run_obs_diag.py

import os, sys, shutil, glob
from config.cfg import exp, cluster
from utils import symlink, copy, sed_inplace, append_file

def run(folder_obs_seq_final):
    rundir_program = '/home/fs71386/lkugler/data/DART-WRF/rundir/'

    files = sorted(glob.glob(folder_obs_seq_final+'/*.final'))  # input for obs_diag program
    fpath = rundir_program+'/obsdiag_inputlist.txt'
    print('writing', fpath)

    if os.path.exists(fpath):
        os.remove(fpath)

    with open(fpath, 'w') as f:
        for fin in files:
            f.write(fin)
            f.write('\n')

    for obserr_iszero in ['.true.', '.false.']:
        print('ensure correct input.nml')
        copy(cluster.scriptsdir+'/../templates/input.prioronly.nml',
             rundir_program+'/input.nml')
        sed_inplace(rundir_program+'/input.nml', '<n_ens>', str(int(exp.n_ens)))
        sed_inplace(rundir_program+'/input.nml', '<zero_error_obs>', obserr_iszero)
        append_file(rundir_program+'/input.nml', cluster.scriptsdir+'/../templates/obs_def_rttov.VIS.nml')

        # run obs_diag
        print('running obs_diag program')
        os.chdir(rundir_program)
        symlink(cluster.dart_srcdir+'/obs_diag', rundir_program+'/obs_diag')
        try:
            os.remove(rundir_program+'/obs_seq_to_netcdf')
        except:
            pass
        os.system('./obs_diag >& obs_diag.log')  # caution, this overwrites obs_seq_to_netcdf

        # move output to archive
        outdir = '/'.join(folder_obs_seq_final.split('/')[:-1])
        if obserr_iszero == '.true.':
            fout = '/obs_diag_wrt_truth.nc'   
        elif obserr_iszero == '.false.':
            fout = '/obs_diag_wrt_obs.nc'
        print('moving output to', outdir+fout)
        copy(rundir_program+'/obs_diag_output.nc', outdir+fout)


    print('running obs_seq_to_netcdf program')
    shutil.copy(cluster.dart_srcdir+'/obs_seq_to_netcdf-bak', cluster.dart_srcdir+'/obs_seq_to_netcdf')
    symlink(cluster.dart_srcdir+'/obs_seq_to_netcdf', rundir_program+'/obs_seq_to_netcdf')
    os.system('./obs_seq_to_netcdf  >& obs_seq_to_netcdf.log')  # caution, overwrites its own binary?!
    print('moving output to', outdir+'/obs_seq...')
    os.system('mv '+rundir_program+'/obs_epoch_*.nc '+outdir+'/')


if __name__ == '__main__':
    #folder_obs_seq_final = '/home/fs71386/lkugler/data/sim_archive/exp_v1.11_LMU_filter2/obs_seq_final/'
    folder_obs_seq_final = str(sys.argv[1])
    run(folder_obs_seq_final)