/* Eigen.cpp
 *
 * Copyright (C) 1993-2018 David Weenink
 *
 * 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 20010719
 djmw 20020402 GPL header.
 djmw 20030701 Modified sorting in Eigen_initFromSquareRootPair.
 djmw 20030703 Added Eigens_alignEigenvectors.
 djmw 20030708 Corrected syntax error in Eigens_alignEigenvectors.
 djmw 20030812 Corrected memory bug in Eigen_initFromSymmetricMatrix.
 djmw 20030825 Removed praat_USE_LAPACK external variable.
 djmw 20031101 Documentation
 djmw 20031107 Moved NUMdmatrix_transpose to NUM2.c
 djmw 20031210 Added rowLabels to Eigen_drawEigenvector and Eigen_Strings_drawEigenvector
 djmw 20030322 Extra test in Eigen_initFromSquareRootPair.
 djmw 20040329 Added fractionOfTotal  and cumulative parameters in Eigen_drawEigenvalues_scree.
 djmw 20040622 Less horizontal labels in Eigen_drawEigenvector.
 djmw 20050706 Shortened horizontal offsets in Eigen_drawEigenvalues from 1 to 0.5
 djmw 20051204 Eigen_initFromSquareRoot adapted for nrows < ncols
 djmw 20071012 Added: oo_CAN_WRITE_AS_ENCODING.h
 djmw 20110304 Thing_new
*/

#include "Eigen.h"
#include "MAT_numerics.h"
#include "NUMmachar.h"
#include "NUMclapack.h"
#include "NUM2.h"
#include "SVD.h"

#include "oo_DESTROY.h"
#include "Eigen_def.h"
#include "oo_COPY.h"
#include "Eigen_def.h"
#include "oo_EQUAL.h"
#include "Eigen_def.h"
#include "oo_CAN_WRITE_AS_ENCODING.h"
#include "Eigen_def.h"
#include "oo_WRITE_TEXT.h"
#include "Eigen_def.h"
#include "oo_READ_TEXT.h"
#include "Eigen_def.h"
#include "oo_WRITE_BINARY.h"
#include "Eigen_def.h"
#include "oo_READ_BINARY.h"
#include "Eigen_def.h"
#include "oo_DESCRIPTION.h"
#include "Eigen_def.h"

Thing_implement (Eigen, Daata, 0);

static void Graphics_ticks (Graphics g, double min, double max, bool hasNumber, bool hasTick, bool hasDottedLine, bool integers) {
	double range = max - min, scale = 1.0, tick = min, dtick = 1.0;

	if (range == 0.0) {
		return;
	} else if (range > 1.0) {
		while (range / scale > 10.0) {
			scale *= 10.0;
		}
		range /= scale;
	} else {
		while (range / scale < 10.0) {
			scale /= 10.0;
		}
		range *= scale;
	}

	if (range < 3.0) {
		dtick = 0.5;
	}
	dtick *= scale;
	tick = dtick * Melder_roundDown (min / dtick);
	if (tick < min) {
		tick += dtick;
	}
	while (tick <= max) {
		double num = integers ? round (tick) : tick;
		Graphics_markBottom (g, num, hasNumber, hasTick, hasDottedLine, nullptr);
		tick += dtick;
	}
}

void Eigen_init (Eigen me, integer numberOfEigenvalues, integer dimension) {
	my numberOfEigenvalues = numberOfEigenvalues;
	my dimension = dimension;
	my eigenvalues = VECzero (numberOfEigenvalues);
	my eigenvectors = MATzero (numberOfEigenvalues, dimension);
}

/*
	Solve: (A'A - lambda)x = 0 for eigenvalues lambda and eigenvectors x.
	svd(A) = UDV' => A'A = (UDV')'(UDV') = VD^2V'
	(VD^2V'-lambda)x = 0 => (D^2 - lambda)V'x = 0 => solution V'x = I => x = V
	Eigenvectors: the columns of the matrix V
	Eigenvalues: D_i^2
*/
void Eigen_initFromSquareRoot (Eigen me, constMAT a) {
	Melder_assert (a.nrow >= 1);
	integer numberOfZeroed, numberOfEigenvalues;
	integer nsv = std::min (a.nrow, a.ncol);
	my dimension = a.ncol;
	autoSVD svd = SVD_createFromGeneralMatrix (a);
	/*
		Make sv's that are too small zero. These values occur automatically
		when the rank of A'A < a.ncol. This could occur when for
		example numberOfRows <= a.ncol.
		(n points in  an n-dimensional space define maximally an n-1
		dimensional surface for which we maximally need an n-1 dimensional
		basis.)
	*/

	numberOfZeroed = SVD_zeroSmallSingularValues (svd.get(), 0.0);

	numberOfEigenvalues = nsv - numberOfZeroed;

