def __init__(self):
self._processCovariance = sp.identity(13)
self._measurementCovariance = sp.identity(3)
self._errorCovariance = sp.identity(13)
self._translationRotorFromBody = vec3(0)
self._gravity = vec3([0.0, 0.0, 1.0])
self._magneticField = mat3.fromEulerXYZ(0.0, -1.22, 0.0) * vec3(
[1.0, 0.0, 0.0])
# the magnetic field vector points to the magnetic north, with a -70 degrees (-1.22 radians) pitch (towards the ground)
self._declinationAngle = 0.0
self.timestamp = 0.0
self.positionNED = vec3(0)
self.velocityBody = vec3(0)
self.orientationBody = quat(1)
self.gyroBiases = vec3(0)
self.gravityBody = self._gravity
def LUP(A):
# throw warning flag when the number is too small
# (close to 0)
ok = 1
small = 1e-12
n = scipy.shape(A)[0]
U = copy.copy(A)
L = scipy.identity(n)
P = scipy.identity(n)
for j in range(1,n):
s = scipy.argmax(abs(U[j-1:n,j-1])) + j-1
# argmax returs the index of that number
if s != j-1:
U = swap(U,s,j-1,n)
P = swap(P,s,j-1,n)
if j > 1:
L = swap(L,s,j-1,j-1)
# Since the multiplier is zero after the
# second row after the pivot row, we only
# need to calculate one row for U and L, which is the
# row under the pivot row
i = j+1
if abs(U[j-1,j-1]) < small:
print("Near-zero pivot!")
ok = 0
break
L[i-1,j-1] = float(U[i-1,j-1])/U[j-1,j-1]
for k in range(j,n+1):
U[i-1,k-1] = U[i-1,k-1] - L[i-1,j-1] * U[j-1,k-1]
return L,U,P,ok
def LUP(A):
small = 1e-12 # a pivot smaller than this will raise the error flag "ok=0"
n = scipy.shape(A)[0] # extract matrix size
U = copy(A) # copy content of A (avoid linking U and A)
L = scipy.identity(n) # initialize L and P
P = scipy.identity(n)
par = 1 # initial permutation (identity) is even
ok = 1 # by default, we assume the matrix is non-singular
for k in range(1, n):
s = scipy.argmax(abs(U[k - 1:n, k - 1])) + k - 1 # find pivot element
if abs(U[s, k - 1]) < small: # check if pivot is too close to zero
print("(nearly) singular matrix, pivot smaller than %e" % small)
ok = 0
break # matrix is too close to singular, exit with error flag up
if s != k - 1: # if the pivot is not on the diagonal...
par = -par # change parity
U = swap(U, s, k - 1, n) # swap rows of U
if k > 1: # swap rows of L left of diagonal element
L = swap(L, s, k - 1, k - 1)
P = swap(P, s, k - 1, n) # swap rows of P
for j in range(k + 1, n + 1): # Gauss elimination of rows below pivot
L[j - 1, k - 1] = U[j - 1, k - 1] / U[k - 1, k - 1]
for i in range(k, n + 1):
U[j - 1,
i - 1] = U[j - 1, i - 1] - L[j - 1, k - 1] * U[k - 1, i - 1]
print('L=', L)
print(" ")
print('U=', U)
print(" ")
print('P=', P)
print(" ")
return L, U, P, par, ok
def test_scipy_inv(self):
invA = inv(self.A)
self.assertAlmostEqual(sum(sum(abs(dot(invA, self.A) - identity(2)))),
0.0, 5)
self.assertAlmostEqual(sum(sum(abs(dot(self.A, invA) - identity(2)))),
0.0, 5)
def __init__(self, respond = None, regressors = None, intercept = False, D = None, d = None, G = None, a = None, b = None, **args):
"""Input: paras where they are expected to be tuple or dictionary"""
ECRegression.__init__(self,respond, regressors, intercept, D, d, **args)
if self.intercept and G != None:
self.G = scipy.zeros((self.n, self.n))
self.G[1:, 1:] = G
elif self.intercept and G == None :
self.G = scipy.identity(self.n)
self.G[0, 0] = 0.0
elif not self.intercept and G != None:
self.G = G
else:
self.G = scipy.identity(self.n)
if self.intercept:
self.a = scipy.zeros((self.n, 1))
self.a[1:] = a
self.b = scipy.zeros((self.n, 1))
self.b[1:] = b
else:
if a is None:
self.a = scipy.matrix( scipy.zeros((self.n,1)))
else: self.a = a
if b is None:
self.b = scipy.matrix( scipy.ones((self.n,1)))
else: self.b = b
def test_scipy_svd(self):
U,D,Vt = svd(self.A)
D = array([[D[0],0],[0,D[1]]],'d')
self.assertAlmostEqual( sum(sum(abs(dot(U,U.transpose())- identity(2)))), 0.0, 5)
self.assertAlmostEqual( sum(sum(abs(dot(Vt,Vt.transpose())- identity(2)))), 0.0, 5)
self.assertAlmostEqual( sum(sum(abs(dot(U,dot(D,Vt)) - self.A))), 0.0, 5)
def find_object_frame_and_bounding_box(self, point_cloud):
#leaving point cloud in the cluster frame
cluster_frame = point_cloud.header.frame_id
self.base_frame = cluster_frame
(points, cluster_to_base_frame) = transform_point_cloud(
self.tf_listener, point_cloud, self.base_frame)
#run PCA on all 3 dimensions
(shifted_points, xyz_mean) = self.mean_shift_xyz(points)
directions = self.pca(shifted_points[0:3, :])
#convert the points to object frame:
#rotate all the points to be in the frame of the eigenvectors (should already be centered around xyz_mean)
rotmat = scipy.matrix(scipy.identity(4))
rotmat[0:3, 0:3] = directions
object_points = rotmat**-1 * shifted_points
#remove outliers from the cluster
#object_points = self.remove_outliers(object_points)
#find the object bounding box in the new object frame as [[xmin, ymin, zmin], [xmax, ymax, zmax]] (coordinates of opposite corners)
object_bounding_box = [[0] * 3 for i in range(2)]
object_bounding_box_dims = [0] * 3
for dim in range(3):
object_bounding_box[0][dim] = object_points[dim, :].min()
object_bounding_box[1][dim] = object_points[dim, :].max()
object_bounding_box_dims[dim] = object_bounding_box[1][
dim] - object_bounding_box[0][dim]
#now shift the object frame and bounding box so that the center is the center of the object
offset_mat = scipy.mat(scipy.identity(4))
for i in range(3):
offset = object_bounding_box[1][
i] - object_bounding_box_dims[i] / 2. #center
object_bounding_box[0][i] -= offset #mins
object_bounding_box[1][i] -= offset #maxes
object_points[i, :] -= offset
offset_mat[i, 3] = offset
rotmat = rotmat * offset_mat
#record the transforms from object frame to base frame and to the original cluster frame,
#broadcast the object frame to tf, and draw the object frame in rviz
unshift_mean = scipy.identity(4)
for i in range(3):
unshift_mean[i, 3] = xyz_mean[i]
object_to_base_frame = unshift_mean * rotmat
object_to_cluster_frame = cluster_to_base_frame**-1 * object_to_base_frame
#broadcast the object frame to tf
(object_frame_pos,
object_frame_quat) = mat_to_pos_and_quat(object_to_cluster_frame)
