def batch_get_sol_params(x_nd, K_nn, bend_coefs, rot_coef=np.r_[1e-4, 1e-4, 1e-1]):
n, d = x_nd.shape
x_gpu = gpuarray.to_gpu(x_nd)
H_arr_gpu = []
for b in bend_coefs:
cur_offset = np.zeros((1 + d + n, 1 + d + n), np.float32)
cur_offset[d+1:, d+1:] = b * K_nn
cur_offset[1:d+1, 1:d+1] = np.diag(rot_coef)
H_arr_gpu.append(gpuarray.to_gpu(cur_offset))
H_ptr_gpu = get_gpu_ptrs(H_arr_gpu)
A = np.r_[np.zeros((d+1,d+1)), np.c_[np.ones((n,1)), x_nd]].T
n_cnts = A.shape[0]
_u,_s,_vh = np.linalg.svd(A.T)
N = _u[:,n_cnts:]
F = np.zeros((n + d + 1, d), np.float32)
F[1:d+1, :d] -= np.diag(rot_coef)
Q = np.c_[np.ones((n,1)), x_nd, K_nn].astype(np.float32)
F = F.astype(np.float32)
N = N.astype(np.float32)
Q_gpu = gpuarray.to_gpu(Q)
Q_arr_gpu = [Q_gpu for _ in range(len(bend_coefs))]
Q_ptr_gpu = get_gpu_ptrs(Q_arr_gpu)
F_gpu = gpuarray.to_gpu(F)
F_arr_gpu = [F_gpu for _ in range(len(bend_coefs))]
F_ptr_gpu = get_gpu_ptrs(F_arr_gpu)
N_gpu = gpuarray.to_gpu(N)
N_arr_gpu = [N_gpu for _ in range(len(bend_coefs))]
N_ptr_gpu = get_gpu_ptrs(N_arr_gpu)
dot_batch_nocheck(Q_arr_gpu, Q_arr_gpu, H_arr_gpu,
Q_ptr_gpu, Q_ptr_gpu, H_ptr_gpu,
transa = 'T')
# N'HN
NHN_arr_gpu, NHN_ptr_gpu = m_dot_batch((N_arr_gpu, N_ptr_gpu, 'T'),
(H_arr_gpu, H_ptr_gpu, 'N'),
(N_arr_gpu, N_ptr_gpu, 'N'))
iH_arr = []
for NHN in NHN_arr_gpu:
iH_arr.append(scipy.linalg.inv(NHN.get()).copy())
iH_arr_gpu = [gpuarray.to_gpu_async(iH) for iH in iH_arr]
iH_ptr_gpu = get_gpu_ptrs(iH_arr_gpu)
proj_mats = m_dot_batch((N_arr_gpu, N_ptr_gpu, 'N'),
(iH_arr_gpu, iH_ptr_gpu, 'N'),
(N_arr_gpu, N_ptr_gpu, 'T'),
(Q_arr_gpu, Q_ptr_gpu, 'T'))
offset_mats = m_dot_batch((N_arr_gpu, N_ptr_gpu, 'N'),
(iH_arr_gpu, iH_ptr_gpu, 'N'),
(N_arr_gpu, N_ptr_gpu, 'T'),
(F_arr_gpu, F_ptr_gpu, 'N'))
return proj_mats, offset_mats
def get_solver(self, x_na, K_nn, bend_coefs, rot_coef=np.r_[1e-4, 1e-4, 1e-1]):
n,d = x_na.shape
assert len(bend_coefs) <= len(self.bend_coefs)
assert n <= self.max_N
if not self.cur_solver is None:
self.cur_solver.valid = False
Q = np.c_[np.ones((n, 1)), x_na, K_nn]
A = np.r_[np.zeros((d+1, d+1)), np.c_[np.ones((n, 1)), x_na]].T
R = np.zeros((n+d+1, d))
R[1:d+1, :d] = np.diag(rot_coef)
n_cnts = A.shape[0]
_u,_s,_vh = np.linalg.svd(A.T)
N = _u[:,n_cnts:].copy()
N_gpu = self.N_gpu[:(n+d+1)*n].reshape(n+d+1, n)
N_gpu.set_async(N)
