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Source code for jax_rb.manifolds.affine_left_invariant

+""":math:`Aff^+`: Positive Component of the Affine group with left invariant metric.
+"""
+
+import jax.numpy.linalg as jla
+from .matrix_left_invariant import MatrixLeftInvariant
+from ..utils.utils import (grand)
+
+
+
+[docs] +class AffineLeftInvariant(MatrixLeftInvariant): + """Group of affine tranformations of :math:`\\mathbb{R}^{n}`, + represented by a pair :math:`(A, v)\\in GL^+(n)\\times \\mathbb{R}^{n}` + with action :math:`(A, v).w = Aw + v` for :math:`w\\in\\mathbb{R}^{n}` . + + Alternatively, it is represented as a matrix :math:`\\begin{bmatrix} A & v \\\\ 0 & 1 \\end{bmatrix}\\in GL(n+1)`. + + :param n: size of A + :param g_mat: a positive definite matrix in :math:`\\mathbb{R}^{n(n+1)\\times n(n+1)}` defining the metric at :math:`I_{n+1}` + """ + def __init__(self, n, g_mat): + """ g_mat is a matrix of size (n(n+1))**2 + used to define the metric + """ + super().__init__(n+1, g_mat) + self.dim = n*(n+1) + + def name(self): + return f"Aff({self.shape[0]-1})" + + def _lie_algebra_proj(self, omg): + """ The projection at identity + """ + return omg.at[-1, :].set(0.) + + def _mat_apply(self, mat, omg): + """ mat is a matrix of size (p(p-1))**2 + """ + p = omg.shape[0] + return omg.at[:-1, :].set( + (mat@omg[:-1, :].reshape(-1)).reshape(p-1, p)) + + def rand_point(self, key): + """ A random point on the manifold + """ + mat, key = grand(key, self.shape) + return mat.at[-1, :].set(0.).at[-1, -1].set(1.), key + + def retract(self, x, v): + """ second order retraction, but simple + """ + return (x + v -0.5*self.gamma(x, v, v)).at[-1, :].set(0.) + + def approx_nearest(self, q): + return q.at[-1, :].set(0.) + + def pseudo_transport(self, x, y, v): + """the easy one + """ + return y@jla.solve(x, v) + + def sigma(self, x, dw): + return x@self._lie_algebra_proj(self._mat_apply(self._i_sqrt_g_mat, dw))
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Source code for jax_rb.manifolds.diag_hypersurface

+"""Hypersurface with a constraint of the form :math:`\\sum_i d_i x_i^p = 1`
+"""
+import jax.numpy as jnp
+import jax.numpy.linalg as jla
+from .global_manifold import GlobalManifold
+from ..utils.utils import (grand)
+
+
+
+[docs] +class DiagHypersurface(GlobalManifold): + """Hypersurface of the form :math:`\\sum_i d_ix_i^p = 1`. + + :param dvec: vector :math:`d_i` of coefficients. + Sort dvec so dvec[-1] is positive. + :param p: :math:`p > 0` is an integer, degree of the constraint. + + Use embedded metric. + """ + def __init__(self, dvec, p): + self.dvec = dvec + self.shape = dvec.shape + self.p = p + self.dim = dvec.shape[0]-1 + + def name(self): + return f"DH{self.shape[0]-1}, {self.p}" + + def g_metric(self, x, omg): + return omg + + def inv_g_metric(self, x, omg): + return omg + + def inner(self, x, a, b): + return jnp.sum(a*b) + + def cfunc(self, x): + """ constraint for the surface is cfunc(x) = 1 + """ + return jnp.sum(self.dvec*x**self.p) + + def grad_c(self, x): + """ gradient of cfunc + """ + return self.p*self.dvec*x**(self.p-1) + + def rand_point(self, key): + """random point on manifold + """ + p = self.p + dvec = self.dvec + x, key = grand(key, self.shape) + val = self.cfunc(x) + if p % 2 == 1: + return x/jnp.abs(val)**(1/p)*jnp.sign(val) + if val < 0: + ret = jnp.concatenate( + [x[:-1], + jnp.array([1/dvec[-1]*(1-jnp.sum(dvec[:-1]*x[:-1]**p))**(1/p)])]) + else: + ret = x/val**(1/p) + return ret, key + + def rand_vec(self, key, x): + """random tangent vector + """ + omg, key = grand(key, self.shape) + return self.proj_scale(x, omg), key + + def proj(self, x, omg): + """ othogonal projection + """ + gcx = self.grad_c(x) + return omg - gcx*jnp.sum(gcx*omg)/jnp.sum(gcx*gcx) + + def approx_nearest(self, q): + """ tubular retraction. Need some work + to show this is actually approx_nearest + """ + val = self.cfunc(q) + return q/val**(1/self.p) + + def retract(self, x, v): + return self.approx_nearest(x + v - 0.5*self.proj_scale(x, self.gamma(x, v, v))) + + def proj_scale(self, x, omg): + """rescale projection + """ + return omg - x*jnp.sum(self.dvec*x**(self.p-1)*omg) + + def gamma(self, x, xi, eta): + """Christoffel function + """ + p = self.p + gcx = self.grad_c(x) + return p*(p-1)*gcx*jnp.sum(self.dvec*x**(p-2)*xi*eta)/jnp.sum(gcx*gcx) + + def ito_drift(self, x): + p = self.p + gcx = self.grad_c(x) + return -0.5*p*(p-1)*gcx*( + jnp.sum(self.dvec*x**(p-2)) - jnp.sum(self.dvec*x**(p-2)*gcx*gcx)/jnp.sum(gcx*gcx) + )/jnp.sum(gcx*gcx) + + def pseudo_transport(self, x, y, v): + gcx = self.grad_c(x) + gcy = self.grad_c(y) + + a = jnp.sum(gcy*v)*(jla.norm(gcx)*jla.norm(gcy) - jnp.sum(gcx*gcy)) \ + / (jnp.sum(gcx*gcx)*jnp.sum(gcy*gcy) - jnp.sum(gcy*gcx)**2) + return v - a*gcx - (jnp.sum(gcy*v) - a*jnp.sum(gcy*gcx))/jnp.sum(gcy*gcy)*gcy + + def sigma(self, x, dw): + return dw + + def rtr_tan_scale(self, yv, dyv): + """retraction to the tangent bundle using rescale + projection + """ + y1 = self.retract(yv[:, 0], dyv[:, 0]) + v1 = self.proj_scale(y1, yv[:, 1] + dyv[:, 1]) + v1 = v1*jnp.sqrt(self.inner(yv[0], yv[:, 1], yv[:, 1])/self.inner(y1, v1, v1)) + return jnp.concatenate([ + y1[:, None], + v1[:, None]], axis=1) + + def geodesic(self, x, v, t, nstep=100): + """ approximate geodesic + using the retraction to the tangent bundle rtr_tan + """ + yv = jnp.concatenate([x[:, None], v[:, None]], axis=1) + h = t/nstep + + def dyvdt(_, yv): + return jnp.concatenate( + [yv[:, [1]], -self.gamma(yv[:, 0], yv[:, 1], yv[:, 1])[:, None]], + axis=1) + + t0 = 0 + for _ in range(1, nstep+1): + # Apply Runge Kutta Formulas to find next value of y + k1 = h * dyvdt(t0, yv) + k2 = h * dyvdt(t0 + 0.5 * h, yv + 0.5 * k1) + k3 = h * dyvdt(t0 + 0.5 * h, yv + 0.5 * k2) + k4 = h * dyvdt(t0 + h, yv + k3) + + yv = self.rtr_tan_scale(yv, (1.0 / 6.0)*(k1 + 2 * k2 + 2 * k3 + k4)) + t0 = t0 + h + return yv[:, 0], yv[:, 1] + + def make_tangent_basis(self, x): + """ tangent basis at x + """ + d = self.dim + gcx = self.grad_c(x) + proj_mat = jnp.eye(self.shape[0]) - gcx[:, None]@gcx[None, :]/jnp.sum(gcx*gcx) + _, ev = jla.eigh(proj_mat) + cmat = ev[:, 1:] + + mat = jnp.empty((d, d)) + for i in range(d): + for j in range(d): + mat = mat.at[i, j].set(self.inner(x, cmat[:, i], cmat[:, j])) + ei, ev = jla.eigh(mat) + return cmat@ev@(1/jnp.sqrt(jnp.abs(ei))[:, None]*ev.T)
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Source code for jax_rb.manifolds.global_manifold

+"""Base class for manifold in global embedded coordinates
+"""
+from functools import partial
+from abc import ABCMeta, abstractmethod
+
+import jax
+import jax.numpy as jnp
+from ..utils.utils import (grand)
+
+
+
+[docs] +class GlobalManifold(metaclass=ABCMeta): + """A manifold :math:`\\mathcal{M}` embedded in a vector space :math:`\\mathcal{E}` . + """ + @abstractmethod + def __init__(self): + """Constructor + + :param shape: shape of the ambient vector space, + :param dim: dimension of the manifold. + """ + self.shape = None + self.dim = None + raise NotImplementedError + +
+[docs] + def name(self): + """ name of the manifold. + """ + raise NotImplementedError
+ + +
+[docs] + def inner(self, x, a, b): + """ Riemannian inner product. + + :param a: a vector in ambient space, + :param b: a vector in ambient space, + :return: the inner product of a and b using the metric :math:`\\mathsf{g}` . + """ + raise NotImplementedError
+ + +
+[docs] + def g_metric(self, x, omg): + """ the metric operator g, which is symmetric. The corresponding metric is + :math:`\\langle \\omega, g(x)\\omega \\rangle_{\\mathcal{E}}` . + """ + raise NotImplementedError
+ + +
+[docs] + def inv_g_metric(self, x, omg): + """ inverse of the metric operator g. + """ + raise NotImplementedError
+ + +
+[docs] + @partial(jax.jit, static_argnums=(0,)) + def proj(self, x, omg): + """ Metric compatible projection + :param x: a point on the manifold, + :param omg: a vector on the ambient manifold :math:`\\mathcal{E}` , + :returns: a point the tangent space at x. + + """ + raise NotImplementedError
+ + +
+[docs] + def rand_ambient(self, key): + """Random ambient vector. + """ + return grand(key, self.shape)
+ + +
+[docs] + def rand_vec(self, key, x): + """Random tangent vector at x. + """ + omg, key = grand(key, self.shape) + return self.proj(x, omg), key
+ + +
+[docs] + def rand_point(self, key): + """ A random point on the manifold. + """ + raise NotImplementedError
+ + +
+[docs] + @partial(jax.jit, static_argnums=(0,)) + def gamma(self, x, xi, eta): + """Christoffel function. Symmetric for two tangent vectors xi, eta. + The corresponding Levi-Civita connection is + :math:`\\nabla_{\\mathtt{X}}\\mathtt{Y} = \\mathrm{D}_{\\mathtt{X}}\\mathtt{Y} + \\Gamma(x; \\mathtt{X}, \\mathtt{Y})` + for two vector fields :math:`\\mathtt{X}, \\mathtt{Y}`. + """ + raise NotImplementedError
+ + +
+[docs] + def retract(self, x, v): + """ Second order retraction + + :param x: a point on the manifold, + :param v: a tangent vector at x, + :returns: a point on the manifold. + """ + # x1 = x + v - 0.5* self.proj(x, self.gamma(x, v, v)) + # return jax.scipy.linalg.polar(x1)[0] + raise NotImplementedError
+ + +
+[docs] + @partial(jax.jit, static_argnums=(0,)) + def ito_drift(self, x): + """Ito Brownian drift as an ambient vector. + """ + raise NotImplementedError
+ + + # @partial(jax.jit, static_argnums=(0,)) +
+[docs] + def laplace_beltrami(self, x, egradx, ehessvp): + """ Laplace Beltrami operator. This works in for vector and matrices. For a specific manifold, this may be simplified. + We assume f is a scalar function in a tubular neighborhood of the manifold. + + :param x: a point on the manifold, + :param egradx: is the Euclidean gradient of :math:`f` , a matrix of the same shape with x, + :param ehessvp: is the Euclidean Hessian Productof :math:`f` , a linear operator on :math:`\\mathcal{E}` , + :returns: the value of the Laplace Beltrami operator of :math:`f` . + """ + ret = 0 + ndim = jnp.prod(jnp.array(self.shape)) + for i in range(ndim): + e_i = jnp.zeros(ndim).at[i].set(1.).reshape(self.shape) + ret += self.proj(x, self.inv_g_metric( + x, ehessvp(x, e_i))).reshape(-1)[i] + return ret + 2*jnp.sum(self.ito_drift(x)*egradx)
+ + +
+[docs] + def pseudo_transport(self, x, y, v): + """ an approximate parallel transport from x to y + + :param x: a point on the manifold, + :param y: a point on the manifold, + :param v: a tangent vector at x, + + :returns: a tangent vector at y. + """ + raise NotImplementedError
+ + +
+[docs] + def sigma(self, x, dw): + """ Sigma map to generate Brownian motion. + + :param x: a point on the manifold, + :param dw: a point on the ambient space, + :return: apoint on the ambient space such that :math:`\\Pi(x) \\sigma(x) \\sigma^{\\mathsf{T}}(x)\\mathsf{g}^{-1}(x) dw = \\Pi(x)dw` + """ + raise NotImplementedError
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Source code for jax_rb.manifolds.glp_left_invariant

+""":math:`GL^+`: Positive Component of the Generalized Linear group with left-invariant metric.
+"""
+
+import jax.numpy.linalg as jla
+from .matrix_left_invariant import MatrixLeftInvariant
+from ..utils.utils import (grand)
+
+
+
+[docs] +class GLpLeftInvariant(MatrixLeftInvariant): + """:math:`GL^+` with left invariant metric defined by g_mat. + + :param p: the size of the matrix + :param g_mat: The matrix defining the inner product at the identity. g_mat is in :math:`\\mathbb{R}^{p^2\\times p^2}` . + + """ + def name(self): + return f"GL+({self.shape[0]})" + + def _mat_apply(self, mat, omg): + return (mat@omg.reshape(-1)).reshape(self.shape) + + def _lie_algebra_proj(self, omg): + return omg + + def rand_ambient(self, key): + """random ambient vector + """ + return grand(key, (self.shape)) + + def rand_point(self, key): + """ A random point on the manifold + """ + ret, key = self.rand_ambient(key) + if jla.det(ret) < 0: + return ret.at[0, :].set(-ret[0, :]), key + return ret, key + + def retract(self, x, v): + """ second order retraction, but simple + """ + return x + v - 0.5* self.proj(x, self.gamma(x, v, v)) + + def approx_nearest(self, q): + return q + + def pseudo_transport(self, x, y, v): + """the easy one + """ + return y@jla.solve(x, v) + + def sigma(self, x, dw): + """ sigma is applied on a vector rather than a matrix + """ + return x@self._mat_apply(self._i_sqrt_g_mat, dw)
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Source code for jax_rb.manifolds.grassmann

