def full_trace(record_file: File, ax: Axes):
activity = DataFrame.load(record_file["spike"])
lever = load_mat(record_file['response'])
new_lever = resample(lever.values[0], lever.sample_rate, record_file.attrs['frame_rate'])
for x in range(activity.shape[0]):
ax.plot(_scale(activity.values[x, :] / 5))
ax.plot(_scale(new_lever) / 2 - 3, color=COLORS[0])
def svr_parameters(data_file: File, info: Dict[str, str]):
lever = load_mat(data_file['response'])
values = devibrate(lever.values[0], sample_rate=lever.sample_rate)
y = InterpolatedUnivariateSpline(lever.axes[0],
values)(data_file['spike']['y'])[1:]
X = data_file['spike']['data'][:, 1:]
gammas = np.linspace(-8, -5, 12, endpoint=False)
Cs = np.linspace(3, 15, 12, endpoint=False)
def pred(gamma, C):
hat = cross_predict(X,
y,
svr.predictor_factory(y,
gamma=10**gamma,
C=C,
epsilon=1E-3),
section_mi=False)
return mutual_info(y, hat)
res = map_table(pred, gammas, Cs)
save_path = join(res_folder,
f"svr_params_test_{info['id']}_{info['session']}.npz")
np.savez_compressed(save_path, values=np.asarray(res), axes=[gammas, Cs])
res_df = DataFrame(np.asarray(res), [gammas, Cs])
with Figure() as (ax, ):
labeled_heatmap(ax, res_df.values, res_df.axes[1], res_df.axes[0])
print('done')
def compare_decoder():
import matplotlib.pyplot as plt
data_file = files['wt'][2]
lever = load_mat(data_file['response'])
y = InterpolatedUnivariateSpline(lever.axes[0], lever.values[0])(
data_file['spike']['y'])[1:]
X = data_file['spike']['data'][:, 1:]
bounds: Bounds = (tuple(np.quantile(y, [0.001, 0.999])), (-2, 1), (-5, 5)
) # type: ignore
print("mutual info:")
plt.plot(y, color=COLORS[0], alpha=0.5, label="trajectory")
path_hats = dict()
powers = dict()
for color, (name, decoder) in zip(
COLORS[1:],
(("particle", particle.decoder_factory(bounds)),
("kalman", kalman.decoder_factory(bounds)),
("linear", linear.decoder_factory(bounds)),
("svr", svr.decoder_factory(SVR('rbf', 3, 1E-7, cache_size=1000))))):
path_hat, power = cross_predict(X, y, decoder)
info = mutual_info(y, path_hat)
path_hats[name] = path_hat
powers[name] = power
plt.plot(path_hat,
color=color,
alpha=0.5,
label="{}: {}".format(name, info))
plt.legend()
def decoder_power(data_file: File,
predictor_factory: Callable[[np.ndarray], Decoder]) -> float:
lever = load_mat(data_file['response'])
y = InterpolatedUnivariateSpline(lever.axes[0], lever.values[0])(
data_file['spike']['y'])[1:]
X = data_file['spike']['data'][:, 1:]
decoder = predictor_factory(y)
lever_hat, powers = cross_predict(X, y, decoder)
return mutual_info(lever_hat, y)
def get_hitrate(data_file: File) -> float:
lever = load_mat(data_file['response'])
params = {
x: y
for x, y in motion_params.items()
if x in ('quiet_var', 'window_size', 'event_thres')
}
_, _, _, correct_trials, _ = find_response_onset(lever, **params)
return correct_trials.mean()
def all_traces(record_file: File, ax: Axes):
"""plot full traces of all neurons and trial onsets"""
lever_trajectory = load_mat(record_file["response"])
calcium_trace = _scale(DataFrame.load(record_file["measurement"]).values)
time = np.linspace(0, lever_trajectory.shape[1] / lever_trajectory.sample_rate, lever_trajectory.shape[1])
ax.plot(time, _scale(lever_trajectory.values[0]) - 5, COLORS[1])
for idx, row in enumerate(calcium_trace):
ax.plot(time, row + idx * 5)
for point in lever_trajectory.timestamps / lever_trajectory.sample_rate: # trial onsets
ax.axvline(x=point, color=COLORS[2])
def test_loadmat():
gerald_log = join(
resource_filename(Requirement.parse("lever"), "lever/test/data"),
"lever.mat")
log = load_mat(gerald_log)
assert (log.trial_time == 5)
assert (log.timestamps.shape[0] == 117)
assert (log.sample_rate == 256)
assert (log.stimulus['config']['reward'] == 6)
assert (abs(log.stimulus['config']['lev_baseline'] - 3.94221418) < 1E-6)
def get_delay(data_file: File) -> float:
lever = load_mat(data_file['response'])
params = {
x: y
for x, y in motion_params.items()
if x in ('quiet_var', 'window_size', 'event_thres')
}
motion_onsets, stim_onsets, _, correct_trials, _ = find_response_onset(
lever, **params)
return np.mean(
(motion_onsets - stim_onsets[correct_trials]) / lever.sample_rate)
def null_fit(data_file):
lever = load_mat(data_file['response'])
y = InterpolatedUnivariateSpline(lever.axes[0], lever.values[0])(
data_file['spike']['y'])[1:]
X = data_file['spike']['data'][:, 1:]
res = list()
for _ in range(200):
y_perm = np.random.permutation(y.copy())
y_hat_perm, _ = cross_predict(X, y_perm, svr.predictor_factory(y_perm))
res.append(mutual_info(y_perm, y_hat_perm))
np.savez_compressed(join(project_folder, "report", "measure", ""), res=res)
def show_traces():
data_file = files['wt'][0]
lever = load_mat(data_file['response'])
values = devibrate(lever.values[0], sample_rate=lever.sample_rate)
y = InterpolatedUnivariateSpline(lever.axes[0],
values)(data_file['spike']['y'])[1:]
X = data_file['spike']['data'][:, 1:]
lever_hat, powers = cross_predict(X, y, svr.predictor_factory(y))
lever_hat = svr.predictor_factory(y)(X, y, X)
plt.plot(y, color='blue')
plt.plot(lever_hat, color='red')
print("mutual info: ", mutual_info(y, lever_hat))
def get_linkage(record_file: File, params: Dict[str, float]) -> np.ndarray:
"""Load record file and get linkage matrix between the trajectories of trials.