QN = Q.dot(N)
QN_gpu = self.QN_gpu[:n*n].reshape(n, n)
QN_gpu.set_async(QN)
WQN_gpu = self.WQN_gpu[:n*n].reshape(n, n)
NHN_gpu = self.NHN_gpu[:n*n].reshape(n, n)
NR = N.T.dot(R)
N_arr_gpu = []
O_gpu = []
ON_gpu = []
NON_gpu = []
for i, b in enumerate(bend_coefs):
O_b = np.zeros((n+d+1, n+d+1), np.float64)
O_b[d+1:, d+1:] += b * K_nn
O_b[1:d+1, 1:d+1] += np.diag(rot_coef)
offset = i * (n+d+1)*(n+d+1)
O_gpu.append(self.O_gpu[offset:offset + (n+d+1)*(n+d+1)].reshape(n+d+1, n+d+1))
O_gpu[-1].set(O_b)
offset = i * (n)*(n+d+1)
ON_gpu.append(self.ON_gpu[offset:offset + n*(n+d+1)].reshape(n+d+1, n))
offset = i * n * n
NON_gpu.append(self.NON_gpu[offset:offset + n*n].reshape(n, n))
N_arr_gpu.append(N_gpu)
O_ptrs = get_gpu_ptrs(O_gpu)
ON_ptrs = get_gpu_ptrs(ON_gpu)
NON_ptrs = get_gpu_ptrs(NON_gpu)
N_ptrs = get_gpu_ptrs(N_arr_gpu)
dot_batch_nocheck(O_gpu, N_arr_gpu, ON_gpu,
O_ptrs, N_ptrs, ON_ptrs,
b = 0)
dot_batch_nocheck(N_arr_gpu, ON_gpu, NON_gpu,
N_ptrs, ON_ptrs, NON_ptrs,
transa='T', b = 0)
NON_gpu = dict(zip(bend_coefs, NON_gpu))
NON = dict([(b, non.get_async()) for b, non in NON_gpu.iteritems()])
self.cur_solver = TPSSolver(bend_coefs, N, QN, NON, NR, x_na, K_nn, rot_coef,
QN_gpu, WQN_gpu, NON_gpu, NHN_gpu)
return self.cur_solver
def check_transform_pts(ctx, i = 0):
import scikits.cuda.linalg as la
n = ctx.dims[i]
w_nd = ctx.w_nd[i].get()[:n]
lin_dd = ctx.lin_dd[i].get()
trans_d = ctx.trans_d[i].get()
k_nn = ctx.kernels[i].get()[:n, :n].reshape(n, n).copy()
x_nd = ctx.pts[i].get()[:n]
xw_nd = ctx.pts_w[i].get()[:n]
_k_gpu = gpuarray.to_gpu(k_nn)
_x_gpu = gpuarray.to_gpu(x_nd)
_lin_gpu = gpuarray.to_gpu(lin_dd)
_trans_gpu = gpuarray.to_gpu(trans_d)
_w_gpu = gpuarray.to_gpu(w_nd)
fill_mat(ctx.pt_w_ptrs, ctx.trans_d_ptrs, ctx.dims_gpu, ctx.N)
dot_batch_nocheck(ctx.pts, ctx.lin_dd, ctx.pts_w,
ctx.pt_ptrs, ctx.lin_dd_ptrs, ctx.pt_w_ptrs)
xw_nd = ctx.pts_w[i].get()[:n]
cpu_xw_nd = np.dot(x_nd, lin_dd) + trans_d[None, :]
# assert np.allclose(xw_nd, cpu_xw_nd)
dot_batch_nocheck(ctx.kernels, ctx.w_nd, ctx.pts_w,
ctx.kernel_ptrs, ctx.w_nd_ptrs, ctx.pt_w_ptrs)
xw_nd = ctx.pts_w[i].get()[:n]
cpu_xw_nd = cpu_xw_nd + np.dot(k_nn, w_nd)
# print "w_nd\n", w_nd[:3], np.max(w_nd)
# print "lin_dd\n", lin_dd[:3]
# print "trans_d\n", trans_d
# print "k_nn\n", k_nn[:3, :3]
# print "x_nd\n", x_nd[:3, :3]
# print cpu_xw_nd[:3]
if not(np.allclose(xw_nd, cpu_xw_nd) ):
