sequenzo 0.1.17__cp312-cp312-macosx_10_13_universal2.whl → 0.1.19__cp312-cp312-macosx_10_13_universal2.whl

sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/chkder.h

@@ -1,66 +0,0 @@
-#define chkder_log10e 0.43429448190325182765
-#define chkder_factor 100.
-
-namespace Eigen { 
-
-namespace internal {
-
-template<typename Scalar>
-void chkder(
-        const Matrix< Scalar, Dynamic, 1 >  &x,
-        const Matrix< Scalar, Dynamic, 1 >  &fvec,
-        const Matrix< Scalar, Dynamic, Dynamic > &fjac,
-        Matrix< Scalar, Dynamic, 1 >  &xp,
-        const Matrix< Scalar, Dynamic, 1 >  &fvecp,
-        int mode,
-        Matrix< Scalar, Dynamic, 1 >  &err
-        )
-{
-    using std::sqrt;
-    using std::abs;
-    using std::log;
-    
-    typedef DenseIndex Index;
-
-    const Scalar eps = sqrt(NumTraits<Scalar>::epsilon());
-    const Scalar epsf = chkder_factor * NumTraits<Scalar>::epsilon();
-    const Scalar epslog = chkder_log10e * log(eps);
-    Scalar temp;
-
-    const Index m = fvec.size(), n = x.size();
-
-    if (mode != 2) {
-        /* mode = 1. */
-        xp.resize(n);
-        for (Index j = 0; j < n; ++j) {
-            temp = eps * abs(x[j]);
-            if (temp == 0.)
-                temp = eps;
-            xp[j] = x[j] + temp;
-        }
-    }
-    else {
-        /* mode = 2. */
-        err.setZero(m); 
-        for (Index j = 0; j < n; ++j) {
-            temp = abs(x[j]);
-            if (temp == 0.)
-                temp = 1.;
-            err += temp * fjac.col(j);
-        }
-        for (Index i = 0; i < m; ++i) {
-            temp = 1.;
-            if (fvec[i] != 0. && fvecp[i] != 0. && abs(fvecp[i] - fvec[i]) >= epsf * abs(fvec[i]))
-                temp = eps * abs((fvecp[i] - fvec[i]) / eps - err[i]) / (abs(fvec[i]) + abs(fvecp[i]));
-            err[i] = 1.;
-            if (temp > NumTraits<Scalar>::epsilon() && temp < eps)
-                err[i] = (chkder_log10e * log(temp) - epslog) / epslog;
-            if (temp >= eps)
-                err[i] = 0.;
-        }
-    }
-}
-
-} // end namespace internal
-
-} // end namespace Eigen

sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/covar.h

@@ -1,70 +0,0 @@
-namespace Eigen { 
-
-namespace internal {
-
-template <typename Scalar>
-void covar(
-        Matrix< Scalar, Dynamic, Dynamic > &r,
-        const VectorXi &ipvt,
-        Scalar tol = std::sqrt(NumTraits<Scalar>::epsilon()) )
-{
-    using std::abs;
-    typedef DenseIndex Index;
-
-    /* Local variables */
-    Index i, j, k, l, ii, jj;
-    bool sing;
-    Scalar temp;
-
-    /* Function Body */
-    const Index n = r.cols();
-    const Scalar tolr = tol * abs(r(0,0));
-    Matrix< Scalar, Dynamic, 1 > wa(n);
-    eigen_assert(ipvt.size()==n);
-
-    /* form the inverse of r in the full upper triangle of r. */
-    l = -1;
-    for (k = 0; k < n; ++k)
-        if (abs(r(k,k)) > tolr) {
-            r(k,k) = 1. / r(k,k);
-            for (j = 0; j <= k-1; ++j) {
-                temp = r(k,k) * r(j,k);
-                r(j,k) = 0.;
-                r.col(k).head(j+1) -= r.col(j).head(j+1) * temp;
