file = params['PROFILE LIMIT FILE']
-    params_file=pd.read_excel(input_file, sheet_name="PARAMS")
+    csv_output_dir = params['CSV OUTPUT FOLDER']
-
+    graph_loc = params['PNG OUTPUT FOLDER']
-    for i, row in params_file.iterrows():
+    volume_output_dir = params['CSV VOLUMES FOLDER']
-        print("Starting to process %s" % row['BEACH'])
+    tmp_dir = params['TMP FOLDER']
-        beach=row['BEACH']
-        survey_date = str(row['SURVEY DATE'])
-        original_las = row['INPUT LAS']
-        classified_las_dir = row['LAS CLASSIFIED FOLDER']
-        shp_swash_dir = row['SHP SWASH FOLDER']
-        crop_heatmap_poly = row['HEATMAP CROP POLY']
-        output_las_dir = row['LAS OUTPUT FOLDER']
-        zone_MGA = row['ZONE MGA']
-        output_poly_dir = row['SHP RASTER FOLDER']
-        output_tif_dir = row['TIF OUTPUT FOLDER']
-        cp_csv = row['INPUT CSV']
-        profile_limit_file = row['PROFILE LIMIT FILE']
-        csv_output_dir = row['CSV OUTPUT FOLDER']
-        graph_loc = row['PNG OUTPUT FOLDER']
-        volume_output_dir = row['CSV VOLUMES FOLDER']
-        tmp_dir = row['TMP FOLDER']
 
     # Get base name of input las
     las_basename = os.path.splitext(os.path.basename(original_las))[0]
@@ -264,5 +250,38 @@ def main():
     remove_temp_files(tmp_dir)
 
 
+def main():
+    example_text = """examples:
+
+    # Process single survey at specific beach
+    python las_outputs.py survey-1-avoca.yaml
+
+    # Process all surveys at specific beach
+    python las_outputs.py *avoca.yaml
+
+    # Process all beaches for specific survey date
+    python las_outputs.py survey-1*.yaml
+    """
+
+    # Set up command line arguments
+    parser = argparse.ArgumentParser(
+        epilog=example_text,
+        formatter_class=argparse.RawDescriptionHelpFormatter)
+    parser.add_argument('input', help='path to yaml file(s)', nargs='*')
+
+    # Print usage if no arguments are provided
+    if len(sys.argv) == 1:
+        parser.print_help(sys.stderr)
+        sys.exit(1)
+
+    # Parse arguments
+    args = parser.parse_args()
+    yaml_files = []
+    [yaml_files.extend(glob(f)) for f in args.input]
+
+    for yaml_file in yaml_files:
+        process(yaml_file)
+
+
 if __name__ == '__main__':
     main()