/* PCA.cpp
 *
 * Principal Component Analysis
 *
 * Copyright (C) 1993-2011 David Weenink
 *
 * This program 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 program 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 program; if not, write to the Free Software
 * Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 */

/*
 djmw 20000511 PCA_and_TableOfReal_to_Configuration: added centralize option.
 	(later removed)
 djmw 20020327 PCA_and_TableOfReal_to_Configuration modified internals.
 djmw 20020418 Removed some causes for compiler warnings.
 djmw 20020502 modified call Eigen_and_TableOfReal_project_into.
 djmw 20030324 Added PCA_and_TableOfReal_getFractionVariance.
 djmw 20061212 Changed info to Melder_writeLine<x> format.
 djmw 20071012 Added: o_CAN_WRITE_AS_ENCODING.h
 djmw 20071201 Melder_warning<n>
 djmw 20081119 Check in TableOfReal_to_PCA if TableOfReal_areAllCellsDefined
  djmw 20110304 Thing_new
*/

#include "PCA.h"
#include "NUMlapack.h"
#include "NUM2.h"
#include "TableOfReal_extensions.h"
#include "Eigen_and_SSCP.h"
#include "Eigen_and_TableOfReal.h"
#include "Configuration.h"

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

Thing_implement (PCA, Eigen, 0);

void structPCA :: v_info () {
	structData :: v_info ();
	MelderInfo_writeLine2 (L"Number of components: ", Melder_integer (numberOfEigenvalues));
	MelderInfo_writeLine2 (L"Number of dimensions: ", Melder_integer (dimension));
	MelderInfo_writeLine2 (L"Number of observations: ", Melder_integer (numberOfObservations));
}

PCA PCA_create (long numberOfComponents, long dimension) {
	try {
		autoPCA me = Thing_new (PCA);
		Eigen_init (me.peek(), numberOfComponents, dimension);
		my labels = NUMvector<wchar_t *> (1, dimension);
		my centroid = NUMvector<double> (1, dimension);
		return me.transfer();
	} catch (MelderError) {
		Melder_throw ("PCA not created");
	}
}

void PCA_setNumberOfObservations (PCA me, long numberOfObservations) {
	my numberOfObservations = numberOfObservations;
}

long PCA_getNumberOfObservations (PCA me) {
	return my numberOfObservations;
}

void PCA_getEqualityOfEigenvalues (PCA me, long from, long to, int conservative, double *probability, double *chisq, long *ndf) {
	double sum = 0, sumln = 0;

	*probability = 1;
	*ndf = 0;
	*chisq = 0;

	if ( (from > 0 && to == from) || to > my numberOfEigenvalues) {
		return;
	}

	if (to <= from) {
		from = 1;
		to = my numberOfEigenvalues;
	}
	long i;
	for (i = from; i <= to; i++) {
		if (my eigenvalues[i] <= 0) {
			break;
		}
		sum += my eigenvalues[i];
		sumln += log (my eigenvalues[i]);
	}
	if (sum == 0) {
		return;
	}
	long r = i - from;
	long n = my numberOfObservations - 1;
	if (conservative) {
		n -= from + (r * (2 * r + 1) + 2) / (6 * r);
	}

	*ndf = r * (r + 1) / 2 - 1;
	*chisq = n * (r * log (sum / r) - sumln);
	*probability = NUMchiSquareQ (*chisq, *ndf);
}

PCA TableOfReal_to_PCA (I) {
	iam (TableOfReal);
	try {
		long m = my numberOfRows, n = my numberOfColumns;

		if (! TableOfReal_areAllCellsDefined (me, 0, 0, 0, 0)) {
			Melder_throw ("Undefined cells.");
		}

		if (m < 2) Melder_throw ("There is not enough data to perform a PCA.\n"
			                         "Your table has less than 2 rows.");

		if (m < n) Melder_warning (L"The number of rows in your table is less than the\n"
			                           "number of columns. ");

		if (NUMfrobeniusnorm (m, n, my data) == 0) {
			Melder_throw ("All values in your table are zero.");
		}
		autoPCA thee = Thing_new (PCA);
		autoNUMmatrix<double> a (NUMmatrix_copy (my data, 1, m, 1, n), 1, 1);
		thy centroid = NUMvector<double> (1, n);

		for (long j = 1; j <= n; j++) {
			double colmean = a[1][j];
			for (long i = 2; i <= m; i++) {
				colmean += a[i][j];
			}
			colmean /= m;
			for (long i = 1; i <= m; i++) {
				a[i][j] -= colmean;
			}
			thy centroid[j] = colmean;
		}
		Eigen_initFromSquareRoot (thee.peek(), a.peek(), m, n);
		thy labels = NUMvector<wchar_t *> (1, n);