-            }
-            l = k;
-        }
-
-    /* form the full upper triangle of the inverse of (r transpose)*r */
-    /* in the full upper triangle of r. */
-    for (k = 0; k <= l; ++k) {
-        for (j = 0; j <= k-1; ++j)
-            r.col(j).head(j+1) += r.col(k).head(j+1) * r(j,k);
-        r.col(k).head(k+1) *= r(k,k);
-    }
-
-    /* form the full lower triangle of the covariance matrix */
-    /* in the strict lower triangle of r and in wa. */
-    for (j = 0; j < n; ++j) {
-        jj = ipvt[j];
-        sing = j > l;
-        for (i = 0; i <= j; ++i) {
-            if (sing)
-                r(i,j) = 0.;
-            ii = ipvt[i];
-            if (ii > jj)
-                r(ii,jj) = r(i,j);
-            if (ii < jj)
-                r(jj,ii) = r(i,j);
-        }
-        wa[jj] = r(j,j);
-    }
-
-    /* symmetrize the covariance matrix in r. */
-    r.topLeftCorner(n,n).template triangularView<StrictlyUpper>() = r.topLeftCorner(n,n).transpose();
-    r.diagonal() = wa;
-}
-
-} // end namespace internal
-
-} // end namespace Eigen

sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/dogleg.h

@@ -1,107 +0,0 @@
-namespace Eigen { 
-
-namespace internal {
-
-template <typename Scalar>
-void dogleg(
-        const Matrix< Scalar, Dynamic, Dynamic >  &qrfac,
-        const Matrix< Scalar, Dynamic, 1 >  &diag,
-        const Matrix< Scalar, Dynamic, 1 >  &qtb,
-        Scalar delta,
-        Matrix< Scalar, Dynamic, 1 >  &x)
-{
-    using std::abs;
-    using std::sqrt;
-    
-    typedef DenseIndex Index;
-
-    /* Local variables */
-    Index i, j;
-    Scalar sum, temp, alpha, bnorm;
-    Scalar gnorm, qnorm;
-    Scalar sgnorm;
-
-    /* Function Body */
-    const Scalar epsmch = NumTraits<Scalar>::epsilon();
-    const Index n = qrfac.cols();
-    eigen_assert(n==qtb.size());
-    eigen_assert(n==x.size());
-    eigen_assert(n==diag.size());
-    Matrix< Scalar, Dynamic, 1 >  wa1(n), wa2(n);
-
-    /* first, calculate the gauss-newton direction. */
-    for (j = n-1; j >=0; --j) {
-        temp = qrfac(j,j);
-        if (temp == 0.) {
-            temp = epsmch * qrfac.col(j).head(j+1).maxCoeff();
-            if (temp == 0.)
-                temp = epsmch;
-        }
-        if (j==n-1)
-            x[j] = qtb[j] / temp;
-        else
-            x[j] = (qtb[j] - qrfac.row(j).tail(n-j-1).dot(x.tail(n-j-1))) / temp;
-    }
-
-    /* test whether the gauss-newton direction is acceptable. */
-    qnorm = diag.cwiseProduct(x).stableNorm();
-    if (qnorm <= delta)
-        return;
-
-    // TODO : this path is not tested by Eigen unit tests
-
-    /* the gauss-newton direction is not acceptable. */
-    /* next, calculate the scaled gradient direction. */
-
-    wa1.fill(0.);
-    for (j = 0; j < n; ++j) {
-        wa1.tail(n-j) += qrfac.row(j).tail(n-j) * qtb[j];
-        wa1[j] /= diag[j];
-    }
-
-    /* calculate the norm of the scaled gradient and test for */
-    /* the special case in which the scaled gradient is zero. */
-    gnorm = wa1.stableNorm();
-    sgnorm = 0.;
-    alpha = delta / qnorm;
-    if (gnorm == 0.)