+"""Grassmann manifold :math:`\\mathrm{Gr}(n, p)` of vector spaces of rank :math:`p` in a :math:`n` -dimension vector space.
+"""
+
+from functools import partial
+
+import jax
+import jax.numpy as jnp
+import jax.numpy.linalg as jla
+from jax.scipy.linalg import expm
+from ..utils.utils import (esqrtm)
+from .global_manifold import GlobalManifold
+
+
+
+
+[docs] +class Grassmann(GlobalManifold): + """ + The lift of the Grassman manifold to to the Stiefel manifold :math:`Y^TY = I` where :math:`Y` is a matrix of :math:`shape=n\\times p` with metric :math:`\\lvert \\omega\\rvert^2_{\\mathsf{g}} = Tr(\\omega^T\\omega)`. The lift is with respect to the submersion defined by the relationship :math:`Y\\sim YU` for an orthogonal matrix :math:`U`. + """ + def __init__(self, shape): + """Constructor + """ + self.shape = shape + n, p = shape + self.dim = (n-p)*p + + def name(self): + return f"Gr({self.shape[0]}, {self.shape[1]})" + + def inner(self, x, a, b): + return jnp.sum(a*b) + + def g_metric(self, x, omg): + """ the metric operator g + """ + return omg + + def inv_g_metric(self, x, omg): + """ inverse of the metric operator g + """ + return omg + + @partial(jax.jit, static_argnums=(0,)) + def proj(self, x, omg): + """ Metric compatible projection + """ + return omg - x@x.T@omg + + def rand_point(self, key): + """ A random point on the manifold + """ + xt, key = self.rand_ambient(key) + x, _ = jla.qr(xt) + return x, key + + @partial(jax.jit, static_argnums=(0,)) + def gamma(self, x, xi, eta): + """Christoffel function + """ + return x@(xi.T@eta) + + @partial(jax.jit, static_argnums=(0,)) + def retract(self, x, v): + """ second order retraction, but simple + """ + x1 = x+ v + ei, ev = jla.eigh(x1.T@x1) + return x1@ev@((1/jnp.sqrt(ei))[:, None]*ev.T) + + @partial(jax.jit, static_argnums=(0,)) + def approx_nearest(self, q): + """ second order retraction, but simple + """ + # return jax.scipy.linalg.polar(q)[0] + ei, ev = jla.eigh(q.T@q) + return q@ev@((1/jnp.sqrt(ei))[:, None]*ev.T) + + @partial(jax.jit, static_argnums=(0,)) + def ito_drift(self, x): + n, p = self.shape + return -0.5*(n-p)*x + + @partial(jax.jit, static_argnums=(0,)) + def stratonovic_drift(self, _): + """ stratnovich drift + """ + return jnp.zeros_like(self.shape) + + def laplace_beltrami(self, x, egradx, ehessvp): + n, p = self.shape + tup = jnp.zeros(self.shape) + ret = 0 + for i in range(n): + for j in range(p): + e_ij = tup.at[i, j].set(1.) + ret += self.proj(x, self.inv_g_metric( + x, ehessvp(x, e_ij)))[i, j] + return ret + 2*jnp.sum(self.ito_drift(x)*egradx) + + def sigma(self, x, dw): + return dw + + def sigma0(self, x, dw0): + """ dw is a vector space of size self.dim. + We use this for the geodesic + walk strategy. Need storage for the complement + """ + n, p = self.shape + ret = jnp.zeros_like(x) + P = esqrtm(x[:p, :].T@x[:p, :]) + Q = jla.solve(P, x[:p, :].T).T + B = dw0.reshape(n-p, p) + ret += jnp.concatenate( + [- Q@x[p:, :].T@B, + B - x[p:, :]@jla.solve(P + jnp.eye(p), x[p:, :].T@B)], + axis=0) + return ret + + def pseudo_transport(self, x, y, v): + """This is the actual parallel transport + """ + # v1 = self.proj(y, v) + # return v1/jnp.sqrt(self.inner(y, v1, v1)) + u, s, w = jla.svd(x.T@y) + return (- x@u - y@w.T)@jnp.diag(1/(1+s))@w@(y.T@v) + v + + def exp(self, x, eta): + """ Geodesics, the formula involves matrices of size 2d + + Parameters + ---------- + x : a manifold point + eta : tangent vector + + Returns + ---------- + gamma(1), where gamma(t) is the geodesics at Y in direction eta + + """ + p = eta.shape[1] + xp, r = jla.qr(eta) + x_mat = jnp.concatenate([ + jnp.concatenate([jnp.zeros((p, p)), -r.T], axis=1), + jnp.concatenate([r, jnp.zeros((p, p))], axis=1)], axis=0) + return jnp.concatenate([x, xp], axis=1) @ expm(x_mat)[:, :p]
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+ + + + \ No newline at end of file diff --git a/_modules/jax_rb/manifolds/matrix_left_invariant.html b/_modules/jax_rb/manifolds/matrix_left_invariant.html new file mode 100644 index 0000000..2079b1c --- /dev/null +++ b/_modules/jax_rb/manifolds/matrix_left_invariant.html @@ -0,0 +1,380 @@ + + + + + + jax_rb.manifolds.matrix_left_invariant — jax_rb documentation + + + + + + + + + + + + + + + + + +
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Source code for jax_rb.manifolds.matrix_left_invariant

+"""Base class for matrix groups with left invariant metrics.
+"""
+
+from functools import partial
+
+import jax
+import jax.numpy as jnp
+import jax.numpy.linalg as jla
+from .global_manifold import GlobalManifold
+from ..utils.utils import (grand, lie)
+
+
+
+[docs] +class MatrixLeftInvariant(GlobalManifold): + """Matrix group with left invariant metric. + + :param p: the size of the matrix + :param g_mat: The matrix defining the inner product at the identity. Typically g_mat is of size :math:`\\dim \\mathrm{G}` . + """ + def __init__(self, p, g_mat): + """Constructor + """ + self.shape = (p, p) + self.dim = p*p + self._g_mat = g_mat + ei, ev = jla.eigh(g_mat) + self._i_sqrt_g_mat = ev@((1/jnp.sqrt(ei))[:, None]*ev.T) + # Stratonovich drift at id + self.v0 = self._make_v0() #: Stratonovich drift at the identity. + self.id_drift = self._make_id_drift() #: Ito drift at the identity. + +
+[docs] + def name(self): + raise NotImplementedError
+ + + def _lie_algebra_proj(self, omg): + """ The projection :math:`p_{\\mathfrak{g}}` at the identity. + """ + raise NotImplementedError + + def _mat_apply(self, mat, omg): + """ Implementing the operator :math:`\\mathcal{I}` applied on omg in :math:`\\mathcal{E}`. + """ + raise NotImplementedError + + def _id_opt(self, omg): + """The metric applied at the identity. + """ + return self._mat_apply(self._g_mat, omg) + + def _inv_id_opt(self, omg): + """Invert of _id_opt. + """ + return self._mat_apply(jla.inv(self._g_mat), omg) + +
+[docs] + def proj(self, x, omg): + return x@self._lie_algebra_proj(jla.solve(x, omg))
+ + + def _d_proj(self, x, xi, eta): + ivx = jla.inv(x) + return xi@self._lie_algebra_proj(jla.solve(x, eta)) \ + - x@self._lie_algebra_proj(ivx@xi@ivx@eta) + +
+[docs] + def rand_ambient(self, key): + return grand(key, (self.shape))
+ + +
+[docs] + def rand_vec(self, key, x): + omg, key = grand(key, self.shape) + return self.proj(x, omg), key
+ + +
+[docs] + def rand_point(self, key): + raise NotImplementedError
+ + +
+[docs] + def inner(self, x, a, b): + return jnp.sum(jla.solve(x, a)*self._id_opt(jla.solve(x, b)))
+ + +
+[docs] + def g_metric(self, x, omg): + return jla.solve(x.T, self._id_opt(jla.solve(x, omg)))
+ + +
+[docs] + def inv_g_metric(self, x, omg): + return x@self._inv_id_opt(x.T@omg)
+ + + @partial(jax.jit, static_argnums=(0,)) + def gamma(self, x, xi, eta): + # return - self.d_proj(x, xi, eta) + # + self.proj(x, self.gamma_ambient(x, xi, eta)) + ivxi = jla.solve(x, xi) + iveta = jla.solve(x, eta) + + return -0.5*(xi@iveta + eta@ivxi) \ + + 0.5*x@self._inv_id_opt( + self._lie_algebra_proj( + lie(self._id_opt(ivxi), iveta.T) \ + + lie(self._id_opt(iveta), ivxi.T))) + +
+[docs] + @partial(jax.jit, static_argnums=(0,)) + def gamma_ambient(self, x, xi, eta): + """Christoffel function for ambient manifold. + """ + ivx = jla.inv(x) + return 0.5*x@self._inv_id_opt( + - self._id_opt(ivx@xi@ivx@eta + ivx@eta@ivx@xi) \ + + lie(self._id_opt(ivx@xi), eta.T@ivx.T) \ + + lie(self._id_opt(ivx@eta), xi.T@ivx.T))
+ + +
+[docs] + def retract(self, x, v): + raise NotImplementedError
+ + + def _make_id_drift_longer(self): + """make the drift at identity. + The longer way, sum gamma.x. + """ + p = self.shape[0] + drft = jnp.zeros(self.shape) + for i in range(p): + for j in range(p): + eij = jnp.zeros((p, p)).at[i, j].set(1.) + drft -= self.gamma(jnp.eye(p), eij, + self._lie_algebra_proj(self._inv_id_opt(eij))) + return 0.5*drft + + def _make_id_drift(self): + """make the drift at identity. + Simplify so we dont need to evaluate gamma. + """ + p = self.shape[0] + v = jnp.zeros((p, p)) + zr = jnp.zeros((p, p)) + + def lp(a): + return self._lie_algebra_proj(a) + for i in range(p): + for j in range(p): + eij = zr.at[i, j].set(1.) + v += - eij@self._inv_id_opt(lp(eij)) \ + + self._inv_id_opt(lp(lie(lp(eij), eij.T))) + + return -0.5*v + + + def _make_v0(self): + """ make v0, the identity tangent vector corresponding to + the Stratonovich drift. + """ + p = self.shape[0] + v = jnp.zeros((p, p)) + zr = jnp.zeros((p, p)) + + for i in range(p): + for j in range(p): + eij = zr.at[i, j].set(1.) + + v += self._inv_id_opt( + self._lie_algebra_proj( + lie(self._lie_algebra_proj(eij), eij.T))) + + return -0.5*v + +
+[docs] + def approx_nearest(self, q): + """ find point on the manifold that + is nearest to q, same order as the nearest point. + """ + raise NotImplementedError
+ + + @partial(jax.jit, static_argnums=(0,)) + def ito_drift(self, x): + return x@self.id_drift + + +
+[docs] + @partial(jax.jit, static_argnums=(0,)) + def stratonovich_drift(self, x): + """ Stratonovich drift. + """ + return x@self.v0
+ + + # @partial(jax.jit, static_argnums=(0,)) +
+[docs] + def laplace_beltrami(self, x, egradx, ehessvp): + p = self.shape[0] + tup = jnp.zeros((p, p)) + ret = 0 + for i in range(p): + for j in range(p): + e_ij = tup.at[i, j].set(1.) + ret += self.proj(x, self.inv_g_metric( + x, ehessvp(x, e_ij)))[i, j] + return ret + 2*jnp.sum(self.ito_drift(x)*egradx)
+ + +
+[docs] + def left_invariant_vector_field(self, x, v): + """ map from a unit vector in the trace metric + to a vector field with unit length in the + left invariant metric. + """ + return x@self._mat_apply(self._i_sqrt_g_mat, v)
+ + +
+[docs] + @partial(jax.jit, static_argnums=(0,)) + def pseudo_transport(self, x, y, v): + """the easy one + """ + return y@jla.solve(x, v)
+ + +
+[docs] + @partial(jax.jit, static_argnums=(0,)) + def sigma_id(self, dw): + """ sigma, to generate the Brownian motion at the identity. + """ + return self._lie_algebra_proj(self._mat_apply(self._i_sqrt_g_mat, dw))
+ + +
+[docs] + @partial(jax.jit, static_argnums=(0,)) + def sigma(self, x, dw): + """ sigma, to generate the Brownian motion. + """ + return x@self.sigma_id(dw)
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+ + + + \ No newline at end of file diff --git a/_modules/jax_rb/manifolds/se_left_invariant.html b/_modules/jax_rb/manifolds/se_left_invariant.html new file mode 100644 index 0000000..babbb61 --- /dev/null +++ b/_modules/jax_rb/manifolds/se_left_invariant.html @@ -0,0 +1,218 @@ + + + + + + jax_rb.manifolds.se_left_invariant — jax_rb documentation + + + + + + + + + + + + + + + + + +
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Source code for jax_rb.manifolds.se_left_invariant

+""":math:`SE`: Special Euclidean group.
+"""
+
+from functools import partial
+
+import jax
+import jax.numpy as jnp
+import jax.numpy.linalg as jla
+from .matrix_left_invariant import MatrixLeftInvariant
+from ..utils.utils import (sym, asym)
+
+
+
+[docs] +class SELeftInvariant(MatrixLeftInvariant): + """Specian Euclidean group of Euclidean transformation of :math:`\\mathbb{R}^{n}`, + represented by a pair :math:`(A, v)\\in SO^(n)\\times \\mathbb{R}^{n}` + with action :math:`(A, v).w = Aw + v` for :math:`w\\in\\mathbb{R}^{n}` . + + Alternatively, it is represented as a matrix :math:`\\begin{bmatrix} A & v \\\\ 0 & 1 \\end{bmatrix}\\in GL(n+1)` where :math:`A\\in SO(n)`. + + :param n: size of A + :param g_mat: a positive definite matrix in :math:`\\mathbb{R}^{\\frac{n(n+1)}{2}\\times\\frac{n(n+1)}{2}}` defining the metric at :math:`I_{n+1}` + """ + def __init__(self, n, g_mat): + """ g_mat is a matrix of size (n(n+1)//2)**2 + used to define the metric + """ + super().__init__(n+1, g_mat) + self.dim = (n*(n+1))//2 + + def name(self): + return f"SE({self.shape[0]-1})" + + @partial(jax.jit, static_argnums=(0,)) + def _lie_algebra_proj(self, omg): + return omg.at[:-1, :-1].set(asym(omg[:-1, :-1])).at[-1, :].set(0.) + + def _mat_apply(self, mat, omg): + """ mat is a matrix of size (p(p+1)/)**2 + Trick is to vectorize both the symmetric + and anti symmetric away from the diagonal + """ + p = omg.shape[0] + sqrt2 = jnp.sqrt(2) + + reta = asym(omg[:-1, :-1]) + rets = sym(omg[:-1, :-1]) + + rows, cols = jnp.triu_indices(p-1, 1) + veca = mat@jnp.concatenate([reta.take(rows*(p-1)+cols)*sqrt2, + omg[:-1, -1]]) + vecs = mat@jnp.concatenate([rets.take(rows*(p-1)+cols)*sqrt2, + omg[-1, :-1]]) + + ret = jnp.empty((p, p)) + ret = ret.at[:-1, -1].set(veca[1-p:]) + ret = ret.at[-1, :-1].set(vecs[1-p:]) + + tota = jnp.zeros((p-1, p-1)) + tota = tota.at[rows, cols].set(veca[:1-p]) + tota = tota.at[cols, rows].set(-veca[:1-p]) + + tots = jnp.zeros((p-1, p-1)) + tots = tots.at[rows, cols].set(vecs[:1-p]) + tots = tots.at[cols, rows].set(vecs[:1-p]) + + ret = ret.at[:-1, :-1].set((tota+tots)/sqrt2) + return ret.at[jnp.diag_indices(p)].set(omg[jnp.diag_indices(p)]) + + def rand_point(self, key): + """ A random point on the manifold + """ + xt, key = self.rand_ambient(key) + xo = jla.qr(xt[:-1, :-1])[0] + if jla.det(xo) < 0: + xo = xo.at[0, :].set(-xo[0, :]) + + return xt.at[:-1, :-1].set(xo).at[-1, :-1].set(0.).at[-1, -1].set(1.), key + + # @partial(jax.jit, static_argnums=(0,)) + def retract(self, x, v): + """ second order retraction, but simple + """ + x1 = x + v - 0.5* self.proj(x, self.gamma(x, v, v)) + u, _, v = jla.svd(x1[:-1, :-1]) + return x1.at[:-1, :-1].set(u@v) + + @partial(jax.jit, static_argnums=(0,)) + def approx_nearest(self, q): + u, _, v = jla.svd(q[:-1, :-1]) + return q.at[:-1, :-1].set(u@v) + + def pseudo_transport(self, x, y, v): + """the easy one + """ + return y@x.T@v + + def sigma(self, x, dw): + return x@self._lie_algebra_proj(self._mat_apply(self._i_sqrt_g_mat, dw))
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+ + + + \ No newline at end of file diff --git a/_modules/jax_rb/manifolds/sl_left_invariant.html b/_modules/jax_rb/manifolds/sl_left_invariant.html new file mode 100644 index 0000000..c132381 --- /dev/null +++ b/_modules/jax_rb/manifolds/sl_left_invariant.html @@ -0,0 +1,216 @@ + + + + + + jax_rb.manifolds.sl_left_invariant — jax_rb documentation + + + + + + + + + + + + + + + + + +
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Source code for jax_rb.manifolds.sl_left_invariant