	Eigen_init (me, numberOfEigenvalues, a.ncol);
	integer k = 0;
	for (integer i = 1; i <= nsv; i ++) {
		double t = svd -> d [i];
		if (t > 0.0) {
			my eigenvalues [++ k] = t * t;
			for (integer j = 1; j <= a.ncol; j ++) {
				my eigenvectors [k] [j] = svd -> v [j] [i];
			}
		}
	}
	Eigen_sort (me);
}


void Eigen_initFromSquareRootPair (Eigen me, constMAT a, constMAT b) {
	//Melder_assert (a.nrow >= a.ncol && b.nrow >= b.ncol);   // pggb: this cannot be an assert, and seems too strict anyway
	Melder_require (a.ncol == b.ncol,
		U"The numbers of columns should be equal, not ", a.ncol, U" and ", b.ncol, U".");
	// Eigen has not been inited yet.
	double *u = nullptr, *v = nullptr, maxsv2 = -10.0;
	char jobu = 'N', jobv = 'N', jobq = 'Q';
	integer k, ll, m = a.nrow, n = a.ncol, p = b.nrow;
	integer lda = m, ldb = p, ldu = lda, ldv = ldb, ldq = n;
	integer lwork = std::max (std::max (3 * n, m), p) + n, info;

	/*	Melder_assert (numberOfRows >= numberOfColumns || numberOfRows_b >= numberOfColumns);*/

	my dimension = a.ncol;

	autoVEC alpha = VECraw (n);
	autoVEC beta = VECraw (n);
	autoVEC work = VECraw (lwork);
	autoINTVEC iwork = INTVECzero (n);
	autoMAT q = MATraw (n, n);
	autoMAT ac = MATtranspose (a);
	autoMAT bc  = MATtranspose (b);

	(void) NUMlapack_dggsvd (& jobu, & jobv, & jobq, & m, & n, & p, & k, & ll,
		& ac [1][1], & lda, & bc [1][1], & ldb, alpha.begin(), beta.begin(), u, & ldu,
		v, & ldv, & q [1][1], & ldq, work.begin(), iwork.begin(), & info);
	Melder_require (info == 0, U"dggsvd fails with code ", info, U".");

	// Calculate the eigenvalues (alpha[i]/beta[i])^2 and store in alpha[i].

	maxsv2 = -1.0;
	for (integer i = k + 1; i <= k + ll; i ++) {
		double t = alpha [i] / beta [i];
		alpha [i] = t * t;
		if (alpha [i] > maxsv2) {
			maxsv2 = alpha [i];
		}
	}

	// Deselect the eigenvalues < eps * max_eigenvalue by making them -1.0

	integer numberOfDeselected = 0;
	for (integer i = k + 1; i <= k + ll; i ++) {
		if (alpha [i] < NUMfpp -> eps * maxsv2) {
			numberOfDeselected ++; 
			alpha [i] = -1.0;
		}
	}

	Melder_require (ll - numberOfDeselected > 0, U"No eigenvectors can be found. Matrix too singular.");

	Eigen_init (me, ll - numberOfDeselected, a.ncol);

	integer numberOfEigenvalues = 0;
	for (integer i = k + 1; i <= k + ll; i ++) {
		if (alpha [i] == -1.0) continue;
		my eigenvalues [++ numberOfEigenvalues] = alpha [i];
		for (integer j = 1; j <= a.ncol; j ++)
			my eigenvectors [numberOfEigenvalues] [j] = q [i] [j];
	}

	Eigen_sort (me);

	MATnormalizeRows_inplace (my eigenvectors.get(), 2.0, 1.0);
}

void Eigen_initFromSymmetricMatrix (Eigen me, constMAT a) {
	Melder_assert (a.ncol == a.nrow);
	if (! my eigenvectors.at) {
		Eigen_init (me, a.ncol, a.ncol);
	}	
	MATtranspose_preallocated (my eigenvectors.get(), a);
	MAT_getEigenSystemFromSymmetricMatrix_inplace (my eigenvectors.get(), true, my eigenvalues.get(), false);
}

autoEigen Eigen_create (integer numberOfEigenvalues, integer dimension) {
	try {
		autoEigen me = Thing_new (Eigen);
		Eigen_init (me.get(), numberOfEigenvalues, dimension);
		return me;
	} catch (MelderError) {
		Melder_throw (U"Eigen not created.");
	}
}

integer Eigen_getNumberOfEigenvectors (Eigen me) {
	return my numberOfEigenvalues;
}

