def quantileReg(t,y,alpha):
# Données de la regression
m=y.size
n=2
A=np.zeros((m,n))
b=np.zeros((m,1))
A[:,0]=t
A[:,1]=np.ones((m,))
b[:,0]=y
# Variables
x = cp.Variable(n)
ep = cp.Variable(m)
em = cp.Variable(m)
# Constitution du problème
objective = cp.Minimize(cp.sum_entries(cp.square(alpha*ep +(1.-alpha)*em)))
constraints = [A*x-b+em-ep==0,ep>=0,em>=0]
prob = cp.Problem(objective, constraints)
# Résolution
prob.solve()
xres=np.array(x.value)
return xres
def solve_sparse(self, y, w, x_mask=None):
assert y.ndim == 1 and w.ndim == 1 and y.shape == w.shape
assert w.shape[0] == self.n
x = cp.Variable(np.count_nonzero(x_mask))
inv_mask = np.logical_not(x_mask)
term1 = cp.square(cp.norm(x-y[x_mask]))
term2 = self.c * cp.norm1(cp.diag(w[x_mask]) * x)
objective = cp.Minimize(term1 + term2)
constraints = [cp.quad_form(x, self.B[np.ix_(x_mask, x_mask)]) <= 1]
problem = cp.Problem(objective, constraints)
result = problem.solve(solver=cp.SCS)
if problem.status != cp.OPTIMAL:
warnings.warn(problem.status)
if problem.status not in (cp.OPTIMAL, cp.OPTIMAL_INACCURATE,
cp.UNBOUNDED_INACCURATE):
raise ValueError(problem.status)
out = np.zeros(self.n)
x = np.asarray(x.value).flatten()
out[x_mask] = x
return out
def find_ideal_pt_for_person_in_ball(center, radius, idealpt_and_radius, constraint="l1"):
X = cvxpy.Variable(5) # 1 point for each item
fun = 0
y = idealpt_and_radius[0]
w = idealpt_and_radius[1]
sumsq = math.sqrt(sum([math.pow(w[i], 2) for i in range(5)]))
w = [w[i] / sumsq for i in range(5)]
for slider in range(5):
fun += w[slider] * cvxpy.abs(X[slider] - y[slider])
obj = cvxpy.Minimize(fun)
constraints = [X >= 0, X[0] + X[1] + X[2] - X[3] + 162 == X[4]]
if constraint == "l1":
constraints += [cvxpy.sum_entries(
cvxpy.abs(X[0:4] - center[0:4])) <= radius]
else:
constraints += [cvxpy.sum_entries(
cvxpy.square(X[0:4] - center[0:4])) <= radius**2]
prob = cvxpy.Problem(obj, constraints)
result = prob.solve()
items = [X.value[i, 0] for i in range(5)]
if constraint == "l1":
credits = [abs(items[i] - center[i]) / radius for i in range(4)]
else:
credits = [(items[i] - center[i])**2 / radius**2 for i in range(4)]
deficit = calculate_deficit(items)
items.append(deficit)
return items, credits
def cbp_taylor(y, F, Delta, penalty=0.1, order=1):
"""
1st order taylor approximation
"""
# generate derivative matrices
dF = list()
current = F
for i in range(order):
dF.append( deriv(current,t) )
current = dF[-1]
# Construct the problem.
Fp = cvxopt.matrix(F)
dFp = cvxopt.matrix(dF[0])
yp = cvxopt.matrix(y)
gamma = cp.Parameter(sign="positive", name='gamma')
gamma.value = penalty
x = cp.Variable(F.shape[1],name='x')
d = cp.Variable(F.shape[1],name='d')
objective = cp.Minimize(sum(cp.square(yp - Fp*x - dFp*d)) + gamma*cp.norm(x, 1))
constraints = [0 <= x, cp.abs(d) <= 0.5*Delta*x]
p = cp.Problem(objective, constraints)
# solve
result = p.solve()
# reconstruct
yhat = F.dot(np.array(x.value)) + dF[0].dot(np.array(d.value))
return np.array(x.value), yhat, np.array(d.value), p.value
def test_signed_curvature(self):
# Convex argument.
expr = cvx.abs(1 + cvx.exp(cvx.Variable()) )
self.assertEqual(expr.curvature, s.CONVEX)
expr = cvx.abs( -cvx.entr(cvx.Variable()) )
self.assertEqual(expr.curvature, s.UNKNOWN)
expr = cvx.abs( -cvx.log(cvx.Variable()) )
self.assertEqual(expr.curvature, s.UNKNOWN)
# Concave argument.
expr = cvx.abs( cvx.log(cvx.Variable()) )
self.assertEqual(expr.curvature, s.UNKNOWN)
expr = cvx.abs( -cvx.square(cvx.Variable()) )
self.assertEqual(expr.curvature, s.CONVEX)
expr = cvx.abs( cvx.entr(cvx.Variable()) )
self.assertEqual(expr.curvature, s.UNKNOWN)
# Affine argument.
expr = cvx.abs( cvx.NonNegative() )
self.assertEqual(expr.curvature, s.CONVEX)
expr = cvx.abs( -cvx.NonNegative() )
self.assertEqual(expr.curvature, s.CONVEX)
expr = cvx.abs( cvx.Variable() )
self.assertEqual(expr.curvature, s.CONVEX)
def constraint_norm1(Ftilde, Sigma_F, positivity=False):
""" Constrain with optimization strategy """
import cvxpy as cvx
m, n = Sigma_F.shape
Sigma_F_inv = np.linalg.inv(Sigma_F)
zeros_F = np.zeros_like(Ftilde[:, np.newaxis])
F = cvx.Variable(n) # Construct the problem. PRIMAL
expression = cvx.quad_form(F - Ftilde[:, np.newaxis], Sigma_F_inv)
objective = cvx.Minimize(expression)
if positivity:
constraints = [F[0] == 0, F[-1] == 0, F >= zeros_F,
cvx.square(cvx.norm(F, 2)) <= 1]
else:
constraints = [F[0] == 0, F[-1] == 0, cvx.square(cvx.norm(F, 2)) <= 1]
prob = cvx.Problem(objective, constraints)
prob.solve(verbose=0, solver=cvx.CVXOPT)
return np.squeeze(np.array((F.value)))
def runndCVXPy(A, b, clambda):
n_vars = A.shape[1]
x = cvxpy.Variable(n_vars)
obj = cvxpy.Minimize(
clambda * cvxpy.sum_entries(cvxpy.abs(x)) +
0.5 * cvxpy.sum_entries(cvxpy.square(A * x - b)))
prob = cvxpy.Problem(obj, [])
prob.solve(verbose=False)
return x.value
def updateEz2(self,sigmaz,ez_):
ez=cvx.Variable()
constraints=[0<=ez]
objective = cvx.Maximize(np.array(sigmaz)*ez-ez*self.omegabg-rho/2*cvx.square(ez-ez_))
prob = cvx.Problem(objective, constraints)
result = prob.solve(solver=slv)
#print(ez.value)
self.ez=ez.value
def l1_solution(A, b, lam=0.5):
N = A.shape[0]
x = Variable(N)
objective = Minimize(sum_entries(square(A * x - b)) + lam * norm(x, 1))
constraints = []
prob = Problem(objective, constraints)
prob.solve()
xhat = x.value
return xhat
def test_linearize(self):
"""
Test the linearize function.
"""
z = cvx.Variable((1,5))
expr = cvx.square(z)
z.value = np.reshape(np.array([1,2,3,4,5]), (1,5))
lin = linearize(expr)
self.assertEqual(lin.shape, (1,5))
self.assertItemsAlmostEqual(lin.value, [1,4,9,16,25])
def transition_to_action(s0,s1, dynamics, max_dtheta, max_ddx, max_iter=30,
max_line_searches=10):
"""recovers a control signal u that can cause a transition from s0 to s1.
specifically, minimize || f(s0,u) - s1 ||^2 as a Sequential
Quadratic Program.
"""
# the current step size along the search direction recovered by the QP
step = 1.
# initial guess
s0 = array(s0)
s1 = array(s1)
u0 = array((0,0))
def cost(u):
"|| f(s0,u) - s1 ||^2"
return sum((dynamics(s0,u)['val'] - s1)**2)
# the value of the initial guess
best_cost = cost(u0)
for it in xrange(max_iter):
f = dynamics(s0, u0, derivs={'du'})
# linearize || f(s0,u) - s1 ||^2 about u0 and solve as a QP
u = CX.Variable(len(u0), name='u')
objective = CX.square(CX.norm( array(f['val']) + vstack(f['du'])*(u-u0) - s1 ))
p = CX.Problem(CX.Minimize(objective),
[CX.abs(u[0]) <= max_ddx,
CX.abs(u[1]) <= max_dtheta])
r = p.solve()
unew = array(u.value.flat)
# line search along unew-u0 from u0
line_search_success = False
for line_searches in xrange(max_line_searches):
new_cost = cost(u0 + step*(unew-u0))
if new_cost < best_cost:
# accept the step
best_cost = new_cost
u0 = u0 + step*(unew-u0)
# grow the step for the next iteration
step *= 1.2
line_search_success = True
else:
# shrink the step size and try again
step *= 0.5
if not line_search_success:
# convergence is when line search fails.
return u0
print 'Warning: failed to converge'
return u0
def cbp_polar(y, F, Fprev, Fnext, Delta, penalty=0.1, order=1):
"""
CBP with polar interpolation
"""
# compute r and theta
a = 0.5 * np.linalg.norm(Fnext-Fprev, axis=0)[int(F.shape[1]/2)]
b = np.linalg.norm(F-Fprev, axis=0)[int(F.shape[1]/2)]
theta = np.pi - 2 * np.arcsin(a/b) # radians
r = a / np.sin(theta)
# build the polar transformation matrix
P = np.array([[1,r*np.cos(theta),-r*np.sin(theta)], [1,r,0], [1,r*np.cos(theta),r*np.sin(theta)]])
# get C, U, and V
pol = np.linalg.inv(P).dot(np.vstack((Fprev.ravel(),F.ravel(),Fnext.ravel())))
C = pol[0,:].reshape(F.shape)
U = pol[1,:].reshape(F.shape)
V = pol[2,:].reshape(F.shape)
## construct the problem
# discretized matrices
Cp = cvxopt.matrix(C)
Up = cvxopt.matrix(U)
Vp = cvxopt.matrix(V)
yp = cvxopt.matrix(y)
# sparsity penalty
gamma = cp.Parameter(sign="positive", name='gamma')
gamma.value = penalty
# variables
dx = cp.Variable(F.shape[1],name='x')
dy = cp.Variable(F.shape[1],name='y')
dz = cp.Variable(F.shape[1],name='z')
# objective and constraints
objective = cp.Minimize(sum(cp.square(yp - Cp*dx - Up*dy - Vp*dz)) + gamma*cp.norm(dx, 1))
#constraints = [0 <= x, cp.sqrt(cp.square(y)+cp.square(z)) <= r*x, r*np.cos(theta)*x <= y, y <= r*x]
sqcon = [cp.norm(cp.vstack(yi,zi),2) <= xi*r for xi, yi, zi in zip(dx,dy,dz)]
constraints = [0 <= dx, dy <= r*dx, r*np.cos(theta)*dx <= dy]
constraints.extend(sqcon)
p = cp.Problem(objective, constraints)
# solve
result = p.solve()
# reconstruct
yhat = C.dot(np.array(dx.value)) + U.dot(np.array(dy.value)) + V.dot(np.array(dz.value))
return np.array(dx.value), yhat, p.value
def solveX(data):
inputs = int(data[len(data)-1])
lamb = data[len(data)-2]
rho = data[len(data)-3]
x = data[0:inputs]
y = data[inputs:2*inputs]
z = data[2*inputs:3*inputs]
a = data[3*inputs:4*inputs]
neighs = data[4*inputs:len(data)-3]
xnew = cp.Variable(inputs, 1)
g = 0.5*cp.square(norm(xnew - a))
h = 0
for i in range(inputs): #This can be written better...
h = h + y[i]*(xnew[i] - z[i])
s = cp.square(norm(xnew - z))
w = 0 #TODO fill in later
for i in range(len(neighs)/(inputs+1)):
w = w + neighs[i*(inputs+1)]*norm(xnew - neighs[i*(inputs+1)+1:i*(inputs+1)+(inputs+1)])
objective = cp.Minimize(g + lamb/2*w + h + rho/2*s)
constraints = []
p = cp.Problem(objective, constraints)
result = p.solve()
return xnew.value
def cvx_test(*args):
n = 5000
p = 100
X = np.random.uniform(-1,1,(n,p))
C = 1e-3
y = np.random.uniform(-1,1, n)
w = cvx.Variable(p)
loss = cvx.sum_entries(cvx.square(X*w - y))
reg = cvx.norm2(w)**2
obj = cvx.Minimize(loss + C*reg)
prob = cvx.Problem(obj, [])
tic()
prob.solve(solver=cvx.SCS, verbose=False)
toc()
def feasibility_regression(X, pairwise_constraints_indices,
bag_indices,upper_p_bound_bags,
diff_upper_bound_pairs,diff_lower_bound_pairs,
lower_p_bound_bags):
theta = cp.Variable(X.shape[1])
reg = cp.square(cp.norm(theta, 2))
constraints = []
added_pairs = []
pair_ind = 0
for pair in pairwise_constraints_indices:
bag_high = bag_indices[pair[0]]
bag_low = bag_indices[pair[1]]
scores_high = (1./len(bag_high))*X[bag_high]*theta
scores_low = (1./len(bag_low))*X[bag_low]*theta
if pair in diff_upper_bound_pairs:
constraints.append(cp.sum_entries(scores_high) - cp.sum_entries(scores_low) < diff_upper_bound_pairs[pair])
if pair in diff_lower_bound_pairs:
constraints.append(cp.sum_entries(scores_high) - cp.sum_entries(scores_low) > diff_lower_bound_pairs[pair])
else:
constraints.append(cp.sum_entries(scores_high) - cp.sum_entries(scores_low) > 0)
if pair[0] not in added_pairs:
if pair[0] in upper_p_bound_bags:
constraints.append(cp.sum_entries(scores_high)<=upper_p_bound_bags[pair[0]])
if pair[0] in lower_p_bound_bags:
constraints.append(cp.sum_entries(scores_high)>=lower_p_bound_bags[pair[0]])
added_pairs.append(pair[0])
if pair[1] not in added_pairs:
if pair[1] in upper_p_bound_bags:
constraints.append(cp.sum_entries(scores_low)<=upper_p_bound_bags[pair[1]])
if pair[1] in lower_p_bound_bags:
constraints.append(cp.sum_entries(scores_low)>=lower_p_bound_bags[pair[1]])
added_pairs.append(pair[1])
pair_ind+=1
prob = cp.Problem(cp.Minimize(1*reg),constraints = constraints)
try:
prob.solve()
except:
prob.solve(solver="SCS")
w_t = np.squeeze(np.asarray(np.copy(theta.value)))
return w_t
def test_convexify_obj(self):
"""
Test convexify objective
"""
obj = cvx.Maximize(cvx.sum(cvx.square(self.x)))
self.x.value = [1,1]
obj_conv = convexify_obj(obj)
prob_conv = cvx.Problem(obj_conv, [self.x <= -1])
prob_conv.solve()
self.assertAlmostEqual(prob_conv.value,-6)
obj = cvx.Minimize(cvx.sqrt(self.a))
self.a.value = [1]
obj_conv = convexify_obj(obj)
prob_conv = cvx.Problem(obj_conv,cvx.sqrt(self.a).domain)
prob_conv.solve()
self.assertAlmostEqual(prob_conv.value,0.5)
def cvxpy_sigma_trace(b, model):
xDim = model.xDim
SqrtSigma = np.zeros([xDim,xDim]).tolist()
idx = xDim
for j in xrange(0,xDim):
for i in xrange(j,xDim):
SqrtSigma[i][j] = b[idx]
SqrtSigma[j][i] = SqrtSigma[i][j]
idx = idx+1
trace = 0
for i in xrange(0,xDim):
trace += sum(cvxpy.square(SqrtSigma[i][j]) for j in xrange(0,xDim))
return trace
def admm(self, rho=0.5, iterations=5, *args, **kwargs):
noncvx_vars = []
for var in self.variables():
if getattr(var, "noncvx", False):
noncvx_vars += [var]
# Form ADMM problem.
obj = self.objective._expr
for var in noncvx_vars:
obj = obj + (rho/2)*cvx.sum_entries(cvx.square(var - var.z + var.u))
prob = cvx.Problem(cvx.Minimize(obj), self.constraints)
# ADMM loop
for i in range(iterations):
result = prob.solve(*args, **kwargs)
for var in noncvx_vars:
var.z.value = var.round(var.value + var.u.value)
var.u.value += var.value - var.z.value
return polish(self, noncvx_vars, *args, **kwargs)
def test_problem_penalty(self):
"""
Compare cvxpy solutions to cvxopt ground truth
"""
from cvxpy import (matrix,variable,program,minimize,
sum,abs,norm2,log,square,zeros,max,
hstack,vstack)
m, n = self.m, self.n
A = matrix(self.A)
b = matrix(self.b)
# set tolerance to 5 significant digits
tol_exp = 5
# l1 approximation
x = variable(n)
p = program(minimize(sum(abs(A*x + b))))
p.solve(True)
np.testing.assert_array_almost_equal(x.value,self.x1,tol_exp)
# l2 approximation
x = variable(n)
p = program(minimize(norm2(A*x + b)))
p.solve(True)
np.testing.assert_array_almost_equal(x.value,self.x2,tol_exp)
# Deadzone approximation - implementation is currently ugly (need max along axis)
x = variable(n)
Axbm = abs(A*x+b)-0.5
Axbm_deadzone = vstack([max(hstack((Axbm[i,0],0.0))) for i in range(m)])
p = program(minimize(sum(Axbm_deadzone)))
p.solve(True)
obj_dz_cvxpy = np.sum(np.max([np.abs(A*x.value+b)-0.5,np.zeros((m,1))],axis=0))
np.testing.assert_array_almost_equal(obj_dz_cvxpy,self.obj_dz,tol_exp)
# Log barrier
x = variable(n)
p = program(minimize(-sum(log(1.0-square(A*x + b)))))
p.solve(True)
np.testing.assert_array_almost_equal(x.value,self.cxlb,tol_exp)
def admm(self, rho=0.5, iterations=5, solver=cvx.ECOS):
vars_ = self.objective.variables()
for constr in self.constraints:
vars_ += constr.variables()
noncvx_vars = [obj for obj in vars_ if isinstance(obj, NonCvxVariable)]