-        goto algo_end;
-
-    /* calculate the point along the scaled gradient */
-    /* at which the quadratic is minimized. */
-    wa1.array() /= (diag*gnorm).array();
-    // TODO : once unit tests cover this part,:
-    // wa2 = qrfac.template triangularView<Upper>() * wa1;
-    for (j = 0; j < n; ++j) {
-        sum = 0.;
-        for (i = j; i < n; ++i) {
-            sum += qrfac(j,i) * wa1[i];
-        }
-        wa2[j] = sum;
-    }
-    temp = wa2.stableNorm();
-    sgnorm = gnorm / temp / temp;
-
-    /* test whether the scaled gradient direction is acceptable. */
-    alpha = 0.;
-    if (sgnorm >= delta)
-        goto algo_end;
-
-    /* the scaled gradient direction is not acceptable. */
-    /* finally, calculate the point along the dogleg */
-    /* at which the quadratic is minimized. */
-    bnorm = qtb.stableNorm();
-    temp = bnorm / gnorm * (bnorm / qnorm) * (sgnorm / delta);
-    temp = temp - delta / qnorm * numext::abs2(sgnorm / delta) + sqrt(numext::abs2(temp - delta / qnorm) + (1.-numext::abs2(delta / qnorm)) * (1.-numext::abs2(sgnorm / delta)));
-    alpha = delta / qnorm * (1. - numext::abs2(sgnorm / delta)) / temp;
-algo_end:
-
-    /* form appropriate convex combination of the gauss-newton */
-    /* direction and the scaled gradient direction. */
-    temp = (1.-alpha) * (std::min)(sgnorm,delta);
-    x = temp * wa1 + alpha * x;
-}
-
-} // end namespace internal
-
-} // end namespace Eigen

sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/fdjac1.h

@@ -1,79 +0,0 @@
-namespace Eigen { 
-
-namespace internal {
-
-template<typename FunctorType, typename Scalar>
-DenseIndex fdjac1(
-        const FunctorType &Functor,
-        Matrix< Scalar, Dynamic, 1 >  &x,
-        Matrix< Scalar, Dynamic, 1 >  &fvec,
-        Matrix< Scalar, Dynamic, Dynamic > &fjac,
-        DenseIndex ml, DenseIndex mu,
-        Scalar epsfcn)
-{
-    using std::sqrt;
-    using std::abs;
-    
-    typedef DenseIndex Index;
-
-    /* Local variables */
-    Scalar h;
-    Index j, k;
-    Scalar eps, temp;
-    Index msum;
-    int iflag;
-    Index start, length;
-
-    /* Function Body */
-    const Scalar epsmch = NumTraits<Scalar>::epsilon();
-    const Index n = x.size();
-    eigen_assert(fvec.size()==n);
-    Matrix< Scalar, Dynamic, 1 >  wa1(n);
-    Matrix< Scalar, Dynamic, 1 >  wa2(n);
-
-    eps = sqrt((std::max)(epsfcn,epsmch));
-    msum = ml + mu + 1;
-    if (msum >= n) {
-        /* computation of dense approximate jacobian. */
-        for (j = 0; j < n; ++j) {
-            temp = x[j];
-            h = eps * abs(temp);
-            if (h == 0.)