Args:
record_file: the record file with at least the lever file
motion_params: param dict including window size and push threshold
"""
lever = load_mat(record_file['response'])
lever.center_on("motion", **params)
lever.fold_trials()
mask, lever_trials = devibrate_trials(lever.values[0], params['pre_time'], sample_rate=lever.sample_rate)
dist_mat = trace_cluster(lever_trials[mask, ...])
return linkage(dist_mat), mask
def svr_power(data_file: File,
neuron_no: int = 20) -> Tuple[float, List[float]]:
lever = load_mat(data_file['response'])
values = devibrate(lever.values[0], sample_rate=lever.sample_rate)
y = InterpolatedUnivariateSpline(lever.axes[0],
values)(data_file['spike']['y'])[1:]
X = data_file['spike']['data'][:, 1:].copy()
decoder = svr.predictor_factory(y, gamma=3E-9, C=12, epsilon=1E-3)
single_power = [
cross_predict(x[newaxis, :], y, decoder,
section_mi=True)[1].mean() for x in X
]
mask = np.greater_equal(single_power, sorted(single_power)[-neuron_no])
path_hat, _ = cross_predict(X[mask, :], y, decoder)
return mutual_info(y, path_hat), single_power
def show_correspondance(ax: Axes, record_file: File,
motion_params: Dict[str, float]):
def scale(x):
x -= x.mean()
x /= x.std()
return x
lever = load_mat(record_file['response'])
lever.center_on("motion", **motion_params)
activity = DataFrame.load(record_file["measurement"])
neuron_rate = record_file.attrs['frame_rate']
trials = filter_empty_trials(ts.fold_by(activity, lever, neuron_rate,
True))
slow_lever = ts.resample(lever.fold_trials().values, lever.sample_rate,
neuron_rate, -1)[:, 0:trials.shape[1], :]
ax.plot(scale(trials.values[0].reshape(-1)), 'green')
ax.plot(scale(slow_lever.reshape(-1)), 'red')
def example_traces(ax: Axes, record_file: File, start: float, end: float, cells: Set[int]):
"""Visualize calcium trace of cells and the lever trajectory"""
lever_trajectory = load_mat(record_file["response"])
calcium_trace = DataFrame.load(record_file["measurement"])
neuron_rate = record_file.attrs['frame_rate']
l_start, l_end = np.rint(np.multiply([start, end], lever_trajectory.sample_rate)).astype(np.int_)
c_start, c_end = np.rint(np.multiply([start, end], neuron_rate)).astype(np.int_)
ax.plot(np.linspace(0, l_end - l_start, l_end - l_start), # lever trajectory
_scale(lever_trajectory.values[0][l_start: l_end]), COLORS[1])
time = np.linspace(0, calcium_trace.shape[1] / neuron_rate, lever_trajectory.shape[1])
spacing = iter(range(0, 500, 2))
for idx, row in enumerate(calcium_trace.values):
if idx in cells:
ax.plot(time[c_start: c_end] - l_start, _scale(row[c_start: c_end]) + next(spacing))
stim_onsets = lever_trajectory.timestamps[
(lever_trajectory.timestamps > l_start) & (lever_trajectory.timestamps < l_end)]\
/ lever_trajectory.sample_rate - l_start
for x in stim_onsets:
ax.axvline(x=x, color=COLORS[2])
def examine_saline(data_file):
data_file = dredd_files['cno'][5]
lever = load_mat(data_file['response'])
values = devibrate(lever.values[0], sample_rate=lever.sample_rate)
y = InterpolatedUnivariateSpline(lever.axes[0],
values)(data_file['spike']['y'])[1:]
X = data_file['spike']['data'][:, 1:]
decoder = svr.predictor_factory(y, gamma=3E-7, C=11, epsilon=1E-3)
single_power = [
mutual_info(y,
cross_predict(x[newaxis, :], y, decoder, section_mi=False))
for x in X
]
hat_0 = cross_predict(X, y, decoder, section_mi=False)
mask = np.greater_equal(single_power, sorted(single_power)[-20])
hat_1 = cross_predict(X[mask, :], y, decoder, section_mi=False)
plt.plot(y, color='blue')
hat = decoder(X, y, X)
plt.plot(hat, color='green')
plt.plot(hat_0, color='red')
plt.plot(hat_1, color='orange')
print("hat_1: ", mutual_info(hat_1, y), " hat_0: ", mutual_info(hat_0, y))
def load(self) -> SparseRec:
log_path = self.file_path.joinpath("original", "log", self.name + ".mat")
return load_mat(str(log_path))
def get_trials(data_file: File, motion_params: MotionParams) -> SparseRec:
lever = load_mat(data_file['response']).center_on(
"motion", **motion_params).fold_trials()
lever.values = np.squeeze(lever.values, 0)
lever.axes = lever.axes[1:]
return lever