git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngine@74500 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
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@ -1,22 +1,3 @@
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/**
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* Copyright 2004-2006 DFKI GmbH.
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* All Rights Reserved. Use is subject to license terms.
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*
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* This file is part of MARY TTS.
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*
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* MARY TTS is free software: you can redistribute it and/or modify
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* it under the terms of the GNU Lesser General Public License as published by
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* the Free Software Foundation, version 3 of the License.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU Lesser General Public License for more details.
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*
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* You should have received a copy of the GNU Lesser General Public License
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* along with this program. If not, see <http://www.gnu.org/licenses/>.
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*
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*/
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package marytts.signalproc.display;
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import java.awt.BorderLayout;
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@ -46,13 +27,11 @@ import javax.swing.ScrollPaneConstants;
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import marytts.util.string.PrintfFormat;
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/**
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* @author Marc Schröder
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*
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*/
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public class FunctionGraphCustom extends FunctionGraph
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{
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public static final int DEFAULT_WIDTH=640;
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private static final long serialVersionUID = 1L;
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public static final int DEFAULT_WIDTH=640;
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public static final int DEFAULT_HEIGHT=480;
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public static final int DRAW_LINE = 1;
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public static final int DRAW_DOTS = 2;
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@ -1,26 +1,5 @@
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package marytts.signalproc.display;
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/**
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* Copyright 2004-2010 DFKI GmbH.
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* All Rights Reserved. Use is subject to license terms.
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*
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* This file is part of MARY TTS.
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*
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* MARY TTS is free software: you can redistribute it and/or modify
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* it under the terms of the GNU Lesser General Public License as published by
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* the Free Software Foundation, version 3 of the License.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU Lesser General Public License for more details.
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*
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* You should have received a copy of the GNU Lesser General Public License
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* along with this program. If not, see <http://www.gnu.org/licenses/>.
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*
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*/
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import java.awt.Color;
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import java.awt.Graphics2D;
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import java.awt.event.ActionEvent;
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@ -35,7 +14,6 @@ import java.util.Arrays;
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import java.util.Hashtable;
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import java.util.List;
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import javax.sound.sampled.AudioFormat;
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import javax.sound.sampled.AudioInputStream;
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import javax.sound.sampled.AudioSystem;
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import javax.swing.BoxLayout;
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@ -53,13 +31,11 @@ import marytts.signalproc.analysis.CepstrumSpeechAnalyser;
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import marytts.signalproc.analysis.FrameBasedAnalyser;
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import marytts.signalproc.analysis.LpcAnalyser;
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import marytts.signalproc.analysis.ShortTermLogSpectrumAnalyser;
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import marytts.signalproc.display.FunctionGraph;
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import marytts.signalproc.filter.FIRFilter;
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import marytts.signalproc.window.HammingWindow;
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import marytts.signalproc.window.RectWindow;
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import marytts.signalproc.window.Window;
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import marytts.util.data.BufferedDoubleDataSource;
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import marytts.util.data.audio.AudioDoubleDataSource;
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import marytts.util.math.ArrayUtils;
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import marytts.util.math.FFT;
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import marytts.util.math.MathUtils;
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@ -67,13 +43,11 @@ import marytts.util.string.PrintfFormat;
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/**
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* @author Marc Schröder
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*
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*/
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public class SpectrogramCustom extends FunctionGraphCustom
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{
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public static final int DEFAULT_WINDOWSIZE = 65;
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private static final long serialVersionUID = 1L;
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public static final int DEFAULT_WINDOWSIZE = 65;
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public static final int DEFAULT_WINDOW = Window.HAMMING;
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public static final int DEFAULT_WINDOWSHIFT = 32;