-                h = eps;
-            x[j] = temp + h;
-            iflag = Functor(x, wa1);
-            if (iflag < 0)
-                return iflag;
-            x[j] = temp;
-            fjac.col(j) = (wa1-fvec)/h;
-        }
-
-    }else {
-        /* computation of banded approximate jacobian. */
-        for (k = 0; k < msum; ++k) {
-            for (j = k; (msum<0) ? (j>n): (j<n); j += msum) {
-                wa2[j] = x[j];
-                h = eps * abs(wa2[j]);
-                if (h == 0.) h = eps;
-                x[j] = wa2[j] + h;
-            }
-            iflag = Functor(x, wa1);
-            if (iflag < 0)
-                return iflag;
-            for (j = k; (msum<0) ? (j>n): (j<n); j += msum) {
-                x[j] = wa2[j];
-                h = eps * abs(wa2[j]);
-                if (h == 0.) h = eps;
-                fjac.col(j).setZero();
-                start = std::max<Index>(0,j-mu);
-                length = (std::min)(n-1, j+ml) - start + 1;
-                fjac.col(j).segment(start, length) = ( wa1.segment(start, length)-fvec.segment(start, length))/h;
-            }
-        }
-    }
-    return 0;
-}
-
-} // end namespace internal
-
-} // end namespace Eigen

sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/lmpar.h

@@ -1,298 +0,0 @@
-namespace Eigen { 
-
-namespace internal {
-
-template <typename Scalar>
-void lmpar(
-        Matrix< Scalar, Dynamic, Dynamic > &r,
-        const VectorXi &ipvt,
-        const Matrix< Scalar, Dynamic, 1 >  &diag,
-        const Matrix< Scalar, Dynamic, 1 >  &qtb,
-        Scalar delta,
-        Scalar &par,
-        Matrix< Scalar, Dynamic, 1 >  &x)
-{
-    using std::abs;
-    using std::sqrt;
-    typedef DenseIndex Index;
-
-    /* Local variables */
-    Index i, j, l;
-    Scalar fp;
-    Scalar parc, parl;
-    Index iter;
-    Scalar temp, paru;
-    Scalar gnorm;
-    Scalar dxnorm;
-
-
-    /* Function Body */
-    const Scalar dwarf = (std::numeric_limits<Scalar>::min)();
-    const Index n = r.cols();
-    eigen_assert(n==diag.size());
-    eigen_assert(n==qtb.size());
-    eigen_assert(n==x.size());
-
-    Matrix< Scalar, Dynamic, 1 >  wa1, wa2;
-
-    /* compute and store in x the gauss-newton direction. if the */
-    /* jacobian is rank-deficient, obtain a least squares solution. */
-    Index nsing = n-1;
-    wa1 = qtb;
-    for (j = 0; j < n; ++j) {
-        if (r(j,j) == 0. && nsing == n-1)
-            nsing = j - 1;
-        if (nsing < n-1)
-            wa1[j] = 0.;
-    }
-    for (j = nsing; j>=0; --j) {
-        wa1[j] /= r(j,j);
-        temp = wa1[j];
-        for (i = 0; i < j ; ++i)
-            wa1[i] -= r(i,j) * temp;
-    }
-
-    for (j = 0; j < n; ++j)
-        x[ipvt[j]] = wa1[j];
-
-    /* initialize the iteration counter. */
-    /* evaluate the function at the origin, and test */
-    /* for acceptance of the gauss-newton direction. */
-    iter = 0;
-    wa2 = diag.cwiseProduct(x);
-    dxnorm = wa2.blueNorm();
-    fp = dxnorm - delta;
-    if (fp <= Scalar(0.1) * delta) {
-        par = 0;
-        return;
-    }
-
-    /* if the jacobian is not rank deficient, the newton */
-    /* step provides a lower bound, parl, for the zero of */
-    /* the function. otherwise set this bound to zero. */
-    parl = 0.;
-    if (nsing >= n-1) {
-        for (j = 0; j < n; ++j) {
-            l = ipvt[j];
-            wa1[j] = diag[l] * (wa2[l] / dxnorm);
-        }
-        // it's actually a triangularView.solveInplace(), though in a weird
-        // way:
-        for (j = 0; j < n; ++j) {
-            Scalar sum = 0.;
-            for (i = 0; i < j; ++i)
-                sum += r(i,j) * wa1[i];
-            wa1[j] = (wa1[j] - sum) / r(j,j);
-        }
-        temp = wa1.blueNorm();
-        parl = fp / delta / temp / temp;
-    }
-
-    /* calculate an upper bound, paru, for the zero of the function. */
-    for (j = 0; j < n; ++j)
-        wa1[j] = r.col(j).head(j+1).dot(qtb.head(j+1)) / diag[ipvt[j]];
-
-    gnorm = wa1.stableNorm();
-    paru = gnorm / delta;
-    if (paru == 0.)
