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Merge branch 'Tethys' of C:\Users\dg50\source\repos\PAMGuardTethys into

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Tethys
This commit is contained in:
Douglas Gillespie 2023-12-14 12:14:44 +00:00
commit 9a0005861c
81 changed files with 2547 additions and 149 deletions
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7
.classpath
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@ -6,7 +6,7 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/jre">
<attributes>
<attribute name="module" value="true"/>
<attribute name="maven.pomderived" value="true"/>
@ -17,5 +17,10 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="lib" path="C:/Users/dg50/Tethys/NilusXMLGenerator/target/nilus-1.5.jar">
<attributes>
<attribute name="javadoc_location" value="jar:file:/C:/Users/dg50/Tethys/NilusXMLGenerator/target/nilus-1.5-javadoc.jar!/"/>
</attributes>
</classpathentry>
<classpathentry kind="output" path="target/classes"/>
</classpath>

23
pom.xml
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@ -555,8 +555,29 @@
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<version>2.3.2</version>
</dependency>-->
<!-- From NilusXMLGenerator POM at https://bitbucket.org/tethysacousticmetadata/nilusxmlgenerator/src/master/-->
<dependency>
<groupId>org.eclipse.persistence</groupId>
<artifactId>org.eclipse.persistence.moxy</artifactId>
<version>2.5.0</version>
</dependency>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>2.4.0-b180830.0359</version>
</dependency>
-->
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
<version>2.4.0-b180830.0438</version>
</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-xjc</artifactId>
<version>2.4.0-b180830.0438</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.jflac/jflac-codec -->
<dependency>

2
src/Acquisition/FolderInputSystem.java
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@ -697,7 +697,7 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings, D
if (currentFile > 0 && currentFile >= allFiles.size()) {
fileListComplete();
}
// System.out.println("FolderinputSytem: daqHasEnded");
System.out.println("FolderinputSytem: daqHasEnded");
}
private void setFolderProgress() {

3
src/GPS/GpsLogger.java
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@ -295,7 +295,8 @@ public class GpsLogger extends SQLLogging {
* time from the UTC column which is NOT the GpsData time which was the real GPS time.
*/
int gpsIntTimeVal = gpsTime.getIntegerValue();
Object ts = getTableDefinition().getTimeStampItem().getValue();
PamTableDefinition pamTableDef = (PamTableDefinition) getTableDefinition();
Object ts = pamTableDef.getTimeStampItem().getValue();
long gpsDate = sqlTypes.millisFromTimeStamp(ts);
if (gpsDate%1000 == 0) {
// some databases may have stored the milliseconds, in which

5
src/IshmaelDetector/IshLogger.java
View File

@ -8,14 +8,13 @@ import java.sql.Types;
import PamguardMVC.PamDataBlock;
import PamguardMVC.PamDataUnit;
import generalDatabase.EmptyTableDefinition;
//import pamDatabase.SQLLogging;
//import PamguardMVC.RecyclingDataBlock;
import generalDatabase.PamDetectionLogging;
public class IshLogger extends PamDetectionLogging {
IshDetControl ishDetControl;
PamTableDefinition tableDefinition;
PamTableItem systemDate, durationSecs, secSinceStart, peakHeight;
// Peak is more important than start time for matched filter & spectrogram correlation
PamTableItem peakSample, peakDelaySecs;
@ -25,7 +24,7 @@ public class IshLogger extends PamDetectionLogging {
super(pamDataBlock, UPDATE_POLICY_WRITENEW);
this.ishDetControl = ishDetControl;
tableDefinition = getTableDefinition();
EmptyTableDefinition tableDefinition = getTableDefinition();
// PamTableItem tableItem;
// setUpdatePolicy(UPDATE_POLICY_WRITENEW);

5
src/IshmaelLocator/IshLocSqlLogging.java
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@ -14,14 +14,13 @@ import IshmaelDetector.IshDetection;
import PamUtils.LatLong;
import PamguardMVC.PamDataBlock;
import PamguardMVC.PamDataUnit;
import generalDatabase.EmptyTableDefinition;
//import pamDatabase.SQLLogging;
//import PamguardMVC.RecyclingDataBlock;
import generalDatabase.PamDetectionLogging;
public class IshLocSqlLogging extends PamDetectionLogging {
IshLocControl ishLocControl;
PamTableDefinition tableDefinition;
PamTableItem systemDate, durationSecs, secSinceStart, peakHeight;
private PamTableItem latitude, longitude, refLatitude, refLongitude, x, y, z;
@ -30,7 +29,7 @@ public class IshLocSqlLogging extends PamDetectionLogging {
super(pamDataBlock, UPDATE_POLICY_WRITENEW);
this.ishLocControl = ishDetControl;
tableDefinition = getTableDefinition();
EmptyTableDefinition tableDefinition = getTableDefinition();
tableDefinition.addTableItem(latitude = new PamTableItem("Latitude", Types.DOUBLE));
tableDefinition.addTableItem(longitude = new PamTableItem("Longitude", Types.DOUBLE));
tableDefinition.addTableItem(refLatitude = new PamTableItem("ReferenceLatitude", Types.DOUBLE));

10
src/Map/GebcoMapFile.java
View File

@ -85,7 +85,15 @@ public class GebcoMapFile implements MapFileManager {
* @see Map.MapFile#readFileData(java.io.File)
*/
public boolean readFileData(File file) {
return readMapFile(file, true);
try {
return readMapFile(file, true);
}
catch (Exception e) {
// trap error someone reported at end November 22. Suspect it was their corrupt map file causing problems.
String err = String.format("Map file %s is missing or corrupt and cannot be loaded", file.getName());
WarnOnce.showWarning("Map File Error", err, WarnOnce.OK_OPTION);
return false;
}
}
private boolean readMapFile(File gebcoFile, boolean readContours) {

