/* NUM2.cpp
 *
 * Copyright (C) 1993-2020 David Weenink, Paul Boersma 2017,2020
 *
 * This code is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or (at
 * your option) any later version.
 *
 * This code is distributed in the hope that it will be useful, but
 * WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 * General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this work. If not, see <http://www.gnu.org/licenses/>.
 */

/*
 djmw 20020819 GPL header
 djmw 20020819 Split nonGLP part off.
 djmw 20001109 Changed stop criteria in NUMsvdcmp and NUMtqli.
 djmw 20020819 Split into GPL and nonGPL part.
 djmw 20021008 Removed SVD_sort.
 djmw 20030619 Removed calls to NRC svd-routines.
 djmw 20030623 Removed tqli en tred calls.
 djmw 20030703 Replaced NUMincompleteBeta with gsl_sf_beta_inc.
 djmw 20030710 NUMminimize_brent now also returns the minimum function value.
 djmw 20030731 NUMridders: better approximation for small d.
			   NUMinvFisherQ better approximation for p < 0.5
 djmw 20030813 Added NUMmad and NUMstatistics_huber.
 djmw 20030825 Replaced gsl_sf_beta_inc with NUMincompleteBeta
 pb   20030828 Improvements for invFisherQ, ridders, studentP, studentQ,
 	invStudentQ, invChiSquareQ: modifications for 'undefined' return values.
 djmw 20030830 Corrected a bug in NUMtriangularfilter_amplitude
 djmw 20031111 Added NUMdmatrix_transpose, NUMdmatrix_printMatlabForm
 djmw 20040105 Added NUMmahalanobisDistanceSquared_chi
 djmw 20040303 Added NUMstring_containsPrintableCharacter.
 djmw 20050406 NUMprocrutus->NUMprocrustes
 djmw 20060319 NUMinverse_cholesky: calculation of determinant is made optional
 djmw 20060517 Added NUMregexp_compile
 djmw 20060518 Treat NULL string as empty string in strs_replace_regexp/literal. Don't accept empty search in replace_regexStr
 djmw 20060626 Extra NULL argument for ExecRE.
 djmw 20070302 NUMclipLineWithinRectangle
 djmw 20070614 updated to version 1.30 of regular expressions.
 djmw 20071022 Removed function NUMfvector_moment2.
 djmw 20071201 Melder_warning<n>
 djmw 20080110 Corrected some bugs in replace_regexStr
 djmw 20080122 Bug in replace_regexStr
 djmw 20080317 +NUMsinc
 pb   20080410 FisherQ from gsl
 djmw 20090630 NUMlogNormalP/Q from gsl
 djmw 20090707 Rename NUMinverse_cholesky to NUMlowerCholeskyInverse,
 	+NUMcovarianceFromColumnCentredMatrix, +NUMmultivariateKurtosis
 djmw 20100311 +NUMsolveQuadraticEquation
 djmw 20100426 replace wcstok by Melder_wcstok
 djmw 20101209 removed NUMwcscmp is Melder_wcscmp now
 djmw 20110304 Thing_new
 djmw 20111110 use autostringvector
*/

#include "SVD.h"
#include "Eigen.h"
#include "NUMlapack.h"
#include "NUM2.h"
#include "NUMmachar.h"
#include "melder.h"

#include "gsl_randist.h"

#include "gsl_errno.h"
#include "gsl_sf_bessel.h"
#include "gsl_sf_gamma.h"
#include "gsl_sf_erf.h"
#include "gsl_sf_trig.h"
#include "gsl_poly.h"
#include "gsl_cdf.h"

#define SIGN(a,b) ((b < 0) ? -fabs(a) : fabs(a))

struct pdf1_struct {
	double p;
	double df;
};
struct pdf2_struct {
	double p;
	double df1;
	double df2;
};

void NUMgetGridDimensions (integer n, integer *out_nrow, integer *out_ncol) {
	integer ncol = 1;
	integer nrow = n;
	if (n > 3) {
		nrow = 1 + Melder_ifloor (sqrt (n - 0.5));
		ncol = 1 + Melder_ifloor ((n - 1) / nrow);
	}
	if (out_nrow)
		*out_nrow = nrow;
	if (out_ncol)
		*out_ncol = ncol;
	
}

void MATprintMatlabForm (constMATVU const& m, conststring32 name) {
	constexpr integer npc = 5;
	const ldiv_t n = ldiv (m.ncol, npc);

	MelderInfo_open ();
	MelderInfo_write (name, U"= [");
	for (integer i = 1; i <= m.nrow; i ++) {
		for (integer j = 1; j <= n.quot; j ++) {
			for (integer k = 1; k <= npc; k ++)
				MelderInfo_write (m [i] [(j - 1) * npc + k], (k < npc ? U", " : U""));
			MelderInfo_write (j < n.quot ? U",\n" : U"");
		}

		for (integer k = 1; k <= n.rem; k ++)
			MelderInfo_write (m [i] [n.quot * npc + k], (k < n.rem ? U", " : U""));
		MelderInfo_write (i < m.nrow ? U";\n" : U"];\n");
	}
	MelderInfo_close ();
}

void VECsmoothByMovingAverage_preallocated (VECVU const& out, constVECVU const& in, integer window) {
	Melder_assert (out.size == in.size);
	Melder_require (window > 0,
		U"The averaging window should be larger than 0.");
	for (integer i = 1; i <= out.size; i ++) {
		integer jfrom = i - window / 2, jto = i + window / 2;
		if (window % 2 == 0)
			jto --;
		Melder_clipLeft (1_integer, & jfrom);
		Melder_clipRight (& jto, out.size);
		out [i] = NUMmean (in.part (jfrom, jto));
	}
}

void VECsmooth_gaussian (VECVU const& out, constVECVU const& in, double sigma, NUMfft_Table fftTable) {
	Melder_require (out.size == in.size,
		U"The sizes of the input and output vectors should be equal.");
	out  <<=  in;
	VECsmooth_gaussian_inplace (out, sigma, fftTable);
}

void VECsmooth_gaussian_inplace (VECVU const& in_out, double sigma, NUMfft_Table fftTable) {
	Melder_require (in_out.size <= fftTable -> n,
		U"The dimension of the table should at least equal the length of the input vector.");
	autoVEC smooth = zero_VEC (fftTable -> n);
	smooth.part (1, in_out.size)  <<=  in_out;
	NUMfft_forward (fftTable, smooth.get());
	/*
		Low pass filter with a Gaussian.
		The Fourier Transform of h(x)= (exp(-a.x^2) is 
			H(f) = sqrt (pi/a) exp (-pi^2.f^2/a).
		A Gaussian g(x)=sqrt(a/pi)h(x), where a = 1/(2s^2)
		The "frequency" region is divided in fftTable -> n steps,
		where one "frequency" unit f equals 1 / fftTable -> n.
	*/
	const double b = 2.0 * NUMpi * sigma * NUMpi * sigma ;
	for (integer k = 2; k <= (fftTable -> n + 1) / 2; k ++) {
		const double f = (k - 1) /  (double) fftTable -> n;
		const double weight = exp (- b * f * f);
		smooth [k * 2 - 2] *= weight; // re
		smooth [k * 2 - 1] *= weight; // im
	}
	if (fftTable -> n % 2 == 0)
		smooth [fftTable -> n] *= exp (- b * 1 / 2  * 1 / 2);
	NUMfft_backward (fftTable, smooth.get());
	/*
		backwardFT (forwardFT (data)) = n * data;
	*/
	const double scaleFacor = 1.0 / fftTable -> n;
	smooth.part (1, in_out.size)  *=  scaleFacor;
	in_out  <<=  smooth.part (1, in_out.size);
}

void VECsmooth_gaussian_inplace (VECVU const& in_out, double sigma) {
	integer nfft = 1;
	while (nfft < in_out.size)
		nfft *= 2;
	autoNUMfft_Table fftTable;
	NUMfft_Table_init (& fftTable, nfft);
	VECsmooth_gaussian_inplace (in_out, sigma, & fftTable);
}

autoMAT MATcovarianceFromColumnCentredMatrix (constMATVU const& x, integer ndf) {
	Melder_require (ndf >= 0 && x.nrow - ndf > 0,
		U"Invalid arguments.");
	autoMAT covar = mtm_MAT (x);
	covar.all()  *=  1.0 / (x.nrow - ndf);
	return covar;
}

static void MATweighRows (MATVU const& x, constVECVU const& y) {
	Melder_assert (x.nrow == y.size);
	for (integer irow = 1; irow <= x.nrow; irow ++)
		x.row (irow)  *=  y [irow];
}

void MATmtm_weighRows (MATVU const& result, constMATVU const& data, constVECVU const& rowWeights) {
	Melder_assert (data.nrow == rowWeights.size);
	Melder_assert (data.ncol == result.ncol);
	Melder_assert (result.nrow == result.ncol);
	result  <<=  0.0;
	if (true) {
		autoMAT outer = raw_MAT (result.ncol, result.ncol);
		for (integer irow = 1; irow <= data.nrow; irow ++) {
			outer_MAT_out (outer.all(), data.row (irow), data.row (irow));
			result  +=  outer.all()  *  rowWeights [irow];
		}
	} else {
		autoVEC w = raw_VEC (rowWeights.size);
		autoMAT d = copy_MAT (data);
		for (integer irow = 1; irow <= w.size; irow ++) 
			w [irow] = sqrt (rowWeights [irow]);
		MATweighRows (d.get(), w.get());
		mtm_MAT_out (result, d.get());
	}
}

inline void MATmultiplyRows_inplace (MATVU const& x, constVECVU const& v) {
	Melder_assert (x.nrow == v.size);
	for (integer irow = 1; irow <= x.nrow; irow ++)
		x.row (irow)  *=  v [irow];  // x[i,j]*v[i]
}
inline void MATmultiplyColumns_inplace (MATVU const& x, constVECVU const& v) {
	Melder_assert (x.ncol == v.size);
	for (integer icol = 1; icol <= x.nrow; icol ++)
		x.column (icol)  *=  v [icol];  // x[i,j]*v[j]
}

double NUMmultivariateKurtosis (constMATVU const& m, integer method) {
	double kurt = undefined;
	if (m.nrow < 5)
		return kurt;
	autoMAT x = copy_MAT (m);
	autoVEC mean = columnMeans_VEC (x.get());
	x.all()  -=  mean.all();
	autoMAT covar = MATcovarianceFromColumnCentredMatrix (x.get(), 1);
	
	if (method == 1) { // Schott (2001, page 33)
		kurt = 0.0;
		for (integer l = 1; l <= x.ncol; l ++) {
			const double sll2 = covar [l] [l] * covar [l] [l];
			double zl = 0.0, wl;
			for (integer j = 1; j <= x.nrow; j ++) {
				const double d = x [j] [l] - mean [l], d2 = d * d;
				zl += d2 * d2;
			}
			zl = (zl - 6.0 * sll2) / (x.nrow - 4);
			wl = (sll2 - zl / x.nrow) * x.nrow / (x.nrow - 1);
			kurt += zl / wl;
		}
		kurt = kurt / (3.0 * x.ncol) - 1.0;
	}
	return kurt;
}

/*
	The following algorithm for monotone regession is on the average
	3.5 times faster than
	Kruskal's algorithm for monotone regression (and much simpler).
	Regression is ascending
*/
autoVEC newVECmonotoneRegression (constVEC x) {
	autoVEC fit = copy_VEC (x);
	double xt = undefined;   // only to stop gcc from complaining "may be used uninitialized"
	for (integer i = 2; i <= x.size; i ++) {
		if (fit [i] >= fit [i - 1])
			continue;
		longdouble sum = fit [i];
		integer nt = 1;
		for (integer j = 1; j <= i - 1; j ++) {
			sum += fit [i - j];
			nt ++;
			xt = (double) sum / nt;   // i >= 2 -> xt always gets a value
			if (j < i - 1 && xt >= fit [i - j - 1])
				break;
		}
		for (integer j = i - nt + 1; j <= i; j ++)
			fit [j] = xt;
	}
	return fit;
}

#undef TINY

double NUMdeterminant_fromSymmetricMatrix (constMAT m) {
	Melder_assert (m.nrow == m.ncol);
	autoMAT a = copy_MAT (m);
	/*
		Cholesky decomposition in lower, leave upper intact
	*/
	integer info;
	NUMlapack_dpotf2_ ("U", a.nrow, & a [1] [1], m.nrow, & info);
	Melder_require (info == 0,
			U"dpotf2_ failed with error = ", info);
	longdouble lnd = 0.0;
	for (integer i = 1; i <= a.nrow; i ++)
		lnd += log (a [i] [i]);
	lnd *= 2.0; // because A = L . L'
	return (double) lnd;
}

autoMAT newMATlowerCholesky (constMATVU const& a, double *out_lnd) {
	Melder_assert (a.nrow == a.ncol);
	autoMAT result = copy_MAT (a);
	MATlowerCholesky_inplace (result.get(), out_lnd);
	for (integer irow = 1; irow <= a.nrow - 1; irow ++)
		for (integer icol = irow + 1; icol <= a.nrow; icol ++)
			result [irow][icol] = 0.0;
	return result;
}


autoMAT newMATlowerCholeslyInverse_fromLowerCholesky (constMAT const& m) {
	Melder_assert (m.nrow == m.ncol);
	autoMAT result = copy_MAT (m);
	MATlowerCholeskyInverse_inplace (result.get(), nullptr);
	return result;
}

void MATlowerCholesky_inplace (MAT a, double *out_lnDeterminant) {
	Melder_assert (a.nrow == a.ncol);
	/*
		Cholesky decomposition in lower, leave upper intact
		Fortran storage -> use uplo='U' to get 'L'.
	*/
	integer info;
	NUMlapack_dpotf2_ ("U", a.nrow, & a [1] [1], a.nrow, & info);
	Melder_require (info == 0,
		U"dpotf2 fails with code ", info, U".");
	/*
		Determinant from diagonal, diagonal is now sqrt (a [i] [i]) !
	*/
	if (out_lnDeterminant) {
		longdouble lnDeterminant = 0.0;
		for (integer i = 1; i <= a.nrow; i ++)
			lnDeterminant += log (a [i] [i]);
		lnDeterminant *= 2.0;   /* because A = L . L' */
		*out_lnDeterminant = double (lnDeterminant);
	}
}

void MATlowerCholeskyInverse_inplace (MAT a, double *out_lnd) {
	Melder_assert (a.nrow == a.ncol);
	MATlowerCholesky_inplace (a, out_lnd);
	/*
		Get the inverse
	*/
	integer info;
	(void) NUMlapack_dtrtri_ ("U", "N", a.nrow, & a [1] [1], a.nrow, & info);
	Melder_require (info == 0,
		U"dtrtri_ fails with code ", info, U".");
}

autoMAT newMATinverse_fromLowerCholeskyInverse (constMAT m) {
	Melder_assert (m.nrow == m.ncol);
	autoMAT result = raw_MAT (m.nrow, m.nrow);
	for (integer irow = 1; irow <= m.nrow; irow ++) {
		for (integer icol = 1; icol <= irow; icol ++) {
			longdouble sum = 0.0;
			for (integer k = irow; k <= m.nrow; k ++)
				sum += m [k] [irow] * m [k] [icol];
			result [irow] [icol] = result [icol] [irow] = (double) sum;
		}
	}
	return result;
}

double NUMmahalanobisDistanceSquared (constMAT lowerInverse, constVEC v, constVEC m) {
	Melder_assert (lowerInverse.ncol == v.size && v.size == m.size);
	longdouble chisq = 0.0;
	if (lowerInverse.nrow == 1) { // diagonal matrix is one row matrix
		for (integer icol = 1; icol <= v.size; icol ++) {
			const double t = lowerInverse [1] [icol] * (v [icol] - m [icol]);
			chisq += t * t;
		}
	} else { // square matrix
		for (integer irow = v.size; irow > 0; irow --) {
			longdouble t = 0.0;
			for (integer icol = 1; icol <= irow; icol ++)
				t += lowerInverse [irow] [icol] * (v [icol] - m [icol]);
			chisq += t * t;
		}
	}
	return (double) chisq;
}

