source: palm/trunk/SCRIPTS/cut_empty_timesteps.py @ 4838

Last change on this file since 4838 was 4810, checked in by gronemeier, 4 years ago

add script to remove empty time steps from netCDF files

File size: 2.0 KB
Line 
1#!/usr/bin/env python3
2
3import subprocess
4import os
5import sys
6import netCDF4
7from netCDF4 import Dataset, stringtochar
8import numpy as np
9
10
11def cut(input_path, output_path):
12    """Cycle through all netCDF files within input_path and remove all
13    empty time levels. Output is saved in output_path"""
14
15    if not os.path.isdir(input_path):
16        raise OSError("Error: input path does not exist: {0}".format(input_path))
17    if not os.path.isdir(output_path):
18        os.makedirs(output_path)
19
20    list_input_data = \
21        [file for file in os.listdir(input_path) if os.path.splitext(file)[1] == '.nc']
22
23    for nc_file in list_input_data:
24        file_in = input_path + "/" + nc_file
25        ncfile = Dataset(file_in, "r", format="NETCDF4", encoding='ascii')
26        time_dim = ncfile.dimensions["time"]
27        time_var = ncfile.variables["time"][:]
28        time_mask = ~np.ma.getmaskarray(time_var)
29
30        print("process file ", file_in)
31        if not time_dim.isunlimited() and any(time_mask):
32            start_index = np.where(time_mask)[0][0]
33            end_index = np.where(time_mask)[0][-1]
34            file_out = output_path + "/" + nc_file
35
36            ncks_command = "ncks -O -d time,{0},{1} {2} {3}".format(
37                start_index,
38                end_index,
39                file_in,
40                file_out,
41                )
42
43            ncks_output = subprocess.run(
44                ncks_command,
45                stdout=subprocess.PIPE,
46                stderr=subprocess.STDOUT,
47                shell=True
48                )
49
50            if ncks_output.returncode != 0:
51                raise RuntimeError("Error: {0}".format(ncks_output.stdout))
52
53
54if __name__ == '__main__':
55    arg_list = sys.argv
56    if arg_list.__len__() == 3:
57        input_path = arg_list[1]
58        output_path = arg_list[2]
59        cut(input_path, output_path)
60    else:
61        sys.exit('Arguments are missing! ' +
62                 'Usage:\n cut_empty_timesteps.py <input_path> <output_path>')
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