self.tf_broadcaster.sendTransform(object_frame_pos, object_frame_quat,
rospy.Time.now(), "object_frame",
cluster_frame)
return (object_points, object_bounding_box_dims, object_bounding_box,
object_to_base_frame, object_to_cluster_frame)
def computeReductions(self, qlist, wlist):
deltalist = qlist / (1. + self.weights)
deltalist_1add = qlist / (2. + self.weights)
reductionlist = deltalist - deltalist_1add
fractionlist = reductionlist / reductionlist.sum()
recclist = matrix(identity(self.dim)[argmax(fractionlist), 0:], "int")
deltalist_1add = arr2lst(deltalist_1add)
reductionlist = arr2lst(reductionlist)
fractionlist = arr2lst(fractionlist)
recclist = arr2lst(recclist)
# These are the recommendations for only one new sample
currentEvalVariance = [
deltalist_1add, reductionlist, fractionlist, recclist
]
# If you want more samples, add four more entries to this list, with this info
if self.nNewSamples > 1:
deltalist_madd = qlist / (1. + self.nNewSamples + self.weights)
reductionlist_m = deltalist - deltalist_madd
self.stateToSampleMore = argmax(reductionlist_m)
fractionlist_m = reductionlist_m / reductionlist_m.sum()
if self.recommendationScheme == 'Nina':
# Nina's scheme: put all nNewSamples at one state
recclist_m = matrix(
self.nNewSamples *
identity(self.dim)[argmax(fractionlist_m), 0:], "int")
elif self.recommendationScheme == 'VAV':
# VAV: a new possible scheme -- pick several to sample, but make sure the total counts are self.nNewSamples
recclist_m = matrix(self.nNewSamples * fractionlist_m, "int")
while recclist_m[0, :].sum() < self.nNewSamples:
recclist_m[0, argmax(fractionlist_m)] += 1
deltalist_madd = arr2lst(deltalist_madd)
reductionlist_m = arr2lst(reductionlist_m)
fractionlist_m = arr2lst(fractionlist_m)
recclist_m = arr2lst(recclist_m)
currentEvalVariance.extend(
[deltalist_madd, reductionlist_m, fractionlist_m, recclist_m])
# add two more things to the beginning of the list: deltalist, and 0....n-1
currentEvalVariance.insert(0, arr2lst(deltalist))
currentEvalVariance.insert(0, range(
self.dim)) # 0 .... n-1 will be the firstthing
#Now, transpose the whole thing so that this information if in column format
currentEvalVariance = matrix(currentEvalVariance, "float64").T
self.varianceContributions.append(currentEvalVariance)
def householder(A, reduced=False) -> Tuple[sp.matrix, sp.matrix]:
'''
Given a matrix A, computes its QR factorisation using Householder
reflections.
Returns (Q, R) such that A = QR, Q is orthogonal and R is triangular.
'''
m, n = A.shape
A_full = sp.ndarray(A.shape)
A_sub = A.copy()
Q_full = sp.identity(m)
# iterate over smaller dimension of A
for i in range(min(A.shape)):
# leftmost vector of A submatrix
v = A_sub[:, 0]
# vector with 1 in the first position.
e_i = sp.zeros(v.shape[0])
e_i[0] = 1
# compute householder vector for P
u = v + sign(v.item(0)) * spla.norm(v) * e_i
# normalise
u = u / spla.norm(u)
# compute submatrix _P
_P = sp.identity(v.shape[0]) - 2 * sp.outer(u, u)
# embed this submatrix _P into the full size P
P = spla.block_diag(sp.identity(i), _P)
# compute next iteration of Q
Q_full = P @ Q_full
# compute next iteration of R
A_sub = _P @ A_sub
# copy first rows/cols to A_full
A_full[i, i:] = A_sub[0, :]
A_full[i:, i] = A_sub[:, 0]
# iterate into submatrix
A_sub = A_sub[1:, 1:]
# Q_full is currently the inverse because it is applied to A.
# thus, Q = Q_full^T.
Q_full = Q_full.T
if reduced:
Q_full = Q_full[:, :n]
A_full = A_full[:n, :]
# A = QR
# note that A has been reduced to R by applying the P's.
return (Q_full, A_full)
def test_scipy_svd(self):
U, D, Vt = svd(self.A)
D = array([[D[0], 0], [0, D[1]]], 'd')
self.assertAlmostEqual(
sum(sum(abs(dot(U, U.transpose()) - identity(2)))), 0.0, 5)
self.assertAlmostEqual(
sum(sum(abs(dot(Vt, Vt.transpose()) - identity(2)))), 0.0, 5)
self.assertAlmostEqual(sum(sum(abs(dot(U, dot(D, Vt)) - self.A))), 0.0,
5)
def Calculate_Beta(X, Pi):
k = Pi.shape[1]
N = X.shape[0]
ones = sc.ones((k, k))
Y = sc.ones((N, N)) - sc.identity(N) - X
Z = sc.ones((k, k)) - 0.5 * sc.identity(k)
beta1 = ones + Z * Pi.T.dot(X.dot(Pi))
beta2 = ones + Z * Pi.T.dot(Y.dot(Pi))
return beta1, beta2
def find_object_frame_and_bounding_box(self, point_cloud):
#leaving point cloud in the cluster frame
cluster_frame = point_cloud.header.frame_id
self.base_frame = cluster_frame
(points, cluster_to_base_frame) = transform_point_cloud(self.tf_listener, point_cloud, self.base_frame)
#run PCA on all 3 dimensions
(shifted_points, xyz_mean) = self.mean_shift_xyz(points)
directions = self.pca(shifted_points[0:3, :])
#convert the points to object frame:
#rotate all the points to be in the frame of the eigenvectors (should already be centered around xyz_mean)
rotmat = scipy.matrix(scipy.identity(4))
rotmat[0:3,0:3] = directions
object_points = rotmat**-1 * shifted_points
#remove outliers from the cluster
#object_points = self.remove_outliers(object_points)
#find the object bounding box in the new object frame as [[xmin, ymin, zmin], [xmax, ymax, zmax]] (coordinates of opposite corners)
object_bounding_box = [[0]*3 for i in range(2)]
object_bounding_box_dims = [0]*3
for dim in range(3):
object_bounding_box[0][dim] = object_points[dim,:].min()
object_bounding_box[1][dim] = object_points[dim,:].max()
object_bounding_box_dims[dim] = object_bounding_box[1][dim] - object_bounding_box[0][dim]
#now shift the object frame and bounding box so that the center is the center of the object
offset_mat = scipy.mat(scipy.identity(4))
for i in range(3):
offset = object_bounding_box[1][i] - object_bounding_box_dims[i]/2. #center
object_bounding_box[0][i] -= offset #mins
object_bounding_box[1][i] -= offset #maxes
object_points[i, :] -= offset
offset_mat[i,3] = offset
rotmat = rotmat * offset_mat
#record the transforms from object frame to base frame and to the original cluster frame,
#broadcast the object frame to tf, and draw the object frame in rviz
unshift_mean = scipy.identity(4)
for i in range(3):
unshift_mean[i,3] = xyz_mean[i]
