Allow input files to be specified from the command line

las_manipulation.py

@@ -360,7 +360,6 @@ def main():
 
     # read the parameters file and scroll through it
     input_file = args.input_file
-    input_file = 'Parameter Files/las-manipulation-survey-2.xlsx'
     params_file=pd.read_excel(input_file, sheet_name="PARAMS")
 
     for i, row in params_file.iterrows():

las_outputs.py

@@ -13,7 +13,9 @@
 import os
 import io
 import re
+import sys
 import math
+import argparse
 import datetime
 import subprocess
 import numpy as np
@@ -91,7 +93,7 @@ def calculate_volumes(profile_name, survey_date, csv_output_dir, ch_limits, volu
         # Get Nielsen erosion volumes
         chainage = profiles.loc[:, current_date].dropna().index
         elevation = profiles.loc[:, current_date].dropna().values
-        volume = neilson_volumes.volume_available(chainage, elevation, ch_min)
+        volume = nielsen_volumes.volume_available(chainage, elevation, ch_min)
 
         # Update spreadsheet
         volumes.loc[profile_name, date] = volume
@@ -101,10 +103,26 @@ def calculate_volumes(profile_name, survey_date, csv_output_dir, ch_limits, volu
     volumes.to_csv(csv_vol)
 
 
-input_file = 'Parameter Files/las-manipulation-survey-2.xlsx'
+def main():
-params_file=pd.read_excel(input_file, sheet_name="PARAMS")
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        'input_file',
+        metavar='PARAMS_FILE',
+        help='name of parameter file',
+        default=None)
 
-for i, row in params_file.iterrows():
+    # Print usage if no arguments are provided
+    if len(sys.argv) == 1:
+        parser.print_help(sys.stderr)
+        sys.exit(1)
+
+    args = parser.parse_args()
+
+    # read the parameters file and scroll through it
+    input_file = args.input_file
+    params_file=pd.read_excel(input_file, sheet_name="PARAMS")
+
+    for i, row in params_file.iterrows():
         print("Starting to process %s" % row['Beach'])
         beach=row['Beach']
         survey_date = row['SURVEY DATE']
@@ -133,23 +151,28 @@ for i, row in params_file.iterrows():
         crop_swash_poly = os.path.join(shp_swash_dir, las_basename + '.shp')
 
         # Crop point cloud to swash boundary
+        print('Cropping swash...')
         las_data = call_lastools('lasclip', input=input_las, output='-stdout',
                                  args=['-poly', crop_swash_poly], verbose=False)
 
         # Apply sea-side clipping polygon
+        print('Cropping back of beach...')
         las_data = call_lastools('lasclip', input=las_data, output='-stdout',
                                  args=['-poly', crop_heatmap_poly], verbose=False)
 
         # Create clipping polygon for heatmap raster
+        print('Creating heat map cropping polygon...')
         shp_name = os.path.join(output_poly_dir, las_basename + '.shp')
         call_lastools('lasboundary', input=las_data, output=shp_name, verbose=False)
 
         # Make a raster from point cloud
+        print('Creating heat map raster...')
         tif_name = os.path.join(output_tif_dir, las_basename + '.tif')
         call_lastools('blast2dem', input=las_data, output=tif_name,
                       args=['-step', 0.2], verbose=False)
 
         # Extract elevations along profiles from triangulated surface
+        print('Extracting profile elevations...')
         df = extract_pts(
             las_data,
             cp_csv,
@@ -165,6 +188,7 @@ for i, row in params_file.iterrows():
         ch_limits = pd.read_excel(profile_limit_file, index_col='Profile')
 
         # Plot profiles, and save sand volumes for current beach
+        print('Updating figures...')
         profile_names = df['Profile'].unique()
         for profile_name in profile_names:
             plot_profiles(profile_name, survey_date, csv_output_dir, graph_loc, ch_limits)
@@ -172,3 +196,7 @@ for i, row in params_file.iterrows():
 
         # Remove temprary files
         remove_temp_files(tmp_dir)
+
+
+if __name__ == '__main__':
+    main()