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Code Issues Packages Projects Releases Wiki Activity

Tidying

Browse Source 
Lots of GUI improvement and code tidying. Functionality to export
gzipped documents to reduce traffic.
This commit is contained in:
Douglas Gillespie 2024-03-20 16:31:53 -07:00
parent b77686ae0f
commit ef1a6cf5ee
41 changed files with 1585 additions and 467 deletions
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3
.classpath
View File

@ -6,9 +6,8 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
<attributes>
<attribute name="module" value="true"/>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>

2
dependency-reduced-pom.xml
View File

@ -4,7 +4,7 @@
<groupId>org.pamguard</groupId>
<artifactId>Pamguard</artifactId>
<name>Pamguard Java12+</name>
<version>2.02.10b</version>
<version>2.02.10ad</version>
<description>Pamguard for Java 12+, using Maven to control dependcies</description>
<url>www.pamguard.org</url>
<organization>

4
src/PamUtils/worker/PamWorkDialog.java
View File

@ -1,5 +1,6 @@
package PamUtils.worker;
import java.awt.Dimension;
import java.awt.Window;
import javax.swing.BoxLayout;
@ -23,6 +24,9 @@ public class PamWorkDialog extends PamDialog {
mainPanel.setBorder(new TitledBorder("Task Progress"));
// GridBagConstraints c = new PamGridBagContraints();
mainPanel.add(progressBar = new JProgressBar(0, 100));
Dimension sz = progressBar.getPreferredSize();
sz.width = 300;
progressBar.setPreferredSize(sz);
textRows = new PamTextDisplay[nTextRows];
for (int i = 0; i < nTextRows; i++) {
// c.gridy++;

38
src/tethys/CollectionHandler.java Normal file
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@ -0,0 +1,38 @@
package tethys;
abstract public class CollectionHandler {
private Collection collection;
protected TethysControl tethysControl;
/**
* @param tethysControl
* @param collection
*/
public CollectionHandler(TethysControl tethysControl, Collection collection) {
this.tethysControl = tethysControl;
this.collection = collection;
}
public String collectionName() {
return collection.collectionName();
}
/**
* @return the collection
*/
public Collection getCollection() {
return collection;
}
/**
* @return the tethysControl
*/
public TethysControl getTethysControl() {
return tethysControl;
}
public abstract String getHelpPoint();
}

2
src/tethys/TethysControl.java
View File

@ -469,6 +469,8 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
// case PamControllerInterface.INITIALIZATION_COMPLETE:
initializationStuff();
break;
case PamControllerInterface.HYDROPHONE_ARRAY_CHANGED:
sendStateUpdate(new TethysState(StateType.UPDATEMETADATA));
}
}

17
src/tethys/calibration/CalibrationHandler.java
View File

@ -1,6 +1,5 @@
package tethys.calibration;
import java.lang.reflect.Field;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
@ -37,6 +36,7 @@ import nilus.MetadataInfo;
import nilus.QualityValueBasic;
import nilus.ResponsibleParty;
import tethys.Collection;
import tethys.CollectionHandler;
import tethys.DocumentInfo;
import tethys.DocumentNilusObject;
import tethys.TethysControl;
@ -52,9 +52,7 @@ import tethys.niluswraps.NilusUnpacker;
import tethys.pamdata.AutoTethysProvider;
import tethys.reporter.TethysReporter;
public class CalibrationHandler implements TethysStateObserver {
private TethysControl tethysControl;
public class CalibrationHandler extends CollectionHandler implements TethysStateObserver {
private ArrayList<DocumentNilusObject<Calibration>> calibrationsList;
@ -65,10 +63,14 @@ public class CalibrationHandler implements TethysStateObserver {
public static final String[] qaTypes = {"unverified", "valid", "invalid"};
private Helper nilusHelper;
public static final String helpPoint = "utilities.tethys.docs.calibrations";
/**
* @param tethysControl
*/
public CalibrationHandler(TethysControl tethysControl) {
super(tethysControl, Collection.Calibrations);
this.tethysControl = tethysControl;
calibrationsList = new ArrayList();
tethysControl.addStateObserver(this); try {
@ -504,7 +506,7 @@ public class CalibrationHandler implements TethysStateObserver {
}
String seachPattern = makeChannelNamePart(iChan);
for (int i = 0; i < calibrationsList.size(); i++) {
String docName = calibrationsList.get(i).getDocumentName();
String docName = calibrationsList.get(i).getDocumentId();
if (docName.endsWith(seachPattern)) {
return true;
}
@ -570,4 +572,9 @@ public class CalibrationHandler implements TethysStateObserver {
}
return theseCals;
}
@Override
public String getHelpPoint() {
return helpPoint;
}
}

33
src/tethys/calibration/swing/CalibrationsContactCard.java
View File

@ -5,6 +5,7 @@ import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.ArrayList;
import java.util.Date;
import javax.swing.BoxLayout;
@ -18,6 +19,9 @@ import javax.xml.datatype.XMLGregorianCalendar;
import org.jdesktop.swingx.JXDatePicker;
import Array.ArrayManager;
import Array.Hydrophone;
import Array.PamArray;
import PamView.dialog.PamDialog;
import PamView.dialog.PamGridBagContraints;
import PamView.panel.WestAlignedPanel;
@ -43,6 +47,8 @@ public class CalibrationsContactCard extends CalibrationsCard {
private JButton copyDown, copyUp;
private JComboBox<String> hydrophoneSelection;
public CalibrationsContactCard(PamWizard pamWizard) {
super(pamWizard, "Contact Details");
// TODO Auto-generated constructor stub
@ -57,17 +63,26 @@ public class CalibrationsContactCard extends CalibrationsCard {
JPanel datePanel = new JPanel(new GridBagLayout());
JPanel lp = new WestAlignedPanel(datePanel);
lp.setBorder(new TitledBorder("Calibration date"));
lp.setBorder(new TitledBorder("Date and hydrophones"));
GridBagConstraints c = new PamGridBagContraints();
datePanel.add(new JLabel("Calibration date: ", JLabel.RIGHT), c);
datePicker = new JXDatePicker();
c.gridx++;
datePanel.add(datePicker, c);
c.gridx = 0;
c.gridy++;
datePanel.add(new JLabel("Update Frequency", JLabel.RIGHT), c);
// c.gridx = 0;
c.gridx++;
datePanel.add(new JLabel(" Update Frequency ", JLabel.RIGHT), c);
c.gridx++;
datePanel.add(updateInterval, c);
c.gridx = 0;
c.gridy++;
datePanel.add(new JLabel(" Hydrophones ", JLabel.RIGHT), c);
c.gridwidth = 5;
c.gridx++;
hydrophoneSelection = new JComboBox<>();
datePanel.add(hydrophoneSelection, c);
hydrophoneSelection.setToolTipText("Select which hydrophone calibrations to export");
calibrator = new ResponsiblePartyPanel("Technical Person");
dataManager = new ResponsiblePartyPanel("Data Manager");
@ -202,6 +217,16 @@ public class CalibrationsContactCard extends CalibrationsCard {
datePicker.setDate(new Date(TethysTimeFuncs.millisFromGregorianXML(ts)));
}
hydrophoneSelection.removeAllItems();
hydrophoneSelection.addItem("All hydrophones");
PamArray array = ArrayManager.getArrayManager().getCurrentArray();
ArrayList<Hydrophone> phones = array.getHydrophoneArray();
int i = 0;
for (Hydrophone phone : phones) {
String txt = String.format("Hydrophone %d, %s, %3.1f dBre1\u00B5Pa", i, phone.getType(), phone.getSensitivity());
hydrophoneSelection.addItem(txt);
i++;
}
}

4
src/tethys/calibration/swing/CalibrationsExportWizard.java
View File

@ -5,6 +5,7 @@ import java.awt.Window;
import PamView.wizard.PamWizard;
import PamView.wizard.PamWizardCard;
import nilus.Calibration;
import tethys.calibration.CalibrationHandler;
public class CalibrationsExportWizard extends PamWizard {
@ -13,8 +14,9 @@ public class CalibrationsExportWizard extends PamWizard {
private CalibrationsExportWizard(Window parentFrame, Calibration sampleDocument) {
super(parentFrame, "Calibrations Export");
this.sampleDocument = sampleDocument;
addCard(new CalibrationProcessCard(this));
addCard(new CalibrationsContactCard(this));
addCard(new CalibrationProcessCard(this));
setHelpPoint(CalibrationHandler.helpPoint);
}
public static Calibration showWizard(Window parentFrame, Calibration sampleDocument) {

98
src/tethys/calibration/swing/CalibrationsMainPanel.java
View File

@ -15,53 +15,47 @@ import PamView.panel.PamPanel;
import tethys.TethysControl;
import tethys.TethysState;
import tethys.calibration.CalibrationHandler;
import tethys.deployment.PInstrument;
import tethys.swing.TethysExportPanel;
import tethys.swing.TethysGUIPanel;
import tethys.swing.TippedButton;
public class CalibrationsMainPanel extends TethysGUIPanel {
public class CalibrationsMainPanel extends TethysExportPanel {
private CalibrationHandler calibrationHandler;
private CalibrationsTable calibrationsTable;
private JPanel mainPanel;
private JPanel ctrlPanel;
private JButton exportButton;
private JLabel warning;
// private JPanel mainPanel;
//
// private JPanel ctrlPanel;
//
// private TippedButton exportButton;
//
// private JLabel warning;
public CalibrationsMainPanel(TethysControl tethysControl, CalibrationHandler calibrationHandler) {
super(tethysControl);
super(tethysControl, calibrationHandler, false);
this.calibrationHandler = calibrationHandler;
mainPanel = new PamPanel(new BorderLayout());
JPanel mainPanel = getMainPanel();
// mainPanel = new PamPanel(new BorderLayout());
mainPanel.setBorder(new TitledBorder("Instrument calibration information"));
calibrationsTable = new CalibrationsTable(tethysControl, calibrationHandler);
mainPanel.add(BorderLayout.CENTER, calibrationsTable.getComponent());
ctrlPanel = new PamPanel(new BorderLayout());
exportButton = new JButton("Export ...");
ctrlPanel.add(BorderLayout.WEST, exportButton);
warning = new JLabel();
ctrlPanel.add(BorderLayout.CENTER, warning);
mainPanel.add(BorderLayout.NORTH, ctrlPanel);
exportButton.setToolTipText("Export calibration data to database");
exportButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
exportCalibrations();
}
});
}
protected void exportCalibrations() {
calibrationHandler.exportAllCalibrations();
}
@Override
public JComponent getComponent() {
return mainPanel;
// ctrlPanel = new PamPanel(new BorderLayout());
// exportButton = new TippedButton("Export ...", "Export calibration data to database");
// ctrlPanel.add(BorderLayout.WEST, exportButton);
// warning = new JLabel();
// ctrlPanel.add(BorderLayout.CENTER, warning);
// mainPanel.add(BorderLayout.NORTH, ctrlPanel);
// exportButton.addActionListener(new ActionListener() {
// @Override
// public void actionPerformed(ActionEvent e) {
// exportCalibrations();
// }
// });
}
@Override
@ -71,7 +65,45 @@ public class CalibrationsMainPanel extends TethysGUIPanel {
}
private void enableControls() {
exportButton.setEnabled(getTethysControl().isServerOk());
if (getTethysControl().isServerOk() == false) {
disableExport("Tethys Server not running");
return;
}
if (isHydrophoneNamed() == false) {
disableExport("Can't export calibrations until the Hydrophone array has been correctly named");
return;
};
enableExport(true);
}
/**
* Check to see if hydrophone is named correctly.
* @return
*/
private boolean isHydrophoneNamed() {
PInstrument currentInstrument = getTethysControl().getDeploymentHandler().getCurrentArrayInstrument();
if (currentInstrument == null) {
return false;
}
if (currentInstrument.instrumentId == null || currentInstrument.instrumentType == null) {
return false;
}
if (currentInstrument.instrumentId.length() == 0 || currentInstrument.instrumentType.length() == 0) {
return false;
}
return true;
}
@Override
protected void exportButtonPressed(ActionEvent e) {
calibrationHandler.exportAllCalibrations();
}
@Override
protected void optionsButtonPressed(ActionEvent e) {
// TODO Auto-generated method stub
}
}