+""":math:`SL`: special linear group of matrices of determinant 1.
+"""
+
+import jax.numpy as jnp
+import jax.numpy.linalg as jla
+from .matrix_left_invariant import MatrixLeftInvariant
+from ..utils.utils import (grand, complement_basis_for_vector)
+
+
+
+[docs] +class SLLeftInvariant(MatrixLeftInvariant): + """:math:`SL(n)` Special linear group, of size :math:`n` with left invariant metric + defined by g_mat. + + :param n: size of the matrix + :param g_mat: a positive definite matrix in :math:`\\mathbb{R}^{(n^2-1)\\times (n^2-1)}` defining the metric at :math:`I_{n}` + """ + def __init__(self, n, g_mat): + """ g_mat is a matrix of size (n**2-1))**2 + used to define the metric + """ + normal = 1/jnp.sqrt(n)*jnp.ones(n) + self._u = jnp.concatenate( + [complement_basis_for_vector(normal), normal[:, None]], axis=1) + + super().__init__(n, g_mat) + self.dim = n*n-1 + + def name(self): + return f"SL({self.shape[0]})" + + def _vec_sl(self, mat): + """ vectorize an n time n matrix + with structure + upper -> first n(n-1)/2 + lower -> next n(n-1)/2 + diagonal + """ + n = mat.shape[0] + ret = jnp.empty(n*n) + n_up = n*(n-1)//2 + ret = ret.at[:n_up].set(mat[jnp.triu_indices(n, 1)]) + ret = ret.at[n_up:2*n_up].set(mat[jnp.tril_indices(n, -1)]) + return ret.at[2*n_up:].set(self._u.T@jnp.diagonal(mat)) + + def _unvec_sl(self, v): + """ unravel a n*n vector to a trace 0 vector + with + """ + n = self.shape[0] + ret = jnp.empty((n, n)) + n_up = n*(n-1)//2 + ret = ret.at[jnp.triu_indices(n, 1)].set(v[:n_up]) + ret = ret.at[jnp.tril_indices(n, -1)].set(v[n_up:2*n_up]) + return ret.at[jnp.diag_indices(n)].set(self._u@v[2*n_up:]) + + def _mat_apply(self, mat, omg): + """ mat is of size (n**-1)**2 + multiply on all cells except for last one + """ + # return (omg.reshape(-1).at[:-1].set(mat@omg.reshape(-1)[:-1])).reshape(self.shape) + v = self._vec_sl(omg) + return self._unvec_sl(v.at[:-1].set(mat@v[:-1])) + + def _lie_algebra_proj(self, omg): + return omg - jnp.diag(jnp.full((self.shape[0]), jnp.trace(omg)/self.shape[0])) + + def rand_ambient(self, key): + """random ambient vector + """ + return grand(key, (self.shape)) + + def rand_point(self, key): + """ A random point on the manifold + """ + ret, key = self.rand_ambient(key) + if jla.det(ret) < 0: + return self.approx_nearest(ret.at[0, :].set(-ret[0, :])), key + return self.approx_nearest(ret), key + + def retract(self, x, v): + """ second order retraction, but simple + """ + return self.approx_nearest(x + v - 0.5* self.proj(x, self.gamma(x, v, v))) + + def approx_nearest(self, q): + return q/jla.det(q)**(1/self.shape[0]) + + def pseudo_transport(self, x, y, v): + """the easy one + """ + return y@jla.solve(x, v) + + def sigma(self, x, dw): + """ sigma is applied on a vector rather than a matrix + """ + return x@self._mat_apply(self._i_sqrt_g_mat, dw)
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+ + + + \ No newline at end of file diff --git a/_modules/jax_rb/manifolds/so_left_invariant.html b/_modules/jax_rb/manifolds/so_left_invariant.html new file mode 100644 index 0000000..d7b7629 --- /dev/null +++ b/_modules/jax_rb/manifolds/so_left_invariant.html @@ -0,0 +1,222 @@ + + + + + + jax_rb.manifolds.so_left_invariant — jax_rb documentation + + + + + + + + + + + + + + + + + +
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Source code for jax_rb.manifolds.so_left_invariant

+""":math:`SO`: Special Orthogonal group.
+"""
+
+from functools import partial
+
+import jax
+import jax.numpy as jnp
+import jax.numpy.linalg as jla
+from .matrix_left_invariant import MatrixLeftInvariant
+from ..utils.utils import (asym, lie)
+
+
+
+[docs] +class SOLeftInvariant(MatrixLeftInvariant): + """The group :math:`SO(n)` of orthogonal matrices :math:`U\\in R^{n\\times n}` + of determinant 1 with metric :math:`Tr(\\omega^TU^T\\mathcal{I}(U^T\\omega))` + where :math:`\\mathcal{I}` is the metric defined by g_mat, a matrix of size + :math:`\\mathbb{R}^{\\frac{n(n-1)}{2}\\times \\frac{n(n-1)}{2}}`. + """ + def __init__(self, n, g_mat): + """ g_mat is a matrix of size :math:`\\frac{n(n-1)}{2}` + used to define the metric. + """ + super().__init__(n, g_mat) + self.dim = (n*(n-1)) // 2 + + def name(self): + return f"SO({self.shape[0]})" + + @partial(jax.jit, static_argnums=(0,)) + def _lie_algebra_proj(self, omg): + return asym(omg) + + @partial(jax.jit, static_argnums=(0,)) + def _mat_apply(self, mat, omg): + """ mat is a matrix of size (p(p-1))**2 + """ + p = omg.shape[0] + rows, cols = jnp.triu_indices(p, 1) + + ret = jnp.empty((p, p)) + ret = ret.at[rows, cols].set(mat@omg.take(rows*p+cols)) + ret = ret.at[cols, rows].set(mat@omg.T.take(rows*p+cols)) + ret = ret.at[jnp.diag_indices(p)].set(omg[jnp.diag_indices(p)]) + + return ret + + def rand_point(self, key): + """ A random point on the manifold + """ + xt, key = self.rand_ambient(key) + x, _ = jla.qr(xt) + return x, key + + # @partial(jax.jit, static_argnums=(0,)) + def retract(self, x, v): + """ second order retraction, but simple + """ + x1 = x + v - 0.5* self.proj_gamma(x, v, v) + u, _, v = jla.svd(x1) + + return u@v + + # @partial(jax.jit, static_argnums=(0,)) + def approx_nearest(self, q): + u, _, v = jla.svd(q) + return u@v + + # @partial(jax.jit, static_argnums=(0,)) + def pseudo_transport(self, x, y, v): + """the easy one + """ + return y@x.T@v + + @partial(jax.jit, static_argnums=(0,)) + def proj_gamma(self, x, xi, eta): + """projection of christoffel function + """ + # return - self.d_proj(x, xi, eta) + # + self.proj(x, self.gamma_ambient(x, xi, eta)) + ivxi = jla.solve(x, xi) + iveta = jla.solve(x, eta) + + return -0.5*x@self._lie_algebra_proj(ivxi@iveta + iveta@ivxi) \ + + 0.5*x@self._inv_id_opt( + self._lie_algebra_proj( + lie(self._id_opt(ivxi), iveta.T) \ + + lie(self._id_opt(iveta), ivxi.T))) + + # @partial(jax.jit, static_argnums=(0,)) + def sigma_la(self, vec_dw): + """ sigma is applied on the lie agebra identified with a vector + """ + p = self.shape[0] + v = jnp.zeros(self.shape) + rows, cols = jnp.triu_indices(p, 1) + for idx in range(vec_dw.shape[0]): + i, j = rows[idx], cols[idx] + v += 1/jnp.sqrt(2)*vec_dw[idx]*self._mat_apply( + self._i_sqrt_g_mat, + jnp.zeros((p, p)).at[i, j].set(1.).at[j, i].set(-1.) + ) + return v
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+ + + + \ No newline at end of file diff --git a/_modules/jax_rb/manifolds/spd.html b/_modules/jax_rb/manifolds/spd.html new file mode 100644 index 0000000..1f7b22f --- /dev/null +++ b/_modules/jax_rb/manifolds/spd.html @@ -0,0 +1,220 @@ + + + + + + jax_rb.manifolds.spd — jax_rb documentation + + + + + + + + + + + + + + + + + +
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Source code for jax_rb.manifolds.spd

+"""Symmetric Positive Definite Matrix Manifold :math:`\\mathrm{S}^+(p)` of positive definite matrices of shape :math:`p\\times p` .
+"""
+
+from functools import partial
+
+import jax
+import jax.numpy as jnp
+import jax.numpy.linalg as jla
+from jax.scipy.linalg import expm
+
+from ..utils.utils import (sym)
+from .global_manifold import GlobalManifold
+
+
+
+[docs] +class PositiveDefiniteManifold(GlobalManifold): + """The manifold of positive definite matrices of size :math:`p` . + """ + def __init__(self, p): + """Constructor + """ + self.shape = (p, p) + self.dim = (p*(p+1))//2 + + def name(self): + return f"S+({self.shape[0]})" + + def inner(self, x, a, b): + return jnp.sum(jla.solve(x, a)*jla.solve(x, b.T).T) + + def g_metric(self, x, omg): + return jla.solve(x, jla.solve(x, omg.T).T) + + def inv_g_metric(self, x, omg): + return x@omg@x + + @partial(jax.jit, static_argnums=(0,)) + def proj(self, x, omg): + return sym(omg) + + def rand_point(self, key): + xt, key = self.rand_ambient(key) + return sym(xt@xt.T), key + + @partial(jax.jit, static_argnums=(0,)) + def gamma(self, x, xi, eta): + return -sym(xi@jla.solve(x, eta)) + + def retract(self, x, v): + return x+ v - 0.5* self.proj(x, self.gamma(x, v, v)) + + def approx_nearest(self, q): + """ point on the manifold nearest to q. + """ + return q + + def gamma_ambient(self, x, omg1, omg2): + """ gamma on the ambient space. + """ + return -sym(omg1@jla.solve(x, omg2)) + + @partial(jax.jit, static_argnums=(0,)) + def ito_drift(self, x): + return (self.shape[0]+1)/4*x + + @partial(jax.jit, static_argnums=(0,)) + def stratonovich_drift(self, x): + """ Brownian Stratonovich drift + """ + ei, ev = jla.eigh(x) + sei = jnp.sqrt(jnp.abs(ei)) + ss = -jnp.array([sei[i]**2*(.5+jnp.sum(sei/(sei[i]+sei))) + for i in range(self.shape[0])]) + return 0.5*ev@(ss[:, None]*ev.T) + (self.shape[0]+1)/4*x + + def laplace_beltrami(self, x, egradx, ehessvp): + n, p = self.shape + tup = jnp.zeros(self.shape) + ret = 0 + for i in range(n): + for j in range(p): + e_ij = tup.at[i, j].set(1.) + ret += self.proj(x, self.inv_g_metric( + x, ehessvp(x, e_ij)))[i, j] + return ret + 2*jnp.sum(self.ito_drift(x)*egradx) + + def pseudo_transport(self, x, y, v): + return v + + def sigma(self, x, dw): + def xhf(x): + ei, ev = jla.eigh(x) + return ev@(jnp.sqrt(ei)[:, None]*ev.T) + + x2 = xhf(x) + # return x2@unvech(dw)@x2 + return x2@sym(dw)@x2 + + def exp(self, x, v): + """ Geodesic.""" + return sym(x@expm(jla.solve(x, v)))
+ +
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+ + + + \ No newline at end of file diff --git a/_modules/jax_rb/manifolds/sphere.html b/_modules/jax_rb/manifolds/sphere.html new file mode 100644 index 0000000..d5e4b44 --- /dev/null +++ b/_modules/jax_rb/manifolds/sphere.html @@ -0,0 +1,247 @@ + + + + + + jax_rb.manifolds.sphere — jax_rb documentation + + + + + + + + + + + + + + + + + +
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+ +
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+ +

Source code for jax_rb.manifolds.sphere

+""" Sphere of constant curvature
+"""
+
+from functools import partial
+
+import jax
+import jax.numpy as jnp
+import jax.numpy.linalg as jla
+from ..utils.utils import (grand, complement_basis_for_vector)
+from .global_manifold import GlobalManifold
+
+
+
+[docs] +class Sphere(GlobalManifold): + """The sphere :math:`x_0^2+x_1^2+\\cdots+x_d^2 = r^2` + with sectional curvature :math:`\\frac{1}{r^2}`. + + :param n: dimension of :math:`\\mathcal{E}` + :param r: the radius. + """ + def __init__(self, n, r): + """ + """ + self.r = r + self.dim = n-1 + self.shape = (n,) + self.x0 = jnp.array([r] + (n-1)*[0.]) + + def name(self): + return f"Sphere S^{self.dim}" + + def inner(self, x, a, b): + return jnp.sum(a*b) + + def g_metric(self, x, omg): + return omg + + def inv_g_metric(self, x, omg): + return omg + + def dist(self, x, y): + """ distance between x and y + """ + return self.r*jnp.arccos(1/self.r**2*jnp.sum(x*y)) + + def log(self, x, y): + """ Riemannian logarithm + """ + al = 1/self.r**2*jnp.sum(x*y) + return jnp.arccos(al)/(1-al**2)**.5*(y-al*x) + + def exp(self, x, v): + """ geodesic + """ + vnr = 1/self.r*jnp.sqrt(jnp.sum(v*v)) + ret = jnp.cos(vnr)*x + jnp.sin(vnr)*v/vnr + return ret/jnp.sqrt(jnp.sum(ret*ret))*self.r + + @partial(jax.jit, static_argnums=(0,)) + def geodesic(self, x, v, t): + """ geodesic + """ + return self.exp(x, t*v) + + def d_exp(self, x, v, t): + """ derivative in t of Exp(x, tv) + """ + vnr = 1/self.r*jnp.sqrt(self.inner(x, v, v)) + return -jnp.sin(t*vnr)*vnr*x + jnp.cos(t*vnr)*v + + def _d2_exp(self, x, v, t): + """ second derivativederivative in t of Exp(x, tv) + """ + vnr = 1/self.r*jnp.sqrt(jnp.sum(v*v)) + # return -jnp.cos(t*vnr)*vnr**2*x - jnp.sin(t*vnr)/vnr*v + return -jnp.cos(t*vnr)*vnr**2*x - jnp.sin(t*vnr)*vnr*v + + def rand_point(self, key): + xt, key = grand(key, (self.shape[0],)) + return xt/jla.norm(xt, 2)*self.r, key + + def proj(self, x, omg): + return omg - 1/self.r**2*x*jnp.sum(x*omg) + + def pseudo_transport(self, x, y, v): + """ This is the real transport + """ + return v - self.inner(x, y, v)/(self.r**2+self.inner(x, x, y))*(x+y) + + def transport_along_geodesic(self, x, v1, v, t): + """ optimal transport along geodesic + """ + vnr1 = 1/self.r*jnp.sqrt(jnp.sum(v1*v1)) + return v - jnp.sin(t*vnr1)/vnr1*self.inner(x, v1, v)/self.r**2*x \ + - 1/self.r**2*jnp.sin(t*vnr1)**2/vnr1**2*self.inner(x, v1, v)/(1+jnp.cos(t*vnr1))*v1 + + def gamma(self, x, xi, eta): + """Christoffel function + """ + return 1/self.r**2*x*jnp.sum(xi*eta) + + def ito_drift(self, x): + return -1*self.dim/(2*self.r**2) * x + + def retract(self, x, v): + return (x+v)/jnp.sqrt(jnp.sum((x+v)**2))*self.r + + def approx_nearest(self, q): + """ find point on the manifold that + is nearest to q, same order as the nearest point + """ + return q/jnp.sqrt(jnp.sum(q*q))*self.r + + def sigma(self, x, dw): + return dw + + @partial(jax.jit, static_argnums=(0,)) + def make_tangent_basis(self, y): + """ yet another way to get complement basis + """ + cmp = complement_basis_for_vector(y) + mat = jax.vmap(lambda v1: jnp.array( + [self.inner(y, v1, cmp[:, i]) for i in range(cmp.shape[1])]), + in_axes=1, + )(cmp) + + ei, ev = jla.eigh(mat) + return cmp@ev@(1/jnp.sqrt(ei)[:, None]*ev.T)
+ +
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+ +
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+ + + + \ No newline at end of file diff --git a/_modules/jax_rb/manifolds/stiefel.html b/_modules/jax_rb/manifolds/stiefel.html new file mode 100644 index 0000000..a864b33 --- /dev/null +++ b/_modules/jax_rb/manifolds/stiefel.html @@ -0,0 +1,291 @@ + + + + + + jax_rb.manifolds.stiefel — jax_rb documentation + + + + + + + + + + + + + + + + + +
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+ +