print "k dot w_nd is difference on cpu and gpu"
k_dot_w = np.dot(k_nn, w_nd)
k_gpu = [gpuarray.to_gpu(k_nn)]
w_gpu = [gpuarray.to_gpu(w_nd)]
res_gpu = [gpuarray.zeros((n, DATA_DIM), np.float32)]
k_ptrs = get_gpu_ptrs(k_gpu)
w_ptrs = get_gpu_ptrs(w_gpu)
res_ptrs = get_gpu_ptrs(res_gpu)
dot_batch_nocheck(k_gpu, w_gpu, res_gpu, k_ptrs, w_ptrs, res_ptrs)
res = res_gpu[0].get()
single_gpu = la.dot(_k_gpu, _w_gpu)
print "retry success {}".format(np.allclose(res, k_dot_w))
print "gpu success {}".format(np.allclose(single_gpu.get(), res))
assert np.allclose(single_gpu.get(), res)
raw_input("go?")
def update_ptrs(self):
self.tps_param_ptrs = get_gpu_ptrs(self.tps_params)
self.trans_d_ptrs = get_gpu_ptrs(self.trans_d)
self.lin_dd_ptrs = get_gpu_ptrs(self.lin_dd)
self.w_nd_ptrs = get_gpu_ptrs(self.w_nd)
for b in self.bend_coefs:
self.proj_mat_ptrs[b] = get_gpu_ptrs(self.proj_mats[b])
self.offset_mat_ptrs[b] = get_gpu_ptrs(self.offset_mats[b])
self.pt_ptrs = get_gpu_ptrs(self.pts)
self.pt_t_pt_ptrs = get_gpu_ptrs(self.pt_t_pt)
self.kernel_ptrs = get_gpu_ptrs(self.kernels)
self.ident_ptrs = get_gpu_ptrs([self.ident_mats[0] for _ in range(self.N)])
self.pt_w_ptrs = get_gpu_ptrs(self.pts_w)
self.pt_t_ptrs = get_gpu_ptrs(self.pts_t)
self.corr_cm_ptrs = get_gpu_ptrs(self.corr_cm)
self.corr_rm_ptrs = get_gpu_ptrs(self.corr_rm)
self.r_coef_ptrs = get_gpu_ptrs(self.r_coefs)
self.c_coef_rn_ptrs = get_gpu_ptrs(self.c_coefs_rn)
self.c_coef_cn_ptrs = get_gpu_ptrs(self.c_coefs_cn)
## temporary space used for bend/warp cost computations
self.warp_err = gpuarray.zeros((self.N, MAX_CLD_SIZE), np.float32)
self.bend_res_mat = gpuarray.zeros((DATA_DIM * self.N, DATA_DIM), np.float32)
self.bend_res =[self.bend_res_mat[i*DATA_DIM:(i+1)*DATA_DIM] for i in range(self.N)]
self.bend_res_ptrs = get_gpu_ptrs(self.bend_res)
self.dims_gpu = gpuarray.to_gpu(np.array(self.dims, dtype=np.int32))
self.ptrs_valid = True
def batch_get_sol_params(x_nd, K_nn, bend_coefs, rot_coef):
n, d = x_nd.shape
x_gpu = gpuarray.to_gpu(x_nd)
H_arr_gpu = []
for b in bend_coefs:
cur_offset = np.zeros((1 + d + n, 1 + d + n), np.float64)
cur_offset[d + 1:, d + 1:] = b * K_nn
cur_offset[1:d + 1, 1:d + 1] = np.diag(rot_coef)
H_arr_gpu.append(gpuarray.to_gpu(cur_offset))