double Eigen_getEigenvectorElement (Eigen me, integer ivec, integer element) {
	if (ivec > my numberOfEigenvalues || element < 1 || element > my dimension) {
		return undefined;
	}
	return my eigenvectors[ivec][element];
}

integer Eigen_getDimensionOfComponents (Eigen me) {
	return my dimension;
}

double Eigen_getSumOfEigenvalues (Eigen me, integer from, integer to) {
	if (from < 1) from = 1;
	if (to < 1) to = my numberOfEigenvalues;
	if (to > my numberOfEigenvalues || from > to)
		return undefined;	
	return NUMsum (my eigenvalues.subview (from, to));
}

double Eigen_getCumulativeContributionOfComponents (Eigen me, integer from, integer to) {
	longdouble partial = 0.0, sum = 0.0;

	if (to == 0) {
		to = my numberOfEigenvalues;
	}
	if (from > 0 && to <= my numberOfEigenvalues && from <= to) {
		for (integer i = 1; i <= my numberOfEigenvalues; i ++) {
			sum += my eigenvalues [i];
			if (i >= from && i <= to) {
				partial += my eigenvalues [i];
			}
		}
	}
	return sum > 0.0 ? partial / sum : 0.0;
}

integer Eigen_getDimensionOfFraction (Eigen me, double fraction) {
	double sum = Eigen_getSumOfEigenvalues (me, 0, 0);

	if (sum == 0.0) {
		return 1;
	}

	integer n = 1;
	longdouble p = my eigenvalues [1];
	while (p / sum < fraction && n < my numberOfEigenvalues) {
		p += my eigenvalues [++ n];
	}
	return n;
}

void Eigen_sort (Eigen me) {
	double *e = my eigenvalues.at, **v = my eigenvectors.at;

	for (integer i = 1; i < my numberOfEigenvalues; i ++) {
		integer k;
		double emax = e [k = i];
		for (integer j = i + 1; j <= my numberOfEigenvalues; j ++) {
			if (e [j] > emax) {
				emax = e [k = j];
			}
		}
		if (k != i) {

			// Swap eigenvalues and eigenvectors

			std::swap (e [i], e [k]);
			for (integer j = 1; j <= my dimension; j ++)
				std::swap (v [i] [j], v [k] [j]);
		}
	}
}

void Eigen_invertEigenvector (Eigen me, integer ivec) {

	if (ivec < 1 || ivec > my numberOfEigenvalues) {
		return;
	}

	for (integer j = 1; j <= my dimension; j ++) {
		my eigenvectors [ivec] [j] = - my eigenvectors [ivec] [j];
	}
}

void Eigen_drawEigenvalues (Eigen me, Graphics g, integer first, integer last, double ymin, double ymax, bool fractionOfTotal, bool cumulative, double size_mm, conststring32 mark, bool garnish) {
	double xmin = first, xmax = last, scale = 1.0, sumOfEigenvalues = 0.0;

	if (first < 1) first = 1;
	if (last < 1 || last > my numberOfEigenvalues) last = my numberOfEigenvalues;
	if (last <= first) {
		first = 1; 
		last = my numberOfEigenvalues;
	}
	xmin = first - 0.5; xmax = last + 0.5;
	if (fractionOfTotal || cumulative) {
		sumOfEigenvalues = Eigen_getSumOfEigenvalues (me, 0, 0);
		if (sumOfEigenvalues <= 0.0)
			sumOfEigenvalues = 1.0;
		scale = sumOfEigenvalues;
	}
	if (ymax <= ymin) {
		ymax = Eigen_getSumOfEigenvalues (me, ( cumulative ? 1 : first ), first) / scale;
		ymin = Eigen_getSumOfEigenvalues (me, ( cumulative ? 1 : last ), last) / scale;
		if (ymin > ymax) {
			double tmp = ymin;
			ymin = ymax; ymax = tmp;
		}
		if (ymin == ymax) { // only one eigenvalue
			ymin -= 0.1 * ymin;
			ymax += 0.1 * ymax;
		}
	}
	Graphics_setInner (g);
	Graphics_setWindow (g, xmin, xmax, ymin, ymax);
	for (integer i = first; i <= last; i ++) {
		double accu = Eigen_getSumOfEigenvalues (me, (cumulative ? 1 : i), i);
		Graphics_mark (g, i, accu / scale, size_mm, mark);
	}
	Graphics_unsetInner (g);
	if (garnish) {
		Graphics_drawInnerBox (g);
		Graphics_textLeft (g, true, (fractionOfTotal ? (cumulative ? U"Cumulative fractional eigenvalue" : U"Fractional eigenvalue" ) :
			                   ( cumulative ? U"Cumulative eigenvalue" : U"Eigenvalue" ) ));
		Graphics_ticks (g, first, last, true, true, false, true);
		Graphics_marksLeft (g, 2, true, true, false);
		Graphics_textBottom (g, true, U"Index");
	}
}