120
src/tethys/dbxml/DBXMLConnect.java
View File

@ -3,14 +3,17 @@ package tethys.dbxml;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.nio.file.Files;
import java.util.ArrayList;
import java.util.zip.GZIPOutputStream;
import javax.xml.bind.JAXBException;
@ -67,7 +70,7 @@ public class DBXMLConnect {
}
return true;
}
/**
* Get the client. The client will only be recreated if the url changes
@ -113,9 +116,9 @@ public class DBXMLConnect {
}
return file;
}
/**
* Create a temporary nilus file.
* Create a temporary nilus file.
* @param nilusObject
* @return
* @throws TethysException
@ -124,20 +127,20 @@ public class DBXMLConnect {
String tempName = getTempFileName(nilusObject);
tempName = tempDirectory.getAbsolutePath() + File.separator + tempName + ".xml";
File tempFile = new File(tempName);
File retFile = createXMLDocument(nilusObject, tempFile);
File retFile = createXMLDocument(nilusObject, tempFile);
retFile.deleteOnExit();
return retFile;
}
public boolean postAndLog(Object nilusObject) throws TethysException
{
return postAndLog(nilusObject, null);
}
/**
* I don't think this should ever be used since everything goes a bit pear
* shaped if the documentName isn't the same as the Id. However, for Calibration
* shaped if the documentName isn't the same as the Id. However, for Calibration
* documents this is no longer the case, since a Calibration can have multiple
* entries on different dates, so allow it !
* @param nilusObject
@ -145,11 +148,11 @@ public class DBXMLConnect {
* @return
* @throws TethysException
*/
public boolean postAndLog(Object nilusObject, String documentName) throws TethysException
{
public boolean postAndLog(Object nilusObject, String documentName) throws TethysException
{
boolean ok = NilusChecker.warnEmptyFields(tethysControl.getGuiFrame(), nilusObject);
TethysException e = null;
boolean success = false;
try {
@ -168,13 +171,13 @@ public class DBXMLConnect {
}
return success;
}
/**
* take a nilus object loaded with PamGuard data and post it to the Tethys database
*
* @param pamGuardObjs a nilus object loaded with PamGuard data
* @return error string, null string means there are no errors
* @throws TethysException
* @throws TethysException
*/
private boolean postToTethys(Object nilusObject, String documentName) throws TethysException
{
@ -192,12 +195,35 @@ public class DBXMLConnect {
MarshalXML marshal = new MarshalXML();
marshal.createInstance(objClass);
marshal.marshal(nilusObject, tempFile.toString());
// above lines have made a file. Are now going to gzip it before sending to Tethys
File zipFile = null;
try {
zipFile = zipOutputFile(tempFile);
}
catch (FileNotFoundException e1){
System.out.println(e1.getMessage());
}
catch (IOException e2) {
System.out.println(e2.getMessage());
}
String finalName;
if (zipFile == null) {
finalName = bodgeName;
}
else {
finalName = zipFile.toString();
}
// tempFile = stripXMLHeader(tempFile);
importReturn = Importer.ImportFiles(params.getFullServerName(), collection.collectionName(),
new String[] { bodgeName }, "", "", false);
new String[] { finalName }, "", "", false);
tempFile.deleteOnExit();
if (zipFile != null) {
zipFile.deleteOnExit();
}
} catch(IllegalArgumentException e) {
throw new TethysException("IllegalArgumentException posting to Tethys: " + e.getMessage(), null);
} catch (IOException e) {
@ -207,21 +233,49 @@ public class DBXMLConnect {
}
/*
* The returned string consists of the file name, then an XML report.
* Quite hard to see much common structure in this, so just look for
* The returned string consists of the file name, then an XML report.
* Quite hard to see much common structure in this, so just look for
* two words, <Success> and <Error>
*/
boolean error = importReturn.contains("<Error");
boolean success = importReturn.contains("<Success>");
String name = tempFile.getName();
TethysReporter.getTethysReporter().addReport(new TethysReport(success, collection, name, name));
// error = !success; might be a better options.
// error = !success; might be a better options.
if (error) {
throw new TethysException("Error posting to Tethys", importReturn);
}
return success;
}
/**
* Zip an xml file (or any file) into a gz file with a new end
* @param xmlFile
* @return
* @throws FileNotFoundException
* @throws IOException
*/
private File zipOutputFile(File xmlFile) throws FileNotFoundException, IOException {
String zipName = xmlFile.toString() + "-temp-.gz";
File zipFile = new File(zipName);
GZIPOutputStream opStream = new GZIPOutputStream(new FileOutputStream(zipFile));
InputStream fis = new FileInputStream(xmlFile);
int chunkSize = 100*1024;
byte[] buffer = new byte[chunkSize];
// ZipEntry zipEntry = new ZipEntry(xmlFile.getName());
int bytesRead;
while ((bytesRead = fis.read(buffer)) >= 0) {
opStream.write(buffer, 0, bytesRead);
}
opStream.close();
fis.close();
return zipFile;
}
/**
* Update a document within Tethys. We're assuming that a
* document with the same name in the same collection already
@ -229,7 +283,7 @@ public class DBXMLConnect {
* the removedocument function
* @param nilusDocument
* @return
* @throws TethysException
* @throws TethysException
*/
public boolean updateDocument(Object nilusDocument) throws TethysException {
deleteDocument(nilusDocument);
@ -242,7 +296,7 @@ public class DBXMLConnect {
* class to identify the correct collection.
* @param nilusDocument
* @return
* @throws TethysException
* @throws TethysException
*/
public boolean deleteDocument(Object nilusDocument) throws TethysException {
@ -259,7 +313,7 @@ public class DBXMLConnect {
<DELETE>
<ITEM> ['ECoastNARW0'] </ITEM>
</DELETE>
An error will throw an exception.
An error will throw an exception.
*/
}
catch (Exception e) {
@ -275,7 +329,7 @@ An error will throw an exception.
* Delete a Deploymnet and any contained Detections document. Doesn't work !
* @param deploymentId
* @return
* @throws TethysException
* @throws TethysException
*/
public boolean deleteDeployment(String deploymentId) throws TethysException {
ArrayList<String> detDocNames = tethysControl.getDbxmlQueries().getDetectionsDocuments(deploymentId);
@ -292,8 +346,8 @@ An error will throw an exception.
}
/**
* Remove a document based on a collection name and a cdocument Id.
* @param collection collection name.
* Remove a document based on a collection name and a cdocument Id.
* @param collection collection name.
* @param documentName document name (not the internal Document Id)
* @return
* @throws TethysException
@ -303,8 +357,8 @@ An error will throw an exception.
}
/**
* Remove a document based on a collection name and a document namw.
* @param collectionName collection name.
* Remove a document based on a collection name and a document namw.
* @param collectionName collection name.
* @param documentName document name (not the internal Document Id)
* @return
* @throws TethysException
@ -319,7 +373,7 @@ An error will throw an exception.
<DELETE>
<ITEM> ['ECoastNARW0'] </ITEM>
</DELETE>
An error will throw an exception.
An error will throw an exception.
*/
}
catch (Exception e) {
@ -330,14 +384,14 @@ An error will throw an exception.
}
/**
* check the return string from importFiles and if it's an
* error, throw an exception. Otherwise do nothing.
* check the return string from importFiles and if it's an
* error, throw an exception. Otherwise do nothing.
* @param fileError
*/
private void checkReturnString(String fileError) {
/**
* Example good string is
*
*
C:\Users\dg50\AppData\Local\Temp\PAMGuardTethys\20080311_2DSimplex_0.xml: 7360 bytes
<?xml version="1.0" encoding="iso-8859-1"?>
<Import>
@ -367,7 +421,7 @@ C:\Users\dg50\AppData\Local\Temp\PAMGuardTethys\20080311_2DSimplex_0.xmlnot: 0 b
/**
* Seems we have to get rid of the line <?xml version="1.0" encoding="UTF-8"?>
* which is being put there by the marshaller ?
* which is being put there by the marshaller ?
* @param tempFile
*/
private File stripXMLHeader(File tempFile) {
@ -377,7 +431,7 @@ C:\Users\dg50\AppData\Local\Temp\PAMGuardTethys\20080311_2DSimplex_0.xmlnot: 0 b
try {
BufferedReader reader = new BufferedReader(new FileReader(tempFile));
BufferedWriter writer = new BufferedWriter(new FileWriter(tempTemp));
String line = reader.readLine();
String line = reader.readLine();
while (line != null) {
// see if the line has any unicode in it
int len = line.length();

3
src/tethys/dbxml/DBXMLQueries.java
View File

@ -515,6 +515,9 @@ public class DBXMLQueries {
* first query for Detections documents associated with this deployment and datablock.
* updated May 23
*/
if (dataBlock == null) {
return null;
}
String queryNoDepl = "{\"species\":{\"query\":{\"op\":\"lib:completename2tsn\",\"optype\":\"function\",\"operands\":[\"%s\"]},\"return\":{\"op\":\"lib:tsn2completename\",\"optype\":\"function\",\"operands\":[\"%s\"]}},\"return\":[\"Detections/Id\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Detections/Algorithm/Software\",\"LongDataName\"],\"optype\":\"binary\"}],\"enclose\":1}";
String queryWithDepl = "{\"species\":{\"query\":{\"op\":\"lib:completename2tsn\",\"optype\":\"function\",\"operands\":[\"%s\"]},\"return\":{\"op\":\"lib:tsn2completename\",\"optype\":\"function\",\"operands\":[\"%s\"]}},\"return\":[\"Detections/Id\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Detections/DataSource/DeploymentId\",\"TheDeploymentId\"],\"optype\":\"binary\"},{\"op\":\"=\",\"operands\":[\"Detections/Algorithm/Software\",\"LongDataName\"],\"optype\":\"binary\"}],\"enclose\":1}";
String query;

