184 lines
4.8 KiB
Python
184 lines
4.8 KiB
Python
#! /usr/bin/env python3
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"""
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|------------------------------------------------------------------|
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|--------------------- Instructions -----------------------------|
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|------------------------------------------------------------------|
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This script is a simple wrapper for neon sites that performs the
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following:
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1) For neon sites, subset surface dataset from global dataset
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(i.e. ./subset_data.py )
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2) Download neon and update the created surface dataset
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based on the downloaded neon data.
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(i.e. modify_singlept_site_neon.py)
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Instructions for running using conda python environments:
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../../py_env_create
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conda activate ctsm_py
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"""
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# Import libraries
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from __future__ import print_function
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import argparse
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import logging
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import os
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import subprocess
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import tqdm
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import pandas as pd
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def get_parser():
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"""
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Get parser object for this script.
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"""
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parser = argparse.ArgumentParser(
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description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter
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)
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parser.print_usage = parser.print_help
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parser.add_argument(
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"-v",
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"--verbose",
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help="Verbose mode will print more information. ",
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action="store_true",
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dest="verbose",
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default=False,
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)
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parser.add_argument(
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"--16pft",
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help="Create and/or modify 16-PFT surface datasets (e.g. for a FATES run) ",
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action="store_true",
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dest="pft_16",
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default=True,
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)
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return parser
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def execute(command):
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"""
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Function for running a command on shell.
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Args:
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command (str):
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command that we want to run.
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Raises:
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Error with the return code from shell.
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"""
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print("\n", " >> ", *command, "\n")
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try:
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subprocess.check_call(command, stdout=open(os.devnull, "w"), stderr=subprocess.STDOUT)
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except subprocess.CalledProcessError as err:
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# raise RuntimeError("command '{}' return with error
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# (code {}): {}".format(e.cmd, e.returncode, e.output))
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# print (e.ouput)
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print(err)
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def main():
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"""
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Read plumber2_sites from csv, iterate through sites, and add dominant PFT
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"""
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args = get_parser().parse_args()
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if args.verbose:
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logging.basicConfig(level=logging.DEBUG)
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plumber2_sites = pd.read_csv("PLUMBER2_sites.csv", skiprows=4)
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for _, row in tqdm.tqdm(plumber2_sites.iterrows()):
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lat = row["Lat"]
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lon = row["Lon"]
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site = row["Site"]
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pft1 = row["pft1"]
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pctpft1 = row["pft1-%"]
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cth1 = row["pft1-cth"]
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cbh1 = row["pft1-cbh"]
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pft2 = row["pft2"]
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pctpft2 = row["pft2-%"]
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cth2 = row["pft2-cth"]
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cbh2 = row["pft2-cbh"]
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# overwrite missing values from .csv file
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if pft1 == -999:
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pft1 = 0
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pctpft1 = 0
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cth1 = 0
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cbh1 = 0
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if pft2 == -999:
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pft2 = 0
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pctpft2 = 0
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cth2 = 0
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cbh2 = 0
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clmsite = "1x1_PLUMBER2_" + site
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print("Now processing site :", site)
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if args.pft_16:
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# use surface dataset with 16 pfts, but overwrite to 100% 1 dominant PFT
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# don't set crop flag
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# set dominant pft
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subset_command = [
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"./subset_data",
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"point",
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"--lat",
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str(lat),
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"--lon",
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str(lon),
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"--site",
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clmsite,
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"--dompft",
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str(pft1),
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str(pft2),
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"--pctpft",
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str(pctpft1),
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str(pctpft2),
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"--cth",
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str(cth1),
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str(cth2),
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"--cbh",
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str(cbh1),
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str(cbh2),
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"--create-surface",
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"--uniform-snowpack",
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"--cap-saturation",
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"--verbose",
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"--overwrite",
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]
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else:
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# use surface dataset with 78 pfts, and overwrite to 100% 1 dominant PFT
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# NOTE: FATES will currently not run with a 78-PFT surface dataset
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# set crop flag
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# set dominant pft
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subset_command = [
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"./subset_data",
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"point",
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"--lat",
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str(lat),
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"--lon",
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str(lon),
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"--site",
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clmsite,
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"--crop",
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"--dompft",
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str(pft1),
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str(pft2),
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"--pctpft",
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str(pctpft1),
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str(pctpft2),
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"--create-surface",
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"--uniform-snowpack",
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"--cap-saturation",
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"--verbose",
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"--overwrite",
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]
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execute(subset_command)
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if __name__ == "__main__":
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main()
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