		NUMstrings_copyElements (my columnLabels, thy labels, 1, n);

		PCA_setNumberOfObservations (thee.peek(), m);

		/*
			The covariance matrix C = A'A / (N-1). However, we have calculated
			the eigenstructure for A'A. This has no consequences for the
			eigenvectors, but the eigenvalues have to be divided by (N-1).
		*/

		for (long i = 1; i <= thy numberOfEigenvalues; i++) {
			thy eigenvalues[i] /= (m - 1);
		}
		return thee.transfer();
	} catch (MelderError) {
		Melder_throw (me, ": PCA not created.");
	}
}

Configuration PCA_and_TableOfReal_to_Configuration (PCA me, thou, long numberOfDimensions) {
	try {
		thouart (TableOfReal);
		if (numberOfDimensions == 0 || numberOfDimensions > my numberOfEigenvalues) {
			numberOfDimensions = my numberOfEigenvalues;
		}

		autoConfiguration him = Configuration_create (thy numberOfRows, numberOfDimensions);
		Configuration thim = him.peek();
		Eigen_and_TableOfReal_project_into (me, thee, 1, thy numberOfColumns, & thim, 1, numberOfDimensions);
		NUMstrings_copyElements (thy rowLabels, his rowLabels, 1, thy numberOfRows);
		TableOfReal_setSequentialColumnLabels (him.peek(), 0, 0, L"pc", 1, 1);
		return him.transfer();
	} catch (MelderError) {
		Melder_throw ("Configuration not created from PCA & TableOfReal.");
	}
}

TableOfReal PCA_and_Configuration_to_TableOfReal_reconstruct (PCA me, thou) {
	try {
		thouart (Configuration);
		long npc = thy numberOfColumns;

		if (thy numberOfColumns > my dimension) {
			Melder_throw ("The dimension of the Configuration must be less than or equal to the dimension of the PCA.");
		}

		if (npc > my numberOfEigenvalues) {
			npc = my numberOfEigenvalues;
		}

		autoTableOfReal him = TableOfReal_create (thy numberOfRows, my dimension);
		NUMstrings_copyElements (my labels, his columnLabels, 1, my dimension);
		NUMstrings_copyElements (thy rowLabels, his rowLabels, 1, thy numberOfRows);

		for (long i = 1; i <= thy numberOfRows; i++) {
			double *hisdata = his data[i];
			for (long k = 1; k <= npc; k++) {
				double *evec = my eigenvectors[k], pc = thy data[i][k];
				for (long j = 1; j <= my dimension; j++) {
					hisdata[j] += pc * evec[j];
				}
			}
		}
		return him.transfer();
	} catch (MelderError) {
		Melder_throw ("TableOfReal not reconstructed.");
	}
}

double PCA_and_TableOfReal_getFractionVariance (PCA me, thou, long from, long to) {
	try {
		thouart (TableOfReal);
		double fraction = NUMundefined;

		if (from < 1 || from > to || to > thy numberOfColumns) {
			return NUMundefined;
		}

		autoSSCP s = TableOfReal_to_SSCP (thee, 0, 0, 0, 0);
		autoSSCP sp = Eigen_and_SSCP_project (me, s.peek());
		fraction = SSCP_getFractionVariation (sp.peek(), from, to);
		return fraction;
	} catch (MelderError) {
		return NUMundefined;
	}
}

TableOfReal PCA_to_TableOfReal_reconstruct1 (PCA me, wchar_t *numstring) {
	try {
		long npc;
		autoNUMvector<double> pc (NUMstring_to_numbers (numstring, & npc), 1);

		autoConfiguration c = Configuration_create (1, npc);
		for (long j = 1; j <= npc; j++) {
			c -> data [1][j] = pc[j];
		}
		autoTableOfReal him = PCA_and_Configuration_to_TableOfReal_reconstruct (me, c.peek());
		return him.transfer();
	} catch (MelderError) {
		Melder_throw (me, " not reconstructed.");
	}
}


/* End of file PCA.cpp */
