mirror of
https://github.com/PAMGuard/PAMGuard.git
synced 2024-11-25 08:32:32 +00:00
Merge branch 'main' of https://github.com/PAMGuard/PAMGuard into main
This commit is contained in:
commit
2dd90f6a32
@ -8,6 +8,7 @@
|
|||||||
</classpathentry>
|
</classpathentry>
|
||||||
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
|
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
|
||||||
<attributes>
|
<attributes>
|
||||||
|
<attribute name="module" value="true"/>
|
||||||
<attribute name="maven.pomderived" value="true"/>
|
<attribute name="maven.pomderived" value="true"/>
|
||||||
</attributes>
|
</attributes>
|
||||||
</classpathentry>
|
</classpathentry>
|
||||||
|
@ -4,7 +4,7 @@
|
|||||||
<groupId>org.pamguard</groupId>
|
<groupId>org.pamguard</groupId>
|
||||||
<artifactId>Pamguard</artifactId>
|
<artifactId>Pamguard</artifactId>
|
||||||
<name>Pamguard Java12+</name>
|
<name>Pamguard Java12+</name>
|
||||||
<version>2.02.09b</version>
|
<version>2.02.09c</version>
|
||||||
<description>Pamguard for Java 12+, using Maven to control dependcies</description>
|
<description>Pamguard for Java 12+, using Maven to control dependcies</description>
|
||||||
<url>www.pamguard.org</url>
|
<url>www.pamguard.org</url>
|
||||||
<organization>
|
<organization>
|
||||||
|
2
pom.xml
2
pom.xml
@ -786,7 +786,7 @@ C:\Users\*yourusername*\.m2\repository\pamguard\org\x3\2.2.2-->
|
|||||||
<dependency>
|
<dependency>
|
||||||
<groupId>pamguard.org</groupId>
|
<groupId>pamguard.org</groupId>
|
||||||
<artifactId>x3</artifactId>
|
<artifactId>x3</artifactId>
|
||||||
<version>2.2.3</version>
|
<version>2.2.6</version>
|
||||||
</dependency>
|
</dependency>
|
||||||
|
|
||||||
|
|
||||||
|
4
repo/pamguard/org/x3/2.2.6/_remote.repositories
Normal file
4
repo/pamguard/org/x3/2.2.6/_remote.repositories
Normal file
@ -0,0 +1,4 @@
|
|||||||
|
#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
|
||||||
|
#Wed Nov 15 12:43:42 GMT 2023
|
||||||
|
x3-2.2.6.jar>=
|
||||||
|
x3-2.2.6.pom>=
|
BIN
repo/pamguard/org/x3/2.2.6/x3-2.2.6.jar
Normal file
BIN
repo/pamguard/org/x3/2.2.6/x3-2.2.6.jar
Normal file
Binary file not shown.
9
repo/pamguard/org/x3/2.2.6/x3-2.2.6.pom
Normal file
9
repo/pamguard/org/x3/2.2.6/x3-2.2.6.pom
Normal file
@ -0,0 +1,9 @@
|
|||||||
|
<?xml version="1.0" encoding="UTF-8"?>
|
||||||
|
<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
|
||||||
|
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
|
||||||
|
<modelVersion>4.0.0</modelVersion>
|
||||||
|
<groupId>pamguard.org</groupId>
|
||||||
|
<artifactId>x3</artifactId>
|
||||||
|
<version>2.2.6</version>
|
||||||
|
<description>POM was created from install:install-file</description>
|
||||||
|
</project>
|
@ -7,57 +7,214 @@ import java.util.Arrays;
|
|||||||
|
|
||||||
import javax.sound.sampled.AudioInputStream;
|
import javax.sound.sampled.AudioInputStream;
|
||||||
import javax.sound.sampled.UnsupportedAudioFileException;
|
import javax.sound.sampled.UnsupportedAudioFileException;
|
||||||
|
import javax.swing.SwingUtilities;
|
||||||
|
|
||||||
|
import org.pamguard.x3.sud.ChunkHeader;
|
||||||
|
import org.pamguard.x3.sud.SudMapListener;
|
||||||
|
|
||||||
|
import PamController.PamController;
|
||||||
|
import PamUtils.worker.PamWorkProgressMessage;
|
||||||
|
import PamUtils.worker.PamWorkWrapper;
|
||||||
|
import PamUtils.worker.PamWorker;
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Opens a .sud audio file.
|
* Opens a .sud audio file.
|
||||||
* <p>
|
* <p>
|
||||||
* Sud files contain X3 compressed audio data. The sud
|
* Sud files contain X3 compressed audio data. The sud file reader opens files,
|
||||||
* file reader opens files, creating a map of the file and saving
|
* creating a map of the file and saving the map as a.sudx file so it can be
|
||||||
* the map as a.sudx file so it can be read more rapidly when the file
|
* read more rapidly when the file is next accessed.
|
||||||
* is next accessed.
|
|
||||||
* <p>
|
* <p>
|
||||||
* The SudioAudioInput stream fully implements AudioInputStream and so
|
* The SudioAudioInput stream fully implements AudioInputStream and so sud files
|
||||||
* sud files can be accessed using much of the same code as .wav files.
|
* can be accessed using much of the same code as .wav files.
|
||||||
*
|
*
|
||||||
* @author Jamie Macaulay
|
* @author Jamie Macaulay
|
||||||
*
|
*
|
||||||
*/
|
*/
|
||||||
public class SudAudioFile extends WavAudioFile {
|
public class SudAudioFile extends WavAudioFile {
|
||||||
|
|
||||||
|
private Object conditionSync = new Object();
|
||||||
|
|
||||||
|
private volatile PamWorker<AudioInputStream> worker;
|
||||||
|
private volatile SudMapWorker sudMapWorker;
|
||||||
|
|
||||||
public SudAudioFile() {
|
public SudAudioFile() {
|
||||||
super();
|
super();
|
||||||
fileExtensions = new ArrayList<String>(Arrays.asList(new String[]{".sud"}));
|
fileExtensions = new ArrayList<String>(Arrays.asList(new String[] { ".sud" }));
|
||||||
}
|
}
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
public String getName() {
|
public String getName() {
|
||||||
return "SUD";
|
return "SUD";
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
public AudioInputStream getAudioStream(File soundFile) {
|
public AudioInputStream getAudioStream(File soundFile) {
|
||||||
if (soundFile.exists() == false) {
|
|
||||||
System.err.println("The sud file does not exist: " + soundFile);
|
|
||||||
return null;
|
|
||||||
}
|
|
||||||
if (soundFile != null) {
|
|
||||||
try {
|
|
||||||
return new SudAudioFileReader().getAudioInputStream(soundFile);
|
|
||||||
}
|
|
||||||
// don't do anything and it will try the built in Audiosystem
|
|
||||||
catch (UnsupportedAudioFileException e) {
|
|
||||||
System.err.println("UnsupportedAudioFileException: Could not open sud file: not a supported file " + soundFile.getName());
|
|
||||||
System.err.println(e.getMessage());
|
|
||||||
// e.printStackTrace();
|
|
||||||
} catch (IOException e) {
|
|
||||||
System.err.println("Could not open sud file: IO Exception: " + soundFile.getName());
|
|
||||||
|
|
||||||
e.printStackTrace();
|
synchronized (conditionSync) {
|
||||||
|
|
||||||
|
// System.out.println("Get SUD getAudioStream : " + soundFile.getName());
|
||||||
|
|
||||||
|
if (soundFile.exists() == false) {
|
||||||
|
System.err.println("The sud file does not exist: " + soundFile);
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
if (soundFile != null) {
|
||||||
|
|
||||||
|
if (new File(soundFile.getAbsolutePath() + "x").exists()) {
|
||||||
|
// System.out.println("----NO NEED TO MAP SUD FILE-----" + soundFile);
|
||||||
|
try {
|
||||||
|
return new SudAudioFileReader().getAudioInputStream(soundFile);
|
||||||
|
} catch (UnsupportedAudioFileException | IOException e) {
|
||||||
|
// TODO Auto-generated catch block
|
||||||
|
e.printStackTrace();
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
|
||||||
|
// System.out.println("----MAP SUD FILE ON OTHER THREAD-----" + soundFile);
|
||||||
|
|
||||||
|
/**
|
||||||
|
* We need to map the sud file. But we don't want this o just freeze the current
|
||||||
|
* GUI thread. Therefore add a listener to the mapping process and show a
|
||||||
|
* blocking dialog to indicate that something is happening. The mapping is put
|
||||||
|
* on a separate thread and blocks stuff from happening until the mapping
|
||||||
|
* process has completed.