/*
	G. Golub & C. van Loan (1996), Matrix computations, third edition,
	The Johns Hopkins University Press Ltd.,
	London, (Par. 7.3.1 The Power Method)
*/
double VECdominantEigenvector_inplace (VEC inout_q, constMAT m, double tolerance) {
	Melder_assert (m.nrow == m.ncol && inout_q.size == m.nrow);

	double lambda0, lambda = NUMmul (inout_q, m, inout_q); //  q'. M . q
	Melder_require (lambda > 0.0,
		U"Zero matrices ??");
	autoVEC z = raw_VEC (m.nrow);
	integer maximunNumberOfIterations = 30;
	for (integer iter = 1; iter <= maximunNumberOfIterations; iter ++) {
		lambda0 = lambda;
		mul_VEC_out (z.get(), m, inout_q);
		VECnormalize_inplace (z.get(), 2.0, 1.0);
		lambda = NUMmul (z.get(), m, z.get()); // z'. M . z
		if (fabs (lambda - lambda0) < tolerance)
			break;
	}
	inout_q  <<=  z.all();
	return lambda;
}

void MATprojectColumnsOnEigenspace_preallocated (MAT projection, constMATVU const& data, constMATVU const& eigenvectors) {
	Melder_assert (data.nrow == eigenvectors.ncol && projection.nrow == eigenvectors.nrow);
	for (integer icol = 1; icol <= data.ncol; icol ++)
		for (integer irow = 1; irow <= eigenvectors.nrow; irow ++)
			projection [irow] [icol] = NUMinner (eigenvectors.row (irow), data.column (icol));
	// MATmul_tt (data.get(), eigenvectors.get()) ??
}

integer NUMsolveQuadraticEquation (double a, double b, double c, double *out_x1, double *out_x2) {
	double x1, x2;
	integer result =  gsl_poly_solve_quadratic (a, b, c, & x1, & x2);
	if (out_x1)
		*out_x1 = x1;
	if (out_x2)
		*out_x2 = x2;
	return result;
}

autoVEC newVECsolve (constMATVU const& a, constVECVU const& b, double tolerance) {
	Melder_assert (a.nrow == b.size);
	autoSVD me = SVD_createFromGeneralMatrix (a);
	SVD_zeroSmallSingularValues (me.get(), tolerance);
	autoVEC x = SVD_solve (me.get(), b);
	return x;
}

autoMAT newMATsolve (constMATVU const& a, constMATVU const& b, double tolerance) {
	Melder_assert (a.nrow == b.nrow);
	const double tol = ( tolerance > 0.0 ? tolerance : NUMfpp -> eps * a.nrow );
	
	autoSVD me = SVD_createFromGeneralMatrix (a);
	autoMAT x = raw_MAT (b.nrow, b.ncol);

	SVD_zeroSmallSingularValues (me.get(), tol);

	for (integer k = 1; k <= b.ncol; k ++) {
		autoVEC xt = SVD_solve (me.get(), b.column (k));
		x.column (k) <<= xt.all();
	}
	return x;
}

void VECsolveNonnegativeLeastSquaresRegression (VECVU const& x, constMATVU const& a, constVECVU const& y, integer maximumNumberOfIterations, double tol, integer infoLevel) {
	Melder_assert (a.nrow == y.size);
	Melder_assert (a.ncol == x.size);
	for (integer i = 1; i <= x.size; i ++)
		if (x [i] < 0.0)
			x [i] = 0.0;
	autoVEC r = raw_VEC (y.size);
	const double normSquared_y = NUMsum2 (y);
	integer iter = 1;
	bool farFromConvergence = true;
	double difsq, difsq_previous = 1e100; // large enough
	while (iter <= maximumNumberOfIterations && farFromConvergence) {
		/*
			Alternating Least Squares: Fixate all except x [icol]
		*/
		for (integer icol = 1; icol <= a.ncol; icol ++) {
			r.all()  <<=  y;
			for (integer jcol = 1; jcol <= a.ncol; jcol ++)
				if (jcol != icol)
					r.get()  -=  x [jcol] * a.column (jcol);
			const double ajr = NUMinner (a.column (icol), r.all());
			const double ajaj = NUMsum2 (a.column (icol));
			x [icol] = std::max (0.0, ajr / ajaj);
		}
		/*
			Calculate t(x) and compare with previous result.
		*/
		mul_VEC_out (r.get(), a, x);
		r.get()  -=  y;
		difsq = NUMsum2 (r.all());
		farFromConvergence = ( fabs (difsq - difsq_previous) > std::max (tol * normSquared_y, NUMeps) );
		if (infoLevel > 1)
			MelderInfo_writeLine (U"Iteration: ", iter, U", error: ", difsq);
		difsq_previous = difsq;
		iter ++;
	}
	iter --;
	if (infoLevel >= 1)
		MelderInfo_writeLine (U"Number of iterations: ", iter, U"; Minimum: ", difsq);
	if (infoLevel > 0)
			MelderInfo_drain();
}

struct nr_struct {
	double *y, *delta;
};

/*
	f (lambda) = sum (y [i]^2 delta [i] / (delta [i]-lambda)^2, i=1..3)
	f'(lambda) = 2 * sum (y [i]^2 delta [i] / (delta [i]-lambda)^3, i=1..3)
*/

static double nr_func (double x, double *df, void *data) {
	const struct nr_struct *me = (struct nr_struct *) data;
	longdouble f = 0.0, derivative = 0.0;
	for (integer i = 1; i <= 3; i ++) {
		const longdouble t1 = (my delta [i] - x);
		const longdouble t2 = my y [i] / t1;
		const longdouble t3 = t2 * t2 * my delta [i];
		f += t3;
		derivative += t3 * 2.0 / t1;
	}
	*df = (double) derivative;
	return (double) f;
}

void NUMsolveConstrainedLSQuadraticRegression (constMAT const& x, constVEC const& d, double *out_alpha, double *out_gamma) {
	Melder_assert (x.ncol == x.nrow && d.size == x.ncol && d.size == 3);
	Melder_assert (x.nrow >= x.ncol);
	integer n3 = 3;
	const double eps = 1e-6;
	/*
		Construct X'.X which will be 3x3
	*/
	autoMAT xtx = mtm_MAT (x);
	/*
		Eq (2): get lower Cholesky decomposition from X'.X (3x3)
		X'X -> lowerCholesky * lowerCholesky.transpose()
		F'^-1 == lowerCholesky
		F^-1 == lowerCholesky.transpose()
		F = lowerCholeskyInverse.transpose()
	*/
	autoMAT lowerCholesky = newMATlowerCholesky (xtx.get(), nullptr);
	autoMAT lowerCholeskyInverse = newMATlowerCholeslyInverse_fromLowerCholesky (lowerCholesky.get());
	/*
		Construct G and its eigen-decomposition (eq. (4,5))
		Sort eigenvalues (& eigenvectors) ascending.
	*/
	autoMAT b = zero_MAT (n3, n3);
	b [3] [1] = b [1] [3] = -0.5;
	b [2] [2] = 1.0;
	/*
		G = F^-1 B (F')^-1 (eq. 4)
	*/
	autoMAT g = zero_MAT (n3, n3);
	MATmul3_XYXt (g.get(), lowerCholesky.transpose(), b.get());
	/*				
		G's eigen-decomposition with eigenvalues (assumed ascending). (eq. 5)
	*/
	autoMAT p;
	autoVEC delta;
	MAT_getEigenSystemFromSymmetricMatrix (g.get(), & p, & delta, true);
	/*
		Construct y = P'*F'*O'*d = (F*P)'*(O'*d)	(page 632)
		We need F*P for later
	*/
	autoVEC otd = mul_VEC (x.transpose(), d);
	autoMAT fp = mul_MAT (p.transpose(), lowerCholeskyInverse.transpose()); // F*P !!
	autoVEC y = mul_VEC (fp.transpose(), otd.get()); // P'F' * O'd
	/*
		The solution (3 cases)
	*/
	autoVEC w = zero_VEC (n3);
	autoVEC chi = raw_VEC (n3);
	autoVEC diag = zero_VEC (n3);

	if (fabs (y [1]) < eps) {
		/*
			Case 1: page 633
		*/
		const double t21 = y [2] / (delta [2] - delta [1]);
		const double t31 = y [3] / (delta [3] - delta [1]);
		w [1] = sqrt (- delta [1] * (t21 * t21 * delta [2] + t31 * t31 * delta [3]));
		w [2] = t21 * delta [2];
		w [3] = t31 * delta [3];

		mul_VEC_out (chi.get(), fp.get(), w.get()); // chi = F*P*w

		if (fabs (chi [3] / chi [1]) < eps) {
			w [1] = - w [1];
			mul_VEC_out (chi.get(), fp.get(), w.get());
		}
	} else if (fabs (y [2]) < eps) {
		/*
			Case 2: page 633
		*/
		const double t12 = y [1] / (delta [1] - delta [2]);
		const double t32 = y [3] / (delta [3] - delta [2]);
		double t2;
		w [1] = t12 * delta [1];
		if ( (delta [2] < delta [3] && (t2 = (t12 * t12 * delta [1] + t32 * t32 * delta [3])) <= 0.0)) {
			w [2] = sqrt (- delta [2] * t2); /* +- */
			w [3] = t32 * delta [3];
			mul_VEC_out (chi.get(), p.get(), w.get());
			if (fabs (chi [3] / chi [1]) < eps) {
				w [2] = -w [2];
				mul_VEC_out (chi.get(), fp.get(), w.get());
			}
		} else if (fabs (delta [2] - delta [3]) < eps && fabs (y [3]) < eps) {
			/*
				Choose one value for w [2] from an infinite number
			*/
			w [2] = w [1];
			w [3] = sqrt (- t12 * t12 * delta [1] * delta [2] - w [2] * w [2]);
			mul_VEC_out (chi.get(), fp.get(), w.get());
		} else {
			// should not be here
		}
	} else {
		/*
			Case 3: page 634 use Newton-Raphson root finder
		*/
		struct nr_struct me;
		me.y = y.asArgumentToFunctionThatExpectsOneBasedArray();
		me.delta = delta.asArgumentToFunctionThatExpectsOneBasedArray();

		double lambda = NUMnrbis (nr_func, delta [1] + eps, delta [2] - eps, & me);

		for (integer i = 1; i <= 3; i++)
			w [i] = y [i] / (1.0 - lambda / delta [i]);
		mul_VEC_out (chi.get(), fp.get(), w.get());
	}
	if (out_alpha)
		*out_alpha = chi [1];
	if (out_gamma)
		*out_gamma = chi [3];
}

/*
	To find the value of b for which the derivative of psi(b) equals zero (Ten Berge, formula 4)
	psi (b) = delta*b - b^2 /(4*alpha) - sum (i=1..n, x [i]^2 / (c [i] - b)) (formula 4)
	psi'(b) = delta - b / (2 alpha) - sum (x [i]^2 / (c [i] - b)^2, i=1..n). (formula 5)
	We use NewTon-Raphson with bisection because we can also use psi'(b)'s derivative:
	f (b) = psi'(b)  = delta - b / (2 alpha) - sum (x [i]^2 / (c [i] - b)^2, i=1..n)
	f'(b) = psi''(b) = - 1 / (2 alpha) + 2 * sum (x [i]^2 / (c [i] - b)^3, i=1..n)
*/
struct nr2_struct {
	integer numberOfTerms;
	double delta, alpha;
	VEC x, c;
};

static double bolzanoFunction (double b, void *data) {
	const struct nr2_struct *me = (struct nr2_struct *) data;
	longdouble f = my delta - 0.5 * b / my alpha;
	for (integer i = 1; i <= my numberOfTerms; i ++) {
		const longdouble c = my x [i] / (my c [i] - b);
		f -= c * c;
	}
	return (double) f;
}

double NUMbolzanoSearch (double (*func) (double x, void *closure), double xmin, double xmax, void *closure) {
	Melder_assert (xmin < xmax);
	double fleft = (*func)(xmin, closure);
	double fright = (*func)(xmax, closure);
	if (fleft == 0.0)
		return fleft;
	if (fright == 0.0)
		return fright;
	Melder_require (fleft * fright < 0.0,
		U"Invalid interval: the function values at the borders should have different signs.");
	double xdifference = fabs (xmax - xmin);
	double xdifference_old = 2.0 * xdifference; // just larger to make the first comparison 'true'.
	while (xdifference < xdifference_old) {
		const double xmid = 0.5 * (xmax + xmin);
		const double fmid = (*func)(xmid, closure);
		if (fmid == 0.0)
			return fmid;
		if (fleft * fmid < 0.0)
			xmax = xmid;
		else
			xmin = xmid;
		xdifference_old = xdifference;
		xdifference = fabs (xmax - xmin);
	}
	return 0.5 * (xmax + xmin);
}

autoVEC newVECsolveWeaklyConstrainedLinearRegression (constMAT const& a, constVEC const& y, double alpha, double delta) {
	Melder_assert (a.nrow == y.size);
	Melder_require (a.nrow >= a.ncol,
		U"The number of rows should not be less than the number of columns.");
	Melder_require (alpha >= 0.0,
		U"The coefficient of the penalty function should not be negative.");
	Melder_require (delta > 0,
		U"The solution's vector length should be positive.");
	
	autoVEC c = zero_VEC (a.ncol);	
	autoSVD svd = SVD_createFromGeneralMatrix (a);