# Form ADMM problem.
obj = self.objective._expr
for var in noncvx_vars:
obj = obj + (rho / 2) * cvx.sum_entries(cvx.square(var - var.z + var.u))
p = cvx.Problem(cvx.Minimize(obj), self.constraints)
# ADMM loop
for i in range(iterations):
result = p.solve(solver=solver)
for var in noncvx_vars:
var.z.value = var.round(var.value + var.u.value)
var.u.value = var.value - var.z.value
# Fix noncvx variables and solve.
fix_constr = []
for var in noncvx_vars:
fix_constr += var.fix(var.z.value)
p = cvx.Problem(self.objective, self.constraints + fix_constr)
return p.solve(solver=solver)
def admm(self, rho=0.5, iterations=5, solver=cvx.ECOS):
noncvx_vars = []
for var in self.variables():
if getattr(var, "noncvx", False):
noncvx_vars += [var]
# Form ADMM problem.
obj = self.objective._expr
for var in noncvx_vars:
obj = obj + (rho/2)*cvx.sum_entries(cvx.square(var - var.z + var.u))
prob = cvx.Problem(cvx.Minimize(obj), self.constraints)
# ADMM loop
for i in range(iterations):
result = prob.solve(solver=solver)
for var in noncvx_vars:
var.z.value = var.round(var.value + var.u.value)
var.u.value += var.value - var.z.value
# Fix noncvx variables and solve.
fix_constr = []
for var in noncvx_vars:
fix_constr += var.fix(var.z.value)
prob = cvx.Problem(self.objective, self.constraints + fix_constr)
return prob.solve(solver=solver)
def admm(self, rho=0.5, iterations=5, solver=cp.ECOS):
objective,constr_map,dims = self.canonicalize()
var_offsets,x_length = self.variables(objective,
constr_map[s.EQ] + constr_map[s.INEQ])
noncvx_vars = [obj for obj in var_offsets.keys() if isinstance(obj, NonCvxVariable)]
# Form ADMM problem.
obj = self.objective.expr
for var in noncvx_vars:
obj = obj + (rho/2)*sum(cp.square(var - var.z + var.u))
p = cp.Problem(cp.Minimize(obj), self.constraints)
# ADMM loop
for i in range(iterations):
result = p.solve(solver=solver)
for var in noncvx_vars:
var.z.value = var.round(var.value + var.u.value)
var.u.value = var.value - var.z.value
# Fix noncvx variables and solve.
fix_constr = []
for var in noncvx_vars:
fix_constr += var.fix(var.z.value)
p = cp.Problem(self.objective, self.constraints + fix_constr)
return p.solve(solver=solver)
def admm(self, rho=0.5, iterations=5, solver=cp.ECOS):
objective,constr_map,dims = self.canonicalize()
new_constr_map = constr_map[s.EQ]
for c in constr_map[s.INEQ]:
new_constr_map.add(c)
vars_ = objective.variables()
for constr in new_constr_map:
vars_ += constr.variables()
var_offsets = OrderedDict()
vert_offset = 0
for var in set(vars_):
var_offsets[var] = vert_offset
vert_offset += var.size[0]*var.size[1]
#var_offsets,x_length = self.variables(objective,
# new_constr_map)
noncvx_vars = [obj for obj in var_offsets.keys() if isinstance(obj, NonCvxVariable)]
#import pdb; pdb.set_trace()
# Form ADMM problem.
obj = self.objective._expr
for var in noncvx_vars:
obj = obj + (rho/2)*sum(cp.square(var - var.z + var.u))
p = cp.Problem(cp.Minimize(obj), self.constraints)
# ADMM loop
for i in range(iterations):
result = p.solve(solver=solver)
for var in noncvx_vars:
var.z.value = var.round(var.value + var.u.value)
var.u.value = var.value - var.z.value
# Fix noncvx variables and solve.
fix_constr = []
for var in noncvx_vars:
fix_constr += var.fix(var.z.value)
p = cp.Problem(self.objective, self.constraints + fix_constr)
return p.solve(solver=solver)
def lasso_cvxpy(dict, target, gamma):
"""
Computes Lasso optimization
:param dict: dictionnary
:type dict: np.array
:param target: image
:typetarget: np.array
:param gamma: regularization factor
:type gamma: float
:rtype: np.array
"""
num_samples = target.shape[1]
patch_size = dict.shape[0]
dic_size = dict.shape[1]
alpha = cp.Variable(dic_size, num_samples)
D = cp.Parameter(patch_size, dic_size, value=dict)
x = cp.Parameter(patch_size, num_samples, value=target)
objective = cp.Minimize(sum(cp.square(D * alpha - x)) / (2 * num_samples) + gamma * cp.norm(alpha, 1))
P = cp.Problem(objective)
P.solve()
# print(P.value)
return alpha.value
def run_MPC(traj_des, cur_state_vec, mpc_acc, mpc_steer, steer_des, goal):
for iter in range(3):
traj_pred = calc_predicted_trajectory(mpc_acc, mpc_steer,
cur_state_vec)
x = cp.Variable([Nx, H + 1])
u = cp.Variable([Nu, H])
cost = 0.0
constraints = []
for i in range(H):
cost += cp.sum(W1 * cp.square(u[:, i])) # input weightage
cost += cp.sum(
W2 *
cp.square(traj_des[:, i] - x[:, i])) # state error weightage
#cost += cp.sum(W2 * cp.square([goal[0],goal[1],0,0] - x[:, i])) # terminal cost
if i < (H - 1):
cost += cp.sum(
W3 * cp.square(u[:, i + 1] -
u[:, i])) # rate of input change weightage
constraints += [
cp.abs(u[1, i + 1] - u[1, i]) <= max_steer_rate * dt
]
A, B, C = dynamic_model(traj_pred[3, i], traj_pred[2, i],
mpc_steer[i])
constraints += [x[:, i + 1] == A * x[:, i] + B * u[:, i] + C]
cost += cp.sum(
W4 *
cp.square(traj_des[:, H] - x[:, H])) # final state error weightage
#cost += cp.sum(10 * cp.square([goal[0],goal[1]] - x[:2, H])) # terminal cost
constraints += [x[:, 0] == cur_state_vec]
constraints += [x[3, :] <= max_speed]
constraints += [x[3, :] >= -max_reverse_speed]
constraints += [u[1, :] <= max_steer_angle]
constraints += [u[1, :] >= -max_steer_angle]
constraints += [u[0, :] <= max_acc]
constraints += [u[0, :] >= -3 * max_acc]
prob = cp.Problem(cp.Minimize(cost), constraints)
prob.solve()
mpc_x = x.value[0, :]
mpc_y = x.value[1, :]
mpc_yaw = x.value[2, :]
mpc_v = x.value[3, :]
mpc_acc = u.value[0, :]
mpc_steer = u.value[1, :]
lyap_val = 0
lap_u = 0
lap_x = 0
lap_du = 0
for i in range(H):
lyap_val += np.sum(W1 *
np.square(u.value[:, i])) # input weightage
lap_u += np.sum(W1 * np.square(u.value[:, i]))
lyap_val += np.sum(
W2 * np.square(traj_des[:, i] -
x.value[:, i])) # state error weightage
lap_x += np.sum(W2 * np.square(traj_des[:, i] - x.value[:, i]))
if i < (H - 1):
lyap_val += np.sum(
W3 *
np.square(u.value[:, i + 1] -
u.value[:, i])) # rate of input change weightage
lap_du += np.sum(W3 *
np.square(u.value[:, i + 1] - u.value[:, i]))
lyap_val += np.sum(W4 * np.square(traj_des[:, H] - x.value[:, H]))
lap_x += np.sum(W4 * np.square(traj_des[:, H] - x.value[:, H]))
#yap_val += np.sum(W2 * np.square(x.value[:, 1]))
aaaa = 5
return mpc_x, mpc_y, mpc_yaw, mpc_v, mpc_acc, mpc_steer, lyap_val, lap_u, lap_x, lap_du
def Main_vbjde_Extension_constrained(graph, Y, Onsets, Thrf, K, TR, beta,
dt, scale=1, estimateSigmaH=True,
sigmaH=0.05, NitMax=-1,
NitMin=1, estimateBeta=True,
PLOT=False, contrasts=[],
computeContrast=False,
gamma_h=0, estimateHRF=True,
TrueHrfFlag=False,
HrfFilename='hrf.nii',
estimateLabels=True,
LabelsFilename='labels.nii',
MFapprox=False, InitVar=0.5,
InitMean=2.0, MiniVEMFlag=False,
NbItMiniVem=5):
# VBJDE Function for BOLD with contraints
logger.info("Fast EM with C extension started ...")
np.random.seed(6537546)
##########################################################################
# INITIALIZATIONS
# Initialize parameters
tau1 = 0.0
tau2 = 0.0
S = 100
Init_sigmaH = sigmaH
Nb2Norm = 1
NormFlag = False
if NitMax < 0:
NitMax = 100
gamma = 7.5
#gamma_h = 1000
gradientStep = 0.003
MaxItGrad = 200
Thresh = 1e-5
Thresh_FreeEnergy = 1e-5
estimateLabels = True # WARNING!! They should be estimated
# Initialize sizes vectors
D = int(np.ceil(Thrf / dt)) + 1 # D = int(np.ceil(Thrf/dt))
M = len(Onsets)
N = Y.shape[0]
J = Y.shape[1]
l = int(np.sqrt(J))
condition_names = []
# Neighbours
maxNeighbours = max([len(nl) for nl in graph])
neighboursIndexes = np.zeros((J, maxNeighbours), dtype=np.int32)
neighboursIndexes -= 1
for i in xrange(J):
neighboursIndexes[i, :len(graph[i])] = graph[i]
# Conditions
X = OrderedDict([])
for condition, Ons in Onsets.iteritems():
X[condition] = vt.compute_mat_X_2(N, TR, D, dt, Ons)
condition_names += [condition]
XX = np.zeros((M, N, D), dtype=np.int32)
nc = 0
for condition, Ons in Onsets.iteritems():
XX[nc, :, :] = X[condition]
nc += 1
# Covariance matrix
order = 2
D2 = vt.buildFiniteDiffMatrix(order, D)
R = np.dot(D2, D2) / pow(dt, 2 * order)
invR = np.linalg.inv(R)
Det_invR = np.linalg.det(invR)
Gamma = np.identity(N)
Det_Gamma = np.linalg.det(Gamma)
p_Wtilde = np.zeros((M, K), dtype=np.float64)
p_Wtilde1 = np.zeros((M, K), dtype=np.float64)
p_Wtilde[:, 1] = 1
Crit_H = 1
Crit_Z = 1
Crit_A = 1
Crit_AH = 1
AH = np.zeros((J, M, D), dtype=np.float64)
AH1 = np.zeros((J, M, D), dtype=np.float64)
Crit_FreeEnergy = 1
cA = []
cH = []
cZ = []
cAH = []
FreeEnergy_Iter = []
cTime = []
cFE = []
SUM_q_Z = [[] for m in xrange(M)]
mu1 = [[] for m in xrange(M)]
h_norm = []
h_norm2 = []
CONTRAST = np.zeros((J, len(contrasts)), dtype=np.float64)
CONTRASTVAR = np.zeros((J, len(contrasts)), dtype=np.float64)
Q_barnCond = np.zeros((M, M, D, D), dtype=np.float64)
XGamma = np.zeros((M, D, N), dtype=np.float64)
m1 = 0
for k1 in X: # Loop over the M conditions
m2 = 0
for k2 in X:
Q_barnCond[m1, m2, :, :] = np.dot(
np.dot(X[k1].transpose(), Gamma), X[k2])
m2 += 1
XGamma[m1, :, :] = np.dot(X[k1].transpose(), Gamma)
m1 += 1
if MiniVEMFlag:
logger.info("MiniVEM to choose the best initialisation...")
"""InitVar, InitMean, gamma_h = MiniVEM_CompMod(Thrf,TR,dt,beta,Y,K,
gamma,gradientStep,
MaxItGrad,D,M,N,J,S,
maxNeighbours,
neighboursIndexes,
XX,X,R,Det_invR,Gamma,
Det_Gamma,
scale,Q_barnCond,XGamma,
NbItMiniVem,
sigmaH,estimateHRF)"""
InitVar, InitMean, gamma_h = vt.MiniVEM_CompMod(Thrf, TR, dt, beta, Y, K, gamma, gradientStep, MaxItGrad, D, M, N, J, S, maxNeighbours,
neighboursIndexes, XX, X, R, Det_invR, Gamma, Det_Gamma, p_Wtilde, scale, Q_barnCond, XGamma, tau1, tau2, NbItMiniVem, sigmaH, estimateHRF)
sigmaH = Init_sigmaH
sigma_epsilone = np.ones(J)
logger.info(
"Labels are initialized by setting active probabilities to ones ...")
q_Z = np.zeros((M, K, J), dtype=np.float64)
q_Z[:, 1, :] = 1
q_Z1 = np.zeros((M, K, J), dtype=np.float64)
Z_tilde = q_Z.copy()
# TT,m_h = getCanoHRF(Thrf-dt,dt) #TODO: check
TT, m_h = getCanoHRF(Thrf, dt) # TODO: check
m_h = m_h[:D]
m_H = np.array(m_h).astype(np.float64)
m_H1 = np.array(m_h)
sigmaH1 = sigmaH
if estimateHRF:
Sigma_H = np.ones((D, D), dtype=np.float64)
else:
Sigma_H = np.zeros((D, D), dtype=np.float64)
Beta = beta * np.ones((M), dtype=np.float64)
P = vt.PolyMat(N, 4, TR)
L = vt.polyFit(Y, TR, 4, P)
PL = np.dot(P, L)
y_tilde = Y - PL
Ndrift = L.shape[0]
sigma_M = np.ones((M, K), dtype=np.float64)
sigma_M[:, 0] = 0.5
sigma_M[:, 1] = 0.6
mu_M = np.zeros((M, K), dtype=np.float64)
for k in xrange(1, K):
mu_M[:, k] = InitMean
Sigma_A = np.zeros((M, M, J), np.float64)
for j in xrange(0, J):
Sigma_A[:, :, j] = 0.01 * np.identity(M)
m_A = np.zeros((J, M), dtype=np.float64)
m_A1 = np.zeros((J, M), dtype=np.float64)
for j in xrange(0, J):
for m in xrange(0, M):
for k in xrange(0, K):
m_A[j, m] += np.random.normal(mu_M[m, k],
np.sqrt(sigma_M[m, k])) * q_Z[m, k, j]
m_A1 = m_A
t1 = time.time()
##########################################################################
# VBJDE num. iter. minimum
ni = 0
while ((ni < NitMin) or (((Crit_FreeEnergy > Thresh_FreeEnergy) or (Crit_AH > Thresh)) and (ni < NitMax))):
logger.info("------------------------------ Iteration n° " +
str(ni + 1) + " ------------------------------")
#####################
# EXPECTATION
#####################
# A
logger.info("E A step ...")
UtilsC.expectation_A(q_Z, mu_M, sigma_M, PL, sigma_epsilone, Gamma,
Sigma_H, Y, y_tilde, m_A, m_H, Sigma_A, XX.astype(np.int32), J, D, M, N, K)
val = np.reshape(m_A, (M * J))
val[np.where((val <= 1e-50) & (val > 0.0))] = 0.0
val[np.where((val >= -1e-50) & (val < 0.0))] = 0.0
# crit. A
DIFF = np.reshape(m_A - m_A1, (M * J))
# To avoid numerical problems
DIFF[np.where((DIFF < 1e-50) & (DIFF > 0.0))] = 0.0
# To avoid numerical problems
DIFF[np.where((DIFF > -1e-50) & (DIFF < 0.0))] = 0.0
Crit_A = (
np.linalg.norm(DIFF) / np.linalg.norm(np.reshape(m_A1, (M * J)))) ** 2
cA += [Crit_A]
m_A1[:, :] = m_A[:, :]
# HRF h
if estimateHRF:
################################
# HRF ESTIMATION
################################
UtilsC.expectation_H(XGamma, Q_barnCond, sigma_epsilone, Gamma, R, Sigma_H, Y,
y_tilde, m_A, m_H, Sigma_A, XX.astype(np.int32), J, D, M, N, scale, sigmaH)
import cvxpy as cvx
m, n = Sigma_H.shape
Sigma_H_inv = np.linalg.inv(Sigma_H)
zeros_H = np.zeros_like(m_H[:, np.newaxis])
# Construct the problem. PRIMAL
h = cvx.Variable(n)
expression = cvx.quad_form(h - m_H[:, np.newaxis], Sigma_H_inv)
objective = cvx.Minimize(expression)
#constraints = [h[0] == 0, h[-1]==0, h >= zeros_H, cvx.square(cvx.norm(h,2))<=1]
constraints = [
h[0] == 0, h[-1] == 0, cvx.square(cvx.norm(h, 2)) <= 1]
prob = cvx.Problem(objective, constraints)
result = prob.solve(verbose=0, solver=cvx.CVXOPT)
# Now we update the mean of h
m_H_old = m_H
Sigma_H_old = Sigma_H
m_H = np.squeeze(np.array((h.value)))
Sigma_H = np.zeros_like(Sigma_H)
h_norm += [np.linalg.norm(m_H)]
# print 'h_norm = ', h_norm
# Plotting HRF
if PLOT and ni >= 0:
import matplotlib.pyplot as plt
plt.figure(M + 1)
plt.plot(m_H)
plt.hold(True)
else:
if TrueHrfFlag:
#TrueVal, head = read_volume(HrfFilename)
TrueVal, head = read_volume(HrfFilename)[:, 0, 0, 0]
print TrueVal
print TrueVal.shape
m_H = TrueVal
# crit. h
Crit_H = (np.linalg.norm(m_H - m_H1) / np.linalg.norm(m_H1)) ** 2
cH += [Crit_H]
m_H1[:] = m_H[:]
# crit. AH
for d in xrange(0, D):
AH[:, :, d] = m_A[:, :] * m_H[d]
DIFF = np.reshape(AH - AH1, (M * J * D))
# To avoid numerical problems
DIFF[np.where((DIFF < 1e-50) & (DIFF > 0.0))] = 0.0
# To avoid numerical problems
DIFF[np.where((DIFF > -1e-50) & (DIFF < 0.0))] = 0.0
if np.linalg.norm(np.reshape(AH1, (M * J * D))) == 0:
Crit_AH = 1000000000.
else:
Crit_AH = (
np.linalg.norm(DIFF) / np.linalg.norm(np.reshape(AH1, (M * J * D)))) ** 2
cAH += [Crit_AH]
AH1[:, :, :] = AH[:, :, :]
# Z labels
if estimateLabels:
logger.info("E Z step ...")