|
||||||
|
*/
|
||||||
|
if (sudMapWorker == null || !sudMapWorker.getSudFile().equals(soundFile)) {
|
||||||
|
|
||||||
|
sudMapWorker = new SudMapWorker(soundFile);
|
||||||
|
worker = new PamWorker<AudioInputStream>(sudMapWorker,
|
||||||
|
PamController.getInstance().getMainFrame(), 1,
|
||||||
|
"Mapping sud file: " + soundFile.getName());
|
||||||
|
// System.out.println("Sud Audio Stream STARTED: " + soundFile.getName());
|
||||||
|
|
||||||
|
SwingUtilities.invokeLater(() -> {
|
||||||
|
worker.start();
|
||||||
|
});
|
||||||
|
// this should block AWT thread but won't block if called on another thread..
|
||||||
|
}
|
||||||
|
|
||||||
|
// this is only ever called if this function is called on another thread other
|
||||||
|
// than the event dispatch thread.
|
||||||
|
while (sudMapWorker == null || !sudMapWorker.isDone()) {
|
||||||
|
// do nothing
|
||||||
|
// System.out.println("Waiting for the SUD file map: " + soundFile.getName() + " worker: " + worker);
|
||||||
|
try {
|
||||||
|
// Thread.sleep(100);
|
||||||
|
Thread.sleep(100);
|
||||||
|
} catch (InterruptedException e) {
|
||||||
|
// TODO Auto-generated catch block
|
||||||
|
e.printStackTrace();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
AudioInputStream stream = sudMapWorker.getSudAudioStream();
|
||||||
|
|
||||||
|
// sudMapWorker= null;
|
||||||
|
// worker = null;
|
||||||
|
|
||||||
|
// System.out.println("----RETURN SUD FILE ON OTHER THREAD-----" + stream);
|
||||||
|
|
||||||
|
return stream;
|
||||||
|
|
||||||
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
return null;
|
return null;
|
||||||
}
|
}
|
||||||
|
|
||||||
}
|
public class SudMapProgress implements SudMapListener {
|
||||||
|
|
||||||
|
PamWorker<AudioInputStream> sudMapWorker;
|
||||||
|
|
||||||
|
public SudMapProgress(PamWorker<AudioInputStream> sudMapWorker) {
|
||||||
|
this.sudMapWorker = sudMapWorker;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void chunkProcessed(ChunkHeader chunkHeader, int count) {
|
||||||
|
// System.out.println("Sud Map Progress: " + count);
|
||||||
|
if (count % 500 == 0) {
|
||||||
|
// don't update too often or everything just freezes
|
||||||
|
sudMapWorker.update(new PamWorkProgressMessage(-1, ("Mapped " + count + " sud file chunks")));
|
||||||
|
}
|
||||||
|
if (count == -1) {
|
||||||
|
sudMapWorker.update(new PamWorkProgressMessage(-1, ("Mapping sud file finished")));
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Opens an sud file on a different thread and adds a listener for a mapping.
|
||||||
|
* This allows a callback to show map progress.
|
||||||
|
*
|
||||||
|
* @author Jamie Macaulay
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
public class SudMapWorker implements PamWorkWrapper<AudioInputStream> {
|
||||||
|
|
||||||
|
private File soundFile;
|
||||||
|
|
||||||
|
private SudMapProgress sudMapListener;
|
||||||
|
|
||||||
|
private volatile boolean done = false;
|
||||||
|
|
||||||
|
private AudioInputStream result;
|
||||||
|
|
||||||
|
public SudMapWorker(File soundFile) {
|
||||||
|
this.soundFile = soundFile;
|
||||||
|
}
|
||||||
|
|
||||||
|
public File getSudFile() {
|
||||||
|
return soundFile;
|
||||||
|
}
|
||||||
|
|
||||||
|
public AudioInputStream getSudAudioStream() {
|
||||||
|
return result;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public AudioInputStream runBackgroundTask(PamWorker<AudioInputStream> pamWorker) {
|
||||||
|
AudioInputStream stream;
|
||||||
|
try {
|
||||||
|
// System.out.println("START OPEN SUD FILE:");
|
||||||
|
|
||||||
|
this.sudMapListener = new SudMapProgress(pamWorker);
|
||||||
|
stream = new SudAudioFileReader().getAudioInputStream(soundFile, sudMapListener);
|
||||||
|
|
||||||
|
// System.out.println("END SUD FILE:");
|
||||||
|
|
||||||
|
// for some reason - task finished may not be called on other
|
||||||
|
// thread so put this here.
|
||||||
|
this.result = stream;
|
||||||
|
this.done = true;
|
||||||
|
|
||||||
|
return stream;
|
||||||
|
} catch (UnsupportedAudioFileException e) {
|
||||||
|
System.err.println("UnsupportedAudioFileException: Could not open sud file: not a supported file "
|
||||||
|
+ soundFile.getName());
|
||||||
|
System.err.println(e.getMessage());
|
||||||
|
// e.printStackTrace();
|
||||||
|
} catch (IOException e) {
|
||||||
|
System.err.println("Could not open sud file: IO Exception: " + soundFile.getName());
|
||||||
|
|
||||||
|
e.printStackTrace();
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void taskFinished(AudioInputStream result) {
|
||||||
|
// System.out.println("TASK FINSIHED:");
|
||||||
|
this.result = result;
|
||||||
|
this.done = true;
|
||||||
|
}
|
||||||
|
|
||||||
|
public boolean isDone() {
|
||||||
|
return done;
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
@ -27,13 +27,14 @@ public class SudAudioFileReader {
|
|||||||
|
|
||||||
|
|
||||||
public SudAudioFileReader() {
|
public SudAudioFileReader() {
|
||||||
sudParams = new SudParams();
|
sudParams = new SudParams();
|
||||||
//set up the sud params for default. i.e. just read files and
|
//set up the sud params for default. i.e. just read files and
|
||||||
//don't save any decompressed or meta data.
|
//don't save any decompressed or meta data.
|
||||||
sudParams.saveWav = false;
|
// sudParams.saveWav = false;
|
||||||
sudParams.saveMeta = false;
|
// sudParams.saveMeta = false;
|
||||||
sudParams.zeroPad = true;
|
sudParams.setFileSave(false, false, false, false);
|
||||||
}
|
sudParams.zeroPad = true;
|
||||||
|
}
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Get the audio input streamn.
|
* Get the audio input streamn.
|
||||||
@ -51,5 +52,25 @@ public class SudAudioFileReader {
|
|||||||
}
|
}
|
||||||
return sudAudioInputStream;
|
return sudAudioInputStream;
|
||||||
}
|
}
|
||||||
|
/**
|
||||||
|
* Get the audio input stream for a sud file.