	if (alpha == 0.0) {
		/*
			Solve by standard least squares
		*/
		autoVEC result = SVD_solve (svd.get(), y);
		return result;
	}
	/*
		Step 1: (page 608)
		Compute U and C from the eigendecomposition F'F = UCU'
		U is from the SVD (F) = VCU' as in the paper (our notation would be: SVD(F)=UDV')
		Therefore, the paper's U is our V but since our V is stored as the transpose: U == svd -> v.transpose()!
	*/
	constMATVU u = svd -> v.transpose();
	for (integer i = 1; i <= a.ncol; i++) {
		const double ci = svd -> d [i];
		c [i] = ci * ci;
	}
	/*
		Evaluate q, the multiplicity of the smallest eigenvalue in C.
		The c[i] are ordered, i.e. c[i] >= c[i+1] for all i.
	*/
	integer q = 1;
	const double tol = 1e-6;
	while (q < a.ncol && (c [a.ncol - q] - c [a.ncol]) < tol)
		q ++;
	/*
		Step 2: x = U'F'y
	*/
	autoVEC ftphi = mul_VEC (a.transpose(), y);
	autoVEC x = mul_VEC (u.transpose(), ftphi.get());
	/*
		Step 3:
	*/
	struct nr2_struct me;
	me.numberOfTerms = a.ncol;
	me.delta = delta;
	me.alpha = alpha;
	me.x = x.get();
	me.c = c.get();

	const double xqsq = NUMsum2 (x.part (a.ncol - q + 1, a.ncol)); // = NUMinner (xq,xq)
	integer r = a.ncol;
	if (xqsq < tol) { // Case3.b page 608
		r = a.ncol - q;
		me.numberOfTerms = r;
		const double fm = bolzanoFunction (c[a.ncol], & me);
		if (fm >= 0.0) { // step 3.b1
			/*
				Get w0 by overwriting vector x.
			*/
			x [r + 1] = sqrt (fm);
			for (integer j = 1; j <= r; j ++)
				x [j] /= c [j] - c [a.ncol]; // eq. 10
			if (q > 1)
				x.part (r + 2, a.ncol) <<= 0.0;
			autoVEC result = mul_VEC (u, x.all());
			return result;
		}
		// else continue with r = m - q
	}
	/*
		Step 3a & 3b2, determine interval lower bound for root finder
	*/
	longdouble xCx = 0.0;
	for (integer j = 1; j <= r; j ++)
		xCx += x [j] * x [j] / c [j];

	const double bmin = ( delta > 0.0 ? - xCx / delta : -2.0 * sqrt (alpha * xCx) );
	//const double eps = (c [a.ncol] - bmin) * tol;
	/*
		Find the root of d(psi(b)/db in interval (bmin, c [m])
	*/
	const double b0 = NUMbolzanoSearch (bolzanoFunction, bmin, c [a.ncol], & me);
	/*
				Get w0 by overwriting vector x.
	*/
	for (integer j = 1; j <= r; j ++)
		x [j] /= c [j] - b0; // eq. 7
	if (q > 1)
		x.part (r + 1, a.ncol) <<= 0.0;
	autoVEC result = mul_VEC (u, x.all());
	return result;
}


void NUMprocrustes (constMATVU const& x, constMATVU const& y, autoMAT *out_rotation, autoVEC *out_translation, double *out_scale) {
	Melder_assert (x.nrow == y.nrow && x.ncol == y.ncol);
	Melder_assert (x.nrow >= x.ncol);
	const bool orthogonal = ! out_translation || ! out_scale; // else similarity transform
	/*
		Reference: Borg & Groenen (1997), Modern multidimensional scaling,
		Springer
		1. Calculate C = X'JY (page 346) for similarity transform
			else X'Y for othogonal (page 341)
			JY amounts to centering the columns of Y.
	*/	
	autoMAT yc = copy_MAT (y);
	if (! orthogonal)
		centreEachColumn_MAT_inout (yc.get());
	autoMAT c = mul_MAT (x.transpose(), yc.get()); // X'(JY)
	/*
		2. Decompose C by SVD: C = UDV' (our SVD has eigenvectors stored row-wise V!)
	*/
	autoSVD svd = SVD_createFromGeneralMatrix (c.get());
	const double trace = NUMsum (svd -> d.all());
	Melder_require (trace > 0.0,
		U"NUMprocrustes: degenerate configuration(s).");
	/*
		3. T = VU'
	*/
	autoMAT rotation = mul_MAT (svd->v.all(), svd->u.transpose());
	
	if (! orthogonal) {
		/*
			4. Dilation factor s = (tr X'JYT) / (tr Y'JY)
			First we need YT.
		*/
		autoMAT yt = mul_MAT (y, rotation.get());
		/*
			X'J = (JX)' centering the columns of X
		*/
		autoMAT xc = copy_MAT (x);
		centreEachColumn_MAT_inout (xc.get());
		/*
			tr X'J YT == tr xc' yt
		*/
		const double traceXtJYT = NUMtrace2 (xc.transpose(), yt.get()); // trace (Xc'.(YT))
		const double traceYtJY = NUMtrace2 (y.transpose(), yc.get()); // trace (Y'.Yc)
		const longdouble scale = traceXtJYT / traceYtJY;
		/*
			5. Translation vector tr = (X - sYT)'1 / x.nrow
		*/
		if (out_translation) {
			autoVEC translation = zero_VEC (x.ncol);
			for (integer i = 1; i <= x.ncol; i ++) {
				longdouble productsum = 0.0;
				for (integer j = 1; j <= x.nrow; j ++)
					productsum += x [j] [i] - scale * yt [j] [i];
				translation [i] = double (productsum / x.nrow);
			}
			*out_translation = translation.move();
		}
		if (out_scale)
			*out_scale = (double) scale;
	}
	if (out_rotation)
		*out_rotation = rotation.move();
}

double NUMmspline (constVEC const & knot, integer order, integer i, double x) {
	const integer nSplines = knot.size - order;
	
	Melder_require (nSplines > 0,
		U"No splines.");
	Melder_require (order > 0 && i <= nSplines,
		U"Combination of order and index not correct.");
	/*
		Find the interval where x is located.
		M-splines of order k have degree k-1.
		M-splines are zero outside interval [ knot [i], knot [i+order] ).
		First and last 'order' knots are equal, i.e.,
		knot [1] = ... = knot [order] && knot [knot.size-order+1] = ... knot [knot.size].
	*/
	integer jj;
	for (jj = order; jj <= knot.size - order + 1; jj ++)
		if (x < knot [jj])
			break;

	if (jj < i || (jj > i + order) || jj == order || jj > (knot.size - order + 1))
		return 0.0;
	/*
		Calculate M [i](x|1,t) according to eq.2.
	*/
	const integer ito = i + order - 1;
	autoVEC m = zero_VEC (order); 
	for (integer j = i; j <= ito; j ++)
		if (x >= knot [j] && x < knot [j + 1])
			m [j - i + 1] = 1 / (knot [j + 1] - knot [j]);
	/*
		Iterate to get M [i](x|k,t)
	*/
	for (integer k = 2; k <= order; k ++) {
		for (integer j = i; j <= i + order - k; j ++) {
			const double kj = knot [j], kjpk = knot [j + k];
			if (kjpk > kj)
                m [j - i + 1] = k * ((x - kj) * m [j - i + 1] + (kjpk - x) * m [j - i + 1 + 1]) / ((k - 1) * (kjpk - kj));
		}
	}
	return m [1];
}

double NUMispline (constVEC const & aknot, integer order, integer i, double x) {
	const integer orderp1 = order + 1;
	integer j;
	for (j = orderp1; j <= aknot.size - order; j ++)
		if (x < aknot [j])
			break;

	if (-- j < i)
		return 0.0;

	if (j > i + order || (j == aknot.size - order && x == aknot [j]))
		return 1.0;

	/*
		Equation 5 in Ramsay's article contains some errors!!!
		1. the interval selection should be 'j-k <= i <= j' instead of
			j-k+1 <= i <= j'
		2. the summation index m starts at 'i+1' instead of 'i'
	*/
	double y = 0.0;
	for (integer m = i + 1; m <= j; m ++) {
		const double r = NUMmspline (aknot, orderp1, m, x);
		y += (aknot [m + orderp1] - aknot [m]) * r;
	}
	y /= orderp1;
	return y;
}

double NUMwilksLambda (constVEC const& lambda, integer from, integer to) {
	Melder_assert (from > 0 && to <= lambda.size && from <= to);
	longdouble result = 1.0;
	for (integer i = from; i <= to; i ++)
		result *= 1.0 / (1.0 + lambda [i]);
	return (double) result;
}

double NUMfactln (integer n) {
	static double table [101];
	if (n < 0)
		return undefined;
	if (n <= 1)
		return 0.0;
	return n > 100 ? NUMlnGamma (n + 1.0) : table [n] != 0.0 ? table [n] : (table [n] = NUMlnGamma (n + 1.0));
}

double NUMnrbis (double (*f) (double x, double *dfx, void *closure), double xmin, double xmax, void *closure) {
	double df, tmp, xh, xl, tol;
	const integer itermax = 80;
	double fl = (*f) (xmin, & df, closure);
	if (fl == 0.0)
		return xmin;;

	double fh = (*f) (xmax, & df, closure);
	if (fh == 0.0)
		return xmax;

	if ((fl > 0.0 && fh > 0.0) || (fl < 0.0 && fh < 0.0))
		return undefined;

	if (fl < 0.0) {
		xl = xmin;
		xh = xmax;
	} else {
		xh = xmin;
		xl = xmax;
	}

	double dxold = fabs (xmax - xmin);
	double dx = dxold;
	double root = 0.5 * (xmin + xmax);
	double fx = (*f) (root, & df, closure);

	for (integer iter = 1; iter <= itermax; iter ++) {
		if ((((root - xh) * df - fx) * ((root - xl) * df - fx) >= 0.0) || (fabs (2.0 * fx) > fabs (dxold * df))) {
			dxold = dx;
			dx = 0.5 * (xh - xl);
			root = xl + dx;
			if (xl == root)
				return root;
		} else {
			dxold = dx;
			dx = fx / df;
			tmp = root;
			root -= dx;
			if (tmp == root)
				return root;
		}
		tol = NUMfpp -> eps	* (root == 0.0 ? 1.0 : fabs (root));
		if (fabs (dx) < tol)
			return root;

		fx = (*f) (root, & df, closure);

		if (fx < 0.0)
			xl = root;
		else
			xh = root;
	}
	Melder_warning (U"NUMnrbis: maximum number of iterations (", itermax, U") exceeded.");
	return root;
}

double NUMridders (double (*f) (double x, void *closure), double x1, double x2, void *closure) {
	/* There is still a problem with this implementation:
		tol may be zero;
	*/
	double d, root = undefined, tol;
	const integer itermax = 100;

	double f1 = f (x1, closure);
	if (f1 == 0.0)
		return x1;
	if (isundef (f1))
		return undefined;

	double f2 = f (x2, closure);
	if (f2 == 0.0)
		return x2;
	if (isundef (f2))
		return undefined;
	if ((f1 < 0.0 && f2 < 0.0) || (f1 > 0.0 && f2 > 0.0))
		return undefined;

	for (integer iter = 1; iter <= itermax; iter ++) {
		const double x3 = 0.5 * (x1 + x2);
		const double f3 = f (x3, closure);
		if (f3 == 0.0)
			return x3;
		if (isundef (f3))
			return undefined;

		// New guess: x4 = x3 + (x3 - x1) * sign(f1 - f2) * f3 / sqrt(f3^2 - f1*f2)

		d = f3 * f3 - f1 * f2;
		if (d < 0.0) {
			Melder_warning (U"d < 0 in ridders (iter = ", iter, U").");
			return undefined;
		}

		if (d == 0.0) {
			// pb test added because f1 f2 f3 may be 1e-170 or so
			tol = NUMfpp -> eps * (x3 == 0.0 ? 1.0 : fabs (x3));
			if (iter > 1 && fabs (x3 - root) < tol)
				return root;
			root = x3;

			// Perform bisection.

			if (f1 > 0.0) {
				// falling curve: f1 > 0, f2 < 0 
				if (f3 > 0.0) {
					x1 = x3;
					f1 = f3; // retain invariant: f1 > 0, f2 < 0
				} else {
					// f3 <= 0.0
					x2 = x3;
					f2 = f3; // retain invariant: f1 > 0, f2 < 0
				}
			} else {
				// rising curve: f1 < 0, f2 > 0 
				if (f3 > 0.0) {
					x2 = x3;
					f2 = f3; // retain invariant: f1 < 0, f2 > 0
				} else {
					// f3 < 0.0
					x1 = x3;
					f1 = f3; // retain invariant: f1 < 0, f2 > 0
				}
			}
		} else {
			d = sqrt (d);
			if (isnan (d)) {
				// pb: square root of denormalized small number fails on some computers
				tol = NUMfpp -> eps * (x3 == 0.0 ? 1.0 : fabs (x3));
				if (iter > 1 && fabs (x3 - root) < tol)
					return root;
				root = x3;

				// Perform bisection.

				if (f1 > 0.0) {
					// falling curve: f1 > 0, f2 < 0
					if (f3 > 0.0) {
						x1 = x3;
						f1 = f3; // retain invariant: f1 > 0, f2 < 0
					} else {
						// f3 <= 0.0
						x2 = x3;
						f2 = f3; // retain invariant: f1 > 0, f2 < 0
					}
				} else {
					// rising curve: f1 < 0, f2 > 0
					if (f3 > 0.0) {
						x2 = x3;
						f2 = f3; // retain invariant: f1 < 0, f2 > 0
					} else {
						// f3 < 0.0
						x1 = x3;
						f1 = f3; // retain invariant: f1 < 0, f2 > 0 */
					}
				}
			} else {
				d = (x3 - x1) * f3 / d;
				const double x4 = f1 - f2 < 0 ? x3 - d : x3 + d;
				tol = NUMfpp -> eps * (x4 == 0.0 ? 1.0 : fabs (x4));
				if (iter > 1 && fabs (x4 - root) < tol)
					return root;
				root = x4;
				const double f4 = f (x4, closure);
				if (f4 == 0.0)
					return root;
				if (isundef (f4))
					return undefined;
				if ((f1 > f2) == (d > 0.0)) { // pb: instead of x3 < x4
					if (SIGN (f3, f4) != f3) {
						x1 = x3;
						f1 = f3;
						x2 = x4;
						f2 = f4;
					} else {
						x1 = x4;
						f1 = f4;
					}
				} else {
					if (SIGN (f3, f4) != f3) {
						x1 = x4;
						f1 = f4;
						x2 = x3;
						f2 = f3;
					} else {
						x2 = x4;
						f2 = f4;
					}
				}
			}
		}
		if (fabs (x1 - x2) < tol)
			return root;
	}