H_ptr_gpu = get_gpu_ptrs(H_arr_gpu)
A = np.r_[np.zeros((d + 1, d + 1)), np.c_[np.ones((n, 1)), x_nd]].T
n_cnts = A.shape[0]
_u, _s, _vh = np.linalg.svd(A.T)
N = _u[:, n_cnts:]
F = np.zeros((n + d + 1, d), np.float64)
F[1:d + 1, :d] += np.diag(rot_coef)
Q = np.c_[np.ones((n, 1)), x_nd, K_nn].astype(np.float64)
F = F.astype(np.float64)
N = N.astype(np.float64)
Q_gpu = gpuarray.to_gpu(Q)
Q_arr_gpu = [Q_gpu for _ in range(len(bend_coefs))]
Q_ptr_gpu = get_gpu_ptrs(Q_arr_gpu)
F_gpu = gpuarray.to_gpu(F)
F_arr_gpu = [F_gpu for _ in range(len(bend_coefs))]
F_ptr_gpu = get_gpu_ptrs(F_arr_gpu)
N_gpu = gpuarray.to_gpu(N)
N_arr_gpu = [N_gpu for _ in range(len(bend_coefs))]
N_ptr_gpu = get_gpu_ptrs(N_arr_gpu)
dot_batch_nocheck(Q_arr_gpu,
Q_arr_gpu,
H_arr_gpu,
Q_ptr_gpu,
Q_ptr_gpu,
H_ptr_gpu,
transa='T')
# N'HN
NHN_arr_gpu, NHN_ptr_gpu = m_dot_batch((N_arr_gpu, N_ptr_gpu, 'T'),
(H_arr_gpu, H_ptr_gpu, 'N'),
(N_arr_gpu, N_ptr_gpu, 'N'))
iH_arr = []
for NHN in NHN_arr_gpu:
iH_arr.append(scipy.linalg.inv(NHN.get()).copy())
iH_arr_gpu = [gpuarray.to_gpu_async(iH) for iH in iH_arr]
iH_ptr_gpu = get_gpu_ptrs(iH_arr_gpu)
proj_mats = m_dot_batch(
(N_arr_gpu, N_ptr_gpu, 'N'), (iH_arr_gpu, iH_ptr_gpu, 'N'),
(N_arr_gpu, N_ptr_gpu, 'T'), (Q_arr_gpu, Q_ptr_gpu, 'T'))
offset_mats = m_dot_batch(
(N_arr_gpu, N_ptr_gpu, 'N'), (iH_arr_gpu, iH_ptr_gpu, 'N'),
(N_arr_gpu, N_ptr_gpu, 'T'), (F_arr_gpu, F_ptr_gpu, 'N'))
return proj_mats, offset_mats
def test_batch_get_sol_params(f, bend_coefs, rot_coef, atol=1e-7, index=0):
seg_info = f.items()[index][1]
inv_group = seg_info['inv']
ds_key = 'DS_SIZE_{}'.format(DS_SIZE)
x_nd = inv_group[ds_key]['scaled_cloud_xyz'][:]
K_nn = inv_group[ds_key]['scaled_K_nn'][:]
n, d = x_nd.shape
x_gpu = gpuarray.to_gpu(x_nd)
H_arr_gpu = []
for b in bend_coefs:
cur_offset = np.zeros((1 + d + n, 1 + d + n), np.float64)
cur_offset[d + 1:, d + 1:] = b * K_nn
cur_offset[1:d + 1, 1:d + 1] = np.diag(rot_coef)
H_arr_gpu.append(gpuarray.to_gpu(cur_offset))
H_ptr_gpu = get_gpu_ptrs(H_arr_gpu)
A = np.r_[np.zeros((d + 1, d + 1)), np.c_[np.ones((n, 1)), x_nd]].T
n_cnts = A.shape[0]
_u, _s, _vh = np.linalg.svd(A.T)
N = _u[:, n_cnts:]
F = np.zeros((n + d + 1, d), np.float64)
F[1:d + 1, :d] += np.diag(rot_coef)
Q = np.c_[np.ones((n, 1)), x_nd, K_nn].astype(np.float64)
F = F.astype(np.float64)