|
||||||
|
* @param file - the .sud file to open.
|
||||||
|
* @param mapListener- a listener for the sud file maps - can be null.
|
||||||
|
* @return the sud AudioStream.
|
||||||
|
* @throws UnsupportedAudioFileException
|
||||||
|
* @throws IOException
|
||||||
|
*/
|
||||||
|
public AudioInputStream getAudioInputStream(File file, SudMapListener mapListener) throws UnsupportedAudioFileException, IOException {
|
||||||
|
|
||||||
|
// System.out.println("Get SUD getAudioInputStream");
|
||||||
|
|
||||||
|
try {
|
||||||
|
sudAudioInputStream = SudAudioInputStream.openInputStream(file, sudParams, mapListener, false);
|
||||||
|
} catch (Exception e) {
|
||||||
|
String msg = String.format("Corrupt sud file %s: %s", file.getName(), e.getMessage());
|
||||||
|
throw new UnsupportedAudioFileException(msg);
|
||||||
|
}
|
||||||
|
return sudAudioInputStream;
|
||||||
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
@ -1,18 +1,12 @@
|
|||||||
package Acquisition.sud;
|
package Acquisition.sud;
|
||||||
|
|
||||||
import java.io.File;
|
import java.io.File;
|
||||||
|
|
||||||
import org.pamguard.x3.sud.ChunkHeader;
|
|
||||||
import org.pamguard.x3.sud.SudAudioInputStream;
|
import org.pamguard.x3.sud.SudAudioInputStream;
|
||||||
import org.pamguard.x3.sud.SudFileMap;
|
|
||||||
import org.pamguard.x3.sud.SudParams;
|
|
||||||
|
|
||||||
import PamUtils.PamCalendar;
|
|
||||||
|
|
||||||
public class SUDFileTime {
|
public class SUDFileTime {
|
||||||
|
|
||||||
private static long sudTime;
|
private static long sudTime;
|
||||||
|
|
||||||
private static String lastFilePath = "";
|
private static String lastFilePath = "";
|
||||||
/**
|
/**
|
||||||
* Temp measure to get the time from the first available sud record.
|
* Temp measure to get the time from the first available sud record.
|
||||||
@ -20,6 +14,7 @@ public class SUDFileTime {
|
|||||||
* @return
|
* @return
|
||||||
*/
|
*/
|
||||||
public static long getSUDFileTime(File file) {
|
public static long getSUDFileTime(File file) {
|
||||||
|
//System.out.println("Get sud file time: " + file.getName());
|
||||||
if (file == null || file.exists() == false) {
|
if (file == null || file.exists() == false) {
|
||||||
return Long.MIN_VALUE;
|
return Long.MIN_VALUE;
|
||||||
}
|
}
|
||||||
@ -36,22 +31,26 @@ public class SUDFileTime {
|
|||||||
*/
|
*/
|
||||||
// long t1 = System.currentTimeMillis();
|
// long t1 = System.currentTimeMillis();
|
||||||
sudTime = Long.MIN_VALUE;
|
sudTime = Long.MIN_VALUE;
|
||||||
SudParams sudParams = new SudParams();
|
// SudParams sudParams = new SudParams();
|
||||||
sudParams.saveMeta = false;
|
// sudParams.saveMeta = false;
|
||||||
sudParams.saveWav = false;
|
// sudParams.saveWav = false;
|
||||||
try {
|
try {
|
||||||
SudAudioInputStream sudAudioInputStream = SudAudioInputStream.openInputStream(file, sudParams, false);
|
//
|
||||||
if (sudAudioInputStream == null) {
|
// SudAudioInputStream sudAudioInputStream = SudAudioInputStream.openInputStream(file, sudParams, false);
|
||||||
return Long.MIN_VALUE;
|
// if (sudAudioInputStream == null) {
|
||||||
}
|
// return Long.MIN_VALUE;
|
||||||
SudFileMap sudMap = sudAudioInputStream.getSudMap();
|
// }
|
||||||
if (sudMap == null) {
|
// SudFileMap sudMap = sudAudioInputStream.getSudMap();
|
||||||
return Long.MIN_VALUE;
|
// if (sudMap == null) {
|
||||||
}
|
// return Long.MIN_VALUE;
|
||||||
long t = sudMap.getFirstChunkTimeMillis();
|
// }
|
||||||
|
// long t = sudMap.getFirstChunkTimeMillis();
|
||||||
|
long t = SudAudioInputStream.quickFileTime(file);
|
||||||
|
t=t/1000; //turn to milliseconds.
|
||||||
if (t != 0) {
|
if (t != 0) {
|
||||||
sudTime = t;
|
sudTime = t;
|
||||||
}
|
}
|
||||||
|
|
||||||
// sudAudioInputStream.addSudFileListener((chunkID, sudChunk)->{
|
// sudAudioInputStream.addSudFileListener((chunkID, sudChunk)->{
|
||||||
// ChunkHeader chunkHead = sudChunk.chunkHeader;
|
// ChunkHeader chunkHead = sudChunk.chunkHeader;
|
||||||
// if (chunkHead == null || sudTime != Long.MIN_VALUE) {
|
// if (chunkHead == null || sudTime != Long.MIN_VALUE) {
|
||||||
@ -70,17 +69,16 @@ public class SUDFileTime {
|
|||||||
// sudAudioInputStream.read();
|
// sudAudioInputStream.read();
|
||||||
// }
|
// }
|
||||||
//
|
//
|
||||||
sudAudioInputStream.close();
|
// sudAudioInputStream.close();
|
||||||
// long t2 = System.currentTimeMillis();
|
// long t2 = System.currentTimeMillis();
|
||||||
// System.out.printf("SUD file time %s extracted in %d milliseconds\n", PamCalendar.formatDBDateTime(sudTime), t2-t1);
|
// System.out.printf("SUD file time %s extracted in %d milliseconds\n", PamCalendar.formatDBDateTime(sudTime), t2-t1);
|
||||||
|
|
||||||
} catch (Exception e) {
|
} catch (Exception e) {
|
||||||
System.err.println("Error getting time from SUD file: " + e.getMessage());
|
System.err.println("Error getting time from SUD file: " + file + " " + e.getMessage());
|
||||||
|
e.printStackTrace();
|
||||||
}
|
}
|
||||||
|
|
||||||
return sudTime;
|
return sudTime;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
}
|
}
|
@ -31,12 +31,12 @@ public class PamguardVersionInfo {
|
|||||||
* Version number, major version.minorversion.sub-release.
|
* Version number, major version.minorversion.sub-release.