object_to_base_frame = unshift_mean*rotmat
object_to_cluster_frame = cluster_to_base_frame**-1 * object_to_base_frame
#broadcast the object frame to tf
(object_frame_pos, object_frame_quat) = mat_to_pos_and_quat(object_to_cluster_frame)
self.tf_broadcaster.sendTransform(object_frame_pos, object_frame_quat, rospy.Time.now(), "object_frame", cluster_frame)
return (object_points, object_bounding_box_dims, object_bounding_box, object_to_base_frame, object_to_cluster_frame)
def IsingHamiltonian_old(n, h, J, g):
### Construct Hamiltonian ###
Z = sp.matrix([[1,0],[0,-1]])
X = sp.matrix([[0,1],[1,0]])
I = sp.identity(2)
alpha = sp.zeros((2**n,2**n))
beta = sp.zeros((2**n,2**n))
delta = sp.zeros((2**n,2**n))
matrices = []
# Calculate alpha
for i in range(0,n):
for m in range(0,n-1):
matrices.append(I)
matrices.insert(i, Z)
temp = matrices[0]
matrices.pop(0)
while (len(matrices) != 0):
temp = sp.kron(temp, matrices[0])
matrices.pop(0)
alpha = alpha + temp*h[i]
temp = 0
# Calculate beta
for i in range(0,n):
for j in range(0,n):
if (i != j):
for m in range(0,n-2):
matrices.append(I)
matrices.insert(i, Z)
matrices.insert(j, Z)
temp = matrices[0]
matrices.pop(0)
while (len(matrices) != 0):
temp = sp.kron(temp, matrices[0])
matrices.pop(0)
beta = beta + temp*J[i,j]
beta = beta + g*sp.identity(2**n)
temp = 0
# Calculate delta
for i in range(0,n) :
for m in range(0,n-1):
matrices.append(I)
matrices.insert(i, X)
temp = matrices[0]
matrices.pop(0)
while (len(matrices) != 0):
temp = sp.kron(temp, matrices[0])
matrices.pop(0)
delta += temp
return [alpha, beta, delta]
def pleiopred_inf(beta_hats1,
beta_hats2,
pr_sig1,
pr_sig2,
rho=0,
n1=1000,
n2=1000,
ref_ld_mats1=None,
ref_ld_mats2=None,
ld_window_size=100):
num_betas = len(beta_hats1)
post_betas1 = sp.empty(num_betas)
post_betas2 = sp.empty(num_betas)
m = len(beta_hats1)
for i, wi in enumerate(range(0, num_betas, ld_window_size)):
start_i = wi
stop_i = min(num_betas, wi + ld_window_size)
curr_window_size = stop_i - start_i
bhats = beta_hats1[start_i:stop_i]
ghats = beta_hats2[start_i:stop_i]
S11 = sp.diag(pr_sig1[start_i:stop_i])
S12 = sp.diag(
rho * np.sqrt(pr_sig1[start_i:stop_i] * pr_sig2[start_i:stop_i]))
S22 = sp.diag(pr_sig2[start_i:stop_i])
D1 = ref_ld_mats1[i]
D2 = ref_ld_mats2[i]
S = np.concatenate((np.concatenate(
(S11, S12), axis=1), np.concatenate((S12, S22), axis=1)),
axis=0)
SD = np.concatenate(
(np.concatenate(
(n1 * np.dot(S11, D1), n2 * np.dot(S12, D2)), axis=1),
np.concatenate(
(n1 * np.dot(S12, D1), n2 * np.dot(S22, D2)), axis=1)),
axis=0)
A = sp.identity(2 * curr_window_size) + SD
A_inv = linalg.pinv(A)
W = sp.identity(2 * curr_window_size) - sp.dot(SD, A_inv)
Sbeta_hats = sp.concatenate(
(n1 * sp.dot(S11, bhats) + n2 * sp.dot(S12, ghats),
n1 * sp.dot(S12, bhats) + n2 * sp.dot(S22, ghats)),
axis=0)
post_both = sp.dot(W, Sbeta_hats)
ll = len(post_both)
post_betas1[start_i:stop_i] = post_both[0:ll / 2]
post_betas2[start_i:stop_i] = post_both[ll / 2:ll]
updated_betas = {'D1': post_betas1, 'D2': post_betas2}
return updated_betas
def measure(self, magneto):
measurementJacobian = sp.zeros((3, 13))
magnetoJacobian = scipy_utils.d_inverse_rotation_d_quaternion_at(
cgkit_to_scipy.convert(self.orientationBody),
cgkit_to_scipy.convert(magneto))
scipy_utils.load_submatrix(measurementJacobian, (0, 6),
magnetoJacobian)
kalmanGain = sp.dot(
sp.dot(self._errorCovariance, measurementJacobian.transpose()),
linalg.inv(
sp.dot(
measurementJacobian,
sp.dot(self._errorCovariance,
measurementJacobian.transpose())) +
self._measurementCovariance))
stateCorrection = sp.dot(
kalmanGain,
(cgkit_to_scipy.convert(magneto - self._predictMagnetoBody())))
self.orientationBody = self.orientationBody + quat(
list(stateCorrection[6:10]))
self._errorCovariance = sp.dot(
(sp.identity(13) - sp.dot(kalmanGain, measurementJacobian)),
self._errorCovariance)
def embedTraversal(cloned, obj,n,suffix):
for i in range(len(obj)):
if isinstance(obj[i],Model):
cloned.body += [obj[i]]
elif (isinstance(obj[i],tuple) or isinstance(obj[i],list)) and (
len(obj[i])==2):
V,EV = obj[i]
V = [v+n*[0.0] for v in V]
cloned.body += [(V,EV)]
elif (isinstance(obj[i],tuple) or isinstance(obj[i],list)) and (
len(obj[i])==3):
V,FV,EV = obj[i]
V = [v+n*[0.0] for v in V]
cloned.body += [(V,FV,EV)]
elif isinstance(obj[i],Mat):
mat = obj[i]
d,d = mat.shape
newMat = scipy.identity(d+n*1)
for h in range(d-1):
for k in range(d-1):
newMat[h,k] = mat[h,k]
newMat[h,d-1+n*1] = mat[h,d-1]
cloned.body += [newMat.view(Mat)]
elif isinstance(obj[i],Struct):
newObj = Struct()
newObj.box = hstack((obj[i].box, [n*[0],n*[0]]))
newObj.name = obj[i].name+suffix
newObj.category = obj[i].category
cloned.body += [embedTraversal(newObj, obj[i], n, suffix)]
return cloned
def solve(self,rhs):
"""
Overrides LinearSolver.solve
Result contains (solution,status)
status is always 0, indicating that the method has converged
"""
if not self.built:
N = len(self.point.getState()[0])
Dt = self.point.system.Dt
dt = self.point.system.dt
k = int(Dt/dt)
I = scipy.identity(N)
A = self.point.computeJacobian()
B = I+dt*A[:N,:N]
AA = B
for i in range(k-1):
AA=scipy.dot(AA,B)
Matrix = A # zo blijven extra rijen en kolommen dezelfde als A
Matrix[:N,:N]= I - AA
self.Matrix = Matrix
self.built = True
else:
Matrix=self.Matrix
x=scipy.linalg.solve(Matrix,rhs)
status = 0
return (x,status)
def solve(self, rhs):
"""
Overrides LinearSolver.solve
Result contains (solution,status)
status is always 0, indicating that the method has converged
"""
if not self.built:
N = len(self.point.getState()[0])
Dt = self.point.system.Dt
dt = self.point.system.dt
k = int(Dt / dt)
I = scipy.identity(N)
A = self.point.computeJacobian()
B = I + dt * A[:N, :N]
AA = B
for i in range(k - 1):
AA = scipy.dot(AA, B)
Matrix = A # zo blijven extra rijen en kolommen dezelfde als A
Matrix[:N, :N] = I - AA
self.Matrix = Matrix
self.built = True
else:
Matrix = self.Matrix
x = scipy.linalg.solve(Matrix, rhs)
status = 0
return (x, status)
def test_correlated_scatter(self) :