N = N.astype(np.float64)
Q_gpu = gpuarray.to_gpu(Q)
Q_arr_gpu = [Q_gpu for _ in range(len(bend_coefs))]
Q_ptr_gpu = get_gpu_ptrs(Q_arr_gpu)
F_gpu = gpuarray.to_gpu(F)
F_arr_gpu = [F_gpu for _ in range(len(bend_coefs))]
F_ptr_gpu = get_gpu_ptrs(F_arr_gpu)
N_gpu = gpuarray.to_gpu(N)
N_arr_gpu = [N_gpu for _ in range(len(bend_coefs))]
N_ptr_gpu = get_gpu_ptrs(N_arr_gpu)
dot_batch_nocheck(Q_arr_gpu,
Q_arr_gpu,
H_arr_gpu,
Q_ptr_gpu,
Q_ptr_gpu,
H_ptr_gpu,
transa='T')
QTQ = Q.T.dot(Q)
H_list = []
for i, bend_coef in enumerate(bend_coefs):
H = QTQ
H[d + 1:, d + 1:] += bend_coef * K_nn
rot_coefs = np.ones(d) * rot_coef if np.isscalar(
rot_coef) else rot_coef
H[1:d + 1, 1:d + 1] += np.diag(rot_coefs)
# ipdb.set_trace()
H_list.append(H)
# N'HN
NHN_arr_gpu, NHN_ptr_gpu = m_dot_batch((N_arr_gpu, N_ptr_gpu, 'T'),
(H_arr_gpu, H_ptr_gpu, 'N'),
(N_arr_gpu, N_ptr_gpu, 'N'))
NHN_list = [N.T.dot(H.dot(N)) for H in H_list]
for i, NHN in enumerate(NHN_list):
assert (np.allclose(NHN, NHN_arr_gpu[i].get(), atol=atol))
iH_arr = []
for NHN in NHN_arr_gpu:
iH_arr.append(scipy.linalg.inv(NHN.get()).copy())
h_inv_list = [scipy.linalg.inv(NHN) for NHN in NHN_list]
assert (np.allclose(iH_arr, h_inv_list, atol=atol))
iH_arr_gpu = [gpuarray.to_gpu_async(iH) for iH in iH_arr]
iH_ptr_gpu = get_gpu_ptrs(iH_arr_gpu)
proj_mats = m_dot_batch(
(N_arr_gpu, N_ptr_gpu, 'N'), (iH_arr_gpu, iH_ptr_gpu, 'N'),
(N_arr_gpu, N_ptr_gpu, 'T'), (Q_arr_gpu, Q_ptr_gpu, 'T'))
proj_mats_list = [N.dot(h_inv.dot(N.T.dot(Q.T))) for h_inv in h_inv_list]
assert (np.allclose(proj_mats_list, proj_mats[0][index].get(), atol=atol))
offset_mats = m_dot_batch(
(N_arr_gpu, N_ptr_gpu, 'N'), (iH_arr_gpu, iH_ptr_gpu, 'N'),
(N_arr_gpu, N_ptr_gpu, 'T'), (F_arr_gpu, F_ptr_gpu, 'N'))
offset_mats_list = [N.dot(h_inv.dot(N.T.dot(F))) for h_inv in h_inv_list]
assert (np.allclose(offset_mats_list,
offset_mats[0][index].get(),
atol=atol))
def test_batch_get_sol_params(f, bend_coefs, rot_coef, atol=1e-7, index=0):
seg_info = f.items()[index][1]
inv_group = seg_info['inv']
ds_key = 'DS_SIZE_{}'.format(DS_SIZE)
x_nd = inv_group[ds_key]['scaled_cloud_xyz'][:]
K_nn = inv_group[ds_key]['scaled_K_nn'][:]
n, d = x_nd.shape
x_gpu = gpuarray.to_gpu(x_nd)
H_arr_gpu = []
for b in bend_coefs:
cur_offset = np.zeros((1 + d + n, 1 + d + n), np.float64)