|
||||||
* Note: can't go higher than sub-release 'f'
|
* Note: can't go higher than sub-release 'f'
|
||||||
*/
|
*/
|
||||||
static public final String version = "2.02.09b";
|
static public final String version = "2.02.09c";
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Release date
|
* Release date
|
||||||
*/
|
*/
|
||||||
static public final String date = "29 June 2023";
|
static public final String date = "10 November 2023";
|
||||||
|
|
||||||
// /**
|
// /**
|
||||||
// * Release type - Beta or Core
|
// * Release type - Beta or Core
|
||||||
|
@ -10,7 +10,7 @@ public class ArraySensorParams implements Serializable, Cloneable, ManagedParame
|
|||||||
|
|
||||||
public static final long serialVersionUID = 1L;
|
public static final long serialVersionUID = 1L;
|
||||||
|
|
||||||
public int readIntervalMillis = 1000;
|
public volatile int readIntervalMillis = 1000;
|
||||||
|
|
||||||
private ArrayDisplayParameters arrayDisplayParameters;
|
private ArrayDisplayParameters arrayDisplayParameters;
|
||||||
|
|
||||||
|
@ -45,7 +45,8 @@ public class ArraySensorProcess extends PamProcess {
|
|||||||
while(true) {
|
while(true) {
|
||||||
readData();
|
readData();
|
||||||
try {
|
try {
|
||||||
Thread.sleep(analogSensorControl.getAnalogSensorParams().readIntervalMillis);
|
int slptime = analogSensorControl.getAnalogSensorParams().readIntervalMillis;
|
||||||
|
Thread.sleep(slptime);
|
||||||
} catch (InterruptedException e) {
|
} catch (InterruptedException e) {
|
||||||
e.printStackTrace();
|
e.printStackTrace();
|
||||||
}
|
}
|
||||||
|
@ -139,7 +139,7 @@ public class BrainBoxDevices implements AnalogDeviceType, PamSettings{
|
|||||||
double sensData = BBED549.hexToEngineering(bbRanges[item], sensInts);
|
double sensData = BBED549.hexToEngineering(bbRanges[item], sensInts);
|
||||||
double paramValue = calibration.rawToValue(sensData, calibrationData[item]);
|
double paramValue = calibration.rawToValue(sensData, calibrationData[item]);
|
||||||
analogDevicesManager.notifyData(new ItemAllData(item, sensInts, sensData, paramValue));
|
analogDevicesManager.notifyData(new ItemAllData(item, sensInts, sensData, paramValue));
|
||||||
// System.out.printf("Read item %d, chan %d, int %d, real %3.5f, param %3.5f\n", iChan, chan, sensInts, sensData, paramValue);
|
// System.out.printf("Read item %d, chan %d, int %d, real %3.5f, param %3.5f\n", 0, chan, sensInts, sensData, paramValue);
|
||||||
sayError(null);
|
sayError(null);
|
||||||
return new AnalogSensorData(sensData, paramValue);
|
return new AnalogSensorData(sensData, paramValue);
|
||||||
|
|
||||||
|
@ -221,7 +221,7 @@ public class AnalogDiagnosticsDisplay extends UserDisplayComponentAdapter implem
|
|||||||
break;
|
break;
|
||||||
case 3:
|
case 3:
|
||||||
if (lastUpdate[rowIndex] > 0) {
|
if (lastUpdate[rowIndex] > 0) {
|
||||||
return PamCalendar.formatTime(lastUpdate[rowIndex]);
|
return PamCalendar.formatTime(lastUpdate[rowIndex], true);
|
||||||
}
|
}
|
||||||
break;
|
break;
|
||||||
case 4:
|
case 4:
|
||||||
|
@ -22,6 +22,7 @@ public class BLOfflineTask extends OfflineTask {
|
|||||||
this.bearingLocaliserControl = bearingLocaliserControl;
|
this.bearingLocaliserControl = bearingLocaliserControl;
|
||||||
bearingProcess = bearingLocaliserControl.getBearingProcess();
|
bearingProcess = bearingLocaliserControl.getBearingProcess();
|
||||||
this.addRequiredDataBlock(rawOrFFTBlock = bearingProcess.getParentDataBlock());
|
this.addRequiredDataBlock(rawOrFFTBlock = bearingProcess.getParentDataBlock());
|
||||||
|
addAffectedDataBlock(detectionBlock);
|
||||||
// PamDataBlock detectionSource = bearingLocaliserControl.getDetectionMonitor().getParentDataBlock();
|
// PamDataBlock detectionSource = bearingLocaliserControl.getDetectionMonitor().getParentDataBlock();
|
||||||
// this.setParentDataBlock(detectionSource);
|
// this.setParentDataBlock(detectionSource);
|
||||||
// setParentDataBlock(bearingProcess.getParentDataBlock());
|
// setParentDataBlock(bearingProcess.getParentDataBlock());
|
||||||
|
@ -26,6 +26,10 @@ public class Group3DOfflineTask extends OfflineTask<PamDataUnit>{
|
|||||||
this.group3DControl = group3DControl;
|
this.group3DControl = group3DControl;
|
||||||
group3DProcess = group3DControl.getGroup3dProcess();
|
group3DProcess = group3DControl.getGroup3dProcess();
|
||||||
addAffectedDataBlock(group3DProcess.getGroup3dDataBlock());
|
addAffectedDataBlock(group3DProcess.getGroup3dDataBlock());
|
||||||
|
PamDataBlock parentData = group3DProcess.getParentDataBlock();
|
||||||
|
if (parentData != null) {
|
||||||
|
this.addRequiredDataBlock(parentData);
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
|
@ -32,6 +32,7 @@ import java.io.IOException;
|
|||||||
import java.util.EnumMap;
|
import java.util.EnumMap;
|
||||||
|
|
||||||
import javax.swing.JFileChooser;
|
import javax.swing.JFileChooser;
|
||||||
|
import javax.swing.filechooser.FileNameExtensionFilter;
|
||||||
|
|
||||||
import PamUtils.PamCalendar;
|
import PamUtils.PamCalendar;
|
||||||
|
|
||||||
@ -126,31 +127,34 @@ public class RoccaClassifyThis {
|
|||||||
/** the field in the RoccaContourStats object which contains all the stats measures */
|
/** the field in the RoccaContourStats object which contains all the stats measures */
|
||||||
private EnumMap<RoccaContourStats.ParamIndx, Double> contourStats;
|
private EnumMap<RoccaContourStats.ParamIndx, Double> contourStats;
|
||||||
|
|
||||||
private String dirIn;
|
/**
|
||||||
|
* Constructor used when allowing user to select training dataset
|
||||||
/** the input filename */
|
* */
|
||||||
private String csvIn;
|
|
||||||
|
|
||||||
/** the input file */
|
|
||||||
private File statsFileIn;
|
|
||||||
|
|
||||||
/** the output filename */
|
|
||||||
private String csvOut;
|
|
||||||
|
|
||||||
/** the output file */
|
|
||||||
private File statsFileOut;
|
|
||||||
|
|
||||||
/** Constructor */
|
|
||||||
public RoccaClassifyThis(RoccaProcess roccaProcess) {
|
public RoccaClassifyThis(RoccaProcess roccaProcess) {
|
||||||
|
File statsFileIn = getTheFile();
|
||||||
// initialize the BufferedReader
|
if (statsFileIn!=null) {
|
||||||
BufferedReader inputFile = null;
|
runTheClassifier(statsFileIn, roccaProcess);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Constructor when we pass in the training dataset
|
||||||
|
*/
|
||||||
|
public RoccaClassifyThis() {
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Ask the user to select the file containing the testing dataset
|
||||||
|
*
|
||||||
|
* @return File the csv file containing the testing dataset
|
||||||
|