n = 50
r = (sp.arange(n, dtype=float) + 10.0*n)/10.0*n
data = sp.sin(sp.arange(n)) * r
amp = 25.0
theory = data/amp
# Generate correlated matrix.
C = random.rand(n, n) # [0, 1)
# Raise to high power to make values near 1 rare.
C = (C**10) * 0.2
C = (C + C.T)/2.0
C += sp.identity(n)
C *= r[:, None]/2.0
C *= r[None, :]/2.0
# Generate random numbers in diagonal frame.
h, R = linalg.eigh(C)
self.assertTrue(sp.alltrue(h>0))
rand_vals = random.normal(size=n)*sp.sqrt(h)
# Rotate back.
data += sp.dot(R.T, rand_vals)
out = utils.ampfit(data, C, theory)
a, s = out['amp'], out['error']
self.assertTrue(sp.allclose(a, amp, atol=5.0*s, rtol=0))
# Expect the next line to fail 1/100 trials.
self.assertFalse(sp.allclose(a, amp, atol=0.01*s, rtol=0))
def test_uncorrelated_noscatter(self):
data = sp.arange(10, dtype=float)
theory = data/2.0
C = sp.identity(10)
out = utils.ampfit(data, C, theory)
a, s = out['amp'], out['error']
self.assertAlmostEqual(a, 2)
def inv_rot_3D(x, y, z, rot="z", angles=[ma.pi]):
""" Rotates a set of vectors by any number of Euler angles, in the reverse direction.
input is as rot_3D, using the inverse order for rotations and angles, but leaving
the angles un-flipped - the matrix inverses will take care of that.
rot is a string of x's, y's and z's describing the order of rotations, left-to-right,
while angles is the corresponding angle (in radians) for each rotation"""
# Build rotation matrix
R = sc.identity(3)
for i in range(len(angles)):
t = angles[i]
if rot[i] == "x":
Rx = LA.inv(Rot_x(t))
R = Rx * R
continue
elif rot[i] == "y":
Ry = LA.inv(Rot_y(t))
R = Ry * R
continue
elif rot[i] == "z":
Rz = LA.inv(Rot_z(t))
R = Rz * R
continue
else:
print "!!! - Invalid rotation axis, {0}".format(rot(i))
# Now do the rotations
if type(x) != type(sc.zeros(1)):
out = R * sc.matrix([[x], [y], [z]])
x, y, z = float(out[0]), float(out[1]), float(out[2])
else:
for i in range(len(x)):
out = R * sc.matrix([[x[i]], [y[i]], [z[i]]])
x[i], y[i], z[i] = float(out[0]), float(out[1]), float(out[2])
return x, y, z
""" MAYBE MAKE THIS ONE TAKE SAME INPUTS AS rot_3D TO MAKE THINGS EASIER """
def evalfREML(logDelta,MCtrials,X,Y,beta_rand,e_rand_unscaled): (N,M) = X.shape delta = sp.exp(logDelta) y_rand = sp.empty((N,MCtrials)) H_inv_y_rand = sp.empty((N,MCtrials)) beta_hat_rand = sp.empty((M,MCtrials)) e_hat_rand = sp.empty((N,MCtrials)) ## Calculating the matrix H=X%*%t(X)/M + delta*I_N H = sp.dot(X,X.T)/M + delta*sp.identity(N) x0 = sp.zeros(N) for t in range(0,MCtrials): ## build random phenotypes using pre-generated components y_rand[:,t] = sp.dot(X,beta_rand[:,t])+sp.sqrt(delta)*e_rand_unscaled[:,t] ## compute H^(-1)%*%y.rand[,t] by the aid of conjugate gradient iteration H_inv_y_rand[:,t] = conjugateGradientSolve(A=H,x0=x0,b=y_rand[:,t]) ## compute BLUP estimated SNP effect sizes and residuals beta_hat_rand[:,t] = 1/M*sp.dot(X.T,H_inv_y_rand[:,t]) e_hat_rand[:,t] = delta*H_inv_y_rand[:,t] ## compute BLUP estimated SNP effect sizes and residuals for real phenotypes H_inv_y_data = conjugateGradientSolve(A=H,x0=x0,b=Y) beta_hat_data = 1/M*sp.dot(X.T,H_inv_y_data) e_hat_data = delta*H_inv_y_data ## evaluate f_REML f = sp.log((sp.sum(beta_hat_data**2)/sp.sum(e_hat_data**2))/(sp.sum(beta_hat_rand**2)/sp.sum(e_hat_rand**2))) return(f)
def update(self, measuredState):
#Compte the residual between measurement and prediction
self.prefitResidual = measuredState - dot(
[self.H, self.predictedState])
#Compute the Klaman gain
intermediate = sp.linalg.inv(self.R +
quadratic_form(self.H, self.predictedP))
self.Kt = dot([self.predictedP, self.H.T, intermediate])
#Update the state
self.state = self.predictedState + dot([self.Kt, self.prefitResidual])
#Update covariance matrix
self.P = quadratic_form(\
sp.identity(self.Kt.shape[0]) - dot([self.Kt,self.H]), self.predictedP)\
+ quadratic_form(self.Kt, self.R)
#Compute the postfit residual to see how well we are doing
self.postfitResidual = measuredState - dot([self.H, self.state])
#Store the results
self.append_data()
self.data.prx.append(self.prefitResidual[0])
self.data.pry.append(self.prefitResidual[1])
def AlphaBetaCoeffs_old(n, a, b):
" Construct the alpha and beta coefficient matrices. "
Z = sp.matrix([[1,0],[0,-1]])
I = sp.identity(2)
alpha = sp.zeros((2**n,2**n))
beta = sp.zeros((2**n,2**n))
m1 = []
m2 = []
for i in range(0,n):
for m in range(0,n-1): m1.append(I)
m1.insert(i, Z)
temp1 = m1[0]
m1.pop(0)
while (len(m1) != 0):
temp1 = sp.kron(temp1, m1[0])
m1.pop(0)
alpha += temp1*a[i]
for j in range(i+1, n):
for m in range(0, n-2): m2.append(I)