# WARNING!!! ParsiMod gives better results, but we need the other
# one.
if MFapprox:
UtilsC.expectation_Z(Sigma_A, m_A, sigma_M, Beta, Z_tilde, mu_M, q_Z, neighboursIndexes.astype(
np.int32), M, J, K, maxNeighbours)
if not MFapprox:
UtilsC.expectation_Z_ParsiMod_RVM_and_CompMod(
Sigma_A, m_A, sigma_M, Beta, mu_M, q_Z, neighboursIndexes.astype(np.int32), M, J, K, maxNeighbours)
else:
logger.info("Using True Z ...")
TrueZ = read_volume(LabelsFilename)
for m in xrange(M):
q_Z[m, 1, :] = np.reshape(TrueZ[0][:, :, :, m], J)
q_Z[m, 0, :] = 1 - q_Z[m, 1, :]
# crit. Z
val = np.reshape(q_Z, (M * K * J))
val[np.where((val <= 1e-50) & (val > 0.0))] = 0.0
DIFF = np.reshape(q_Z - q_Z1, (M * K * J))
# To avoid numerical problems
DIFF[np.where((DIFF < 1e-50) & (DIFF > 0.0))] = 0.0
# To avoid numerical problems
DIFF[np.where((DIFF > -1e-50) & (DIFF < 0.0))] = 0.0
if np.linalg.norm(np.reshape(q_Z1, (M * K * J))) == 0:
Crit_Z = 1000000000.
else:
Crit_Z = (
np.linalg.norm(DIFF) / np.linalg.norm(np.reshape(q_Z1, (M * K * J)))) ** 2
cZ += [Crit_Z]
q_Z1 = q_Z
#####################
# MAXIMIZATION
#####################
# HRF: Sigma_h
if estimateHRF:
if estimateSigmaH:
logger.info("M sigma_H step ...")
if gamma_h > 0:
sigmaH = vt.maximization_sigmaH_prior(
D, Sigma_H_old, R, m_H_old, gamma_h)
else:
sigmaH = vt.maximization_sigmaH(D, Sigma_H, R, m_H)
logger.info('sigmaH = %s', str(sigmaH))
# (mu,sigma)
logger.info("M (mu,sigma) step ...")
mu_M, sigma_M = vt.maximization_mu_sigma(
mu_M, sigma_M, q_Z, m_A, K, M, Sigma_A)
for m in xrange(M):
SUM_q_Z[m] += [sum(q_Z[m, 1, :])]
mu1[m] += [mu_M[m, 1]]
# Drift L
UtilsC.maximization_L(
Y, m_A, m_H, L, P, XX.astype(np.int32), J, D, M, Ndrift, N)
PL = np.dot(P, L)
y_tilde = Y - PL
# Beta
if estimateBeta:
logger.info("estimating beta")
for m in xrange(0, M):
if MFapprox:
Beta[m] = UtilsC.maximization_beta(beta, q_Z[m, :, :].astype(np.float64), Z_tilde[m, :, :].astype(
np.float64), J, K, neighboursIndexes.astype(np.int32), gamma, maxNeighbours, MaxItGrad, gradientStep)
if not MFapprox:
#Beta[m] = UtilsC.maximization_beta(beta,q_Z[m,:,:].astype(np.float64),q_Z[m,:,:].astype(np.float64),J,K,neighboursIndexes.astype(int32),gamma,maxNeighbours,MaxItGrad,gradientStep)
Beta[m] = UtilsC.maximization_beta_CB(beta, q_Z[m, :, :].astype(
np.float64), J, K, neighboursIndexes.astype(np.int32), gamma, maxNeighbours, MaxItGrad, gradientStep)
logger.info("End estimating beta")
logger.info(Beta)
# Sigma noise
logger.info("M sigma noise step ...")
UtilsC.maximization_sigma_noise(
Gamma, PL, sigma_epsilone, Sigma_H, Y, m_A, m_H, Sigma_A, XX.astype(np.int32), J, D, M, N)
#### Computing Free Energy ####
if ni > 0:
FreeEnergy1 = FreeEnergy
"""FreeEnergy = vt.Compute_FreeEnergy(y_tilde,m_A,Sigma_A,mu_M,sigma_M,
m_H,Sigma_H,R,Det_invR,sigmaH,
p_Wtilde,q_Z,neighboursIndexes,
maxNeighbours,Beta,sigma_epsilone,
XX,Gamma,Det_Gamma,XGamma,J,D,M,
N,K,S,"CompMod")"""
FreeEnergy = vt.Compute_FreeEnergy(y_tilde, m_A, Sigma_A, mu_M, sigma_M, m_H, Sigma_H, R, Det_invR, sigmaH, p_Wtilde, tau1,
tau2, q_Z, neighboursIndexes, maxNeighbours, Beta, sigma_epsilone, XX, Gamma, Det_Gamma, XGamma, J, D, M, N, K, S, "CompMod")
if ni > 0:
Crit_FreeEnergy = (FreeEnergy1 - FreeEnergy) / FreeEnergy1
FreeEnergy_Iter += [FreeEnergy]
cFE += [Crit_FreeEnergy]
# Update index
ni += 1
t02 = time.time()
cTime += [t02 - t1]
t2 = time.time()
##########################################################################
# PLOTS and SNR computation
FreeEnergyArray = np.zeros((ni), dtype=np.float64)
for i in xrange(ni):
FreeEnergyArray[i] = FreeEnergy_Iter[i]
SUM_q_Z_array = np.zeros((M, ni), dtype=np.float64)
mu1_array = np.zeros((M, ni), dtype=np.float64)
h_norm_array = np.zeros((ni), dtype=np.float64)
for m in xrange(M):
for i in xrange(ni):
SUM_q_Z_array[m, i] = SUM_q_Z[m][i]
mu1_array[m, i] = mu1[m][i]
h_norm_array[i] = h_norm[i]
if PLOT and 0:
import matplotlib.pyplot as plt
import matplotlib
font = {'size': 15}
matplotlib.rc('font', **font)
plt.savefig('./HRF_Iter_CompMod.png')
plt.hold(False)
plt.figure(2)
plt.plot(cAH[1:-1], 'lightblue')
plt.hold(True)
plt.plot(cFE[1:-1], 'm')
plt.hold(False)
#plt.legend( ('CA','CH', 'CZ', 'CAH', 'CFE') )
plt.legend(('CAH', 'CFE'))
plt.grid(True)
plt.savefig('./Crit_CompMod.png')
plt.figure(3)
plt.plot(FreeEnergyArray)
plt.grid(True)
plt.savefig('./FreeEnergy_CompMod.png')
plt.figure(4)
for m in xrange(M):
plt.plot(SUM_q_Z_array[m])
plt.hold(True)
plt.hold(False)
#plt.legend( ('m=0','m=1', 'm=2', 'm=3') )
#plt.legend( ('m=0','m=1') )
plt.savefig('./Sum_q_Z_Iter_CompMod.png')
plt.figure(5)
for m in xrange(M):
plt.plot(mu1_array[m])
plt.hold(True)
plt.hold(False)
plt.savefig('./mu1_Iter_CompMod.png')
plt.figure(6)
plt.plot(h_norm_array)
plt.savefig('./HRF_Norm_CompMod.png')
Data_save = xndarray(h_norm_array, ['Iteration'])
Data_save.save('./HRF_Norm_Comp.nii')
CompTime = t2 - t1
cTimeMean = CompTime / ni
sigma_M = np.sqrt(np.sqrt(sigma_M))
logger.info("Nb iterations to reach criterion: %d", ni)
logger.info("Computational time = %s min %s s", str(
int(CompTime // 60)), str(int(CompTime % 60)))
# print "Computational time = " + str(int( CompTime//60 ) ) + " min " + str(int(CompTime%60)) + " s"
# print "sigma_H = " + str(sigmaH)
logger.info('mu_M: %f', mu_M)
logger.info('sigma_M: %f', sigma_M)
logger.info("sigma_H = %s" + str(sigmaH))
logger.info("Beta = %s" + str(Beta))
StimulusInducedSignal = vt.computeFit(m_H, m_A, X, J, N)
SNR = 20 * \
np.log(
np.linalg.norm(Y) / np.linalg.norm(Y - StimulusInducedSignal - PL))
SNR /= np.log(10.)
logger.info("SNR = %d", SNR)
return ni, m_A, m_H, q_Z, sigma_epsilone, mu_M, sigma_M, Beta, L, PL, CONTRAST, CONTRASTVAR, cA[2:], cH[2:], cZ[2:], cAH[2:], cTime[2:], cTimeMean, Sigma_A, StimulusInducedSignal, FreeEnergyArray
r1 = np.sqrt(3.4 * np.random.rand(Nt1, 1)) # Radius
t1 = 2 * np.pi * np.random.rand(Nt1, 1) # Angle
testdata1 = np.concatenate((r1 * np.cos(t1), r1 * np.sin(t1)),
axis=1) # Points
r2 = np.sqrt(2.4 * np.random.rand(Nt2, 1)) # Radius
t2 = 2 * np.pi * np.random.rand(Nt2, 1) # Angle
testdata2 = np.concatenate((3 + r2 * np.cos(t2), r2 * np.sin(t2)),
axis=1) # points
## training linear SVM based on CVX optimizer
X = np.concatenate((data1, data2), axis=0)
y = np.concatenate((np.ones((N1, 1)), -np.ones((N2, 1))), axis=0)
w = cp.Variable((D, 1))
b = cp.Variable()
objective = cp.Minimize(cp.sum(cp.square(w)) * 0.5)
constraints = [cp.multiply(y, (X @ w + b)) >= 1]
prob = cp.Problem(objective, constraints)
prob.solve()
print("status:", prob.status)
print("optimal value", prob.value)
print("optimal var w = {}, b = {}".format(w.value, b.value))
## visualize decision boundary for training data
d = 0.02
x1 = np.arange(np.min(X[:, 0]), np.max(X[:, 0]), d)
x2 = np.arange(np.min(X[:, 1]), np.max(X[:, 1]), d)
x1Grid, x2Grid = np.meshgrid(x1, x2)
xGrid = np.stack((x1Grid.flatten('F'), x2Grid.flatten('F')), axis=1)
scores1 = xGrid.dot(w.value) + b.value
scores2 = -xGrid.dot(w.value) - b.value
def Main_vbjde_Extension_constrained(graph, Y, Onsets, Thrf, K, TR, beta,
dt, scale=1, estimateSigmaH=True,
sigmaH=0.05, NitMax=-1,
NitMin=1, estimateBeta=True,
PLOT=False, contrasts=[],
computeContrast=False,
gamma_h=0, estimateHRF=True,
TrueHrfFlag=False,
HrfFilename='hrf.nii',
estimateLabels=True,
LabelsFilename='labels.nii',
MFapprox=False, InitVar=0.5,
InitMean=2.0, MiniVEMFlag=False,
NbItMiniVem=5):
# VBJDE Function for BOLD with contraints
logger.info("Fast EM with C extension started ...")
np.random.seed(6537546)
##########################################################################
# INITIALIZATIONS
# Initialize parameters
tau1 = 0.0
tau2 = 0.0
S = 100
Init_sigmaH = sigmaH
Nb2Norm = 1
NormFlag = False
if NitMax < 0:
NitMax = 100
gamma = 7.5
#gamma_h = 1000
gradientStep = 0.003
MaxItGrad = 200
Thresh = 1e-5
Thresh_FreeEnergy = 1e-5
estimateLabels = True # WARNING!! They should be estimated
# Initialize sizes vectors
D = int(np.ceil(Thrf / dt)) + 1 # D = int(np.ceil(Thrf/dt))
M = len(Onsets)
N = Y.shape[0]
J = Y.shape[1]
l = int(np.sqrt(J))
condition_names = []
# Neighbours
maxNeighbours = max([len(nl) for nl in graph])
neighboursIndexes = np.zeros((J, maxNeighbours), dtype=np.int32)
neighboursIndexes -= 1
for i in xrange(J):
neighboursIndexes[i, :len(graph[i])] = graph[i]
# Conditions
X = OrderedDict([])
for condition, Ons in Onsets.iteritems():
X[condition] = vt.compute_mat_X_2(N, TR, D, dt, Ons)
condition_names += [condition]
XX = np.zeros((M, N, D), dtype=np.int32)
nc = 0
for condition, Ons in Onsets.iteritems():
XX[nc, :, :] = X[condition]
nc += 1
# Covariance matrix
order = 2
D2 = vt.buildFiniteDiffMatrix(order, D)
R = np.dot(D2, D2) / pow(dt, 2 * order)
invR = np.linalg.inv(R)
Det_invR = np.linalg.det(invR)
Gamma = np.identity(N)
Det_Gamma = np.linalg.det(Gamma)
p_Wtilde = np.zeros((M, K), dtype=np.float64)
p_Wtilde1 = np.zeros((M, K), dtype=np.float64)
p_Wtilde[:, 1] = 1
Crit_H = 1
Crit_Z = 1
Crit_A = 1
Crit_AH = 1
AH = np.zeros((J, M, D), dtype=np.float64)
AH1 = np.zeros((J, M, D), dtype=np.float64)
Crit_FreeEnergy = 1
cA = []
cH = []
cZ = []
cAH = []
FreeEnergy_Iter = []
cTime = []
cFE = []
SUM_q_Z = [[] for m in xrange(M)]
mu1 = [[] for m in xrange(M)]
h_norm = []
h_norm2 = []
CONTRAST = np.zeros((J, len(contrasts)), dtype=np.float64)
CONTRASTVAR = np.zeros((J, len(contrasts)), dtype=np.float64)
Q_barnCond = np.zeros((M, M, D, D), dtype=np.float64)
XGamma = np.zeros((M, D, N), dtype=np.float64)
m1 = 0
for k1 in X: # Loop over the M conditions
m2 = 0
for k2 in X:
Q_barnCond[m1, m2, :, :] = np.dot(
np.dot(X[k1].transpose(), Gamma), X[k2])
m2 += 1
XGamma[m1, :, :] = np.dot(X[k1].transpose(), Gamma)
m1 += 1
if MiniVEMFlag:
logger.info("MiniVEM to choose the best initialisation...")
"""InitVar, InitMean, gamma_h = MiniVEM_CompMod(Thrf,TR,dt,beta,Y,K,
gamma,gradientStep,
MaxItGrad,D,M,N,J,S,
maxNeighbours,
neighboursIndexes,
XX,X,R,Det_invR,Gamma,
Det_Gamma,
scale,Q_barnCond,XGamma,
NbItMiniVem,
sigmaH,estimateHRF)"""
InitVar, InitMean, gamma_h = vt.MiniVEM_CompMod(Thrf, TR, dt, beta, Y, K, gamma, gradientStep, MaxItGrad, D, M, N, J, S, maxNeighbours,
neighboursIndexes, XX, X, R, Det_invR, Gamma, Det_Gamma, p_Wtilde, scale, Q_barnCond, XGamma, tau1, tau2, NbItMiniVem, sigmaH, estimateHRF)
sigmaH = Init_sigmaH
sigma_epsilone = np.ones(J)
logger.info(
"Labels are initialized by setting active probabilities to ones ...")
q_Z = np.zeros((M, K, J), dtype=np.float64)
q_Z[:, 1, :] = 1
q_Z1 = np.zeros((M, K, J), dtype=np.float64)
Z_tilde = q_Z.copy()
# TT,m_h = getCanoHRF(Thrf-dt,dt) #TODO: check
TT, m_h = getCanoHRF(Thrf, dt) # TODO: check
m_h = m_h[:D]
m_H = np.array(m_h).astype(np.float64)
m_H1 = np.array(m_h)
sigmaH1 = sigmaH
if estimateHRF:
Sigma_H = np.ones((D, D), dtype=np.float64)
else:
Sigma_H = np.zeros((D, D), dtype=np.float64)
Beta = beta * np.ones((M), dtype=np.float64)
P = vt.PolyMat(N, 4, TR)
L = vt.polyFit(Y, TR, 4, P)
PL = np.dot(P, L)
y_tilde = Y - PL
Ndrift = L.shape[0]
sigma_M = np.ones((M, K), dtype=np.float64)
sigma_M[:, 0] = 0.5
sigma_M[:, 1] = 0.6
mu_M = np.zeros((M, K), dtype=np.float64)
for k in xrange(1, K):
mu_M[:, k] = InitMean
Sigma_A = np.zeros((M, M, J), np.float64)
for j in xrange(0, J):
Sigma_A[:, :, j] = 0.01 * np.identity(M)
m_A = np.zeros((J, M), dtype=np.float64)
m_A1 = np.zeros((J, M), dtype=np.float64)
for j in xrange(0, J):
for m in xrange(0, M):
for k in xrange(0, K):
m_A[j, m] += np.random.normal(mu_M[m, k],
np.sqrt(sigma_M[m, k])) * q_Z[m, k, j]
m_A1 = m_A
t1 = time.time()
##########################################################################
# VBJDE num. iter. minimum
ni = 0
while ((ni < NitMin) or (((Crit_FreeEnergy > Thresh_FreeEnergy) or (Crit_AH > Thresh)) and (ni < NitMax))):
logger.info("------------------------------ Iteration n° " +
str(ni + 1) + " ------------------------------")
#####################
# EXPECTATION
#####################
# A
logger.info("E A step ...")