Source code for jax_rb.manifolds.stiefel

+"""Stiefel manifold :math:`\\mathrm{St}(n, p, \\alpha_0, \\alpha_1)` with metric defined by two parameters.
+"""
+
+from functools import partial
+
+import jax
+import jax.numpy as jnp
+import jax.numpy.linalg as jla
+from jax.scipy.linalg import expm
+from ..utils.utils import (grand, sym, asym, esqrtm, unvec_skew)
+from .global_manifold import GlobalManifold
+
+
+
+[docs] +class RealStiefelAlpha(GlobalManifold): + """The manifold :math:`Y^TY = I` where :math:`Y` is a matrix of size :math:`shape=n\\times p` with metric :math:`\\lvert \\omega\\rvert^2_{\\mathsf{g}} =\\alpha_0 Tr(\\omega^T\\omega) +(\\alpha_0-\\alpha_1)Tr(\\omega^TYY^T\\omega)` . + + :param shape: tuple (n, p), + :param alpha: array of 2 positive numbers. + """ + def __init__(self, shape, alpha): + """Constructor + """ + self.shape = shape + n, p = shape + self.dim = (n-p)*p+(p*(p-1))//2 + self.alpha = alpha + + def name(self): + return f"Stiefel({self.shape}) alpha={self.alpha}" + + def inner(self, x, a, b): + al = self.alpha + return al[0]*jnp.sum(a*b) + (al[1]-al[0])*jnp.sum((x.T@a)*(x.T@b)) + + def g_metric(self, x, omg): + """ the metric operator g + """ + al = self.alpha + return al[0]*omg + (al[1]-al[0])*x@(x.T@omg) + + def inv_g_metric(self, x, omg): + """ inverse of the metric operator g + """ + al = self.alpha + return 1/al[0]*omg + (1/al[1]-1/al[0])*x@(x.T@omg) + + @partial(jax.jit, static_argnums=(0,)) + def proj(self, x, omg): + """ Metric compatible projection + """ + return omg - x@sym(x.T@omg) + + def rand_vec(self, key, x): + """random tangent vector + """ + omg, key = grand(key, self.shape) + return self.proj(x, omg), key + + def rand_point(self, key): + """ A random point on the manifold + """ + xt, key = self.rand_ambient(key) + x, _ = jla.qr(xt) + return x, key + + @partial(jax.jit, static_argnums=(0,)) + def gamma(self, x, xi, eta): + """Christoffel function + """ + + def grass_proj(omg): + return omg - x@(x.T@omg) + + al = self.alpha + return x@sym(xi.T@eta) \ + + (al[0] - al[1])/al[0]*grass_proj(xi@(eta.T@x) + eta@(xi.T@x)) + + @partial(jax.jit, static_argnums=(0,)) + def retract(self, x, v): + """ second order retraction, but simple + """ + x1 = x+ v - 0.5* self.proj(x, self.gamma(x, v, v)) + ei, ev = jla.eigh(x1.T@x1) + return x1@ev@((1/jnp.sqrt(ei))[:, None]*ev.T) + + @partial(jax.jit, static_argnums=(0,)) + def approx_nearest(self, q): + """ second order retraction, but simple + """ + # return jax.scipy.linalg.polar(q)[0] + ei, ev = jla.eigh(q.T@q) + return q@ev@((1/jnp.sqrt(ei))[:, None]*ev.T) + + def gamma_ambient(self, x, omg1, omg2): + """ gamma of the metric on the ambient space + """ + al = self.alpha + return (al[1]-al[0])*self.inv_g_metric( + x, + omg1@asym(x.T@omg2) + + x@sym(omg1.T@omg2) + + omg2@asym(x.T@omg1) + ) + + @partial(jax.jit, static_argnums=(0,)) + def ito_drift(self, x): + al = self.alpha + n, p = self.shape + return -0.5*((n-p)/al[0] + 0.5*(p-1)/al[1])*x + + def laplace_beltrami(self, x, egradx, ehessvp): + n, p = self.shape + tup = jnp.zeros(self.shape) + ret = 0 + for i in range(n): + for j in range(p): + e_ij = tup.at[i, j].set(1.) + ret += self.proj(x, self.inv_g_metric( + x, ehessvp(x, e_ij)))[i, j] + return ret + 2*jnp.sum(self.ito_drift(x)*egradx) + + def sigma(self, x, dw): + alh = 1/jnp.sqrt(self.alpha) + return alh[0]*dw + (alh[1]-alh[0])*x@(x.T@dw) + + def sigma0(self, x, dw0): + """ dw is a vector space of size self.dim. + We use this for the geodesic + walk strategy. Need storage for the complement + """ + alh = 1/jnp.sqrt(self.alpha) + n, p = self.shape + # ret = alh[1]*x@unvecah(dw0[((p*(p-1)))//2]) + pk = ((p*(p-1)))//2 + ret = alh[1]*x@unvec_skew(dw0[:pk]) + P = esqrtm(x[:p, :].T@x[:p, :]) + Q = jla.solve(P, x[:p, :].T).T + B = dw0[pk:].reshape(n-p, p) + ret += alh[0]*jnp.concatenate( + [- Q@x[p:, :].T@B, + B - x[p:, :]@jla.solve(P + jnp.eye(p), x[p:, :].T@B)], + axis=0) + return ret + + def pseudo_transport(self, x, y, v): + v1 = self.proj(y, v) + return v1/jnp.sqrt(self.inner(y, v1, v1)) + + def exp(self, x, eta): + """ Geodesics, the formula involves matrices of size 2d + + Parameters + ---------- + x : a manifold point + eta : tangent vector + + Returns + ---------- + gamma(1), where gamma(t) is the geodesics at Y in direction eta + + """ + p = eta.shape[1] + K = eta - x @ (x.T @ eta) + xp, R = jla.qr(K) + alf = self.alpha[1]/self.alpha[0] + A = x.T @ eta + x_mat = jnp.concatenate([ + jnp.concatenate([2*alf*A, -R.T], axis=1), + jnp.concatenate([R, jnp.zeros((p, p))], axis=1)], axis=0) + return jnp.array( + jnp.concatenate([x, xp], axis=1) @ expm(x_mat)[:, :p] @ expm((1-2*alf)*A))
+ +
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+ + + + \ No newline at end of file diff --git a/_modules/jax_rb/simulation/global_manifold_integrator.html b/_modules/jax_rb/simulation/global_manifold_integrator.html new file mode 100644 index 0000000..492df8a --- /dev/null +++ b/_modules/jax_rb/simulation/global_manifold_integrator.html @@ -0,0 +1,198 @@ + + + + + + jax_rb.simulation.global_manifold_integrator — jax_rb documentation + + + + + + + + + + + + + + + + + +
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Source code for jax_rb.simulation.global_manifold_integrator

+"""Module implementing simulation methods for embedded manifolds
+"""
+from functools import partial
+
+
+import jax.numpy as jnp
+from jax import jit
+
+
+
+[docs] +@partial(jit, static_argnums=(0,)) +def geodesic_move(mnf, x, unit_move, scale): + """ simulate using a second order retraction. + The move is :math:`x_{new} = \\mathfrak{r}(x, \\Pi(x)\\sigma(x)(\\text{unit_move}(\\text{scale})^{\\frac{1}{2}}))` + """ + return mnf.retract(x, mnf.proj(x, mnf.sigma(x, unit_move.reshape(mnf.shape)*jnp.sqrt(scale))))
+ + + +
+[docs] +@partial(jit, static_argnums=(0,)) +def geodesic_move_normalized(mnf, x, unit_move, scale): + """ similar to geodesic_move, but the move is normalized to have fixed length :math:`scale^{\\frac{1}{2}}` + """ + # stochastic dx + v = mnf.proj(x, mnf.sigma(x, unit_move.reshape(mnf.shape))) + v = v/jnp.sqrt(mnf.inner(x, v, v))*jnp.sqrt(scale) + return mnf.retract(x, v)
+ + + +
+[docs] +@partial(jit, static_argnums=(0,)) +def geodesic_move_exact(mnf, x, unit_move, scale): + """ similar to geodesic_move, but use exact geodesic + """ + return mnf.exp(x, mnf.proj(x, mnf.sigma(x, unit_move.reshape(mnf.shape)*jnp.sqrt(scale))))
+ + + +
+[docs] +@partial(jit, static_argnums=(0,)) +def geodesic_move_exact_normalized(mnf, x, unit_move, scale): + """ similar to geodesic_move_exact, but use normalize the unit_move + """ + # stochastic dx + v = mnf.proj(x, mnf.sigma(x, unit_move.reshape(mnf.shape))) + v = v/jnp.sqrt(mnf.inner(x, v, v))*jnp.sqrt(scale) + return mnf.exp(x, v)
+ + + +
+[docs] +@partial(jit, static_argnums=(0,)) +def rbrownian_ito_move(mnf, x, unit_move, scale): + """ + Use Euler Maruyama and projection method to solve the Ito equation. + """ + return mnf.approx_nearest( + x + mnf.proj(x, mnf.sigma(x, unit_move.reshape(mnf.shape)*jnp.sqrt(scale))) + + mnf.ito_drift(x)*scale)
+ + + +
+[docs] +@partial(jit, static_argnums=(0,)) +def rbrownian_stratonovich_move(mnf, x, unit_move, scale): + """ Use Euler Heun and projection method to solve the Stratonovich equation. + """ + # stochastic dx + dxs = mnf.sigma(x, unit_move.reshape(mnf.shape)*jnp.sqrt(scale)) + xbk = x + mnf.proj(x, dxs) + return mnf.approx_nearest(x + mnf.proj(0.5*(x + xbk), dxs) + + mnf.proj(x, mnf.ito_drift(x)*scale))
+ +
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+ + + + \ No newline at end of file diff --git a/_modules/jax_rb/simulation/matrix_group_integrator.html b/_modules/jax_rb/simulation/matrix_group_integrator.html new file mode 100644 index 0000000..a99e84d --- /dev/null +++ b/_modules/jax_rb/simulation/matrix_group_integrator.html @@ -0,0 +1,233 @@ + + + + + + jax_rb.simulation.matrix_group_integrator — jax_rb documentation + + + + + + + + + + + + + + + + + +
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Source code for jax_rb.simulation.matrix_group_integrator

+"""Module implementing simulation methods for left invariant matrix Lie group
+"""
+from functools import partial
+
+
+import jax.numpy as jnp
+from jax import jit
+
+
+
+[docs] +@partial(jit, static_argnums=(0,)) +def geodesic_move(mnf, x, unit_move, scale): + """ unit_move is reshaped to the shape conforming with sigma., usually the shape of the ambient space. + The move is :math:`x_{new} = \\mathfrak{r}(x, \\sigma(x)(\\text{unit_move}(\\text{scale})^{\\frac{1}{2}}))` + """ + return x@mnf.retract(jnp.eye(mnf.shape[0]), + mnf.sigma_id( + jnp.sqrt(scale)*unit_move.reshape(mnf.shape)))
+ + + +
+[docs] +@partial(jit, static_argnums=(0,)) +def geodesic_move_normalized(mnf, x, unit_move, scale): + """ Similar to geodesic_move, but unit move is rescaled to have fixed length 1 + in the metric of the group. + """ + v = mnf.sigma_id(unit_move.reshape(mnf.shape)) + v = v / jnp.sqrt(mnf.inner(jnp.eye(mnf.shape[0]), v, v)) * jnp.sqrt(scale) + return x@mnf.retract(jnp.eye(mnf.shape[0]), v)
+ + + +
+[docs] +@partial(jit, static_argnums=(0,)) +def geodesic_move_dim_g(mnf, x, unit_move, scale): + """Unit_move is of dimension :math:`\\dim \\mathrm{G}`. + The move is :math:`x_{new} = \\mathfrak{r}(x, \\sigma_{la}(x)(\\text{unit_move}(\\text{scale})^{\\frac{1}{2}}))` + """ + return x@mnf.retract(jnp.eye(mnf.shape[0]), + mnf.sigma_la(jnp.sqrt(scale)*unit_move))
+ + + +
+[docs] +@partial(jit, static_argnums=(0,)) +def geodesic_move_dim_g_normalized(mnf, x, unit_move, scale): + """ Similar to geodesic_move_dim_g, but unit move is rescaled to have fixed length 1 + in the metric of the group. + """ + nu = unit_move/jnp.sqrt(jnp.sum(unit_move**2)) + return x@mnf.retract(jnp.eye(mnf.shape[0]), + mnf.sigma_la(jnp.sqrt(scale)*nu))
+ + + +
+[docs] +@partial(jit, static_argnums=(0,)) +def rbrownian_ito_move(mnf, x, unit_move, scale): + """ Use stochastic projection method to solve the Ito equation. + Use Euler Maruyama here. + """ + n = mnf.shape[0] + return mnf.approx_nearest( + x@jnp.eye(n) + x@mnf.sigma_id(unit_move.reshape(mnf.shape)*jnp.sqrt(scale)) + + x@mnf.id_drift*scale)
+ + + +
+[docs] +@partial(jit, static_argnums=(0,)) +def rbrownian_stratonovich_move(mnf, x, unit_move, scale): + """ Using projection method to solve the Stratonovich equation. + In many cases :math:`v_0` is zero (unimodular group). + Use Euler Heun. + """ + n = mnf.shape[0] + # stochastic dx + dxs = mnf.sigma_id(unit_move.reshape(mnf.shape)*jnp.sqrt(scale)) + + move = jnp.eye(n) + 0.5*(2*jnp.eye(n)+dxs)@dxs + mnf.v0*scale + return x@mnf.approx_nearest(move)
+ + +
+[docs] +@partial(jit, static_argnums=(0,)) +def ito_move_dim_g(mnf, x, unit_move, scale): + """Similar to rbrownian_ito_move, but driven with a Wiener + process of dimension :math:`\\dim \\mathrm{G}`. + """ + return x@mnf.approx_nearest( + jnp.eye(mnf.shape[0]) + mnf.sigma_la(unit_move*jnp.sqrt(scale)) + + mnf.id_drift*scale)
+ + +
+[docs] +@partial(jit, static_argnums=(0,)) +def stratonovich_move_dim_g(mnf, x, unit_move, scale): + """Similar to rbrownian_stratonovich_move, but driven with a Wiener + process of dimension :math:`\\dim \\mathrm{G}`. + """ + n = mnf.shape[0] + # stochastic dx + dxs = mnf.sigma_la(unit_move*jnp.sqrt(scale)) + + move = jnp.eye(n) + 0.5*(2*jnp.eye(n)+dxs)@dxs + mnf.v0*scale + return x@mnf.approx_nearest(move)
+ +
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+ + + + \ No newline at end of file diff --git a/_modules/jax_rb/simulation/retractive_integrator.html b/_modules/jax_rb/simulation/retractive_integrator.html new file mode 100644 index 0000000..d9d172b --- /dev/null +++ b/_modules/jax_rb/simulation/retractive_integrator.html @@ -0,0 +1,171 @@ + + + + + + jax_rb.simulation.retractive_integrator — jax_rb documentation + + + + + + + + + + + + + + + + + +
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Source code for jax_rb.simulation.retractive_integrator