25
src/PamController/PamController.java
View File

@ -1155,6 +1155,8 @@ public class PamController implements PamControllerInterface, PamSettings {
}
if (saveSettings) {
startTime = PamCalendar.getSessionStartTime();
// System.out.printf("Saving settings for start time %s\n", PamCalendar.formatDBDateTime(startTime));
saveSettings(PamCalendar.getSessionStartTime());
}
@ -1313,6 +1315,9 @@ public class PamController implements PamControllerInterface, PamSettings {
}
guiFrameManager.pamEnded();
long stopTime = PamCalendar.getTimeInMillis();
saveEndSettings(stopTime);
// no good having this here since it get's called at the end of every file.
// if (GlobalArguments.getParam(PamController.AUTOEXIT) != null) {
//// can exit here, since we've auto started, can auto exit.
@ -1431,6 +1436,26 @@ public class PamController implements PamControllerInterface, PamSettings {
pamConfiguration.saveSettings(timeNow);
}
/**
* Gets called in pamStart and may / will attempt to store all
* PAMGUARD settings via the database and binary storage modules.
*/
private void saveEndSettings(long timeNow) {
// System.out.printf("Updating settings with end time %s\n", PamCalendar.formatDBDateTime(timeNow));
ArrayList<PamControlledUnit> pamControlledUnits = pamConfiguration.getPamControlledUnits();
PamControlledUnit pcu;
PamSettingsSource settingsSource;
for (int iU = 0; iU < pamControlledUnits.size(); iU++) {
pcu = pamControlledUnits.get(iU);
if (PamSettingsSource.class.isAssignableFrom(pcu.getClass())) {
settingsSource = (PamSettingsSource) pcu;
settingsSource.saveEndSettings(timeNow);
}
}
}
/**
* Export configuration into an XML file
* @param parentFrame

8
src/PamController/PamSettingsSource.java
View File

@ -20,6 +20,14 @@ public interface PamSettingsSource {
*/
public boolean saveStartSettings(long timeNow);
/**
* Save settings when processing ends.
* This may just be an update of the settings saves with saveStartSettings, e.g. an end time.
* @param timeNow
* @return true if saved correctly.
*/
public boolean saveEndSettings(long timeNow);
/**
* Get the number of different settings
* within the settings source.

35
src/PamController/settings/output/xml/PamguardXMLWriter.java
View File

@ -371,6 +371,32 @@ public class PamguardXMLWriter implements PamSettings {
* @return xml content as a a string.
*/
public String getAsString(Document doc) {
return getAsString(doc, true);
// try {
// DOMSource domSource = new DOMSource(doc);
// StringWriter writer = new StringWriter();
// StreamResult result = new StreamResult(writer);
// TransformerFactory tf = TransformerFactory.newInstance();
// Transformer transformer = tf.newTransformer();
// transformer.setOutputProperty(OutputKeys.METHOD, "xml");
// transformer.setOutputProperty(OutputKeys.ENCODING, "ISO-8859-1");
//// transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
// transformer.setOutputProperty(OutputKeys.INDENT, "yes");
// transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "4");
// transformer.transform(domSource, result);
// return writer.toString();
// } catch (TransformerException e) {
// e.printStackTrace();
// return null;
// }
}
/**
* Get the xml document as a String.
* @param doc xml document
* @param indent Indent / format the document.
* @return xml content as a a string.
*/
public String getAsString(Document doc, boolean indent) {
try {
DOMSource domSource = new DOMSource(doc);
StringWriter writer = new StringWriter();
@ -380,7 +406,7 @@ public class PamguardXMLWriter implements PamSettings {
transformer.setOutputProperty(OutputKeys.METHOD, "xml");
transformer.setOutputProperty(OutputKeys.ENCODING, "ISO-8859-1");
// transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
transformer.setOutputProperty(OutputKeys.INDENT, indent ? "yes" : "no");
transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "4");
transformer.transform(domSource, result);
return writer.toString();
@ -765,9 +791,10 @@ public class PamguardXMLWriter implements PamSettings {
processData.setAttribute("Name", process.getProcessName());
PamDataBlock source = process.getParentDataBlock();
if (source != null) {
Element inputEl = doc.createElement("Input");
inputEl.setAttribute("Name", source.getLongDataName());
inputEl.setAttribute("Channels", String.format("0x%X", source.getChannelMap()));
Element inputEl = source.getDataBlockXML(doc);
// Element inputEl = doc.createElement("Input");
// inputEl.setAttribute("Name", source.getLongDataName());
// inputEl.setAttribute("Channels", String.format("0x%X", source.getChannelMap()));
processData.appendChild(inputEl);
}
int nOut = process.getNumOutputDataBlocks();

15
src/PamModel/PamModel.java
View File

@ -44,9 +44,11 @@ import whistlesAndMoans.AbstractWhistleDataUnit;
import fftManager.FFTDataUnit;
import fftManager.PamFFTControl;
import group3dlocaliser.Group3DLocaliserControl;
import metadata.MetaDataContol;
import meygenturbine.MeygenTurbine;
import printscreen.PrintScreenControl;
import rockBlock.RockBlockControl;
import tethys.TethysControl;
import turbineops.TurbineOperationControl;
import GPS.GpsDataUnit;
import NMEA.NMEADataUnit;
@ -454,6 +456,19 @@ final public class PamModel implements PamSettings {
mi.setToolTipText("Manage automated data backups");
mi.setModulesMenuGroup(utilitiesGroup);
mi.setMaxNumber(1);
mi = PamModuleInfo.registerControlledUnit(MetaDataContol.class.getName(), MetaDataContol.unitType);
mi.setToolTipText("Deployment Meta Data");
mi.setModulesMenuGroup(utilitiesGroup);
mi.setMaxNumber(1);
if (isViewer) {
mi = PamModuleInfo.registerControlledUnit(TethysControl.class.getName(), TethysControl.defaultName);
mi.setToolTipText("Interface to Tethys Database");
mi.setModulesMenuGroup(utilitiesGroup);
mi.setMaxNumber(1);
}
/*
* ************* End Utilities Group *******************