UtilsC.expectation_A(q_Z, mu_M, sigma_M, PL, sigma_epsilone, Gamma,
Sigma_H, Y, y_tilde, m_A, m_H, Sigma_A, XX.astype(np.int32), J, D, M, N, K)
val = np.reshape(m_A, (M * J))
val[np.where((val <= 1e-50) & (val > 0.0))] = 0.0
val[np.where((val >= -1e-50) & (val < 0.0))] = 0.0
# crit. A
DIFF = np.reshape(m_A - m_A1, (M * J))
# To avoid numerical problems
DIFF[np.where((DIFF < 1e-50) & (DIFF > 0.0))] = 0.0
# To avoid numerical problems
DIFF[np.where((DIFF > -1e-50) & (DIFF < 0.0))] = 0.0
Crit_A = (
np.linalg.norm(DIFF) / np.linalg.norm(np.reshape(m_A1, (M * J)))) ** 2
cA += [Crit_A]
m_A1[:, :] = m_A[:, :]
# HRF h
if estimateHRF:
################################
# HRF ESTIMATION
################################
UtilsC.expectation_H(XGamma, Q_barnCond, sigma_epsilone, Gamma, R, Sigma_H, Y,
y_tilde, m_A, m_H, Sigma_A, XX.astype(np.int32), J, D, M, N, scale, sigmaH)
import cvxpy as cvx
m, n = Sigma_H.shape
Sigma_H_inv = np.linalg.inv(Sigma_H)
zeros_H = np.zeros_like(m_H[:, np.newaxis])
# Construct the problem. PRIMAL
h = cvx.Variable(n)
expression = cvx.quad_form(h - m_H[:, np.newaxis], Sigma_H_inv)
objective = cvx.Minimize(expression)
#constraints = [h[0] == 0, h[-1]==0, h >= zeros_H, cvx.square(cvx.norm(h,2))<=1]
constraints = [
h[0] == 0, h[-1] == 0, cvx.square(cvx.norm(h, 2)) <= 1]
prob = cvx.Problem(objective, constraints)
result = prob.solve(verbose=0, solver=cvx.CVXOPT)
# Now we update the mean of h
m_H_old = m_H
Sigma_H_old = Sigma_H
m_H = np.squeeze(np.array((h.value)))
Sigma_H = np.zeros_like(Sigma_H)
h_norm += [np.linalg.norm(m_H)]
# print 'h_norm = ', h_norm
# Plotting HRF
if PLOT and ni >= 0:
import matplotlib.pyplot as plt
plt.figure(M + 1)
plt.plot(m_H)
plt.hold(True)
else:
if TrueHrfFlag:
#TrueVal, head = read_volume(HrfFilename)
TrueVal, head = read_volume(HrfFilename)[:, 0, 0, 0]
print TrueVal
print TrueVal.shape
m_H = TrueVal
# crit. h
Crit_H = (np.linalg.norm(m_H - m_H1) / np.linalg.norm(m_H1)) ** 2
cH += [Crit_H]
m_H1[:] = m_H[:]
# crit. AH
for d in xrange(0, D):
AH[:, :, d] = m_A[:, :] * m_H[d]
DIFF = np.reshape(AH - AH1, (M * J * D))
# To avoid numerical problems
DIFF[np.where((DIFF < 1e-50) & (DIFF > 0.0))] = 0.0
# To avoid numerical problems
DIFF[np.where((DIFF > -1e-50) & (DIFF < 0.0))] = 0.0
if np.linalg.norm(np.reshape(AH1, (M * J * D))) == 0:
Crit_AH = 1000000000.
else:
Crit_AH = (
np.linalg.norm(DIFF) / np.linalg.norm(np.reshape(AH1, (M * J * D)))) ** 2
cAH += [Crit_AH]
AH1[:, :, :] = AH[:, :, :]
# Z labels
if estimateLabels:
logger.info("E Z step ...")
# WARNING!!! ParsiMod gives better results, but we need the other
# one.
if MFapprox:
UtilsC.expectation_Z(Sigma_A, m_A, sigma_M, Beta, Z_tilde, mu_M, q_Z, neighboursIndexes.astype(
np.int32), M, J, K, maxNeighbours)
if not MFapprox:
UtilsC.expectation_Z_ParsiMod_RVM_and_CompMod(
Sigma_A, m_A, sigma_M, Beta, mu_M, q_Z, neighboursIndexes.astype(np.int32), M, J, K, maxNeighbours)
else:
logger.info("Using True Z ...")
TrueZ = read_volume(LabelsFilename)
for m in xrange(M):
q_Z[m, 1, :] = np.reshape(TrueZ[0][:, :, :, m], J)
q_Z[m, 0, :] = 1 - q_Z[m, 1, :]
# crit. Z
val = np.reshape(q_Z, (M * K * J))
val[np.where((val <= 1e-50) & (val > 0.0))] = 0.0
DIFF = np.reshape(q_Z - q_Z1, (M * K * J))
# To avoid numerical problems
DIFF[np.where((DIFF < 1e-50) & (DIFF > 0.0))] = 0.0
# To avoid numerical problems
DIFF[np.where((DIFF > -1e-50) & (DIFF < 0.0))] = 0.0
if np.linalg.norm(np.reshape(q_Z1, (M * K * J))) == 0:
Crit_Z = 1000000000.
else:
Crit_Z = (
np.linalg.norm(DIFF) / np.linalg.norm(np.reshape(q_Z1, (M * K * J)))) ** 2
cZ += [Crit_Z]
q_Z1 = q_Z
#####################
# MAXIMIZATION
#####################
# HRF: Sigma_h
if estimateHRF:
if estimateSigmaH:
logger.info("M sigma_H step ...")
if gamma_h > 0:
sigmaH = vt.maximization_sigmaH_prior(
D, Sigma_H_old, R, m_H_old, gamma_h)
else:
sigmaH = vt.maximization_sigmaH(D, Sigma_H, R, m_H)
logger.info('sigmaH = %s', str(sigmaH))
# (mu,sigma)
logger.info("M (mu,sigma) step ...")
mu_M, sigma_M = vt.maximization_mu_sigma(
mu_M, sigma_M, q_Z, m_A, K, M, Sigma_A)
for m in xrange(M):
SUM_q_Z[m] += [sum(q_Z[m, 1, :])]
mu1[m] += [mu_M[m, 1]]
# Drift L
UtilsC.maximization_L(
Y, m_A, m_H, L, P, XX.astype(np.int32), J, D, M, Ndrift, N)
PL = np.dot(P, L)
y_tilde = Y - PL
# Beta
if estimateBeta:
logger.info("estimating beta")
for m in xrange(0, M):
if MFapprox:
Beta[m] = UtilsC.maximization_beta(beta, q_Z[m, :, :].astype(np.float64), Z_tilde[m, :, :].astype(
np.float64), J, K, neighboursIndexes.astype(np.int32), gamma, maxNeighbours, MaxItGrad, gradientStep)
if not MFapprox:
#Beta[m] = UtilsC.maximization_beta(beta,q_Z[m,:,:].astype(np.float64),q_Z[m,:,:].astype(np.float64),J,K,neighboursIndexes.astype(int32),gamma,maxNeighbours,MaxItGrad,gradientStep)
Beta[m] = UtilsC.maximization_beta_CB(beta, q_Z[m, :, :].astype(
np.float64), J, K, neighboursIndexes.astype(np.int32), gamma, maxNeighbours, MaxItGrad, gradientStep)
logger.info("End estimating beta")
logger.info(Beta)
# Sigma noise
logger.info("M sigma noise step ...")
UtilsC.maximization_sigma_noise(
Gamma, PL, sigma_epsilone, Sigma_H, Y, m_A, m_H, Sigma_A, XX.astype(np.int32), J, D, M, N)
#### Computing Free Energy ####
if ni > 0:
FreeEnergy1 = FreeEnergy
"""FreeEnergy = vt.Compute_FreeEnergy(y_tilde,m_A,Sigma_A,mu_M,sigma_M,
m_H,Sigma_H,R,Det_invR,sigmaH,
p_Wtilde,q_Z,neighboursIndexes,
maxNeighbours,Beta,sigma_epsilone,
XX,Gamma,Det_Gamma,XGamma,J,D,M,
N,K,S,"CompMod")"""
FreeEnergy = vt.Compute_FreeEnergy(y_tilde, m_A, Sigma_A, mu_M, sigma_M, m_H, Sigma_H, R, Det_invR, sigmaH, p_Wtilde, tau1,
tau2, q_Z, neighboursIndexes, maxNeighbours, Beta, sigma_epsilone, XX, Gamma, Det_Gamma, XGamma, J, D, M, N, K, S, "CompMod")
if ni > 0:
Crit_FreeEnergy = (FreeEnergy1 - FreeEnergy) / FreeEnergy1
FreeEnergy_Iter += [FreeEnergy]
cFE += [Crit_FreeEnergy]
# Update index
ni += 1
t02 = time.time()
cTime += [t02 - t1]
t2 = time.time()
##########################################################################
# PLOTS and SNR computation
FreeEnergyArray = np.zeros((ni), dtype=np.float64)
for i in xrange(ni):
FreeEnergyArray[i] = FreeEnergy_Iter[i]
SUM_q_Z_array = np.zeros((M, ni), dtype=np.float64)
mu1_array = np.zeros((M, ni), dtype=np.float64)
h_norm_array = np.zeros((ni), dtype=np.float64)
for m in xrange(M):
for i in xrange(ni):
SUM_q_Z_array[m, i] = SUM_q_Z[m][i]
mu1_array[m, i] = mu1[m][i]
h_norm_array[i] = h_norm[i]
if PLOT and 0:
import matplotlib.pyplot as plt
import matplotlib
font = {'size': 15}
matplotlib.rc('font', **font)
plt.savefig('./HRF_Iter_CompMod.png')
plt.hold(False)
plt.figure(2)
plt.plot(cAH[1:-1], 'lightblue')
plt.hold(True)
plt.plot(cFE[1:-1], 'm')
plt.hold(False)
#plt.legend( ('CA','CH', 'CZ', 'CAH', 'CFE') )
plt.legend(('CAH', 'CFE'))
plt.grid(True)
plt.savefig('./Crit_CompMod.png')
plt.figure(3)
plt.plot(FreeEnergyArray)
plt.grid(True)
plt.savefig('./FreeEnergy_CompMod.png')
plt.figure(4)
for m in xrange(M):
plt.plot(SUM_q_Z_array[m])
plt.hold(True)
plt.hold(False)
#plt.legend( ('m=0','m=1', 'm=2', 'm=3') )
#plt.legend( ('m=0','m=1') )
plt.savefig('./Sum_q_Z_Iter_CompMod.png')
plt.figure(5)
for m in xrange(M):
plt.plot(mu1_array[m])
plt.hold(True)
plt.hold(False)
plt.savefig('./mu1_Iter_CompMod.png')
plt.figure(6)
plt.plot(h_norm_array)
plt.savefig('./HRF_Norm_CompMod.png')
Data_save = xndarray(h_norm_array, ['Iteration'])
Data_save.save('./HRF_Norm_Comp.nii')
CompTime = t2 - t1
cTimeMean = CompTime / ni
sigma_M = np.sqrt(np.sqrt(sigma_M))
logger.info("Nb iterations to reach criterion: %d", ni)
logger.info("Computational time = %s min %s s", str(
int(CompTime // 60)), str(int(CompTime % 60)))
# print "Computational time = " + str(int( CompTime//60 ) ) + " min " + str(int(CompTime%60)) + " s"
# print "sigma_H = " + str(sigmaH)
logger.info('mu_M: %f', mu_M)
logger.info('sigma_M: %f', sigma_M)
logger.info("sigma_H = %s" + str(sigmaH))
logger.info("Beta = %s" + str(Beta))
StimulusInducedSignal = vt.computeFit(m_H, m_A, X, J, N)
SNR = 20 * \
np.log(
np.linalg.norm(Y) / np.linalg.norm(Y - StimulusInducedSignal - PL))
SNR /= np.log(10.)
logger.info("SNR = %d", SNR)
return ni, m_A, m_H, q_Z, sigma_epsilone, mu_M, sigma_M, Beta, L, PL, CONTRAST, CONTRASTVAR, cA[2:], cH[2:], cZ[2:], cAH[2:], cTime[2:], cTimeMean, Sigma_A, StimulusInducedSignal, FreeEnergyArray
X_normalized = MinMaxScaler().fit_transform(X.values)
X = pd.DataFrame(X_normalized)
relaxation = 100
points_per_agent = 200
var = 4
#defining van variables
W = cp.Variable((var, 1))
b = cp.Variable()
eps = cp.Variable((4000, 1), nonneg=True)
loss = cp.sum(eps)
reg = cp.square(cp.norm(W))
#cost function, kloopt waarschijnlijk niet
opt = cp.Minimize(0.5 * reg + relaxation * loss)
#loop om mijn agents te vullen met neighbours en
X_train_total = np.zeros((1, 4))
X_test_total = np.zeros((1, 4))
y_test_total = np.zeros((1, 1))
y_train_total = np.zeros((1, 1))
for i in range(agents):
X_train = X[400 * i:400 * i + 200]
X_test = X[400 * i + 200:400 * (i + 1)]
y_train = Y[400 * i:400 * i + 200]
def reachable(T,
s0,
sT,
cost,
dynamics,
max_dtheta,
max_theta,
max_ddx,
max_line_search=30,
show_results=lambda *a: None):
"""Find control signals u_1...u_T, u_t=(ddx_t,dtheta_t) and the
ensuing states s_1...s_T that
minimize L(s_0,...,s_{T-1})
subject to s_t = f(s_{t-1}, u_t)
| dtheta_t | < max_dtheta
| ddx_t | < max_ddx
One of sT or cost must be None. if sT is set, then
L = || s_{t-1} - sT ||
otherwise, it is
L = sum_{t=0}^{T-1} cost(s_t)
Solves this as a Sequential Quadratic program by approximating L by
a quadratic and f by an affine function.
"""
s0 = array(s0)
if sT is not None:
sT = array(sT)
assert (cost is None) != (sT is
None), 'only one of cost or sT may be specified'
# initial iterates and objective terms
Sv = [s0] * T
Uv = [None] + [zeros(2)] * T
L = None
if cost:
L = [cost(s0)['val']] * T
last_obj = None # last objective value attained
step = 1. # last line search step size
iters = 0
n_line_searches = 0
while True:
show_results(
Sv, L, '%d, %d line searches so far. step size %g' %
(iters, n_line_searches, step))
iters += 1
# variables, objective, and constraints of the quadratic problem
S = [None] * T
U = [None] * T
S[0] = CX.Parameter(5, name='s0')
S[0].value = s0
constraints = []
if cost:
objective = zeros(1)
# define the QP
for t in xrange(1, T):
# f(u_t, s_{t-1}) and its derivatives
f = dynamics(Sv[t - 1], Uv[t], {'du', 'ds'})
dfds = vstack(f['ds'])
dfdu = vstack(f['du'])
# define u_t and s_t
U[t] = CX.Variable(2, name='u%d' % t)
S[t] = CX.Variable(5, name='s%d' % t)
# constraints:
# s_t = linearized f(s_t-1, u_t) about previous iterate
# and bounds on s_t and u_t
constraints += [
S[t] == f['val'] + dfds * (S[t - 1] - Sv[t - 1]) + dfdu *
(U[t] - Uv[t]),
CX.abs(U[t][0]) <= max_ddx,
CX.abs(U[t][1]) <= max_dtheta,
CX.abs(S[t][4]) <= max_theta
]
if cost:
# accumulate objective
c = cost(Sv[t], derivs={'ds', 'ds2'})
c['ds2'] = make_psd(c['ds2'])
objective += c['val'] + (
S[t] - Sv[t]).T * c['ds'] + 0.5 * CX.quad_form(
S[t] - Sv[t], c['ds2'])
if sT is not None:
# objective is || s_t - sT ||
objective = CX.square(CX.norm(S[T - 1] - sT))
# solve for S and U
p = CX.Problem(CX.Minimize(objective), constraints)
r = p.solve(solver=CX.CVXOPT, verbose=False)
assert isfinite(r)
# line search on U, from Uv along U-Uv
line_search_failed = True
while n_line_searches < max_line_search:
n_line_searches += 1
# compute and apply the controls along the step
Us = []
Svs = [s0]
for u, u0 in zip(U[1:], Uv[1:]):
# a step along the search direction
us = u0 + step * (ravel(u.value) - u0)
# make it feasible
us[0] = clip(us[0], -max_ddx, max_ddx)
us[1] = clip(us[1], -max_dtheta, max_dtheta)
Us.append(us)
# apply controls
Svs.append(sim.apply_control(Svs[-1], us)['val'])
# objective value based on the last state
if cost:
L = [cost(s)['val'] for s in Svs]
obj = sum(L)
else:
obj = sum((Svs[-1] - sT)**2)
if last_obj is None or obj < last_obj:
step *= 1.1 # lengthen the step for the next round
line_search_failed = False # converged
break
else:
step *= 0.7 # shorten the step and try again
if line_search_failed: # converged
break # throw away this iterate
else:
# accept the iterate
Sv = Svs
Uv = [None] + Us
last_obj = obj
return Sv, Uv
def test_readme_examples(self):
import cvxopt
import numpy
# Problem data.
m = 30
n = 20
A = cvxopt.normal(m, n)
b = cvxopt.normal(m)
# Construct the problem.
x = cp.Variable(n)
objective = cp.Minimize(sum(cp.square(A * x - b)))
constraints = [0 <= x, x <= 1]
p = cp.Problem(objective, constraints)
# The optimal objective is returned by p.solve().
result = p.solve()
# The optimal value for x is stored in x.value.
print x.value
# The optimal Lagrange multiplier for a constraint
# is stored in constraint.dual_value.
print constraints[0].dual_value
####################################################
# Scalar variable.
a = cp.Variable()
# Column vector variable of length 5.
x = cp.Variable(5)
# Matrix variable with 4 rows and 7 columns.
A = cp.Variable(4, 7)
####################################################
# Positive scalar parameter.
m = cp.Parameter(sign="positive")
# Column vector parameter with unknown sign (by default).
c = cp.Parameter(5)
# Matrix parameter with negative entries.
G = cp.Parameter(4, 7, sign="negative")
# Assigns a constant value to G.
G.value = -numpy.ones((4, 7))
# Raises an error for assigning a value with invalid sign.
with self.assertRaises(Exception) as cm:
G.value = numpy.ones((4, 7))
self.assertEqual(str(cm.exception),
"Invalid sign for Parameter value.")