cur_offset[d+1:, d+1:] = b * K_nn
cur_offset[1:d+1, 1:d+1] = np.diag(rot_coef)
H_arr_gpu.append(gpuarray.to_gpu(cur_offset))
H_ptr_gpu = get_gpu_ptrs(H_arr_gpu)
A = np.r_[np.zeros((d+1,d+1)), np.c_[np.ones((n,1)), x_nd]].T
n_cnts = A.shape[0]
_u,_s,_vh = np.linalg.svd(A.T)
N = _u[:,n_cnts:]
F = np.zeros((n + d + 1, d), np.float64)
F[1:d+1, :d] += np.diag(rot_coef)
Q = np.c_[np.ones((n,1)), x_nd, K_nn].astype(np.float64)
F = F.astype(np.float64)
N = N.astype(np.float64)
Q_gpu = gpuarray.to_gpu(Q)
Q_arr_gpu = [Q_gpu for _ in range(len(bend_coefs))]
Q_ptr_gpu = get_gpu_ptrs(Q_arr_gpu)
F_gpu = gpuarray.to_gpu(F)
F_arr_gpu = [F_gpu for _ in range(len(bend_coefs))]
F_ptr_gpu = get_gpu_ptrs(F_arr_gpu)
N_gpu = gpuarray.to_gpu(N)
N_arr_gpu = [N_gpu for _ in range(len(bend_coefs))]
N_ptr_gpu = get_gpu_ptrs(N_arr_gpu)
dot_batch_nocheck(Q_arr_gpu, Q_arr_gpu, H_arr_gpu,
Q_ptr_gpu, Q_ptr_gpu, H_ptr_gpu,
transa = 'T')
QTQ = Q.T.dot(Q)
H_list = []
for i, bend_coef in enumerate(bend_coefs):
H = QTQ
H[d+1:,d+1:] += bend_coef * K_nn
rot_coefs = np.ones(d) * rot_coef if np.isscalar(rot_coef) else rot_coef
H[1:d+1, 1:d+1] += np.diag(rot_coefs)
# ipdb.set_trace()
H_list.append(H)
# N'HN
NHN_arr_gpu, NHN_ptr_gpu = m_dot_batch((N_arr_gpu, N_ptr_gpu, 'T'),
(H_arr_gpu, H_ptr_gpu, 'N'),
(N_arr_gpu, N_ptr_gpu, 'N'))
NHN_list = [N.T.dot(H.dot(N)) for H in H_list]
for i, NHN in enumerate(NHN_list):
assert(np.allclose(NHN, NHN_arr_gpu[i].get(), atol=atol))
iH_arr = []
for NHN in NHN_arr_gpu:
iH_arr.append(scipy.linalg.inv(NHN.get()).copy())
h_inv_list = [scipy.linalg.inv(NHN) for NHN in NHN_list]
assert(np.allclose(iH_arr, h_inv_list, atol=atol))
iH_arr_gpu = [gpuarray.to_gpu_async(iH) for iH in iH_arr]
iH_ptr_gpu = get_gpu_ptrs(iH_arr_gpu)
proj_mats = m_dot_batch((N_arr_gpu, N_ptr_gpu, 'N'),
(iH_arr_gpu, iH_ptr_gpu, 'N'),
(N_arr_gpu, N_ptr_gpu, 'T'),
(Q_arr_gpu, Q_ptr_gpu, 'T'))
proj_mats_list = [N.dot(h_inv.dot(N.T.dot(Q.T))) for h_inv in h_inv_list]
assert(np.allclose(proj_mats_list, proj_mats[0][index].get(), atol=atol))
offset_mats = m_dot_batch((N_arr_gpu, N_ptr_gpu, 'N'),
(iH_arr_gpu, iH_ptr_gpu, 'N'),
(N_arr_gpu, N_ptr_gpu, 'T'),
(F_arr_gpu, F_ptr_gpu, 'N'))
offset_mats_list = [N.dot(h_inv.dot(N.T.dot(F))) for h_inv in h_inv_list]
assert(np.allclose(offset_mats_list, offset_mats[0][index].get(), atol=atol))