52
src/PamModel/parametermanager/PamParameterData.java
View File

@ -34,6 +34,11 @@ abstract public class PamParameterData {
*/
private String postTitle;
/**
* field length for automatic dialogs.
*/
private int fieldLength;
/**
* @param parentObject
@ -45,6 +50,21 @@ abstract public class PamParameterData {
this.field = field;
}
/**
* @param parentObject
* @param field
* @param shortName
* @param toolTip
* @param fieldLength length of text in automatic dialogs.
*/
public PamParameterData(Object parentObject, Field field, String shortName, String toolTip, int fieldLength) {
super();
this.field = field;
this.shortName = shortName;
this.toolTip = toolTip;
this.fieldLength = fieldLength;
}
/**
* @param parentObject
* @param field
@ -58,7 +78,6 @@ abstract public class PamParameterData {
this.toolTip = toolTip;
}
/**
* @param shortName the shortName to set
*/
@ -66,6 +85,20 @@ abstract public class PamParameterData {
this.shortName = shortName;
}
/**
* Set info about a parameter
* @param shortName short name, e.g. to use in a dialog
* @param postTitle post title, e.g. text coming after a data entry field in a dialog
* @param toolTip tool tip to display over the component in a dialog.
* @param fieldLength length of text in automatic dialogs.
*/
public void setInfo(String shortName, String postTitle, String toolTip, int fieldLength) {
this.shortName = shortName;
this.postTitle = postTitle;
this.toolTip = toolTip;
this.fieldLength = fieldLength;
}
/**
* Set info about a parameter
* @param shortName short name, e.g. to use in a dialog
@ -136,6 +169,9 @@ abstract public class PamParameterData {
* @return a short name for the field, suitable for use in dialogs.
*/
public String getShortName() {
if (shortName == null) {
return getFieldName();
}
return shortName;
}
@ -166,5 +202,19 @@ abstract public class PamParameterData {
return String.format("Param %s class %s", getFieldName(), getDataClass());
}
/**
* @return the fieldLength
*/
public int getFieldLength() {
return fieldLength;
}
/**
* @param fieldLength the fieldLength to set
*/
public void setFieldLength(int fieldLength) {
this.fieldLength = fieldLength;
}
}

7
src/PamModel/parametermanager/PamParameterDataGetter.java
View File

@ -59,9 +59,12 @@ public class PamParameterDataGetter extends PrivatePamParameterData {
if (setter == null) {
return false;
}
// need to convert the type
Object convObj = convertStringType(data);
try {
setter.invoke(getParentObject(), data);
} catch (IllegalAccessException | IllegalArgumentException | InvocationTargetException e) {
Object parentObj = getParentObject();
setter.invoke(parentObj, convObj);
} catch (InvocationTargetException e) {
e.printStackTrace();
return false;
}

1
src/PamModel/parametermanager/PamParameterSet.java
View File

@ -286,4 +286,5 @@ public class PamParameterSet {
public PamParameterData removeParameterData(String paramName) {
return parameterDatas.remove(paramName);
}
}

73
src/PamModel/parametermanager/ParameterSetManager.java Normal file
View File

@ -0,0 +1,73 @@
package PamModel.parametermanager;
import java.awt.Window;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.swing.JMenuItem;
import PamModel.parametermanager.swing.ManagedParameterDialog;
import generalDatabase.parameterstore.ParameterDatabaseStore;
/**
* Just about everything giving overall control of some managed parameters.
* May be a bit too specific on first cut and need to be abstracted.
* Testing on 'Deployment' data.
* @author dg50
*
* @param <T>
*/
public class ParameterSetManager<T extends ManagedParameters> {
private T managedParams;
private String name;
public ParameterSetManager(T defaultParams, String name) {
setManagedParams(defaultParams);
this.name = name;
// if (managedParams == null) {
// managedParams = new T();
// }
}
/**
* @return the managedParams
*/
public T getManagedParams() {
return managedParams;
}
/**
* @param managedParams the managedParams to set
*/
public void setManagedParams(T managedParams) {
this.managedParams = managedParams;
}
public JMenuItem getMenuItem(Window parent) {
if (managedParams == null) {
return null;
}
JMenuItem menuItem = new JMenuItem(name + " ...");
menuItem.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
showDialog(parent);
}
});
return menuItem;
}
protected void showDialog(Window parent) {
ManagedParameterDialog<T> dialog = new ManagedParameterDialog<T>(parent, name, managedParams);
T newParams = dialog.showDialog(parent, name, managedParams);
if (newParams != null) {
ParameterDatabaseStore paramDatabase = new ParameterDatabaseStore("MetaData");
paramDatabase.saveParameterSet(newParams);
}
}
}