*/
|
||||||
|
public File getTheFile() {
|
||||||
// set the directory
|
// set the directory
|
||||||
// this.dirIn = new String("C:\\Users\\Mike\\Documents\\Work\\Java\\EclipseWorkspace\\testing\\RoccaClassifyThis_testing");
|
// this.dirIn = new String("C:\\Users\\Mike\\Documents\\Work\\Java\\EclipseWorkspace\\testing\\RoccaClassifyThis_testing");
|
||||||
// this.dirIn = new String("C:\\Users\\Mike\\Documents\\Work\\Tom\\Atlantic Classifier\\manual 2-stage data");
|
// this.dirIn = new String("C:\\Users\\Mike\\Documents\\Work\\Tom\\Atlantic Classifier\\manual 2-stage data");
|
||||||
// this.dirIn = new String("C:\\Users\\Mike\\Documents\\Work\\Tom\\Hawaii dataset problems");
|
// this.dirIn = new String("C:\\Users\\Mike\\Documents\\Work\\Tom\\Hawaii dataset problems");
|
||||||
this.dirIn = new String("C:\\Users\\SCANS\\Documents\\Work\\Biowaves\\ONR classifier");
|
// this.dirIn = new String("C:\\Users\\SCANS\\Documents\\Work\\Biowaves\\ONR classifier");
|
||||||
|
|
||||||
// Define the input and output filenames
|
// Define the input and output filenames
|
||||||
// Hard-coded for now. To Do: query the user for the filename
|
// Hard-coded for now. To Do: query the user for the filename
|
||||||
@ -158,35 +162,54 @@ public class RoccaClassifyThis {
|
|||||||
// this.csvIn = new String("Manual_5sp_April 9 2013.csv");
|
// this.csvIn = new String("Manual_5sp_April 9 2013.csv");
|
||||||
// this.csvIn = new String("CombinedContourStats-fixed.csv");
|
// this.csvIn = new String("CombinedContourStats-fixed.csv");
|
||||||
// this.csvOut = new String("RoccaContourStatsReclassified.csv");
|
// this.csvOut = new String("RoccaContourStatsReclassified.csv");
|
||||||
this.csvIn = new String("Atl_TestDFNoTrain_Call_W_160831.csv");
|
// this.csvIn = new String("Atl_TestDFNoTrain_Call_W_160831.csv");
|
||||||
statsFileIn = new File(dirIn, csvIn);
|
// statsFileIn = new File(dirIn, csvIn);
|
||||||
this.csvOut = new String("Atl_TestDFNoTrain_Call_W_160829-classified.csv");
|
// this.csvOut = new String("Atl_TestDFNoTrain_Call_W_160829-classified.csv");
|
||||||
statsFileOut = new File(dirIn, csvOut);
|
// statsFileOut = new File(dirIn, csvOut);
|
||||||
|
|
||||||
|
// let the user select the arff file
|
||||||
|
JFileChooser fileChooser = new JFileChooser();
|
||||||
|
fileChooser.setDialogTitle("Select spreadsheet to recalculate...");
|
||||||
|
fileChooser.setFileHidingEnabled(true);
|
||||||
|
fileChooser.setApproveButtonText("Select");
|
||||||
|
fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
|
||||||
|
FileNameExtensionFilter restrict = new FileNameExtensionFilter("Only .csv files", "csv");
|
||||||
|
fileChooser.addChoosableFileFilter(restrict);
|
||||||
|
|
||||||
|
int state = fileChooser.showOpenDialog(null);
|
||||||
|
File statsFileIn = null;
|
||||||
|
if (state == JFileChooser.APPROVE_OPTION) {
|
||||||
|
|
||||||
|
// load the file
|
||||||
|
statsFileIn = fileChooser.getSelectedFile();
|
||||||
|
return statsFileIn;
|
||||||
|
|
||||||
|
} else {
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Run the classifier
|
||||||
|
* @param statsFileIn the File containing the testing dataset
|
||||||
|
* @param roccaProcess the RoccaProcess instance
|
||||||
|
*/
|
||||||
|
public void runTheClassifier(File statsFileIn, RoccaProcess roccaProcess) {
|
||||||
|
|
||||||
// JFileChooser fileChooser = new JFileChooser();
|
int index = statsFileIn.getAbsolutePath().lastIndexOf(".");
|
||||||
// fileChooser.setDialogTitle("Select spreadsheet to recalculate...");
|
String csvOut = statsFileIn.getAbsolutePath().substring(0,index) + "-classified.csv";
|
||||||
// fileChooser.setFileHidingEnabled(true);
|
File statsFileOut = new File(csvOut);
|
||||||
// fileChooser.setApproveButtonText("Select");
|
|
||||||
// fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
|
|
||||||
//
|
|
||||||
// int state = fileChooser.showOpenDialog(this.dirIn);
|
|
||||||
// if (state == JFileChooser.APPROVE_OPTION) {
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
// load the classifier
|
// load the classifier
|
||||||
System.out.println("Loading classifier...");
|
System.out.println("Loading classifier...");
|
||||||
roccaProcess.setClassifierLoaded
|
roccaProcess.setClassifierLoaded
|
||||||
(roccaProcess.roccaClassifier.setUpClassifier());
|
(roccaProcess.roccaClassifier.setUpClassifier());
|
||||||
|
|
||||||
|
// initialize the BufferedReader
|
||||||
|
BufferedReader inputFile = null;
|
||||||
|
|
||||||
// open the input file
|
// open the input file
|
||||||
try {
|
try {
|
||||||
System.out.println("Opening input file "+statsFileIn);
|
System.out.println("Opening input file "+statsFileIn);
|
||||||
@ -263,12 +286,45 @@ public class RoccaClassifyThis {
|
|||||||
contourStats.put(RoccaContourStats.ParamIndx.FREQPOSSLOPEMEAN, Double.parseDouble(dataArray[34]));
|
contourStats.put(RoccaContourStats.ParamIndx.FREQPOSSLOPEMEAN, Double.parseDouble(dataArray[34]));
|
||||||
contourStats.put(RoccaContourStats.ParamIndx.FREQNEGSLOPEMEAN, Double.parseDouble(dataArray[35]));
|
contourStats.put(RoccaContourStats.ParamIndx.FREQNEGSLOPEMEAN, Double.parseDouble(dataArray[35]));
|
||||||
contourStats.put(RoccaContourStats.ParamIndx.FREQSLOPERATIO, Double.parseDouble(dataArray[36]));
|
contourStats.put(RoccaContourStats.ParamIndx.FREQSLOPERATIO, Double.parseDouble(dataArray[36]));
|
||||||
contourStats.put(RoccaContourStats.ParamIndx.FREQBEGSWEEP, Double.parseDouble(dataArray[37]));
|
|
||||||
//contourStats.put(RoccaContourStats.ParamIndx.FREQBEGUP, Double.parseDouble(dataArray[38]));
|
// Note that we have to modify the FREQBEGSWEEP value. Weka is trained with the FREQBEGSWEEP param
|
||||||
//contourStats.put(RoccaContourStats.ParamIndx.FREQBEGDWN, Double.parseDouble(dataArray[39]));
|
// as -1=down, 0=flat and 1=up, and that would be how the test data comes through as well. HOWEVER,
|
||||||
contourStats.put(RoccaContourStats.ParamIndx.FREQENDSWEEP, Double.parseDouble(dataArray[40]));
|
// Weka assumes that for nominal parameters, the value is the index location (0,1 or 2) and NOT the actual trained
|
||||||
//contourStats.put(RoccaContourStats.ParamIndx.FREQENDUP, Double.parseDouble(dataArray[41]));
|
// value (-1,0 or 1). So if the whistle has a down sweep, Weka needs the FREQBEGSWEEP value to be 0 indicating the
|
||||||
//contourStats.put(RoccaContourStats.ParamIndx.FREQENDDWN, Double.parseDouble(dataArray[42]));
|
// first location in the array (which was 'down'). If it was up, the value would need to be 2 indicating the third
|
||||||
|
// location in the array (which was 'up').