98
src/tethys/deployment/DeploymentHandler.java
View File

@ -73,6 +73,7 @@ import nilus.UnknownSensor;
import pamMaths.PamVector;
import pamMaths.STD;
import tethys.Collection;
import tethys.CollectionHandler;
import tethys.TethysControl;
import tethys.TethysLocationFuncs;
import tethys.TethysState;
@ -83,6 +84,7 @@ import tethys.TethysState.StateType;
import tethys.dbxml.DBXMLConnect;
import tethys.dbxml.TethysException;
import tethys.deployment.swing.DeploymentWizard;
import tethys.deployment.swing.EffortProblemDialog;
import tethys.deployment.swing.RecordingGapDialog;
import tethys.niluswraps.PDeployment;
import tethys.output.TethysExportParams;
@ -98,16 +100,9 @@ import tethys.swing.DeploymentTableObserver;
* @author dg50
*
*/
public class DeploymentHandler implements TethysStateObserver, DeploymentTableObserver {
public class DeploymentHandler extends CollectionHandler implements TethysStateObserver, DeploymentTableObserver {
private TethysControl tethysControl;
/**
* @return the tethysControl
*/
public TethysControl getTethysControl() {
return tethysControl;
}
// private TethysControl tethysControl;
private EffortFunctions effortFunctions;
@ -119,8 +114,11 @@ public class DeploymentHandler implements TethysStateObserver, DeploymentTableOb
private DeploymentExportOpts deploymentExportOptions = new DeploymentExportOpts();
public static final String helpPoint = "utilities.tethys.docs.deployments";
public DeploymentHandler(TethysControl tethysControl) {
super();
super(tethysControl, Collection.Deployments);
this.tethysControl = tethysControl;
@ -368,8 +366,39 @@ public class DeploymentHandler implements TethysStateObserver, DeploymentTableOb
public void createPamguardOverview() {
deploymentOverview = effortFunctions.makeRecordingOverview();
checkDeploymentOverview(deploymentOverview);
updateProjectDeployments();
matchPamguard2Tethys(deploymentOverview, projectDeployments);
tethysControl.sendStateUpdate(new TethysState(StateType.NEWPAMGUARDSELECTION));
}
/**
* Check the deployment overview for consistency.<br>
* Take the raw audio information and the binary information and check they are similar.
* if not, ask the user what to do.
* @param deploymentOverview
*/
private void checkDeploymentOverview(DeploymentOverview overview) {
RecordingList rawList = overview.getRawDataList();
RecordingList binList = overview.getBinaryDataList();
if (rawList == null || binList == null) {
return; // nothing to do
}
double similarity = rawList.getSimilarity(binList);
if (similarity > 0.95) {
return;
}
/*
* if we get here, it seems like the two lists are very different, so
* show a dialog to ask the user what to do.
*/
RecordingList selList = EffortProblemDialog.showDialog(tethysControl.getGuiFrame(), overview);
if (selList != null) {
tethysControl.getTethysExportParams().setEffortSourceName(selList.getSourceName());
}
}
/**
@ -381,22 +410,22 @@ public class DeploymentHandler implements TethysStateObserver, DeploymentTableOb
if (exportOptions != null) {
this.deploymentExportOptions = exportOptions;
deploymentOverview = getDeploymentOverview();
ArrayList<RecordingPeriod> allPeriods = deploymentOverview.getRecordingPeriods();
RecordingList allPeriods = deploymentOverview.getMasterList(getTethysControl());
exportDeployments(allPeriods);
}
}
/**
* Export deployments docs. Playing with a couple of different ways of doing this.
* @param selectedDeployments
* @param allPeriods
*/
public void exportDeployments(ArrayList<RecordingPeriod> selectedDeployments) {
public void exportDeployments(RecordingList allPeriods) {
TethysReporter.getTethysReporter().clear();
if (deploymentExportOptions.separateDeployments) {
exportSeparateDeployments(selectedDeployments);
exportSeparateDeployments(allPeriods);
}
else {
exportOneDeploymnet(selectedDeployments);
exportOneDeploymnet(allPeriods);
}
TethysReporter.getTethysReporter().showReport(tethysControl.getGuiFrame(), true);
}
@ -404,7 +433,7 @@ public class DeploymentHandler implements TethysStateObserver, DeploymentTableOb
/**
* Make one big deployment document with all the recording periods in it.
*/
private void exportOneDeploymnet(ArrayList<RecordingPeriod> selectedDeployments) {
private void exportOneDeploymnet(RecordingList recordingList) {
// do the lot, whatever ...
Float sampleRate = null;
AcquisitionControl daq = (AcquisitionControl) PamController.getInstance().findControlledUnit(AcquisitionControl.class, null);
@ -414,10 +443,9 @@ public class DeploymentHandler implements TethysStateObserver, DeploymentTableOb
sampleRate = daqParams.sampleRate;
}
selectedDeployments = getDeploymentOverview().getRecordingPeriods();
int freeId = getTethysControl().getDeploymentHandler().getFirstFreeDeploymentId();
RecordingPeriod onePeriod = new RecordingPeriod(selectedDeployments.get(0).getRecordStart(),
selectedDeployments.get(selectedDeployments.size()-1).getRecordStop());
RecordingPeriod onePeriod = new RecordingPeriod(recordingList.getStart(),
recordingList.getEnd());
TethysExportParams exportParams = tethysControl.getTethysExportParams();
String id = String.format("%s_%s", exportParams.getDatasetName(), "all");
Deployment deployment = createDeploymentDocument(freeId, onePeriod, id);
@ -425,7 +453,8 @@ public class DeploymentHandler implements TethysStateObserver, DeploymentTableOb
Deployment globalMeta = getTethysControl().getGlobalDeplopymentData();
deployment.setCruise(globalMeta.getCruise());
deployment.setSite(globalMeta.getSite());
if (selectedDeployments.size() > 1) {
ArrayList<RecordingPeriod> effortPeriods = recordingList.getEffortPeriods();
if (recordingList.size() > 1) {
// // now need to remove the sampling details - don't though, add invalid periods instead.
// SamplingDetails samplingDetails = deployment.getSamplingDetails();
// samplingDetails.getChannel().clear();
@ -440,9 +469,9 @@ public class DeploymentHandler implements TethysStateObserver, DeploymentTableOb
deployment.setQualityAssurance(qa = new AcousticDataQAType());
}
List<Quality> qualityList = qa.getQuality();
for (int i = 1; i < selectedDeployments.size(); i++) {
long end = selectedDeployments.get(i-1).getRecordStop();
long start = selectedDeployments.get(i).getRecordStart();
for (int i = 1; i < recordingList.size(); i++) {
long end = effortPeriods.get(i-1).getRecordStop();
long start = effortPeriods.get(i).getRecordStart();
Quality q = new Quality();
q.setStart(TethysTimeFuncs.xmlGregCalFromMillis(end));
q.setEnd(TethysTimeFuncs.xmlGregCalFromMillis(start));
@ -479,14 +508,15 @@ public class DeploymentHandler implements TethysStateObserver, DeploymentTableOb
/**
* Make a separate deployment document for every recording period.
*/
private void exportSeparateDeployments(ArrayList<RecordingPeriod> selectedDeployments) {
private void exportSeparateDeployments(RecordingList recordingList) {
int freeId = getTethysControl().getDeploymentHandler().getFirstFreeDeploymentId();
// fill in a few things from here
Deployment globalMeta = getTethysControl().getGlobalDeplopymentData();
TethysExportParams exportParams = tethysControl.getTethysExportParams();
for (int i = 0; i < selectedDeployments.size(); i++) {
RecordingPeriod recordPeriod = selectedDeployments.get(i);
ArrayList<RecordingPeriod> effortPeriods = recordingList.getEffortPeriods();
for (int i = 0; i < recordingList.size(); i++) {
RecordingPeriod recordPeriod = effortPeriods.get(i);
PDeployment exDeploymnet = recordPeriod.getMatchedTethysDeployment();
Deployment deployment = null;
String id = String.format("%s_%d", exportParams.getDatasetName(), i);
@ -532,8 +562,9 @@ public class DeploymentHandler implements TethysStateObserver, DeploymentTableOb
if (deployments == null || deploymentOverview == null) {
return;
}
ArrayList<RecordingPeriod> recordingPeriods = deploymentOverview.getRecordingPeriods();
for (RecordingPeriod aPeriod : recordingPeriods) {
RecordingList recordingList = deploymentOverview.getMasterList(getTethysControl());
ArrayList<RecordingPeriod> effortPeriods = recordingList.getEffortPeriods();
for (RecordingPeriod aPeriod : effortPeriods) {
PDeployment closestDeployment = findClosestDeployment(aPeriod, deployments);
aPeriod.setMatchedTethysDeployment(closestDeployment);
if (closestDeployment != null) {
@ -592,7 +623,8 @@ public class DeploymentHandler implements TethysStateObserver, DeploymentTableOb
if (deploymentOverview == null) {
return matched;
}
for (RecordingPeriod period : deploymentOverview.getRecordingPeriods()) {
ArrayList<RecordingPeriod> effortPeriods = deploymentOverview.getMasterList(getTethysControl()).getEffortPeriods();
for (RecordingPeriod period : effortPeriods) {
PDeployment deployment = period.getMatchedTethysDeployment();
if (deployment != null) {
if (matched.contains(deployment) == false) {
@ -1230,7 +1262,8 @@ public class DeploymentHandler implements TethysStateObserver, DeploymentTableOb
}
regimens.add(regimen);
DutyCycleInfo dutyCycleInf = deploymentOverview.getDutyCycleInfo();
RecordingList recordingList = deploymentOverview.getMasterList(getTethysControl());
DutyCycleInfo dutyCycleInf = recordingList.assessDutyCycle();
boolean isDS = dutyCycleInf != null && dutyCycleInf.isDutyCycled;
if (isDS) {
DutyCycle dutyCycle = new DutyCycle();
@ -1307,4 +1340,9 @@ public class DeploymentHandler implements TethysStateObserver, DeploymentTableOb
return deploymentExportOptions;
}
@Override
public String getHelpPoint() {
return helpPoint;
}
}

110
src/tethys/deployment/DeploymentOverview.java
View File

@ -1,16 +1,6 @@
package tethys.deployment;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.ListIterator;
import Acquisition.AcquisitionControl;
import Acquisition.AcquisitionParameters;
import Acquisition.DaqStatusDataUnit;
import PamController.PamControlledUnit;
import PamController.PamController;
import PamguardMVC.PamDataBlock;
import tethys.TethysControl;
/**
* Class to give a general overview of all the effort in PAMGuard which will form the
@ -22,59 +12,83 @@ import PamguardMVC.PamDataBlock;
*/
public class DeploymentOverview {
private ArrayList<RecordingPeriod> recordingPeriods = new ArrayList<>();
private RecordingList rawDataList;
private DutyCycleInfo dutyCycleInfo;
private RecordingList binaryDataList;
// private DutyCycleInfo dutyCycleInfo;
public DeploymentOverview(DutyCycleInfo dutyCycleInfo) {
super();
this.dutyCycleInfo = dutyCycleInfo;
}
// public DeploymentOverview(DutyCycleInfo dutyCycleInfo) {
// super();
// this.dutyCycleInfo = dutyCycleInfo;
// }
public DeploymentOverview(DutyCycleInfo dutyCycleInfo, ArrayList<RecordingPeriod> tempPeriods) {
this.dutyCycleInfo = dutyCycleInfo;
this.recordingPeriods = tempPeriods;
}
public void addRecordingPeriod(long start, long stop) {
addRecordingPeriod(new RecordingPeriod(start, stop));
public DeploymentOverview(DutyCycleInfo dutyCycleInfo, RecordingList rawDataList, RecordingList binaryDataList) {
// this.dutyCycleInfo = dutyCycleInfo;
this.rawDataList = rawDataList;
this.binaryDataList = binaryDataList;
}
private void addRecordingPeriod(RecordingPeriod recordingPeriod) {
recordingPeriods.add(recordingPeriod);
/**
* @return the rawDataList
*/
public RecordingList getRawDataList() {
return rawDataList;
}
public ArrayList<RecordingPeriod> getRecordingPeriods() {
return recordingPeriods;
/**
* @return the binaryDataList
*/
public RecordingList getBinaryDataList() {
return binaryDataList;
}
public DutyCycleInfo getDutyCycleInfo() {
return dutyCycleInfo;
// /**
// * @return the dutyCycleInfo
// */
// public DutyCycleInfo getDutyCycleInfo() {
// return dutyCycleInfo;
// }
public RecordingList getMasterList(TethysControl tethysControl) {
return getMasterList(tethysControl.getTethysExportParams().getEffortSourceName());
}
public RecordingList getMasterList(String effortSourceName) {
if (effortSourceName == null) {
return getLongestList();
}
if (binaryDataList != null & binaryDataList.getSourceName().equals(effortSourceName)) {
return binaryDataList;
}
if (rawDataList != null & rawDataList.getSourceName().equals(effortSourceName)) {
return rawDataList;
}
return getLongestList();
}
/**
* Get the start time of the first recording
* Get the recording list with the greatest duration (start to end)
* not looking at coverage between those times.
* @return
*/
public Long getFirstStart() {
if (recordingPeriods.size() > 0) {
return recordingPeriods.get(0).getRecordStart();
public RecordingList getLongestList() {
if (binaryDataList == null) {
return rawDataList;
}
return null;
}
/**
* Get the end time of the last recording
* @return
*/
public Long getLastEnd() {
if (recordingPeriods.size() > 0) {
return recordingPeriods.get(recordingPeriods.size()-1).getRecordStop();
if (rawDataList == null) {
return binaryDataList;
}
long lRaw = rawDataList.duration();
long lBin = binaryDataList.duration();
if (lRaw > lBin) {
return rawDataList;
}
else {
return binaryDataList;
}
return null;
}
}