42
src/PamModel/parametermanager/PrivatePamParameterData.java
View File

@ -1,6 +1,7 @@
package PamModel.parametermanager;
import java.lang.reflect.Field;
import java.lang.reflect.Type;
/**
* Abstract instance of PamParameterDataInterface which implements everything
@ -36,9 +37,48 @@ public abstract class PrivatePamParameterData extends PamParameterData {
* This should really be implemented in every concrete class, but no time to do that now. Aim to delete
* this function here, then go through and implement everywhere ...
*/
return false;
// return false;
Object convData = convertStringType(data);
getField().set(this, convData);
return true;
}
/**
* convert a string type to a different type appropriate for the field in
* question.
* @param value
* @return
*/
public Object convertStringType(Object value) {
if (value == null) {
return null;
}
if (value instanceof String == false) {
return value;
}
String str = (String) value;
Type type = getField().getGenericType();
Class<?> cls = getField().getType();
String clsName = cls.getName();
switch (clsName) {
case "int":
case "Integer":
return Integer.valueOf(str);
case "double":
case "Double":
return Double.valueOf(str);
case "float":
case "Float":
return Float.valueOf(str);
case "short":
case "Short":
return Short.valueOf(str);
}
return value;
}
}

49
src/PamModel/parametermanager/swing/ManagedParameterDialog.java Normal file
View File

@ -0,0 +1,49 @@
package PamModel.parametermanager.swing;
import java.awt.Window;
import PamModel.parametermanager.ManagedParameters;
import PamView.dialog.PamDialog;
public class ManagedParameterDialog<T extends ManagedParameters> extends PamDialog {
private T params;
private ManagedParameterPanel<T> parameterPanel;
public ManagedParameterDialog(Window parentFrame, String title, T params) {
super(parentFrame, title, false);
parameterPanel = new ManagedParameterPanel<T>(params);
setDialogComponent(parameterPanel.getPanel());
}
public T showDialog(Window parentFrame, String title, T parameters) {
// ManagedParameterDialog dialog = new ManagedParameterDialog<>(parentFrame, title, parameters);
setParams(parameters);
setVisible(true);
return params;
}
private void setParams(T params) {
this.params = params;
this.parameterPanel.setParams(params);
}
@Override
public boolean getParams() {
return parameterPanel.getParams(params);
}
@Override
public void cancelButtonPressed() {
params = null;
}
@Override
public void restoreDefaultSettings() {
// TODO Auto-generated method stub
}
}

149
src/PamModel/parametermanager/swing/ManagedParameterPanel.java Normal file
View File

@ -0,0 +1,149 @@
package PamModel.parametermanager.swing;
import java.awt.Color;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.util.Collection;
import javax.swing.BorderFactory;
import javax.swing.JComponent;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JTextArea;
import javax.swing.JTextField;
import javax.swing.text.JTextComponent;
import PamModel.parametermanager.FieldNotFoundException;
import PamModel.parametermanager.ManagedParameters;
import PamModel.parametermanager.PamParameterData;
import PamModel.parametermanager.PamParameterSet;
import PamView.dialog.PamDialog;
import PamView.dialog.PamGridBagContraints;
public class ManagedParameterPanel<T extends ManagedParameters> {
private JPanel mainPanel;
private Collection<PamParameterData> parameterSet;
private static final int DEFAULT_TEXT_LENGTH = 6;
private static final int MAX_SINGLE_LINE_LENGTH = 40;
private JTextComponent[] textComponents;
public ManagedParameterPanel(T parameterExample) {
mainPanel = new JPanel(new GridBagLayout());
GridBagConstraints c = new PamGridBagContraints();
PamParameterSet exampleSet = parameterExample.getParameterSet();
parameterSet = exampleSet.getParameterCollection();
int n = parameterSet.size();
textComponents = new JTextComponent[n];
int i = 0;
for (PamParameterData paramData : parameterSet) {
textComponents[i] = createComponent(paramData);
c.gridx = 0;
c.fill = GridBagConstraints.NONE;
c.anchor = GridBagConstraints.NORTHEAST;
mainPanel.add(new JLabel(paramData.getShortName(), JLabel.RIGHT), c);
c.gridx++;
if (textComponents[i] instanceof JTextArea) {
c.fill = GridBagConstraints.HORIZONTAL;
}
else {
c.fill = GridBagConstraints.NONE;
}
c.anchor = GridBagConstraints.WEST;
mainPanel.add(textComponents[i], c);
textComponents[i].setToolTipText(getTipText(paramData));
c.gridy++;
i++;
}
}
private String getTipText(PamParameterData paramData) {
String tip = paramData.getToolTip();
if (tip != null) {
return tip;
}
else {
return paramData.getFieldName();
}
}
private JTextComponent createComponent(PamParameterData paramData) {
int textLen = paramData.getFieldLength();
if (textLen == 0) {
textLen = DEFAULT_TEXT_LENGTH;
}
if (textLen <= MAX_SINGLE_LINE_LENGTH) {
return new JTextField(textLen);
}
else {
JTextField dummyField = new JTextField(2);
// dummyField.getBorder().
JTextArea textArea = new JTextArea(textLen/MAX_SINGLE_LINE_LENGTH+1, MAX_SINGLE_LINE_LENGTH);
textArea.setBorder(BorderFactory.createLineBorder(Color.LIGHT_GRAY));
return textArea;
}
}
public JComponent getPanel() {
return mainPanel;
}
public void setParams(T params) {
int i = 0;
PamParameterData newParamData = null;
Object data = null;
for (PamParameterData paramData : this.parameterSet) {
// find the parameter in the new parameters (parameterSet is just a formatting placeholder)
try {
newParamData = params.getParameterSet().findParameterData(paramData.getFieldName());
} catch (FieldNotFoundException e) {
e.printStackTrace();
}
try {
data = newParamData.getData();
} catch (IllegalArgumentException e) {
e.printStackTrace();
} catch (IllegalAccessException e) {
e.printStackTrace();
}
if (data != null) {
textComponents[i].setText(data.toString());
}
else {
textComponents[i].setText(null);
}
i++;
}
}
public boolean getParams(T params) {
int i = 0;
PamParameterData newParamData = null;
Object data = null;
for (PamParameterData paramData : this.parameterSet) {
// find the parameter in the new parameters (parameterSet is just a formatting placeholder)
try {
newParamData = params.getParameterSet().findParameterData(paramData.getFieldName());
} catch (FieldNotFoundException e) {
e.printStackTrace();
}
String txt = textComponents[i].getText();
try {
newParamData.setData(txt);
} catch (IllegalArgumentException | IllegalAccessException e) {
String msg = "Invalid parameter. Data type should be " + paramData.getField().getType().getName();
return PamDialog.showWarning(null, newParamData.getShortName(), msg);
}
i++;
}
return true;
}
}