	{
		static integer nwarnings = 0;
		nwarnings ++;
		Melder_warning (U"NUMridders: maximum number of iterations (", itermax, U") exceeded.");
	}
	return root;
}

double NUMlogNormalP (double x, double zeta, double sigma) {
	return gsl_cdf_lognormal_P (x, zeta, sigma);
}

double NUMlogNormalQ (double x, double zeta, double sigma) {
	return gsl_cdf_lognormal_Q (x, zeta, sigma);
}

double NUMstudentP (double t, double df) {
	if (df < 1.0) return undefined;
	const double ib = NUMincompleteBeta (0.5 * df, 0.5, df / (df + t * t));
	if (isundef (ib))
		return undefined;
	return t < 0.0 ? 0.5 * ib : 1.0 - 0.5 * ib;
}

double NUMstudentQ (double t, double df) {
	if (df < 1)
		return undefined;
	const double ib = NUMincompleteBeta (0.5 * df, 0.5, df / (df + t * t));
	if (isundef (ib))
		return undefined;
	return t > 0.0 ? 0.5 * ib : 1.0 - 0.5 * ib;
}

double NUMfisherP (double f, double df1, double df2) {
	if (f < 0.0 || df1 < 1.0 || df2 < 1.0)
		return undefined;
	const double ib = NUMincompleteBeta (0.5 * df2, 0.5 * df1, df2 / (df2 + f * df1));
	if (isundef (ib))
		return undefined;
	return 1.0 - ib;
}

double NUMfisherQ (double f, double df1, double df2) {
	if (f < 0.0 || df1 < 1.0 || df2 < 1.0)
		return undefined;
	if (Melder_debug == 28) {
		return NUMincompleteBeta (0.5 * df2, 0.5 * df1, df2 / (df2 + f * df1));
	} else {
		const double result = gsl_cdf_fdist_Q (f, df1, df2);
		if (isnan (result))
			return undefined;
		return result;
	}
}

double NUMinvGaussQ (double p) {
	double pc = p;
	if (p <= 0.0 || p >= 1.0)
		return undefined;
	if (p > 0.5)
		pc = 1.0 - p;
	double t = sqrt (- 2.0 * log (pc));
	t -= (2.515517 + (0.802853 + 0.010328 * t) * t) /
		 (1.0 + (1.432788 + (0.189269 + 0.001308 * t) * t) * t);
	return p > 0.5 ? -t : t;
}

static double studentQ_func (double x, void *voidParams) {
	const struct pdf1_struct *params = (struct pdf1_struct *) voidParams;
	const double q = NUMstudentQ (x, params -> df);
	return isundef (q) ? undefined : q - params -> p;
}

double NUMinvStudentQ (double p, double df) {
	struct pdf1_struct params;
	const double pc = ( p > 0.5 ? 1.0 - p : p );

	if (p < 0.0 || p >= 1.0)
		return undefined;
	/*
		Bracket the function f(x) = NUMstudentQ (x, df) - p.
	*/
	double xmax = 1.0;
	for (;;) {
		const double q = NUMstudentQ (xmax, df);
		if (isundef (q))
			return undefined;
		if (q < pc)
			break;
		xmax *= 2.0;
	}

	const double xmin = ( xmax > 1.0 ? xmax / 2.0 : 0.0 );
	/*
		Find zero of f(x) with Ridders' method.
	*/
	params. df = df;
	params. p = pc;
	const double x = NUMridders (studentQ_func, xmin, xmax, & params);
	if (isundef (x))
		return undefined;
	return p > 0.5 ? -x : x;
}

static double chiSquareQ_func (double x, void *voidParams) {
	const struct pdf1_struct *params = (struct pdf1_struct *) voidParams;
	const double q = NUMchiSquareQ (x, params -> df);
	return isundef (q) ? undefined : q - params -> p;
}

double NUMinvChiSquareQ (double p, double df) {
	struct pdf1_struct params;

	if (p < 0.0 || p >= 1.0)
		return undefined;
	/*
		Bracket the function f(x) = NUMchiSquareQ (x, df) - p.
	*/
	double xmax = 1.0;
	for (;;) {
		const double q = NUMchiSquareQ (xmax, df);
		if (isundef (q))
			return undefined;
		if (q < p)
			break;
		xmax *= 2.0;
	}
	const double xmin = ( xmax > 1.0 ? xmax / 2.0 : 0.0 );
	/*
		Find zero of f(x) with Ridders' method.
	*/
	params. df = df;
	params. p = p;
	return NUMridders (chiSquareQ_func, xmin, xmax, & params);
}

static double fisherQ_func (double x, void *voidParams) {
	struct pdf2_struct *params = (struct pdf2_struct *) voidParams;
	const double q = NUMfisherQ (x, params -> df1, params -> df2);
	return ( isundef (q) ? undefined : q - params -> p );
}

double NUMinvFisherQ (double p, double df1, double df2) {
	if (p <= 0.0 || p > 1.0 || df1 < 1.0 || df2 < 1.0)
		return undefined;
	if (Melder_debug == 29) {
		//if (p == 1.0) return 0.0;
		return gsl_cdf_fdist_Qinv (p, df1, df2);
	} else {
		struct pdf2_struct params;
		if (p == 1.0)
			return 0.0;
		params. p = p;
		params. df1 = df1;
		params. df2 = df2;
		double top = 1000.0;
		for (;;) {
			const double q = NUMfisherQ (top, df1, df2);
			if (isundef (q))
				return undefined;
			if (q < p)
				break;
			if (top > 0.9e300)
				return undefined;
			top *= 1e9;
		}
		return NUMridders (fisherQ_func, 0.0, p > 0.5 ? 2.2 : top, & params);
	}
}

double NUMbeta2 (double z, double w) {
	gsl_sf_result result;
	const integer status = gsl_sf_beta_e (z, w, &result);
	return status == GSL_SUCCESS ? result.val : undefined;
}

double NUMlnBeta (double a, double b) {
	gsl_sf_result result;
	const integer status = gsl_sf_lnbeta_e (a, b, & result);
	return status == GSL_SUCCESS ? result.val : undefined;
}

void MATscaledResiduals (MAT const& residuals, constMAT const& data, constMAT const& covariance, constVEC const& means) {
	try {
		Melder_require (residuals.nrow == data.nrow && residuals.ncol == data.ncol,
			U"The data and the residuals should have the same dimensions.");
		Melder_require (covariance.ncol == means.size && data.ncol == means.size,
			U"The dimensions of the means and the covariance have to conform with the data.");
		autoVEC dif = raw_VEC (data.ncol);
		autoMAT lowerInverse = copy_MAT (covariance);
		MATlowerCholeskyInverse_inplace (lowerInverse.get(), nullptr);
		for (integer irow = 1; irow <= data.nrow; irow ++) {
			dif.all() <<= data.row (irow)  -  means;
			residuals.row(irow) <<= 0.0;
			if (lowerInverse.nrow == 1) { // diagonal matrix is one row matrix
				residuals.row(irow) <<= lowerInverse.row(1)  *  dif.get();
			} else {// square matrix
				for (integer icol = 1; icol <= data.ncol; icol ++)
					residuals [irow] [icol] = NUMinner (lowerInverse.row(icol).part (1, icol), dif.part (1, icol));
			}
		}
	} catch (MelderError) {
		Melder_throw (U"MATscaleResiduals: not performed.");
	}
}

/*************** Hz <--> other freq reps *********************/

double NUMmelToHertz3 (double mel) {
	if (mel < 0.0)
		return undefined;
	return mel < 1000.0 ? mel : 1000.0 * (exp (mel * log10 (2.0) / 1000.0) - 1.0);
}

double NUMhertzToMel3 (double hz) {
	if (hz < 0.0)
		return undefined;
	return hz < 1000.0 ? hz : 1000.0 * log10 (1.0 + hz / 1000.0) / log10 (2.0);
}

double NUMmelToHertz2 (double mel) {
	if (mel < 0.0)
		return undefined;
	return 700.0 * (pow (10.0, mel / 2595.0) - 1.0);
}

double NUMhertzToMel2 (double hz) {
	if (hz < 0.0)
		return undefined;
	return 2595.0 * log10 (1.0 + hz / 700.0);
}

double NUMhertzToBark_traunmueller (double hz) {
	if (hz < 0.0)
		return undefined;
	return 26.81 * hz / (1960.0 + hz) - 0.53;
}

double NUMbarkToHertz_traunmueller (double bark) {
	if (bark < 0.0 || bark > 26.28)
		return undefined;
	return 1960.0 * (bark + 0.53) / (26.28 - bark);
}

double NUMbarkToHertz_schroeder (double bark) {
	return 650.0 * sinh (bark / 7.0);
}

double NUMbarkToHertz_zwickerterhardt (double hz) {
	if (hz < 0.0)
		return undefined;
	return 13.0 * atan (0.00076 * hz) + 3.5 * atan (hz / 7500.0);
}

double NUMhertzToBark_schroeder (double hz) {
	if (hz < 0.0)
		return undefined;
	const double h650 = hz / 650.0;
	return 7.0 * log (h650 + sqrt (1.0 + h650 * h650));
}

double NUMbarkToHertz2 (double bark) {
	if (bark < 0.0)
		return undefined;
	return 650.0 * sinh (bark / 7.0);
}

double NUMhertzToBark2 (double hz) {
	if (hz < 0)
		return undefined;
	const double h650 = hz / 650.0;
	return 7.0 * log (h650 + sqrt (1.0 + h650 * h650));
}

double NUMbladonlindblomfilter_amplitude (double zc, double z) {
	const double dz = zc - z + 0.474;
	return pow (10.0, 1.581 + 0.75 * dz - 1.75 * sqrt (1.0 + dz * dz));
}

double NUMsekeyhansonfilter_amplitude (double zc, double z) {
	const double dz = zc - z - 0.215;
	return pow (10.0, 0.7 - 0.75 * dz - 1.75 * sqrt (0.196 + dz * dz));
}

double NUMtriangularfilter_amplitude (double fl, double fc, double fh, double f) {
	double a = 0.0;
	if (f > fl && f < fh) {
		a = f < fc ? (f - fl) / (fc - fl) : (fh - f) / (fh - fc);

		/* Normalize such that area under the filter is always 1. ???

		a /= 2 * (fh - fl);*/
	}
	return a;
}

double NUMformantfilter_amplitude (double fc, double bw, double f) {
	const double dq = (fc * fc - f * f) / (bw * f);
	return 1.0 / (dq * dq + 1.0);
}

/* Childers (1978), Modern Spectrum analysis, IEEE Press, 252-255) */
/* work [1..n+n+n];
b1 = & work [1];
b2 = & work [n+1];
aa = & work [n+n+1];
for (i=1; i<=n+n+n; i ++) work [i]=0;
*/
double VECburg (VEC const& a, constVEC const& x) {
	const integer n = x.size, m = a.size;
	for (integer j = 1; j <= m; j ++)
		a [j] = 0.0;

	autoVEC b1 = zero_VEC (n), b2 = zero_VEC (n), aa = zero_VEC (m);

	// (3)

	longdouble p = 0.0;
	for (integer j = 1; j <= n; j ++)
		p += x [j] * x [j];

	longdouble xms = p / n;
	if (xms <= 0.0)
		return xms;	// warning empty

	// (9)

	b1 [1] = x [1];
	b2 [n - 1] = x [n];
	for (integer j = 2; j <= n - 1; j ++)
		b1 [j] = b2 [j - 1] = x [j];

	for (integer i = 1; i <= m; i ++) {
		// (7)

		longdouble num = 0.0, denum = 0.0;
		for (integer j = 1; j <= n - i; j ++) {
			num += b1 [j] * b2 [j];
			denum += b1 [j] * b1 [j] + b2 [j] * b2 [j];
		}

		if (denum <= 0.0)
			return 0.0;	// warning ill-conditioned

		a [i] = 2.0 * num / denum;

		// (10)

		xms *= 1.0 - a [i] * a [i];

		// (5)

		for (integer j = 1; j <= i - 1; j ++)
			a [j] = aa [j] - a [i] * aa [i - j];

		if (i < m) {

			// (8) Watch out: i -> i+1

			for (integer j = 1; j <= i; j ++)
				aa [j] = a [j];
			for (integer j = 1; j <= n - i - 1; j ++) {
				b1 [j] -= aa [i] * b2 [j];
				b2 [j] = b2 [j + 1] - aa [i] * b1 [j + 1];
			}
		}
	}
	return xms;
}

autoVEC newVECburg (constVEC const& x, integer numberOfPredictionCoefficients, double *out_xms) {
	autoVEC a = raw_VEC (numberOfPredictionCoefficients);
	const double xms = VECburg (a.get(), x);
	if (out_xms)
		*out_xms = xms;
	return a;
}

void VECfilterInverse_inplace (VEC const& s, constVEC const& filter, VEC const& filterMemory) {
	Melder_assert (filterMemory.size >= filter.size);
	filterMemory  <<=  0.0;
	for (integer i = 1; i <= s.size; i ++) {
		const double y0 = s [i];
		for (integer j = 1; j <= filter.size; j ++)
			s [i] += filter [j] * filterMemory [j];
		for (integer j = filter.size; j > 1; j --)
			filterMemory [j] = filterMemory [j - 1];
		filterMemory [1] = y0;
	}
}

void NUMdmatrix_to_dBs (MAT const& m, double ref, double factor, double floor) {
	const double factor10 = factor * 10.0;
	MelderExtremaWithInit extrema;

	Melder_assert (ref > 0 && factor > 0);

	for (integer irow = 1; irow <= m.nrow; irow ++)
		for (integer icol = 1; icol <= m.ncol; icol ++)
			extrema.update (m [irow] [icol]);
				
