def batch_tps_rpm_bij( src_ctx, tgt_ctx, T_init=1e-1, T_final=5e-3, outlierfrac=1e-2, outlierprior=1e-1, outliercutoff=1e-2, em_iter=EM_ITER_CHEAP, component_cost=False, ): """ computes tps rpm for the clouds in src and tgt in batch TODO: Fill out comment cleanly """ ##TODO: add check to ensure that src_ctx and tgt_ctx are formatted properly n_iter = len(src_ctx.bend_coefs) T_vals = loglinspace(T_init, T_final, n_iter) src_ctx.reset_tps_params() tgt_ctx.reset_tps_params() for i, b in enumerate(src_ctx.bend_coefs): T = T_vals[i] for _ in range(em_iter): src_ctx.transform_points() tgt_ctx.transform_points() src_ctx.get_target_points(tgt_ctx, outlierprior, outlierfrac, outliercutoff, T) src_ctx.update_transform(b) # check_update(src_ctx, b) tgt_ctx.update_transform(b) return src_ctx.bidir_tps_cost(tgt_ctx, return_components=component_cost)
def __init__(self, bend_coefs=None): if bend_coefs is None: lambda_init, lambda_final = DEFAULT_LAMBDA bend_coefs = np.around(loglinspace(lambda_init, lambda_final, N_ITER_CHEAP), BEND_COEF_DIGITS) self.bend_coefs = bend_coefs self.ptrs_valid = False self.N = 0 self.tps_params = [] self.tps_param_ptrs = None self.trans_d = [] self.trans_d_ptrs = None self.lin_dd = [] self.lin_dd_ptrs = None self.w_nd = [] self.w_nd_ptrs = None """ TPS PARAM FORMAT [ np.zeros(DATA_DIM) ] [ trans_d ] [1 x d] [ np.eye(DATA_DIM) ] = [ lin_dd ] = [d x d] [np.zeros((np.zeros, DATA_DIM))] [ w_nd ] [n x d] """ self.default_tps_params = gpuarray.zeros((DATA_DIM + 1 + MAX_CLD_SIZE, DATA_DIM), np.float32) self.default_tps_params[1 : DATA_DIM + 1, :].set(np.eye(DATA_DIM, dtype=np.float32)) self.proj_mats = dict([(b, []) for b in bend_coefs]) self.proj_mat_ptrs = dict([(b, None) for b in bend_coefs]) self.offset_mats = dict([(b, []) for b in bend_coefs]) self.offset_mat_ptrs = dict([(b, None) for b in bend_coefs]) self.pts = [] self.pt_ptrs = None self.kernels = [] self.kernel_ptrs = None self.pts_w = [] self.pt_w_ptrs = None self.pts_t = [] self.pt_t_ptrs = None self.dims = [] self.dims_gpu = None self.scale_params = [] self.warp_err = None self.bend_res = [] self.bend_res_ptrs = None self.corr_cm = [] self.corr_cm_ptrs = None self.corr_rm = [] self.corr_rm_ptrs = None self.r_coefs = [] self.r_coef_ptrs = None self.c_coefs_rn = [] self.c_coef_rn_ptrs = None self.c_coefs_cn = [] self.c_coef_cn_ptrs = None self.seg_names = [] self.names2inds = {}
def test_batch_tps_rpm_bij( src_ctx, tgt_ctx, T_init=1e-1, T_final=5e-3, outlierfrac=1e-2, outlierprior=1e-1, outliercutoff=0.5, em_iter=EM_ITER_CHEAP, test_ind=0, ): from lfd.tpsopt.transformations import ThinPlateSpline, set_ThinPlateSpline n_iter = len(src_ctx.bend_coefs) T_vals = loglinspace(T_init, T_final, n_iter) x_nd = src_ctx.pts[test_ind].get()[: src_ctx.dims[test_ind]] y_md = tgt_ctx.pts[0].get()[: tgt_ctx.dims[0]] (n, d) = x_nd.shape (m, _) = y_md.shape f = ThinPlateSpline(d) g = ThinPlateSpline(d) src_ctx.reset_tps_params() tgt_ctx.reset_tps_params() for i, b in enumerate(src_ctx.bend_coefs): T = T_vals[i] for _ in range(em_iter): src_ctx.transform_points() tgt_ctx.transform_points() xwarped_nd = f.transform_points(x_nd) ywarped_md = g.transform_points(y_md) gpu_xw = src_ctx.pts_w[test_ind].get()[:n, :] gpu_yw = tgt_ctx.pts_w[test_ind].get()[:m, :] assert np.allclose(xwarped_nd, gpu_xw, atol=1e-5) assert np.allclose(ywarped_md, gpu_yw, atol=1e-5) xwarped_nd = gpu_xw ywarped_md = gpu_yw