/* EEG_extensions.cpp
 *
 * Copyright (C) 2012-2015 David Weenink, 2015 Paul Boersma
 *
 * 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.
 */


#include "ICA.h"
#include "EEG_extensions.h"
#include "NUM2.h"
#include "Sound_and_PCA.h"
#include "Sound_extensions.h"
#include "Spectrum_extensions.h"
#include "Sound_and_Spectrum.h"

static autoEEG EEG_copyWithoutSound (EEG me) {
	try {
 		autoEEG thee = EEG_create (my xmin, my xmax);
		thy numberOfChannels = my numberOfChannels;
		thy textgrid = Data_copy (my textgrid.get());
		autostring32vector channelNames (1, my numberOfChannels);
		for (long i = 1; i <= my numberOfChannels; i++) {
			channelNames[i] = Melder_dup (my channelNames[i]);
		}
		thy channelNames = channelNames.transfer();
		return thee;
	} catch (MelderError) {
		Melder_throw (me, U": not copied.");
	}
}

static long *EEG_channelNames_to_channelNumbers (EEG me, char32 **channelNames, long numberOfChannelNames) {
	try {
		autoNUMvector<long> channelNumbers (1, numberOfChannelNames);
		for (long i = 1; i <= numberOfChannelNames; i++) {
			for (long j = 1; j <= my numberOfChannels; j++) {
				if (Melder_equ (channelNames[i], my channelNames[j])) {
					channelNumbers[i] = j;
				}
			}
			if (channelNumbers[i] == 0) {
				Melder_throw (U"Channel name \"", channelNames[i], U"\" not found.");
			}
		}
		return channelNumbers.transfer();
	} catch (MelderError) {
		Melder_throw (me, U": channelNames not found.");
	}
}

static void EEG_setChannelNames_selected (EEG me, const char32 *precursor, long *channelNumbers, long numberOfChannels) {
	autoMelderString name;
	const char32 *zero = U"0";
	for (long i = 1; i <= numberOfChannels; i++) {
		MelderString_copy (&name, precursor);
		if (my numberOfChannels > 100) {
			if (i < 10) {
				MelderString_append (&name, zero);
			}
			if (i < 100) {
				MelderString_append (&name, zero);
			}
		} else if (i < 10) {
			MelderString_append (&name, zero);
		}
		MelderString_append (&name, i);
		EEG_setChannelName (me, channelNumbers[i], name.string);
	}
}

autoCrossCorrelationTable EEG_to_CrossCorrelationTable (EEG me, double startTime, double endTime, double lagStep, const char32 *channelRanges)
{
	try {
		// autowindow
		if (startTime == endTime) {
			startTime = my xmin; endTime = my xmax;
		}
		// don't allow times outside domain
		if (startTime < my xmin) {
			startTime = my xmin;
		}
		if (endTime > my xmax) {
			endTime = my xmax;
		}
		autoEEG thee = EEG_extractPart (me, startTime, endTime, true);
		long numberOfChannels;
		autoNUMvector <long> channels (NUMstring_getElementsOfRanges (channelRanges, thy numberOfChannels, & numberOfChannels, nullptr, U"channel", true), 1);
		autoSound soundPart = Sound_copyChannelRanges (thy sound.get(), channelRanges);
		autoCrossCorrelationTable him = Sound_to_CrossCorrelationTable (soundPart.peek(), startTime, endTime, lagStep);
		// assign channel names
		for (long i = 1; i <= numberOfChannels; i++) {
			long ichannel = channels[i];
			char32 *label = my channelNames[ichannel];
			TableOfReal_setRowLabel (him.peek(), i, label);
			TableOfReal_setColumnLabel (him.peek(), i, label);
		}
		return him;
	} catch (MelderError) {
		Melder_throw (me, U": no CrossCorrelationTable calculated.");
	}
}

autoCovariance EEG_to_Covariance (EEG me, double startTime, double endTime, const char32 *channelRanges)
{
	try {
		double lagStep = 0.0;
		autoCrossCorrelationTable thee = EEG_to_CrossCorrelationTable (me, startTime, endTime, lagStep, channelRanges);
        autoCovariance him = Thing_new (Covariance);
        thy structCrossCorrelationTable :: v_copy (him.peek());
		return him;
	} catch (MelderError) {
		Melder_throw (me, U": no Covariance calculated.");
	}
}