####################################################
a = cp.Variable()
x = cp.Variable(5)
# expr is an Expression object after each assignment.
expr = 2 * x
expr = expr - a
expr = sum(expr) + cp.norm(x, 2)
####################################################
import numpy as np
import cvxopt
from multiprocessing import Pool
# Problem data.
n = 10
m = 5
A = cvxopt.normal(n, m)
b = cvxopt.normal(n)
gamma = cp.Parameter(sign="positive")
# Construct the problem.
x = cp.Variable(m)
objective = cp.Minimize(
sum(cp.square(A * x - b)) + gamma * cp.norm(x, 1))
p = cp.Problem(objective)
# Assign a value to gamma and find the optimal x.
def get_x(gamma_value):
gamma.value = gamma_value
result = p.solve()
return x.value
gammas = np.logspace(-1, 2, num=2)
# Serial computation.
x_values = [get_x(value) for value in gammas]
####################################################
n = 10
mu = cvxopt.normal(1, n)
sigma = cvxopt.normal(n, n)
sigma = sigma.T * sigma
gamma = cp.Parameter(sign="positive")
gamma.value = 1
x = cp.Variable(n)
# Constants:
# mu is the vector of expected returns.
# sigma is the covariance matrix.
# gamma is a Parameter that trades off risk and return.
# Variables:
# x is a vector of stock holdings as fractions of total assets.
expected_return = mu * x
risk = cp.quad_form(x, sigma)
objective = cp.Maximize(expected_return - gamma * risk)
p = cp.Problem(objective, [sum(x) == 1])
result = p.solve()
# The optimal expected return.
print expected_return.value
# The optimal risk.
print risk.value
###########################################
N = 50
M = 40
n = 10
data = []
for i in range(N):
data += [(1, cvxopt.normal(n, mean=1.0, std=2.0))]
for i in range(M):
data += [(-1, cvxopt.normal(n, mean=-1.0, std=2.0))]
# Construct problem.
gamma = cp.Parameter(sign="positive")
gamma.value = 0.1
# 'a' is a variable constrained to have at most 6 non-zero entries.
a = cp.Variable(n) #mi.SparseVar(n, nonzeros=6)
b = cp.Variable()
slack = [
cp.pos(1 - label * (sample.T * a - b)) for (label, sample) in data
]
objective = cp.Minimize(cp.norm(a, 2) + gamma * sum(slack))
p = cp.Problem(objective)
# Extensions can attach new solve methods to the CVXPY Problem class.
#p.solve(method="admm")
p.solve()
# Count misclassifications.
errors = 0
for label, sample in data:
if label * (sample.T * a - b).value < 0:
errors += 1
print "%s misclassifications" % errors
print a.value
print b.value
def test_sum_of_qccv_not_dqcp(self):
t = cp.Variable(5, pos=True)
expr = cp.sum(cp.square(t) / t)
self.assertFalse(expr.is_dqcp())
v = npy.random.random((m, 1)) * 2 - 1
b = npy.dot(A, x_known) + v
r = cvx.Variable(m, 1)
x = cvx.Variable(n, 1)
z = npy.zeros((n, 1))
a = .25
cst = [r == A * x - b]
f, (ax) = plt.subplots(4, sharex=True)
bins = npy.linspace(-2, 2, 81) + .025
bins = bins[:-1]
for idx in [0, 1, 2, 3]:
if idx == 0:
fcn = cvx.sum_entries(cvx.abs(r))
elif idx == 1:
fcn = cvx.sum_entries(cvx.square(r))
elif idx == 2:
fcn = cvx.sum_entries(
cvx.max_entries(cvx.hstack(cvx.abs(r) - a, npy.zeros((m, 1))),
axis=1))
elif idx == 3:
fcn = cvx.sum_entries(-cvx.log(1 - cvx.square(r)))
else:
print('bad')
print(idx)
prb = cvx.Problem(cvx.Minimize(fcn), cst)
prb.solve()
print(prb.status)
ax[idx].hist(r.value, bins)
plt.show()
#!/usr/bin/python
import numpy as np
import cvxpy as cvx
from qcqp import *
n, m = 10, 15
np.random.seed(1)
A = np.random.randn(m, n)
b = np.random.randn(m, 1)
x = cvx.Variable(n)
obj = cvx.sum_squares(A*x - b)
cons = [cvx.square(x) == 1]
prob = cvx.Problem(cvx.Minimize(obj), cons)
qcqp = QCQP(prob)
# sample from the semidefinite relaxation
qcqp.suggest(SDR)
print("SDR lower bound: %.3f" % qcqp.sdr_bound)
f_cd, v_cd = qcqp.improve(COORD_DESCENT)
x_cd = x.value
print("Coordinate descent: objective %.3f, violation %.3f" % (f_cd, v_cd))
# SDR solution is cached and not solved again
qcqp.suggest(SDR)
f_dccp, v_dccp = qcqp.improve(DCCP)
print("Penalty CCP: objective %.3f, violation %.3f" % (f_dccp, v_dccp))
f_dccp, v_dccp = qcqp.improve(COORD_DESCENT, phase1=False)
x_dccp = x.value
def main():
# x[0] == x(k)
x0, y0 = (2, 3)
ux0, uy0 = (3, 4)
(x_target, y_target) = (22, 25)
steps = 50
delta_t = 0.1
x_limits, y_limits = (1, 30), (1, 30)
ux_limits, uy_limits = (1, 10), (1, 10)
x = cvx.Variable(steps)
ux = cvx.Variable(steps - 1)
constraint_x = [x[0] == x0, ux[0] == ux0]
constraint_x += [
x[index + 1] == x[index] + delta_t * ux[index]
for index in xrange(0, steps - 1)
]
constraint_x += [
x >= x_limits[0], x <= x_limits[1], ux >= ux_limits[0],
ux <= ux_limits[1]
]
objective_xpath = cvx.Minimize(cvx.square(x_target - x[steps - 1]))
delta_xvelocity = np.sum([(ux[index] - ux[index + 1])**2
for index in xrange(0, steps - 2)])
objective_xvelocity = cvx.Minimize((delta_xvelocity))
objective_x = objective_xpath + objective_xvelocity
y = cvx.Variable(steps)
uy = cvx.Variable(steps - 1)
constraint_y = [y[0] == y0, uy[0] == uy0]
constraint_y += [
y[index + 1] == y[index] + delta_t * uy[index]
for index in xrange(0, steps - 1)
]
constraint_y += [
y >= y_limits[0], y <= y_limits[1], uy >= uy_limits[0],
uy <= uy_limits[1]
]
objective_ypath = cvx.Minimize(cvx.square(y_target - y[steps - 1]))
delta_yvelocity = np.sum([(uy[index] - uy[index + 1])**2
for index in xrange(0, steps - 2)])
objective_yvelocity = cvx.Minimize((delta_yvelocity))
objective_y = objective_ypath + objective_yvelocity
constraints = constraint_x + constraint_y
objective = objective_x + objective_y
prob = cvx.Problem(objective, constraints)
print 'DCP followed:', prob.is_dcp()
prob.solve()
print prob.status
print 'cost function: ', np.round(prob.value, 5)
print 'x coordinates: ', np.round(x.value, 3)
print 'y coordinates:', np.round(y.value, 3)
# print 'ux velocity: ', np.round(ux.value, 3)
# print 'uy velocity: ', np.round(uy.value, 3)
plt.figure(1)
plt.subplot(211)
plt.plot(x.value, y.value, 'ro', x0, y0, 'go', x_target, y_target, 'go')
plt.xlabel('x coordinate')
plt.ylabel('y coordinate')
plt.subplot(212)
velocity = np.array(
[np.sqrt(vx**2 + vy**2) for vx, vy in zip(ux.value, uy.value)])
time = np.linspace(0.1, 5, 49)
print 'velocity:', velocity
plt.plot(time, velocity, 'bo', time[0], np.sqrt(ux0**2 + uy0**2), 'go')
plt.xlabel('Time')
plt.ylabel('Velocity')
plt.show()
import cvxpy as cp w = cp.Variable(2) d = cp.Variable() probconst = ([2 * w[0] + w[1] + d >= 1, 0.8 * w[0] - 0.6 * w[1] + d <= -1]) probobj = cp.Minimize(0.5 * cp.square(cp.norm(w))) prob = cp.Problem(probobj, probconst) prob.solve() print(prob.value) print(w.value) print(d.value)
def q3_partd(A, b):
lambdValues = [.0001, .001, .01, .1, .5, 1, 5, 10, 50, 100]
indexArray = list(range(0, A.shape[0]))
subsetList = []
subsets = []
classes = []
#PART i
print('Runing q3 partd, section i')
#Make 5 random subset index lists of size 29.
for i in range(0, 5):
subsetList.append([])
for m in range(0, 29):
randi = rand.randint(0, len(indexArray) - 1)
subsetList[i].append(indexArray[randi])
del indexArray[randi]
#Make 5 random subset index lists of size 30.
for i in range(5, 10):
subsetList.append([])
for m in range(0, 30):
randi = rand.randint(0, len(indexArray) - 1)
subsetList[i].append(indexArray[randi])
del indexArray[randi]
#Make actual data subsets out of the
for i in range(0, len(subsetList)):
subsets.append(A[subsetList[i]])
classes.append(b[subsetList[i]])
#PART ii (data sets 0 through 7)
print('Runing q3 partd, section ii')
Atrain = None
btrain = None
for i in range(0, 8):
if Atrain == None:
Atrain = subsets[i]
btrain = classes[i]
else:
Atrain = np.vstack((Atrain, subsets[i]))
btrain = np.vstack((btrain, classes[i]))
# Set up the parameters of the equation for LASSO.
lambd = cvx.Parameter(sign="positive")
lambd.value = 0.01
x = cvx.Variable(A.shape[1])
objective = cvx.Minimize(
cvx.sum_squares(Atrain * x - btrain) + (lambd * cvx.norm1(x)))
prob = cvx.Problem(objective)
optimalRidgeX = []
optimalLassoX = []
#Find optimal lasso x's
for val in lambdValues:
print('Solving lambda: %f' % (val))
# Solve the problem with the new lambda.
lambd.value = val
prob.solve()
optimalLassoX.append(np.array(x.value))
#Find optimal ridge x's
prob.objective = cvx.Minimize(
cvx.sum_squares(Atrain * x - btrain) +
(lambd * cvx.sum_entries(cvx.square(x))))
for val in lambdValues:
print('Solving lambda: %f' % (val))
# Solve the problem with the new lambda.
lambd.value = val
prob.solve()
optimalRidgeX.append(np.array(x.value))
#PART iii
print('Runing q3 partd, section iii')
Atuning = subsets[8]
btuning = classes[8]
bestLassoX = optimalLassoX[0]
bestLassoAccuracy = 0
bestRidgeX = optimalRidgeX[0]
bestRidgeAccuracy = 0
#Find best Lasso
for xopt in optimalLassoX:
ypredicted = []
for data in Atuning:
predVal = data.reshape(1,
data.size).dot(xopt.reshape(xopt.size, 1))
if predVal > 0:
predVal = 1
else:
predVal = -1
ypredicted.append(predVal)
accuracy = calculateAccuracy(btuning, ypredicted)
if accuracy > bestLassoAccuracy:
bestLassoAccuracy = accuracy
bestLassoX = xopt
#Find best Ridge
for xopt in optimalRidgeX:
ypredicted = []
for data in Atuning:
predVal = data.reshape(1,
data.size).dot(xopt.reshape(xopt.size, 1))
if predVal > 0:
predVal = 1
else:
predVal = -1
ypredicted.append(predVal)
accuracy = calculateAccuracy(btuning, ypredicted)
if accuracy > bestRidgeAccuracy:
bestRidgeAccuracy = accuracy
bestRidgeX = xopt
#PART iv
print('Runing q3 partd, section iv')
#Calculate test accuracy for LASSO.
Atest = subsets[9]
btest = classes[9]
ypredicted = []
for data in Atest:
predVal = data.reshape(1, data.size).dot(
bestLassoX.reshape(bestLassoX.size, 1))
if predVal > 0:
predVal = 1
else:
predVal = -1
ypredicted.append(predVal)
lassoAccuracy = calculateAccuracy(btest, ypredicted)
#Calculate test accuracy for RIDGE.
ypredicted = []
for data in Atest:
predVal = data.reshape(1, data.size).dot(
bestRidgeX.reshape(bestRidgeX.size, 1))
if predVal > 0:
predVal = 1
else:
predVal = -1
ypredicted.append(predVal)
ridgeAccuracy = calculateAccuracy(btest, ypredicted)
print('Ridge test accuracy: %f' % (ridgeAccuracy))
print('LASSO test accuracy: %f' % (lassoAccuracy))
import cvxpy as cvx
# Create two scalar optimization variables.
x = cvx.Variable()
y = cvx.Variable()
constraints = [x + y == 1, x - y >= 1]
# Form objective.
obj = cvx.Minimize(cvx.square(x - y))
# Form and solve problem.
prob = cvx.Problem(obj, constraints)
prob.solve() # Returns the optimal value.
print("status:", prob.status)
print("optimal value", prob.value)
print("optimal var", x.value, y.value)
def lasso_sure_cvxpy(X, y, alpha, sigma, random_state=42):
# lambda_alpha = [alpha, alpha]
n_samples, n_features = X.shape
epsilon = 2 * sigma / n_samples**0.3
rng = check_random_state(random_state)
delta = rng.randn(n_samples)
y2 = y + epsilon * delta
Xth, yth, y2th, deltath = map(torch.from_numpy, [X, y, y2, delta])
# set up variables and parameters
beta_cp = cp.Variable(n_features)
lambda_cp = cp.Parameter(nonneg=True)
# set up objective
loss = ((1 / (2 * n_samples)) * cp.sum(cp.square(Xth @ beta_cp - yth)))
reg = lambda_cp * cp.norm1(beta_cp)
objective = loss + reg
# define problem
problem1 = cp.Problem(cp.Minimize(objective))
assert problem1.is_dpp()
# solve problem1
layer = CvxpyLayer(problem1, [lambda_cp], [beta_cp])
alpha_th1 = torch.tensor(alpha, requires_grad=True)
beta1, = layer(alpha_th1)
# get test loss and it's gradient
test_loss1 = (Xth @ beta1 - yth).pow(2).sum()
test_loss1 -= 2 * sigma**2 / epsilon * (Xth @ beta1) @ deltath
test_loss1.backward()
val1 = test_loss1.detach().numpy()
grad1 = np.array(alpha_th1.grad)
# set up variables and parameters
beta_cp = cp.Variable(n_features)
lambda_cp = cp.Parameter(nonneg=True)
# set up objective
loss = ((1 / (2 * n_samples)) * cp.sum(cp.square(Xth @ beta_cp - y2th)))
reg = lambda_cp * cp.norm1(beta_cp)
objective = loss + reg
# define problem
problem2 = cp.Problem(cp.Minimize(objective))
assert problem2.is_dpp()
# solve problem2
layer = CvxpyLayer(problem2, [lambda_cp], [beta_cp])
alpha_th2 = torch.tensor(alpha, requires_grad=True)
beta2, = layer(alpha_th2)
# get test loss and it's gradient
test_loss2 = 2 * sigma**2 / epsilon * (Xth @ beta2) @ deltath
test_loss2.backward()
val2 = test_loss2.detach().numpy()
grad2 = np.array(alpha_th2.grad)
val = val1 + val2 - len(y) * sigma**2
grad = grad1 + grad2
return val, grad
def sparse_kmeans(AllDataMatrix, s, niter, group):
w = [1 / np.sqrt(AllDataMatrix.shape[1])] * AllDataMatrix.shape[1]
wx = np.zeros((len(AllDataMatrix), AllDataMatrix.shape[1]))
for j in range(AllDataMatrix.shape[1]):
wx[:, j] = AllDataMatrix[:, j] * (np.sqrt(w)[j])
alpha_group = s
s_orig = s
nclust = 6
#kmt = KMeans(n_clusters=nclust, init='random', n_init=100,verbose=False, tol=0.0000000001)
#kmt.fit(wx)
#print kmt.labels_
#print adjusted_rand_score(labels, kmt.labels_)
kmt = rkmeans(x=numpy2ri(wx), centers=nclust, nstart=100)
kmlabels = np.array(kmt[0])
print adjusted_rand_score(labels, np.array(kmt[0]))
#overall iterations
for i in range(niter):
#print i
#1.get bcssj
aj_list = []
for j in range(AllDataMatrix.shape[1]):
dat_j = AllDataMatrix[:, j].reshape((len(AllDataMatrix), 1))
djall = euclidean_distances(dat_j, dat_j)
sumd_all = np.sum(djall**2) / len(AllDataMatrix)
nk_list = []
sumd_k_list = []
for k in range(nclust):
dat_j = AllDataMatrix[kmlabels == k, j]
dat_j = dat_j.reshape((len(dat_j), 1))
if (len(dat_j) < 1):
d = 0
else:
d = euclidean_distances(dat_j, dat_j)
nk = len(dat_j)
sumd_k = np.sum(d**2)
nk_list.append(nk)
sumd_k_list.append(sumd_k)
nk_list = np.array(nk_list)
sumd_k_list = np.array(sumd_k_list)
#compute within-sum of squares over feature j
nk_list[nk_list == 0] = -1
one_nk_list = 1. / nk_list
one_nk_list[np.sign(one_nk_list) == -1] = 0
withinssj = np.sum(one_nk_list * sumd_k_list)
#aj = totalss/n - wss/nk
aj = sumd_all - withinssj
aj_list.append(aj)
#2. get w
a = np.array(aj_list)
lenseq = np.array([256, 128, 64, 32, 16, 8, 4, 2, 1, 1])
lenseq = np.array([256, 128, 64, 32, 16, 8, 8])
nlevels = len(lenseq)
sqrtlenseq = np.sqrt(lenseq)
indseq = np.cumsum(lenseq)
wvar = cvx.Variable(len(a))
t = cvx.Variable(nlevels)