src_ctx.get_target_points(tgt_ctx, outlierprior, outlierfrac, outliercutoff, T) fwddist_nm = ssd.cdist(xwarped_nd, y_md, "euclidean") invdist_nm = ssd.cdist(x_nd, ywarped_md, "euclidean") prob_nm = outlierprior * np.ones((n + 1, m + 1), np.float32) prob_nm[:n, :m] = np.exp(-(fwddist_nm + invdist_nm) / float(2 * T)) prob_nm[n, m] = outlierfrac * np.sqrt(n * m) gpu_corr = src_ctx.corr_rm[test_ind].get() gpu_corr = gpu_corr.flatten() gpu_corr = gpu_corr[: (n + 1) * (m + 1)].reshape(n + 1, m + 1).astype(np.float32) assert np.allclose(prob_nm[:n, :m], gpu_corr[:n, :m], atol=1e-5) save_prob_nm = np.array(prob_nm) save_gpu_corr = np.array(gpu_corr) prob_nm[:n, :m] = gpu_corr[:n, :m] r_coefs = np.ones(n + 1, np.float32) c_coefs = np.ones(m + 1, np.float32) a_N = np.ones((n + 1), dtype=np.float32) a_N[n] = m * outlierfrac b_M = np.ones((m + 1), dtype=np.float32) b_M[m] = n * outlierfrac for norm_iter_i in range(DEFAULT_NORM_ITERS): r_coefs = a_N / prob_nm.dot(c_coefs) rn_c_coefs = c_coefs c_coefs = b_M / r_coefs.dot(prob_nm) gpu_r_coefs = src_ctx.r_coefs[test_ind].get()[: n + 1].reshape(n + 1) gpu_c_coefs_cn = src_ctx.c_coefs_cn[test_ind].get()[: m + 1].reshape(m + 1) gpu_c_coefs_rn = src_ctx.c_coefs_rn[test_ind].get()[: m + 1].reshape(m + 1) r_diff = np.abs(r_coefs - gpu_r_coefs) rn_diff = np.abs(rn_c_coefs - gpu_c_coefs_rn) cn_diff = np.abs(c_coefs - gpu_c_coefs_cn) assert np.allclose(r_coefs, gpu_r_coefs, atol=1e-5) assert np.allclose(c_coefs, gpu_c_coefs_cn, atol=1e-5) assert np.allclose(rn_c_coefs, gpu_c_coefs_rn, atol=1e-5) prob_nm = prob_nm[:n, :m] prob_nm *= gpu_r_coefs[:n, None] rn_p_nm = prob_nm * gpu_c_coefs_rn[None, :m] cn_p_nm = prob_nm * gpu_c_coefs_cn[None, :m] wt_n = rn_p_nm.sum(axis=1) gpu_corr_cm = src_ctx.corr_cm[test_ind].get().flatten()[: (n + 1) * (m + 1)] gpu_corr_cm = gpu_corr_cm.reshape(m + 1, n + 1) ## b/c it is column major assert np.allclose(wt_n, gpu_corr_cm[m, :n], atol=1e-4) inlier = wt_n > outliercutoff xtarg_nd = np.empty((n, DATA_DIM), np.float32) xtarg_nd[inlier, :] = rn_p_nm.dot(y_md)[inlier, :] xtarg_nd[~inlier, :] = xwarped_nd[~inlier, :] wt_m = cn_p_nm.sum(axis=0) assert np.allclose(wt_m, gpu_corr[n, :m], atol=1e-4) inlier = wt_m > outliercutoff ytarg_md = np.empty((m, DATA_DIM), np.float32) ytarg_md[inlier, :] = cn_p_nm.T.dot(x_nd)[inlier, :] ytarg_md[~inlier, :] = ywarped_md[~inlier, :] xt_gpu = src_ctx.pts_t[test_ind].get()[:n, :] yt_gpu = tgt_ctx.pts_t[test_ind].get()[:m, :] assert np.allclose(xtarg_nd, xt_gpu, atol=1e-4) assert np.allclose(ytarg_md, yt_gpu, atol=1e-4) src_ctx.update_transform(b) tgt_ctx.update_transform(b) f_p_mat = src_ctx.proj_mats[b][test_ind].get()[: n + d + 1, :n] f_o_mat = src_ctx.offset_mats[b][test_ind].get()[: n + d + 1] b_p_mat = tgt_ctx.proj_mats[b][0].get()[: m + d + 1, :m] b_o_mat = tgt_ctx.offset_mats[b][0].get()[: m + d + 1] f_params = f_p_mat.dot(xtarg_nd) + f_o_mat g_params = b_p_mat.dot(ytarg_md) + b_o_mat gpu_fparams = src_ctx.tps_params[test_ind].get()[: n + d + 1] gpu_gparams = tgt_ctx.tps_params[test_ind].get()[: m + d + 1] assert np.allclose(f_params, gpu_fparams, atol=1e-4) assert np.allclose(g_params, gpu_gparams, atol=1e-4) set_ThinPlateSpline(f, x_nd, gpu_fparams) set_ThinPlateSpline(g, y_md, gpu_gparams) f._cost = tps.tps_cost(f.lin_ag, f.trans_g, f.w_ng, f.x_na, xtarg_nd, 1) g._cost = tps.tps_cost(g.lin_ag, g.trans_g, g.w_ng, g.x_na, ytarg_md, 1) gpu_cost = src_ctx.bidir_tps_cost(tgt_ctx) cpu_cost = f._cost + g._cost assert np.isclose(gpu_cost[test_ind], cpu_cost, atol=1e-4)
