test_extract_ts_xr.py

#!/usr/bin/env python
'''
MIT License

Copyright (c) 2022, Renaissance Computing Institute

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
'''

'''
test_extract_ts_xr.py
tests/times extraction of timeserires from an ADCIRC fort nc file
Brian Blanton, RENCI
V0.1, 12 Sep 2022

python test_extract_ts_xr.py --file http://tds.renci.org/thredds/dodsC/Reanalysis/ADCIRC/ERA5/hsofs/1979-post/fort.63.d0.no-unlim.T.rc.nc --screen

'''

import sys
import random
import time
import numpy as np
import netCDF4 as nc4
import xarray as xr

dropvars=['neta', 'nvel',  'max_nvdll', 'max_nvell']

def main(args):

    f=args.f
    if f == None:
        print('Must specify fort nc file with --file.')
        sys.exit(1)

    N=args.N
    Screen=args.screen
    Seed=args.seed

    if Seed: random.seed(Seed)
    if Screen: print(f'Screen={Screen}')
    if Screen: print(f'NC File={f}')

    ds=xr.open_dataset(f,drop_variables=dropvars)
    zeta=ds.zeta

    # check if file is transposed
    T=False
    if zeta.dims[0] == 'node':
        T=True
        nnodes, ntimes = zeta.shape
        if Screen: 
            print('file is transposed')
            print(f"Nnodes,Ntimes = {nnodes, ntimes}")
    else:
        ntimes, nnodes = zeta.shape
        if Screen: 
            print('file is NOT transposed')
            print(f"Ntimes,Nnodes = {ntimes,nnodes}")

    Nsamp=np.sort(random.sample(range(0, nnodes),N))
    if Screen: print(Nsamp, " (0-based)")

    overall_start_time = time.time()
    if Screen: 
        print("Starting Loop...\ni     n    shape[0]  time[sec]\n----------------------------------------")
        print(f'Start time = {overall_start_time}')
    inner_dt=[]
    for j,i in enumerate(Nsamp):
        inner_start_time=time.time()
        # this is the extraction step
        if T: z=zeta[i,:].values
        else: z=zeta[:,i].values
        inner_end_time=time.time()
        inner_dt.append(inner_end_time-inner_start_time)
        if Screen: 
            temp=inner_dt[-1]
            print(f'{j:3d} {i:6d} {z.shape[0]:6d} {temp:7.4f}')

    if Screen: print("----------------------------------------")
    overall_end_time = time.time()
    print(f'Stop time = {overall_end_time}')
    overall_dt=overall_end_time-overall_start_time
    average_dt_no_first=np.sum(inner_dt[1:-1])/(N-1)
    average_dt=overall_dt/N
    std_dt=np.std(inner_dt)
    std_dt_no_first=np.std(inner_dt[1:-1])
    if Screen: 
        print(f"Elapsed seconds = {overall_dt:.4f}")
        print(f"Average seconds = {average_dt:.4f}")
        print(f"Std Dev seconds = {std_dt:.4f}\n")
        print(f"Average w/o first = {average_dt_no_first:.4f}")
        print(f"Std Dev w/o first = {std_dt_no_first:.4f}\n")
    else: print(overall_dt,average_dt,std_dt,std_dt_no_first)


if __name__ == '__main__':

    from argparse import ArgumentParser
    import sys
    parser = ArgumentParser()

    parser.add_argument('--file', action='store', dest='f', default=None, help='String: file to process.')
    parser.add_argument('--nsamp', action='store', dest='N', default=10, type=int, help='Int: number of accesses. default=10')
    parser.add_argument('--seed', action='store', dest='seed', default=None, type=int, help='Int: random gen seed, default=None.')
    parser.add_argument('--screen', dest='screen', action='store_true')

    args = parser.parse_args()
    sys.exit(main(args))