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public static final int DEFAULT_FFTSIZE = 256;
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@ -6,6 +6,9 @@ import java.util.Arrays;
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import javax.swing.JPanel;
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import org.gcube.contentmanagement.graphtools.data.BigSamplesTable;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import marytts.signalproc.display.SpectrogramCustom;
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import marytts.signalproc.window.Window;
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@ -100,7 +103,7 @@ public class SignalConversions {
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return cutSpectrum;
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}
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public static void exampleSet2Signal(double[] rebuiltSignal, ExampleSet es) {
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public static void exampleSet2Signal(double[] rebuiltSignal, ExampleSet es, Double fillerValueFormissingEntries) {
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MemoryExampleTable met = (MemoryExampleTable) es.getExampleTable();
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int numCol = met.getAttributeCount();
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@ -115,24 +118,32 @@ public class SignalConversions {
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Example e = es.getExample(i);
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// System.out.println(es.getExample(i)+"->"+signal[i]);
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for (Attribute a : e.getAttributes()) {
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rebuiltSignal[id] = e.getValue(a);
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Double value = e.getValue(a);
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if (value.equals(Double.NaN) && !fillerValueFormissingEntries.equals(Double.NaN))
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value = fillerValueFormissingEntries;
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rebuiltSignal[id] = value;
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}
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}
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}
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public static void exampleSet2Signal(double[] rebuiltSignal, ExampleSet es) {
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exampleSet2Signal(rebuiltSignal, es, null);
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}
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public static int[] fftBinIndices(double samplingRate, int frameSize, int numMelFilters, int numFequencies, float lowerFilterFreq, float upperFilterFreq) {
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int cbin[] = new int[numFequencies+2];
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System.out.println("New Filter banks: "+numFequencies);
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AnalysisLogger.getLogger().debug("New Filter banks: "+numFequencies);
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cbin[0] = (int) Math.round(lowerFilterFreq / samplingRate * frameSize);
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cbin[cbin.length - 1] = frequencyIndex(upperFilterFreq, frameSize, (float)samplingRate);
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System.out.println("F0: "+lowerFilterFreq);
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AnalysisLogger.getLogger().debug("F0: "+lowerFilterFreq);
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for (int i = 1; i <= numFequencies; i++) {
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double fc = centerFreq(i, samplingRate, lowerFilterFreq, numMelFilters);
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System.out.println("F"+(i)+": "+fc);
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AnalysisLogger.getLogger().debug("F"+(i)+": "+fc);
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cbin[i] = (int) Math.round(fc / samplingRate * frameSize);
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}
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System.out.println("F"+(cbin.length - 1)+": "+upperFilterFreq);
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AnalysisLogger.getLogger().debug("F"+(cbin.length - 1)+": "+upperFilterFreq);
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return cbin;
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}
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@ -213,7 +224,7 @@ public class SignalConversions {
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int bestIndex=1;
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for (int i = 1; i <= numMelFilters; i++) {
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double fc = centerFreq(i, samplingRate, lowerFilterFreq, numMelFilters);
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System.out.println("fc "+fc);
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AnalysisLogger.getLogger().debug("fc "+fc);
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if (fc>maxFilterFreq){
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bestIndex=i;
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break;
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@ -234,7 +245,7 @@ public class SignalConversions {
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for (int i = 0; i < signalLength; i++) {
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time[i] = (double) i / (double) samplingRate;
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}
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System.out.println("time " + time[signalLength - 1] * samplingRate + " vs " + signalLength);
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AnalysisLogger.getLogger().debug("time " + time[signalLength - 1] * samplingRate + " vs " + signalLength);
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return time;
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}
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@ -242,6 +253,15 @@ public class SignalConversions {
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return linearTime / windowShiftTime;
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}
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public static ExampleSet signal2ExampleSet(double[] signal){
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BigSamplesTable samples = new BigSamplesTable();
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for (int k = 0; k < signal.length; k++) {
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samples.addSampleRow("" + k, signal[k]);
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}
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AnalysisLogger.getLogger().debug("Example Set Created");
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return samples.generateExampleSet();
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}
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public static double[][] spectrogram(String name, double[] signal, int samplingRate, int windowshift, int frameslength, boolean display) throws Exception {
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SpectrogramCustom spec = new SpectrogramCustom(signal, samplingRate, Window.get(Window.HAMMING, frameslength), windowshift, frameslength, 640, 480);
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double[][] spectrum = spec.spectra.toArray(new double[spec.spectra.size()][]);
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@ -11,12 +11,13 @@ import java.util.List;
