def initialize_stim_with_sta(population, data, x0, Ns=None):
""" Initialize the stimulus response parameters with the STA
TODO: Move this to the bkgd model once we have decided upon the
correct function signature
"""
if Ns is None:
Ns = np.arange(population.N)
if isinstance(Ns,int):
Ns = [Ns]
temporal = isinstance(population.glm.bkgd_model, BasisStimulus)
spatiotemporal = isinstance(population.glm.bkgd_model, SpatiotemporalStimulus)
if not (temporal or spatiotemporal):
return
# Compute the STA
print "Initializing with the STA"
# TODO Fix these super hacky calls
if temporal:
s = sta(data['stim'],
data,
population.glm.bkgd_model.ibasis.get_value().shape[0],
Ns=Ns)
elif spatiotemporal:
s = sta(data['stim'],
data,
population.glm.bkgd_model.ibasis_t.get_value().shape[0],
Ns=Ns)
else:
# We're only initializing the basis function stim models now
return
# Compute the initial weights for each neuron
for i,n in enumerate(Ns):
sn = np.squeeze(s[i,:,:])
if sn.ndim == 1:
sn = np.reshape(sn, [sn.size, 1])
if spatiotemporal:
# Factorize the STA into a spatiotemporal filter using SVD
# CAUTION! Numpy svd returns V transpose whereas Matlab svd returns V!
U,Sig,V = np.linalg.svd(sn)
f_t = U[:,0] * np.sqrt(Sig[0])
f_x = V[0,:] * np.sqrt(Sig[0])
# Project this onto the spatial and temporal bases
w_t = project_onto_basis(f_t, population.glm.bkgd_model.ibasis_t.get_value())
w_x = project_onto_basis(f_x, population.glm.bkgd_model.ibasis_x.get_value())
# Flatten into 1D vectors
w_t = np.ravel(w_t)
w_x = np.ravel(w_x)
x0['glms'][n]['bkgd']['w_x'] = w_x
x0['glms'][n]['bkgd']['w_t'] = w_t
elif temporal:
# Only using a temporal filter
D_stim = sn.shape[1]
B = population.glm.bkgd_model.ibasis.get_value().shape[1]
# Project this onto the spatial and temporal bases
w_t = np.zeros((B*D_stim,1))
for d in np.arange(D_stim):
w_t[d*B:(d+1)*B] = project_onto_basis(sn[:,d],
population.glm.bkgd_model.ibasis.get_value())
# Flatten into a 1D vector
w_t = np.ravel(w_t)
x0['glms'][n]['bkgd']['w_stim'] = w_t
def convert_stimulus_filters_to_sharedtc(from_popn, from_model, from_vars, to_popn, to_model, to_vars):
"""
Convert a set of stimulus filters to a shared set of tuning curves
"""
# Get the spatial component of the stimulus filter for each neuron
N = from_popn.N
R = to_model['latent']['sharedtuningcurves']['R']
from_state = from_popn.eval_state(from_vars)
locs = np.zeros((N,2))
local_stim_xs = []
local_stim_ts = []
for n in range(N):
s_glm = from_state['glms'][n]
# to_state = to_popn.eval_state(to_vars)
assert 'stim_response_x' in s_glm['bkgd']
# Get the stimulus responses
stim_x = s_glm['bkgd']['stim_response_x']
stim_t = s_glm['bkgd']['stim_response_t']
loc_max = np.argmax(np.abs(stim_x))
if stim_x.ndim == 2:
locsi, locsj = np.unravel_index(loc_max, stim_x.shape)
locs[n,0], locs[n,1] = locsi.ravel(), locsj.ravel()
# # TODO: Test whether we have an issue with unraveling the data.
# locs[n,0], locs[n,1] = locsj.ravel(), locsi.ravel()
# Get the stimulus response in the vicinity of the mode
# Create a meshgrid of the correct shape, centered around the max
max_rb = to_model['latent']['latent_location']['location_prior']['max0']
max_ub = to_model['latent']['latent_location']['location_prior']['max1']
gsz = to_model['latent']['sharedtuningcurves']['spatial_shape']
gwidth = (np.array(gsz) - 1)//2
lb = max(0, locs[n,0]-gwidth[0])
rb = min(locs[n,0]-gwidth[0]+gsz[0], max_rb)
db = max(0, locs[n,1]-gwidth[1])
ub = min(locs[n,1]-gwidth[1]+gsz[1], max_ub)
grid = np.ix_(np.arange(lb, rb).astype(np.int),
np.arange(db, ub).astype(np.int))
# grid = grid.astype(np.int)
# Add this local filter to the list
local_stim_xs.append(stim_x[grid])
local_stim_ts.append(stim_t)
# Cluster the local stimulus filters
from sklearn.cluster import KMeans
flattened_filters_x = np.array(map(lambda f: f.ravel(), local_stim_xs))
flattened_filters_t = np.array(map(lambda f: f.ravel(), local_stim_ts))
km = KMeans(n_clusters=R)
km.fit(flattened_filters_x)
Y = km.labels_
print 'Filter cluster labels from kmeans: ', Y
# Initialize type based on stimulus filter
to_vars['latent']['sharedtuningcurve_provider']['Y'] = Y
# Initialize shared tuning curves (project onto the bases)
from pyglm.utils.basis import project_onto_basis
for r in range(R):
mean_filter_xr = flattened_filters_x[Y==r].mean(axis=0)
mean_filter_tr = flattened_filters_t[Y==r].mean(axis=0)
# TODO: Make sure the filters are being normalized properly!
# Project the mean filters onto the basis
to_vars['latent']['sharedtuningcurve_provider']['w_x'][:,r] = \
project_onto_basis(mean_filter_xr,
to_popn.glm.bkgd_model.spatial_basis).ravel()
# Temporal part of the filter
temporal_basis = to_popn.glm.bkgd_model.temporal_basis
t_temporal_basis = np.arange(temporal_basis.shape[0])
t_mean_filter_tr = np.linspace(0, temporal_basis.shape[0]-1, mean_filter_tr.shape[0])
interp_mean_filter_tr = np.interp(t_temporal_basis, t_mean_filter_tr, mean_filter_tr)
to_vars['latent']['sharedtuningcurve_provider']['w_t'][:,r] = \
project_onto_basis(interp_mean_filter_tr, temporal_basis).ravel()
# Initialize locations based on stimuls filters
to_vars['latent']['location_provider']['L'] = locs.ravel().astype(np.int)