/*
The contents of this file are subject to the Mozilla Public License Version 1.1
(the "License"); you may not use this file except in compliance with the License.
You may obtain a copy of the License at http://www.mozilla.org/MPL/
Software distributed under the License is distributed on an "AS IS" basis, WITHOUT
WARRANTY OF ANY KIND, either express or implied. See the License for the specific
language governing rights and limitations under the License.
The Original Code is "MatlabExporter.java". Description:
"A tool for exporting data to Matlab .mat files"
The Initial Developer of the Original Code is Bryan Tripp & Centre for Theoretical Neuroscience, University of Waterloo. Copyright (C) 2006-2008. All Rights Reserved.
Alternatively, the contents of this file may be used under the terms of the GNU
Public License license (the GPL License), in which case the provisions of GPL
License are applicable instead of those above. If you wish to allow use of your
version of this file only under the terms of the GPL License and not to allow
others to use your version of this file under the MPL, indicate your decision
by deleting the provisions above and replace them with the notice and other
provisions required by the GPL License. If you do not delete the provisions above,
a recipient may use your version of this file under either the MPL or the GPL License.
*/
package ca.nengo.io;
import java.io.File;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
import ca.nengo.plot.Plotter;
import ca.nengo.util.MU;
import ca.nengo.util.SpikePattern;
import ca.nengo.util.TimeSeries;
import com.jmatio.io.MatFileWriter;
import com.jmatio.types.MLArray;
import com.jmatio.types.MLDouble;
/**
* <p>A tool for exporting data to Matlab .mat files. Use like this:</p>
*
* <p><code>
* MatlabExport me = new MatlabExport();<br>
* me.add("series1", series1);<br>
* ... <br>
* me.add("series1", series1);<br>
* me.write(new File("c:\\foo.mat"));<br>
* </code></p>
*
* @author Bryan Tripp
*/
public class MatlabExporter {
private Map<String, MLArray> myData;
/**
* Export data to Matlab .mat files
*/
public MatlabExporter() {
myData = new HashMap<String, MLArray>(10);
}
/**
* @param name Matlab variable name
* @param data Data to be stored in Matlab variable
*/
public void add(String name, TimeSeries data) {
add(name+"_time", new float[][]{data.getTimes()});
add(name, data.getValues());
}
/**
* Filters TimeSeries data with given time constant (this is usually a good
* idea for spike output, which is a sum of impulses).
*
* TODO: this filter is prohibitively slow for large datasets
*
* @param name Matlab variable name
* @param data Data to be stored in Matlab variable
* @param tau Time constant of filter to apply to data
*/
public void add(String name, TimeSeries data, float tau) {
TimeSeries filtered = Plotter.filter(data, tau);
add(name+"_time", new float[][]{filtered.getTimes()});
add(name+"_data", filtered.getValues());
}
/**
* @param name Matlab variable name
* @param pattern Spike times for a group of neurons
*/
public void add(String name, SpikePattern pattern) {
int n = pattern.getNumNeurons();
int maxSpikes = 0;
for (int i = 0; i < n; i++) {
float[] times = pattern.getSpikeTimes(i);
if (times.length > maxSpikes) {
maxSpikes = times.length;
}
}
float[][] timesMatrix = new float[n][];
for (int i = 0; i < n; i++) {
timesMatrix[i] = new float[maxSpikes];
float[] times = pattern.getSpikeTimes(i);
System.arraycopy(times, 0, timesMatrix[i], 0, times.length);
}
add(name, timesMatrix);
}
/**
* @param name Matlab variable name
* @param data A matrix
*/
public void add(String name, float[][] data) {
if (!MU.isMatrix(data)) {
throw new IllegalArgumentException("Data must be a matrix (same number of columns in each row)");
}
name=makeVariableNameValid(name);
MLDouble mld = new MLDouble(name, MU.convert(data));
myData.put(name, mld);
}
/**
* @param name original possibly invalid name
* @return valid name that Matlab can use
*/
public static String makeVariableNameValid(String name) {
// replace all invalid characters with underscores
name=name.replaceAll("[^a-zA-Z0-9_]","_");
// make sure the variable name starts with a letter
if (name.length()==0) {
name="data";
} else if (name.matches("[^a-zA-Z].*")) {
name="data"+name;
}
return name;
}
/**
* Clears all variables
*/
public void removeAll() {
myData.clear();
}
/**
* Writes to given destination the data that have been added to this exporter.
*
* @param destination File to which data are to be written (should have extension .mat)
* @throws IOException if there's a problem writing to disk
*/
public void write(File destination) throws IOException {
new MatFileWriter(destination, myData.values());
}
}