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save2matfile_or_pkl.py
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save2matfile_or_pkl.py
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from scipy.io import savemat
from IPython.display import FileLink, display
import numpy as np
def save2matfile_or_pkl(data, file_name, obs, params = {}, save_mat = True, save_pkl = False):
"""
Takes an mcdata object and the observables and stores the states, expectations, times,
observable labels (str and latex), random seeds, number of trajectories as:
{
"psis": psis, # shape (ntraj, ntimes, dim_psi) complex128
"expects": expects, # shape (ntraj, ntimes, num_observables) complex128
"times": times, # shape (ntimes) float64
"observable_str": observable_str, # shape (num_observables) string
"observable_latex": observable_latex, # shape (num_observables) string
"seeds": seeds, # shape (ntraj) int
}
Additional parameters can be passed using the params argument, as a python dictionary.
"""
ntraj = data['psis'].shape[0]
assert ntraj == data['obsq_expects'].shape[0]
assert ntraj >= 1
psis = data['psis']
expects = data['obsq_expects']
times = data['tspan']
observable_str = [str(o) for o in obs]
observable_latex = [o._repr_latex_() for o in obs]
seeds = data['seeds']
mdict = {
"psis": psis,
"expects": expects,
"times": times,
"observable_str": observable_str,
"observable_latex": observable_latex,
"seeds": seeds,
}
mdict.update(params) ## other paramters (optional)
if save_mat:
savemat(file_name, mdict)
display(FileLink(file_name+".mat"))
if save_pkl:
import pickle
output = open(file_name + ".pkl", 'wb')
pickle.dump( mdict, output,protocol=0)
output.close()
display(FileLink(file_name+".pkl"))
return mdict