	
	Melder_require (extrema.min >= 0.0 && extrema.max >= 0.0,
		U"All matrix elements should be positive.");
	
	const double ref_db = factor10 * log10 (ref);

	for (integer irow = 1; irow <= m.nrow; irow ++) {
		for (integer icol = 1; icol <= m.ncol; icol ++) {
			double mij = floor;
			if (m [irow] [icol] > 0.0) {
				mij = factor10 * log10 (m [irow] [icol]) - ref_db;
				if (mij < floor)
					mij = floor;
			}
			m [irow] [icol] = mij;
		}
	}
}

autoMAT MATcosinesTable (integer n) {
	autoMAT result = raw_MAT (n, n);
	for (integer irow = 1; irow <= n; irow ++)
		for (integer icol = 1; icol <= n; icol ++)
			result [irow] [icol] = cos (NUMpi * (irow - 1) * (icol - 0.5) / n);
	return result;
}

void VECcosineTransform_preallocated (VEC const& target, constVEC const& x, constMAT const& cosinesTable) {
	Melder_assert (cosinesTable.nrow == cosinesTable.ncol);
	Melder_assert (x.size == target.size && x.size == cosinesTable.nrow);
	for (integer k = 1; k <= target.size; k ++)
		target [k] = NUMinner (x, cosinesTable.row (k));
}

void VECinverseCosineTransform_preallocated (VEC const& target, constVEC const& x, constMAT const& cosinesTable) {
	Melder_assert (cosinesTable.nrow == cosinesTable.ncol);
	Melder_assert (x.size == target.size && x.size == cosinesTable.nrow);
	for (integer j = 1; j <= target.size; j ++) {
		target [j] = 0.5 * x [1] * cosinesTable [1] [j];
		for (integer k = 2; k <= target.size; k ++)
			target [j] += x [k] * cosinesTable [k] [j];
		target [j] *= 2.0 / target.size;
	}
}

void NUMcubicSplineInterpolation_getSecondDerivatives (VEC const& out_y, constVEC const& x, constVEC const& y, double yp1, double ypn) {
	Melder_assert (x.size == y.size && out_y.size == y.size);
	
	autoVEC u = raw_VEC (x.size - 1);

	if (yp1 > 0.99e30)
		out_y [1] = u [1] = 0.0;
	else {
		out_y [1] = -0.5;
		u [1] = (3.0 / (x [2] - x [1])) * ( (y [2] - y [1]) / (x [2] - x [1]) - yp1);
	}

	for (integer i = 2; i <= x.size - 1; i ++) {
		const double sig = (x [i] - x [i - 1]) / (x [i + 1] - x [i - 1]);
		const double p = sig * out_y [i - 1] + 2.0;
		out_y [i] = (sig - 1.0) / p;
		u [i] = (y [i + 1] - y [i]) / (x [i + 1] - x [i]) - (y [i] - y [i - 1]) / (x [i] - x [i - 1]);
		u [i] = (6.0 * u [i] / (x [i + 1] - x [i - 1]) - sig * u [i - 1]) / p;
	}

	double qn, un;
	if (ypn > 0.99e30)
		qn = un = 0.0;
	else {
		qn = 0.5;
		un = (3.0 / (x [x.size] - x [x.size - 1])) * (ypn - (y [x.size] - y [x.size - 1]) / (x [x.size] - x [x.size - 1]));
	}

	out_y [x.size] = (un - qn * u [x.size - 1]) / (qn * out_y [x.size - 1] + 1.0);
	for (integer k = x.size - 1; k >= 1; k--)
		out_y [k] = out_y [k] * out_y [k + 1] + u [k];
}

double NUMcubicSplineInterpolation (constVEC const& x, constVEC const& y, constVEC const& y2, double xin) {
	Melder_assert (x.size == y.size && x.size == y2.size);
	integer klo = 1, khi = x.size;
	while (khi - klo > 1) {
		integer k = (khi + klo) >> 1;
		if (x [k] > xin)
			khi = k;
		else
			klo = k;
	}
	const double h = x [khi] - x [klo];
	Melder_require (h != 0.0,
		U"NUMcubicSplineInterpolation: bad input value.");
	
	const double a = (x [khi] - xin) / h;
	const double b = (xin - x [klo]) / h;
	const double yint = a * y [klo] + b * y [khi] + ((a * a * a - a) * y2 [klo] + (b * b * b - b) * y2 [khi]) * (h * h) / 6.0;
	return yint;
}

double NUMsinc (const double x) {
	struct gsl_sf_result_struct result;
	const integer status = gsl_sf_sinc_e (x / NUMpi, &result);
	return status == GSL_SUCCESS ? result. val : undefined;
}

double NUMsincpi (const double x) {
	struct gsl_sf_result_struct result;
	const integer status = gsl_sf_sinc_e (x, &result);
	return status == GSL_SUCCESS ? result. val : undefined;
}

/* Does the line segment from (x1,y1) to (x2,y2) intersect with the line segment from (x3,y3) to (x4,y4)? */
bool NUMdoLineSegmentsIntersect (double x1, double y1, double x2, double y2, double x3, double y3, double x4, double y4) {
	const integer o11 = NUMgetOrientationOfPoints (x1, y1, x2, y2, x3, y3);
	const integer o12 = NUMgetOrientationOfPoints (x1, y1, x2, y2, x4, y4);
	const integer o21 = NUMgetOrientationOfPoints (x3, y3, x4, y4, x1, y1);
	const integer o22 = NUMgetOrientationOfPoints (x3, y3, x4, y4, x2, y2);
	return ((o11 * o12 < 0) && (o21 * o22 < 0)) || (o11 *o12 *o21 *o22 == 0);
}

integer NUMgetOrientationOfPoints (double x1, double y1, double x2, double y2, double x3, double y3) {
	integer orientation;
	const longdouble dx2 = x2 - x1, dy2 = y2 - y1;
	const longdouble dx3 = x3 - x1, dy3 = y3 - y1;
	if (dx2 * dy3 > dy2 * dx3)
		orientation = -1;
	else if (dx2 * dy3 < dy2 * dx3)
		orientation = 1;
	else {
		if ((dx2 * dx3 < 0) || (dy2 * dy3 < 0))
			orientation = -1;
		else if ((dx2 * dx2 + dy2 * dy2) >= (dx3 * dx3 + dy3 * dy3))
			orientation = 0;
		else
			orientation = 1;
	}
	return orientation;
}

integer NUMgetIntersectionsWithRectangle (double x1, double y1, double x2, double y2, double xmin, double ymin, double xmax, double ymax, double *xi, double *yi) {
	double x [6], y [6];
	integer ni = 0;

	x [1] = x [4] = x [5] = xmin;
	x [2] = x [3] = xmax;
	y [1] = y [2] = y [5] = ymin;
	y [3] = y [4] = ymax;
	/*
		Calculate intersection of line segment through p1=(x1,y1) to p2(x2,y2) with line segment
		through p3=(x3,y3) to p4=(x4,y4).
		Parametrisation of the lines:
		l1 = p1 + s (p2 - p1), s in (-inf,+inf)
		l2 = p3 + t (p4 - p3), t in (-inf,+inf).
		When s and t are in [0,1] we have line segments between the points.
		At the intersection l1 == l2. We get for the x and y coordinates:
			x1 + s (x2 - x1) = x3 + t (x4 - x3).............(1)
			y1 + s (y2 - y1) = y3 + t (y4 - y3).............(2)
		Multiply (1)*(y2 - y1) and (2)*(x2 - x1):
			x1 (y2 - y1) + s (x2 - x1)(y2 - y1) = x3 (y2 - y1) + t (x4 - x3)(y2 - y1).......(3)
			y1 (x2 - x1) + s (y2 - y1)(x2 - x1) = y3 (x2 - x1) + t (y4 - y3)(x2 - x1).......(4)
		(3)-(4) with y21 = y2 -y1, x21 = x2 - x1, x43 = x4 - x3, ...
			x1 y21 - y1 x21 = x3 y21 - y3 x21 +t (x43 y21 - y43 x21)
		Combining:
			y31 x21 - x31 y21 = t (x43 y21 - y43 x21)
		Therefore at the intersection we have:

			t = (y31 x21 - x31 y21) / (x43 y21 - y43 x21)

		If (x43 y21 - y43 x21) == 0
			There is no intersection.
		If (t < 0 || t >= 1)
			No intersection in the segment l2
			To count intersections in a corner only once we have t < 0 instead of t <= 0!
	*/

	for (integer i = 1; i <= 4; i ++) {
		const double denom = (x [i + 1] - x [i]) * (y2 - y1) - (y [i + 1] - y [i]) * (x2 - x1);
		if (denom == 0.0)
			continue;
		
		// We have an intersection.
		
		const double t = ((y [i] - y1) * (x2 - x1) - (x [i] - x1) * (y2 - y1)) / denom;
		if (t < 0.0 || t >= 1.0)
			continue;
		
		// Intersection is within rectangle side.
		
		const double x3 = x [i] + t * (x [i + 1] - x [i]);
		const double y3 = y [i] + t * (y [i + 1] - y [i]);
		
		// s must also be valid
		
		const double s = ( x1 != x2 ? (x3 - x1) / (x2 - x1) : (y3 - y1) / (y2 - y1) );
		if (s < 0.0 || s >= 1.0)
			continue;

		ni ++;
		Melder_require (ni <= 3,
			U"Too many intersections.");
		
		xi [ni] = x3;
		yi [ni] = y3;
	}
	return ni;
}

bool NUMclipLineWithinRectangle (double line_x1, double line_y1, double line_x2, double line_y2, double rect_x1, double rect_y1, double rect_x2, double rect_y2, double *out_line_x1, double *out_line_y1, double *out_line_x2, double *out_line_y2) {
	integer numberOfRectangleCrossings = 0;
	double x, y, a, b;
	double crossing_x [5], crossing_y [5], xmin, xmax, ymin, ymax;
	double segment_x1 = line_x1, segment_y1 = line_y1, segment_x2 = line_x2, segment_y2 = line_y2;
	/*
		This test first because we expect the majority of the tested segments to be within the rectangle
	*/
	if (line_x1 >= rect_x1 && line_x1 <= rect_x2 && line_y1 >= rect_y1 && line_y1 <= rect_y2 &&
			line_x2 >= rect_x1 && line_x2 <= rect_x2 && line_y2 >= rect_y1 && line_y2 <= rect_y2)
		goto end;
	/*
		All lines that are completely outside the rectangle
	*/
	if ( (line_x1 <= rect_x1 && line_x2 <= rect_x1) || (line_x1 >= rect_x2 && line_x2 >= rect_x2) ||
			(line_y1 <= rect_y1 && line_y2 <= rect_y1) || (line_y1 >= rect_y2 && line_y2 >= rect_y2))
		return false;
	/*
		At least line spans (part of) the rectangle.
		Get extremes in x and y of the line for easy testing further on.
	*/
	bool xswap, yswap;
	if (line_x1 < line_x2) {
		xmin = line_x1;
		xmax = line_x2;
		xswap = false;
	} else {
		xmin = line_x2;
		xmax = line_x1;
		xswap = true;
	}
	if (line_y1 < line_y2) {
		ymin = line_y1;
		ymax = line_y2;
		yswap = false;
	} else {
		ymin = line_y2;
		ymax = line_y1;
		yswap = true;
	}
	
	if (line_y1 == line_y2) {
		if (xmin < rect_x1)
			segment_x1 = rect_x1;
		if (xmax > rect_x2)
			segment_x2 = rect_x2;
		if (xswap)
			std::swap (segment_x1, segment_x2);
		goto end;
	}
	if (line_x1 == line_x2) {
		if (ymin < rect_y1)
			segment_y1 = rect_y1;
		if (ymax > rect_y2)
			segment_y2 = rect_y2;
		if (yswap)
			std::swap (segment_y1, segment_y2);
		goto end;
	}
	/*
		Now we know that the line from (line_x1,line_y1) to (line_x2,line_y2) is neither horizontal nor vertical.
		We can parametrize it as y = ax + b
	*/
	a = (line_y1 - line_y2) / (line_x1 - line_x2);
	b = line_y1 - a * line_x1;
	
	/*
		To determine the crossings we have to avoid counting the crossings in a corner twice.
		Therefore we test the corners inclusive (..<=..<=..) on the vertical borders of the rectangle
		and exclusive (..<..<) at the horizontal borders.
	*/
	
	y = a * rect_x1 + b; // Crossing at y with left border: x = rect_x1
	
	if (y >= rect_y1 && y <= rect_y2 && xmin < rect_x1) { // Within vertical range?
		crossing_x [++ numberOfRectangleCrossings] = rect_x1;
		crossing_y [numberOfRectangleCrossings] = y;
		crossing_x [2] = xmax;
		crossing_y [2] = line_x1 > line_x2 ? line_y1 : line_y2;
	}

	x = (rect_y2 - b) / a; // Crossing at x with top border: y = rect_y2
	
	if (x > rect_x1 && x < rect_x2 && ymax > rect_y2) { // Within horizontal range?
		crossing_x [++ numberOfRectangleCrossings] = x;
		crossing_y [numberOfRectangleCrossings] = rect_y2;
		if (numberOfRectangleCrossings == 1) {
			crossing_y [2] = ymin;
			crossing_x [2] = line_y1 < line_y2 ? line_x1 : line_x2;
		}
	}

	y = a * rect_x2 + b; // Crossing at y with right border: x = rect_x2

	if (y >= rect_y1 && y <= rect_y2 && xmax > rect_x2) { // Within vertical range?
		crossing_x [++ numberOfRectangleCrossings] = rect_x2;
		crossing_y [numberOfRectangleCrossings] = y;
		if (numberOfRectangleCrossings == 1) {
			crossing_x [2] = xmin;
			crossing_y [2] = line_x1 < line_x2 ? line_y1 : line_y2;
		}
	}

	x = (rect_y1 - b) / a; // Crossing at x with bottom border: y = rect_y1

	if (x > rect_x1 && x < rect_x2 && ymin < rect_y1) {
		crossing_x [++ numberOfRectangleCrossings] = x;
		crossing_y [numberOfRectangleCrossings] = rect_y1;
		if (numberOfRectangleCrossings == 1) {
			crossing_y [2] = ymax;
			crossing_x [2] = line_y1 > line_y2 ? line_x1 : line_x2;
		}
	}
	if (numberOfRectangleCrossings == 0)
		return false;
	Melder_require (numberOfRectangleCrossings <= 2,
		U"Too many crossings found.");

	/*
		If start and endpoint of line are outside rectangle and numberOfRectangleCrossings == 1, than the line only touches.
	*/
	
	if (numberOfRectangleCrossings == 1 && (line_x1 < rect_x1 || line_x1 > rect_x2 || line_y1 < rect_y1 || line_y1 > rect_y2) &&
		(line_x2 < rect_x1 || line_x2 > rect_x2 || line_y2 < rect_y1 || line_y2 > rect_y2))
		goto end;

	if ((crossing_x [1] > crossing_x [2] && ! xswap) || (crossing_x [1] < crossing_x [2] && xswap)) {
		std::swap (crossing_x [1], crossing_x [2]);
		std::swap (crossing_y [1], crossing_y [2]);
	}
	segment_x1 = crossing_x [1];
	segment_y1 = crossing_y [1];
	segment_x2 = crossing_x [2];
	segment_y2 = crossing_y [2];
	
end:
	
	if (out_line_x1)
		*out_line_x1 = segment_x1;
	if (out_line_y1)
		*out_line_y1 = segment_y1;
	if (out_line_x2)
		*out_line_x2 = segment_x2;
	if (out_line_y2)
		*out_line_y2 = segment_y2;
	return true;
}

void NUMgetEllipseBoundingBox (double a, double b, double cospsi, double *out_width, double *out_height) {
	Melder_require (cospsi >= -1.0 && cospsi <= 1.0,
		U"NUMgetEllipseBoundingBox: abs (cospi) should not exceed 1.", cospsi);
	double width, height;
	if (cospsi == 1.0) { // a-axis along x-axis
		width = a;
		height = b;
	} else if (cospsi == 0.0) { // a-axis along y-axis
		width = b;
		height = a;
	} else {
		const double psi = acos (cospsi), sinpsi = sin (psi);
		double phi = atan2 (-b * sinpsi, a * cospsi);
		width = fabs (a * cospsi * cos (phi) - b * sinpsi * sin (phi));
		phi = atan2 (b * cospsi, a * sinpsi);
		height = fabs (a * sinpsi * cos (phi) + b * cospsi * sin (phi));
	}
	if (out_width)
		*out_width = width;
	if (out_height)
		*out_height = height;
}