def main(): scikits.cuda.linalg.init() args = parse_arguments() f = h5py.File(args.datafile, 'r+') bend_coefs = np.around( loglinspace(args.bend_coef_init, args.bend_coef_final, args.n_iter), BEND_COEF_DIGITS) for seg_name, seg_info in f.iteritems(): if 'inv' in seg_info: if args.replace: del seg_info['inv'] inv_group = seg_info.create_group('inv') else: inv_group = seg_info['inv'] else: inv_group = seg_info.create_group('inv') ds_key = 'DS_SIZE_{}'.format(DS_SIZE) if ds_key in inv_group: scaled_x_na = inv_group[ds_key]['scaled_cloud_xyz'][:] K_nn = inv_group[ds_key]['scaled_K_nn'][:] else: ds_g = inv_group.create_group(ds_key) x_na = downsample_cloud(seg_info[args.cloud_name][:, :3]) scaled_x_na, scale_params = unit_boxify(x_na) K_nn = tps_kernel_matrix(scaled_x_na) if args.fill_traj: r_traj = seg_info['r_gripper_tool_frame']['hmat'][:, :3, 3] l_traj = seg_info['l_gripper_tool_frame']['hmat'][:, :3, 3] scaled_r_traj = r_traj * scale_params[0] + scale_params[1] scaled_l_traj = l_traj * scale_params[0] + scale_params[1] scaled_r_traj_K = tps_kernel_matrix2(scaled_r_traj, scaled_x_na) scaled_l_traj_K = tps_kernel_matrix2(scaled_l_traj, scaled_x_na) ds_g['scaled_r_traj'] = scaled_r_traj ds_g['scaled_l_traj'] = scaled_l_traj ds_g['scaled_r_traj_K'] = scaled_r_traj_K ds_g['scaled_l_traj_K'] = scaled_l_traj_K # Precompute l,r closing indices lr2finger_traj = {} for lr in 'lr': arm_name = {"l": "leftarm", "r": "rightarm"}[lr] lr2finger_traj[ lr] = gripper_joint2gripper_l_finger_joint_values( np.asarray(seg_info['%s_gripper_joint' % lr]))[:, None] opening_inds, closing_inds = get_opening_closing_inds( lr2finger_traj[lr]) if '%s_closing_inds' % lr in seg_info: del seg_info['%s_closing_inds' % lr] if not closing_inds: closing_inds = False seg_info['%s_closing_inds' % lr] = closing_inds # ds_g['cloud_xyz'] = x_na ds_g['scaled_cloud_xyz'] = scaled_x_na ds_g['scaling'] = scale_params[0] ds_g['scaled_translation'] = scale_params[1] ds_g['scaled_K_nn'] = K_nn for bend_coef in bend_coefs: if str(bend_coef) in inv_group: continue bend_coef_g = inv_group.create_group(str(bend_coef)) _, res = get_sol_params(scaled_x_na, K_nn, bend_coef) for k, v in res.iteritems(): bend_coef_g[k] = v if args.verbose: sys.stdout.write( '\rprecomputed tps solver for segment {}'.format(seg_name)) sys.stdout.flush() print "" if args.test: atol = 1e-7 print 'Running batch get sol params test with atol = ', atol test_batch_get_sol_params(f, [bend_coef], atol=atol) print 'batch sol params test succeeded' print "" bend_coefs = np.around( loglinspace(args.exact_bend_coef_init, args.exact_bend_coef_final, args.exact_n_iter), BEND_COEF_DIGITS) for seg_name, seg_info in f.iteritems(): if 'solver' in seg_info: if args.replace: del seg_info['solver'] solver_g = seg_info.create_group('solver') else: solver_g = seg_info['solver'] else: solver_g = seg_info.create_group('solver') x_nd = seg_info['inv'][ds_key]['scaled_cloud_xyz'][:] K_nn = seg_info['inv'][ds_key]['scaled_K_nn'][:] N, QN, NON, NR = get_exact_solver(x_nd, K_nn, bend_coefs) solver_g['N'] = N solver_g['QN'] = QN solver_g['NR'] = NR solver_g['x_nd'] = x_nd solver_g['K_nn'] = K_nn NON_g = solver_g.create_group('NON') for b in bend_coefs: NON_g[str(b)] = NON[b] if args.verbose: sys.stdout.write( '\rprecomputed exact tps solver for segment {}'.format( seg_name)) sys.stdout.flush() print "" f.close()