|
||||||
|
// Ideally we would map the values in the test data to the positions in the training array, but as a quick and
|
||||||
|
// dirty hack we'll simply add 1 to the value since the difference between the nominal values (-1,0,1) and the
|
||||||
|
/// index positions (0,1,2) is an offset of 1
|
||||||
|
// Note also that we don't have to do the same thing for FREQBEGUP and FREQBEGDWN since, by coincidence, the training
|
||||||
|
// values of 0 and 1 happen to match the index locations of 0 and 1
|
||||||
|
//contourStats.put(RoccaContourStats.ParamIndx.FREQBEGSWEEP, Double.parseDouble(dataArray[37]));
|
||||||
|
double tempVal = Double.parseDouble(dataArray[37]);
|
||||||
|
tempVal++;
|
||||||
|
contourStats.put(RoccaContourStats.ParamIndx.FREQBEGSWEEP, tempVal);
|
||||||
|
contourStats.put(RoccaContourStats.ParamIndx.FREQBEGUP, Double.parseDouble(dataArray[38]));
|
||||||
|
contourStats.put(RoccaContourStats.ParamIndx.FREQBEGDWN, Double.parseDouble(dataArray[39]));
|
||||||
|
|
||||||
|
// Note that we have to modify the FREQENDSWEEP value. Weka is trained with the FREQENDSWEEP param
|
||||||
|
// as -1=down, 0=flat and 1=up, and that would be how the test data comes through as well. HOWEVER,
|
||||||
|
// Weka assumes that for nominal parameters, the value is the index location (0,1 or 2) and NOT the actual trained
|
||||||
|
// value (-1,0 or 1). So if the whistle has a down sweep, Weka needs the FREQENDSWEEP value to be 0 indicating the
|
||||||
|
// first location in the array (which was 'down'). If it was up, the value would need to be 2 indicating the third
|
||||||
|
// location in the array (which was 'up').
|
||||||
|
// Ideally we would map the values in the test data to the positions in the training array, but as a quick and
|
||||||
|
// dirty hack we'll simply add 1 to the value since the difference between the nominal values (-1,0,1) and the
|
||||||
|
/// index positions (0,1,2) is an offset of 1
|
||||||
|
// Note also that we don't have to do the same thing for FREQENDUP and FREQENDDWN since, by coincidence, the training
|
||||||
|
// values of 0 and 1 happen to match the index locations of 0 and 1
|
||||||
|
//contourStats.put(RoccaContourStats.ParamIndx.FREQENDSWEEP, Double.parseDouble(dataArray[40]));
|
||||||
|
tempVal = Double.parseDouble(dataArray[40]);
|
||||||
|
tempVal++;
|
||||||
|
contourStats.put(RoccaContourStats.ParamIndx.FREQENDSWEEP, tempVal);
|
||||||
|
contourStats.put(RoccaContourStats.ParamIndx.FREQENDUP, Double.parseDouble(dataArray[41]));
|
||||||
|
contourStats.put(RoccaContourStats.ParamIndx.FREQENDDWN, Double.parseDouble(dataArray[42]));
|
||||||
|
// end of hack
|
||||||
|
|
||||||
|
|
||||||
contourStats.put(RoccaContourStats.ParamIndx.NUMSWEEPSUPDWN, Double.parseDouble(dataArray[43]));
|
contourStats.put(RoccaContourStats.ParamIndx.NUMSWEEPSUPDWN, Double.parseDouble(dataArray[43]));
|
||||||
contourStats.put(RoccaContourStats.ParamIndx.NUMSWEEPSDWNUP, Double.parseDouble(dataArray[44]));
|
contourStats.put(RoccaContourStats.ParamIndx.NUMSWEEPSDWNUP, Double.parseDouble(dataArray[44]));
|
||||||
contourStats.put(RoccaContourStats.ParamIndx.NUMSWEEPSUPFLAT, Double.parseDouble(dataArray[45]));
|
contourStats.put(RoccaContourStats.ParamIndx.NUMSWEEPSUPFLAT, Double.parseDouble(dataArray[45]));
|
||||||
@ -285,8 +341,8 @@ public class RoccaClassifyThis {
|
|||||||
contourStats.put(RoccaContourStats.ParamIndx.INFLMEANDELTA, Double.parseDouble(dataArray[56]));
|
contourStats.put(RoccaContourStats.ParamIndx.INFLMEANDELTA, Double.parseDouble(dataArray[56]));
|
||||||
contourStats.put(RoccaContourStats.ParamIndx.INFLSTDDEVDELTA, Double.parseDouble(dataArray[57]));
|
contourStats.put(RoccaContourStats.ParamIndx.INFLSTDDEVDELTA, Double.parseDouble(dataArray[57]));
|
||||||
contourStats.put(RoccaContourStats.ParamIndx.INFLMEDIANDELTA, Double.parseDouble(dataArray[58]));
|
contourStats.put(RoccaContourStats.ParamIndx.INFLMEDIANDELTA, Double.parseDouble(dataArray[58]));
|
||||||
contourStats.put(RoccaContourStats.ParamIndx.INFLDUR, Double.parseDouble(dataArray[59]));
|
//contourStats.put(RoccaContourStats.ParamIndx.INFLDUR, Double.parseDouble(dataArray[59]));
|
||||||
contourStats.put(RoccaContourStats.ParamIndx.STEPDUR, Double.parseDouble(dataArray[60]));
|
//contourStats.put(RoccaContourStats.ParamIndx.STEPDUR, Double.parseDouble(dataArray[60]));
|
||||||
|
|
||||||
// Run the classifier
|
// Run the classifier
|
||||||
roccaProcess.roccaClassifier.classifyContour2(rcdb);
|
roccaProcess.roccaClassifier.classifyContour2(rcdb);
|
||||||
|
@ -169,6 +169,7 @@ public class RoccaParametersDialog extends PamDialog implements ActionListener,
|
|||||||
JButton classifier2Button;
|
JButton classifier2Button;
|
||||||
JButton recalcButton;
|
JButton recalcButton;
|
||||||
JButton reclassifyButton;
|
JButton reclassifyButton;
|
||||||
|
JButton trainThenTestButton;
|
||||||
JButton clearClassifier;
|
JButton clearClassifier;
|
||||||
JComboBox<DefaultComboBoxModel<Vector<String>>> stage1Classes;
|
JComboBox<DefaultComboBoxModel<Vector<String>>> stage1Classes;
|
||||||
DefaultComboBoxModel<Vector<String>> stage1ClassModel;
|
DefaultComboBoxModel<Vector<String>> stage1ClassModel;
|
||||||
@ -513,6 +514,10 @@ public class RoccaParametersDialog extends PamDialog implements ActionListener,
|
|||||||
reclassifyButton.addActionListener(this);
|
reclassifyButton.addActionListener(this);
|
||||||
reclassifyButton.setToolTipText("Load the whistle data from the contour stats output file, and run it through the current Classifier");
|
reclassifyButton.setToolTipText("Load the whistle data from the contour stats output file, and run it through the current Classifier");
|
||||||
reclassifyButton.setVisible(true);
|
reclassifyButton.setVisible(true);
|
||||||
|
trainThenTestButton = new JButton("Train then Test");
|
||||||
|
trainThenTestButton.addActionListener(this);
|
||||||
|
trainThenTestButton.setToolTipText("Train a classifier on a set of training data, then test it with a set of testing data");
|
||||||
|
trainThenTestButton.setVisible(true);
|
||||||
|
|
||||||
// ******** THIS LINES CONTROLS THE VISIBILITY ********
|
// ******** THIS LINES CONTROLS THE VISIBILITY ********
|
||||||
if (RoccaDev.isEnabled()) {
|
if (RoccaDev.isEnabled()) {
|
||||||
@ -528,13 +533,15 @@ public class RoccaParametersDialog extends PamDialog implements ActionListener,
|
|||||||
extraPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
|
extraPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
|
||||||
.addGroup(extraPanelLayout.createSequentialGroup()
|
.addGroup(extraPanelLayout.createSequentialGroup()
|
||||||
.addComponent(recalcButton)
|
