Read STILT particle trajectories from python

read_traj.py

#!/usr/bin/env python3

import io
import os
import subprocess

import pandas as pd


class ReadTrajException(Exception):
    """Raised if non-zero error code returned by R"""


def read_traj(path):
    """Read STILT particle trajectories from rds file and return as pd.DataFrame"""
    if not os.path.exists(path):
        raise OSError(f'{path} not found')

    cmd = ['Rscript', '-e',
           f'write.table(readRDS("{path}")$particle, quote=F, sep=",", row.names=F)']
    proc = subprocess.run(cmd, capture_output=True)

    if proc.returncode != 0:
        raise(ReadTrajException(proc.stderr))

    stdout = io.StringIO(proc.stdout.decode('utf-8'))
    return pd.read_csv(stdout)


if __name__ == '__main__':
    df = read_traj('example_traj.rds')
    print(df)

#        time  indx      long     lati       zagl   sigw  ...      wout     mlht      rain  crai    pres  foot_no_hnf_dilution
# 0        -2     1 -111.8611  40.7437    27.5031  0.595  ... -0.024151  2480.77  0.000000  -0.9  859.34              0.003202
# 1        -2     2 -111.8610  40.7436    16.0465  0.595  ... -0.024151  2480.77  0.000000  -0.9  860.46              0.003202
# 2        -2     3 -111.8590  40.7412     0.1241  0.595  ... -0.024151  2480.77  0.000000  -0.9  861.10              0.003202
# 3        -2     4 -111.8598  40.7422     9.8509  0.595  ... -0.024151  2480.77  0.000000  -0.9  861.06              0.003202
# 4        -2     5 -111.8596  40.7420     3.6314  0.595  ... -0.024151  2480.77  0.000000  -0.9  861.10              0.003202
# ...     ...   ...       ...      ...        ...    ...  ...       ...      ...       ...   ...     ...                   ...
# 72575 -1440   191 -111.8181  40.2887  1101.1840  0.316  ...  1.504116   257.03  0.000003  -0.9  756.43              0.000000
# 72576 -1440   192 -111.8295  40.2660    17.6724  0.211  ...  0.012469   250.00  0.000008  -0.9  857.17              0.028139
# 72577 -1440   195 -114.2375  41.2536  1737.6335  2.880  ...  0.242759  4127.43  0.000000  -0.9  686.65              0.001895
# 72578 -1440   196 -112.3814  40.1736  1790.1379  0.709  ... -0.014207   712.07  0.000000  -0.9  676.88              0.000000
# 72579 -1440   200 -113.9733  37.5461  1152.4561  1.934  ...  0.535018  2353.55  0.000000  -0.9  705.82              0.000742

# [72580 rows x 28 columns]