242
src/tethys/deployment/EffortFunctions.java
View File

@ -41,36 +41,40 @@ public class EffortFunctions {
this.tethysControl = tethysControl;
}
private DeploymentOverview createOverview(RecordingList tempPeriods) {
DutyCycleInfo dutyCycleinfo = assessDutyCycle(tempPeriods);
if (dutyCycleinfo == null) {
return null;
}
// if it's duty cycles, then we only want a single entry.
RecordingList deploymentPeriods;
if (dutyCycleinfo.isDutyCycled == false) {
deploymentPeriods = tempPeriods;
}
else {
deploymentPeriods = new RecordingList();
deploymentPeriods.add(new RecordingPeriod(tempPeriods.get(0).getRecordStart(), tempPeriods.get(tempPeriods.size()-1).getRecordStop()));
}
/*
* do another sort of the deploymentPeriods. The start stops were in the order they went into the
* database in the hope that pairs were the right way round. Now check all data are/
*/
Collections.sort(deploymentPeriods, new Comparator<RecordingPeriod>() {
@Override
public int compare(RecordingPeriod o1, RecordingPeriod o2) {
return (int) (o1.getRecordStart()-o2.getRecordStart());
}
});
DeploymentOverview deploymentOverview = new DeploymentOverview(dutyCycleinfo, deploymentPeriods);
return deploymentOverview;
}
// private DeploymentOverview createOverview(RecordingList tempPeriods) {
//
// tempPeriods.sort();
//
// DutyCycleInfo dutyCycleinfo = assessDutyCycle(tempPeriods);
// if (dutyCycleinfo == null) {
// return null;
// }
//
//
// // if it's duty cycles, then we only want a single entry.
// RecordingList deploymentPeriods;
// if (dutyCycleinfo.isDutyCycled == false) {
// deploymentPeriods = tempPeriods;
// }
// else {
// deploymentPeriods = new RecordingList(tempPeriods.getSourceName());
// deploymentPeriods.add(new RecordingPeriod(tempPeriods.get(0).getRecordStart(), tempPeriods.get(tempPeriods.size()-1).getRecordStop()));
// }
// /*
// * do another sort of the deploymentPeriods. The start stops were in the order they went into the
// * database in the hope that pairs were the right way round. Now check all data are/
// */
// deploymentPeriods.sort();
//// Collections.sort(deploymentPeriods, new Comparator<RecordingPeriod>() {
//// @Override
//// public int compare(RecordingPeriod o1, RecordingPeriod o2) {
//// return (int) (o1.getRecordStart()-o2.getRecordStart());
//// }
//// });
//
// DeploymentOverview deploymentOverview = new DeploymentOverview(dutyCycleinfo, deploymentPeriods);
// return deploymentOverview;
// }
public DeploymentOverview makeRecordingOverview() {
@ -79,13 +83,18 @@ public class EffortFunctions {
RecordingList binaryPeriods = listBinaryFiles();
long l1 = listDuration(recordingPeriods);
long l2 = listDuration(binaryPeriods);
if (listDuration(binaryPeriods) > listDuration(recordingPeriods)) {
recordingPeriods = binaryPeriods;
}
// see what the similarity is between them
// double sim = recordingPeriods.getSimilarity(binaryPeriods);
// double testSim = recordingPeriods.getSimilarity(recordingPeriods);
DeploymentOverview deploymentOverview = createOverview(recordingPeriods);
// long l1 = listDuration(recordingPeriods);
// long l2 = listDuration(binaryPeriods);
// if (listDuration(binaryPeriods) > listDuration(recordingPeriods)) {
// recordingPeriods = binaryPeriods;
// }
//
// DeploymentOverview deploymentOverview = createOverview(recordingPeriods);
DeploymentOverview deploymentOverview = new DeploymentOverview(null, recordingPeriods, binaryPeriods);
return deploymentOverview;
}
@ -128,7 +137,8 @@ public class EffortFunctions {
}
}
}
bestList = mergeRecordings(bestList);
DeploymentExportOpts exportOptions = tethysControl.getDeploymentHandler().getDeploymentExportOptions();
bestList.mergeRecordingPeriods(exportOptions.maxRecordingGapSeconds*1000);
return bestList;
}
@ -138,7 +148,7 @@ public class EffortFunctions {
if (mapPoints == null) {
return null;
}
RecordingList periods = new RecordingList();
RecordingList periods = new RecordingList(dataMap.getDataMapName());
for (OfflineDataMapPoint mapPoint : mapPoints) {
periods.add(new RecordingPeriod(mapPoint.getStartTime(), mapPoint.getEndTime()));
}
@ -219,117 +229,60 @@ public class EffortFunctions {
// PamCalendar.formatDBDateTime(aP.getRecordStop()));
// }
tempPeriods = mergeRecordings(tempPeriods);
return tempPeriods;
}
/**
* Merge close recordings and discard ones that are too short.
* @param tempPeriods all recording periods, may be from consecutive files.
* @return merged list.
*/
private RecordingList mergeRecordings(RecordingList tempPeriods) {
// now go through those and merge into longer periods where there is no gap between files.
if (tempPeriods == null) {
return null;
}
tempPeriods.sort();
DeploymentExportOpts exportOptions = tethysControl.getDeploymentHandler().getDeploymentExportOptions();
ListIterator<RecordingPeriod> iterator = tempPeriods.listIterator();
RecordingPeriod prevPeriod = null;
while (iterator.hasNext()) {
RecordingPeriod nextPeriod = iterator.next();
long nextDur = nextPeriod.getRecordStop()-nextPeriod.getRecordStart();
if (nextDur == 0) {
continue;
}
if (prevPeriod != null) {
long gap = nextPeriod.getRecordStart() - prevPeriod.getRecordStop();
long prevDur = prevPeriod.getRecordStop()-prevPeriod.getRecordStart();
if (gap < exportOptions.maxRecordingGapSeconds*1000) {
// ignoring up to 3s gap or a sample error < 2%.Dunno if this is sensible or not.
prevPeriod.setRecordStop(nextPeriod.getRecordStop());
iterator.remove();
nextPeriod = prevPeriod;
}
}
prevPeriod = nextPeriod;
}
// now remove ones which are too short even after merging.
iterator = tempPeriods.listIterator();
while (iterator.hasNext()) {
RecordingPeriod nextPeriod = iterator.next();
long duration = nextPeriod.getDuration();
if (duration < exportOptions.minRecordingLengthSeconds*1000L) {
iterator.remove();
}
}
tempPeriods.mergeRecordingPeriods(exportOptions.maxRecordingGapSeconds*1000);
return tempPeriods;
}
/**
* Work out whether or not the data are evenly duty cycled by testing the
* distributions of on and off times.
* @param tempPeriods
* @return
*/
private DutyCycleInfo assessDutyCycle(RecordingList tempPeriods) {
if (tempPeriods == null) {
return null;
}
int n = tempPeriods.size();
if (n < 2) {
return new DutyCycleInfo(false, 0,0,n);
}
double[] ons = new double[n-1]; // ignore the last one since it may be artificially shortened which is OK
double[] gaps = new double[n-1];
for (int i = 0; i < n-1; i++) {
ons[i] = tempPeriods.get(i).getDuration()/1000.;
gaps[i] = (tempPeriods.get(i+1).getRecordStart()-tempPeriods.get(i).getRecordStop())/1000.;
}
/* now look at how consistent those values are
* But some data gets messed by small gaps, so want to
* remove outliers and concentrate on say 80% of the data.
*/
ons = getDistributionCentre(ons, 80);
gaps = getDistributionCentre(gaps, 80);
Arrays.sort(gaps);
// /**
// * Merge close recordings and discard ones that are too short.
// * @param tempPeriods all recording periods, may be from consecutive files.
// * @return merged list.
// */
// private RecordingList mergeRecordings(RecordingList tempPeriods) {
// // now go through those and merge into longer periods where there is no gap between files.
// if (tempPeriods == null) {
// return null;
// }
//
// DeploymentExportOpts exportOptions = tethysControl.getDeploymentHandler().getDeploymentExportOptions();
//
// ListIterator<RecordingPeriod> iterator = tempPeriods.listIterator();
// RecordingPeriod prevPeriod = null;
// while (iterator.hasNext()) {
// RecordingPeriod nextPeriod = iterator.next();
// long nextDur = nextPeriod.getRecordStop()-nextPeriod.getRecordStart();
// if (nextDur == 0) {
// continue;
// }
// if (prevPeriod != null) {
// long gap = nextPeriod.getRecordStart() - prevPeriod.getRecordStop();
// long prevDur = prevPeriod.getRecordStop()-prevPeriod.getRecordStart();
// if (gap < exportOptions.maxRecordingGapSeconds*1000) {
// // ignoring up to 3s gap or a sample error < 2%.Dunno if this is sensible or not.
// prevPeriod.setRecordStop(nextPeriod.getRecordStop());
// iterator.remove();
// nextPeriod = prevPeriod;
// }
// }
// prevPeriod = nextPeriod;
// }
// // now remove ones which are too short even after merging.
// iterator = tempPeriods.listIterator();
// while (iterator.hasNext()) {
// RecordingPeriod nextPeriod = iterator.next();
// long duration = nextPeriod.getDuration();
// if (duration < exportOptions.minRecordingLengthSeconds*1000L) {
// iterator.remove();
// }
// }
//
// return tempPeriods;
// }
STD std = new STD();
double onsMean = std.getMean(ons);
double onsSTD = std.getSTD(ons);
double gapsMean = std.getMean(gaps);
double gapsSTD = std.getSTD(gaps);
boolean dutyCycle = onsSTD/onsMean < .05 && gapsSTD/gapsMean < 0.05;
DutyCycleInfo cycleInfo = new DutyCycleInfo(dutyCycle, onsMean, gapsMean, tempPeriods.size());
return cycleInfo;
}
/**
* Get the central part of a distribution without any outliers so
* that we can get a better assessment of duty cycle.
* @param data unsorted distribution data.
* @param percent percentage to include (half this removed from top and bottom)
* @return
*/
private double[] getDistributionCentre(double[] data, double percent) {
if (data == null) {
return null;
}
Arrays.sort(data);
int nRem = (int) Math.round(data.length * (100-percent)/200);
int newLen = data.length-nRem*2;
double[] subdata = Arrays.copyOfRange(data, nRem, data.length-2*nRem);
if (subdata.length < 2) {
return data;
}
return subdata;
}
/**
* Get data times from any other datamap, since this will generally match the acquisition anyway
@ -360,16 +313,17 @@ public class EffortFunctions {
return null;
}
// get the times out of it.
RecordingList recPeriods = new RecordingList();
RecordingList recPeriods = new RecordingList(bestMap.getDataMapName());
List<OfflineDataMapPoint> mapPoints = bestMap.getMapPoints();
for (OfflineDataMapPoint mapPoint : mapPoints) {
recPeriods.add(new RecordingPeriod(mapPoint.getStartTime(), mapPoint.getEndTime()));
recPeriods.add(mapPoint.getStartTime(), mapPoint.getEndTime());
}
return recPeriods;
}
private RecordingList extractTimesFromStatus(ArrayList<DaqStatusDataUnit> allStatusData) {
RecordingList tempPeriods = new RecordingList();
RecordingList tempPeriods = new RecordingList("Data acquisition status");
long dataStart = Long.MAX_VALUE;
long dataEnd = Long.MIN_VALUE;
Long lastStart = null;

211
src/tethys/deployment/RecordingList.java
View File

@ -1,12 +1,43 @@
package tethys.deployment;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
import java.util.Iterator;
public class RecordingList extends ArrayList<RecordingPeriod> {
import PamUtils.PamCalendar;
import pamMaths.STD;
/**
* Information about periods of effort that might come from either the raw data recordings or
* an analysis of binary data maps.
* @author dg50
*
*/
public class RecordingList implements Serializable {
private static final long serialVersionUID = 1L;
private ArrayList<RecordingPeriod> effortPeriods = new ArrayList();
/**
* Name / source of this list.
*/
private String sourceName;
/**
* @param sourceName
*/
public RecordingList(String sourceName) {
this.sourceName = sourceName;
}
public RecordingList(String sourceName, ArrayList<RecordingPeriod> selectedDeployments) {
this.sourceName = sourceName;
this.effortPeriods = selectedDeployments;
}
/**
* Get the duration of the recording periods from start to end.
@ -21,27 +52,27 @@ public class RecordingList extends ArrayList<RecordingPeriod> {
* @return
*/
public long getStart() {
if (size() == 0) {
if (effortPeriods.size() == 0) {
return 0;
}
return get(0).getRecordStart();
return effortPeriods.get(0).getRecordStart();
}
/**
* get the end of the last in the list.
*/
public long getEnd() {
if (size() == 0) {
if (effortPeriods.size() == 0) {
return 0;
}
return get(size()-1).getRecordStop();
return effortPeriods.get(effortPeriods.size()-1).getRecordStop();
}
/**
* Sort the list in ascending order.
*/
public void sort() {
Collections.sort(this, new Comparator<RecordingPeriod>() {
Collections.sort(effortPeriods, new Comparator<RecordingPeriod>() {
@Override
public int compare(RecordingPeriod o1, RecordingPeriod o2) {
@ -49,4 +80,172 @@ public class RecordingList extends ArrayList<RecordingPeriod> {
}
});
}
/**
* Get the coverage as a fraction. This is the sum of the individual periods divided
* by the start to end times
* @return
*/
public double getCoverage() {
long cov = 0;
long durTot = 0;
if (effortPeriods.size() == 0) {
return 0;
}
Iterator<RecordingPeriod> it = effortPeriods.iterator();
while (it.hasNext()) {
RecordingPeriod rp = it.next();
cov += rp.getDuration();
}
durTot = getEnd()-getStart();
return (double) cov / (double) durTot;
}
/**
* Merge recording periods, with a max gap between periods in milliseconds.
* @param maxGap
* @return the number of periods removed.
*/
public int mergeRecordingPeriods(long maxGap) {
if (effortPeriods.size() < 2) {
return 0;
}
Iterator<RecordingPeriod> it = effortPeriods.iterator();
RecordingPeriod prev = it.next();
int removed = 0;
while (it.hasNext()) {
RecordingPeriod curr = it.next();
if (curr.getRecordStart() - prev.getRecordStop() <= maxGap) {
prev.setRecordStop(curr.getRecordStop());
it.remove();
removed++;
}
else {
prev = curr;
}
}
return removed;
}
/**
* Work out whether or not the data are evenly duty cycled by testing the
* distributions of on and off times.
* @param tempPeriods
* @return
*/
public DutyCycleInfo assessDutyCycle() {
if (effortPeriods == null) {
return null;
}
int n = effortPeriods.size();
if (n < 2) {
return new DutyCycleInfo(false, 0,0,n);
}
double[] ons = new double[n-1]; // ignore the last one since it may be artificially shortened which is OK
double[] gaps = new double[n-1];
for (int i = 0; i < n-1; i++) {
ons[i] = effortPeriods.get(i).getDuration()/1000.;
gaps[i] = (effortPeriods.get(i+1).getRecordStart()-effortPeriods.get(i).getRecordStop())/1000.;
}
/* now look at how consistent those values are
* But some data gets messed by small gaps, so want to
* remove outliers and concentrate on say 80% of the data.
*/
ons = getDistributionCentre(ons, 80);
gaps = getDistributionCentre(gaps, 80);
Arrays.sort(gaps);
STD std = new STD();
double onsMean = std.getMean(ons);
double onsSTD = std.getSTD(ons);
double gapsMean = std.getMean(gaps);
double gapsSTD = std.getSTD(gaps);
boolean dutyCycle = onsSTD/onsMean < .05 && gapsSTD/gapsMean < 0.05;
DutyCycleInfo cycleInfo = new DutyCycleInfo(dutyCycle, onsMean, gapsMean, effortPeriods.size());
return cycleInfo;
}
/**
* Get the central part of a distribution without any outliers so
* that we can get a better assessment of duty cycle.
* @param data unsorted distribution data.
* @param percent percentage to include (half this removed from top and bottom)
* @return
*/
private double[] getDistributionCentre(double[] data, double percent) {
if (data == null) {
return null;
}
Arrays.sort(data);
int nRem = (int) Math.round(data.length * (100-percent)/200);
int newLen = data.length-nRem*2;
double[] subdata = Arrays.copyOfRange(data, nRem, data.length-2*nRem);
if (subdata.length < 2) {
return data;
}
return subdata;
}
/**
* @return the sourceName
*/
public String getSourceName() {
return sourceName;
}
@Override
public String toString() {
if (effortPeriods.size() == 0) {
return "Empty recording list";
}
String str = String.format("%s: %s to %s, %3.1f%% coverage", getSourceName(),
PamCalendar.formatDBDateTime(getStart()),
PamCalendar.formatDBDateTime(getEnd()), getCoverage()*100);
return str;
}
/**
* Get similarity to another recording list. 1 = identical, 0 means not even overlapping.
* @param other other recording list.
* @return measure of similarity.
*/
public double getSimilarity(RecordingList other) {
double sim1 = (double) other.duration() / (double) this.duration();
if (sim1 > 1) {
sim1 = 1./sim1;
}
long overlap = Math.min(other.getEnd(), this.getEnd()) - Math.max(other.getStart(), this.getStart());
overlap = Math.max(0, overlap);
long longest = Math.max(other.duration(), this.duration());
double sim2 = (double) overlap / (double) longest;
return Math.min(sim1, sim2);
}
/**
* Add a recording period to the list.
* @param recordingPeriod
*/
public void add(RecordingPeriod recordingPeriod) {
effortPeriods.add(recordingPeriod);
}
/**
* Add a recording period to the list.
* @param startTime
* @param endTime
*/
public void add(long startTime, long endTime) {
add (new RecordingPeriod(startTime, endTime));
}
public int size() {
return effortPeriods.size();
}
/**
* @return the effortPeriods
*/
public ArrayList<RecordingPeriod> getEffortPeriods() {
return effortPeriods;
}
}