-        paru = dwarf / (std::min)(delta,Scalar(0.1));
-
-    /* if the input par lies outside of the interval (parl,paru), */
-    /* set par to the closer endpoint. */
-    par = (std::max)(par,parl);
-    par = (std::min)(par,paru);
-    if (par == 0.)
-        par = gnorm / dxnorm;
-
-    /* beginning of an iteration. */
-    while (true) {
-        ++iter;
-
-        /* evaluate the function at the current value of par. */
-        if (par == 0.)
-            par = (std::max)(dwarf,Scalar(.001) * paru); /* Computing MAX */
-        wa1 = sqrt(par)* diag;
-
-        Matrix< Scalar, Dynamic, 1 > sdiag(n);
-        qrsolv<Scalar>(r, ipvt, wa1, qtb, x, sdiag);
-
-        wa2 = diag.cwiseProduct(x);
-        dxnorm = wa2.blueNorm();
-        temp = fp;
-        fp = dxnorm - delta;
-
-        /* if the function is small enough, accept the current value */
-        /* of par. also test for the exceptional cases where parl */
-        /* is zero or the number of iterations has reached 10. */
-        if (abs(fp) <= Scalar(0.1) * delta || (parl == 0. && fp <= temp && temp < 0.) || iter == 10)
-            break;
-
-        /* compute the newton correction. */
-        for (j = 0; j < n; ++j) {
-            l = ipvt[j];
-            wa1[j] = diag[l] * (wa2[l] / dxnorm);
-        }
-        for (j = 0; j < n; ++j) {
-            wa1[j] /= sdiag[j];
-            temp = wa1[j];
-            for (i = j+1; i < n; ++i)
-                wa1[i] -= r(i,j) * temp;
-        }
-        temp = wa1.blueNorm();
-        parc = fp / delta / temp / temp;
-
-        /* depending on the sign of the function, update parl or paru. */
-        if (fp > 0.)
-            parl = (std::max)(parl,par);
-        if (fp < 0.)
-            paru = (std::min)(paru,par);
-
-        /* compute an improved estimate for par. */
-        /* Computing MAX */
-        par = (std::max)(parl,par+parc);
-
-        /* end of an iteration. */
-    }
-
-    /* termination. */
-    if (iter == 0)
-        par = 0.;
-    return;
-}
-
-template <typename Scalar>
-void lmpar2(
-        const ColPivHouseholderQR<Matrix< Scalar, Dynamic, Dynamic> > &qr,
-        const Matrix< Scalar, Dynamic, 1 >  &diag,
-        const Matrix< Scalar, Dynamic, 1 >  &qtb,
-        Scalar delta,
-        Scalar &par,
-        Matrix< Scalar, Dynamic, 1 >  &x)
-
-{
-    using std::sqrt;
-    using std::abs;
-    typedef DenseIndex Index;
-
-    /* Local variables */
-    Index j;
-    Scalar fp;
-    Scalar parc, parl;
-    Index iter;
-    Scalar temp, paru;
-    Scalar gnorm;
-    Scalar dxnorm;
-
-
-    /* Function Body */
-    const Scalar dwarf = (std::numeric_limits<Scalar>::min)();
-    const Index n = qr.matrixQR().cols();
-    eigen_assert(n==diag.size());
-    eigen_assert(n==qtb.size());
-
-    Matrix< Scalar, Dynamic, 1 >  wa1, wa2;
-
-    /* compute and store in x the gauss-newton direction. if the */
-    /* jacobian is rank-deficient, obtain a least squares solution. */
-
-//    const Index rank = qr.nonzeroPivots(); // exactly double(0.)