/*
	Closely modeled after the netlib code by Oleg Keselyov.
*/
double NUMminimize_brent (double (*f) (double x, void *closure), double a, double b, void *closure, double tol, double *fx) {
	double x, v, fv, w, fw;
	const double golden = 1 - NUM_goldenSection;
	const double sqrt_epsilon = sqrt (NUMfpp -> eps);
	const integer itermax = 60;

	Melder_assert (tol > 0 && a < b);

	/*
		First step - golden section
	*/
	v = a + golden * (b - a);
	fv = (*f) (v, closure);
	x = v;
	w = v;
	*fx = fv;
	fw = fv;

	for (integer iter = 1; iter <= itermax; iter ++) {
		const double middle_range = (a + b) / 2.0;
		const double tol_act = sqrt_epsilon * fabs (x) + tol / 3.0;
		double range = b - a;
		if (fabs (x - middle_range) + range / 2.0 <= 2.0 * tol_act)
			return x;

		// Obtain the golden section step

		double new_step = golden * (x < middle_range ? b - x : a - x);

		// Decide if the parabolic interpolation can be tried

		if (fabs (x - w) >= tol_act) {
			/*
				Interpolation step is calculated as p/q;
				division operation is delayed until last moment.
			*/

			const double t = (x - w) * (*fx - fv);
			double q = (x - v) * (*fx - fw);
			double p = (x - v) * q - (x - w) * t;
			q = 2.0 * (q - t);

			if (q > 0.0)
				p = -p;
			else
				q = -q;

			/*
				If x+p/q falls in [a,b], not too close to a and b,
				and isn't too large, it is accepted.
				If p/q is too large then the golden section procedure can
				reduce [a,b] range.
			*/

			if (fabs (p) < fabs (new_step * q) &&
					p > q * (a - x + 2.0 * tol_act) &&
					p < q * (b - x - 2.0 * tol_act)) {
				new_step = p / q;
			}
		}

		// Adjust the step to be not less than tolerance.

		if (fabs (new_step) < tol_act)
			new_step = new_step > 0.0 ? tol_act : - tol_act;

		// Obtain the next approximation to min	and reduce the enveloping range

		{
			const double t = x + new_step;	// Tentative point for the min
			const double ft = (*f) (t, closure);

			/*
				If t is a better approximation, reduce the range so that
				t would fall within it. If x remains the best, reduce the range
				so that x falls within it.
			*/

			if (ft <= *fx) {
				if (t < x)
					b = x;
				else
					a = x;

				v = w;
				w = x;
				x = t;
				fv = fw;
				fw = *fx;
				*fx = ft;
			} else {
				if (t < x)
					a = t;
				else
					b = t;

				if (ft <= fw || w == x) {
					v = w;
					w = t;
					fv = fw;
					fw = ft;
				} else if (ft <= fv || v == x || v == w) {
					v = t;
					fv = ft;
				}
			}
		}
	}
	Melder_warning (U"NUMminimize_brent: maximum number of iterations (", itermax, U") exceeded.");
	return x;
}

/*
	probs is probability vector, i.e. all 0 <= probs [i] <= 1 and sum(i=1...probs.size, probs [i])= 1
*/
integer NUMgetIndexFromProbability (constVEC probs, double p) {
	integer index = 1;
	double psum = probs [index];
	while (p > psum && index < probs.size)
		psum += probs [++ index];
	return index;
}

// straight line fitting

void NUMlineFit_theil (constVEC const& x, constVEC const& y, double *out_m, double *out_intercept, bool completeMethod) {
	try {
		Melder_require (x.size == y.size,
			U"NUMlineFit_theil: the sizes of the two vectors should be equal.");
		/*
			Theil's incomplete method:
			Split (x [i],y [i]) as
			(x [i],y [i]), (x [N+i],y [N+i], i=1..numberOfPoints/2
			m [i] = (y [N+i]-y [i])/(x [N+i]-x [i])
			m = median (m [i])
			b = median(y [i]-m*x [i])
		 */
		double m, intercept;
		if (x.size == 1) {
			intercept = y [1];
			m = 0.0;
		} else if (x.size == 2) {
			m = (y [2] - y [1]) / (x [2] - x [1]);
			intercept = y [1] - m * x [1];
		} else {
			integer numberOfCombinations;
			autoVEC mbs;
			if (! completeMethod) {
				numberOfCombinations = x.size / 2;
				mbs = zero_VEC (x.size); // allocate for the intercept calculation too
				integer n2 = x.size % 2 == 1 ? numberOfCombinations + 1 : numberOfCombinations;
				for (integer i = 1; i <= numberOfCombinations; i ++)
					mbs [i] = (y [n2 + i] - y [i]) / (x [n2 + i] - x [i]);
			} else { // use all combinations
				numberOfCombinations = (x.size - 1) * x.size / 2;
				mbs = zero_VEC (numberOfCombinations);
				integer index = 0;
				for (integer i = 1; i < x.size; i ++)
					for (integer j = i + 1; j <= x.size; j ++)
						mbs [++ index] = (y [j] - y [i]) / (x [j] - x [i]);
				Melder_assert (index == numberOfCombinations);
			}
			sort_VEC_inout (mbs.part (1, numberOfCombinations));
			m = NUMquantile (mbs.part (1, numberOfCombinations), 0.5);
			for (integer i = 1; i <= x.size; i ++)
				mbs [i] = y [i] - m * x [i];
			sort_VEC_inout (mbs.part (1, x.size));
			intercept = NUMquantile (mbs.part (1, x.size), 0.5);
		}
		if (out_m)
			*out_m = m;
		if (out_intercept)
			*out_intercept = intercept;
	} catch (MelderError) {
		Melder_throw (U"No line fit (Theil's method).");
	}
}

void NUMlineFit_LS (constVEC const& x, constVEC const& y, double *out_m, double *out_intercept) {
	Melder_require (x.size == y.size,
		U"NUMlineFit_LS: the sizes of the two vectors should be equal.");
	const double sx = NUMsum (x);
	const double xmean = sx / x.size;
	longdouble st2 = 0.0, m = 0.0;
	for (integer i = 1; i <= x.size; i ++) {
		const double t = x [i] - xmean;
		st2 += t * t;
		m += t * y [i];
	}
	// y = m*x + b
	m /= st2;
	if (out_intercept) {
		const double sy = NUMsum (y);
		*out_intercept = (sy - m * sx) / x.size;
	}
	if (out_m)
		*out_m = m;
}

void NUMlineFit (constVEC x, constVEC y, double *out_m, double *out_intercept, integer method) {
	if (method == 1)
		NUMlineFit_LS (x, y, out_m, out_intercept);
	else if (method == 3)
		NUMlineFit_theil (x, y, out_m, out_intercept, true);
	else
		NUMlineFit_theil (x, y, out_m, out_intercept, false);
}

// IEEE: Programs for digital signal processing section 4.3 LPTRN
// lpc [1..n] to rc [1..n]

void VECrc_from_lpc (VEC rc, constVEC lpc) {
	Melder_assert (rc.size == lpc.size);
	autoVEC b = raw_VEC (lpc.size);
	autoVEC a = raw_VEC (lpc.size);
	a.all()  <<=  lpc;
	for (integer m = lpc.size; m > 0; m--) {
		rc [m] = a [m];
		Melder_require (fabs (rc [m]) <= 1.0,
			U"Relection coefficient [", m, U"] larger than 1.");
		b.part (1, m) <<= a.part (1, m);
		for (integer i = 1; i < m; i ++)
			a [i] = (b [i] - rc [m] * b [m - i]) / (1.0 - rc [m] * rc [m]);
	}
}

void VEClpc_from_rc (VEC lpc, constVEC rc) {
	Melder_assert (lpc.size == rc.size);
	lpc  <<=  rc;
	for (integer j = 2; j <= lpc.size; j ++) {
		for (integer k = 1; k <= j / 2; k ++) {
			double at = lpc [k] + rc [j] * lpc [j - k];
			lpc [j - k] += rc [j] * lpc [k];
			lpc [k] = at;
		}
	}
}

void VECarea_from_rc (VEC area, constVEC rc) {
	Melder_assert (area.size == rc.size);
	longdouble s = 0.0001; // 1.0 cm^2 at glottis
	for (integer i = area.size; i > 0; i --) {
		s *= (1.0 + rc [i]) / (1.0 - rc [i]);
		area [i] = s;
	}
}

void VECrc_from_area (VEC rc, constVEC area) {
	Melder_assert (rc.size == area.size);
	double ar;
	for (integer j = 1; j <= rc.size - 1; j ++) {
		ar = area [j + 1] / area [j];
		rc [j] = (1.0 - ar) / (1.0 + ar);
	}
	ar = 0.0001 / area [rc.size];  // 1.0 cm^2 at glottis
	rc [rc.size] = (1.0 - ar) / (1.0 + ar);
}

void VEClpc_from_area (VEC lpc, constVEC area) {
	Melder_assert (lpc.size == area.size);
	autoVEC rc = zero_VEC (lpc.size);
	VECrc_from_area (rc.get(), area);
	VEClpc_from_rc (lpc, rc.get());
}

void VECarea_from_lpc (VEC area, constVEC lpc) {
	Melder_assert (area.size == lpc.size);
	autoVEC rc = raw_VEC (lpc.size);
	VECrc_from_lpc (rc.get(), lpc);
	VECarea_from_rc (area, rc.get());
}

#if 0
/*********** Begin deprecated LPC routines ***********************************/
void NUMlpc_lpc_to_rc (double *lpc, integer p, double *rc) {
	autoVEC b = zero_VEC (p);
	autoVEC a  <<=  VEC(lpc, p);
	for (integer m = p; m > 0; m--) {
		rc [m] = a [m];
		Melder_require (fabs (rc [m]) <= 1.0,
			U"Relection coefficient [", m, U"] larger than 1.");
		for (integer i = 1; i < m; i ++) {
			b [i] = a [i];
		}
		for (integer i = 1; i < m; i ++) {
			a [i] = (b [i] - rc [m] * b [m - i]) / (1.0 - rc [m] * rc [m]);
		}
	}
}

void NUMlpc_rc_to_area2 (double *rc, integer n, double *area);
void NUMlpc_rc_to_area2 (double *rc, integer n, double *area) {
	double s = 0.0001; /* 1.0 cm^2 at glottis */
	for (integer i = n; i > 0; i--) {
		s *= (1.0 + rc [i]) / (1.0 - rc [i]);
		area [i] = s;
	}
}

void NUMlpc_area_to_lpc2 (double *area, integer n, double *lpc);
void NUMlpc_area_to_lpc2 (double *area, integer n, double *lpc) {
	// from area to reflection coefficients
	autoVEC rc =raw_VEC (n);
	// normalisation: area [n+1] = 0.0001
	for (integer j = n; j > 0; j--) {
		double ar = area [j+1] / area [j];
		rc [j] = (1 - ar) / (1 + ar);
	}
	// LPTRAN works from mouth to lips:
	for (integer j = 1; j <= n; j ++) {
		lpc [j] = rc [n - j + 1];
	}
	for (integer j = 2; j <= n; j ++) {
		integer nh = j / 2;
		double q = rc [j];
		for (integer k = 1; k <= nh; k ++) {
			double at = lpc [k] + q * lpc [j - k];
			lpc [j - k] += q * lpc [k];
			lpc [k] = at;
		}
	}
}

void NUMlpc_lpc_to_rc2 (double *lpc, integer m, double *rc);
void NUMlpc_lpc_to_rc2 (double *lpc, integer m, double *rc) { // klopt nog niet
	rc.part(1,m) <<= lpc.part (1,m)
	for (integer j = 2; j <= m; j ++) {
		integer jb = m + 1 - j;
		integer mh = (jb + 1) / 2;
		double rct = rc [jb+1];
		double d = 1.0 - rct * rct;
		for (integer k = 1; k <= mh; k ++) {
			rc [k] *= (1 - rct) / d;
		}
	}
}
// area [1] at lips generates n+1 areas from n rc's
void NUMlpc_rc_to_area (double *rc, integer m, double *area) {
	area [m+1] = 0.0001; /* 1.0 cm^2 */
	for (integer j = 1; j <= m; j ++) {
		double ar = (1.0 - rc [m+1-j]) / (1.0 + rc [m+1-j]);
		area [m+1-j] = area [m+2-j] / ar;
	}
}

// returns m-1 reflection coefficients from m areas
void NUMlpc_area_to_rc (double *area, integer m, double *rc) {
	for (integer j = 1; j <= m - 1; j ++) {
		double ar = area [j+1] / area [j];
		rc [j] = (1.0 - ar) / (1.0 + ar);
	}
}

void NUMlpc_rc_to_lpc (double *rc, integer m, double *lpc);
void NUMlpc_rc_to_lpc (double *rc, integer m, double *lpc) {
	lpc.part (1,m) <<= rc. part (1.m)
	for (integer j = 2; j <= m; j ++) {
		for (integer k = 1; k <= j / 2; k ++) {
			double at = lpc [k] + rc [j] * lpc [j - k];
			lpc [j - k] += rc [j] * lpc [k];
			lpc [k] = at;
		}
	}
}

void NUMlpc_area_to_lpc (double *area, integer m, double *lpc) {
	// from area to reflection coefficients
	autoVEC rc = zero_VEC (m);
	// normalisation: area [n+1] = 0.0001
	NUMlpc_area_to_rc (area, m, rc.peek());
	NUMlpc_rc_to_lpc (rc.peek(), m - 1, lpc); // m-1 ???
}

void NUMlpc_lpc_to_area (double *lpc, integer m, double *area) {
	autoVEC rc = zero_VEC (m);
	NUMlpc_lpc_to_rc (lpc, m, rc.peek());
	NUMlpc_rc_to_area (rc.peek(), m, area);

}
/*********** End deprecated LPC routines ***********************************/
#endif

#undef SIGN

#define SMALL_MEAN 14
/* If n*p < SMALL_MEAN then use BINV algorithm. The ranlib implementation used cutoff=30;
 * but on my (Brian Gough) computer 14 works better
 */

#define BINV_CUTOFF 110
/* In BINV, do not permit ix too large */

#define FAR_FROM_MEAN 20
/* If ix-n*p is larger than this, then use the "squeeze" algorithm.
 * Ranlib used 20, and this seems to be the best choice on my (Brian Gough) machine as well.
 */

#define LNFACT(x) gsl_sf_lnfact(x)

inline static double Stirling (double y1)
{
	const double y2 = y1 * y1;
	const double s = (13860.0 - (462.0 - (132.0 - (99.0 - 140.0 / y2) / y2) / y2) / y2) / y1 / 166320.0;
	return s;
}

// djmw 20121211 replaced calls to gsl_rng_uniform with NUMrandomUniform (0,1)

integer NUMrandomBinomial (double p, integer n) {
	if (p < 0.0 || p > 1.0 || n < 0) {
		return -100000000;
	}
	integer ix;			// return value
	bool flipped = false;

	if (n == 0)
		return 0;
	if (p > 0.5) {
		p = 1.0 - p;	// work with small p
		flipped = true;
	}

	const double q = 1.0 - p;
	const double s = p / q;
	const double np = n * p;

	/*
		Inverse cdf logic for small mean (BINV in K+S)
	*/

	if (np < SMALL_MEAN) {
		const double f0 = pow (q, n); // djmw gsl_pow_int (q, n); f(x), starting with x=0

		while (1) {
			/*
				This while(1) loop will almost certainly only loop once; but
				if u=1 to within a few epsilons of machine precision, then it
				is possible for roundoff to prevent the main loop over ix to
				achieve its proper value. Following the ranlib implementation,
				we introduce a check for that situation, and when it occurs,
				we just try again.
			*/

			double f = f0;
			double u = NUMrandomUniform (0.0, 1.0); // djmw gsl_rng_uniform (rng);

			for (ix = 0; ix <= BINV_CUTOFF; ++ ix) {
				if (u < f)
					goto Finish;
				u -= f;
				// Use recursion f(x+1) = f(x)* [(n-x)/(x+1)]* [p/(1-p)]
				f *= s * (n - ix) / (ix + 1.0);
			}

			/*
				It should be the case that the 'goto Finish' was encountered
				before this point was ever reached. But if we have reached
				this point, then roundoff has prevented u from decreasing
				all the way to zero. This can happen only if the initial u
				was very nearly equal to 1, which is a rare situation. In
				that rare situation, we just try again.