10
src/PamguardMVC/AcousticDataBlock.java
View File

@ -1,5 +1,8 @@
package PamguardMVC;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import PamController.PamControllerInterface;
import PamguardMVC.nanotime.NanosFromSamples;
@ -90,5 +93,12 @@ abstract public class AcousticDataBlock <Tunit extends PamDataUnit> extends PamD
return parentSourceData;
}
@Override
public Element getDataBlockXML(Document doc) {
Element el = super.getDataBlockXML(doc);
el.setAttribute("SampleRate", String.format("%3.1f", getSampleRate()));
return el;
}
}

17
src/PamguardMVC/DataBlock2D.java
View File

@ -1,5 +1,8 @@
package PamguardMVC;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import dataPlotsFX.data.DataTypeInfo;
abstract public class DataBlock2D<Tunit extends PamDataUnit> extends AcousticDataBlock<Tunit> {
@ -39,4 +42,18 @@ abstract public class DataBlock2D<Tunit extends PamDataUnit> extends AcousticDat
* @return data type information.
*/
abstract public DataTypeInfo getScaleInfo();
public Element getDataBlockXML(Document doc) {
Element el = super.getDataBlockXML(doc);
DataTypeInfo dti = getScaleInfo();
if (dti != null) {
if (dti.dataType != null) {
el.setAttribute("DataType", dti.dataType.toString());
}
if (dti.dataUnits != null) {
el.setAttribute("DataUnits", dti.dataUnits.toString());
}
}
return el;
}
}

47
src/PamguardMVC/PamDataBlock.java
View File

@ -44,10 +44,14 @@ import javax.swing.Timer;
import javax.swing.border.EmptyBorder;
import org.springframework.core.GenericTypeResolver;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import Acquisition.AcquisitionControl;
import Acquisition.AcquisitionProcess;
import pamScrollSystem.ViewLoadObserver;
import tethys.pamdata.AutoTethysProvider;
import tethys.pamdata.TethysDataProvider;
import dataGram.DatagramProvider;
import dataMap.BespokeDataMapGraphic;
import dataMap.OfflineDataMap;
@ -62,6 +66,7 @@ import PamController.PamController;
import PamController.PamControllerInterface;
import PamDetection.LocContents;
import PamDetection.LocalisationInfo;
import PamDetection.PamDetection;
import PamUtils.PamCalendar;
import PamUtils.PamUtils;
import PamView.symbol.PamSymbolManager;
@ -2863,8 +2868,11 @@ public class PamDataBlock<Tunit extends PamDataUnit> extends PamObservable {
private Vector<OfflineDataMap> offlineDataMaps = null;
private SQLLogging logging;
private TethysDataProvider tethysDataProvider;
private JSONObjectDataSource jsonDataSource;
public Vector<ProcessAnnotation> getProcessAnnotations() {
return processAannotations;
@ -3074,6 +3082,26 @@ public class PamDataBlock<Tunit extends PamDataUnit> extends PamObservable {
public SQLLogging getLogging() {
return logging;
}
/**
* Gets a data provider for Tethys. These will probably need
* to be bespoke, but for now will autogenerate based on the SALLogging information.
* @return the tethysDataProvider
*/
public TethysDataProvider getTethysDataProvider() {
if (tethysDataProvider == null && PamDetection.class.isAssignableFrom(unitClass) && getLogging() != null) {
tethysDataProvider = new AutoTethysProvider(this);
}
return tethysDataProvider;
}
/**
* Set a data provider for Tethys.
* @param tethysDataProvider the tethysDataProvider to set
*/
public void setTethysDataProvider(TethysDataProvider tethysDataProvider) {
this.tethysDataProvider = tethysDataProvider;
}
final public boolean getCanLog() {
return (logging != null);
@ -4229,4 +4257,23 @@ public class PamDataBlock<Tunit extends PamDataUnit> extends PamObservable {
public void setBackgroundManager(BackgroundManager backgroundManager) {
this.backgroundManager = backgroundManager;
}
/**
* Get a brief summary of datablock to include in XML descriptions.
* Basic output is very simple. Expect other datablock to extend this by
* adding additional attributes.
* @param doc
* @return XML element with description of data.
*/
public Element getDataBlockXML(Document doc) {
Element inputEl = doc.createElement("Input");
if (getParentProcess() != null && getParentProcess().getPamControlledUnit() != null) {
PamControlledUnit pcu = getParentProcess().getPamControlledUnit();
inputEl.setAttribute("ModuleType", pcu.getUnitType());
inputEl.setAttribute("ModuleName", pcu.getUnitName());
}
inputEl.setAttribute("Name", getLongDataName());
inputEl.setAttribute("Channels", String.format("0x%X", getChannelMap()));
return inputEl;
}
}

3
src/RightWhaleEdgeDetector/RWESQLLogging.java
View File

@ -7,6 +7,7 @@ import PamDetection.AcousticSQLLogging;
import PamUtils.PamUtils;
import PamguardMVC.PamDataBlock;
import PamguardMVC.PamDataUnit;
import generalDatabase.EmptyTableDefinition;
import generalDatabase.PamTableDefinition;
import generalDatabase.PamTableItem;
import generalDatabase.SQLTypes;
@ -26,7 +27,7 @@ public class RWESQLLogging extends AcousticSQLLogging {
angles = new PamTableItem[maxAngles];
angleErrors = new PamTableItem[maxAngles];
PamTableDefinition tableDef = getTableDefinition();
EmptyTableDefinition tableDef = getTableDefinition();
tableDef.addTableItem(score = new PamTableItem("score", Types.INTEGER));
tableDef.addTableItem(signal = new PamTableItem("signal", Types.DOUBLE));
tableDef.addTableItem(noise = new PamTableItem("noise", Types.DOUBLE));