-    const Index rank = qr.rank(); // use a threshold
-    wa1 = qtb;
-    wa1.tail(n-rank).setZero();
-    qr.matrixQR().topLeftCorner(rank, rank).template triangularView<Upper>().solveInPlace(wa1.head(rank));
-
-    x = qr.colsPermutation()*wa1;
-
-    /* initialize the iteration counter. */
-    /* evaluate the function at the origin, and test */
-    /* for acceptance of the gauss-newton direction. */
-    iter = 0;
-    wa2 = diag.cwiseProduct(x);
-    dxnorm = wa2.blueNorm();
-    fp = dxnorm - delta;
-    if (fp <= Scalar(0.1) * delta) {
-        par = 0;
-        return;
-    }
-
-    /* if the jacobian is not rank deficient, the newton */
-    /* step provides a lower bound, parl, for the zero of */
-    /* the function. otherwise set this bound to zero. */
-    parl = 0.;
-    if (rank==n) {
-        wa1 = qr.colsPermutation().inverse() *  diag.cwiseProduct(wa2)/dxnorm;
-        qr.matrixQR().topLeftCorner(n, n).transpose().template triangularView<Lower>().solveInPlace(wa1);
-        temp = wa1.blueNorm();
-        parl = fp / delta / temp / temp;
-    }
-
-    /* calculate an upper bound, paru, for the zero of the function. */
-    for (j = 0; j < n; ++j)
-        wa1[j] = qr.matrixQR().col(j).head(j+1).dot(qtb.head(j+1)) / diag[qr.colsPermutation().indices()(j)];
-
-    gnorm = wa1.stableNorm();
-    paru = gnorm / delta;
-    if (paru == 0.)
-        paru = dwarf / (std::min)(delta,Scalar(0.1));
-
-    /* if the input par lies outside of the interval (parl,paru), */
-    /* set par to the closer endpoint. */
-    par = (std::max)(par,parl);
-    par = (std::min)(par,paru);
-    if (par == 0.)
-        par = gnorm / dxnorm;
-
-    /* beginning of an iteration. */
-    Matrix< Scalar, Dynamic, Dynamic > s = qr.matrixQR();
-    while (true) {
-        ++iter;
-
-        /* evaluate the function at the current value of par. */
-        if (par == 0.)
-            par = (std::max)(dwarf,Scalar(.001) * paru); /* Computing MAX */
-        wa1 = sqrt(par)* diag;
-
-        Matrix< Scalar, Dynamic, 1 > sdiag(n);
-        qrsolv<Scalar>(s, qr.colsPermutation().indices(), wa1, qtb, x, sdiag);
-
-        wa2 = diag.cwiseProduct(x);
-        dxnorm = wa2.blueNorm();
-        temp = fp;
-        fp = dxnorm - delta;
-
-        /* if the function is small enough, accept the current value */
-        /* of par. also test for the exceptional cases where parl */
-        /* is zero or the number of iterations has reached 10. */
-        if (abs(fp) <= Scalar(0.1) * delta || (parl == 0. && fp <= temp && temp < 0.) || iter == 10)
-            break;
-
-        /* compute the newton correction. */
-        wa1 = qr.colsPermutation().inverse() * diag.cwiseProduct(wa2/dxnorm);
-        // we could almost use this here, but the diagonal is outside qr, in sdiag[]
-        // qr.matrixQR().topLeftCorner(n, n).transpose().template triangularView<Lower>().solveInPlace(wa1);
-        for (j = 0; j < n; ++j) {
-            wa1[j] /= sdiag[j];
-            temp = wa1[j];
-            for (Index i = j+1; i < n; ++i)
-                wa1[i] -= s(i,j) * temp;
-        }
-        temp = wa1.blueNorm();
-        parc = fp / delta / temp / temp;
-
-        /* depending on the sign of the function, update parl or paru. */
-        if (fp > 0.)
-            parl = (std::max)(parl,par);
-        if (fp < 0.)
-            paru = (std::min)(paru,par);
-
-        /* compute an improved estimate for par. */
-        par = (std::max)(parl,par+parc);
-    }
-    if (iter == 0)
-        par = 0.;
-    return;
-}
-
-} // end namespace internal
-
-} // end namespace Eigen