7
src/tethys/deployment/RecordingPeriod.java
View File

@ -1,5 +1,6 @@
package tethys.deployment;
import PamUtils.PamCalendar;
import tethys.niluswraps.PDeployment;
public class RecordingPeriod {
@ -71,5 +72,11 @@ public class RecordingPeriod {
selected = !selected;
return selected;
}
@Override
public String toString() {
return String.format("%s to %s, %s", PamCalendar.formatDBDateTime(recordStart),
PamCalendar.formatDBDateTime(recordStop), PamCalendar.formatDuration(getDuration()));
}
}

163
src/tethys/deployment/swing/EffortProblemDialog.java Normal file
View File

@ -0,0 +1,163 @@
package tethys.deployment.swing;
import java.awt.BorderLayout;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.GridLayout;
import java.awt.Window;
import javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBox;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
import javax.swing.border.TitledBorder;
import PamUtils.PamCalendar;
import PamView.dialog.PamDialog;
import PamView.dialog.PamGridBagContraints;
import tethys.deployment.DeploymentOverview;
import tethys.deployment.RecordingList;
/**
* Handle problems when binary and raw effort don't add up
* @author dg50
*
*/
public class EffortProblemDialog extends PamDialog {
private JRadioButton useRaw, useBinary, useNeither;
private JLabel generalInfo;
private InfoSet[] infoSets = new InfoSet[2];
private RecordingList chosenList;
private DeploymentOverview deploymentOverview;
private static EffortProblemDialog singleInstance;
private static final String[] setNames = {"Raw data", "Binary data"};
private EffortProblemDialog(Window parentFrame) {
super(parentFrame, "Deployment Effort", false);
JPanel mainPanel = new JPanel();
mainPanel.setLayout(new BorderLayout());
mainPanel.setBorder(new TitledBorder("Effort information"));
String info = "<html>There is a mismatch between the time period covered by the raw<br>"
+ "data recordings and the time covered in the binary data.<br> "
+ "Select the one you wish to use, or Cancel and sort out your data<br>"
+ "prior to restarting the Tethys export process</html>";
generalInfo = new JLabel(info);
// generalInfo.setBorder(new TitledBorder("General"));
mainPanel.add(generalInfo, BorderLayout.NORTH);
JPanel botPanel = new JPanel(new GridLayout(2, 1));
mainPanel.add(botPanel, BorderLayout.CENTER);
ButtonGroup bg = new ButtonGroup();
for (int i = 0; i < 2; i++) {
GridBagConstraints c = new PamGridBagContraints();
JPanel subPanel = new JPanel(new GridBagLayout());
botPanel.add(subPanel);
infoSets[i] = new InfoSet(setNames[i]);
c.gridwidth = 2;
subPanel.add(infoSets[i].name, c);
c.gridx += c.gridwidth;
subPanel.add(infoSets[i].select, c);
c.gridx = 0;
c.gridy++;
c.gridwidth = 1;
subPanel.add(new JLabel("Start: ", JLabel.RIGHT), c);
c.gridx++;
subPanel.add(infoSets[i].start, c);
c.gridx++;
subPanel.add(new JLabel("End: ", JLabel.RIGHT), c);
c.gridx++;
subPanel.add(infoSets[i].end, c);
c.gridy++;
c.gridx = 0;
subPanel.add(new JLabel("Duration: ", JLabel.RIGHT), c);
c.gridx++;
subPanel.add(infoSets[i].duration, c);
c.gridx++;
subPanel.add(new JLabel("Coverage: ", JLabel.RIGHT), c);
c.gridx++;
subPanel.add(infoSets[i].occupancy, c);
bg.add(infoSets[i].select);
}
setDialogComponent(mainPanel);
setResizable(true);
}
public static RecordingList showDialog(Window parentFrame, DeploymentOverview deploymentOverview) {
singleInstance = new EffortProblemDialog(parentFrame);
singleInstance.setData(deploymentOverview);
singleInstance.setVisible(true);
return singleInstance.chosenList;
}
private void setData(DeploymentOverview deploymentOverview) {
this.deploymentOverview = deploymentOverview;
RecordingList rl;
for (int i = 0; i < 2; i++) {
if (i == 0) {
rl = deploymentOverview.getRawDataList();
}
else {
rl = deploymentOverview.getBinaryDataList();
}
infoSets[i].start.setText(PamCalendar.formatDBDateTime(rl.getStart()));
infoSets[i].end.setText(PamCalendar.formatDBDateTime(rl.getEnd()));
infoSets[i].duration.setText(PamCalendar.formatDuration(rl.duration()));
infoSets[i].occupancy.setText(String.format("%3.0f%%", rl.getCoverage()*100.));
}
invalidate();
pack();
}
@Override
public boolean getParams() {
if (infoSets[0].select.isSelected()) {
chosenList = deploymentOverview.getRawDataList();
return true;
}
if (infoSets[1].select.isSelected()) {
chosenList = deploymentOverview.getBinaryDataList();
return true;
}
return false;
}
@Override
public void cancelButtonPressed() {
// TODO Auto-generated method stub
}
@Override
public void restoreDefaultSettings() {
// TODO Auto-generated method stub
}
private class InfoSet {
JLabel name, start, end, duration, occupancy;
JCheckBox select;
/**
*
*/
public InfoSet(String name) {
super();
this.name = new JLabel(name);
this.start = new JLabel(" ");
this.end = new JLabel(" ");
this.select = new JCheckBox("Select " + name);
duration = new JLabel(" ");
occupancy = new JLabel(" ");
}
}
}

3
src/tethys/deployment/swing/RecordingGapDialog.java
View File

@ -36,7 +36,7 @@ public class RecordingGapDialog extends PamDialog {
c.gridx++;
mainPanel.add(new JLabel(" seconds", JLabel.RIGHT), c);
maxGap.setToolTipText("Maximum gap between recording periods. Periods with a gap less than this will be counted as one");
maxGap.setToolTipText("Maximum gap between recording periods. Sequential periods with a gap less than this will be counted as one");
minLength.setToolTipText("Minimum recording length. Recording sections shorter than this will be ignored");
setDialogComponent(mainPanel);
@ -80,6 +80,7 @@ public class RecordingGapDialog extends PamDialog {
@Override
public void restoreDefaultSettings() {
DeploymentExportOpts defaults = new DeploymentExportOpts();
setParams(defaults);
}
}

1
src/tethys/detection/DetectionExportProgress.java
View File

@ -17,6 +17,7 @@ public class DetectionExportProgress {
public int exportCount;
public int skipCount;
public int state;
public int totalDeployments, deploymentsDone;
public DetectionExportProgress(PDeployment currentDeployment, Detections currentDetections, long lastUnitTime,
long totalUnits, int exportCount, int skipCount, int state) {

70
src/tethys/detection/DetectionsHandler.java
View File

@ -11,7 +11,6 @@ import PamController.PamguardVersionInfo;
import PamModel.PamPluginInterface;
import PamUtils.PamCalendar;
import PamView.dialog.PamDialog;
import PamView.dialog.warn.WarnOnce;
import PamguardMVC.PamDataBlock;
import PamguardMVC.PamDataUnit;
import PamguardMVC.PamProcess;
@ -32,6 +31,7 @@ import nilus.Detections;
import nilus.GranularityEnumType;
import nilus.Helper;
import tethys.Collection;
import tethys.CollectionHandler;
import tethys.TethysControl;
import tethys.TethysTimeFuncs;
import tethys.dbxml.DBXMLConnect;
@ -39,7 +39,6 @@ import tethys.dbxml.TethysException;
import tethys.deployment.DeploymentHandler;
import tethys.niluswraps.PDeployment;
import tethys.niluswraps.PDetections;
import tethys.output.DatablockSynchInfo;
import tethys.output.StreamExportParams;
import tethys.output.TethysExportParams;
import tethys.pamdata.TethysDataProvider;
@ -54,9 +53,7 @@ import tethys.swing.export.DetectionsExportWizard;
* @author dg50
*
*/
public class DetectionsHandler {
private TethysControl tethysControl;
public class DetectionsHandler extends CollectionHandler {
public int uniqueDetectionsId=1;
public int uniqueDetectionId;
@ -65,12 +62,14 @@ public class DetectionsHandler {
private ExportWorker exportWorker;
public static final String helpPoint = "utilities.tethys.docs.detect_localize";
/**
*
* @param tethysControl
*/
public DetectionsHandler(TethysControl tethysControl) {
super();
super(tethysControl, Collection.Detections);
this.tethysControl = tethysControl;
}
@ -296,6 +295,9 @@ public class DetectionsHandler {
viewerLoadPolicy = ViewerLoadPolicy.LOAD_UTCNORMAL;
}
GranularityHandler granularityHandler = GranularityHandler.getHandler(streamExportParams.granularity, tethysControl, dataBlock, exportParams, streamExportParams);
int totalMaps = 0;
int totalMappedPoints = 0;
int totalLoadedDatas = 0;
for (PDeployment deployment : deployments) {
int documentCount = 0;
prog = new DetectionExportProgress(deployment, null,
@ -311,6 +313,7 @@ public class DetectionsHandler {
prog = new DetectionExportProgress(deployment, null,
lastUnitTime, totalCount, exportCount, skipCount, DetectionExportProgress.STATE_CANCELED);
exportObserver.update(prog);
break;
}
if (mapPoint.getEndTime() < deployment.getAudioStart()) {
@ -319,10 +322,13 @@ public class DetectionsHandler {
if (mapPoint.getStartTime() >= deployment.getAudioEnd()) {
break;
}
totalMaps ++;
totalMappedPoints += mapPoint.getNDatas();
dataBlock.loadViewerData(mapPoint.getStartTime(), mapPoint.getEndTime(), null);
ArrayList<PamDataUnit> dataCopy = dataBlock.getDataCopy(deployment.getAudioStart(), deployment.getAudioEnd(), true, dataSelector);
// System.out.printf("%d loaded from %s to %s %d kept\n", dataBlock.getUnitsCount(), PamCalendar.formatDateTime(mapPoint.getStartTime()),
// PamCalendar.formatDateTime(mapPoint.getEndTime()), dataCopy.size());
totalLoadedDatas += dataCopy.size();
System.out.printf("%d loaded from %s to %s %d kept\n", dataBlock.getUnitsCount(), PamCalendar.formatDateTime(mapPoint.getStartTime()),
PamCalendar.formatDateTime(mapPoint.getEndTime()), dataCopy.size());
skipCount += dataBlock.getUnitsCount() - dataCopy.size();
for (PamDataUnit dataUnit : dataCopy) {
/*
@ -353,7 +359,9 @@ public class DetectionsHandler {
if (viewerLoadPolicy == ViewerLoadPolicy.LOAD_ALWAYS_EVERYTHING) {
break;
}
if (!activeExport) {
return 0;
}
}
Detection dets[] = granularityHandler.cleanup(deployment.getAudioEnd());
if (dets != null) {
@ -405,10 +413,6 @@ public class DetectionsHandler {
exportObserver.update(prog);
granularityHandler.prepare(deployment.getAudioStart());
if (currentDetections == null) {
currentDetections = startDetectionsDocument(deployment, dataBlock, streamExportParams);
currentDetections.getEffort().setStart(TethysTimeFuncs.xmlGregCalFromMillis(deployment.getAudioStart()));
}
// export everything in that deployment.
// need to loop through all map points in this interval.
List<OfflineDataMapPoint> mapPoints = dataMap.getMapPoints();
@ -417,8 +421,15 @@ public class DetectionsHandler {
prog = new DetectionExportProgress(deployment, currentDetections,
lastUnitTime, totalCount, exportCount, skipCount, DetectionExportProgress.STATE_CANCELED);
exportObserver.update(prog);
break;
}
if (currentDetections == null) {
// needed in inner loop in case doc gets written at 500000.
currentDetections = startDetectionsDocument(deployment, dataBlock, streamExportParams);
currentDetections.getEffort().setStart(TethysTimeFuncs.xmlGregCalFromMillis(deployment.getAudioStart()));
}
if (mapPoint.getEndTime() < deployment.getAudioStart()) {
continue;
}
@ -453,7 +464,7 @@ public class DetectionsHandler {
lastUnitTime, totalCount, exportCount, skipCount, DetectionExportProgress.STATE_GATHERING);
exportObserver.update(prog);
if (documentCount > 500000 && mapPoint != dataMap.getLastMapPoint()) {
if (documentCount > 50000000 && mapPoint != dataMap.getLastMapPoint()) {
prog = new DetectionExportProgress(deployment, currentDetections,
lastUnitTime, totalCount, exportCount, skipCount, DetectionExportProgress.STATE_WRITING);
exportObserver.update(prog);
@ -469,8 +480,14 @@ public class DetectionsHandler {
if (viewerLoadPolicy == ViewerLoadPolicy.LOAD_ALWAYS_EVERYTHING) {
break;
}
if (!activeExport) {
break;
}
}
if (!activeExport) {
return DetectionExportProgress.STATE_CANCELED;
}
if (currentDetections != null) {
Detection dets[] = granularityHandler.cleanup(deployment.getAudioEnd());
@ -552,7 +569,7 @@ public class DetectionsHandler {
supportSoft.setVersion(getSupportSoftwareVersion(dataBlock));
supSoft.add(supportSoft);
detections.setAlgorithm(algorithm);
detections.setUserId("Unknown user");
detections.setUserId("PAMGuard user");
detections.setEffort(getDetectorEffort(deployment, dataBlock, exportParams));
return detections;
@ -599,13 +616,16 @@ public class DetectionsHandler {
protected Integer doInBackground() throws Exception {
Integer ans = null;
try {
int count = countDetections(dataBlock, exportParams, exportObserver);
String msg = String.format("Do you want to go ahead and output %d %s detections to Tethys?",
count, exportParams.granularity);
int doit = WarnOnce.showWarning("Tethys Detections Export", msg, WarnOnce.OK_CANCEL_OPTION);
if (doit == WarnOnce.OK_OPTION) {
// int count = countDetections(dataBlock, exportParams, exportObserver);
// if (activeExport == false) {
// return 0;
// }
// String msg = String.format("Do you want to go ahead and output %d %s detections to Tethys?",
// count, exportParams.granularity);
// int doit = WarnOnce.showWarning("Tethys Detections Export", msg, WarnOnce.OK_CANCEL_OPTION);
// if (doit == WarnOnce.OK_OPTION) {
ans = exportDetections(dataBlock, exportParams, this);
}
// }
}
catch (Exception e) {
e.printStackTrace();
@ -661,4 +681,10 @@ public class DetectionsHandler {
DetectionsExportWizard.showDialog(tethysControl.getGuiFrame(), tethysControl, dataBlock);
}
@Override
public String getHelpPoint() {
return helpPoint;
}
}