void Eigen_drawEigenvector (Eigen me, Graphics g, integer ivec, integer first, integer last,
	double ymin, double ymax, bool weigh, double size_mm, conststring32 mark, bool connect, char32 **rowLabels, bool garnish)
{
	double xmin = first, xmax = last;

	if (ivec < 1 || ivec > my numberOfEigenvalues) return;

	if (last <= first) {
		first = 1;
		last = my dimension;
		xmin = 0.5; 
		xmax = last + 0.5;
	}
	double *vec = my eigenvectors [ivec];
	double w = weigh ? sqrt (my eigenvalues [ivec]) : 1.0;

	// If ymax < ymin the eigenvector will automatically be drawn inverted.

	if (ymax == ymin) {
		NUMvector_extrema (vec, first, last, & ymin, & ymax);
		ymax *= w; ymin *= w;
	}
	Graphics_setInner (g);
	Graphics_setWindow (g, xmin, xmax, ymin, ymax);

	for (integer i = first; i <= last; i ++) {
		Graphics_mark (g, i, w * vec [i], size_mm, mark);
		if (connect && i > first)
			Graphics_line (g, i - 1.0, w * vec [i - 1], i, w * vec [i]);
	}
	Graphics_unsetInner (g);
	if (garnish) {
		Graphics_markBottom (g, first, false, true, false, rowLabels ? rowLabels [first] : Melder_integer (first));
		Graphics_markBottom (g, last, false, true, false, rowLabels ? rowLabels [last] : Melder_integer (last));
		Graphics_drawInnerBox (g);
		if (ymin * ymax < 0.0)
			Graphics_markLeft (g, 0.0, true, true, true, nullptr);
		Graphics_marksLeft (g, 2, true, true, false);
		if (! rowLabels)
			Graphics_textBottom (g, true, U"Element number");
	}
}

void Eigens_alignEigenvectors (OrderedOf<structEigen>* me) {
	if (my size < 2) return;

	Eigen e1 = my at [1];
	integer nev1 = e1 -> numberOfEigenvalues;
	integer dimension = e1 -> dimension;

	for (integer i = 2; i <= my size; i ++)
		Melder_require (my at [i] -> dimension == dimension,
			U"The dimension of the eigenvectors should be equal (offending object is ",  i, U").");

	/*
		Correlate eigenvectors.
		If r < 0 then mirror the eigenvector.
	*/

	for (integer i = 2; i <= my size; i ++) {
		Eigen e2 = my at [i];
		for (integer j = 1; j <= std::min (nev1, e2 -> numberOfEigenvalues); j ++) {
			double ip = NUMinner (e1 -> eigenvectors.row(j), e2 -> eigenvectors.row(j));
			if (ip < 0.0)
				for (integer k = 1; k <= dimension; k ++)
					e2 -> eigenvectors [j] [k] = - e2 -> eigenvectors [j] [k];
		}
	}
}

static autoVEC Eigens_getAnglesBetweenSubspaces (Eigen me, Eigen thee, integer ivec_from, integer ivec_to) {
	integer nvectors = ivec_to - ivec_from + 1;
	integer nmin = my numberOfEigenvalues < thy numberOfEigenvalues ? my numberOfEigenvalues : thy numberOfEigenvalues;

	Melder_require (my dimension == thy dimension, U"The eigenvectors should have equal dimensions.");
	Melder_require (ivec_from > 0 && ivec_from <= ivec_to && ivec_to <= nmin, U"Eigenvector range too large.");

	/*
		Algorithm 12.4.3 Golub & van Loan
		Because we deal with eigenvectors we don't have to do the QR decomposition,
			the columns in the Q's are the eigenvectors.
		Compute C.
	*/
	autoVEC angles_degrees = VECraw (nvectors);
	autoMAT c = MATmul_nt (my eigenvectors.horizontalBand (ivec_from, ivec_to), thy eigenvectors.horizontalBand (ivec_from, ivec_to));
	autoSVD svd = SVD_createFromGeneralMatrix (c.get());
	for (integer i = 1; i <= nvectors; i ++) {
		angles_degrees [i] = acos (svd -> d [i]) * 180.0 / NUMpi;
	}
	return angles_degrees;
}

double Eigens_getAngleBetweenEigenplanes_degrees (Eigen me, Eigen thee) {
	autoVEC angles_degrees = Eigens_getAnglesBetweenSubspaces (me, thee, 1, 2);
	return angles_degrees [2];
}

/* End of file Eigen.cpp */