+"""Module implementing the retractive Euler-Maruyama integrator.
+"""
+from functools import partial
+
+
+import jax.numpy as jnp
+from jax import jit
+
+
+
+[docs] +@partial(jit, static_argnums=(0,2,5,6)) +def retractive_move(rtr, x, t, unit_move, scale, sigma, mu): + """ Simulating the equation :math:`dX_t = \\mu(X_t, t) dt + \\sigma(X_t, t) dW_t` using the retraction rtr. + We do not assume a Riemanian metric on the manifold, :math:`\\sigma\\sigma^T` could be degenerated on :math:`T\\mathcal{M}`. + + W is a Wiener process driving the equation, defined on :math:`\\mathbb{R}^k`. W is given by unit_move. + + :math:`\\sigma(X_t, t)` maps :math:`\\mathbb{R}^k` to :math:`\\mathcal{E}`, but the image belongs + to :math:`T_{X_t}\\mathcal{M}`. + + The retraction rtr is assume to have the method :math:`\\text{drift_adj}` for an adjustment. + + The move is :math:`x_{new} = \\mathfrak{r}(x, \\Pi(x)\\sigma(x)(\\text{unit_move}(\\text{scale})^{\\frac{1}{2}}) + \\text{scale} (\\mu + \\text{drift_adj}))`. + + :param rtr: the retraction, + :param x: a point on the manifold, + :param t: time + :param unit_move: a random normal draw + :param scale: scaling + :param sigma: a function implementing the map :math:`\\sigma` + :param mu: a function implementing the Ito drift :math:`\\mu` + """ + return rtr.retract(x, + sigma(x, t, unit_move)*jnp.sqrt(scale) + + scale*(mu(x, t) + rtr.drift_adjust(sigma, x, t, unit_move.shape[0])))
+ + + +
+[docs] +@partial(jit, static_argnums=(0,2,5,6)) +def retractive_move_normalized(rtr, x, t, unit_move, scale, sigma, mu): + """ Similar to retractive_move, but the stochastic part is normalized to have fixed length :math:`scale^{\\frac{1}{2}}` + """ + # v = mnf.proj(x, mnf.sigma(x, unit_move.reshape(mnf.shape))) + # v = v/jnp.sqrt(mnf.inner(x, v, v))*jnp.sqrt(scale) + # return mnf.retract(x, v) + v = sigma(x, t, unit_move) + mnf = rtr.mnf + return rtr.retract(x, + sigma(x, t, v/jnp.sqrt(mnf.inner(x, v, v))*jnp.sqrt(scale*mnf.dim)) + + scale*(mu(x, t) + rtr.drift_adjust(sigma, x, t, unit_move.shape[0])))
+ +
+ +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/_modules/jax_rb/simulation/simulator.html b/_modules/jax_rb/simulation/simulator.html new file mode 100644 index 0000000..2ef8d5f --- /dev/null +++ b/_modules/jax_rb/simulation/simulator.html @@ -0,0 +1,242 @@ + + + + + + jax_rb.simulation.simulator — jax_rb documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +

Source code for jax_rb.simulation.simulator

+"""Simulator for global_manifold
+"""
+from collections import namedtuple
+
+import jax.numpy as jnp
+# import jax.numpy.linalg as jla
+from jax import random, vmap
+
+
+
+[docs] +class RunParams(namedtuple('RunParams', + ['x_0', 'key', 't_final', 'n_path', + 'n_div', 'd_coeff', + 'wiener_dim', 'm_size', 'normalize', 'run_type'])): + """Parameters to save a run in simulator. + + :param x_0: starting point of the simulation + :param key: key to generate the random numbers used in simulation. Created from jax.random.PRNGKey, then jax.random.split. + :param t_final: The final time of simulation. Starting time is :math:`t=0`. + :param n_path: number of paths used in simulation + :param n_div: number of subdivision (interval will be t_final/n_div + :param d_coeff: difusion coefficient, d_coeff = 0.5 for the Riemannian Brownian motion. + :param wiener_dim: dimension of the Wienner process used in simulation. Usually it is the dimension of the ambient space :math:`\\mathcal{E}`. In some cases, we can simulate using the dimension of the manifold itself. + :param m_size: a param indicating the size of the manifold, use to differentiate when simulating several manifolds, + :param normalize: whether to normalize the move to a fixed lengh, + :param run_type: string indicating one of the simulation moves. This is a tag to distinguish the output, does not affect the results. + """
+ + + +
+[docs] +def simulate(x_0, + integrator, + path_pay_off, + final_pay_off, + params): + """A simulation from :math:`t=0` up to time :math:`t=t_final`, with time increment + :math:`t=\\frac{t_final}{n_div}`, run :math:`n_path` path. + Return the full distribution of the simulation. We use the minimum cut-off with accuracy level 0.5 in this version. + + :param x_0: starting point of the simulation + :param integrator: one of the integrators (geodesic, ito, stratonovich + :param path_pay_off: the cost evaluated along the path + :param final_pay_off: the contribution evaluated at the final time + :param params: additional parameters for the simulations: sk, t_final, n_path, n_div, d_coeff, wiener_dim + """ + sk, t_final, n_path, n_div, d_coeff, wiener_dim = params + p2 = 0.5 + a_h = (2*p2*jnp.log(t_final/n_div))**.5 + + x_all = random.normal(sk, (wiener_dim, n_div, n_path)) + x_all = x_all.at[jnp.where(x_all > a_h)].set(a_h).at[jnp.where(x_all < -a_h)].set(-a_h) + + def do_one_path(seq): + path_sum = 0. + x_i = x_0.copy() + for j in range(n_div): + x_i = integrator(x_i, seq[:, j], t_final/n_div*2*d_coeff) + + if path_pay_off: + path_sum += path_pay_off(x_i, j*t_final/n_div)*t_final/n_div + + return path_sum + final_pay_off(x_i) + + # batch_do_one_path = jax.vmap(do_one_path, in_axes=2) + pay_offs = vmap(do_one_path, in_axes=2)(x_all) + + return pay_offs, x_all
+ + + +
+[docs] +class Simulator(): + """ Class to do simulation on a manifold + with particular funtion or simulators. Run results is saved in self.runs. + + :param path_pay_off is the function value evaluated along the path + :param final_pay_off is the function value evaluated at final time + """ + def __init__(self, path_pay_off, + final_pay_off): + self.path_pay_off = path_pay_off + self.final_pay_off = final_pay_off + self.runs = [] + +
+[docs] + def run(self, integrator, params): + """ run a simulation + + :param integrator the integrator used + :param params is of class RunParams + """ + sim_params = (params.key, params.t_final, params.n_path, + params.n_div, params.d_coeff, + params.wiener_dim) + pay_offs, _ = simulate(params.x_0, integrator, self.path_pay_off, + self.final_pay_off, sim_params) + self.runs.append([params, pay_offs])
+ + +
+[docs] + def save_runs(self, save_path): + """ save all the runs to save_path + """ + idx = 0 + pay_offs = [] + prms = [] + while idx < len(self.runs): + pay_offs.append(self.runs[idx][1]) + fi = self.runs[idx][0]._fields + pp = {} + for i in range(len(fi)): + if fi[i] != 'x_0': + pp[fi[i]] = self.runs[idx][0][i] + prms.append(pp) + idx += 1 + jnp.savez(save_path, pay_offs=pay_offs, + params=prms, allow_pickle=True)
+
+ +
+ +
+
+ +
+
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+
+ + + + \ No newline at end of file diff --git a/_modules/jax_rb/utils/utils.html b/_modules/jax_rb/utils/utils.html new file mode 100644 index 0000000..bf2595b --- /dev/null +++ b/_modules/jax_rb/utils/utils.html @@ -0,0 +1,445 @@ + + + + + + jax_rb.utils.utils — jax_rb documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +

Source code for jax_rb.utils.utils

+"""various utils for the project
+"""
+import jax.numpy as jnp
+import jax.numpy.linalg as jla
+from jax import random, jit
+
+
+def pos(x):
+    """ max(x, 0), jit friendly
+    """
+    return 0.5*(x+jnp.abs(x))
+
+
+def asym(mat):
+    return 0.5*(mat - mat.T)
+
+
+def sym2(mat):
+    return mat + mat.T
+
+
+def sym(a):
+    return 0.5*sym2(a)
+
+
+
+[docs] +def grand(key, dims): + """ generate a random array of shape dim using key + """ + key, sk = random.split(key) + return random.normal(sk, dims), key
+ + + +def lyapunov(a, b): + """solve aU + Ua = b + A, B, U are symmetric + """ + yei, yv = jla.eigh(a) + return yv@((yv.T@b@yv)/(yei[:, None] + yei[None, :]))@yv.T + + +def vcat(x, y): + """vertical concatenate + """ + return jnp.concatenate([x, y], axis=0) + + +def sinc(x): + """ better sinc than + """ + if jnp.abs(x) <= 1e-20: + return 1 + return jnp.sin(x)/x + + +def sinc1(x): + """sinc1 is dsinc/x + """ + if jnp.abs(x) < 1e-6: + return -1/3 + x*x/2/3/5 + return (x*jnp.cos(x)-jnp.sin(x))/x/x/x + + +def sinc2(x): + """ helper function, derivative of sinc1 = x*sinc2(x) + """ + if jnp.abs(x) < 1e-3: + return 1/15 - x*x/210 + x*x*x*x / 7560 + return -((x*x-3)*jnp.sin(x) + 3*x*jnp.cos(x))/x**5 + + +def dsinc(x): + """Derivative of sinc + """ + if jnp.abs(x) < 1e-6: + return -1/3*x + x*x*x/30 + return (x*jnp.cos(x)-jnp.sin(x))/x/x + + +def dsinc1(x): + """sinc1 is dsinc/x + dsinc1 is its derivative + """ + return x*sinc2(x) + +
+[docs] +def complement_basis_for_vector(xraw): + """ complement basis of xraw, a non zero vector. Assume x[0] !=0 + """ + x = xraw/jnp.sqrt(jnp.sum(xraw*xraw)) + q = 2.*(x[0] > 0) - 1 + p = x[0]/q + + return jnp.concatenate( + [-q*x[1:].reshape(1, -1), + jnp.eye(x.shape[0]-1)-1/(1+p)*x[1:][:, None]@x[1:][None, :]])
+ + + +
+[docs] +def esqrtm(x): + """ sqrtm by eigenvalue + """ + ei, ev = jla.eigh(x) + return ev@(jnp.sqrt(ei)[:, None]*ev.T)
+ + + +
+[docs] +def make_complement_basis(x): + """ make complement basis of + """ + n, p = x.shape + P = esqrtm(x[:p, :].T@x[:p, :]) + Q = jla.solve(P, x[:p, :].T).T + return jnp.concatenate([- Q@x[p:, :].T, + jnp.eye(n-p) - x[p:, :]@jla.solve(P + jnp.eye(p), x[p:, :].T)], + axis=0)
+ + + +
+[docs] +def generate_symmetric_tensor(key, k, m): + """Generating symmetric tensor size k,m + """ + mat = jnp.full(tuple(m*[k]), jnp.nan) + current_idx = m*[0] + active_i = m - 1 + tval, key = grand(key, (1,)) + mat = mat.at[tuple(current_idx)].set(tval[0]) + while True: + if current_idx[active_i] < k - 1: + current_idx[active_i] += 1 + if jnp.isnan(mat[tuple(current_idx)]): + i_s = tuple(sorted(current_idx)) + if jnp.isnan(mat[i_s]): + tval, key = grand(key, (1,)) + mat = mat.at[i_s].set(tval[0]) + # print('Doing %s' % str(i_s)) + mat = mat.at[tuple(current_idx)].set(mat[i_s]) + # print('Doing %s' % str(current_idx)) + elif active_i == 0: + break + else: + next_pos = jnp.where(jnp.array(current_idx)[:active_i] < k-1)[0] + if next_pos.shape[0] == 0: + break + current_idx[next_pos[-1]] += 1 + for jx in range(next_pos[-1]+1, m): + current_idx[jx] = 0 + + active_i = m - 1 + if jnp.isnan(mat[tuple(current_idx)]): + i_s = tuple(sorted(current_idx)) + if jnp.isnan(mat[i_s]): + tval, key = grand(key, (1,)) + mat = mat.at[i_s].set(tval) + # print('Doing %s' % str(i_s)) + mat = mat.at[tuple(current_idx)].set(mat[i_s]) + # print('Doing %s' % str(current_idx)) + return mat, key
+ + + +def _fill_symmetric(p_raw, k): + """Fill a k by k matrix with p_raw symmetrically + """ + p = jnp.zeros((k, k)) + start = 0 + for i in range(k-1): + p = p.at[i, i+1:].set(p_raw[start:start+k-i-1]) + p = p.at[i+1:, i].set(p_raw[start:start+k-i-1]) + start += k-i-1 + return jnp.fill_diagonal(p, p_raw[-k:], inplace=False) + + +def tv_mode_product(tensor, x, modes): + """ Evaluating tensor subsituting x for the last modes times indices + """ + v = tensor + for _ in range(modes): + v = jnp.tensordot(v, x, axes=1) + return v + + +def _gen_so_inertia_matrix(key, n): + """ generate an n times n symmetric matrix + with diagonal 1 + """ + i_mat, key = grand(key, (n , n)) + i_mat = sym(jnp.abs(i_mat)) + i_mat = i_mat.at[jnp.diag_indices(n)].set(1.) + return i_mat, key + + +def _old_rand_positive_definite(key, n): + """ generate a positive definite matrix of size n + """ + # n2 = (n*(n-1)) // 2 + mat, key = grand(key, (n, n)) + mat = mat@mat.T + return sym(mat), key + + +
+[docs] +def rand_positive_definite(key, n, bounds=None): + """ generate a positive definite matrix of size n + """ + # n2 = (n*(n-1)) // 2 + mat, key = grand(key, (n, n)) + if not bounds: + return sym(mat@mat.T), key + mat, _ = jla.qr(mat) + key, sk = random.split(key) + ei = random.uniform(sk, (n,), minval =bounds[0], maxval=bounds[1]) + mat = mat@(ei[:, None]*mat.T) + return sym(mat), key
+ + + +def _so_metric_opt(lu_mat, a): + """ bilinear form given by lu_mat operates on a. + lu_mat is a (n(n-1)/2)*(n(n-1)/2) matrix, operates on vectorization + of the upper and lower triangular matrices so the overall operation is + self-adjoint. + """ + p = a.shape[0] + rows, cols = jnp.triu_indices(p, 1) + + ret = jnp.empty((p, p)) + ret = ret.at[rows, cols].set(lu_mat@a.take(rows*p+cols)) + ret = ret.at[cols, rows].set(lu_mat@a.T.take(rows*p+cols)) + ret = ret.at[jnp.diag_indices(p)].set(a[jnp.diag_indices(p)]) + + return ret + + +def _inv_so_metric_opt(lu_mat, a): + """ invert of lu_mat + """ + p = a.shape[0] + rows, cols = jnp.triu_indices(p, 1) + + ret = jnp.empty((p, p)) + ret = ret.at[rows, cols].set(jla.solve(lu_mat, a.take(rows*p+cols))) + # rows, cols = jnp.tril_indices(p, -1) + ret = ret.at[cols, rows].set(jla.solve(lu_mat, a.T.take(rows*p+cols))) + ret = ret.at[jnp.diag_indices(p)].set(a[jnp.diag_indices(p)]) + + return ret + + +
+[docs] +def unvec_skew(v): + """ unravel a n(n-1)//2 vector to anti hermitian matrix + """ + sqrt2 = jnp.sqrt(2.) + rows = .5 * (1 + jnp.sqrt(1 + 8 * v.shape[0])) + rows = jnp.round(rows).astype(int) + result = jnp.zeros((rows, rows)) + result = result.at[jnp.triu_indices(rows, 1)].set(v) + + return (result.T - result)/sqrt2
+ + + +def unvec_anti_hermitian(v): + """ unravel a n(n-1)//2 vector to anti hermitian matrix + """ + sqrt2 = jnp.sqrt(2) + rows = .5 * (1 + jnp.sqrt(1 + 8 * len(v))) + rows = int(jnp.round(rows)) + result = jnp.zeros((rows, rows)) + result = result.at[jnp.triu_indices(rows, 1)].set(v) + return (result.T.conjugate() - result)/sqrt2 + + +def unvech(v): + """ Unvvectorize a symmetric matrix to a real vector + Undoing the vech operation. + sqrt2*upper triangular part concatenate with diagonal + This is compatible with the trace(a@b) metric + + Parameters + ---------- + v : A vector + Returns + ---------- + the symmetric matrix undoing the vech operation + """ + sqrt2 = jnp.sqrt(2) + # quadratic formula, correct fp error + rows = .5 * (-1 + jnp.sqrt(1 + 8 * v.shape[0])) + rows = jnp.round(rows).astype(int) + + result = jnp.zeros((rows, rows)) + result = result.at[jnp.triu_indices(rows)].set(v/jnp.sqrt(2)) + result = result.at[jnp.diag_indices(rows)].set( + result[jnp.diag_indices(rows)]/sqrt2) + # result = (result + result.T)/sqrt2 + # divide diagonal elements by 2 + + return result + result.T + + + +def lie(a, b): + """ Lie Bracket + """ + return a@b - b@a + + +
+[docs] +@jit +def jpolar(x): + """ jax polar decomposition + """ + return jla.solve(esqrtm(x.T@x), x.T).T
+ +
+ +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/_sources/animation.rst.txt b/_sources/animation.rst.txt new file mode 100644 index 0000000..84d787b --- /dev/null +++ b/_sources/animation.rst.txt @@ -0,0 +1,21 @@ +Animation +================= +Click on the images to view the animation. + +.. image:: _static/se2_animation.png + :width: 400 + :alt: Riemannian Brownian motion on SE(2). + :target: _static/se2_animation.mp4 + + +.. image:: _static/se3_animation.png + :width: 400 + :alt: Riemannian Brownian motion on SE(3). + :target: _static/se3_animation.mp4 + + +.. image:: _static/af2_animation.png + :width: 400 + :alt: Riemannian Brownian motion on :math:`Aff^+(2)` + :target: _static/af2_animation.mp4 + diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt new file mode 100644 index 0000000..92718df --- /dev/null +++ b/_sources/index.rst.txt @@ -0,0 +1,50 @@ +.. jax_rb documentation master file, created by + sphinx-quickstart on Mon Apr 1 23:16:45 2024. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +JAX RB: Riemannian Brownian motion on manifolds +=============================================== +JAX RB is a library for Riemannian Brownian motion on constrained manifolds embedded in a vector space, or on quotient of such manifolds by a compact group. The theory is developed in [NgSo24]_. Please refer to the `github repository `_ for installation instruction. + +.. math:: +.. toctree:: + :maxdepth: 2 + :caption: Manifolds + + manifolds + +.. toctree:: + :maxdepth: 2 + :caption: Simulation + + simulation + + +.. toctree:: + :maxdepth: 2 + :caption: Utils + + utils + + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + + +.. toctree:: + :maxdepth: 2 + :caption: Other Resources: + + Wikipedia + GitHub + + animation + +.. rubric:: References +.. [NgSo24] Nguyen, D.; Sommer, S...: Second-order differential operators, stochastic differential equations and Brownian motions on embedded manifolds `arXiv:2406.02879 `_. diff --git a/_sources/manifolds.rst.txt b/_sources/manifolds.rst.txt new file mode 100644 index 0000000..922df1f --- /dev/null +++ b/_sources/manifolds.rst.txt @@ -0,0 +1,117 @@ +jax\_rb.manifolds +================= + +.. automodule:: jax_rb.manifolds + + Global Manifold + =============== + .. autosummary:: + :toctree: _autosummary + + .. automodule:: jax_rb.manifolds.global_manifold + :members: + + Sphere + =============== + .. autosummary:: + :toctree: _autosummary + + .. automodule:: jax_rb.manifolds.sphere + .. autoclass:: Sphere + + Symmetric Positive Definite Matrix Manifold + ============================================ + .. autosummary:: + :toctree: _autosummary + + .. automodule:: jax_rb.manifolds.spd + .. autoclass:: PositiveDefiniteManifold + + Stiefel Manifold + ================= + .. autosummary:: + :toctree: _autosummary + + .. automodule:: jax_rb.manifolds.stiefel + .. autoclass:: RealStiefelAlpha + + Grassmann Manifold + ========================== + .. autosummary:: + :toctree: _autosummary + + .. automodule:: jax_rb.manifolds.grassmann + .. autoclass:: Grassmann + + Hypersurface with Diagonal constraints Manifold + ================================================ + .. autosummary:: + :toctree: _autosummary + + .. automodule:: jax_rb.manifolds.diag_hypersurface + .. autoclass:: DiagHypersurface + + + Matrix Lie Group Left Invariant Metric + ======================================= + .. autosummary:: + :toctree: _autosummary + + .. automodule:: jax_rb.manifolds.matrix_left_invariant + :members: + + Required implementations + ========================= + .. autofunction:: jax_rb.manifolds.matrix_left_invariant.MatrixLeftInvariant._lie_algebra_proj + .. autofunction:: jax_rb.manifolds.matrix_left_invariant.MatrixLeftInvariant._mat_apply + + + Base class + =========== + + :math:`\mathrm{GL}^+(n)` Generalized Linear Group Positive Determinant + ======================================================================== + .. autosummary:: + :toctree: _autosummary + + .. automodule:: jax_rb.manifolds.glp_left_invariant + .. autoclass:: GLpLeftInvariant + + :math:`\mathrm{Aff}^+(n)` Affine Linear Group Positive Determinant + ==================================================================== + .. autosummary:: + :toctree: _autosummary + + .. automodule:: jax_rb.manifolds.affine_left_invariant + .. autoclass:: AffineLeftInvariant + + :math:`\mathrm{SL}(n)` Special Linear Group + =============================================================== + .. autosummary:: + :toctree: _autosummary + + .. automodule:: jax_rb.manifolds.sl_left_invariant + .. autoclass:: SLLeftInvariant + + :math:`\mathrm{SO}(n)` Special Orthogonal Group + =============================================================== + .. autosummary:: + :toctree: _autosummary + + .. automodule:: jax_rb.manifolds.so_left_invariant + .. autoclass:: SOLeftInvariant + + :math:`\mathrm{SE}(n)` Special Euclidean Group + =============================================================== + .. autosummary:: + :toctree: _autosummary + + .. automodule:: jax_rb.manifolds.se_left_invariant + .. autoclass:: SELeftInvariant + + + + + + + diff --git a/_sources/simulation.rst.txt b/_sources/simulation.rst.txt new file mode 100644 index 0000000..0b872ca --- /dev/null +++ b/_sources/simulation.rst.txt @@ -0,0 +1,53 @@ +jax\_rb.simulation +================== + +.. automodule:: jax_rb.simulation + + Simulator + =============== + .. autosummary:: + :toctree: _autosummary + + .. automodule:: jax_rb.simulation.simulator + :members: + + + Matrix Lie Group Integrator + ============================= + .. autosummary:: + :toctree: _autosummary + + .. automodule:: jax_rb.simulation.matrix_group_integrator + :members: + + Global Manifold Integrator + ============================= + .. autosummary:: + :toctree: _autosummary + + .. automodule:: jax_rb.simulation.global_manifold_integrator + :members: + + Retractive Integrator + ============================= + .. autosummary:: + :toctree: _autosummary + + .. automodule:: jax_rb.simulation.retractive_integrator + :members: + + + + + + + + + + + + + + + + diff --git a/_sources/utils.rst.txt b/_sources/utils.rst.txt new file mode 100644 index 0000000..46c3231 --- /dev/null +++ b/_sources/utils.rst.txt @@ -0,0 +1,19 @@ +jax\_rb.utils +============= + +.. automodule:: jax_rb.utils + + Utils + ====== + .. autosummary:: + :toctree: _autosummary + + .. automodule:: jax_rb.utils.utils + .. autofunction:: jax_rb.utils.utils.complement_basis_for_vector + .. autofunction:: jax_rb.utils.utils.make_complement_basis + .. autofunction:: jax_rb.utils.utils.generate_symmetric_tensor + .. autofunction:: jax_rb.utils.utils.esqrtm + .. autofunction:: jax_rb.utils.utils.unvec_skew + .. autofunction:: jax_rb.utils.utils.jpolar + .. autofunction:: jax_rb.utils.utils.rand_positive_definite + .. autofunction:: jax_rb.utils.utils.grand diff --git a/_static/_sphinx_javascript_frameworks_compat.js b/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8141580 --- /dev/null +++ b/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. 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+ +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + "Search finished, found ${resultCount} page(s) matching the search query." + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlinks", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/animation.html b/animation.html new file mode 100644 index 0000000..c671de4 --- /dev/null +++ b/animation.html @@ -0,0 +1,127 @@ + + + + + + + Animation — jax_rb documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Animation

