diff --git a/figures/Schmidt2018_dyn/compute_bold_signal.py b/figures/Schmidt2018_dyn/compute_bold_signal.py index ac72a790db177e98733d05980fb3da277e17d855..9c249e0127648771991b9737964bb2eaca73a56b 100644 --- a/figures/Schmidt2018_dyn/compute_bold_signal.py +++ b/figures/Schmidt2018_dyn/compute_bold_signal.py @@ -1,5 +1,6 @@ import numpy as np import os +import subprocess import sys @@ -32,7 +33,6 @@ fn = os.path.join(load_path, 'synaptic_input_{}.npy'.format(area)) synaptic_input = np.load(fn) - def bold_R_parser(fn): f = open(fn, 'r') # skip first line @@ -51,7 +51,10 @@ out_fn = os.path.join(save_path, 'bold_syn_input_{}.txt'.format(area)) np.savetxt(fn, synaptic_input / np.max(synaptic_input)) -os.system('Rscript --vanilla compute_bold_signal.R {} {}'.format(fn, out_fn)) +try: + subprocess.run(['Rscript', '--vanilla', 'compute_bold_signal.R {} {}'.format(fn, out_fn)]) +except FileNotFoundError: + raise FileNotFoundError("Executing R failed. Did you install R?") bold_signal = bold_R_parser(out_fn) fn = os.path.join(save_path,