m2.insert(i, Z)
m2.insert(j, Z)
temp2 = m2[0]
m2.pop(0)
while (len(m2) != 0):
temp2 = sp.kron(temp2, m2[0])
m2.pop(0)
beta += (temp2)*b[i,j]
return [alpha, beta]
def computeProjectionVectors( self, P, L, U ) : eK = matrix( identity( self.dim, float64 )[ 0: ,( self.dim - 1 ) ] ).T U = matrix(U, float64) U[ self.dim - 1, self.dim - 1 ] = 1.0 # Sergio: I added this exception because in rare cases, the matrix # U is singular, which gives rise to a LinAlgError. try: x1 = matrix( solve( U, eK ), float64 ) except LinAlgError: print "Matrix U was singular, so we input a fake x1\n" print "U: ", U x1 = matrix(ones(self.dim)) #print "x1", x1 del U LT = matrix( L, float64, copy=False ).T PT = matrix( P, float64, copy=False ).T x2 = matrix( solve( LT*PT, eK ), float64 ) del L del P del LT del PT del eK return ( x1, x2 )
def embedTraversal(cloned, obj, n, suffix):
for i in range(len(obj)):
if isinstance(obj[i], Model):
cloned.body += [obj[i]]
elif (isinstance(obj[i], tuple) or isinstance(obj[i], list)) and (len(
obj[i]) == 2):
V, EV = obj[i]
V = [v + n * [0.0] for v in V]
cloned.body += [(V, EV)]
elif (isinstance(obj[i], tuple) or isinstance(obj[i], list)) and (len(
obj[i]) == 3):
V, FV, EV = obj[i]
V = [v + n * [0.0] for v in V]
cloned.body += [(V, FV, EV)]
elif isinstance(obj[i], Mat):
mat = obj[i]
d, d = mat.shape
newMat = scipy.identity(d + n * 1)
for h in range(d - 1):
for k in range(d - 1):
newMat[h, k] = mat[h, k]
newMat[h, d - 1 + n * 1] = mat[h, d - 1]
cloned.body += [newMat.view(Mat)]
elif isinstance(obj[i], Struct):
newObj = Struct()
newObj.box = hstack((obj[i].box, [n * [0], n * [0]]))
newObj.name = obj[i].name + suffix
newObj.category = obj[i].category
cloned.body += [embedTraversal(newObj, obj[i], n, suffix)]
return cloned
def rot_3D(x, y, z, rot="z", angles=[ma.pi]):
""" Rotates a set of vectors by any number of Euler angles.
rot is a string of x's, y's and z's describing the order of rotations, left-to-right,
while angles is the corresponding angle (in radians) for each rotation"""
# Build rotation matrix
R = sc.identity(3)
for i in range(len(angles)):
t = angles[i]
if rot[i] == "x":
Rx = Rot_x(t)
R = Rx * R
continue
elif rot[i] == "y":
Ry = Rot_y(t)
R = Ry * R
continue
elif rot[i] == "z":
Rz = Rot_z(t)
R = Rz * R
continue
else:
print "!!! - Invalid rotation axis, {0}".format(rot(i))
# Now do the rotations
if type(x) != type(sc.zeros(1)):
out = R * sc.matrix([[x], [y], [z]])
x, y, z = float(out[0]), float(out[1]), float(out[2])
else:
for i in range(len(x)):
out = R * sc.matrix([[x[i]], [y[i]], [z[i]]])
x[i], y[i], z[i] = float(out[0]), float(out[1]), float(out[2])
return x, y, z
def GP_covmat(X1, X2, par, typ = 'SE', sigma = None):
'''
Compute covariance matrix with or without white noise for a range of
GP kernels. Currently implemented:
- SE (squared exponential 1D, default)
- SE_ARD (squared exponential with separate length scales for each input dimension)
- M32 (Matern 32, 1D)
- QP (quasi-periodic SE, 1D)
'''
if typ == 'QP':
DD = ssp.distance.cdist(X1, X2, 'euclidean')
K = par[0]**2 * \
scipy.exp(- (scipy.sin(scipy.pi * DD / par[1]))**2 / 2. / par[2]**2 \
- DD**2 / 2. / par[3]**2)
if typ == 'Per':
DD = ssp.distance.cdist(X1, X2, 'euclidean')
K = par[0]**2 * \
scipy.exp(- (scipy.sin(scipy.pi * DD / par[1]))**2 / 2. / par[2]**2)
elif typ == 'M32':
DD = ssp.distance.cdist(X1, X2, 'euclidean')
arg = scipy.sqrt(3) * abs(DD) / par[1]
K = par[0]**2 * (1 + arg) * scipy.exp(- arg)
elif typ == 'SE_ARD':
V = numpy.abs(numpy.matrix( numpy.diag( 1. / numpy.sqrt(2) / par[1:]) ))
D2 = ssp.distance.cdist(X1 * V, X2 * V, 'sqeuclidean')
K = par[0]**2 * numpy.exp( -D2 )
else: # 'SE (radial)'
D2 = ssp.distance.cdist(X1, X2, 'sqeuclidean')
K = par[0]**2 * scipy.exp(- D2 / 2. / par[1]**2)
if sigma != None:
N = X1.shape[0]
K += sigma**2 * scipy.identity(N)
return scipy.matrix(K)
def test_correlated_scatter(self):
n = 50
r = (sp.arange(n, dtype=float) + 10.0 * n) / 10.0 * n
data = sp.sin(sp.arange(n)) * r
amp = 25.0
theory = data / amp
# Generate correlated matrix.
C = random.rand(n, n) # [0, 1)
# Raise to high power to make values near 1 rare.
C = (C**10) * 0.2
C = (C + C.T) / 2.0
C += sp.identity(n)
C *= r[:, None] / 2.0
C *= r[None, :] / 2.0
# Generate random numbers in diagonal frame.
h, R = linalg.eigh(C)
self.assertTrue(sp.alltrue(h > 0))
rand_vals = random.normal(size=n) * sp.sqrt(h)
# Rotate back.
data += sp.dot(R.T, rand_vals)
out = utils.ampfit(data, C, theory)
a, s = out['amp'], out['error']
self.assertTrue(sp.allclose(a, amp, atol=5.0 * s, rtol=0))