+

Click on the images to view the animation.

+Riemannian Brownian motion on SE(2). +Riemannian Brownian motion on SE(3). +Riemannian Brownian motion on :math:`Aff^+(2)` +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/genindex.html b/genindex.html new file mode 100644 index 0000000..a3cb04c --- /dev/null +++ b/genindex.html @@ -0,0 +1,620 @@ + + + + + + Index — jax_rb documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
  • + +
  • +
  • +
+
+
+
+
+ + +

Index

+ +
+ _ + | A + | C + | D + | E + | G + | I + | J + | L + | M + | N + | P + | R + | S + | U + | V + +
+

_

+ + + +
+ +

A

+ + + +
+ +

C

+ + +
+ +

D

+ + +
+ +

E

+ + +
+ +

G

+ + + +
+ +

I

+ + + +
+ +

J

+ + + +
    +
  • + jax_rb.manifolds + +
  • +
  • + jax_rb.manifolds.affine_left_invariant + +
  • +
  • + jax_rb.manifolds.diag_hypersurface + +
  • +
  • + jax_rb.manifolds.global_manifold + +
  • +
  • + jax_rb.manifolds.glp_left_invariant + +
  • +
  • + jax_rb.manifolds.grassmann + +
  • +
  • + jax_rb.manifolds.matrix_left_invariant + +
  • +
  • + jax_rb.manifolds.se_left_invariant + +
  • +
  • + jax_rb.manifolds.sl_left_invariant + +
  • +
  • + jax_rb.manifolds.so_left_invariant + +
  • +
    +
  • + jax_rb.manifolds.spd + +
  • +
  • + jax_rb.manifolds.sphere + +
  • +
  • + jax_rb.manifolds.stiefel + +
  • +
  • + jax_rb.simulation + +
  • +
  • + jax_rb.simulation.global_manifold_integrator + +
  • +
  • + jax_rb.simulation.matrix_group_integrator + +
  • +
  • + jax_rb.simulation.retractive_integrator + +
  • +
  • + jax_rb.simulation.simulator + +
  • +
  • + jax_rb.utils + +
  • +
  • + jax_rb.utils.utils + +
  • +
  • jpolar() (in module jax_rb.utils.utils) +
  • +
+ +

L

+ + + +
+ +

M

+ + +
+ +

N

+ + +
+ +

P

+ + + +
+ +

R

+ + + +
+ +

S

+ + + +
+ +

U

+ + +
+ +

V

+ + +
+ + + +
+
+
+ +
+ +
+

© Copyright 2024, Du Nguyen, Stefan Sommer.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/index.html b/index.html new file mode 100644 index 0000000..10c9614 --- /dev/null +++ b/index.html @@ -0,0 +1,191 @@ + + + + + + + JAX RB: Riemannian Brownian motion on manifolds — jax_rb documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

JAX RB: Riemannian Brownian motion on manifolds

+

JAX RB is a library for Riemannian Brownian motion on constrained manifolds embedded in a vector space, or on quotient of such manifolds by a compact group. The theory is developed in [NgSo24]. Please refer to the github repository for installation instruction.

+
+\[\]
+ + +
+

Utils

+ +
+
+
+

Indices and tables

+ +
+

Other Resources:

+ +
+

References

+
+
+[NgSo24] +

Nguyen, D.; Sommer, S...: Second-order differential operators, stochastic differential equations and Brownian motions on embedded manifolds arXiv:2406.02879.

+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/manifolds.html b/manifolds.html new file mode 100644 index 0000000..4826ff7 --- /dev/null +++ b/manifolds.html @@ -0,0 +1,768 @@ + + + + + + + jax_rb.manifolds — jax_rb documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

jax_rb.manifolds

+
+

Global Manifold

+ + + +
+

Base class for manifold in global embedded coordinates

+
+
+class jax_rb.manifolds.global_manifold.GlobalManifold[source]
+

A manifold \(\mathcal{M}\) embedded in a vector space \(\mathcal{E}\) .

+
+
+g_metric(x, omg)[source]
+

the metric operator g, which is symmetric. The corresponding metric is +\(\langle \omega, g(x)\omega \rangle_{\mathcal{E}}\) .

+
+ +
+
+gamma(x, xi, eta)[source]
+

Christoffel function. Symmetric for two tangent vectors xi, eta. +The corresponding Levi-Civita connection is +\(\nabla_{\mathtt{X}}\mathtt{Y} = \mathrm{D}_{\mathtt{X}}\mathtt{Y} + \Gamma(x; \mathtt{X}, \mathtt{Y})\) +for two vector fields \(\mathtt{X}, \mathtt{Y}\).

+
+ +
+
+inner(x, a, b)[source]
+

Riemannian inner product.

+
+
Parameters:
+
    +
  • a -- a vector in ambient space,

  • +
  • b -- a vector in ambient space,

  • +
+
+
Returns:
+

the inner product of a and b using the metric \(\mathsf{g}\) .

+
+
+
+ +
+
+inv_g_metric(x, omg)[source]
+

inverse of the metric operator g.

+
+ +
+
+ito_drift(x)[source]
+

Ito Brownian drift as an ambient vector.

+
+ +
+
+laplace_beltrami(x, egradx, ehessvp)[source]
+

Laplace Beltrami operator. This works in for vector and matrices. For a specific manifold, this may be simplified. +We assume f is a scalar function in a tubular neighborhood of the manifold.

+
+
Parameters:
+
    +
  • x -- a point on the manifold,

  • +
  • egradx -- is the Euclidean gradient of \(f\) , a matrix of the same shape with x,

  • +
  • ehessvp -- is the Euclidean Hessian Productof \(f\) , a linear operator on \(\mathcal{E}\) ,

  • +
+
+
Returns:
+

the value of the Laplace Beltrami operator of \(f\) .

+
+
+
+ +
+
+name()[source]
+

name of the manifold.

+
+ +
+
+proj(x, omg)[source]
+

Metric compatible projection +:param x: a point on the manifold, +:param omg: a vector on the ambient manifold \(\mathcal{E}\) , +:returns: a point the tangent space at x.

+
+ +
+
+pseudo_transport(x, y, v)[source]
+

an approximate parallel transport from x to y

+
+
Parameters:
+
    +
  • x -- a point on the manifold,

  • +
  • y -- a point on the manifold,

  • +
  • v -- a tangent vector at x,

  • +
+
+
Returns:
+

a tangent vector at y.

+
+
+
+ +
+
+rand_ambient(key)[source]
+

Random ambient vector.

+
+ +
+
+rand_point(key)[source]
+

A random point on the manifold.

+
+ +
+
+rand_vec(key, x)[source]
+

Random tangent vector at x.

+
+ +
+
+retract(x, v)[source]
+

Second order retraction

+
+
Parameters:
+
    +
  • x -- a point on the manifold,

  • +
  • v -- a tangent vector at x,

  • +
+
+
Returns:
+

a point on the manifold.

+
+
+
+ +
+
+sigma(x, dw)[source]
+

Sigma map to generate Brownian motion.

+
+
Parameters:
+
    +
  • x -- a point on the manifold,

  • +
  • dw -- a point on the ambient space,

  • +
+
+
Returns:
+

apoint on the ambient space such that \(\Pi(x) \sigma(x) \sigma^{\mathsf{T}}(x)\mathsf{g}^{-1}(x) dw = \Pi(x)dw\)

+
+
+
+ +
+ +
+
+

Sphere

+ + + +
+

Sphere of constant curvature

+
+
+class jax_rb.manifolds.sphere.Sphere(n, r)[source]
+

The sphere \(x_0^2+x_1^2+\cdots+x_d^2 = r^2\) +with sectional curvature \(\frac{1}{r^2}\).