				Note, following the ranlib implementation, we loop ix only to
				a hardcoded value of SMALL_MEAN_LARGE_N=110; we could have
				looped to n, and 99.99...% of the time it won't matter. This
				choice, I think is a little more robust against the rare
				roundoff error. If n>LARGE_N, then it is technically
				possible for ix>LARGE_N, but it is astronomically rare, and
				if ix is that large, it is more likely due to roundoff than
				probability, so better to nip it at LARGE_N than to take a
				chance that roundoff will somehow conspire to produce an even
				larger (and more improbable) ix. If n<LARGE_N, then once
				ix=n, f=0, and the loop will continue until ix=LARGE_N.
			*/
		}
	} else {
		
		/*
			For n >= SMALL_MEAN, we invoke the BTPE algorithm
		*/

		const double ffm = np + p;		// ffm = n*p+p
		const integer m = (integer) ffm;	// m = int floor [n*p+p]
		const double fm = m;				// fm = double m
		const double xm = fm + 0.5;	 	// xm = half integer mean (tip of triangle)
		const double npq = np * q;		// npq = n*p*q

		/*
			Compute cumulative area of tri, para, exp tails

			p1: radius of triangle region; since height=1, also: area of region
			p2: p1 + area of parallelogram region
			p3: p2 + area of left tail
			p4: p3 + area of right tail
			pi/p4: probability of i'th area (i=1,2,3,4)

			Note: magic numbers 2.195, 4.6, 0.134, 20.5, 15.3
			These magic numbers are not adjustable...at least not easily!
		*/
		
		const double p1 = Melder_roundDown (2.195 * sqrt (npq) - 4.6 * q) + 0.5;

		// xl, xr: left and right edges of triangle
		const double xl = xm - p1;
		const double xr = xm + p1;

		/*
			Parameter of exponential tails
			Left tail:  t(x) = c*exp(-lambda_l* [xl - (x+0.5)])
			Right tail: t(x) = c*exp(-lambda_r* [(x+0.5) - xr])
		*/

		const double c = 0.134 + 20.5 / (15.3 + fm);
		const double p2 = p1 * (1.0 + c + c);
		const double al = (ffm - xl) / (ffm - xl * p);
		const double lambda_l = al * (1.0 + 0.5 * al);
		const double ar = (xr - ffm) / (xr * q);
		const double lambda_r = ar * (1.0 + 0.5 * ar);
		const double p3 = p2 + c / lambda_l;
		const double p4 = p3 + c / lambda_r;
		double var, accept;

TryAgain:

		/*
			Generate random variates, u specifies which region: Tri, Par, Tail
		*/
		
		const double u = p4 * NUMrandomUniform (0.0, 1.0); // djmw gsl_rng_uniform (rng) * p4;
		double v = NUMrandomUniform (0.0, 1.0); // djmw gsl_rng_uniform (rng);

		if (u <= p1) {
			// Triangular region
			ix = (integer) (xm - p1 * v + u);
			goto Finish;
		} else if (u <= p2) {
			// Parallelogram region
			const double x = xl + (u - p1) / c;
			v = v * c + 1.0 - fabs (x - xm) / p1;
			if (v > 1.0 || v <= 0.0)
				goto TryAgain;
			ix = (integer) x;
		} else if (u <= p3) {
			// Left tail
			ix = (integer) (xl + log (v) / lambda_l);
			if (ix < 0)
				goto TryAgain;
			v *= ((u - p2) * lambda_l);
		} else {
			// Right tail
			ix = (integer) (xr - log (v) / lambda_r);
			if (ix > (double) n)
				goto TryAgain;
			v *= ((u - p3) * lambda_r);
		}

		/*
			At this point, the goal is to test whether v <= f(x)/f(m)
			v <= f(x)/f(m) = (m!(n-m)! / (x!(n-x)!)) * (p/q)^{x-m}

			Here is a direct test using logarithms. It is a little
			slower than the various "squeezing" computations below, but
			if things are working, it should give exactly the same answer
			(given the same random number seed).
		*/

		#ifdef DIRECT
		var = log (v);

		accept = LNFACT (m) + LNFACT (n - m) - LNFACT (ix) - LNFACT (n - ix) + (ix - m) * log (p / q);

		#else // SQUEEZE METHOD

		/*
			More efficient determination of whether v < f(x)/f(M)
		 */

		const integer k = integer_abs (ix - m);

		if (k <= FAR_FROM_MEAN) {
			/*
				If ix near m (ie, |ix-m|<FAR_FROM_MEAN), then do
				explicit evaluation using recursion relation for f(x)
			*/
			const double g = (n + 1) * s;
			double f = 1.0;

			var = v;

			if (m < ix) {
				for (integer i = m + 1; i <= ix; i ++)
					f *= (g / i - s);
			} else if (m > ix) {
				for (integer i = ix + 1; i <= m; i ++)
					f /= (g / i - s);
			}

			accept = f;
		} else {
			// If ix is far from the mean m: k=ABS(ix-m) large

			var = log (v);

			if (k < npq / 2 - 1) {
				/* 
					"Squeeze" using upper and lower bounds on
					log(f(x)) The squeeze condition was derived
					under the condition k < npq/2-1
				*/
				const double amaxp = k / npq * ((k * (k / 3.0 + 0.625) + (1.0 / 6.0)) / npq + 0.5);
				const double ynorm = -(k * k / (2.0 * npq));
				if (var < ynorm - amaxp)
					goto Finish;
				if (var > ynorm + amaxp)
					goto TryAgain;
			}

			/*
				Now, again: do the test log(v) vs. log f(x)/f(M)
			*/

			#if USE_EXACT
			/*
				This is equivalent to the above, but is a little (~20%) slower
				There are five log's vs three above, maybe that's it?
			*/

			accept = LNFACT (m) + LNFACT (n - m) - LNFACT (ix) - LNFACT (n - ix) + (ix - m) * log (p / q);

			#else
			/* USE STIRLING:
				The "#define Stirling" above corresponds to the first five
				terms in asymptotic formula for
				log Gamma (y) - (y-0.5)log(y) + y - 0.5 log(2*pi);
				See Abramowitz and Stegun, eq 6.1.40


				Note below: two Stirling's are added, and two are
				subtracted. In both K+S, and in the ranlib
				implementation, all four are added. I (jt) believe that
				is a mistake -- this has been confirmed by personal
				correspondence w/ Dr. Kachitvichyanukul. Note, however,
				the corrections are so small, that I couldn't find an
				example where it made a difference that could be
				observed, let alone tested. In fact, define'ing Stirling
				to be zero gave identical results!! In practice, alv is
				O(1), ranging 0 to -10 or so, while the Stirling
				correction is typically O(10^{-5}) ...setting the
				correction to zero gives about a 2% performance boost;
				might as well keep it just to be pedantic.
			*/

			{
				const double x1 = ix + 1.0;
				const double w1 = n - ix + 1.0;
				const double f1 = fm + 1.0;
				const double z1 = n + 1.0 - fm;

				accept = xm * log (f1 / x1) + (n - m + 0.5) * log (z1 / w1) + (ix - m) * log (w1 * p / (x1 * q))
					+ Stirling (f1) + Stirling (z1) - Stirling (x1) - Stirling (w1);
			}
			#endif
			#endif
		}


		if (var <= accept)
			goto Finish;
		else
			goto TryAgain;
	}

Finish:

	return flipped ? (n - ix) : ix;
}

double NUMrandomBinomial_real (double p, integer n) {
	if (p < 0.0 || p > 1.0 || n < 0)
		return undefined;
	else
		return (double) NUMrandomBinomial (p, n);
}

double NUMrandomGamma (const double alpha, const double beta) {
	Melder_require (alpha > 0 && beta > 0,
		U"Both arguments should be positive.");
	double result;
	if (alpha >= 1.0) {
		double x, v, d = alpha - 1.0 / 3.0;
		double c = (1.0 / 3.0) / sqrt (d);
		while (1) {
			do {
				x = NUMrandomGauss (0.0, 1.0);
				v = 1.0 + c * x;
			} while (v <= 0.0);
			v = v * v * v;
			double u = NUMrandomUniform (0.0, 1.0);
			if (u < 1.0 - 0.0331 * (x * x) * (x * x))
				break;
			if (log(u) < 0.5 * x * x + d * (1.0 - v + log(v)))
				break;
		}
		result = d * v / beta;
	} else {
		double u = NUMrandomUniform (0.0, 1.0);
		result = NUMrandomGamma (alpha + 1.0, beta) * pow (u, 1.0 / alpha);
	}
	return result;
}

void NUMlngamma_complex (double zr, double zi, double *out_lnr, double *out_arg) {
	double ln_re = undefined, ln_arg = undefined;
	gsl_sf_result gsl_lnr, gsl_arg;
	if (gsl_sf_lngamma_complex_e (zr, zi, & gsl_lnr, & gsl_arg)) {
		ln_re = gsl_lnr.val;
		ln_arg = gsl_arg.val;
	}
	if (out_lnr)
		*out_lnr = ln_re;
	if (out_arg)
		*out_arg = ln_arg;
}

autoVEC newVECbiharmonic2DSplineInterpolation_getWeights (constVECVU const& x, constVECVU const& y, constVECVU const& z) {
	Melder_assert (x.size == y.size && x.size == z.size);
	autoMAT g = raw_MAT (x.size, x.size);
	/*
		1. Calculate the Green matrix G = |point [i]-point [j]|^2 (ln (|point [i]-point [j]|) - 1.0)
		2. Solve z = G.w for w
	*/
	for (integer i = 1; i <= x.size; i ++) {
		for (integer j = i + 1; j <= x.size; j ++) {
			double dx = x [i] - x [j], dy = y [i] - y [j];
			double distanceSquared = dx * dx + dy * dy;
			g [i] [j] = g [j] [i] = distanceSquared * (0.5 * log (distanceSquared) - 1.0); // Green's function
		}
		g [i] [i] = 0.0;
	}
	autoVEC w = newVECsolve (g.get(), z, 0.0);
	return w;
}

double NUMbiharmonic2DSplineInterpolation (constVECVU const& x, constVECVU const& y, constVECVU const& w, double xp, double yp) {
	Melder_assert (x.size == y.size && x.size == w.size);
	longdouble result = 0.0;
	for (integer i = 1; i <= x.size; i ++) {
		double dx = xp - x [i], dy = yp - y [i];
		double d = dx * dx + dy * dy;
		result += w [i] * d * (0.5 * log (d) - 1.0);
	}
	return (double) result;
}

void NUMfixIndicesInRange (integer lowerLimit, integer upperLimit, integer *lowIndex, integer *highIndex) {
	Melder_require (lowerLimit <= upperLimit, U"The lower limit should not exceed the upper limit.");
	if (*highIndex < *lowIndex) {
		*lowIndex = lowerLimit; *highIndex = upperLimit;
	} else if (*highIndex == *lowIndex) {
		Melder_require (*lowIndex >= lowerLimit && *highIndex <= upperLimit,
			U"Both lower and upper indices are out of range.");
	} else { // low < high
		Melder_require (*lowIndex < upperLimit && *highIndex > lowerLimit,
			U"Both lower and upper indices are out of range.");
		if (*lowIndex < lowerLimit)
			*lowIndex = lowerLimit;
		if (*highIndex > upperLimit)
			*highIndex = upperLimit;
	}
}

void NUMgetEntropies (constMATVU const& m, double *out_h, double *out_hx, double *out_hy, double *out_hygx, double *out_hxgy, double *out_uygx, double *out_uxgy, double *out_uxy) {
	
	double h = undefined, hx = undefined, hy = undefined;
	double hxgy = undefined, hygx = undefined, uygx = undefined, uxgy = undefined, uxy = undefined;
	
	// Get total sum and check if all elements are not negative.
	
	longdouble totalSum = 0.0;
	for (integer i = 1; i <= m.nrow; i ++) {
		for (integer j = 1; j <= m.ncol; j++) {
			Melder_require (m [i] [j] >= 0.0,
				U"Matrix elements should not be negative.");
			totalSum += m [i] [j];
		}
	}
	
	if (totalSum > 0.0) {
		longdouble hy_t = 0.0;
		for (integer i = 1; i <= m.nrow; i ++) {
			double rowsum = NUMsum (m.row (i));
			if (rowsum > 0.0) {
				double p = rowsum / totalSum;
				hy_t -= p * NUMlog2 (p);
			}
		}
		hy = (double) hy_t;
		
		longdouble hx_t = 0.0;
		for (integer j = 1; j <= m.ncol; j ++) {
			double colsum = NUMsum (m.column (j));
			if (colsum > 0.0) {
				double p = colsum / totalSum;
				hx_t -= p * NUMlog2 (p);
			}
		}
		hx = (double) hx_t;
				
