Include grain size inputs

Makefile

@@ -86,6 +86,11 @@ impacts: ./data/interim/impacts_forecasted_foreshore_slope_sto06.csv ./data/inte
 	--profiles-csv "./data/interim/profiles.csv" \
 	--output-file "./data/interim/profile_features_crest_toes.csv" \
 
+./data/interim/sites_grain_size.csv : ./data/raw/grain_size/sites_grain_size.csv
+	$(PYTHON_CLI) create-grain-size-csv \
+	--grain-size-csv "./data/raw/grain_size/sites_grain_size.csv" \
+	--output-file "./data/interim/sites_grain_size.csv" \
+
 
 ### TWLs
 

src/cli.py

@@ -33,4 +33,5 @@ if __name__ == "__main__":
     cli.add_command(parse_mat.create_sites_and_profiles_csv)
     cli.add_command(parse_mat.create_tides_csv)
     cli.add_command(parse_mat.create_waves_csv)
+    cli.add_command(parse_mat.create_grain_size_csv)
     cli()

src/data/parse_mat.py

@@ -546,6 +546,23 @@ def create_tides_csv(tides_mat, sites_csv, output_file):
     logger.info("Created %s", output_file)
 
 
+@click.command(short_help="create sites_grain_size.csv")
+@click.option(
+    "--grain-size-csv",
+    required=True,
+    help=".csv file description of cross section sites",
+)
+@click.option("--output-file", required=True, help="where to save sites_grain_size.csv")
+def create_grain_size_csv(grain_size_csv, output_file):
+    logger.info("Creating %s", output_file)
+    df_sites_grain_size = pd.read_csv(grain_size_csv, index_col=[0])
+
+    # Calculate roughness, refer to Power et al (2018)
+    df_sites_grain_size["r"] = 2.5 * df_sites_grain_size["d_50"]
+    df_sites_grain_size.to_csv(output_file)
+    logger.info("Created %s", output_file)
+
+
 @click.group()
 def cli():
     pass