+
+
Parameters:
+
    +
  • n -- dimension of \(\mathcal{E}\)

  • +
  • r -- the radius.

  • +
+
+
+
+ +
+
+

Symmetric Positive Definite Matrix Manifold

+ + + +
+

Symmetric Positive Definite Matrix Manifold \(\mathrm{S}^+(p)\) of positive definite matrices of shape \(p\times p\) .

+
+
+class jax_rb.manifolds.spd.PositiveDefiniteManifold(p)[source]
+

The manifold of positive definite matrices of size \(p\) .

+
+ +
+
+

Stiefel Manifold

+ + + +
+

Stiefel manifold \(\mathrm{St}(n, p, \alpha_0, \alpha_1)\) with metric defined by two parameters.

+
+
+class jax_rb.manifolds.stiefel.RealStiefelAlpha(shape, alpha)[source]
+

The manifold \(Y^TY = I\) where \(Y\) is a matrix of size \(shape=n\times p\) with metric \(\lvert \omega\rvert^2_{\mathsf{g}} =\alpha_0 Tr(\omega^T\omega) +(\alpha_0-\alpha_1)Tr(\omega^TYY^T\omega)\) .

+
+
Parameters:
+
    +
  • shape -- tuple (n, p),

  • +
  • alpha -- array of 2 positive numbers.

  • +
+
+
+
+ +
+
+

Grassmann Manifold

+ + + +
+

Grassmann manifold \(\mathrm{Gr}(n, p)\) of vector spaces of rank \(p\) in a \(n\) -dimension vector space.

+
+
+class jax_rb.manifolds.grassmann.Grassmann(shape)[source]
+

The lift of the Grassman manifold to to the Stiefel manifold \(Y^TY = I\) where \(Y\) is a matrix of \(shape=n\times p\) with metric \(\lvert \omega\rvert^2_{\mathsf{g}} = Tr(\omega^T\omega)\). The lift is with respect to the submersion defined by the relationship \(Y\sim YU\) for an orthogonal matrix \(U\).

+
+ +
+
+

Hypersurface with Diagonal constraints Manifold

+ + + +
+

Hypersurface with a constraint of the form \(\sum_i d_i x_i^p = 1\)

+
+
+class jax_rb.manifolds.diag_hypersurface.DiagHypersurface(dvec, p)[source]
+

Hypersurface of the form \(\sum_i d_ix_i^p = 1\).

+
+
Parameters:
+
    +
  • dvec -- vector \(d_i\) of coefficients. +Sort dvec so dvec[-1] is positive.

  • +
  • p -- \(p > 0\) is an integer, degree of the constraint.

  • +
+
+
+

Use embedded metric.

+
+ +
+
+

Matrix Lie Group Left Invariant Metric

+ + + +
+

Base class for matrix groups with left invariant metrics.

+
+

Required implementations

+
+
+jax_rb.manifolds.matrix_left_invariant.MatrixLeftInvariant._lie_algebra_proj(self, omg)
+

The projection \(p_{\mathfrak{g}}\) at the identity.

+
+ +
+
+jax_rb.manifolds.matrix_left_invariant.MatrixLeftInvariant._mat_apply(self, mat, omg)
+

Implementing the operator \(\mathcal{I}\) applied on omg in \(\mathcal{E}\).

+
+ +
+
+

Base class

+
+
+class jax_rb.manifolds.matrix_left_invariant.MatrixLeftInvariant(p, g_mat)[source]
+

Matrix group with left invariant metric.

+
+
Parameters:
+
    +
  • p -- the size of the matrix

  • +
  • g_mat -- The matrix defining the inner product at the identity. Typically g_mat is of size \(\dim \mathrm{G}\) .

  • +
+
+
+
+
+approx_nearest(q)[source]
+

find point on the manifold that +is nearest to q, same order as the nearest point.

+
+ +
+
+g_metric(x, omg)[source]
+

the metric operator g, which is symmetric. The corresponding metric is +\(\langle \omega, g(x)\omega \rangle_{\mathcal{E}}\) .

+
+ +
+
+gamma_ambient(x, xi, eta)[source]
+

Christoffel function for ambient manifold.

+
+ +
+
+id_drift
+

Ito drift at the identity.

+
+ +
+
+inner(x, a, b)[source]
+

Riemannian inner product.

+
+
Parameters:
+
    +
  • a -- a vector in ambient space,

  • +
  • b -- a vector in ambient space,

  • +
+
+
Returns:
+

the inner product of a and b using the metric \(\mathsf{g}\) .

+
+
+
+ +
+
+inv_g_metric(x, omg)[source]
+

inverse of the metric operator g.

+
+ +
+
+laplace_beltrami(x, egradx, ehessvp)[source]
+

Laplace Beltrami operator. This works in for vector and matrices. For a specific manifold, this may be simplified. +We assume f is a scalar function in a tubular neighborhood of the manifold.

+
+
Parameters:
+
    +
  • x -- a point on the manifold,

  • +
  • egradx -- is the Euclidean gradient of \(f\) , a matrix of the same shape with x,

  • +
  • ehessvp -- is the Euclidean Hessian Productof \(f\) , a linear operator on \(\mathcal{E}\) ,

  • +
+
+
Returns:
+

the value of the Laplace Beltrami operator of \(f\) .

+
+
+
+ +
+
+left_invariant_vector_field(x, v)[source]
+

map from a unit vector in the trace metric +to a vector field with unit length in the +left invariant metric.

+
+ +
+
+name()[source]
+

name of the manifold.

+
+ +
+
+proj(x, omg)[source]
+

Metric compatible projection +:param x: a point on the manifold, +:param omg: a vector on the ambient manifold \(\mathcal{E}\) , +:returns: a point the tangent space at x.

+
+ +
+
+pseudo_transport(x, y, v)[source]
+

the easy one

+
+ +
+
+rand_ambient(key)[source]
+

Random ambient vector.

+
+ +
+
+rand_point(key)[source]
+

A random point on the manifold.

+
+ +
+
+rand_vec(key, x)[source]
+

Random tangent vector at x.

+
+ +
+
+retract(x, v)[source]
+

Second order retraction

+
+
Parameters:
+
    +
  • x -- a point on the manifold,

  • +
  • v -- a tangent vector at x,

  • +
+
+
Returns:
+

a point on the manifold.

+
+
+
+ +
+
+sigma(x, dw)[source]
+

sigma, to generate the Brownian motion.

+
+ +
+
+sigma_id(dw)[source]
+

sigma, to generate the Brownian motion at the identity.

+
+ +
+
+stratonovich_drift(x)[source]
+

Stratonovich drift.

+
+ +
+
+v0
+

Stratonovich drift at the identity.

+
+ +
+ +
+
+
+

\(\mathrm{GL}^+(n)\) Generalized Linear Group Positive Determinant

+ + + +
+

\(GL^+\): Positive Component of the Generalized Linear group with left-invariant metric.

+
+
+class jax_rb.manifolds.glp_left_invariant.GLpLeftInvariant(p, g_mat)[source]
+

\(GL^+\) with left invariant metric defined by g_mat.

+
+
Parameters:
+
    +
  • p -- the size of the matrix

  • +
  • g_mat -- The matrix defining the inner product at the identity. g_mat is in \(\mathbb{R}^{p^2\times p^2}\) .

  • +
+
+
+
+ +
+
+

\(\mathrm{Aff}^+(n)\) Affine Linear Group Positive Determinant

+ + + +
+

\(Aff^+\): Positive Component of the Affine group with left invariant metric.

+
+
+class jax_rb.manifolds.affine_left_invariant.AffineLeftInvariant(n, g_mat)[source]
+

Group of affine tranformations of \(\mathbb{R}^{n}\), +represented by a pair \((A, v)\in GL^+(n)\times \mathbb{R}^{n}\) +with action \((A, v).w = Aw + v\) for \(w\in\mathbb{R}^{n}\) .

+

Alternatively, it is represented as a matrix \(\begin{bmatrix} A & v \\ 0 & 1 \end{bmatrix}\in GL(n+1)\).

+
+
Parameters:
+
    +
  • n -- size of A

  • +
  • g_mat -- a positive definite matrix in \(\mathbb{R}^{n(n+1)\times n(n+1)}\) defining the metric at \(I_{n+1}\)

  • +
+
+
+
+ +
+
+

\(\mathrm{SL}(n)\) Special Linear Group

+ + + +
+

\(SL\): special linear group of matrices of determinant 1.

+
+
+class jax_rb.manifolds.sl_left_invariant.SLLeftInvariant(n, g_mat)[source]
+

\(SL(n)\) Special linear group, of size \(n\) with left invariant metric +defined by g_mat.

+
+
Parameters:
+
    +
  • n -- size of the matrix

  • +
  • g_mat -- a positive definite matrix in \(\mathbb{R}^{(n^2-1)\times (n^2-1)}\) defining the metric at \(I_{n}\)

  • +
+
+
+
+ +
+
+

\(\mathrm{SO}(n)\) Special Orthogonal Group

+ + + +
+

\(SO\): Special Orthogonal group.

+
+
+class jax_rb.manifolds.so_left_invariant.SOLeftInvariant(n, g_mat)[source]
+

The group \(SO(n)\) of orthogonal matrices \(U\in R^{n\times n}\) +of determinant 1 with metric \(Tr(\omega^TU^T\mathcal{I}(U^T\omega))\) +where \(\mathcal{I}\) is the metric defined by g_mat, a matrix of size +\(\mathbb{R}^{\frac{n(n-1)}{2}\times \frac{n(n-1)}{2}}\).

+
+ +
+
+

\(\mathrm{SE}(n)\) Special Euclidean Group

+ + + +
+

\(SE\): Special Euclidean group.

+
+
+class jax_rb.manifolds.se_left_invariant.SELeftInvariant(n, g_mat)[source]
+

Specian Euclidean group of Euclidean transformation of \(\mathbb{R}^{n}\), +represented by a pair \((A, v)\in SO^(n)\times \mathbb{R}^{n}\) +with action \((A, v).w = Aw + v\) for \(w\in\mathbb{R}^{n}\) .

+

Alternatively, it is represented as a matrix \(\begin{bmatrix} A & v \\ 0 & 1 \end{bmatrix}\in GL(n+1)\) where \(A\in SO(n)\).

+
+
Parameters:
+
    +
  • n -- size of A

  • +
  • g_mat -- a positive definite matrix in \(\mathbb{R}^{\frac{n(n+1)}{2}\times\frac{n(n+1)}{2}}\) defining the metric at \(I_{n+1}\)

  • +
+
+
+
+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/objects.inv b/objects.inv new file mode 100644 index 0000000..4062a60 Binary files /dev/null and b/objects.inv differ diff --git a/py-modindex.html b/py-modindex.html new file mode 100644 index 0000000..ab897a7 --- /dev/null +++ b/py-modindex.html @@ -0,0 +1,236 @@ + + + + + + Python Module Index — jax_rb documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
  • + +
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  • +
+
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+
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+ + +

Python Module Index

+ +
+ j +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
 
+ j
+ jax_rb +
    + jax_rb.manifolds +
    + jax_rb.manifolds.affine_left_invariant +
    + jax_rb.manifolds.diag_hypersurface +
    + jax_rb.manifolds.global_manifold +
    + jax_rb.manifolds.glp_left_invariant +
    + jax_rb.manifolds.grassmann +
    + jax_rb.manifolds.matrix_left_invariant +
    + jax_rb.manifolds.se_left_invariant +
    + jax_rb.manifolds.sl_left_invariant +
    + jax_rb.manifolds.so_left_invariant +
    + jax_rb.manifolds.spd +
    + jax_rb.manifolds.sphere +
    + jax_rb.manifolds.stiefel +
    + jax_rb.simulation +
    + jax_rb.simulation.global_manifold_integrator +
    + jax_rb.simulation.matrix_group_integrator +
    + jax_rb.simulation.retractive_integrator +
    + jax_rb.simulation.simulator +
    + jax_rb.utils +
    + jax_rb.utils.utils +
+ + +
+
+
+ +
+ +
+

© Copyright 2024, Du Nguyen, Stefan Sommer.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
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+
+
+
+ + + + \ No newline at end of file diff --git a/search.html b/search.html new file mode 100644 index 0000000..a65db9b --- /dev/null +++ b/search.html @@ -0,0 +1,136 @@ + + + + + + Search — jax_rb documentation + + + + + + + + + + + + + + + + + + + + +
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+ +
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+