.addComponent(recalcButton)
|
||||||
.addComponent(reclassifyButton))
|
.addComponent(reclassifyButton)
|
||||||
|
.addComponent(trainThenTestButton))
|
||||||
);
|
);
|
||||||
extraPanelLayout.setVerticalGroup(
|
extraPanelLayout.setVerticalGroup(
|
||||||
extraPanelLayout.createSequentialGroup()
|
extraPanelLayout.createSequentialGroup()
|
||||||
.addGroup(extraPanelLayout.createParallelGroup(GroupLayout.Alignment.BASELINE)
|
.addGroup(extraPanelLayout.createParallelGroup(GroupLayout.Alignment.BASELINE)
|
||||||
.addComponent(recalcButton)
|
.addComponent(recalcButton)
|
||||||
.addComponent(reclassifyButton))
|
.addComponent(reclassifyButton)
|
||||||
|
.addComponent(trainThenTestButton))
|
||||||
);
|
);
|
||||||
classifierPanel.add(extraButtonsSubPanel);
|
classifierPanel.add(extraButtonsSubPanel);
|
||||||
|
|
||||||
@ -892,7 +899,9 @@ public class RoccaParametersDialog extends PamDialog implements ActionListener,
|
|||||||
} else if (e.getSource() == recalcButton) {
|
} else if (e.getSource() == recalcButton) {
|
||||||
RoccaFixParams recalc = new RoccaFixParams(roccaControl.roccaProcess);
|
RoccaFixParams recalc = new RoccaFixParams(roccaControl.roccaProcess);
|
||||||
} else if (e.getSource() == reclassifyButton) {
|
} else if (e.getSource() == reclassifyButton) {
|
||||||
RoccaClassifyThisEvent reclassify = new RoccaClassifyThisEvent(roccaControl.roccaProcess);
|
RoccaClassifyThis reclassify = new RoccaClassifyThis(roccaControl.roccaProcess);
|
||||||
|
} else if (e.getSource() == trainThenTestButton) {
|
||||||
|
RoccaTrainThenTest trainThenTest = new RoccaTrainThenTest(roccaControl.roccaProcess);
|
||||||
} else if (e.getSource() == fftButton) {
|
} else if (e.getSource() == fftButton) {
|
||||||
roccaParameters.setUseFFT(true);
|
roccaParameters.setUseFFT(true);
|
||||||
this.enableTheCorrectSource();
|
this.enableTheCorrectSource();
|
||||||
|
@ -145,6 +145,7 @@ public class RoccaRFModel implements java.io.Serializable {
|
|||||||
|
|
||||||
} catch (Exception ex) {
|
} catch (Exception ex) {
|
||||||
System.err.println("1st Classification failed: " + ex.getMessage());
|
System.err.println("1st Classification failed: " + ex.getMessage());
|
||||||
|
ex.printStackTrace();
|
||||||
rcdb.setClassifiedAs("Err");
|
rcdb.setClassifiedAs("Err");
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
@ -24,10 +24,14 @@
|
|||||||
package rocca;
|
package rocca;
|
||||||
|
|
||||||
import java.io.BufferedReader;
|
import java.io.BufferedReader;
|
||||||
|
import java.io.File;
|
||||||
import java.io.FileReader;
|
import java.io.FileReader;
|
||||||
import java.util.Date;
|
import java.util.Date;
|
||||||
import java.util.Enumeration;
|
import java.util.Enumeration;
|
||||||
|
|
||||||
|
import javax.swing.JFileChooser;
|
||||||
|
import javax.swing.filechooser.FileNameExtensionFilter;
|
||||||
|
|
||||||
import weka.classifiers.trees.RandomForest;
|
import weka.classifiers.trees.RandomForest;
|
||||||
import weka.core.Instances;
|
import weka.core.Instances;
|
||||||
import weka.core.SerializationHelper;
|
import weka.core.SerializationHelper;
|
||||||
@ -42,13 +46,64 @@ import weka.core.SerializationHelper;
|
|||||||
*/
|
*/
|
||||||
public class RoccaTrainClassifier {
|
public class RoccaTrainClassifier {
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Standalone implementation
|
||||||
|
*
|
||||||
|
* @param args
|
||||||
|
*/
|
||||||
public static void main(String[] args) {
|
public static void main(String[] args) {
|
||||||
|
|
||||||
|
RoccaTrainClassifier rtc = new RoccaTrainClassifier();
|
||||||
|
File arffFile = rtc.getArff();
|
||||||
|
if (arffFile!=null) {
|
||||||
|
String modelName = rtc.trainClassifier(arffFile);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Let user choose arff file training dataset
|
||||||
|
*
|
||||||
|
* @return File the arff file containing the training dataset
|
||||||
|
*/
|
||||||
|
public File getArff() {
|
||||||
|
// String arffFile = "C:\\Users\\SCANS\\Documents\\Work\\Biowaves\\ONR classifier\\TP_TrainEvtDF_170408";
|
||||||
|
|
||||||
|
// let the user select the arff file
|
||||||
|
JFileChooser fileChooser = new JFileChooser();
|
||||||
|
fileChooser.setDialogTitle("Select arff file containing training data");
|
||||||
|
fileChooser.setFileHidingEnabled(true);
|
||||||
|
fileChooser.setApproveButtonText("Select");
|
||||||
|
fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
|
||||||
|
FileNameExtensionFilter restrict = new FileNameExtensionFilter("Only .arff files", "arff");
|
||||||
|
fileChooser.addChoosableFileFilter(restrict);
|
||||||
|
File arffFile;
|
||||||
|
|
||||||
|
int state = fileChooser.showOpenDialog(null);
|
||||||
|
if (state == JFileChooser.APPROVE_OPTION) {
|
||||||
|
|
||||||
|
// load the file
|
||||||
|
arffFile = fileChooser.getSelectedFile();
|
||||||
|
return arffFile;
|
||||||
|
|
||||||
|
} else {
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Actual code to train the classifier
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
public String trainClassifier(File arffFile) {
|
||||||
|
|
||||||
RandomForest model = new RandomForest ();
|
RandomForest model = new RandomForest ();
|
||||||
Instances trainData = null;
|
Instances trainData = null;
|
||||||
String arffFile = "C:\\Users\\SCANS\\Documents\\Work\\Biowaves\\ONR classifier\\TP_TrainEvtDF_170408";
|
|
||||||
|
|
||||||
// load the ARFF file containing the training set
|
// load the ARFF file containing the training set
|
||||||
System.out.println("Loading data...");
|
System.out.println("Loading data..." + arffFile.getAbsolutePath());
|
||||||
try {
|
try {
|
||||||
trainData = new Instances
|
trainData = new Instances
|
||||||
(new BufferedReader
|
(new BufferedReader
|
||||||
@ -56,10 +111,13 @@ public class RoccaTrainClassifier {
|
|||||||
// ("C:\\Users\\Mike\\Documents\\Work\\Java\\WEKA\\allwhists 12 vars 8sp update 1-28-10.arff")));
|
// ("C:\\Users\\Mike\\Documents\\Work\\Java\\WEKA\\allwhists 12 vars 8sp update 1-28-10.arff")));
|
||||||
// ("C:\\Users\\Mike\\Documents\\Work\\Java\\WEKA\\weka vs R\\ETP_orcawale_whists2 modified-subset110perspecies-no_harm_ratios.arff")));
|
// ("C:\\Users\\Mike\\Documents\\Work\\Java\\WEKA\\weka vs R\\ETP_orcawale_whists2 modified-subset110perspecies-no_harm_ratios.arff")));
|
||||||
// ("C:\\Users\\SCANS\\Documents\\Work\\Biowaves\\ONR classifier\\Atl_TrainDF_Event_160829.arff")));
|
// ("C:\\Users\\SCANS\\Documents\\Work\\Biowaves\\ONR classifier\\Atl_TrainDF_Event_160829.arff")));
|
||||||
(arffFile + ".arff")));
|
// (arffFile + ".arff")));
|
||||||
|
(arffFile)));
|
||||||
trainData.setClassIndex(trainData.numAttributes()-1);
|