3
src/analogarraysensor/ArraySensorLogging.java
View File

@ -56,7 +56,8 @@ public class ArraySensorLogging extends SQLLogging {
AnalogSensorData aData = new AnalogSensorData(rawValue, calValue);
sensorData[i] = aData;
}
int chanMap = getTableDefinition().getChannelBitmap().getIntegerValue();
PamTableDefinition pamTableDef = (PamTableDefinition) getTableDefinition();
int chanMap = pamTableDef.getChannelBitmap().getIntegerValue();
int streamer = PamUtils.getSingleChannel(chanMap);
if (streamer < 0) streamer = 0;
AnalogArraySensorDataUnit asdu = new AnalogArraySensorDataUnit(timeMilliseconds, streamer, sensorData);

7
src/annotation/calcs/snr/SnrSqlAddon.java
View File

@ -3,6 +3,7 @@ package annotation.calcs.snr;
import java.sql.Types;
import PamguardMVC.PamDataUnit;
import generalDatabase.EmptyTableDefinition;
import generalDatabase.PamTableDefinition;
import generalDatabase.PamTableItem;
import generalDatabase.SQLLoggingAddon;
@ -21,13 +22,13 @@ public class SnrSqlAddon implements SQLLoggingAddon {
}
@Override
public void addTableItems(PamTableDefinition pamTableDefinition) {
public void addTableItems(EmptyTableDefinition pamTableDefinition) {
pamTableDefinition.addTableItem(snr);
}
@Override
public boolean saveData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition,
public boolean saveData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition,
PamDataUnit pamDataUnit) {
SNRAnnotation snrAnnotation = (SNRAnnotation) pamDataUnit.findDataAnnotation(SNRAnnotation.class);
if (snrAnnotation == null) {
@ -40,7 +41,7 @@ public class SnrSqlAddon implements SQLLoggingAddon {
}
@Override
public boolean loadData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition,
public boolean loadData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition,
PamDataUnit pamDataUnit) {
Double snrVal = (Double) snr.getValue();
if (snrVal != null) {

7
src/annotation/calcs/spl/SPLSqlAddon.java
View File

@ -3,6 +3,7 @@ package annotation.calcs.spl;
import java.sql.Types;
import PamguardMVC.PamDataUnit;
import generalDatabase.EmptyTableDefinition;
import generalDatabase.PamTableDefinition;
import generalDatabase.PamTableItem;
import generalDatabase.SQLLoggingAddon;
@ -25,7 +26,7 @@ public class SPLSqlAddon implements SQLLoggingAddon {
}
@Override
public void addTableItems(PamTableDefinition pamTableDefinition) {
public void addTableItems(EmptyTableDefinition pamTableDefinition) {
pamTableDefinition.addTableItem(rms);
pamTableDefinition.addTableItem(zeroPeak);
pamTableDefinition.addTableItem(peakPeak);
@ -33,7 +34,7 @@ public class SPLSqlAddon implements SQLLoggingAddon {
}
@Override
public boolean saveData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition,
public boolean saveData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition,
PamDataUnit pamDataUnit) {
SPLAnnotation splAnnotation = (SPLAnnotation) pamDataUnit.findDataAnnotation(SPLAnnotation.class);
if (splAnnotation == null) {
@ -52,7 +53,7 @@ public class SPLSqlAddon implements SQLLoggingAddon {
}
@Override
public boolean loadData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition,
public boolean loadData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition,
PamDataUnit pamDataUnit) {
SPLAnnotation splAnnotation = new SPLAnnotation(splAnnotationType);
if (splAnnotation != null) {

7
src/annotation/calcs/wav/WavSqlAddon.java
View File

@ -3,6 +3,7 @@ package annotation.calcs.wav;
import java.sql.Types;
import PamguardMVC.PamDataUnit;
import generalDatabase.EmptyTableDefinition;
import generalDatabase.PamTableDefinition;
import generalDatabase.PamTableItem;
import generalDatabase.SQLLoggingAddon;
@ -21,13 +22,13 @@ public class WavSqlAddon implements SQLLoggingAddon {
}
@Override
public void addTableItems(PamTableDefinition pamTableDefinition) {
public void addTableItems(EmptyTableDefinition pamTableDefinition) {
pamTableDefinition.addTableItem(wavFileName);
}
@Override
public boolean saveData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition,
public boolean saveData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition,
PamDataUnit pamDataUnit) {
WavAnnotation annotation = (WavAnnotation) pamDataUnit.findDataAnnotation(WavAnnotation.class);
if (annotation == null) {
@ -40,7 +41,7 @@ public class WavSqlAddon implements SQLLoggingAddon {
}
@Override
public boolean loadData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition,
public boolean loadData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition,
PamDataUnit pamDataUnit) {
String fileName = (String) wavFileName.getValue();
if (fileName != null) {