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import org.gcube.contentmanagement.graphtools.data.BigSamplesTable;
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import org.gcube.contentmanagement.graphtools.plotting.graphs.NumericSeriesGraph;
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import org.gcube.contentmanagement.graphtools.plotting.graphs.TimeSeriesGraph;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.contentmanagement.lexicalmatcher.utils.MathFunctions;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.jfree.data.time.FixedMillisecond;
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import org.jfree.data.time.TimeSeriesCollection;
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import org.jfree.data.xy.XYSeriesCollection;
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import com.rapidminer.RapidMiner;
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import com.rapidminer.example.ExampleSet;
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import com.rapidminer.operator.preprocessing.sampling.AbsoluteSampling;
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import com.rapidminer.operator.preprocessing.series.filter.SeriesMissingValueReplenishment;
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@ -54,20 +55,20 @@ public class SignalProcessing {
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public static double[][] calculateSumSpectrum(List<double[]> signals, int windowShiftSamples, int frameLength, int samplingRate) throws Exception {
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int signalLenght = signals.get(0).length;
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System.out.println("TRIALS LENGHT " + signalLenght);
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AnalysisLogger.getLogger().debug("TRIALS LENGHT " + signalLenght);
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List<double[][]> spectrograms = new ArrayList<double[][]>();
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System.out.println("Getting Spectra");
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AnalysisLogger.getLogger().debug("Getting Spectra");
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int j = 0;
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// get all spectrograms
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for (double[] signal : signals) {
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double[][] spectro = SignalConversions.spectrogram("Spectrogram", signal, samplingRate, windowShiftSamples, frameLength, false);
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System.out.println("Signal Number " + (j + 1) + " spectrum lenght " + ((spectro.length * windowShiftSamples) / samplingRate));
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AnalysisLogger.getLogger().debug("Signal Number " + (j + 1) + " spectrum lenght " + ((spectro.length * windowShiftSamples) / samplingRate));
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spectrograms.add(spectro);
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j++;
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}
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System.out.println("Summing Spectra");
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AnalysisLogger.getLogger().debug("Summing Spectra");
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// sum all spectrograms
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double[][] sumSpectro = SignalProcessing.sumSpectra(spectrograms);
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spectrograms = null;
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tsg.render(dataset);
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}
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public static double[] downSample(double[] signal, int numElements) throws Exception {
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System.setProperty("rapidminer.init.operators", "operators.xml");
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RapidMiner.init();
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public static double[] downSample(double[] signal, int numElements, AlgorithmConfiguration config) throws Exception {
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config.initRapidMiner();
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double[] rebuiltSignal = new double[signal.length];
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Arrays.fill(rebuiltSignal, Double.NaN);
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BigSamplesTable samples = new BigSamplesTable();
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}
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ExampleSet es = samples.generateExampleSet();
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System.out.println("Example Set Created");
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AnalysisLogger.getLogger().debug("Example Set Created");
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AbsoluteSampling sampler = (AbsoluteSampling) OperatorService.createOperator("AbsoluteSampling");
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sampler.setParameter("sample_size", "" + numElements);
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sampler.setParameter("local_random_seed", "-1");
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es = sampler.apply(es);
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System.out.println("Finished");
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AnalysisLogger.getLogger().debug("Finished");
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SignalConversions.exampleSet2Signal(rebuiltSignal, es);
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List<double[][]> sumspectrograms = new ArrayList<double[][]>();
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List<double[][]> spectrograms = new ArrayList<double[][]>();
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System.out.println("Getting Spectra");
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AnalysisLogger.getLogger().debug("Getting Spectra");
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int j = 0;
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// get all spectrograms
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for (double[] signal : signals) {
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System.out.println("Signal Number " + (j + 1));
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AnalysisLogger.getLogger().debug("Signal Number " + (j + 1));
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double[][] spectro = SignalConversions.spectrogram("Spectrogram", signal, samplingRate, windowShiftSamples, frameLength, false);
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spectrograms.add(spectro);
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j++;
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}
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System.out.println("Summing Spectra");
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AnalysisLogger.getLogger().debug("Summing Spectra");
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// sum all spectrograms
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double[][] sumSpectro = SignalProcessing.sumSpectra(spectrograms);
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spectrograms = null;
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return sumSpectro;
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}
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public static Date[] fillTimeLine(double[] timeseconds, double samplingRate) throws Exception {