# Expect the next line to fail 1/100 trials.
self.assertFalse(sp.allclose(a, amp, atol=0.01 * s, rtol=0))
def __init__(self, respond=None, regressors=None, intercept=False, **args):
"""
:param respond: Dependent time series
:type respond: TimeSeriesFrame<double>
:param regressors: Independent time serieses
:type regressors: TimeSeriesFrame<dobule>
:param intercept: include/exclude intercept
:type intercept: boolean
:param args: reserve for future developement
"""
self.intercept = intercept
self.respond = respond
self.regressors = regressors
self.respond = respond
self.weight = args.get("weight")
self.t, self.n = regressors.size()
if self.intercept:
self.regressors.data = scipy.hstack((scipy.ones(
(self.t, 1)), self.regressors.data))
self.regressors.cheader.insert(0, "Intercept")
self.n = self.n + 1
if self.weight is None:
self.weight = scipy.identity(self.t)
self.X, self.y, self.W = map(
scipy.matrix,
(self.regressors.data, self.respond.data, self.weight))
def __init__(self, f, shape, gradient=None, hessian=None):
"""Solves an optimization problem, except that it doesn't
Arguments:
f -- the function
shape -- Dimension of input argument to function
(if f: ℝⁿ->ℝ then shape=n)
gradient -- the gradient (default to numerical approximation)
hessian -- function returning hessian matrix (default to numerical approximation)
"""
self.f = f
self.shape = shape
if gradient:
self.gradient = gradient
else:
def df(x):
return numpy.array([
(self.f(x + df.h[i] * self.dx / 2.) -
self.f(x - df.h[i] * self.dx / 2.)) / self.dx
for i in xrange(shape)
])
df.h = scipy.identity(self.shape)
self.gradient = df
if hessian:
self.hessian = hessian
else:
self.hessian = self._approx_hess()
def pcg(A, b, x_0, P=None):
if P is None:
P = sp.identity(A.shape[0])
P_inv = spla.inv(P)
print('starting')
r_0 = b - A @ x_0
r_prev = r = r_0
r_prod = (r.T @ P_inv @ (r))
x = x_0
p = P_inv @ r_0
k = 0
while True:
k += 1
Ap = A @ p
alpha = (r_prod / (p.T @ Ap)).item()
x = x + alpha*p # x_k initially stores x_{k-1}
r_prev = r
r_prev_prod = r_prod
r = r - alpha * Ap
r_prod = (r.T @ P_inv @ (r))
beta = (r_prod / r_prev_prod).item()
p = P_inv @ (r) + beta * p
print(k, spla.norm(r))
if spla.norm(r) <= 10**-12:
print('terminating from residual')
break
print(x)
print(A @ x)
return x
def argmin(self, start=None, tolerance=0.0001, maxit=100, stepsize=1.0):
xold = start if start is not None else scipy.zeros(self.shape)
# Initial hessian inverse guess
B = scipy.identity(self.shape)
grad = (tolerance + 1) * scipy.ones(self.shape)
for it in xrange(maxit):
if (it != 0 and numpy.linalg.norm(grad) < tolerance): break
grad = self.gradient(xold)
# Search direction
s = numpy.dot(B, -1 * grad)
# Use scipy line search until implemented here
a = scipy.optimize.linesearch.line_search_wolfe2(
self.f, self.gradient, xold, s, grad)
s = a[0] * s
xnew = xold + s
if numpy.isnan(self.f(xnew)): break
y = self.gradient(xnew) - grad
ytb = numpy.dot(y, B)
by = numpy.dot(B, y)
B = B + numpy.outer(s, s) / numpy.dot(y, s) - numpy.outer(
by, ytb) / numpy.dot(ytb, y)
xold = xnew
return xnew
def kalman_filter(b,
V,
Phi,
y,
X,
sigma,
Sigma,
switch = 0,
D = None,
d = None,
G = None,
a = None,
c = None):
r"""
.. math::
:nowrap:
\begin{eqnarray*}
\beta_{t|t-1} = \Phi \: \beta_{t-1|t-1}\\
V_{t|t-1} = \Phi V_{t-1|t-1} \Phi ^T + \Sigma \\
e_t = y_t - X_t \beta_{t|t-1}\\
K_t = V_{t|t-1} X_t^T (\sigma + X_t V_{t|t-1} X_t )^{-1}\\
\beta_{t|t} = \beta_{t|t-1} + K_t e_t\\
V_{t|t} = (I - K_t X_t^T) V_{t|t-1}\\
\end{eqnarray*}
"""
n = scipy.shape(X)[1]
beta = scipy.empty(scipy.shape(X))
n = len(b)
if D is None:
D = scipy.ones((1, n))
if d is None:
d = scipy.matrix(1.)
if G is None:
G = scipy.identity(n)
if a is None:
a = scipy.zeros((n, 1))
if c is None:
c = scipy.ones((n, 1))
# import code; code.interact(local=locals())
(b, V) = kalman_predict(b, V, Phi, Sigma)
for i in xrange(len(X)):
beta[i] = scipy.array(b).T
(b, V, e, K) = kalman_upd(b,
V,
y[i],
X[i],
sigma,
Sigma,
switch,
D,
d,
G,
a,
c)
(b, V) = kalman_predict(b, V, Phi, Sigma)
return beta
def test():
'''a = mx('1,2,3;0,4,5;9,0,8')
print a.shape
print a.I
print mx.A'''
a = mx('1,2;3,2')
b = mx('1,0,0;0,1,1')
c = mx('1,0;0,1;1,0')
# print c*(a*b)
print a.shape[0]
ai = sp.identity(a.shape[1])
# aif = ai.flat
ail = ai.tolist()
newit = ail[0]
ail.append(newit)
print ail #.repeat(2,1)#.reshape((2,))
ailm = sp.asmatrix(ail)
print ailm
# c = mx('1,2;0,4;9,2')
# d = mx('1,2,0;4,9,2')
# print a*b
#每加入一个节点，得一A同型+1单位阵，，修改Isi+=1，与A相乘得新输出矩阵
linec = 0
def decompose( matrix ): # Returns the decomposition of a matrix A where # # Q.A.Q = P.L.U # # P.L.U is the factoring of Q.A.Q such that L is a lower triangular matrix with 1's # on the diagonal and U is an upper triangular matrix; P is the permutation (row-swapping # operations) required for this procedure. The permutation matrix Q is chosen such that # the last element of U is its smallest diagnoal element. If A has a zero eigenvalue, # then U's last element will be zero. dim = matrix.shape[ 0 ] # first decomposition ( P, L, U ) = lu( matrix ) # detect the smallest element of U smallestIndex = findsmallestdiag( U ) smallest = U[ smallestIndex, smallestIndex ] #show( matrix, "M" ) #show( U, "U" ) #print "Smallest element is %f at %d" % ( smallest, smallestIndex ) # is the permutation Q not just the identity matrix? Q = identity( dim ) if smallestIndex+1 != dim : # trick: exchange row 'smallestIndex' with row 'dim-1' of the identity matrix swaprow( Q, smallestIndex, dim-1 ) return ( P, L, U, Q )
def process_collision_geometry_for_table(self,
firsttable,
additional_tables=[]):
table_object = CollisionObject()
table_object.operation.operation = CollisionObjectOperation.ADD
table_object.header.frame_id = firsttable.pose.header.frame_id
table_object.header.stamp = rospy.Time.now()
#create a box for each table
for table in [
firsttable,
] + additional_tables:
object = Shape()
object.type = Shape.BOX
object.dimensions.append(math.fabs(table.x_max - table.x_min))
