nnet_params_filename, input_filename, output_filename = sys.argv[1:4]
moviedir = sys.argv[4] if len(sys.argv) == 5 else None
sigmasq_states = 0.1**2
with open(nnet_params_filename, 'r') as infile:
nnet_params = pickle.load(infile)
print 'loading from {}...'.format(input_filename)
with open_pkl_or_pklgz(input_filename, 'r') as infile:
datadict = pickle.load(infile)
print '...done!'
# reorient each video
print 're-orienting video sequences...'
reoriented_datadict = \
{name: reorient_video(nnet_params, frames, sigmasq_states, inflate_vars=1.)
for name, frames in iteritems(datadict)}
print '...done!'
# save the result
print 'saving to {}...'.format(output_filename)
with open(output_filename, 'w') as outfile:
pickle.dump(reoriented_datadict, outfile, protocol=-1)
print '...done!'
# make some movies
if moviedir:
print 'making movies...'
for name, frames in reoriented_datadict.iteritems():
name = os.path.split(name)[-1] + '.mp4'
make_movie(frames, os.path.join(moviedir, name))
from mouse_orientation.canonicalize import infer_angles, reorient_video
from mouse_orientation.regression import predict
from mouse_orientation.kalman import kalman_smoother
if __name__ == "__main__":
sigmasq_states = 0.1**2
with open('data/nnet_params.pkl', 'r') as infile:
nnet_params = pickle.load(infile)
with open('data/test_frames_dict.pkl', 'r') as infile:
datadict = pickle.load(infile)
### manual viz
frames = clean_frames(datadict['test'])
mus, log_sigmasqs = predict(frames.reshape(frames.shape[0], -1), nnet_params)
plt.errorbar(np.arange(len(frames)), mus, np.exp(log_sigmasqs / 2.))
plt.plot(kalman_smoother(
0., 100., 1., sigmasq_states, mus, np.exp(log_sigmasqs))[0], 'g-')
### a look at results
sl = slice(270, 290)
# sl = slice(None)
rotated_frames = reorient_video(nnet_params, frames, sigmasq_states)
plt.matshow(np.vstack((np.hstack(frames), np.hstack(rotated_frames))), cmap='plasma')
plt.xlim(sl.start*30, sl.stop*30)
plt.show()
plt.show()
nnet_params_filename, input_filename, output_filename = sys.argv[1:4]
moviedir = sys.argv[4] if len(sys.argv) == 5 else None
sigmasq_states = 0.1**2
with open(nnet_params_filename, 'r') as infile:
nnet_params = pickle.load(infile)
print 'loading from {}...'.format(input_filename)
with open_pkl_or_pklgz(input_filename, 'r') as infile:
datadict = pickle.load(infile)
print '...done!'
# reorient each video
print 're-orienting video sequences...'
reoriented_datadict = \
{name: reorient_video(nnet_params, frames, sigmasq_states, inflate_vars=1.)
for name, frames in iteritems(datadict)}
print '...done!'
# save the result
print 'saving to {}...'.format(output_filename)
with open(output_filename, 'w') as outfile:
pickle.dump(reoriented_datadict, outfile, protocol=-1)
print '...done!'
# make some movies
if moviedir:
print 'making movies...'
for name, frames in reoriented_datadict.iteritems():
name = os.path.split(name)[-1] + '.mp4'
make_movie(frames, os.path.join(moviedir, name))