## Form objective.
if group:
####GROUP SPARSE
#obj = cvx.Minimize(sum(-1*a*wvar) + alpha_group*sum(t))
obj = cvx.Minimize(sum(-1 * a * wvar))
group0 = [cvx.norm(wvar[0:(indseq[0] - 1)], 2) <= t[0]]
group1 = [cvx.norm(wvar[indseq[0]:(indseq[1])], 2) <= t[1]]
group2 = [cvx.norm(wvar[indseq[1]:(indseq[2])], 2) <= t[2]]
group3 = [cvx.norm(wvar[indseq[2]:(indseq[3])], 2) <= t[3]]
group4 = [cvx.norm(wvar[indseq[3]:(indseq[4])], 2) <= t[4]]
group5 = [cvx.norm(wvar[indseq[4]:(indseq[5])], 2) <= t[5]]
group6 = [cvx.norm(wvar[indseq[5]:(indseq[6])], 2) <= t[6]]
# group0 = [cvx.norm(wvar[0:indseq[0]],2)<=t[0]]
# group1 = [cvx.norm(wvar[indseq[0]:indseq[1]],2)<=t[1]]
# group0 = [sqrtlenseq[0]*cvx.norm(wvar[0:(indseq[0]-1)],2)<=t[0]]
# group1 = [sqrtlenseq[1]*cvx.norm(wvar[indseq[0]:(indseq[1])],2)<=t[1]]
# group2 = [sqrtlenseq[2]*cvx.norm(wvar[indseq[1]:(indseq[2])],2)<=t[2]]
# group3 = [sqrtlenseq[3]*cvx.norm(wvar[indseq[2]:(indseq[3])],2)<=t[3]]
# group4 = [sqrtlenseq[4]*cvx.norm(wvar[indseq[3]:(indseq[4])],2)<=t[4]]
# group5 = [sqrtlenseq[5]*cvx.norm(wvar[indseq[4]:(indseq[5])],2)<=t[5]]
# group6 = [sqrtlenseq[6]*cvx.norm(wvar[indseq[5]:(indseq[6])],2)<=t[6]]
#
#group7 = [cvx.norm(wvar[indseq[6]:(indseq[7])],2)<=t[7]]
# group8 = [cvx.norm(wvar[indseq[7]:(indseq[8])],2)<=t[8]]
# group9 = [cvx.norm(wvar[indseq[8]:(indseq[9])],2)<=t[9]]
###"correct" constraints
#constr = [wvar>=0,sum(wvar)==1] + group0 + group1 + group2 + group3 + group4 + group5 + group6
##l2 constraints
#constr = [cvx.square(cvx.norm2(wvar))<=1,wvar>=0] + group0 + group1 + group2 + group3 + group4 + group5 + group6 + group7 + group8 + group9
#constr = [cvx.square(cvx.norm2(wvar))<=1,wvar>=0] + group0 + group1 + group2 + group3 + group4 + group5 + group6 + group7
constr = [
cvx.square(cvx.norm2(wvar)) <= 1, wvar >= 0
] + group0 + group1 + group2 + group3 + group4 + group5 + group6
constr = constr + [sum(t) <= alpha_group] #cvx.norm1(wvar)<=s_orig
####GROUP NORM AS IN LASSO
# groupnormvec = [cvx.norm(wvar[0:(indseq[0]-1)],2),cvx.norm(wvar[indseq[0]:(indseq[1])],2),
# cvx.norm(wvar[indseq[1]:(indseq[2])],2),cvx.norm(wvar[indseq[2]:(indseq[3])],2),
# cvx.norm(wvar[indseq[3]:(indseq[4])],2),cvx.norm(wvar[indseq[4]:(indseq[5])],2),
# cvx.norm(wvar[indseq[5]:(indseq[6])],2)]
# obj = cvx.Minimize(sum(-1*a*wvar) + alpha_group*sum(groupnormvec))
# constr = [cvx.square(cvx.norm2(wvar))<=1,wvar>=0]
else:
####ORIGINAL SPARSE KMEANS PROBLEM
#obj = cvx.Minimize(cvx.sum(cvx.mul_elemwise(-1*a,wvar)))
obj = cvx.Minimize(sum(-1 * a * wvar))
constr = [
cvx.square(cvx.norm2(wvar)) <= 1,
cvx.norm1(wvar) <= s_orig, wvar >= 0
]
#constr = [cvx.square(cvx.norm2(wvar))<=1, wvar>=0]
prob = cvx.Problem(obj, constr)
#prob.solve()
try:
prob.solve()
#print "default solver"
except:
#print "SCS SOLVER"
#prob.solve(solver =cvx.CVXOPT)
prob.solve(solver=cvx.SCS, verbose=False) #use_indirect=True
#print prob.value
w = wvar.value
#3. update kmeans
wx = np.zeros((len(AllDataMatrix), AllDataMatrix.shape[1]))
for j in range(AllDataMatrix.shape[1]):
wj = np.sqrt(w[j][0, 0])
#wj = w[j][0,0]
if np.isnan(wj):
#print "bad"
wj = 10**-20
# else:
# #print "yes"
# #print wj
wx[:, j] = AllDataMatrix[:, j] * wj
# kmt = KMeans(n_clusters=nclust, init='random', n_init=100,verbose=False,tol=0.0000000001)
# kmt.fit(wx)
kmt = rkmeans(x=numpy2ri(wx), centers=nclust, nstart=100)
kmlabels = np.array(kmt[0])
return prob.value, kmlabels
x[2 * k + 2, :] - x[2 * k, :] ==
(linf(np_x[2 * k, :], np_u[k, :], x[2 * k, :], u[k, :]) +
4 * linf(np_x[2 * k + 1, :],
(np_u[k, :] + np_u[k + 1, :]) / 2, x[2 * k + 1],
(u[k, :] + u[k + 1, :]) / 2) +
linf(np_x[2 * k + 2, :], np_u[k + 1, :], x[2 * k + 2], u[k, :])) *
dt / 6
]
#const += [x[k+1,:] - x[k,:] == 0.5*dt*(linf(np_x[k+1,:],np_u[k+1,:],x[k+1,:],u[k+1,:])+linf(np_x[k,:],np_u[k,:],x[k,:],u[k,:]))]
cost = cost + 0.5 * cvx.huber(
x[k, 0] - np.pi, M=0.5) + 0.01 * cvx.huber(
u[k, :]) + 0.5 * cvx.huber(x[k, 1] - 0, M=0.25)
cost = cost + 100 * cvx.square(x[K, 0] -
np.pi) + 100 * cvx.square(x[K, 1] - 0)
objective = cvx.Minimize(cost)
print("Iteration", j + 1)
prob = cvx.Problem(objective, const)
sol = prob.solve(verbose=True)
np_x = x.value
np_u = u.value
#print((np_x))
# print(np.shape(np_u))
plt.plot(np_x[:, 0])
plt.plot(np_x[:, 1])
plt.plot(np_u[:, 0])
plt.show()
def cost(self):
p = self.terminals[0].power_var
return self.alpha * cvx.square(p) - self.beta * p + self.gamma
def reachable(T, s0, sT, cost, dynamics, max_dtheta, max_theta, max_ddx,
max_line_search=30, show_results=lambda *a:None):
"""Find control signals u_1...u_T, u_t=(ddx_t,dtheta_t) and the
ensuing states s_1...s_T that
minimize L(s_0,...,s_{T-1})
subject to s_t = f(s_{t-1}, u_t)
| dtheta_t | < max_dtheta
| ddx_t | < max_ddx
One of sT or cost must be None. if sT is set, then
L = || s_{t-1} - sT ||
otherwise, it is
L = sum_{t=0}^{T-1} cost(s_t)
Solves this as a Sequential Quadratic program by approximating L by
a quadratic and f by an affine function.
"""
s0 = array(s0)
if sT is not None:
sT = array(sT)
assert (cost is None) != (sT is None), 'only one of cost or sT may be specified'
# initial iterates and objective terms
Sv = [s0] * T
Uv = [None] + [zeros(2)]*T
L = None
if cost:
L = [cost(s0)['val']] * T
last_obj = None # last objective value attained
step = 1. # last line search step size
iters = 0
n_line_searches = 0
while True:
show_results(Sv, L, '%d, %d line searches so far. step size %g'%(iters,
n_line_searches,
step))
iters += 1
# variables, objective, and constraints of the quadratic problem
S = [None] * T
U = [None] * T
S[0] = CX.Parameter(5, name='s0')
S[0].value = s0
constraints = []
if cost:
objective = zeros(1)
# define the QP
for t in xrange(1,T):
# f(u_t, s_{t-1}) and its derivatives
f = dynamics(Sv[t-1], Uv[t], {'du','ds'})
dfds = vstack(f['ds'])
dfdu = vstack(f['du'])
# define u_t and s_t
U[t] = CX.Variable(2, name='u%d'%t)
S[t] = CX.Variable(5, name='s%d'%t)
# constraints:
# s_t = linearized f(s_t-1, u_t) about previous iterate
# and bounds on s_t and u_t
constraints += [
S[t] == f['val'] + dfds*(S[t-1]-Sv[t-1]) + dfdu*(U[t]-Uv[t]),
CX.abs(U[t][0]) <= max_ddx,
CX.abs(U[t][1]) <= max_dtheta,
CX.abs(S[t][4]) <= max_theta ]
if cost:
# accumulate objective
c = cost(Sv[t], derivs={'ds','ds2'})
c['ds2'] = make_psd(c['ds2'])
objective += c['val'] + (S[t]-Sv[t]).T*c['ds'] + 0.5*CX.quad_form(S[t]-Sv[t],
c['ds2'])
if sT is not None:
# objective is || s_t - sT ||
objective = CX.square(CX.norm(S[T-1] - sT))
# solve for S and U
p = CX.Problem(CX.Minimize(objective), constraints)
r = p.solve(solver=CX.CVXOPT, verbose=False)
assert isfinite(r)
# line search on U, from Uv along U-Uv
line_search_failed = True
while n_line_searches < max_line_search:
n_line_searches += 1
# compute and apply the controls along the step
Us = []
Svs = [s0]
for u,u0 in zip(U[1:],Uv[1:]):
# a step along the search direction
us = u0 + step * (ravel(u.value)-u0)
# make it feasible
us[0] = clip(us[0], -max_ddx, max_ddx)
us[1] = clip(us[1], -max_dtheta, max_dtheta)
Us.append(us)
# apply controls
Svs.append( sim.apply_control(Svs[-1], us)['val'] )
# objective value based on the last state
if cost:
L = [ cost(s)['val'] for s in Svs ]
obj = sum(L)
else:
obj = sum((Svs[-1]-sT)**2)
if last_obj is None or obj < last_obj:
step *= 1.1 # lengthen the step for the next round
line_search_failed = False # converged
break
else:
step *= 0.7 # shorten the step and try again
if line_search_failed: # converged
break # throw away this iterate
else:
# accept the iterate
Sv = Svs
Uv = [None] + Us
last_obj = obj
return Sv,Uv
def flow_x_travel_time(self, link, flow):
return square(flow) * self.a + self.b * flow
def loss_x4(x, y, rho):
norm = cp.norm(y - x[0], p=2, axis=0)
return 1 / 2 * rho * cp.square(norm)
delimiter=',',
quotechar='"',
quoting=csv.QUOTE_MINIMAL)
writer.writerow(
[epoch, epoch_w, loss_l_cum, loss_u_cum, loss_ent_cum])
# update unlabel estimates with cumulative loss:
target_var_list = [{'params': estimated_y, 'lr': ETA_Y}]
optimizer_y = optim.SGD(target_var_list, momentum=0, weight_decay=0)
optimizer_y.step()
optimizer_y.zero_grad()
estimated_y.grad.data.zero_()
# Project onto probability polytope
est_y_num = estimated_y.data.cpu().numpy()
U = cvxpy.Variable((est_y_num.shape[0], est_y_num.shape[1]))
objective = cvxpy.Minimize(cvxpy.sum(cvxpy.square(U - est_y_num)))
constraints = [U >= EPSILON, cvxpy.sum(U, axis=1) == 1]
prob = cvxpy.Problem(objective, constraints)
prob.solve()
estimated_y.data = torch.from_numpy(np.float32(U.value)).cuda()
# save estimated labels and labeled indexes on unlabeled data:
state = {
"lab_inds": lab_inds,
"estimated_y": estimated_y.data.cpu().numpy(),
"epoch": epoch,
"y_acc": y_acc,
}
np.save(Y_U_FOLDER + file_name + '.npy', state)
def Main_vbjde_Extension_constrained_stable(graph, Y, Onsets, Thrf, K, TR, beta,
dt, scale=1, estimateSigmaH=True,
sigmaH=0.05, NitMax=-1,
NitMin=1, estimateBeta=True,
PLOT=False, contrasts=[],
computeContrast=False,
gamma_h=0):
""" Version modified by Lofti from Christine's version """
logger.info(
"Fast EM with C extension started ... Here is the stable version !")
np.random.seed(6537546)
# Initialize parameters
S = 100
if NitMax < 0:
NitMax = 100
gamma = 7.5 # 7.5
gradientStep = 0.003
MaxItGrad = 200
Thresh = 1e-5
# Initialize sizes vectors
D = np.int(np.ceil(Thrf / dt)) + 1
M = len(Onsets)
N = Y.shape[0]
J = Y.shape[1]
l = np.int(np.sqrt(J))
condition_names = []
# Neighbours
maxNeighbours = max([len(nl) for nl in graph])
neighboursIndexes = np.zeros((J, maxNeighbours), dtype=np.int32)
neighboursIndexes -= 1
for i in xrange(J):
neighboursIndexes[i, :len(graph[i])] = graph[i]
# Conditions
X = OrderedDict([])
for condition, Ons in Onsets.iteritems():
X[condition] = vt.compute_mat_X_2(N, TR, D, dt, Ons)
condition_names += [condition]
XX = np.zeros((M, N, D), dtype=np.int32)
nc = 0
for condition, Ons in Onsets.iteritems():
XX[nc, :, :] = X[condition]
nc += 1
# Covariance matrix
order = 2
D2 = vt.buildFiniteDiffMatrix(order, D)
R = np.dot(D2, D2) / pow(dt, 2 * order)
invR = np.linalg.inv(R)
Det_invR = np.linalg.det(invR)
Gamma = np.identity(N)
Det_Gamma = np.linalg.det(Gamma)
Crit_H = 1
Crit_Z = 1
Crit_A = 1
Crit_AH = 1
AH = np.zeros((J, M, D), dtype=np.float64)
AH1 = np.zeros((J, M, D), dtype=np.float64)
Crit_FreeEnergy = 1
cTime = []
cA = []
cH = []
cZ = []
cAH = []
CONTRAST = np.zeros((J, len(contrasts)), dtype=np.float64)
CONTRASTVAR = np.zeros((J, len(contrasts)), dtype=np.float64)
Q_barnCond = np.zeros((M, M, D, D), dtype=np.float64)
XGamma = np.zeros((M, D, N), dtype=np.float64)
m1 = 0
for k1 in X: # Loop over the M conditions
m2 = 0
for k2 in X:
Q_barnCond[m1, m2, :, :] = np.dot(
np.dot(X[k1].transpose(), Gamma), X[k2])
m2 += 1
XGamma[m1, :, :] = np.dot(X[k1].transpose(), Gamma)
m1 += 1
sigma_epsilone = np.ones(J)
logger.info(
"Labels are initialized by setting active probabilities to ones ...")
q_Z = np.zeros((M, K, J), dtype=np.float64)
q_Z[:, 1, :] = 1
q_Z1 = np.zeros((M, K, J), dtype=np.float64)
Z_tilde = q_Z.copy()
TT, m_h = getCanoHRF(Thrf, dt) # TODO: check
m_h = m_h[:D]
m_H = np.array(m_h).astype(np.float64)
m_H1 = np.array(m_h)
sigmaH1 = sigmaH
Sigma_H = np.ones((D, D), dtype=np.float64)
Beta = beta * np.ones((M), dtype=np.float64)
P = vt.PolyMat(N, 4, TR)
L = vt.polyFit(Y, TR, 4, P)
PL = np.dot(P, L)
y_tilde = Y - PL
Ndrift = L.shape[0]
sigma_M = np.ones((M, K), dtype=np.float64)
sigma_M[:, 0] = 0.5
sigma_M[:, 1] = 0.6
mu_M = np.zeros((M, K), dtype=np.float64)
for k in xrange(1, K):
mu_M[:, k] = 1 # InitMean
Sigma_A = np.zeros((M, M, J), np.float64)
for j in xrange(0, J):
Sigma_A[:, :, j] = 0.01 * np.identity(M)
m_A = np.zeros((J, M), dtype=np.float64)
m_A1 = np.zeros((J, M), dtype=np.float64)
for j in xrange(0, J):
for m in xrange(0, M):
for k in xrange(0, K):
m_A[j, m] += np.random.normal(mu_M[m, k],
np.sqrt(sigma_M[m, k])) * q_Z[m, k, j]
m_A1 = m_A
t1 = time.time()
##########################################################################
# VBJDE num. iter. minimum
ni = 0
while ((ni < NitMin + 1) or ((Crit_AH > Thresh) and (ni < NitMax))):
logger.info("------------------------------ Iteration n° " +
str(ni + 1) + " ------------------------------")
#####################
# EXPECTATION
#####################
# A
logger.info("E A step ...")