17
src/tethys/localization/LocalizationHandler.java Normal file
View File

@ -0,0 +1,17 @@
package tethys.localization;
import nilus.CylindricalCoordinateType;
import nilus.LocalizationType;
import nilus.Localize.Effort.CoordinateReferenceSystem;
public class LocalizationHandler {
public LocalizationType getLoc() {
LocalizationType lt = new LocalizationType();
CylindricalCoordinateType cct = new CylindricalCoordinateType();
// cct.set
CoordinateReferenceSystem cr;
return null;
}
}

4
src/tethys/niluswraps/NilusSettingsWrapper.java
View File

@ -129,7 +129,9 @@ public class NilusSettingsWrapper<T extends Object> implements Serializable, Clo
Document doc = builder.parse(new InputSource(new StringReader(xmlString)));
return doc;
} catch (Exception e) {
e.printStackTrace();
System.out.println(e.getMessage());
System.out.println("Nilus Settings wrapper - Error parsing string\n" + xmlString);
// e.printStackTrace();
}
return null;
}

6
src/tethys/output/StreamExportParams.java
View File

@ -98,7 +98,11 @@ public class StreamExportParams implements Serializable {
* @return
*/
public DescriptionType getNilusDetectionDescription() {
return getDetectionDescription().getDescription();
WrappedDescriptionType desc = getDetectionDescription();
if (desc == null) {
return null;
}
return desc.getDescription();
}
}

18
src/tethys/output/TethysExportParams.java
View File

@ -45,6 +45,8 @@ public class TethysExportParams implements Serializable, Cloneable{
private String datasetName;
public boolean listDocsInPamguard;
private String effortSourceName;
/**
@ -121,6 +123,22 @@ public class TethysExportParams implements Serializable, Cloneable{
return streamParamsMap.get(longDataName);
}
/**
* Source name for type of effort.
* @param sourceName
*/
public void setEffortSourceName(String sourceName) {
this.effortSourceName = sourceName;
}
/**
* Source name for type of effort.
* @return the effortSourceName
*/
public String getEffortSourceName() {
return effortSourceName;
}
}

26
src/tethys/species/DataBlockSpeciesManager.java
View File

@ -97,7 +97,10 @@ abstract public class DataBlockSpeciesManager<T extends PamDataUnit> {
public SpeciesMapItem getSpeciesItem(T dataUnit) {
String speciesString = getSpeciesCode(dataUnit);
if (speciesString == null) {
return getDefaultDefaultSpecies();
SpeciesMapItem def = getDefaultDefaultSpecies();
if (def != null) {
speciesString = def.getPamguardName();
}
}
DataBlockSpeciesMap speciesMap = getDatablockSpeciesMap();
if (speciesMap == null) {
@ -127,7 +130,26 @@ abstract public class DataBlockSpeciesManager<T extends PamDataUnit> {
if (allCodes.size() == 0) {
allCodes.add("Unknown");
}
return allCodes;
return makeUniqueList(allCodes);
}
/**
* Make sure all entries in an array list are unique.
* @param list
* @return updated list.
*/
public ArrayList<String> makeUniqueList(ArrayList<String> list) {
if (list == null) {
return null;
}
ArrayList<String> newList = new ArrayList();
for (String aStr : list) {
if (newList.contains(aStr)) {
continue;
}
newList.add(aStr);
}
return newList;
}
public DataBlockSpeciesMap getDatablockSpeciesMap() {

41
src/tethys/species/ITISFunctions.java
View File

@ -70,7 +70,7 @@ public class ITISFunctions {
// PAMGuardXMLPreview xmlPreview = new PAMGuardXMLPreview(null, "returned", qResult.queryResult)
PamguardXMLWriter pamXMLWriter = PamguardXMLWriter.getXMLWriter();
String fDoc = pamXMLWriter.getAsString(doc, true);
System.out.println(fDoc);
// System.out.println(fDoc);
String tsn = dbQueries.getElementData(docEl, "tsn");
if (tsn == null) {
@ -91,7 +91,46 @@ public class ITISFunctions {
return new TethysITISResult(itisCode, taxunit, latin, vernacular);
}
/**
* Search species codes. If the search term is a valid Integer number
* then it's assumed to be an ITIS code and the function should
* return a single map item. If it's non-integer, it's assumed to
* be a common or latin name search
* @param searchTerm
* @return array list of possible matches.
*/
public ArrayList<SpeciesMapItem> searchSpecies(String searchTerm) {
Integer intVal = null;
try {
intVal = Integer.valueOf(searchTerm);
}
catch (NumberFormatException e) {
intVal = null;
}
if (intVal != null) {
return searchCodes(intVal);
}
else { // assume name search
return searchNames(searchTerm);
}
}
private ArrayList<SpeciesMapItem> searchCodes(Integer intCode) {
ArrayList<SpeciesMapItem> mapItems = new ArrayList();
TethysITISResult result = getITISInformation(intCode);
if (result != null) {
mapItems.add(new SpeciesMapItem(intCode, "", "", result.getLatin(), result.getVernacular()));
}
return mapItems;
}
/**
* Search common and latin names for partial matched of the search term
* and return an array list of all possible matches.
* @param searchTerm
* @return
*/
public ArrayList<SpeciesMapItem> searchNames(String searchTerm) {
ArrayList<SpeciesMapItem> items = new ArrayList<SpeciesMapItem>();
String xQ = "let $target := \"thespeciessearchterm\" \r\n"
+ "return\r\n"

4
src/tethys/species/ITISTypes.java
View File

@ -7,8 +7,8 @@ package tethys.species;
*/
public class ITISTypes {
public static final int OTHER = 0;
public static final int ANTHROPOGENIC = 1;
public static final int OTHER = -10;
public static final int ANTHROPOGENIC = 1758;
public static final String getName(int code) {
switch (code) {

14
src/tethys/species/SpeciesMapItem.java
View File

@ -41,6 +41,14 @@ public class SpeciesMapItem implements Serializable, Cloneable {
*/
private String callType;
/**
*
* @param itisCode
* @param callType
* @param pamguardName
* @param latinName
* @param commonName
*/
public SpeciesMapItem(int itisCode, String callType, String pamguardName, String latinName, String commonName) {
super();
this.itisCode = itisCode;
@ -50,6 +58,12 @@ public class SpeciesMapItem implements Serializable, Cloneable {
this.commonName = commonName;
}
/**
*
* @param itisCode
* @param callType
* @param pamguardName
*/
public SpeciesMapItem(int itisCode, String callType, String pamguardName) {
super();
this.itisCode = itisCode;

11
src/tethys/species/swing/DataBlockSpeciesDialog.java
View File

@ -49,16 +49,7 @@ public class DataBlockSpeciesDialog extends PamDialog {
+ "\"Other Phenomena\" (-10). "
+ "<br>When known, a call or sound type should "
+ "be specified (see help for more information).</html>";
nPanel.add(BorderLayout.CENTER, new JLabel(otherMsg , JLabel.LEFT));
// JPanel nwBit = new JPanel(new FlowLayout());
// JButton exportButton = new JButton("Export");
// exportButton.addActionListener(SpeciesMapManager.getInstance().getExportAction(parentFrame));
// nwBit.add(exportButton);
// JButton importButton = new JButton("Import");
// importButton.addActionListener(SpeciesMapManager.getInstance().getImportAction(parentFrame));
// nwBit.add(importButton);
// nPanel.add(BorderLayout.WEST, nwBit);
nPanel.add(BorderLayout.CENTER, new JLabel(otherMsg , JLabel.LEFT));
mainPanel.add(BorderLayout.NORTH, nPanel);
setDialogComponent(mainPanel);

33
src/tethys/species/swing/SpeciesSearchDialog.java
View File

@ -104,11 +104,11 @@ public class SpeciesSearchDialog extends PamDialog {
setResizable(true);
setDialogComponent(mainPanel);
}
public static SpeciesMapItem showDialog(Window parentFrame, TethysControl tethysControl) {
public static SpeciesMapItem showDialog(Window parentFrame, TethysControl tethysControl, Integer currentCode) {
if (singleInstance == null) {
singleInstance = new SpeciesSearchDialog(parentFrame, tethysControl);
}
singleInstance.setParams();
singleInstance.setParams(currentCode);
singleInstance.setVisible(true);
return singleInstance.selectedItem;
}
@ -131,6 +131,9 @@ public class SpeciesSearchDialog extends PamDialog {
public void setMapItems(ArrayList<SpeciesMapItem> newMapItems) {
this.speciesMapItems = newMapItems;
if (newMapItems != null && newMapItems.size() == 1) {
setSelectedItem(newMapItems.get(0));
}
tableModel.fireTableDataChanged();
}
@ -188,14 +191,20 @@ public class SpeciesSearchDialog extends PamDialog {
}
private void setParams() {
searchText.setText(null);
clearResults();
private void setParams(Integer currentCode) {
if (currentCode == null) {
searchText.setText(null);
clearResults();
}
else {
searchText.setText(currentCode.toString());
searchTethys();
}
}
private void clearResults() {
speciesMapItems = null;
selectedItem = null;
setSelectedItem(null);
}
@Override
public boolean getParams() {
@ -216,6 +225,10 @@ public class SpeciesSearchDialog extends PamDialog {
}
private void enableControls() {
getOkButton().setEnabled(selectedItem != null);
}
private class TableMouse extends MouseAdapter {
@Override
@ -225,12 +238,18 @@ public class SpeciesSearchDialog extends PamDialog {
}
int selectedRow = resultTable.getSelectedRow();
if (selectedRow >= 0 && selectedRow < speciesMapItems.size()) {
selectedItem = speciesMapItems.get(selectedRow);
setSelectedItem(speciesMapItems.get(selectedRow));
}
tableModel.fireTableDataChanged();
}
}
private void setSelectedItem(SpeciesMapItem selItem) {
this.selectedItem = selItem;
enableControls();
}
private class DataModel extends AbstractTableModel {
private String[] colNames = {"Select", "TSN", "Name", "Common Name"};

20
src/tethys/species/swing/SpeciesSubPanel.java
View File

@ -114,12 +114,12 @@ public class SpeciesSubPanel {
}
ITISFunctions itisFunctions = tethysControl.getItisFunctions();
String itisString = this.itisCode.getText();
if (itisString == null || itisString.length() == 0) {
// if (itisString == null || itisString.length() == 0) {
searchForCode(tethysControl, itisFunctions);
}
else {
getCodeInformation(tethysControl, itisFunctions, itisString);
}
// }
// else {
// getCodeInformation(tethysControl, itisFunctions, itisString);
// }
// System.out.println(itisInfo);
}
@ -144,7 +144,15 @@ public class SpeciesSubPanel {
}
private void searchForCode(TethysControl tethysControl, ITISFunctions itisFunctions) {
SpeciesMapItem speciesItem = SpeciesSearchDialog.showDialog(tethysControl.getGuiFrame(), tethysControl);
Integer currentCode = null;
try {
currentCode = Integer.valueOf(itisCode.getText());
}
catch (NumberFormatException e) {
}
SpeciesMapItem speciesItem = SpeciesSearchDialog.showDialog(tethysControl.getGuiFrame(), tethysControl, currentCode);
if (speciesItem != null) {
itisCode.setText(String.format("%d", speciesItem.getItisCode()));
latinName.setText(speciesItem.getLatinName());