object.dimensions.append(math.fabs(table.y_max - table.y_min))
object.dimensions.append(0.01)
table_object.shapes.append(object)
#set the origin of the table object in the middle of the firsttable
table_mat = self.pose_to_mat(firsttable.pose.pose)
table_offset = scipy.matrix([
(firsttable.x_min + firsttable.x_max) / 2.0,
(firsttable.y_min + firsttable.y_max) / 2.0, 0.0
]).T
table_offset_mat = scipy.matrix(scipy.identity(4))
table_offset_mat[0:3, 3] = table_offset
table_center = table_mat * table_offset_mat
origin_pose = self.mat_to_pose(table_center)
table_object.poses.append(origin_pose)
table_object.id = "table"
self.object_in_map_pub.publish(table_object)
def process_collision_geometry_for_table(self, firsttable, additional_tables = []):
table_object = CollisionObject()
table_object.operation.operation = CollisionObjectOperation.ADD
table_object.header.frame_id = firsttable.pose.header.frame_id
table_object.header.stamp = rospy.Time.now()
#create a box for each table
for table in [firsttable,]+additional_tables:
object = Shape()
object.type = Shape.BOX;
object.dimensions.append(math.fabs(table.x_max-table.x_min))
object.dimensions.append(math.fabs(table.y_max-table.y_min))
object.dimensions.append(0.01)
table_object.shapes.append(object)
#set the origin of the table object in the middle of the firsttable
table_mat = self.pose_to_mat(firsttable.pose.pose)
table_offset = scipy.matrix([(firsttable.x_min + firsttable.x_max)/2.0, (firsttable.y_min + firsttable.y_max)/2.0, 0.0]).T
table_offset_mat = scipy.matrix(scipy.identity(4))
table_offset_mat[0:3,3] = table_offset
table_center = table_mat * table_offset_mat
origin_pose = self.mat_to_pose(table_center)
table_object.poses.append(origin_pose)
table_object.id = "table"
self.object_in_map_pub.publish(table_object)
def test_uncorrelated_noscatter(self):
data = sp.arange(10, dtype=float)
theory = data / 2.0
C = sp.identity(10)
out = utils.ampfit(data, C, theory)
a, s = out['amp'], out['error']
self.assertAlmostEqual(a, 2)
def argmin(self,start=None,tolerance=0.0001,maxit=100,stepsize=1.0):
xold = start if start is not None else scipy.zeros(self.shape)
# Initial hessian inverse guess
B = scipy.identity(self.shape)
grad=(tolerance+1)*scipy.ones(self.shape)
for it in xrange(maxit):
if (it != 0 and numpy.linalg.norm(grad)<tolerance): break
grad = self.gradient(xold)
# Search direction
s = numpy.dot(B,-1*grad)
# Use scipy line search until implemented here
a=scipy.optimize.linesearch.line_search_wolfe2(
self.f,
self.gradient,
xold,
s,
grad
)
s = a[0] * s
xnew = xold + s
if numpy.isnan(self.f(xnew)): break
y = self.gradient(xnew) -grad
ytb = numpy.dot(y,B)
by = numpy.dot(B,y)
B = B + numpy.outer(s,s)/numpy.dot(y,s) - numpy.outer(by,ytb)/numpy.dot(ytb,y)
xold = xnew
return xnew
def computeProjectionVectors(self, P, L, U):
eK = matrix(identity(self.dim, float64)[0:, (self.dim - 1)]).T
U = matrix(U, float64)
U[self.dim - 1, self.dim - 1] = 1.0
# Sergio: I added this exception because in rare cases, the matrix
# U is singular, which gives rise to a LinAlgError.
try:
x1 = matrix(solve(U, eK), float64)
except LinAlgError:
print "Matrix U was singular, so we input a fake x1\n"
print "U: ", U
x1 = matrix(ones(self.dim))
#print "x1", x1
del U
LT = matrix(L, float64, copy=False).T
PT = matrix(P, float64, copy=False).T
x2 = matrix(solve(LT * PT, eK), float64)
del L
del P
del LT
del PT
del eK
return (x1, x2)
def DfN(x, N, l): # Jacobian for second test case
J = scipy.identity(N) # Initialize as N-by-N array
S = sum(x) # Compute sum
for i in range(0, N): # Assign values
J[i, :] = J[i, :] + (i + 1.0) * l * math.sin(
(i + 1.0) * S) * math.exp(l * math.cos(
(i + 1.0) * S)) * scipy.ones((1, N))
return J
def generate_gaussians(k):
"""Generate k iid spherical k-dim Gaussians g_1, ..., g_k"""
mean = [0 for x in range(0, k)]
covariance = sp.matrix(sp.identity(k), copy=False)
g = []
for i in range(0, k):
tmp = sp.random.multivariate_normal(mean, covariance)
g.append(tmp)
return g
def ellipsoid(R=np.array([[2, 0, 0],[0, 1, 0],[0, 0, 1] ]),position=(0,0,0),thetares=20,phires=20,color=(0,0,1),opacity=1,tessel=0):
''' Create a ellipsoid actor.
Stretch a unit sphere to make it an ellipsoid under a 3x3 translation matrix R
R=sp.array([[2, 0, 0],
[0, 1, 0],
[0, 0, 1] ])
'''
Mat=sp.identity(4)
Mat[0:3,0:3]=R
'''
Mat=sp.array([[2, 0, 0, 0],
[0, 1, 0, 0],
[0, 0, 1, 0],
[0, 0, 0, 1] ])
'''
mat=vtk.vtkMatrix4x4()
for i in sp.ndindex(4,4):
mat.SetElement(i[0],i[1],Mat[i])
radius=1
sphere = vtk.vtkSphereSource()
sphere.SetRadius(radius)
sphere.SetLatLongTessellation(tessel)
sphere.SetThetaResolution(thetares)
sphere.SetPhiResolution(phires)
trans=vtk.vtkTransform()
trans.Identity()
#trans.Scale(0.3,0.9,0.2)
trans.SetMatrix(mat)
trans.Update()
transf=vtk.vtkTransformPolyDataFilter()
transf.SetTransform(trans)
transf.SetInput(sphere.GetOutput())
transf.Update()
spherem = vtk.vtkPolyDataMapper()
spherem.SetInput(transf.GetOutput())
spherea = vtk.vtkActor()
spherea.SetMapper(spherem)
spherea.SetPosition(position)
spherea.GetProperty().SetColor(color)
spherea.GetProperty().SetOpacity(opacity)
#spherea.GetProperty().SetRepresentationToWireframe()
return spherea
def get_algebraic_page_rank(transition_matrix, dumping_factor=0.85):
"""Computes the page ranks in an algebraic way"""
n = transition_matrix.shape[0]
m_a = transition_matrix
d = dumping_factor
ls = la.inv(sp.identity(n) - d*m_a)
rs = sp.matrix([(1-d)/n]*n).reshape(n, 1)
return sp.dot(ls, rs)
def get_transform(tf_listener, frame1, frame2):
temp_header = Header()
temp_header.frame_id = frame1
temp_header.stamp = rospy.Time(0)
try:
frame1_to_frame2 = tf_listener.asMatrix(frame2, temp_header)
except:
rospy.logerr("tf transform was not there between %s and %s"%(frame1, frame2))
return scipy.matrix(scipy.identity(4))
return scipy.matrix(frame1_to_frame2)
def kalman_upd(beta,
V,
y,
X,
s,
S,
switch = 0,
D = None,
d = None,
G = None,
a = None,
b = None):
r"""
This is the update step of kalman filter.
