/* ===========================================================
* WFDB Java : Interface to WFDB Applications.
*
* ===========================================================
*
* (C) Copyright 2012, by Ikaro Silva
*
* Project Info:
* Code: http://code.google.com/p/wfdb-java/
* WFDB: http://www.physionet.org/physiotools/wfdb.shtml
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation, either version 3 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 Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*
*
*
* Original Author: Ikaro Silva
* Contributor(s): -;
*
* Changes
* -------
* Check: http://code.google.com/p/wfdb-java/list
*/
package org.physionet.wfdb.physiobank;
import java.util.ArrayList;
import java.util.logging.Logger;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.physionet.wfdb.Wfdbexec;
public class PhysioNetRecord {
private String name=new String();
private ArrayList<String> signalStringList;
private ArrayList<PhysioNetSignal> signalList;
private static Logger logger =
Logger.getLogger(PhysioNetRecord.class.getName());
public PhysioNetRecord(String RecordName) throws Exception{
name=RecordName;
signalStringList = new ArrayList<String>();
signalList=new ArrayList<PhysioNetSignal>();
setSignalList();
}
public ArrayList<String> getSignalStringList() {
return signalStringList;
}
public void printRecord(){
for(PhysioNetSignal sig: signalList){
sig.printSignalInfo();
}
}
public void setSignalList() throws Exception{
setSignalList(null);
}
public void setSignalList(String descFilter) throws Exception {
//Parse information from wfdbdesc to populate the record list
String[] args=new String[1];
args[0]=name;
Wfdbexec wfdbdesc = new Wfdbexec("wfdbdesc", Wfdbexec.customArchFlag);
wfdbdesc.setArguments(args);
logger.finest("\n\t***Executing wfdb command");
ArrayList<String> tmpList= wfdbdesc.execToStringList();
String startTime=null;
String lengthTime=null;
String lengthSample=null;
String samplingFrequency=null;
PhysioNetSignal tmpSignal=null;
//REGEXP Parsers
String groupRegex="^Group (\\d+), Signal (\\d+):";
//Regex to parse something like: "Length: 30:05.556 (650000 sample intervals)"
//TODO: find a way to make one single expression with optional day field
String lengthRegex="Length:\\s+(\\d+:\\d+.\\d+)\\s+\\((\\d+)\\s+sample\\s+intervals\\)";
String lengthRegex2="Length:\\s+(\\d+:\\d+:\\d+.\\d+)\\s+\\((\\d+)\\s+sample\\s+intervals\\)";
Pattern groupPattern = Pattern.compile(groupRegex);
Pattern lengthPattern = Pattern.compile(lengthRegex);
Pattern lengthPattern2 = Pattern.compile(lengthRegex2);
Matcher groupMatch=null;
Matcher lengthMatch=null;
logger.fine("parsing list, size= " + tmpList.size());
for(String i : tmpList){
logger.finest("parsing :" + i);
if(i.startsWith("Starting time: ")){
startTime=i.replace("Starting time: ","");
}
else if (i.startsWith("Length: ") && !(i.contains("Length: not specified")) ) {
try{
//String should have a format similar to :Length: 30:05.556 (650000 sample intervals)
lengthMatch=lengthPattern.matcher(i);
if (!lengthMatch.find() ){
//Attempt second matcher for length
lengthMatch=lengthPattern2.matcher(i);
lengthMatch.find();
}
if(! lengthMatch.group(1).isEmpty())
lengthTime=lengthMatch.group(1);
if(! lengthMatch.group(2).isEmpty())
lengthSample=lengthMatch.group(2);
} catch (IllegalStateException e){
System.err.println("Could not match : " +i );
System.err.println("Attempting to continue...");
}
}else if (i.startsWith("Sampling frequency: ")) {
samplingFrequency=i.replace("Sampling frequency: ","");
}else if (i.startsWith("Group ")) {
if(tmpSignal != null){
if(descFilter == null){
signalList.add(tmpSignal);
}else if(descFilter.equals(tmpSignal.getDescription())){
signalList.add(tmpSignal);
}
}
tmpSignal=new PhysioNetSignal(signalList.size()+1,name);
tmpSignal.setStartTime(startTime);
tmpSignal.setLengthTime(lengthTime);
tmpSignal.setLengthSamples(lengthSample);
tmpSignal.setSamplingFrequency(samplingFrequency);
groupMatch=groupPattern.matcher(i);
groupMatch.find();
if(! groupMatch.group(1).isEmpty())
tmpSignal.setGroup(groupMatch.group(1));
if(! groupMatch.group(2).isEmpty())
tmpSignal.setSignalIndex(groupMatch.group(2));
}else if (i.startsWith(" File: ")) {
tmpSignal.setFile(i.replace(" File: ",""));
}else if (i.startsWith(" Description: ")) {
tmpSignal.setDescription(i.replace(" Description: ",""));
}else if (i.startsWith(" Gain: ")) {
tmpSignal.setGain(i.replace(" Gain: ",""));
}else if (i.startsWith(" Initial value: ")) {
tmpSignal.setInitialValue(i.replace(" Initial value: ",""));
}else if (i.startsWith(" Storage format: ")) {
tmpSignal.setFormat(i.replace(" Storage format: ",""));
}else if (i.startsWith(" I/O: ")) {
tmpSignal.setIo(i.replace(" I/O: ",""));
}else if (i.startsWith(" ADC resolution: ")) {
tmpSignal.setAdcResolution(i.replace(" ADC resolution: ",""));
}else if (i.startsWith(" ADC zero: ")) {
tmpSignal.setAdcZero(i.replace(" ADC zero: ",""));
}else if (i.startsWith(" Baseline: ")) {
tmpSignal.setBaseline(i.replace(" Baseline: ",""));
}else if (i.startsWith(" Checksum: ")) {
tmpSignal.setCheckSum(i.replace(" Checksum: ",""));
}
} //end of for loop
//Add last signal to list
if(tmpSignal != null){
if(descFilter == null){
signalList.add(tmpSignal);
}else if(descFilter.equals(tmpSignal.getDescription())){
signalList.add(tmpSignal);
}
}
logger.fine("Done parsing!");
}
public ArrayList<PhysioNetSignal> getSignalList() {
return signalList;
}
public String getRecordName(){
return name;
}
public static void main(String[] args) throws Exception {
PhysioNetRecord re = new PhysioNetRecord(args[0]);
ArrayList<PhysioNetSignal> sg= re.getSignalList();
for(PhysioNetSignal mysig : sg)
mysig.printSignalInfo();
}
}