30
src/tethys/swing/DatablockDetectionsPanel.java
View File

@ -19,6 +19,8 @@ import javax.swing.table.AbstractTableModel;
import javax.swing.table.JTableHeader;
import javax.xml.datatype.XMLGregorianCalendar;
import PamUtils.worker.PamWorkWrapper;
import PamUtils.worker.PamWorker;
import PamView.PamGui;
import PamView.dialog.warn.WarnOnce;
import PamView.tables.SwingTableColumnWidths;
@ -42,7 +44,7 @@ import tethys.niluswraps.PDetections;
* @author dg50
*
*/
public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTableObserver {
public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTableObserver, PamWorkWrapper<String> {
private JPanel mainPanel;
@ -118,15 +120,37 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
@Override
public void selectDataBlock(PamDataBlock dataBlock) {
if (this.dataBlock == dataBlock) {
return; // stops lots of requerying, which matters when database is large.
}
this.dataBlock = dataBlock;
dataBlockName.setText(dataBlock.getLongDataName());
streamDetectionsSummary = getTethysControl().getDetectionsHandler().getStreamDetections(dataBlock);
if (dataBlock == null) {
dataBlockName.setText("Select data in panel on the left");
}
else {
dataBlockName.setText(dataBlock.getLongDataName());
}
// need to re-thread this to stop user panicing that nothing is happening.
PamWorker w = new PamWorker<String>(this, getTethysControl().getGuiFrame(), 0, "Searching database");
w.start();
}
@Override
public void taskFinished(String result) {
tableModel.fireTableDataChanged();
}
@Override
public String runBackgroundTask(PamWorker<String> pamWorker) {
streamDetectionsSummary = getTethysControl().getDetectionsHandler().getStreamDetections(dataBlock);
return null;
}
@Override
public void updateState(TethysState tethysState) {
if (dataBlock != null) {
PamDataBlock currBlock = dataBlock;
selectDataBlock(null);
selectDataBlock(dataBlock);
}
}

101
src/tethys/swing/DatablockSynchPanel.java
View File

@ -1,6 +1,7 @@
package tethys.swing;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ComponentEvent;
@ -13,6 +14,7 @@ import java.util.ArrayList;
import javax.swing.JButton;
import javax.swing.JComponent;
import javax.swing.JLabel;
import javax.swing.JMenuItem;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
@ -36,9 +38,9 @@ import tethys.niluswraps.PDeployment;
import tethys.output.DatablockSynchInfo;
import tethys.species.DataBlockSpeciesManager;
public class DatablockSynchPanel extends TethysGUIPanel {
public class DatablockSynchPanel extends TethysExportPanel {
public JPanel mainPanel;
// public JPanel mainPanel;
private JTable synchTable;
@ -48,39 +50,46 @@ public class DatablockSynchPanel extends TethysGUIPanel {
private ArrayList<StreamTableObserver> tableObservers = new ArrayList<>();
private JButton exportButton;
// private TippedButton exportButton;
// private JLabel exportWarning;
public DatablockSynchPanel(TethysControl tethysControl) {
super(tethysControl);
mainPanel = new PamPanel(new BorderLayout());
super(tethysControl, tethysControl.getDetectionsHandler(), false);
// mainPanel = new PamPanel(new BorderLayout());
JPanel mainPanel = getMainPanel();
mainPanel.setBorder(new TitledBorder("PAMGuard data blocks"));
synchTableModel = new SynchTableModel();
synchTable = new JTable(synchTableModel);
new SwingTableColumnWidths(tethysControl.getUnitName()+"SynchTable", synchTable);
JScrollPane scrollPane = new JScrollPane(synchTable);
mainPanel.add(BorderLayout.CENTER, scrollPane);
PamPanel ctrlPanel = new PamPanel(new BorderLayout());
exportButton = new JButton("Export ...");
ctrlPanel.add(BorderLayout.WEST, exportButton);
mainPanel.add(BorderLayout.NORTH, ctrlPanel);
// PamPanel ctrlPanel = new PamPanel(new BorderLayout());
// exportButton = new TippedButton("Export ...", "Export Detections document");
// exportWarning = new JLabel(" ");
// exportWarning.setForeground(Color.RED);
// ctrlPanel.add(BorderLayout.WEST, exportButton);
// ctrlPanel.add(BorderLayout.CENTER, exportWarning);
// mainPanel.add(BorderLayout.NORTH, ctrlPanel);
synchTable.addMouseListener(new MouseActions());
synchTable.addKeyListener(new KeyActions());
exportButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
exportData();
}
});
// exportButton.addActionListener(new ActionListener() {
// @Override
// public void actionPerformed(ActionEvent e) {
// exportData();
// }
// });
enableExportButton();
}
@Override
public JComponent getComponent() {
return mainPanel;
}
// @Override
// public JComponent getComponent() {
// return mainPanel;
// }
private class KeyActions extends KeyAdapter {
@Override
@ -141,13 +150,50 @@ public class DatablockSynchPanel extends TethysGUIPanel {
}
private void enableExportButton() {
if (!getTethysControl().isServerOk()) {
disableExport("Tethys Server not running");
return;
}
int[] rows = synchTable.getSelectedRows();
boolean en = rows != null && rows.length == 1;
ArrayList<PDeployment> deployments = getTethysControl().getDeploymentHandler().getMatchedDeployments();
if (deployments == null || deployments.size() == 0) {
en = false;
disableExport("No Deployment document(s). Export Deployments prior to exporting Detections");
return;
}
exportButton.setEnabled(getTethysControl().isServerOk() & en);
boolean en = rows != null && rows.length == 1;
if (!en) {
disableExport("No PAMGuard datablock selected (click a row on the table below)");
return;
}
PamDataBlock dataBlock = dataBlockSynchInfo.get(rows[0]).getDataBlock();
String mapError = checkSpeciesManager(dataBlock);
if (mapError != null) {
disableExport("Unable to export due to species map error: " + mapError + ". Right click table row to edit species list");
return;
}
enableExport(true);
}
// public void disableExport(String reason) {
// if (reason == null) {
// exportButton.setEnabled(true);
// exportWarning.setText(null);
// }
// else {
// exportButton.disable(reason);
// exportWarning.setText(" " + reason);
// }
// }
private String checkSpeciesManager(PamDataBlock dataBlock) {
DataBlockSpeciesManager spManager = dataBlock.getDatablockSpeciesManager();
if (spManager == null) {
return "No species manager";
}
String error = spManager.checkSpeciesMapError();
return error;
}
public void showPopup(MouseEvent e, int row) {
@ -259,4 +305,15 @@ public class DatablockSynchPanel extends TethysGUIPanel {
}
}
@Override
protected void exportButtonPressed(ActionEvent e) {
exportData();
}
@Override
protected void optionsButtonPressed(ActionEvent e) {
// TODO Auto-generated method stub
}
}

5
src/tethys/swing/DeploymentExportPanel.java
View File

@ -34,6 +34,7 @@ import tethys.TethysState;
import tethys.TethysState.StateType;
import tethys.dbxml.DBXMLConnect;
import tethys.deployment.DeploymentHandler;
import tethys.deployment.RecordingList;
import tethys.deployment.RecordingPeriod;
import tethys.niluswraps.PDeployment;
@ -241,7 +242,9 @@ public class DeploymentExportPanel extends TethysGUIPanel implements DeploymentT
if (selectedDeployments == null || selectedDeployments.size() == 0) {
return;
};
getTethysControl().getDeploymentHandler().exportDeployments(selectedDeployments);
// need to turn that list back into a RecordingList object.
RecordingList tempList = new RecordingList("eport list", selectedDeployments);
getTethysControl().getDeploymentHandler().exportDeployments(tempList);
}

112
src/tethys/swing/DeploymentsPanel.java
View File

@ -16,81 +16,38 @@ import javax.swing.border.TitledBorder;
import PamView.panel.PamPanel;
import tethys.TethysControl;
import tethys.TethysState;
import tethys.calibration.CalibrationHandler;
import tethys.deployment.DeploymentHandler;
import tethys.deployment.RecordingList;
import tethys.deployment.RecordingPeriod;
public class DeploymentsPanel extends TethysGUIPanel implements DeploymentTableObserver {
public class DeploymentsPanel extends TethysExportPanel implements DeploymentTableObserver {
private JPanel mainPanel;
// private JPanel mainPanel;
private PAMGuardDeploymentsTable pamDeploymentsTable;
private DeploymentExportPanel exportPanel;
private JButton exportButton, optionsButton;
// private TethysDeploymentsTable tethysDeploymentsTable;
private JLabel exportWarning;
private JLabel effortName;
public DeploymentsPanel(TethysControl tethysControl) {
super(tethysControl);
super(tethysControl, tethysControl.getDeploymentHandler(), true);
DeploymentHandler deploymentHandler = tethysControl.getDeploymentHandler();
pamDeploymentsTable = new PAMGuardDeploymentsTable(tethysControl);
exportPanel = new DeploymentExportPanel(tethysControl, pamDeploymentsTable);
pamDeploymentsTable.addObserver(exportPanel);
// tethysDeploymentsTable = new TethysDeploymentsTable(tethysControl);
mainPanel = new PamPanel(new BorderLayout());
JPanel mainPanel = getMainPanel();
mainPanel.setBorder(new TitledBorder("Recording periods and deployment information"));
pamDeploymentsTable.addObserver(this);
pamDeploymentsTable.addObserver(deploymentHandler);
// JSplitPane splitPane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT);
// splitPane.add(pamDeploymentsTable.getComponent());
// splitPane.add(tethysDeploymentsTable.getComponent());
// mainPanel.add(splitPane,BorderLayout.CENTER);
// SwingUtilities.invokeLater(new Runnable() {
//
// @Override
// public void run() {
// splitPane.setDividerLocation(0.6);
// }
// });
JPanel ctrlPanel = new PamPanel(new BorderLayout());
JPanel ctrlButtons = new JPanel();
ctrlButtons.setLayout(new BoxLayout(ctrlButtons, BoxLayout.X_AXIS));
optionsButton = new JButton("Options ...");
exportButton = new JButton("Export ...");
ctrlButtons.add(optionsButton);
ctrlButtons.add(exportButton);
ctrlPanel.add(BorderLayout.WEST, ctrlButtons);
optionsButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
getTethysControl().getDeploymentHandler().showOptions(null);
}
});
exportButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
exportDeployments();
}
});
exportWarning = new JLabel(" ");
ctrlPanel.add(BorderLayout.CENTER, exportWarning);
mainPanel.add(BorderLayout.CENTER, pamDeploymentsTable.getComponent());
mainPanel.add(BorderLayout.NORTH, ctrlPanel);
// mainPanel.add(BorderLayout.EAST, exportPanel.getComponent());
exportButton.setEnabled(false);
}
protected void exportDeployments() {
getTethysControl().getDeploymentHandler().exportDeployments();
}
@Override
public JComponent getComponent() {
return mainPanel;
effortName = new JLabel(" ");
JPanel centralPanel = new JPanel(new BorderLayout());
centralPanel.add(BorderLayout.NORTH, effortName);
centralPanel.add(BorderLayout.CENTER,pamDeploymentsTable.getComponent());
mainPanel.add(BorderLayout.CENTER, centralPanel);
}
@Override
@ -98,12 +55,21 @@ public class DeploymentsPanel extends TethysGUIPanel implements DeploymentTableO
enableExportButton();
}
private void enableExportButton() {
if (!getTethysControl().isServerOk()) {
disableExport("Tethys server not running");
return;
}
CalibrationHandler calHandler = getTethysControl().getCalibrationHandler();
if (calHandler.haveAllChannelCalibrations() == false) {
disableExport("Calibration data for each channel must be exported before creating Deployment documents");
return;
}
ArrayList<RecordingPeriod> selected = pamDeploymentsTable.getSelectedPeriods();
if (selected == null) {
exportButton.setEnabled(false);
if (selected == null || selected.size() == 0) {
disableExport("You must select one or more deployment periods to export");
return;
}
boolean existing = false;
@ -118,17 +84,35 @@ public class DeploymentsPanel extends TethysGUIPanel implements DeploymentTableO
}
String warning = null;
if (existing) {
warning = " One or more deployment documents already exist. These must be deleted prior to exporting new documents";
exportWarning.setText(warning);
warning = "One or more deployment documents already exist. These must be deleted prior to exporting new documents";
disableExport(warning);
return;
}
exportButton.setEnabled(selected.size()>0 & existing == false && getTethysControl().isServerOk());
enableExport(true);
}
@Override
public void updateState(TethysState tethysState) {
super.updateState(tethysState);
enableExportButton();
RecordingList recordingList = pamDeploymentsTable.getMasterList();
if (recordingList == null) {
effortName.setText(" No available effort data");
}
else {
effortName.setText(" Effort from " + recordingList.getSourceName());
}
}
@Override
protected void exportButtonPressed(ActionEvent e) {
getTethysControl().getDeploymentHandler().exportDeployments();
}
@Override
protected void optionsButtonPressed(ActionEvent e) {
getTethysControl().getDeploymentHandler().showOptions(null);
}

30
src/tethys/swing/FancyClientButton.java
View File

@ -1,12 +1,15 @@
package tethys.swing;
import java.awt.BorderLayout;
import java.awt.Desktop;
import java.awt.FlowLayout;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Insets;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.File;
import java.io.IOException;
import javax.swing.AbstractButton;
import javax.swing.BoxLayout;
@ -30,14 +33,14 @@ import tethys.dbxml.DBXMLConnect;
*/
public class FancyClientButton extends JPanel {
private TethysControl tethysControl;
private JButton clientButton;
private JButton dropButton;
private JPopupMenu collectionsMenu;
private TethysControl tethysControl;
private JCheckBoxMenuItem showBrowser;
private AbstractButton showPAMGuard;
public FancyClientButton(TethysControl tethysControl) {
this.tethysControl = tethysControl;
setLayout(new GridBagLayout());
@ -105,6 +108,16 @@ public class FancyClientButton extends JPanel {
menuItem.addActionListener(new OpenCollection(collections[i]));
collectionsMenu.add(menuItem);
}
collectionsMenu.addSeparator();
JMenuItem tmpItem = new JMenuItem("Open temp folder");
collectionsMenu.add(tmpItem);
tmpItem.setToolTipText("Open folder used for temporary document files during export in Windows Explorer");
tmpItem.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
openTempFolder();
}
});
dropButton.addActionListener(new ActionListener() {
@Override
@ -115,6 +128,19 @@ public class FancyClientButton extends JPanel {
enableItems();
}
protected void openTempFolder() {
File tempFolder = tethysControl.getDbxmlConnect().checkTempFolder();
if (tempFolder == null) {
return;
}
try {
Desktop.getDesktop().open(tempFolder);
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
protected void enableItems() {
boolean isP = tethysControl.getTethysExportParams().listDocsInPamguard;
showBrowser.setSelected(!isP);