.. math::
:nowrap:
\begin{eqnarray*}
e_t &=& y_t - X_t \beta_{t|t-1} \\
K_t &=& V_{t|t-1} X_t^T (\sigma + X_t V_{t|t-1} X_t )^{-1}\\
\beta_{t|t} &=& \beta_{t|t-1} + K_t e_t\\
V_{t|t} &=& (I - K_t X_t^T) V_{t|t-1}\\
\end{eqnarray*}
"""
e = y - X * beta
K = V * X.T * ( s + X * V * X.T).I
beta = beta + K * e
if switch == 1:
D = scipy.matrix(D)
d = scipy.matrix(d)
if DEBUG: print "beta: ", beta
beta = beta - S * D.T * ( D * S * D.T).I * ( D * beta - d)
if DEBUG: print "beta: ", beta
elif switch == 2:
G = scipy.matrix(G)
a = scipy.matrix(a)
b = scipy.matrix(b)
n = len(beta)
P = 2* V.I
q = -2 * V.I.T * beta
bigG = scipy.empty((2*n, n))
h = scipy.empty((2*n, 1))
bigG[:n, :] = -G
bigG[n:, :] = G
h[:n, :] = -a
h[n:, :] = b
paraset = map(cvxopt.matrix, (P, q, bigG, h, D, d))
beta = qp(*paraset)['x']
temp = K*X
V = (scipy.identity(temp.shape[0]) - temp) * V
return (beta, V, e, K)
def diffmat(x):
n= sp.size(x)
e= sp.ones((n,1))
Xdiff= sp.outer(x,e)-sp.outer(e,x)+sp.identity(n)
xprod= -reduce(mul, Xdiff)
W= sp.outer(1/xprod,e)
D= W/sp.multiply(W.T,Xdiff)
d= 1-sum(D)
for k in range(0,n):
D[k,k] = d[k]
return -D.T
def my_matrixinv(mat):
width = mat.shape[0]
det = np.linalg.det
if det == 0 :
print "det = 0; matrix not invertable"
identity = sp.identity(width)
inv = sp.linalg.solve(mat,identity)
return inv
def diffmat(x): # x is an ordered array of grid points n = sp.size(x) e = sp.ones((n,1)) Xdiff = sp.outer(x,e)-sp.outer(e,x)+sp.identity(n) xprod = -reduce(mul,Xdiff) # product of rows W = sp.outer(1/xprod,e) D = W/sp.multiply(W.T,Xdiff) d = 1-sum(D) for k in range(0,n): # Set diagonal elements D[k,k] = d[k] return -D.T
def __init__(self,
respond = None,
regressors = None,
intercept = False,
lamb = 1.,
W1 = None,
W2 = None,
Phi = None,
D = None,
d = scipy.matrix(1.00),
G = None,
a = None,
b = None):
"""Input: paras where they are expected to be tuple or dictionary"""
ICRegression.__init__(self,
respond,
regressors,
intercept,
D,
d,
G,
a,
b)
if W1 is not None:
self.W1 = W1
else:
self.W1 = 1.
if W2 is None:
self.W2 = scipy.identity(self.n)
else:
self.W2 = W2
if Phi is None:
self.Phi = scipy.identity(self.n)
else:
self.Phi = Phi
self.lamb = lamb
def __init__(self, R, size):
# cheat for now, use expm
self.R = R
w, vr = linalg.eig(R)
self.size = size
self.Eigvals = scipy.array(w, dtype=scipy.float64)
self.S = scipy.identity(self.size)
self.T = vr
self.T_inv = linalg.inv(vr)
self.Q_of_t_cache = {} # t --> Q(t)
def argmin(self,start=None,tolerance=0.0001,maxit=100,call=None):
"""
Find a minimum
start: starting point, default 0
tolerance: break when ||gradient|| is less than
maxit: iteration limit
call: function to call at end of each iteration, is passed locals() as argument
"""
xold = start if start is not None else scipy.zeros(self.shape)
B = scipy.identity(self.shape)
for it in xrange(maxit):
grad = self.gradient(xold)
if (it != 0 and numpy.linalg.norm(grad)<tolerance): break
s = numpy.dot(B,-1*grad)
# Use scipy line search until implemented here
a=scipy.optimize.linesearch.line_search_wolfe2(
self.f,
self.gradient,
xold,
s,
grad
)
s = a[0] * s
xnew = xold + s
# Break on nan
if numpy.isnan(xnew).any():
xnew=xold
break
y = self.gradient(xnew) - grad
# Update inverse hessian approximation
# Using Sherman-Morisson updating
ytb = numpy.dot(y,B)
ys = numpy.dot(s,y)
ss = numpy.outer(s,s)
by = numpy.dot(B,y)
bys = numpy.outer(by,s)
B = B + (1 + numpy.dot(ytb,y)/ys)*ss/ys - (bys+ numpy.transpose(bys))/ys
xold = xnew
if call:
call(locals())
return xnew
def __init__(self, A=_A, H=_H, R=_R, Q = _Q):
dim = A.shape[0]
self.A = A # Transition matrix
self.H = H # Extraction matrix
self.R = R # Covariance matrix, measurement noise
self.Q = Q # Covariance matrix, process noise
self.x_mu_prior = sp.zeros([dim, 1])
self.x_mu = sp.zeros([dim, 1])
self.P_prior = sp.zeros([dim, dim])
self.P = sp.zeros([dim, dim])
self.P[-1][-1] = .001
self.I = sp.identity(dim)
def calcDistanceMatrix(nDimPoints,
distFunc=lambda deltaPoint: sqrt(sum(deltaPoint[d]**2 for d in xrange(len(deltaPoint))))):
nDimPoints = array(nDimPoints)
dim = len(nDimPoints[0])
delta = [None]*dim
for d in xrange(dim):
data = nDimPoints[:,d]
delta[d] = data - reshape(data,(len(data),1)) # computes all possible combinations
dist = distFunc(delta)
dist = dist + identity(len(data))*dist.max() # eliminate self matching
# dist is the matrix of distances from one coordinate to any other
return dist
def diffmat(x):
"""Compute the differentiation matrix for x is an ordered array
of grid points. Uses barycentric formulas for stability.
"""
n = sp.size(x)
e = sp.ones((n,1))
Xdiff = sp.outer(x,e)-sp.outer(e,x)+sp.identity(n)
xprod = -reduce(mul,Xdiff) # product of rows
W = sp.outer(1/xprod,e)
D = W/sp.multiply(W.T,Xdiff)
d = 1-sum(D)
for k in range(0,n): # Set diagonal elements
D[k,k] = d[k]
return -D.T
def generate_data(N):
'''
Generate N data points form a 2D Gaussian Gaussian distribution
with mean [1, 2]
Usage: x = generate_data(N)
Returns: x : a 2xN array
Instructions: Use sp.random.mutivariate_normal
'''
mean = [1, 2]
cov = sp.identity(2)
return sp.random.multivariate_normal(mean, cov, (N)).T