3
src/annotation/handler/OneStopAnnotationHandler.java
View File

@ -15,6 +15,7 @@ import PamView.dialog.GenericSwingDialog;
import PamguardMVC.PamDataBlock;
import PamguardMVC.PamDataUnit;
import generalDatabase.DBControlUnit;
import generalDatabase.EmptyTableDefinition;
import generalDatabase.PamTableDefinition;
import generalDatabase.SQLLogging;
@ -126,7 +127,7 @@ public abstract class OneStopAnnotationHandler extends AnnotationChoiceHandler i
return;
}
// get, modify and set the modified tabelDef
PamTableDefinition tableDef = logging.getBaseTableDefinition();
EmptyTableDefinition tableDef = logging.getBaseTableDefinition();
logging.setTableDefinition(tableDef);
addAnnotationSqlAddons(logging); // this will add the additional columns.
DBControlUnit dbc = DBControlUnit.findDatabaseControl();

3
src/annotation/localise/targetmotion/TMAnnotationLogging.java
View File

@ -3,6 +3,7 @@ package annotation.localise.targetmotion;
import Localiser.detectionGroupLocaliser.GroupLocalisation;
import PamDetection.AbstractLocalisation;
import PamguardMVC.PamDataUnit;
import generalDatabase.EmptyTableDefinition;
import generalDatabase.PamTableDefinition;
import generalDatabase.SQLTypes;
import targetMotionOld.TargetMotionSQLLogging;
@ -17,7 +18,7 @@ public class TMAnnotationLogging extends TargetMotionSQLLogging {
}
@Override
public boolean loadData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
public boolean loadData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
boolean ans = super.loadData(sqlTypes, pamTableDefinition, pamDataUnit);
if (ans == false) return false;
AbstractLocalisation loc = pamDataUnit.getLocalisation();

7
src/annotation/string/StringSQLLogging.java
View File

@ -3,6 +3,7 @@ package annotation.string;
import java.sql.Types;
import PamguardMVC.PamDataUnit;
import generalDatabase.EmptyTableDefinition;
import generalDatabase.PamTableDefinition;
import generalDatabase.PamTableItem;
import generalDatabase.SQLLoggingAddon;
@ -24,12 +25,12 @@ public class StringSQLLogging implements SQLLoggingAddon {
}
@Override
public void addTableItems(PamTableDefinition pamTableDefinition) {
public void addTableItems(EmptyTableDefinition pamTableDefinition) {
pamTableDefinition.addTableItem(notes);
}
@Override
public boolean saveData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
public boolean saveData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
StringAnnotation stringAnnotation = (StringAnnotation) pamDataUnit.findDataAnnotation(StringAnnotation.class,
stringAnnotationType.getAnnotationName());
if (stringAnnotation == null) {
@ -42,7 +43,7 @@ public class StringSQLLogging implements SQLLoggingAddon {
}
@Override
public boolean loadData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
public boolean loadData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
try {
String note = notes.getDeblankedStringValue();
if (note != null && note.length() > 0) {

7
src/annotation/timestamp/TimestampSQLLogging.java
View File

@ -3,6 +3,7 @@ package annotation.timestamp;
import java.sql.Types;
import PamguardMVC.PamDataUnit;
import generalDatabase.EmptyTableDefinition;
import generalDatabase.PamTableDefinition;
import generalDatabase.PamTableItem;
import generalDatabase.SQLLoggingAddon;
@ -22,12 +23,12 @@ public class TimestampSQLLogging implements SQLLoggingAddon {
}
@Override
public void addTableItems(PamTableDefinition pamTableDefinition) {
public void addTableItems(EmptyTableDefinition pamTableDefinition) {
pamTableDefinition.addTableItem(timestamp);
}
@Override
public boolean saveData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
public boolean saveData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
TimestampAnnotation timestampAnnotation = (TimestampAnnotation) pamDataUnit.findDataAnnotation(TimestampAnnotation.class,
timestampAnnotationType.getAnnotationName());
if (timestampAnnotation == null) {
@ -40,7 +41,7 @@ public class TimestampSQLLogging implements SQLLoggingAddon {
}
@Override
public boolean loadData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
public boolean loadData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
try {
TimestampAnnotation timestampAnnotation = new TimestampAnnotation(timestampAnnotationType);
Long note = sqlTypes.millisFromTimeStamp(timestamp.getValue());

7
src/annotation/userforms/UserFormSQLAddon.java
View File

@ -3,6 +3,7 @@ package annotation.userforms;
import java.util.ArrayList;
import PamguardMVC.PamDataUnit;
import generalDatabase.EmptyTableDefinition;
import generalDatabase.PamTableDefinition;
import generalDatabase.PamTableItem;
import generalDatabase.SQLLoggingAddon;
@ -32,7 +33,7 @@ public class UserFormSQLAddon implements SQLLoggingAddon {
@Override
public void addTableItems(PamTableDefinition pamTableDefinition) {
public void addTableItems(EmptyTableDefinition pamTableDefinition) {
loggerTableItems.clear();
FormDescription formDescription = userFormAnnotationType.findFormDescription();
if (formDescription == null) {
@ -58,7 +59,7 @@ public class UserFormSQLAddon implements SQLLoggingAddon {
}
@Override
public boolean saveData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
public boolean saveData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
if (pamDataUnit == null) {
clearTableItems();
return false;
@ -103,7 +104,7 @@ public class UserFormSQLAddon implements SQLLoggingAddon {
}
@Override
public boolean loadData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
public boolean loadData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
FormDescription formDescription = userFormAnnotationType.findFormDescription();
if (formDescription == null) {
return false;

