scripts/channelClasses/standard/ExtraEog.java

/////////////////////////////////////////////////////////////////
// Processes data by creating EOGV,EOGH channels, and then performing 
// standard filtering
//
// This code is compiled at runtime, but compilation can be tested by:
//    javac -cp build scripts/channelClasses/standard/ExtraEog.java
//    rm scripts/channelClasses/standard/ExtraEog.class 
/////////////////////////////////////////////////////////////////
package standard;

import java.io.*;
import java.util.*;

import generalClasses.*;
import recordingClasses.Recording;
import seriesClasses.*;
import channelClasses.ChannelScript;
import static channelClasses.Channel.*;

/////////////////////////////////////////////////////////////////
/** Processes data by creating EOGV,EOGH channels, and then performing 
 * standard filtering
 */
public class ExtraEog extends ChannelScript
{
    /** Recording instance to be operated on */
    Recording rec = null;
    /** Cutoff in Hz, applied only to EEG,EMG,EOG */
    float highpassCutoff;
    /** SD in uV, to detect flat channels */
    float sdLowerThreshold;
    /** SD in uV, to detect noisy channels */
    float sdUpperThreshold;
    /** Log of warnings generated during update */
    ArrayList<String> warnings = null;


    ////////////////////////////////////////////////////////////////////
    /** Initialize instance by setting its parameters to specified values.
     * @param highpassCutoff Highpass cutoff applied to EEG,EMG and EOG
     * @param sdLowerThreshold SD in uV, to detect flat channels
     * @param sdUpperThreshold SD in uV, to detect noisy channels
     */
    public ExtraEog(Recording rec, float highpassCutoff,
                 float sdLowerThreshold, float sdUpperThreshold) {
        this.rec = rec;
        this.highpassCutoff = highpassCutoff;
        this.sdLowerThreshold = sdLowerThreshold;
        this.sdUpperThreshold = sdUpperThreshold;
        warnings = new ArrayList<String>();
    } // ExtraEog

    ////////////////////////////////////////////////////////////////////
    /** Initialize instance by setting its parameters to default values.
     */
    public ExtraEog(Recording rec) {
        this(rec, 0.5f,1.0f,50.0f);
    } // ExtraEog

    ////////////////////////////////////////////////////////////////////
    /** Update recording data by performing channel-oriented operations.
     * <p>Available modes are EEG, EOG, REF, EMG, EDA, RES, ECG, EVE.
     */
    public void update() {
        // Create EOGV = VPVA-VNVB and EOGH = HPHL-HNHR.
        ArrayList<SeriesAnalog> vp = selectSite(rec, "VPVA");
        ArrayList<SeriesAnalog> vn = selectSite(rec, "VNVB");
        ArrayList<SeriesAnalog> hp = selectSite(rec, "HPHL");
        ArrayList<SeriesAnalog> hn = selectSite(rec, "HNHR");
        ArrayList<SeriesAnalog> subsetEOG = new ArrayList<SeriesAnalog>();
        if(vp.size()==1 && vn.size()==1) {
            SeriesAnalog s = vp.get(0).clone();
            s.sub(vn.get(0));
            s.setSites(new SiteSet(new Site("EOGV")));
            subsetEOG.add(s);
        }
        if(hp.size()==1 && hn.size()==1) {
            SeriesAnalog s = hp.get(0).clone();
            s.sub(hn.get(0));
            s.setSites(new SiteSet(new Site("EOGH")));
            subsetEOG.add(s);
        }
        ArrayList<SeriesAnalog> result = subsetEOG;

        // Process EEG
        ArrayList<SeriesAnalog> subset = selectMode(rec, DataMode.EEG);
        filterHP(highpassCutoff, subset); // NB: this does not remove DC
        subtractTemporalMean(subset);
        ArrayList<SeriesAnalog> subsetThresholded=new ArrayList<SeriesAnalog>();
        for(int i=0; i<subset.size(); i++) {
            SeriesAnalog s = subset.get(i);
            BasicStats bs = s.getStats();
            boolean ok = bs.sd > sdLowerThreshold && bs.sd < sdUpperThreshold;
            if(ok) subsetThresholded.add(s);
            else warnings.add("Channel "+s.getPrimaryLabel()+" has SD="+bs.sd);
        }
        result = listsUnion(result, subsetThresholded);

        // Process EMG
        subset = selectMode(rec, DataMode.EMG);
        filterHP(highpassCutoff, subset);
        subtractTemporalMean(subset);
        result = listsUnion(result, subset);

        // Process EDA,EVE: do nothing to them
        subset = selectMode(rec, DataMode.EDA);
        subset = listsUnion(subset,selectMode(rec, DataMode.EVE));
        result = listsUnion(result, subset);

        // Process RES,ECG,REF: subtract temporal mean
        subset = selectMode(rec, DataMode.ECG);
        subset = listsUnion(subset,selectMode(rec, DataMode.RES));
        subset = listsUnion(subset,selectMode(rec, DataMode.REF));
        subtractTemporalMean(subset);
        result = listsUnion(result, subset);

        // Update Recording object
        replaceAllSeries(rec, result);

    } // update

    ////////////////////////////////////////////////////////////////////
    /** Dump summary of this class or object
     * @return String representation of this object
     */
    public String toString() {
        String s = "<<<"+this.getClass().toString()+">>>\n";
        s += "Highpass (Hz) = "+ highpassCutoff+"\n";
        s += "Allowed range of SD = ["+sdLowerThreshold+","+sdUpperThreshold+"]";
        for(String w: warnings)
            s += w+"\n";
        return s;
    } // toString
}