autoCrossCorrelationTableList EEG_to_CrossCorrelationTableList (EEG me, double startTime, double endTime, double lagStep, long ncovars, const char32 *channelRanges) {
	try {
		// autowindow
		if (startTime == endTime) {
			startTime = my xmin; endTime = my xmax;
		}
		// don't allow times outside domain
		if (startTime < my xmin) {
			startTime = my xmin;
		}
		if (endTime > my xmax) {
			endTime = my xmax;
		}
		autoEEG thee = EEG_extractPart (me, startTime, endTime, true);
		long numberOfChannels;
		autoNUMvector <long> channels (NUMstring_getElementsOfRanges (channelRanges, thy numberOfChannels, & numberOfChannels, nullptr, U"channel", true), 1);
		autoSound soundPart = Sound_copyChannelRanges (thy sound.get(), channelRanges);
		autoCrossCorrelationTableList him = Sound_to_CrossCorrelationTableList (soundPart.peek(), startTime, endTime, lagStep, ncovars);
		return him;
	} catch (MelderError) {
		Melder_throw (me, U": no CrossCorrelationTables calculated.");
	}
}

autoPCA EEG_to_PCA (EEG me, double startTime, double endTime, const char32 *channelRanges, int fromCorrelation) {
	try {
		autoCovariance cov = EEG_to_Covariance (me, startTime, endTime, channelRanges);
		autoPCA him;
		if (fromCorrelation) {
			autoCorrelation cor = SSCP_to_Correlation (cov.peek());
			him = SSCP_to_PCA (cor.peek());
		} else {
			him = SSCP_to_PCA (cov.peek());
		}
		return him;
	} catch (MelderError) {
		Melder_throw (me, U": no PCA calculated.");
	}
}

autoEEG EEG_and_PCA_to_EEG_whiten (EEG me, PCA thee, long numberOfComponents) {
	try {
		if (numberOfComponents <= 0 || numberOfComponents > thy numberOfEigenvalues) {
			numberOfComponents = thy numberOfEigenvalues;
		}
		numberOfComponents = numberOfComponents > my numberOfChannels ? my numberOfChannels : numberOfComponents;

		autoNUMvector<long> channelNumbers (EEG_channelNames_to_channelNumbers (me, thy labels, thy dimension), 1);

		autoEEG him = Data_copy (me);
		autoSound white = Sound_and_PCA_whitenSelectedChannels (my sound.get(), thee, numberOfComponents, channelNumbers.peek(), thy dimension);
		for (long i = 1; i <= thy dimension; i++) {
			long ichannel = channelNumbers[i];
			NUMvector_copyElements<double> (white -> z[i], his sound -> z[ichannel], 1, his sound -> nx);
		}
		EEG_setChannelNames_selected (him.peek(), U"wh", channelNumbers.peek(), thy dimension);
		return him;
	} catch(MelderError) {
		Melder_throw (me, U": not whitened with ", thee);
	}
}

autoEEG EEG_and_PCA_to_EEG_principalComponents (EEG me, PCA thee, long numberOfComponents) {
	try {
		if (numberOfComponents <= 0 || numberOfComponents > thy numberOfEigenvalues) {
			numberOfComponents = thy numberOfEigenvalues;
		}
		numberOfComponents = numberOfComponents > my numberOfChannels ? my numberOfChannels : numberOfComponents;

		autoNUMvector<long> channelNumbers (EEG_channelNames_to_channelNumbers (me, thy labels, thy dimension), 1);
		autoEEG him = Data_copy (me);
		autoSound pc = Sound_and_PCA_to_Sound_pc_selectedChannels (my sound.get(), thee, numberOfComponents, channelNumbers.peek(), thy dimension);
		for (long i = 1; i <= thy dimension; i++) {
			long ichannel = channelNumbers[i];
			NUMvector_copyElements<double> (pc -> z[i], his sound -> z[ichannel], 1, his sound -> nx);
		}
		EEG_setChannelNames_selected (him.peek(), U"pc", channelNumbers.peek(), thy dimension);
		return him;
	} catch (MelderError) {
		Melder_throw (me, U": not projected.");
	}
}