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public static Date[] fillTimeLine(double[] timeseconds, double samplingRate, AlgorithmConfiguration config) throws Exception {
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double[] values = new double[timeseconds.length];
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for (int i = 0; i < timeseconds.length; i++)
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values[i] = timeseconds[i] * 1000d;
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double[] milliseconds = fillTimeSeries(values, timeseconds, samplingRate);
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double[] milliseconds = fillTimeSeries(values, timeseconds, samplingRate, config);
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Date[] dates = new Date[milliseconds.length];
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for (int i = 0; i < milliseconds.length; i++)
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dates[i] = new Date((long) milliseconds[i]);
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@ -184,10 +184,21 @@ public class SignalProcessing {
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return dates;
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}
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public static double[] fillTimeSeries(double[] values, double[] timeseconds, double samplingRate) throws Exception {
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System.setProperty("rapidminer.init.operators", "operators.xml");
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RapidMiner.init();
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public static double[] fillSignal(double[] signal) throws Exception{
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ExampleSet es = SignalConversions.signal2ExampleSet(signal);
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SeriesMissingValueReplenishment sampler = (SeriesMissingValueReplenishment) OperatorService.createOperator("SeriesMissingValueReplenishment");
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sampler.setParameter("attribute_name", "att0");
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sampler.setParameter("replacement", "3");
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es = sampler.apply(es);
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AnalysisLogger.getLogger().debug("Finished");
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double[] rebuiltSignal = new double[signal.length];
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SignalConversions.exampleSet2Signal(rebuiltSignal, es,0d);
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return rebuiltSignal;
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}
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public static double[] fillTimeSeries(double[] values, double[] timeseconds, double samplingRate, AlgorithmConfiguration config) throws Exception {
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config.initRapidMiner();
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double t0 = timeseconds[0];
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double t1 = timeseconds[timeseconds.length - 1];
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int signalength = (int) ((t1 - t0) * samplingRate) + 1;
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@ -207,13 +218,13 @@ public class SignalProcessing {
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}
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ExampleSet es = samples.generateExampleSet();
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System.out.println("Example Set Created");
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AnalysisLogger.getLogger().debug("Example Set Created");
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SeriesMissingValueReplenishment sampler = (SeriesMissingValueReplenishment) OperatorService.createOperator("SeriesMissingValueReplenishment");
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sampler.setParameter("attribute_name", "att0");
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sampler.setParameter("replacement", "3");
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es = sampler.apply(es);
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System.out.println("Finished");
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AnalysisLogger.getLogger().debug("Finished");
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SignalConversions.exampleSet2Signal(rebuiltSignal, es);
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@ -278,15 +289,15 @@ public class SignalProcessing {
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float centralTime = (maxTime / (2f * numOfCentralSeconds));
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System.out.println("Max Time in the Spectrum " + maxTime + " Central time " + centralTime);
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AnalysisLogger.getLogger().debug("Max Time in the Spectrum " + maxTime + " Central time " + centralTime);
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int startIndex = (int) (centralTime / windowShiftTime);
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int endIndex = (int) ((centralTime + numOfCentralSeconds) / windowShiftTime);
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System.out.println("Recalculated lenght " + maxTime + " sec");
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System.out.println("Lenght " + spectrum.length);
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AnalysisLogger.getLogger().debug("Recalculated lenght " + maxTime + " sec");
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AnalysisLogger.getLogger().debug("Lenght " + spectrum.length);
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System.out.println("Start " + startIndex + " End " + endIndex + " max " + spectrum.length + " Cut lenght " + (endIndex - startIndex + 1) * windowShiftTime);
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AnalysisLogger.getLogger().debug("Start " + startIndex + " End " + endIndex + " max " + spectrum.length + " Cut lenght " + (endIndex - startIndex + 1) * windowShiftTime);
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double[][] cutSpectrum = new double[endIndex - startIndex + 1][spectrum[0].length];
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@ -297,4 +308,16 @@ public class SignalProcessing {
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return cutSpectrum;
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}
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public static void main(String[] args) throws Exception{
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AlgorithmConfiguration conf = new AlgorithmConfiguration();
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conf.setConfigPath("./cfg/");
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conf.initRapidMiner();
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// double[] signal = new double[] {1,2,Double.NaN,4,5};
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double[] signal = new double[] {Double.NaN,1,2,3,4,5,Double.NaN};
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// double[] signal = new double[] {Double.NaN,Double.NaN,Double.NaN};
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// double[] signal = new double[] {Double.NaN,Double.NaN,0};
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double[] resignal = fillSignal(signal);
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System.out.println(resignal);
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}
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}
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