		// Total entropy
		longdouble h_t = 0.0;
		for (integer i = 1; i <= m.nrow; i ++) {
			for (integer j = 1; j <= m.ncol; j ++) {
				if (m [i] [j] > 0.0) {
					double p = m [i] [j] / totalSum;
					h_t -= p * NUMlog2 (p);
				}
			}
		}
		h = (double) h_t;
		hygx = h - hx;
		hxgy = h - hy;
		uygx = (hy - hygx) / hy;
		uxgy = (hx - hxgy) / hx;
		uxy = 2.0 * (hx + hy - h) / (hx + hy);
	}
	if (out_h)
		*out_h = h;
	if (out_hx)
		*out_hx = hx;
	if (out_hy)
		*out_hy = hy;
	// Conditional entropies
	if (out_hygx)
		*out_hygx = hygx;
	if (out_hxgy)
		*out_hxgy = hxgy;
	if (out_uygx)
		*out_uygx = uygx;
	if (out_uxgy)
		*out_uxgy = uxgy;
	if (out_uxy)
		*out_uxy = uxy;
}
#undef TINY

double NUMtrace (const constMATVU& a) {
	Melder_assert (a.nrow == a.ncol);
	longdouble trace = 0.0;
	for (integer i = 1; i <= a.nrow; i ++)
		trace += a [i] [i];
	return (double) trace;
}

double NUMtrace2 (const constMATVU& x, const constMATVU& y) {
	Melder_assert (x.ncol == y.nrow && x.nrow == y.ncol);
	longdouble trace = 0.0;
	for (integer irow = 1; irow <= x.nrow; irow ++)
		for (integer k = 1; k <= x.ncol; k ++)
			trace += x [irow] [k] * y [k] [irow];
	return (double) trace;
}

void NUMeigencmp22 (double a, double b, double c, double *out_rt1, double *out_rt2, double *out_cs1, double *out_sn1) {
	const longdouble sm = a + c, df = a - c, adf = fabs (df);
	const longdouble tb = b + b, ab = fabs (tb);
	longdouble acmx = c, acmn = a;
	if (fabs (a) > fabs (c)) {
		acmx = a;
		acmn = c;
	}
	longdouble rt, tn;
	if (adf > ab) {
		tn = ab / adf;
		rt = adf * sqrt (1.0 + tn * tn);
	} else if (adf < ab) {
		tn = adf / ab;
		rt = ab * sqrt (1.0 + tn * tn);
	} else
		rt = ab * sqrt (2.0);
	
	longdouble rt1, rt2;
	integer sgn1, sgn2;
	if (sm < 0.0) {
		rt1 = 0.5 * (sm - rt);
		sgn1 = -1;
		/*
			Order of execution important.
			To get fully accurate smaller eigenvalue,
			next line needs to be executed in higher precision.
		*/
		rt2 = (acmx / rt1) * acmn - (b / rt1) * b;
	} else if (sm > 0.0) {
		rt1 = 0.5 * (sm + rt);
		sgn1 = 1;
		/*
			Order of execution important.
			To get fully accurate smaller eigenvalue,
			next line needs to be executed in higher precision.
		*/
		rt2 = (acmx / rt1) * acmn - (b / rt1) * b;
	} else {
		rt1 = 0.5 * rt;
		rt2 = -0.5 * rt;
		sgn1 = 1;
	}

	// Compute the eigenvector

	longdouble cs;
	if (df >= 0.0) {
		cs = df + rt;
		sgn2 = 1;
	} else {
		cs = df - rt;
		sgn2 = -1;
	}
	const longdouble acs = fabs (cs);
	longdouble cs1, sn1;
	if (acs > ab) {
		const longdouble ct = -tb / cs;
		sn1 = 1.0 / sqrt (1.0 + ct * ct);
		cs1 = ct * sn1;
	} else {
		if (ab == 0.0) {
			cs1 = 1.0;
			sn1 = 0.0;
		} else {
			tn = -cs / tb;
			cs1 = 1.0 / sqrt (1.0 + tn * tn);
			sn1 = tn * cs1;
		}
	}
	if (sgn1 == sgn2) {
		tn = cs1;
		cs1 = -sn1;
		sn1 = tn;
	}
	if (fabs (cs1) > 1.0)
		cs1 = copysign (1.0, cs1);
	if (fabs (sn1) > 1.0)
		sn1 = copysign (1.0, sn1);
	if (out_rt1)
		*out_rt1 = (double) rt1;
	if (out_rt2)
		*out_rt2 = (double) rt2;
	if (out_cs1)
		*out_cs1 = (double) cs1;
	if (out_sn1)
		*out_sn1 = (double) sn1;
}

void MATmul3_XYXt (MATVU const& target, constMATVU const& x, constMATVU const& y) { // X.Y.X'
	Melder_assert (x.ncol == y.nrow && y.ncol == x.ncol);
	Melder_assert (target.nrow == target.ncol && target.nrow == x.nrow);
	for (integer irow = 1; irow <= target.nrow; irow ++)
		for (integer icol = 1; icol <= target.ncol; icol ++) {
			longdouble sum = 0.0;
			for (integer k = 1; k <= x.ncol; k ++)
				sum += x [irow] [k] * NUMinner (y.row (k), x.row (icol));
			target [irow] [icol] = sum;
		}
}

void MATmul3_XYsXt (MATVU const& target, constMAT const& x, constMAT const& y) { // X.Y.X'
	Melder_assert (x.ncol == y.nrow && y.ncol == x.ncol);
	Melder_assert (target.nrow == target.ncol && target.nrow == x.nrow);
	for (integer irow = 1; irow <= target.nrow; irow ++)
		for (integer icol = irow; icol <= target.ncol; icol ++) {
			longdouble sum = 0.0;
			for (integer k = 1; k <= x.ncol; k ++)
				sum += x [irow] [k] * NUMinner (y.row (k), x.row (icol));
			target [irow] [icol] = sum;
		}
	for (integer irow = 1; irow <= target.nrow; irow ++)
		for (integer icol = irow + 1; icol <= target.ncol; icol ++)
			target [icol] [irow] = target [irow] [icol];
}

/*
	1. Take absolute value of v.
	2. Sort abs(v) and its index together.
	3. Make all elements of v zero, except the numberOfNonZeros largest elements.
	4. Set the support of these largest elements to 1 and the rest to zero.
*/
static void VECupdateDataAndSupport_inplace (VECVU const& v, BOOLVECVU const& support, integer numberOfNonZeros) {
	Melder_assert (v.size == support.size);
	autoVEC abs = newVECabs (v);
	autoINTVEC index = to_INTVEC (v.size);
	NUMsortTogether <double, integer> (abs.get(), index.get()); // sort is always increasing
	for (integer i = 1; i <= v.size - numberOfNonZeros; i ++) {
		v [index [i]] = 0.0;
		support [index [i]] = false;
	}
	for (integer i = v.size - numberOfNonZeros + 1; i <= v.size; i ++)
		support [index [i]] = true;
}

static double update (VEC const& x_new, VEC const& y_new, BOOLVECVU const& support_new, constVECVU const& xn, double stepSize, constVEC const& gradient, constMATVU const& dictionary, constVEC const& yn, integer numberOfNonZeros, VEC buffer) {
	Melder_assert (x_new.size == xn.size && buffer.size == x_new.size);
	Melder_assert (gradient.size == support_new.size && gradient.size == x_new.size);
	Melder_assert (y_new.size == yn.size);
	Melder_assert (dictionary.nrow == yn.size && dictionary.ncol == xn.size);
	
	buffer <<=  stepSize * gradient;
	x_new  <<=  xn  +  buffer; // x(n) + stepSize * gradient
	VECupdateDataAndSupport_inplace (x_new, support_new, numberOfNonZeros);
	buffer  <<=  x_new  -  xn; // x(n+1) - x (n)
	const double xdifsq = NUMsum2 (buffer); // ||x(n+1) - x (n)||^2
	
	mul_VEC_out (y_new, dictionary, x_new); // y(n+1) = D. x(n+1)
	buffer.part (1, yn.size) <<= y_new  -  yn; // y(n+1) - y(n) = D.(x(n+1) - x(n))
	const double ydifsq = NUMsum2 (buffer.part (1, yn.size)); // ||y(n+1) - y(n)||^2
	return xdifsq / ydifsq;
}

autoVEC newVECsolveSparse_IHT (constMATVU const& dictionary, constVECVU const& y, integer numberOfNonZeros, integer maximumNumberOfIterations, double tolerance, integer infoLevel) {
	try {
		Melder_assert (dictionary.ncol > dictionary.nrow); // must be underdetermined system
		Melder_assert (dictionary.nrow == y.size); // y = D.x + e
		autoVEC result = zero_VEC (dictionary.ncol);
		VECsolveSparse_IHT (result.get(), dictionary, y, numberOfNonZeros, maximumNumberOfIterations, tolerance, infoLevel);
		return result;
	} catch (MelderError) {
		Melder_throw (U"Solution of sparse problem not found.");
	}
}

/* temporarily until present in melder_tensor.h */
inline void operator<<= (BOOLVECVU const& target, constBOOLVECVU const& source) {
	Melder_assert (target.size == source.size);
	for (integer i = 1; i <= target.size; i ++)
		target [i] = source [i];
}

void VECsolveSparse_IHT (VECVU const& x, constMATVU const& dictionary, constVECVU const& y, integer numberOfNonZeros, integer maximumNumberOfIterations, double tolerance, integer infoLevel) {
	try {
		Melder_assert (dictionary.ncol > dictionary.nrow); // must be underdetermined system
		Melder_assert (dictionary.ncol == x.size); // we calculate D.x
		Melder_assert (dictionary.nrow == y.size); // y = D.x + e
		
		autoVEC gradient = raw_VEC (x.size);
		autoVEC x_new = raw_VEC (x.size); // x(n+1), x == x(n)
		autoVEC yfromx = raw_VEC (y.size); // D.x(n)
		autoVEC yfromx_new = raw_VEC (y.size); // D.x(n+1)
		autoVEC ydif = raw_VEC (y.size); // y - D.x(n)
		autoVEC buffer = raw_VEC (x.size);
		autoBOOLVEC support = raw_BOOLVEC (x.size);
		autoBOOLVEC support_new = raw_BOOLVEC (x.size);
		
		const double xnormSq = NUMsum2 (x);
		const double rms_y = NUMsum2 (y) / y.size;
		double rms = rms_y;
		
		if (xnormSq == 0.0) {
			/*
				Start with x == 0.
				Get initial support supp (Hard_K (D'y))
				Hard_K (v) is a hard thresholder which only keeps the largest K elements from the vector v
			*/
			mul_VEC_out (buffer.get(), dictionary.transpose(), y);
			VECupdateDataAndSupport_inplace (buffer.get(), support.get(), numberOfNonZeros);
			yfromx.all() <<= 0.0;
			ydif.all() <<= y; // ydif = y - D.x(1) = y - D.0 = y
		} else {
			/*
				We improve a current solution x
			*/
			VECupdateDataAndSupport_inplace (x, support.get(), numberOfNonZeros);
			mul_VEC_out (yfromx.get(), dictionary, x); // D.x(n)
			ydif.all() <<= y  -  yfromx.all(); // y - D.x(n)
			rms = NUMsum2 (ydif.get()) / y.size; // ||y - D.x(n)||^2
		}
		
		bool convergence = false;
		integer iter = 1;
		while (iter <= maximumNumberOfIterations && not convergence) {			
			
			mul_VEC_out (gradient.get(), dictionary.transpose(), ydif.get()); // D'.(y - D.x(n))
			/*
				Calculate stepSize mu according to Eq. (13)
				mu = || g_sparse ||^2 / || D_sparse * g_sparse ||^2
				where g_sparse only contains the supported elements from the gradient and D_sparse only the supported columns from the dictionary.
			*/
			longdouble normsq_gs = 0.0; // squared norm of the sparse gradient
			for (integer ig = 1; ig <= gradient.size; ig ++) {
				if (support [ig])
					normsq_gs += gradient [ig] * gradient [ig];
			}
			longdouble normsq_dgs = 0.0; // squared norm of the transformed sparse gradient
			for (integer irow = 1; irow <= dictionary.nrow; irow ++) {
				longdouble sum = 0.0;
				for (integer icol = 1; icol <= dictionary.ncol; icol ++)
					if (support [icol])
						sum += dictionary [irow] [icol] * gradient [icol];
				normsq_dgs += sum * sum;
			}
						
			double stepSize = normsq_gs / normsq_dgs;
			
			double normsq_ratio = update (x_new.get(), yfromx_new.get(), support_new.get(), x, stepSize, gradient.get(), dictionary, yfromx.get(), numberOfNonZeros, buffer.get());
			
			if (! NUMequal (support.get(), support_new.get())) {
				double omega;
				const double kappa = 2.0, c = 0.0;
				while (stepSize > (omega = (1.0 - c) * normsq_ratio)) { // stepSize > omega, from Eq. 14
					stepSize *= 1.0 / (kappa * (1.0 - c));
					normsq_ratio = update (x_new.get(), yfromx_new.get(), support_new.get(), x, stepSize, gradient.get(), dictionary, yfromx.get(), numberOfNonZeros, buffer.get());
				}
			}

			ydif.all() <<= y  -  yfromx_new.all();   // y - D.x(n+1)

			const double rms_new = NUMsum2 (ydif.get()) / y.size;
			const double relativeError = fabs (rms - rms_new) / rms_y;
			convergence = relativeError < tolerance;
			if (infoLevel > 1)
				MelderInfo_writeLine (U"Iteration: ", iter, U", error: ", rms_new, U" relative: ", relativeError, U" stepSize: ", stepSize);
			
			x  <<=  x_new.all();
			support.all() <<= support_new.all();
			yfromx.all() <<= yfromx_new.all();
			rms = rms_new;
			iter ++;
		}
		iter = std::min (iter, maximumNumberOfIterations);
		if (infoLevel >= 1)
			MelderInfo_writeLine (U"Number of iterations: ", iter, U" Difference squared: ", rms);
		if (infoLevel > 0)
			MelderInfo_drain();
	} catch (MelderError) {
		Melder_throw (U"Solution of sparse problem not found.");
	}
}

void NUMpolynomial_recurrence (VEC const& pn, double a, double b, double c, constVEC const& pnm1, constVEC const& pnm2) {
	const integer degree = pn.size - 1;
	Melder_assert (degree > 1 && pnm1.size >= pn.size && pnm2.size >= pn.size);

	pn [1] = b * pnm1 [1] + c * pnm2 [1];
	for (integer i = 2; i <= degree - 1; i ++)
		pn [i] = a * pnm1 [i - 1] + b * pnm1 [i] + c * pnm2 [i];
	pn [degree] = a * pnm1 [degree - 1] + b * pnm1 [degree];
	pn [degree + 1] = a * pnm1 [degree];
}

/* End of file NUM2.cpp */