autoEEG EEG_to_EEG_bss (EEG me, double startTime, double endTime, long ncovars, double lagStep, const char32 *channelRanges, int whiteningMethod, int diagonalizerMethod, long maxNumberOfIterations, double tol) {
	try {
		// autowindow
		if (startTime == endTime) {
			startTime = my xmin; endTime = my xmax;
		}
		// don't allow times outside domain
		if (startTime < my xmin) {
			startTime = my xmin;
		}
		if (endTime > my xmax) {
			endTime = my xmax;
		}
		long numberOfChannels;
		autoNUMvector <long> channelNumbers (NUMstring_getElementsOfRanges (channelRanges, my numberOfChannels, & numberOfChannels, nullptr, U"channel", true), 1);
		autoEEG thee = EEG_extractPart (me, startTime, endTime, true);
		if (whiteningMethod != 0) {
			bool fromCorrelation = ( whiteningMethod == 2 );
			autoPCA pca = EEG_to_PCA (thee.peek(), thy xmin, thy xmax, channelRanges, fromCorrelation);
			autoEEG white = EEG_and_PCA_to_EEG_whiten (thee.peek(), pca.peek(), 0);
			thee = white.move();
		}
		autoMixingMatrix mm = Sound_to_MixingMatrix (thy sound.get(), startTime, endTime, ncovars, lagStep, maxNumberOfIterations, tol, diagonalizerMethod);

		autoEEG him = EEG_copyWithoutSound (me);
		his sound = Sound_and_MixingMatrix_unmix (my sound.get(), mm.peek());
		EEG_setChannelNames_selected (him.peek(), U"ic", channelNumbers.peek(), numberOfChannels);

		// Calculate the cross-correlations between eye-channels and the ic's


		return him;

	} catch (MelderError) {
		Melder_throw (me, U": no independent components determined.");
	}
}

autoSound EEG_to_Sound_modulated (EEG me, double baseFrequency, double channelBandwidth, const char32 *channelRanges) {
	try {
		long numberOfChannels;
		autoNUMvector <long> channelNumbers (NUMstring_getElementsOfRanges (channelRanges, my numberOfChannels, & numberOfChannels, nullptr, U"channel", true), 1);
		double maxFreq = baseFrequency + my numberOfChannels * channelBandwidth;
		double samplingFrequency = 2 * maxFreq;
		samplingFrequency = samplingFrequency < 44100 ? 44100 : samplingFrequency;
		autoSound thee = Sound_createSimple (1, my xmax - my xmin, samplingFrequency);
		for (long i = 1; i <= numberOfChannels; i++) {
			long ichannel = channelNumbers[i];
			double fbase = baseFrequency;// + (ichannel - 1) * channelBandwidth;
			autoSound si = Sound_extractChannel (my sound.get(), ichannel);
			autoSpectrum spi = Sound_to_Spectrum (si.peek(), 1);
			Spectrum_passHannBand (spi.peek(), 0.5, channelBandwidth - 0.5, 0.5);
			autoSpectrum spi_shifted = Spectrum_shiftFrequencies (spi.peek(), fbase, samplingFrequency / 2.0, 30);
			autoSound resampled = Spectrum_to_Sound (spi_shifted.peek());
			long nx = resampled -> nx < thy nx ? resampled -> nx : thy nx;
			for (long j = 1; j <= nx; j++) {
				thy z[1][j] += resampled -> z[1][j];
			}
		}
		Vector_scale (thee.peek(), 0.99);
		return thee;
	} catch (MelderError) {
		Melder_throw (me, U": no playable sound created.");
	}
}

autoSound EEG_to_Sound_frequencyShifted (EEG me, long channel, double frequencyShift, double samplingFrequency, double maxAmp) {
	try {
		autoSound si = Sound_extractChannel (my sound.get(), channel);
		autoSpectrum spi = Sound_to_Spectrum (si.peek(), 1);
		autoSpectrum spi_shifted = Spectrum_shiftFrequencies (spi.peek(), frequencyShift, samplingFrequency / 2.0, 30);
		autoSound thee = Spectrum_to_Sound (spi_shifted.peek());
		if (maxAmp > 0) {
			Vector_scale (thee.peek(), maxAmp);
		}
		return thee;
	} catch (MelderError) {
		Melder_throw (me, U": channel not converted to sound.");
	}
}

/* End of file EEG_extensions.cpp */
