From 821e5c34cf2986d1be4c5fc6250fcca3125be3e6 Mon Sep 17 00:00:00 2001
From: Chris Leaman <ckleaman@gmail.com>
Date: Wed, 13 Feb 2019 14:18:26 +1100
Subject: [PATCH] Include grain size inputs

---
 Makefile              |  5 +++++
 src/cli.py            |  1 +
 src/data/parse_mat.py | 17 +++++++++++++++++
 3 files changed, 23 insertions(+)

diff --git a/Makefile b/Makefile
index 0816220..fc8635f 100644
--- a/Makefile
+++ b/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
 
diff --git a/src/cli.py b/src/cli.py
index c290548..0d29ad9 100644
--- a/src/cli.py
+++ b/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()
diff --git a/src/data/parse_mat.py b/src/data/parse_mat.py
index 2afa87a..855479b 100644
--- a/src/data/parse_mat.py
+++ b/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