27
src/tethys/swing/PAMGuardDeploymentsTable.java
View File

@ -32,6 +32,7 @@ import tethys.TethysState.StateType;
import tethys.dbxml.TethysException;
import tethys.deployment.DeploymentHandler;
import tethys.deployment.DeploymentOverview;
import tethys.deployment.RecordingList;
import tethys.deployment.RecordingPeriod;
import tethys.niluswraps.PDeployment;
@ -55,6 +56,8 @@ public class PAMGuardDeploymentsTable extends TethysGUIPanel {
private ArrayList<DeploymentTableObserver> observers = new ArrayList<>();
private RecordingList masterList;
public PAMGuardDeploymentsTable(TethysControl tethysControl) {
super(tethysControl);
// deploymentHandler = new DeploymentHandler(getTethysControl());
@ -74,6 +77,10 @@ public class PAMGuardDeploymentsTable extends TethysGUIPanel {
public JComponent getComponent() {
return mainPanel;
}
public RecordingList getMasterList() {
return masterList;
}
private class TableMouse extends MouseAdapter {
@ -95,7 +102,7 @@ public class PAMGuardDeploymentsTable extends TethysGUIPanel {
public void mouseClicked(MouseEvent e) {
int aRow = table.getSelectedRow();
int col = table.getSelectedColumn();
ArrayList<RecordingPeriod> periods = deploymentOverview.getRecordingPeriods();
ArrayList<RecordingPeriod> periods = getMasterList().getEffortPeriods();
if (aRow >= 0 && aRow < periods.size() && col == TableModel.SELECTCOLUMN) {
periods.get(aRow).toggleSelected();
notifyObservers();
@ -118,7 +125,8 @@ public class PAMGuardDeploymentsTable extends TethysGUIPanel {
}
// make a list of RecordingPeriods which don't currently have a Deployment document
ArrayList<RecordingPeriod> newPeriods = new ArrayList<>();
ArrayList<RecordingPeriod> allPeriods = deploymentOverview.getRecordingPeriods();
ArrayList<RecordingPeriod> allPeriods = getMasterList().getEffortPeriods();
// ArrayList<RecordingPeriod> allPeriods = deploymentOverview.getRecordingPeriods();
ArrayList<PDeployment> matchedDeployments = new ArrayList<>();
for (int i = 0; i < selRows.length; i++) {
PDeployment tethysDeployment = allPeriods.get(selRows[i]).getMatchedTethysDeployment();
@ -200,7 +208,8 @@ public class PAMGuardDeploymentsTable extends TethysGUIPanel {
}
protected void selectAll(boolean select) {
ArrayList<RecordingPeriod> recordingPeriods = deploymentOverview.getRecordingPeriods();
ArrayList<RecordingPeriod> recordingPeriods = getMasterList().getEffortPeriods();
// ArrayList<RecordingPeriod> recordingPeriods = deploymentOverview.getRecordingPeriods();
for (int i = 0; i < recordingPeriods.size(); i++) {
recordingPeriods.get(i).setSelected(select);
}
@ -329,7 +338,7 @@ public class PAMGuardDeploymentsTable extends TethysGUIPanel {
if (deploymentOverview == null) {
return null;
}
ArrayList<RecordingPeriod> allPeriods = deploymentOverview.getRecordingPeriods();
ArrayList<RecordingPeriod> allPeriods = getMasterList().getEffortPeriods();
ArrayList<RecordingPeriod> selPeriods = new ArrayList();
int n = allPeriods.size();
for (int i = 0; i < n; i++) {
@ -348,6 +357,7 @@ public class PAMGuardDeploymentsTable extends TethysGUIPanel {
private void updateDeployments() {
DeploymentHandler deploymentHandler = getTethysControl().getDeploymentHandler();
deploymentOverview = deploymentHandler.getDeploymentOverview();
masterList = deploymentOverview.getMasterList(getTethysControl());
if (deploymentOverview == null) {
return;
}
@ -373,7 +383,7 @@ public class PAMGuardDeploymentsTable extends TethysGUIPanel {
return 0;
}
else {
return deploymentOverview.getRecordingPeriods().size();
return getMasterList().size();
}
}
@ -398,13 +408,14 @@ public class PAMGuardDeploymentsTable extends TethysGUIPanel {
@Override
public Object getValueAt(int rowIndex, int columnIndex) {
RecordingPeriod period = deploymentOverview.getRecordingPeriods().get(rowIndex);
RecordingList masterList = getMasterList();
RecordingPeriod period = masterList.getEffortPeriods().get(rowIndex);
// DeploymentRecoveryPair deplInfo = deploymentInfo.get(rowIndex);
if (columnIndex == 6) {
return deploymentOverview.getDutyCycleInfo();
return masterList.assessDutyCycle();
}
if (columnIndex == 4 && rowIndex > 0) {
RecordingPeriod prevPeriod = deploymentOverview.getRecordingPeriods().get(rowIndex-1);
RecordingPeriod prevPeriod = masterList.getEffortPeriods().get(rowIndex-1);
long gap = period.getRecordStart() - prevPeriod.getRecordStop();
return PamCalendar.formatDuration(gap);
}

11
src/tethys/swing/TethysConnectionPanel.java
View File

@ -277,12 +277,17 @@ public class TethysConnectionPanel extends TethysGUIPanel {
@Override
public void updateState(TethysState tethysState) {
super.updateState(tethysState);
if (tethysState.stateType == StateType.UPDATESERVER) {
switch (tethysState.stateType) {
case UPDATESERVER:
fillServerControl();
updateProjectList();
}
if (tethysState.stateType == StateType.NEWPROJECTSELECTION) {
break;
case NEWPROJECTSELECTION:
updateProjectList();
break;
case UPDATEMETADATA:
updateInstrumentsList();
break;
}
}

9
src/tethys/swing/TethysDeploymentsTable.java
View File

@ -21,6 +21,7 @@ import tethys.TethysControl;
import tethys.TethysMenuActions;
import tethys.TethysState;
import tethys.deployment.DeploymentOverview;
import tethys.deployment.RecordingList;
import tethys.niluswraps.PDeployment;
public class TethysDeploymentsTable extends TethysGUIPanel {
@ -121,8 +122,7 @@ public class TethysDeploymentsTable extends TethysGUIPanel {
@Override
public String getColumnName(int column) {
return columnNames[column];
}
}
public String getMatchText(PDeployment deployment) {
// TODO Auto-generated method stub
@ -132,8 +132,9 @@ public class TethysDeploymentsTable extends TethysGUIPanel {
if (deploymentOverview == null) {
return "No PAMGuard data";
}
Long depStart = deploymentOverview.getFirstStart();
Long depEnd = deploymentOverview.getLastEnd();
RecordingList masterList = deploymentOverview.getMasterList(getTethysControl());
Long depStart = masterList.getStart();
Long depEnd = masterList.getEnd();
if (depStart == null) {
return "No PAMGuard recordings";
}

227
src/tethys/swing/TethysExportPanel.java Normal file
View File

@ -0,0 +1,227 @@
package tethys.swing;
import java.awt.BorderLayout;
import java.awt.FlowLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.swing.BoxLayout;
import javax.swing.JButton;
import javax.swing.JComponent;
import javax.swing.JLabel;
import javax.swing.JPanel;
import PamView.dialog.NorthPanel;
import PamView.dialog.SettingsButton;
import PamView.help.PamHelp;
import tethys.Collection;
import tethys.CollectionHandler;
import tethys.TethysControl;
/**
* Common panel used by Calibrations, Deployments and Detections to show an export button and other
* common components, such as help, a table, etc..
* @author dg50
*
*/
abstract public class TethysExportPanel extends TethysGUIPanel {
private TippedButton exportButton;
private JButton optionsButton, helpButton;
private JPanel mainPanel, northPanel;
private JLabel message;
private CollectionHandler collectionHandler;
private String helpPoint;
private boolean showOptions;
public TethysExportPanel(TethysControl tethysControl, CollectionHandler collectionHandler, boolean showOptions) {
super(tethysControl);
this.collectionHandler = collectionHandler;
this.showOptions = showOptions;
this.helpPoint = collectionHandler.getHelpPoint();
mainPanel = new JPanel(new BorderLayout());
northPanel = new JPanel(new BorderLayout());
JPanel nwPanel = new JPanel();
nwPanel.setLayout(new BoxLayout(nwPanel, BoxLayout.X_AXIS));
JPanel nePanel = new JPanel();
nePanel.setLayout(new BoxLayout(nePanel, BoxLayout.X_AXIS));
northPanel.add(BorderLayout.CENTER, nwPanel);
northPanel.add(BorderLayout.EAST, nePanel);
mainPanel.add(BorderLayout.NORTH, northPanel);
optionsButton = new SettingsButton();
exportButton = new TippedButton("Export ...", "Export " + collectionHandler.collectionName() + " to Tethys");
helpButton = new JButton("?");
helpButton.setToolTipText("Show context sensitive help");
JLabel space = new JLabel(" ");
message = new JLabel (" ");
nwPanel.add(optionsButton);
nwPanel.add(exportButton);
nwPanel.add(space);
nwPanel.add(message);
nePanel.add(helpButton);
showAndHide();
optionsButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
optionsButtonPressed(e);
}
});
exportButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
exportButtonPressed(e);
}
});
helpButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
helpButtonPressed(e);
}
});
}
/**
* Show the help.
* @param e
*/
protected void helpButtonPressed(ActionEvent e) {
if (helpPoint == null) {
return;
}
PamHelp.getInstance().displayContextSensitiveHelp(helpPoint);
}
/**
* Export button has been pressed.
* @param e
*/
protected abstract void exportButtonPressed(ActionEvent e);
/**
* Options button has been pressed.
* @param e
*/
protected abstract void optionsButtonPressed(ActionEvent e);
private void showAndHide() {
optionsButton.setVisible(showOptions);
helpButton.setVisible(helpPoint != null);
}
@Override
public JComponent getComponent() {
return mainPanel;
}
/**
* @return the helpPoint
*/
public String getHelpPoint() {
return helpPoint;
}
/**
* @param helpPoint the helpPoint to set
*/
public void setHelpPoint(String helpPoint) {
this.helpPoint = helpPoint;
showAndHide();
}
/**
* @return the showOptions
*/
public boolean isShowOptions() {
return showOptions;
}
/**
* @param showOptions the showOptions to set
*/
public void setShowOptions(boolean showOptions) {
this.showOptions = showOptions;
showAndHide();
}
/**
* @return the exportButton
*/
public TippedButton getExportButton() {
return exportButton;
}
/**
* @return the optionsButton
*/
public JButton getOptionsButton() {
return optionsButton;
}
/**
* @return the helpButton
*/
public JButton getHelpButton() {
return helpButton;
}
/**
* @return the mainPanel
*/
public JPanel getMainPanel() {
return mainPanel;
}
/**
* @return the northPanel
*/
public JPanel getNorthPanel() {
return northPanel;
}
/**
* @return the message
*/
public JLabel getMessage() {
return message;
}
/**
* @return the collectionHandler
*/
public CollectionHandler getCollectionHandler() {
return collectionHandler;
}
/**
* Enable or disable export button, leaving tool tips alone
* @param enable
*/
public void enableExport(boolean enable) {
exportButton.setEnabled(enable);
if (enable) {
message.setText(null);
}
}
/**
* Disable the export button and set the tooltip.
* @param disabledTip
*/
public void disableExport(String disabledTip) {
exportButton.disable(disabledTip);
message.setText(disabledTip);
}
}

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src/tethys/swing/TippedButton.java Normal file
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@ -0,0 +1,77 @@
package tethys.swing;
import javax.swing.JButton;
public class TippedButton extends JButton {
private static final long serialVersionUID = 1L;
private String enabledTip;
private String disabledTip;
/**
* Create a button with standard tips which will be used for enabled state
* @param text
* @param enabledTip
*/
public TippedButton(String text, String enabledTip) {
this(text, enabledTip, null);
}
/**
* Create a button with standard tips which will be used for enabled and disabled state
* @param text
* @param enabledTip
* @param disabledTip
*/
public TippedButton(String text, String enabledTip, String disabledTip) {
super(text);
this.enabledTip = enabledTip;
this.disabledTip = disabledTip;
setToolTipText(enabledTip);
}
@Override
public void setEnabled(boolean enable) {
super.setEnabled(enable);
setToolTipText(enable ? enabledTip : disabledTip);
}
/*
* Call to disable the button and at the same time
* set a tooltip giving the reason.
*/
public void disable(String newTip) {
disabledTip = newTip;
setEnabled(false);
}
/**
* @return the enabledTip
*/
public String getEnabledTip() {
return enabledTip;
}
/**
* @param enabledTip the enabledTip to set
*/
public void setEnabledTip(String enabledTip) {
this.enabledTip = enabledTip;
}
/**
* @return the disabledTip
*/
public String getDisabledTip() {
return disabledTip;
}
/**
* @param disabledTip the disabledTip to set
*/
public void setDisabledTip(String disabledTip) {
this.disabledTip = disabledTip;
}
}