def main(): scikits.cuda.linalg.init() args = parse_arguments() f = h5py.File(args.datafile, 'r+') bend_coefs = np.around(loglinspace(args.bend_coef_init, args.bend_coef_final, args.n_iter), BEND_COEF_DIGITS) for seg_name, seg_info in f.iteritems(): if 'inv' in seg_info: if args.replace: del seg_info['inv'] inv_group = seg_info.create_group('inv') else: inv_group = seg_info['inv'] else: inv_group = seg_info.create_group('inv') ds_key = 'DS_SIZE_{}'.format(DS_SIZE) if ds_key in inv_group: scaled_x_na = inv_group[ds_key]['scaled_cloud_xyz'][:] K_nn = inv_group[ds_key]['scaled_K_nn'][:] else: ds_g = inv_group.create_group(ds_key) x_na = downsample_cloud(seg_info[args.cloud_name][:, :3]) scaled_x_na, scale_params = unit_boxify(x_na) K_nn = tps_kernel_matrix(scaled_x_na) if args.fill_traj: r_traj = seg_info['r_gripper_tool_frame']['hmat'][:, :3, 3] l_traj = seg_info['l_gripper_tool_frame']['hmat'][:, :3, 3] scaled_r_traj = r_traj * scale_params[0] + scale_params[1] scaled_l_traj = l_traj * scale_params[0] + scale_params[1] scaled_r_traj_K = tps_kernel_matrix2(scaled_r_traj, scaled_x_na) scaled_l_traj_K = tps_kernel_matrix2(scaled_l_traj, scaled_x_na) ds_g['scaled_r_traj'] = scaled_r_traj ds_g['scaled_l_traj'] = scaled_l_traj ds_g['scaled_r_traj_K'] = scaled_r_traj_K ds_g['scaled_l_traj_K'] = scaled_l_traj_K # Precompute l,r closing indices lr2finger_traj = {} for lr in 'lr': arm_name = {"l":"leftarm", "r":"rightarm"}[lr] lr2finger_traj[lr] = gripper_joint2gripper_l_finger_joint_values(np.asarray(seg_info['%s_gripper_joint'%lr]))[:,None] opening_inds, closing_inds = get_opening_closing_inds(lr2finger_traj[lr]) if '%s_closing_inds'%lr in seg_info: del seg_info['%s_closing_inds'%lr] if not closing_inds: closing_inds = False seg_info['%s_closing_inds'%lr] = closing_inds # ds_g['cloud_xyz'] = x_na ds_g['scaled_cloud_xyz'] = scaled_x_na ds_g['scaling'] = scale_params[0] ds_g['scaled_translation'] = scale_params[1] ds_g['scaled_K_nn'] = K_nn for bend_coef in bend_coefs: if str(bend_coef) in inv_group: continue bend_coef_g = inv_group.create_group(str(bend_coef)) _, res = get_sol_params(scaled_x_na, K_nn, bend_coef) for k, v in res.iteritems(): bend_coef_g[k] = v if args.verbose: sys.stdout.write('\rprecomputed tps solver for segment {}'.format(seg_name)) sys.stdout.flush() print "" if args.test: atol = 1e-7 print 'Running batch get sol params test with atol = ', atol test_batch_get_sol_params(f, [bend_coef], atol=atol) print 'batch sol params test succeeded' print "" bend_coefs = np.around(loglinspace(args.exact_bend_coef_init, args.exact_bend_coef_final, args.exact_n_iter), BEND_COEF_DIGITS) for seg_name, seg_info in f.iteritems(): if 'solver' in seg_info: if args.replace: del seg_info['solver'] solver_g = seg_info.create_group('solver') else: solver_g = seg_info['solver'] else: solver_g = seg_info.create_group('solver') x_nd = seg_info['inv'][ds_key]['scaled_cloud_xyz'][:] K_nn = seg_info['inv'][ds_key]['scaled_K_nn'][:] N, QN, NON, NR = get_exact_solver(x_nd, K_nn, bend_coefs) solver_g['N'] = N solver_g['QN'] = QN solver_g['NR'] = NR solver_g['x_nd'] = x_nd solver_g['K_nn'] = K_nn NON_g = solver_g.create_group('NON') for b in bend_coefs: NON_g[str(b)] = NON[b] if args.verbose: sys.stdout.write('\rprecomputed exact tps solver for segment {}'.format(seg_name)) sys.stdout.flush() print "" f.close()