trainData.setClassIndex(trainData.numAttributes()-1);
|
||||||
} catch (Exception ex) {
|
} catch (Exception ex) {
|
||||||
System.out.println("Error Loading...");
|
System.out.println("Error Loading...");
|
||||||
|
ex.printStackTrace();
|
||||||
|
return null;
|
||||||
}
|
}
|
||||||
|
|
||||||
// set the classifier parameters
|
// set the classifier parameters
|
||||||
@ -78,6 +136,8 @@ public class RoccaTrainClassifier {
|
|||||||
model.setOptions(options);
|
model.setOptions(options);
|
||||||
} catch (Exception ex) {
|
} catch (Exception ex) {
|
||||||
System.out.println("Error setting options...");
|
System.out.println("Error setting options...");
|
||||||
|
ex.printStackTrace();
|
||||||
|
return null;
|
||||||
}
|
}
|
||||||
|
|
||||||
// train the classifier
|
// train the classifier
|
||||||
@ -90,23 +150,29 @@ public class RoccaTrainClassifier {
|
|||||||
new Date());
|
new Date());
|
||||||
} catch (Exception ex) {
|
} catch (Exception ex) {
|
||||||
System.out.println("Error training classifier...");
|
System.out.println("Error training classifier...");
|
||||||
|
ex.printStackTrace();
|
||||||
|
return null;
|
||||||
}
|
}
|
||||||
|
|
||||||
// save the classifier
|
// save the classifier
|
||||||
String[] curOptions = model.getOptions();
|
// String[] curOptions = model.getOptions();
|
||||||
Enumeration test = model.listOptions();
|
// Enumeration test = model.listOptions();
|
||||||
System.out.println("Saving Classifier...");
|
|
||||||
Instances header = new Instances(trainData,0);
|
Instances header = new Instances(trainData,0);
|
||||||
|
int index = arffFile.getAbsolutePath().lastIndexOf(".");
|
||||||
|
String modelName = arffFile.getAbsolutePath().substring(0,index) + ".model";
|
||||||
|
System.out.println("Saving Classifier..." + modelName);
|
||||||
try {
|
try {
|
||||||
SerializationHelper.writeAll
|
SerializationHelper.writeAll
|
||||||
// ("C:\\Users\\Mike\\Documents\\Work\\Java\\WEKA\\weka vs R\\RF_8sp_54att_110whistle-subset.model",
|
// ("C:\\Users\\Mike\\Documents\\Work\\Java\\WEKA\\weka vs R\\RF_8sp_54att_110whistle-subset.model",
|
||||||
(arffFile + ".model",
|
// (arffFile + ".model",
|
||||||
|
(modelName,
|
||||||
new Object[]{model,header});
|
new Object[]{model,header});
|
||||||
|
System.out.println("Finished!");
|
||||||
|
return modelName;
|
||||||
} catch (Exception ex) {
|
} catch (Exception ex) {
|
||||||
System.out.println("Error saving classifier...");
|
System.out.println("Error saving classifier...");
|
||||||
|
ex.printStackTrace();
|
||||||
}
|
}
|
||||||
|
return null;
|
||||||
System.out.println("Finished!");
|
|
||||||
}
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
109
src/rocca/RoccaTrainThenTest.java
Normal file
109
src/rocca/RoccaTrainThenTest.java
Normal file
@ -0,0 +1,109 @@
|
|||||||
|
/*
|
||||||
|
* PAMGUARD - Passive Acoustic Monitoring GUARDianship.
|
||||||
|
* To assist in the Detection Classification and Localisation
|
||||||
|
* of marine mammals (cetaceans).
|
||||||
|
*
|
||||||
|
* Copyright (C) 2006
|
||||||
|
*
|
||||||
|
* 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 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 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., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
|
||||||
|
*/
|
||||||
|
|
||||||
|
package rocca;
|
||||||
|
|
||||||
|
import java.io.BufferedReader;
|
||||||
|
import java.io.File;
|
||||||
|
import java.io.FileNotFoundException;
|
||||||
|
import java.io.FileReader;
|
||||||
|
import java.io.IOException;
|
||||||
|
|
||||||
|
import javax.swing.JFileChooser;
|
||||||
|
import javax.swing.filechooser.FileNameExtensionFilter;
|
||||||
|
|
||||||
|
public class RoccaTrainThenTest {
|
||||||
|
|
||||||
|
RoccaTrainClassifier roccaTrainClassifier;
|
||||||
|
|
||||||
|
RoccaClassifyThis roccaClassifyThis;
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Main Constructor
|
||||||
|
* @param roccaProcess
|
||||||
|
*/
|
||||||
|
public RoccaTrainThenTest(RoccaProcess roccaProcess) {
|
||||||
|
|
||||||
|
|
||||||
|
// let the user select the csv file containing the training and testing dataset(s)
|
||||||
|
JFileChooser fileChooser = new JFileChooser();
|
||||||
|
fileChooser.setDialogTitle("Select csv file with the training/testing pairs");
|
||||||
|
fileChooser.setFileHidingEnabled(true);
|
||||||
|
fileChooser.setApproveButtonText("Select");
|
||||||
|
fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
|
||||||
|
FileNameExtensionFilter restrict = new FileNameExtensionFilter("Only .csv files", "csv");
|
||||||
|
fileChooser.addChoosableFileFilter(restrict);
|
||||||
|
|
||||||
|
int state = fileChooser.showOpenDialog(null);
|
||||||
|
if (state == JFileChooser.APPROVE_OPTION) {
|
||||||
|
|
||||||
|
// load the file
|
||||||
|
try {
|
||||||
|
File csvDataPairs = fileChooser.getSelectedFile();
|
||||||
|
BufferedReader br = new BufferedReader(new FileReader(csvDataPairs));
|
||||||
|
String curPath = csvDataPairs.getParent();
|
||||||
|
|
||||||
|
// main loop
|
||||||
|
// read through the csv file one line at a time. The first column should contain the training dataset filename,
|
||||||
|
// and the second column the testing dataset filename. Paths should be relative to the path containing
|
||||||
|
// the csv file
|
||||||
|
String line = "";
|
||||||
|
String splitBy = ",";
|
||||||
|
while ((line=br.readLine())!=null) {
|
||||||
|
|
||||||
|
String[] filenames = line.split(splitBy);
|
||||||
|
|
||||||
|
// train the classifier
|
||||||
|
File arffFile = new File(curPath + File.separator + filenames[0]);
|
||||||
|
roccaTrainClassifier = new RoccaTrainClassifier();
|
||||||
|
String modelName = roccaTrainClassifier.trainClassifier(arffFile);
|
||||||
|
if (modelName == null) {
|
||||||
|
System.out.println("ERROR: could not create classifier model from "+arffFile);
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
|
||||||
|
// set the classifier as the current one in RoccaParameters
|
||||||
|
roccaProcess.roccaControl.roccaParameters.setRoccaClassifierModelFilename(new File(modelName));
|
||||||
|
|
||||||
|
|
||||||
|
// test the classifier with the testing dataset
|
||||||
|
File testFile = new File(curPath + File.separator + filenames[1]);
|
||||||
|
roccaClassifyThis = new RoccaClassifyThis();
|
||||||
|
roccaClassifyThis.runTheClassifier(testFile, roccaProcess);
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
} catch (FileNotFoundException e) {
|
||||||
|
e.printStackTrace();
|
||||||
|
return;
|
||||||
|
} catch (IOException e) {
|
||||||
|
e.printStackTrace();
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
Loading…
Reference in New Issue
Block a user