UtilsC.expectation_A(q_Z, mu_M, sigma_M, PL, sigma_epsilone, Gamma,
Sigma_H, Y, y_tilde, m_A, m_H, Sigma_A, XX.astype(np.int32), J, D, M, N, K)
# crit. A
DIFF = np.reshape(m_A - m_A1, (M * J))
Crit_A = (
np.linalg.norm(DIFF) / np.linalg.norm(np.reshape(m_A1, (M * J)))) ** 2
cA += [Crit_A]
m_A1[:, :] = m_A[:, :]
# HRF h
UtilsC.expectation_H(XGamma, Q_barnCond, sigma_epsilone, Gamma, R, Sigma_H, Y,
y_tilde, m_A, m_H, Sigma_A, XX.astype(np.int32), J, D, M, N, scale, sigmaH)
#m_H[0] = 0
#m_H[-1] = 0
# Constrain with optimization strategy
import cvxpy as cvx
m, n = Sigma_H.shape
Sigma_H_inv = np.linalg.inv(Sigma_H)
zeros_H = np.zeros_like(m_H[:, np.newaxis])
# Construct the problem. PRIMAL
h = cvx.Variable(n)
expression = cvx.quad_form(h - m_H[:, np.newaxis], Sigma_H_inv)
objective = cvx.Minimize(expression)
#constraints = [h[0] == 0, h[-1]==0, h >= zeros_H, cvx.square(cvx.norm(h,2))<=1]
constraints = [h[0] == 0, h[-1] == 0, cvx.square(cvx.norm(h, 2)) <= 1]
prob = cvx.Problem(objective, constraints)
result = prob.solve(verbose=0, solver=cvx.CVXOPT)
# Now we update the mean of h
m_H_old = m_H
Sigma_H_old = Sigma_H
m_H = np.squeeze(np.array((h.value)))
Sigma_H = np.zeros_like(Sigma_H)
# and the norm
h_norm += [np.linalg.norm(m_H)]
# crit. h
Crit_H = (np.linalg.norm(m_H - m_H1) / np.linalg.norm(m_H1)) ** 2
cH += [Crit_H]
m_H1[:] = m_H[:]
# crit. AH
for d in xrange(0, D):
AH[:, :, d] = m_A[:, :] * m_H[d]
DIFF = np.reshape(AH - AH1, (M * J * D))
Crit_AH = (np.linalg.norm(
DIFF) / (np.linalg.norm(np.reshape(AH1, (M * J * D))) + eps)) ** 2
cAH += [Crit_AH]
AH1[:, :, :] = AH[:, :, :]
# Z labels
logger.info("E Z step ...")
UtilsC.expectation_Z(Sigma_A, m_A, sigma_M, Beta, Z_tilde, mu_M,
q_Z, neighboursIndexes.astype(np.int32), M, J, K, maxNeighbours)
# crit. Z
DIFF = np.reshape(q_Z - q_Z1, (M * K * J))
Crit_Z = (np.linalg.norm(DIFF) /
(np.linalg.norm(np.reshape(q_Z1, (M * K * J))) + eps)) ** 2
cZ += [Crit_Z]
q_Z1[:, :, :] = q_Z[:, :, :]
#####################
# MAXIMIZATION
#####################
# HRF: Sigma_h
if estimateSigmaH:
logger.info("M sigma_H step ...")
if gamma_h > 0:
sigmaH = vt.maximization_sigmaH_prior(
D, Sigma_H, R, m_H, gamma_h)
else:
sigmaH = vt.maximization_sigmaH(D, Sigma_H, R, m_H)
logger.info('sigmaH = %s', str(sigmaH))
# (mu,sigma)
logger.info("M (mu,sigma) step ...")
mu_M, sigma_M = vt.maximization_mu_sigma(
mu_M, sigma_M, q_Z, m_A, K, M, Sigma_A)
# Drift L
UtilsC.maximization_L(
Y, m_A, m_H, L, P, XX.astype(np.int32), J, D, M, Ndrift, N)
PL = np.dot(P, L)
y_tilde = Y - PL
# Beta
if estimateBeta:
logger.info("estimating beta")
for m in xrange(0, M):
Beta[m] = UtilsC.maximization_beta(beta, q_Z[m, :, :].astype(np.float64), Z_tilde[m, :, :].astype(
np.float64), J, K, neighboursIndexes.astype(np.int32), gamma, maxNeighbours, MaxItGrad, gradientStep)
logger.info("End estimating beta")
logger.info(Beta)
# Sigma noise
logger.info("M sigma noise step ...")
UtilsC.maximization_sigma_noise(
Gamma, PL, sigma_epsilone, Sigma_H, Y, m_A, m_H, Sigma_A, XX.astype(np.int32), J, D, M, N)
t02 = time.time()
cTime += [t02 - t1]
t2 = time.time()
##########################################################################
# PLOTS and SNR computation
if PLOT and 0:
font = {'size': 15}
matplotlib.rc('font', **font)
savefig('./HRF_Iter_CompMod.png')
hold(False)
figure(2)
plot(cAH[1:-1], 'lightblue')
hold(True)
plot(cFE[1:-1], 'm')
hold(False)
legend(('CAH', 'CFE'))
grid(True)
savefig('./Crit_CompMod.png')
figure(3)
plot(FreeEnergyArray)
grid(True)
savefig('./FreeEnergy_CompMod.png')
figure(4)
for m in xrange(M):
plot(SUM_q_Z_array[m])
hold(True)
hold(False)
savefig('./Sum_q_Z_Iter_CompMod.png')
figure(5)
for m in xrange(M):
plot(mu1_array[m])
hold(True)
hold(False)
savefig('./mu1_Iter_CompMod.png')
figure(6)
plot(h_norm_array)
savefig('./HRF_Norm_CompMod.png')
Data_save = xndarray(h_norm_array, ['Iteration'])
Data_save.save('./HRF_Norm_Comp.nii')
CompTime = t2 - t1
cTimeMean = CompTime / ni
"""
Norm = np.linalg.norm(m_H)
m_H /= Norm
Sigma_H /= Norm**2
sigmaH /= Norm**2
m_A *= Norm
Sigma_A *= Norm**2
mu_M *= Norm
sigma_M *= Norm**2
sigma_M = np.sqrt(np.sqrt(sigma_M))
"""
logger.info("Nb iterations to reach criterion: %d", ni)
logger.info("Computational time = %s min %s s", str(
np.int(CompTime // 60)), str(np.int(CompTime % 60)))
logger.info('mu_M: %f', mu_M)
logger.info('sigma_M: %f', sigma_M)
logger.info("sigma_H = %s", str(sigmaH))
logger.info("Beta = %s", str(Beta))
StimulusInducedSignal = vt.computeFit(m_H, m_A, X, J, N)
SNR = 20 * \
np.log(
np.linalg.norm(Y) / np.linalg.norm(Y - StimulusInducedSignal - PL))
SNR /= np.log(10.)
print 'SNR comp =', SNR
return ni, m_A, m_H, q_Z, sigma_epsilone, mu_M, sigma_M, Beta, L, PL, CONTRAST, CONTRASTVAR, cA[2:], cH[2:], cZ[2:], cAH[2:], cTime[2:], cTimeMean, Sigma_A, StimulusInducedSignal
def test_intro(self):
"""Test examples from cvxpy.org introduction.
"""
import numpy
# Problem data.
m = 30
n = 20
numpy.random.seed(1)
A = numpy.random.randn(m, n)
b = numpy.random.randn(m, 1)
# Construct the problem.
x = Variable(n)
objective = Minimize(sum_squares(A * x - b))
constraints = [0 <= x, x <= 1]
prob = Problem(objective, constraints)
# The optimal objective is returned by p.solve().
result = prob.solve()
# The optimal value for x is stored in x.value.
print(x.value)
# The optimal Lagrange multiplier for a constraint
# is stored in constraint.dual_value.
print(constraints[0].dual_value)
########################################
# Create two scalar variables.
x = Variable()
y = Variable()
# Create two constraints.
constraints = [x + y == 1, x - y >= 1]
# Form objective.
obj = Minimize(square(x - y))
# Form and solve problem.
prob = Problem(obj, constraints)
prob.solve() # Returns the optimal value.
print("status:", prob.status)
print("optimal value", prob.value)
print("optimal var", x.value, y.value)
########################################
import cvxpy as cvx
# Create two scalar variables.
x = cvx.Variable()
y = cvx.Variable()
# Create two constraints.
constraints = [x + y == 1, x - y >= 1]
# Form objective.
obj = cvx.Minimize(cvx.square(x - y))
# Form and solve problem.
prob = cvx.Problem(obj, constraints)
prob.solve() # Returns the optimal value.
print("status:", prob.status)
print("optimal value", prob.value)
print("optimal var", x.value, y.value)
self.assertEqual(prob.status, OPTIMAL)
self.assertAlmostEqual(prob.value, 1.0)
self.assertAlmostEqual(x.value, 1.0)
self.assertAlmostEqual(y.value, 0)
########################################
# Replace the objective.
prob.objective = Maximize(x + y)
print("optimal value", prob.solve())
self.assertAlmostEqual(prob.value, 1.0)
# Replace the constraint (x + y == 1).
prob.constraints[0] = (x + y <= 3)
print("optimal value", prob.solve())
self.assertAlmostEqual(prob.value, 3.0)
########################################
x = Variable()
# An infeasible problem.
prob = Problem(Minimize(x), [x >= 1, x <= 0])
prob.solve()
print("status:", prob.status)
print("optimal value", prob.value)
self.assertEqual(prob.status, INFEASIBLE)
self.assertAlmostEqual(prob.value, np.inf)
# An unbounded problem.
prob = Problem(Minimize(x))
prob.solve()
print("status:", prob.status)
print("optimal value", prob.value)
self.assertEqual(prob.status, UNBOUNDED)
self.assertAlmostEqual(prob.value, -np.inf)
########################################
# A scalar variable.
a = Variable()
# Column vector variable of length 5.
x = Variable(5)
# Matrix variable with 4 rows and 7 columns.
A = Variable(4, 7)
########################################
import numpy
# Problem data.
m = 10
n = 5
numpy.random.seed(1)
A = numpy.random.randn(m, n)
b = numpy.random.randn(m, 1)
# Construct the problem.
x = Variable(n)
objective = Minimize(sum_entries(square(A * x - b)))
constraints = [0 <= x, x <= 1]
prob = Problem(objective, constraints)
print("Optimal value", prob.solve())
print("Optimal var")
print(x.value) # A numpy matrix.
self.assertAlmostEqual(prob.value, 4.14133859146)
########################################
# Positive scalar parameter.
m = Parameter(sign="positive")
# Column vector parameter with unknown sign (by default).
c = Parameter(5)
# Matrix parameter with negative entries.
G = Parameter(4, 7, sign="negative")
# Assigns a constant value to G.
G.value = -numpy.ones((4, 7))
########################################
# Create parameter, then assign value.
rho = Parameter(sign="positive")
rho.value = 2
# Initialize parameter with a value.
rho = Parameter(sign="positive", value=2)
########################################
import numpy
# Problem data.
n = 15
m = 10
numpy.random.seed(1)
A = numpy.random.randn(n, m)
b = numpy.random.randn(n, 1)
# gamma must be positive due to DCP rules.
gamma = Parameter(sign="positive")
# Construct the problem.
x = Variable(m)
error = sum_squares(A * x - b)
obj = Minimize(error + gamma * norm(x, 1))
prob = Problem(obj)
# Construct a trade-off curve of ||Ax-b||^2 vs. ||x||_1
sq_penalty = []
l1_penalty = []
x_values = []
gamma_vals = numpy.logspace(-4, 6)
for val in gamma_vals:
gamma.value = val
prob.solve()
# Use expr.value to get the numerical value of
# an expression in the problem.
sq_penalty.append(error.value)
l1_penalty.append(norm(x, 1).value)
x_values.append(x.value)
########################################
import numpy
X = Variable(5, 4)
A = numpy.ones((3, 5))
# Use expr.size to get the dimensions.
print("dimensions of X:", X.size)
print("dimensions of sum_entries(X):", sum_entries(X).size)
print("dimensions of A*X:", (A * X).size)
# ValueError raised for invalid dimensions.
try:
A + X
except ValueError as e:
print(e)
def loss_y2(rho, x, y, workers):
val = 1 / 2 * rho * cp.sum([
cp.square(cp.norm(y[i] - x[i + 1][0], p=2, axis=0))
for i in range(0, workers)
])
return val
print('Reading vecA ... done!')
else:
for f in trange(numFaces,
desc='Computing vecA',
ncols=100,
leave=False):
vA = []
for i in range(9):
A = cvx.Variable(7)
err = 0
for m in range(numMeshes_POSE):
err += cvx.square((deltaR[m][faceBone[f]] * A) -
np.matrix(matQ[m][f]).A1[i])
obj = cvx.Minimize(err)
prob = cvx.Problem(obj)
prob.solve()
vA.append(A.value.A1)
vecA[f] = np.array(vA)
vecA = np.array(vecA)
test_vecA()
print('Computing vecA ... done!')
if WRITE_VECA_TO_DISK:
write_vecA(DATA_DIR + '/vecA.dat', vecA)
def Main_vbjde_Extension_constrained_stable(graph, Y, Onsets, Thrf, K, TR, beta,
dt, scale=1, estimateSigmaH=True,
sigmaH=0.05, NitMax=-1,
NitMin=1, estimateBeta=True,
PLOT=False, contrasts=[],
computeContrast=False,
gamma_h=0):
""" Version modified by Lofti from Christine's version """
logger.info(
"Fast EM with C extension started ... Here is the stable version !")
np.random.seed(6537546)
# Initialize parameters
S = 100
if NitMax < 0:
NitMax = 100
gamma = 7.5 # 7.5
gradientStep = 0.003
MaxItGrad = 200
Thresh = 1e-5
# Initialize sizes vectors
D = np.int(np.ceil(Thrf / dt)) + 1
M = len(Onsets)
N = Y.shape[0]
J = Y.shape[1]
l = np.int(np.sqrt(J))
condition_names = []
# Neighbours
maxNeighbours = max([len(nl) for nl in graph])
neighboursIndexes = np.zeros((J, maxNeighbours), dtype=np.int32)
neighboursIndexes -= 1
for i in xrange(J):
neighboursIndexes[i, :len(graph[i])] = graph[i]
# Conditions
X = OrderedDict([])
for condition, Ons in Onsets.iteritems():
X[condition] = vt.compute_mat_X_2(N, TR, D, dt, Ons)
condition_names += [condition]
XX = np.zeros((M, N, D), dtype=np.int32)
nc = 0
for condition, Ons in Onsets.iteritems():
XX[nc, :, :] = X[condition]
nc += 1
# Covariance matrix
order = 2
D2 = vt.buildFiniteDiffMatrix(order, D)
R = np.dot(D2, D2) / pow(dt, 2 * order)
invR = np.linalg.inv(R)
Det_invR = np.linalg.det(invR)
Gamma = np.identity(N)
Det_Gamma = np.linalg.det(Gamma)
Crit_H = 1
Crit_Z = 1
Crit_A = 1
Crit_AH = 1
AH = np.zeros((J, M, D), dtype=np.float64)
AH1 = np.zeros((J, M, D), dtype=np.float64)
Crit_FreeEnergy = 1
cTime = []
cA = []
cH = []
cZ = []
cAH = []
CONTRAST = np.zeros((J, len(contrasts)), dtype=np.float64)
CONTRASTVAR = np.zeros((J, len(contrasts)), dtype=np.float64)
Q_barnCond = np.zeros((M, M, D, D), dtype=np.float64)
XGamma = np.zeros((M, D, N), dtype=np.float64)
m1 = 0
for k1 in X: # Loop over the M conditions
m2 = 0
for k2 in X:
Q_barnCond[m1, m2, :, :] = np.dot(
np.dot(X[k1].transpose(), Gamma), X[k2])
m2 += 1
XGamma[m1, :, :] = np.dot(X[k1].transpose(), Gamma)
m1 += 1
sigma_epsilone = np.ones(J)
logger.info(
"Labels are initialized by setting active probabilities to ones ...")
q_Z = np.zeros((M, K, J), dtype=np.float64)
q_Z[:, 1, :] = 1
q_Z1 = np.zeros((M, K, J), dtype=np.float64)
Z_tilde = q_Z.copy()
TT, m_h = getCanoHRF(Thrf, dt) # TODO: check
m_h = m_h[:D]
m_H = np.array(m_h).astype(np.float64)
m_H1 = np.array(m_h)
sigmaH1 = sigmaH
Sigma_H = np.ones((D, D), dtype=np.float64)
Beta = beta * np.ones((M), dtype=np.float64)
P = vt.PolyMat(N, 4, TR)
L = vt.polyFit(Y, TR, 4, P)
PL = np.dot(P, L)
y_tilde = Y - PL
Ndrift = L.shape[0]
sigma_M = np.ones((M, K), dtype=np.float64)
sigma_M[:, 0] = 0.5
sigma_M[:, 1] = 0.6
mu_M = np.zeros((M, K), dtype=np.float64)
for k in xrange(1, K):
mu_M[:, k] = 1 # InitMean
Sigma_A = np.zeros((M, M, J), np.float64)
for j in xrange(0, J):
Sigma_A[:, :, j] = 0.01 * np.identity(M)
m_A = np.zeros((J, M), dtype=np.float64)
m_A1 = np.zeros((J, M), dtype=np.float64)
for j in xrange(0, J):
for m in xrange(0, M):
for k in xrange(0, K):
m_A[j, m] += np.random.normal(mu_M[m, k],
np.sqrt(sigma_M[m, k])) * q_Z[m, k, j]
m_A1 = m_A
t1 = time.time()
##########################################################################
# VBJDE num. iter. minimum
ni = 0
while ((ni < NitMin + 1) or ((Crit_AH > Thresh) and (ni < NitMax))):
logger.info("------------------------------ Iteration n° " +
str(ni + 1) + " ------------------------------")
#####################
# EXPECTATION
#####################
# A
logger.info("E A step ...")