© Copyright 2024, Du Nguyen, Stefan Sommer.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
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+ + + + + + + + + \ No newline at end of file diff --git a/searchindex.js b/searchindex.js new file mode 100644 index 0000000..ab77ee2 --- /dev/null +++ b/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"alltitles": {"Animation": [[0, "animation"]], "Base class": [[2, "base-class"]], "Global Manifold": [[2, "global-manifold"]], "Global Manifold Integrator": [[3, "global-manifold-integrator"]], "Grassmann Manifold": [[2, "grassmann-manifold"]], "Hypersurface with Diagonal constraints Manifold": [[2, "hypersurface-with-diagonal-constraints-manifold"]], "Indices and tables": [[1, "indices-and-tables"]], "JAX RB: Riemannian Brownian motion on manifolds": [[1, "jax-rb-riemannian-brownian-motion-on-manifolds"]], "Manifolds": [[1, null]], "Matrix Lie Group Integrator": [[3, "matrix-lie-group-integrator"]], "Matrix Lie Group Left Invariant Metric": [[2, "matrix-lie-group-left-invariant-metric"]], "Other Resources:": [[1, null]], "Required implementations": [[2, "required-implementations"]], "Retractive Integrator": [[3, "retractive-integrator"]], "Simulation": [[1, null]], "Simulator": [[3, "simulator"]], "Sphere": [[2, "sphere"]], "Stiefel Manifold": [[2, "stiefel-manifold"]], "Symmetric Positive Definite Matrix Manifold": [[2, "symmetric-positive-definite-matrix-manifold"]], "Utils": [[1, null], [4, "utils"]], "\\mathrm{Aff}^+(n) Affine Linear Group Positive Determinant": [[2, "mathrm-aff-n-affine-linear-group-positive-determinant"]], "\\mathrm{GL}^+(n) Generalized Linear Group Positive Determinant": [[2, "mathrm-gl-n-generalized-linear-group-positive-determinant"]], "\\mathrm{SE}(n) Special Euclidean Group": [[2, "mathrm-se-n-special-euclidean-group"]], "\\mathrm{SL}(n) Special Linear Group": [[2, "mathrm-sl-n-special-linear-group"]], "\\mathrm{SO}(n) Special Orthogonal Group": [[2, "mathrm-so-n-special-orthogonal-group"]], "jax_rb.manifolds": [[2, "module-jax_rb.manifolds"]], "jax_rb.simulation": [[3, "module-jax_rb.simulation"]], "jax_rb.utils": [[4, "module-jax_rb.utils"]]}, "docnames": ["animation", "index", "manifolds", "simulation", "utils"], "envversion": {"sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1}, "filenames": ["animation.rst", "index.rst", "manifolds.rst", "simulation.rst", "utils.rst"], "indexentries": {"_lie_algebra_proj() (in module jax_rb.manifolds.matrix_left_invariant.matrixleftinvariant)": [[2, "jax_rb.manifolds.matrix_left_invariant.MatrixLeftInvariant._lie_algebra_proj", false]], "_mat_apply() (in module jax_rb.manifolds.matrix_left_invariant.matrixleftinvariant)": [[2, "jax_rb.manifolds.matrix_left_invariant.MatrixLeftInvariant._mat_apply", false]], "affineleftinvariant (class in jax_rb.manifolds.affine_left_invariant)": [[2, "jax_rb.manifolds.affine_left_invariant.AffineLeftInvariant", false]], "approx_nearest() (jax_rb.manifolds.matrix_left_invariant.matrixleftinvariant method)": [[2, "jax_rb.manifolds.matrix_left_invariant.MatrixLeftInvariant.approx_nearest", false]], "complement_basis_for_vector() (in module jax_rb.utils.utils)": [[4, "jax_rb.utils.utils.complement_basis_for_vector", false]], "diaghypersurface (class in jax_rb.manifolds.diag_hypersurface)": [[2, "jax_rb.manifolds.diag_hypersurface.DiagHypersurface", false]], "esqrtm() (in module jax_rb.utils.utils)": [[4, "jax_rb.utils.utils.esqrtm", false]], "g_metric() (jax_rb.manifolds.global_manifold.globalmanifold method)": [[2, "jax_rb.manifolds.global_manifold.GlobalManifold.g_metric", false]], "g_metric() (jax_rb.manifolds.matrix_left_invariant.matrixleftinvariant method)": [[2, "jax_rb.manifolds.matrix_left_invariant.MatrixLeftInvariant.g_metric", false]], "gamma() (jax_rb.manifolds.global_manifold.globalmanifold method)": [[2, "jax_rb.manifolds.global_manifold.GlobalManifold.gamma", false]], "gamma_ambient() (jax_rb.manifolds.matrix_left_invariant.matrixleftinvariant method)": [[2, "jax_rb.manifolds.matrix_left_invariant.MatrixLeftInvariant.gamma_ambient", false]], "generate_symmetric_tensor() (in module jax_rb.utils.utils)": [[4, "jax_rb.utils.utils.generate_symmetric_tensor", false]], "geodesic_move() (in module jax_rb.simulation.global_manifold_integrator)": [[3, "jax_rb.simulation.global_manifold_integrator.geodesic_move", false]], "geodesic_move() (in module jax_rb.simulation.matrix_group_integrator)": [[3, "jax_rb.simulation.matrix_group_integrator.geodesic_move", false]], "geodesic_move_dim_g() (in module jax_rb.simulation.matrix_group_integrator)": [[3, "jax_rb.simulation.matrix_group_integrator.geodesic_move_dim_g", false]], "geodesic_move_dim_g_normalized() (in module jax_rb.simulation.matrix_group_integrator)": [[3, "jax_rb.simulation.matrix_group_integrator.geodesic_move_dim_g_normalized", false]], "geodesic_move_exact() (in module jax_rb.simulation.global_manifold_integrator)": [[3, "jax_rb.simulation.global_manifold_integrator.geodesic_move_exact", false]], "geodesic_move_exact_normalized() (in module jax_rb.simulation.global_manifold_integrator)": [[3, "jax_rb.simulation.global_manifold_integrator.geodesic_move_exact_normalized", false]], "geodesic_move_normalized() (in module jax_rb.simulation.global_manifold_integrator)": [[3, "jax_rb.simulation.global_manifold_integrator.geodesic_move_normalized", false]], "geodesic_move_normalized() (in module jax_rb.simulation.matrix_group_integrator)": [[3, "jax_rb.simulation.matrix_group_integrator.geodesic_move_normalized", false]], "globalmanifold (class in jax_rb.manifolds.global_manifold)": [[2, "jax_rb.manifolds.global_manifold.GlobalManifold", false]], "glpleftinvariant (class in jax_rb.manifolds.glp_left_invariant)": [[2, "jax_rb.manifolds.glp_left_invariant.GLpLeftInvariant", false]], "grand() (in module jax_rb.utils.utils)": [[4, "jax_rb.utils.utils.grand", false]], "grassmann (class in jax_rb.manifolds.grassmann)": [[2, "jax_rb.manifolds.grassmann.Grassmann", false]], "id_drift (jax_rb.manifolds.matrix_left_invariant.matrixleftinvariant attribute)": [[2, "jax_rb.manifolds.matrix_left_invariant.MatrixLeftInvariant.id_drift", false]], "inner() (jax_rb.manifolds.global_manifold.globalmanifold method)": [[2, "jax_rb.manifolds.global_manifold.GlobalManifold.inner", false]], "inner() (jax_rb.manifolds.matrix_left_invariant.matrixleftinvariant method)": [[2, "jax_rb.manifolds.matrix_left_invariant.MatrixLeftInvariant.inner", false]], "inv_g_metric() (jax_rb.manifolds.global_manifold.globalmanifold method)": [[2, "jax_rb.manifolds.global_manifold.GlobalManifold.inv_g_metric", false]], "inv_g_metric() (jax_rb.manifolds.matrix_left_invariant.matrixleftinvariant method)": [[2, "jax_rb.manifolds.matrix_left_invariant.MatrixLeftInvariant.inv_g_metric", false]], "ito_drift() (jax_rb.manifolds.global_manifold.globalmanifold method)": [[2, "jax_rb.manifolds.global_manifold.GlobalManifold.ito_drift", false]], "ito_move_dim_g() (in module jax_rb.simulation.matrix_group_integrator)": [[3, "jax_rb.simulation.matrix_group_integrator.ito_move_dim_g", false]], "jax_rb.manifolds": [[2, "module-jax_rb.manifolds", false]], "jax_rb.manifolds.affine_left_invariant": [[2, "module-jax_rb.manifolds.affine_left_invariant", false]], "jax_rb.manifolds.diag_hypersurface": [[2, "module-jax_rb.manifolds.diag_hypersurface", false]], "jax_rb.manifolds.global_manifold": [[2, "module-jax_rb.manifolds.global_manifold", false]], "jax_rb.manifolds.glp_left_invariant": [[2, "module-jax_rb.manifolds.glp_left_invariant", false]], "jax_rb.manifolds.grassmann": [[2, "module-jax_rb.manifolds.grassmann", false]], "jax_rb.manifolds.matrix_left_invariant": [[2, "module-jax_rb.manifolds.matrix_left_invariant", false]], "jax_rb.manifolds.se_left_invariant": [[2, 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"gener": 2, "gl": 2, "global": [2, 3], "grassmann": 2, "group": [2, 3], "hypersurfac": 2, "implement": 2, "indic": 1, "integr": 3, "invari": 2, "jax": 1, "jax_rb": [2, 3, 4], "left": 2, "lie": [2, 3], "linear": 2, "manifold": [1, 2, 3], "mathrm": 2, "matrix": [2, 3], "metric": 2, "motion": 1, "n": 2, "orthogon": 2, "other": 1, "posit": 2, "rb": 1, "requir": 2, "resourc": 1, "retract": 3, "riemannian": 1, "se": 2, "simul": [1, 3], "sl": 2, "so": 2, "special": 2, "sphere": 2, "stiefel": 2, "symmetr": 2, "tabl": 1, "util": [1, 4]}}) \ No newline at end of file diff --git a/simulation.html b/simulation.html new file mode 100644 index 0000000..756f1d7 --- /dev/null +++ b/simulation.html @@ -0,0 +1,384 @@ + + + + + + + jax_rb.simulation — jax_rb documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

jax_rb.simulation

+
+

Simulator

+ + + +
+

Simulator for global_manifold

+
+
+class jax_rb.simulation.simulator.RunParams(x_0, key, t_final, n_path, n_div, d_coeff, wiener_dim, m_size, normalize, run_type)[source]
+

Parameters to save a run in simulator.

+
+
Parameters:
+
    +
  • x_0 -- starting point of the simulation

  • +
  • key -- key to generate the random numbers used in simulation. Created from jax.random.PRNGKey, then jax.random.split.

  • +
  • t_final -- The final time of simulation. Starting time is \(t=0\).

  • +
  • n_path -- number of paths used in simulation

  • +
  • n_div -- number of subdivision (interval will be t_final/n_div

  • +
  • d_coeff -- difusion coefficient, d_coeff = 0.5 for the Riemannian Brownian motion.

  • +
  • wiener_dim -- dimension of the Wienner process used in simulation. Usually it is the dimension of the ambient space \(\mathcal{E}\). In some cases, we can simulate using the dimension of the manifold itself.

  • +
  • m_size -- a param indicating the size of the manifold, use to differentiate when simulating several manifolds,

  • +
  • normalize -- whether to normalize the move to a fixed lengh,

  • +
  • run_type -- string indicating one of the simulation moves. This is a tag to distinguish the output, does not affect the results.

  • +
+
+
+
+ +
+
+class jax_rb.simulation.simulator.Simulator(path_pay_off, final_pay_off)[source]
+

Class to do simulation on a manifold +with particular funtion or simulators. Run results is saved in self.runs.

+

:param path_pay_off is the function value evaluated along the path +:param final_pay_off is the function value evaluated at final time

+
+
+run(integrator, params)[source]
+

run a simulation

+

:param integrator the integrator used +:param params is of class RunParams

+
+ +
+
+save_runs(save_path)[source]
+

save all the runs to save_path

+
+ +
+ +
+
+jax_rb.simulation.simulator.simulate(x_0, integrator, path_pay_off, final_pay_off, params)[source]
+

A simulation from \(t=0\) up to time \(t=t_final\), with time increment +\(t=\frac{t_final}{n_div}\), run \(n_path\) path. +Return the full distribution of the simulation. We use the minimum cut-off with accuracy level 0.5 in this version.

+
+
Parameters:
+
    +
  • x_0 -- starting point of the simulation

  • +
  • integrator -- one of the integrators (geodesic, ito, stratonovich

  • +
  • path_pay_off -- the cost evaluated along the path

  • +
  • final_pay_off -- the contribution evaluated at the final time

  • +
  • params -- additional parameters for the simulations: sk, t_final, n_path, n_div, d_coeff, wiener_dim

  • +
+
+
+
+ +
+
+

Matrix Lie Group Integrator

+ + + +
+

Module implementing simulation methods for left invariant matrix Lie group

+
+
+jax_rb.simulation.matrix_group_integrator.geodesic_move(mnf, x, unit_move, scale)[source]
+

unit_move is reshaped to the shape conforming with sigma., usually the shape of the ambient space. +The move is \(x_{new} = \mathfrak{r}(x, \sigma(x)(\text{unit_move}(\text{scale})^{\frac{1}{2}}))\)

+
+ +
+
+jax_rb.simulation.matrix_group_integrator.geodesic_move_dim_g(mnf, x, unit_move, scale)[source]
+

Unit_move is of dimension \(\dim \mathrm{G}\). +The move is \(x_{new} = \mathfrak{r}(x, \sigma_{la}(x)(\text{unit_move}(\text{scale})^{\frac{1}{2}}))\)

+
+ +
+
+jax_rb.simulation.matrix_group_integrator.geodesic_move_dim_g_normalized(mnf, x, unit_move, scale)[source]
+

Similar to geodesic_move_dim_g, but unit move is rescaled to have fixed length 1 +in the metric of the group.

+
+ +
+
+jax_rb.simulation.matrix_group_integrator.geodesic_move_normalized(mnf, x, unit_move, scale)[source]
+

Similar to geodesic_move, but unit move is rescaled to have fixed length 1 +in the metric of the group.

+
+ +
+
+jax_rb.simulation.matrix_group_integrator.ito_move_dim_g(mnf, x, unit_move, scale)[source]
+

Similar to rbrownian_ito_move, but driven with a Wiener +process of dimension \(\dim \mathrm{G}\).

+
+ +
+
+jax_rb.simulation.matrix_group_integrator.rbrownian_ito_move(mnf, x, unit_move, scale)[source]
+

Use stochastic projection method to solve the Ito equation. +Use Euler Maruyama here.

+
+ +
+
+jax_rb.simulation.matrix_group_integrator.rbrownian_stratonovich_move(mnf, x, unit_move, scale)[source]
+

Using projection method to solve the Stratonovich equation. +In many cases \(v_0\) is zero (unimodular group). +Use Euler Heun.

+
+ +
+
+jax_rb.simulation.matrix_group_integrator.stratonovich_move_dim_g(mnf, x, unit_move, scale)[source]
+

Similar to rbrownian_stratonovich_move, but driven with a Wiener +process of dimension \(\dim \mathrm{G}\).

+
+ +
+
+

Global Manifold Integrator

+ + + +
+

Module implementing simulation methods for embedded manifolds

+
+
+jax_rb.simulation.global_manifold_integrator.geodesic_move(mnf, x, unit_move, scale)[source]
+

simulate using a second order retraction. +The move is \(x_{new} = \mathfrak{r}(x, \Pi(x)\sigma(x)(\text{unit_move}(\text{scale})^{\frac{1}{2}}))\)

+
+ +
+
+jax_rb.simulation.global_manifold_integrator.geodesic_move_exact(mnf, x, unit_move, scale)[source]
+

similar to geodesic_move, but use exact geodesic

+
+ +
+
+jax_rb.simulation.global_manifold_integrator.geodesic_move_exact_normalized(mnf, x, unit_move, scale)[source]
+

similar to geodesic_move_exact, but use normalize the unit_move

+
+ +
+
+jax_rb.simulation.global_manifold_integrator.geodesic_move_normalized(mnf, x, unit_move, scale)[source]
+

similar to geodesic_move, but the move is normalized to have fixed length \(scale^{\frac{1}{2}}\)

+
+ +
+
+jax_rb.simulation.global_manifold_integrator.rbrownian_ito_move(mnf, x, unit_move, scale)[source]
+

Use Euler Maruyama and projection method to solve the Ito equation.

+
+ +
+
+jax_rb.simulation.global_manifold_integrator.rbrownian_stratonovich_move(mnf, x, unit_move, scale)[source]
+

Use Euler Heun and projection method to solve the Stratonovich equation.

+
+ +
+
+

Retractive Integrator

+ + + +
+

Module implementing the retractive Euler-Maruyama integrator.

+
+
+jax_rb.simulation.retractive_integrator.retractive_move(rtr, x, t, unit_move, scale, sigma, mu)[source]
+

Simulating the equation \(dX_t = \mu(X_t, t) dt + \sigma(X_t, t) dW_t\) using the retraction rtr. +We do not assume a Riemanian metric on the manifold, \(\sigma\sigma^T\) could be degenerated on \(T\mathcal{M}\).

+

W is a Wiener process driving the equation, defined on \(\mathbb{R}^k\). W is given by unit_move.

+

\(\sigma(X_t, t)\) maps \(\mathbb{R}^k\) to \(\mathcal{E}\), but the image belongs +to \(T_{X_t}\mathcal{M}\).

+

The retraction rtr is assume to have the method \(\text{drift_adj}\) for an adjustment.

+

The move is \(x_{new} = \mathfrak{r}(x, \Pi(x)\sigma(x)(\text{unit_move}(\text{scale})^{\frac{1}{2}}) + \text{scale} (\mu + \text{drift_adj}))\).

+
+
Parameters:
+
    +
  • rtr -- the retraction,

  • +
  • x -- a point on the manifold,

  • +
  • t -- time

  • +
  • unit_move -- a random normal draw

  • +
  • scale -- scaling

  • +
  • sigma -- a function implementing the map \(\sigma\)

  • +
  • mu -- a function implementing the Ito drift \(\mu\)

  • +
+
+
+
+ +
+
+jax_rb.simulation.retractive_integrator.retractive_move_normalized(rtr, x, t, unit_move, scale, sigma, mu)[source]
+

Similar to retractive_move, but the stochastic part is normalized to have fixed length \(scale^{\frac{1}{2}}\)

+
+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/utils.html b/utils.html new file mode 100644 index 0000000..7395783 --- /dev/null +++ b/utils.html @@ -0,0 +1,194 @@ + + + + + + + jax_rb.utils — jax_rb documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

jax_rb.utils

+
+

Utils

+ + + +
+

various utils for the project

+
+
+jax_rb.utils.utils.complement_basis_for_vector(xraw)[source]
+

complement basis of xraw, a non zero vector. Assume x[0] !=0

+
+ +
+
+jax_rb.utils.utils.make_complement_basis(x)[source]
+

make complement basis of

+
+ +
+
+jax_rb.utils.utils.generate_symmetric_tensor(key, k, m)[source]
+

Generating symmetric tensor size k,m

+
+ +
+
+jax_rb.utils.utils.esqrtm(x)[source]
+

sqrtm by eigenvalue

+
+ +
+
+jax_rb.utils.utils.unvec_skew(v)[source]
+

unravel a n(n-1)//2 vector to anti hermitian matrix

+
+ +
+
+jax_rb.utils.utils.jpolar(x)[source]
+

jax polar decomposition

+
+ +
+
+jax_rb.utils.utils.rand_positive_definite(key, n, bounds=None)[source]
+

generate a positive definite matrix of size n

+
+ +
+
+jax_rb.utils.utils.grand(key, dims)[source]
+

generate a random array of shape dim using key

+
+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file