UtilsC.expectation_A(q_Z, mu_M, sigma_M, PL, sigma_epsilone, Gamma,
Sigma_H, Y, y_tilde, m_A, m_H, Sigma_A, XX.astype(np.int32), J, D, M, N, K)
# crit. A
DIFF = np.reshape(m_A - m_A1, (M * J))
Crit_A = (
np.linalg.norm(DIFF) / np.linalg.norm(np.reshape(m_A1, (M * J)))) ** 2
cA += [Crit_A]
m_A1[:, :] = m_A[:, :]
# HRF h
UtilsC.expectation_H(XGamma, Q_barnCond, sigma_epsilone, Gamma, R, Sigma_H, Y,
y_tilde, m_A, m_H, Sigma_A, XX.astype(np.int32), J, D, M, N, scale, sigmaH)
#m_H[0] = 0
#m_H[-1] = 0
# Constrain with optimization strategy
import cvxpy as cvx
m, n = Sigma_H.shape
Sigma_H_inv = np.linalg.inv(Sigma_H)
zeros_H = np.zeros_like(m_H[:, np.newaxis])
# Construct the problem. PRIMAL
h = cvx.Variable(n)
expression = cvx.quad_form(h - m_H[:, np.newaxis], Sigma_H_inv)
objective = cvx.Minimize(expression)
#constraints = [h[0] == 0, h[-1]==0, h >= zeros_H, cvx.square(cvx.norm(h,2))<=1]
constraints = [h[0] == 0, h[-1] == 0, cvx.square(cvx.norm(h, 2)) <= 1]
prob = cvx.Problem(objective, constraints)
result = prob.solve(verbose=0, solver=cvx.CVXOPT)
# Now we update the mean of h
m_H_old = m_H
Sigma_H_old = Sigma_H
m_H = np.squeeze(np.array((h.value)))
Sigma_H = np.zeros_like(Sigma_H)
# and the norm
h_norm += [np.linalg.norm(m_H)]
# crit. h
Crit_H = (np.linalg.norm(m_H - m_H1) / np.linalg.norm(m_H1)) ** 2
cH += [Crit_H]
m_H1[:] = m_H[:]
# crit. AH
for d in xrange(0, D):
AH[:, :, d] = m_A[:, :] * m_H[d]
DIFF = np.reshape(AH - AH1, (M * J * D))
Crit_AH = (np.linalg.norm(
DIFF) / (np.linalg.norm(np.reshape(AH1, (M * J * D))) + eps)) ** 2
cAH += [Crit_AH]
AH1[:, :, :] = AH[:, :, :]
# Z labels
logger.info("E Z step ...")
UtilsC.expectation_Z(Sigma_A, m_A, sigma_M, Beta, Z_tilde, mu_M,
q_Z, neighboursIndexes.astype(np.int32), M, J, K, maxNeighbours)
# crit. Z
DIFF = np.reshape(q_Z - q_Z1, (M * K * J))
Crit_Z = (np.linalg.norm(DIFF) /
(np.linalg.norm(np.reshape(q_Z1, (M * K * J))) + eps)) ** 2
cZ += [Crit_Z]
q_Z1[:, :, :] = q_Z[:, :, :]
#####################
# MAXIMIZATION
#####################
# HRF: Sigma_h
if estimateSigmaH:
logger.info("M sigma_H step ...")
if gamma_h > 0:
sigmaH = vt.maximization_sigmaH_prior(
D, Sigma_H, R, m_H, gamma_h)
else:
sigmaH = vt.maximization_sigmaH(D, Sigma_H, R, m_H)
logger.info('sigmaH = %s', str(sigmaH))
# (mu,sigma)
logger.info("M (mu,sigma) step ...")
mu_M, sigma_M = vt.maximization_mu_sigma(
mu_M, sigma_M, q_Z, m_A, K, M, Sigma_A)
# Drift L
UtilsC.maximization_L(
Y, m_A, m_H, L, P, XX.astype(np.int32), J, D, M, Ndrift, N)
PL = np.dot(P, L)
y_tilde = Y - PL
# Beta
if estimateBeta:
logger.info("estimating beta")
for m in xrange(0, M):
Beta[m] = UtilsC.maximization_beta(beta, q_Z[m, :, :].astype(np.float64), Z_tilde[m, :, :].astype(
np.float64), J, K, neighboursIndexes.astype(np.int32), gamma, maxNeighbours, MaxItGrad, gradientStep)
logger.info("End estimating beta")
logger.info(Beta)
# Sigma noise
logger.info("M sigma noise step ...")
UtilsC.maximization_sigma_noise(
Gamma, PL, sigma_epsilone, Sigma_H, Y, m_A, m_H, Sigma_A, XX.astype(np.int32), J, D, M, N)
t02 = time.time()
cTime += [t02 - t1]
t2 = time.time()
##########################################################################
# PLOTS and SNR computation
if PLOT and 0:
font = {'size': 15}
matplotlib.rc('font', **font)
savefig('./HRF_Iter_CompMod.png')
hold(False)
figure(2)
plot(cAH[1:-1], 'lightblue')
hold(True)
plot(cFE[1:-1], 'm')
hold(False)
legend(('CAH', 'CFE'))
grid(True)
savefig('./Crit_CompMod.png')
figure(3)
plot(FreeEnergyArray)
grid(True)
savefig('./FreeEnergy_CompMod.png')
figure(4)
for m in xrange(M):
plot(SUM_q_Z_array[m])
hold(True)
hold(False)
savefig('./Sum_q_Z_Iter_CompMod.png')
figure(5)
for m in xrange(M):
plot(mu1_array[m])
hold(True)
hold(False)
savefig('./mu1_Iter_CompMod.png')
figure(6)
plot(h_norm_array)
savefig('./HRF_Norm_CompMod.png')
Data_save = xndarray(h_norm_array, ['Iteration'])
Data_save.save('./HRF_Norm_Comp.nii')
CompTime = t2 - t1
cTimeMean = CompTime / ni
"""
Norm = np.linalg.norm(m_H)
m_H /= Norm
Sigma_H /= Norm**2
sigmaH /= Norm**2
m_A *= Norm
Sigma_A *= Norm**2
mu_M *= Norm
sigma_M *= Norm**2
sigma_M = np.sqrt(np.sqrt(sigma_M))
"""
logger.info("Nb iterations to reach criterion: %d", ni)
logger.info("Computational time = %s min %s s", str(
np.int(CompTime // 60)), str(np.int(CompTime % 60)))
logger.info('mu_M: %f', mu_M)
logger.info('sigma_M: %f', sigma_M)
logger.info("sigma_H = %s", str(sigmaH))
logger.info("Beta = %s", str(Beta))
StimulusInducedSignal = vt.computeFit(m_H, m_A, X, J, N)
SNR = 20 * \
np.log(
np.linalg.norm(Y) / np.linalg.norm(Y - StimulusInducedSignal - PL))
SNR /= np.log(10.)
logger.info('SNR comp = %f', SNR)
return ni, m_A, m_H, q_Z, sigma_epsilone, mu_M, sigma_M, Beta, L, PL, CONTRAST, CONTRASTVAR, cA[2:], cH[2:], cZ[2:], cAH[2:], cTime[2:], cTimeMean, Sigma_A, StimulusInducedSignal
def __init__(self, m, K):
# Variables:
self.var = dict()
self.var['X'] = cvxpy.Variable((m.n_x, K))
self.var['U'] = cvxpy.Variable((m.n_u, K))
self.var['sigma'] = cvxpy.Variable(nonneg=True)
self.var['nu'] = cvxpy.Variable((m.n_x, K - 1))
self.var['delta_norm'] = cvxpy.Variable(nonneg=True)
self.var['sigma_norm'] = cvxpy.Variable(nonneg=True)
# Parameters:
self.par = dict()
self.par['A_bar'] = cvxpy.Parameter((m.n_x * m.n_x, K - 1))
self.par['B_bar'] = cvxpy.Parameter((m.n_x * m.n_u, K - 1))
self.par['C_bar'] = cvxpy.Parameter((m.n_x * m.n_u, K - 1))
self.par['S_bar'] = cvxpy.Parameter((m.n_x, K - 1))
self.par['z_bar'] = cvxpy.Parameter((m.n_x, K - 1))
self.par['X_last'] = cvxpy.Parameter((m.n_x, K))
self.par['U_last'] = cvxpy.Parameter((m.n_u, K))
self.par['sigma_last'] = cvxpy.Parameter(nonneg=True)
self.par['weight_sigma'] = cvxpy.Parameter(nonneg=True)
self.par['weight_delta'] = cvxpy.Parameter(nonneg=True)
self.par['weight_delta_sigma'] = cvxpy.Parameter(nonneg=True)
self.par['weight_nu'] = cvxpy.Parameter(nonneg=True)
# Constraints:
constraints = []
# Model:
constraints += m.get_constraints(self.var['X'], self.var['U'],
self.par['X_last'],
self.par['U_last'])
# Dynamics:
# x_t+1 = A_*x_t+B_*U_t+C_*U_T+1*S_*sigma+zbar+nu
constraints += [
self.var['X'][:, k + 1] == cvxpy.reshape(self.par['A_bar'][:, k],
(m.n_x, m.n_x)) *
self.var['X'][:, k] +
cvxpy.reshape(self.par['B_bar'][:, k],
(m.n_x, m.n_u)) * self.var['U'][:, k] +
cvxpy.reshape(self.par['C_bar'][:, k],
(m.n_x, m.n_u)) * self.var['U'][:, k + 1] +
self.par['S_bar'][:, k] * self.var['sigma'] +
self.par['z_bar'][:, k] + self.var['nu'][:, k]
for k in range(K - 1)
]
# Trust regions:
dx = cvxpy.sum(cvxpy.square(self.var['X'] - self.par['X_last']),
axis=0)
du = cvxpy.sum(cvxpy.square(self.var['U'] - self.par['U_last']),
axis=0)
ds = self.var['sigma'] - self.par['sigma_last']
constraints += [cvxpy.norm(dx + du, 1) <= self.var['delta_norm']]
constraints += [cvxpy.norm(ds, 'inf') <= self.var['sigma_norm']]
# Flight time positive:
constraints += [self.var['sigma'] >= 0.1]
# Objective:
sc_objective = cvxpy.Minimize(
self.par['weight_sigma'] * self.var['sigma'] +
self.par['weight_nu'] * cvxpy.norm(self.var['nu'], 'inf') +
self.par['weight_delta'] * self.var['delta_norm'] +
self.par['weight_delta_sigma'] * self.var['sigma_norm'])
objective = sc_objective
self.prob = cvxpy.Problem(objective, constraints)
def test_intro(self):
"""Test examples from cvxpy.org introduction.
"""
import numpy
# Problem data.
m = 30
n = 20
numpy.random.seed(1)
A = numpy.random.randn(m, n)
b = numpy.random.randn(m, 1)
# Construct the problem.
x = Variable(n)
objective = Minimize(sum_squares(A*x - b))
constraints = [0 <= x, x <= 1]
prob = Problem(objective, constraints)
# The optimal objective is returned by p.solve().
result = prob.solve()
# The optimal value for x is stored in x.value.
print(x.value)
# The optimal Lagrange multiplier for a constraint
# is stored in constraint.dual_value.
print(constraints[0].dual_value)
########################################
# Create two scalar variables.
x = Variable()
y = Variable()
# Create two constraints.
constraints = [x + y == 1,
x - y >= 1]
# Form objective.
obj = Minimize(square(x - y))
# Form and solve problem.
prob = Problem(obj, constraints)
prob.solve() # Returns the optimal value.
print("status:", prob.status)
print("optimal value", prob.value)
print("optimal var", x.value, y.value)
########################################
import cvxpy as cvx
# Create two scalar variables.
x = cvx.Variable()
y = cvx.Variable()
# Create two constraints.
constraints = [x + y == 1,
x - y >= 1]
# Form objective.
obj = cvx.Minimize(cvx.square(x - y))
# Form and solve problem.
prob = cvx.Problem(obj, constraints)
prob.solve() # Returns the optimal value.
print("status:", prob.status)
print("optimal value", prob.value)
print("optimal var", x.value, y.value)
self.assertEqual(prob.status, OPTIMAL)
self.assertAlmostEqual(prob.value, 1.0)
self.assertAlmostEqual(x.value, 1.0)
self.assertAlmostEqual(y.value, 0)
########################################
# Replace the objective.
prob.objective = Maximize(x + y)
print("optimal value", prob.solve())
self.assertAlmostEqual(prob.value, 1.0)
# Replace the constraint (x + y == 1).
prob.constraints[0] = (x + y <= 3)
print("optimal value", prob.solve())
self.assertAlmostEqual(prob.value, 3.0)
########################################
x = Variable()
# An infeasible problem.
prob = Problem(Minimize(x), [x >= 1, x <= 0])
prob.solve()
print("status:", prob.status)
print("optimal value", prob.value)
self.assertEquals(prob.status, INFEASIBLE)
self.assertAlmostEqual(prob.value, np.inf)
# An unbounded problem.
prob = Problem(Minimize(x))
prob.solve()
print("status:", prob.status)
print("optimal value", prob.value)
self.assertEquals(prob.status, UNBOUNDED)
self.assertAlmostEqual(prob.value, -np.inf)
########################################
# A scalar variable.
a = Variable()
# Column vector variable of length 5.
x = Variable(5)
# Matrix variable with 4 rows and 7 columns.
A = Variable(4, 7)
########################################
import numpy
# Problem data.
m = 10
n = 5
numpy.random.seed(1)
A = numpy.random.randn(m, n)
b = numpy.random.randn(m, 1)
# Construct the problem.
x = Variable(n)
objective = Minimize(sum_entries(square(A*x - b)))
constraints = [0 <= x, x <= 1]
prob = Problem(objective, constraints)
print("Optimal value", prob.solve())
print("Optimal var")
print(x.value) # A numpy matrix.
self.assertAlmostEqual(prob.value, 4.14133859146)
########################################
# Positive scalar parameter.
m = Parameter(sign="positive")
# Column vector parameter with unknown sign (by default).
c = Parameter(5)
# Matrix parameter with negative entries.
G = Parameter(4, 7, sign="negative")
# Assigns a constant value to G.
G.value = -numpy.ones((4, 7))
########################################
# Create parameter, then assign value.
rho = Parameter(sign="positive")
rho.value = 2
# Initialize parameter with a value.
rho = Parameter(sign="positive", value=2)
########################################
import numpy
# Problem data.
n = 15
m = 10
numpy.random.seed(1)
A = numpy.random.randn(n, m)
b = numpy.random.randn(n, 1)
# gamma must be positive due to DCP rules.
gamma = Parameter(sign="positive")
# Construct the problem.
x = Variable(m)
error = sum_squares(A*x - b)
obj = Minimize(error + gamma*norm(x, 1))
prob = Problem(obj)
# Construct a trade-off curve of ||Ax-b||^2 vs. ||x||_1
sq_penalty = []
l1_penalty = []
x_values = []
gamma_vals = numpy.logspace(-4, 6)
for val in gamma_vals:
gamma.value = val
prob.solve()
# Use expr.value to get the numerical value of
# an expression in the problem.
sq_penalty.append(error.value)
l1_penalty.append(norm(x, 1).value)
x_values.append(x.value)
########################################
import numpy
X = Variable(5, 4)
A = numpy.ones((3, 5))
# Use expr.size to get the dimensions.
print("dimensions of X:", X.size)
print("dimensions of sum_entries(X):", sum_entries(X).size)
print("dimensions of A*X:", (A*X).size)
# ValueError raised for invalid dimensions.
try:
A + X
except ValueError as e:
print(e)
def graph_reg(beta, edges, weight):
# Graph regularization (squared).
return weight @ cp.square(
cp.pnorm(beta[edges[:, 0], :] - beta[edges[:, 1], :],
axis=1,
keepdims=True))