7
src/beamformer/annotation/BFAnnotationLogging.java
View File

@ -6,6 +6,7 @@ import PamDetection.LocContents;
import PamguardMVC.PamDataBlock;
import PamguardMVC.PamDataUnit;
import beamformer.loc.BeamFormerLocalisation;
import generalDatabase.EmptyTableDefinition;
import generalDatabase.PamTableDefinition;
import generalDatabase.PamTableItem;
import generalDatabase.SQLLoggingAddon;
@ -29,7 +30,7 @@ public class BFAnnotationLogging implements SQLLoggingAddon {
}
@Override
public void addTableItems(PamTableDefinition pamTableDefinition) {
public void addTableItems(EmptyTableDefinition pamTableDefinition) {
pamTableDefinition.addTableItem(bfPhones);
pamTableDefinition.addTableItem(bfArrayType);
pamTableDefinition.addTableItem(bfContents);
@ -38,7 +39,7 @@ public class BFAnnotationLogging implements SQLLoggingAddon {
}
@Override
public boolean saveData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
public boolean saveData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
bfPhones.setValue(null);
bfArrayType.setValue(null);
bfContents.setValue(null);
@ -64,7 +65,7 @@ public class BFAnnotationLogging implements SQLLoggingAddon {
}
@Override
public boolean loadData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
public boolean loadData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
Float[] Angles = new Float[2];
for (int i = 0; i < 2; i++) {
Angles[i] = (Float) angle[i].getFloatValue();

7
src/bearinglocaliser/annotation/BearingAnnotationSQL.java
View File

@ -4,6 +4,7 @@ import java.sql.Types;
import PamguardMVC.PamDataUnit;
import bearinglocaliser.BearingLocalisation;
import generalDatabase.EmptyTableDefinition;
import generalDatabase.PamTableDefinition;
import generalDatabase.PamTableItem;
import generalDatabase.SQLLoggingAddon;
@ -34,7 +35,7 @@ public class BearingAnnotationSQL implements SQLLoggingAddon {
}
@Override
public void addTableItems(PamTableDefinition pamTableDefinition) {
public void addTableItems(EmptyTableDefinition pamTableDefinition) {
pamTableDefinition.addTableItem(algoName);
pamTableDefinition.addTableItem(bfPhones);
pamTableDefinition.addTableItem(bfArrayType);
@ -48,7 +49,7 @@ public class BearingAnnotationSQL implements SQLLoggingAddon {
}
@Override
public boolean saveData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
public boolean saveData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
algoName.setValue(null);
bfPhones.setValue(null);
bfArrayType.setValue(null);
@ -96,7 +97,7 @@ public class BearingAnnotationSQL implements SQLLoggingAddon {
}
@Override
public boolean loadData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
public boolean loadData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
Float[] Angles = new Float[2];
int nNans = 0;
for (int i = 0; i < 2; i++) {

6
src/binaryFileStorage/BinarySettingsStorage.java
View File

@ -110,6 +110,12 @@ public class BinarySettingsStorage implements PamSettingsSource {
return false;*/
}
@Override
public boolean saveEndSettings(long timeNow) {
// do nothing at the end of a run with binary store.
return true;
}
// private boolean writeData(DataOutputStream dos, int objectId, byte[] data) {
// int totalLen = data.length + 16;
// int dataLen = data.length;

6
src/binaryFileStorage/BinaryStore.java
View File

@ -540,6 +540,12 @@ PamSettingsSource, DataOutputStore {
return binarySettingsStorage.saveStartSettings(timeNow);
}
@Override
public boolean saveEndSettings(long timeNow) {
// TODO Auto-generated method stub
return false;
}
@Override
public int getNumSettings() {
if (binarySettingsStorage == null) {

1
src/binaryFileStorage/BinaryStoreProcess.java
View File

@ -46,6 +46,7 @@ public class BinaryStoreProcess extends PamProcess {
startTime = PamCalendar.getTimeInMillis();
long round = binaryStore.binaryStoreSettings.fileSeconds * 1000;
nextFileTime = (startTime/round) * round + round;
// this was a print of the time of the NEXT binary file. Not really of interest.
// System.out.println("Next file start at " + PamCalendar.formatDateTime(nextFileTime));
timer = new Timer();
timer.schedule(new FileTimerTask(), 1000, 1000);

7
src/clickDetector/ClickClassifiers/annotation/ClickAnnotationSQL.java
View File

@ -3,6 +3,7 @@ package clickDetector.ClickClassifiers.annotation;
import java.sql.Types;
import PamguardMVC.PamDataUnit;
import generalDatabase.EmptyTableDefinition;
import generalDatabase.PamTableDefinition;
import generalDatabase.PamTableItem;
import generalDatabase.SQLLoggingAddon;
@ -33,12 +34,12 @@ public class ClickAnnotationSQL implements SQLLoggingAddon {
}
@Override
public void addTableItems(PamTableDefinition pamTableDefinition) {
public void addTableItems(EmptyTableDefinition pamTableDefinition) {
pamTableDefinition.addTableItem(classifierSetTable);
}
@Override
public boolean saveData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
public boolean saveData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
ClickClassifierAnnotation clickAnnotation = (ClickClassifierAnnotation) pamDataUnit.findDataAnnotation(ClickClassificationType.class);
//create a comma delimited string
@ -53,7 +54,7 @@ public class ClickAnnotationSQL implements SQLLoggingAddon {
@Override
public boolean loadData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
public boolean loadData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
String array = classifierSetTable.getDeblankedStringValue();
//read in the classification set. This a list of all the classifiers the clicks passed.

4
src/clickDetector/TrackedClickGroupLogging.java
View File

@ -1,5 +1,6 @@
package clickDetector;
import generalDatabase.PamTableDefinition;
import generalDatabase.SQLTypes;
import PamguardMVC.PamDataUnit;
import clickDetector.offlineFuncs.OfflineEventDataUnit;
@ -30,7 +31,8 @@ public class TrackedClickGroupLogging extends ClickGroupLogging {
boolean isUpdate = true;
// Timestamp ts = (Timestamp) getTableDefinition().getTimeStampItem().getValue();
// long t = PamCalendar.millisFromTimeStamp(ts);
int updateIndex = (Integer) getTableDefinition().getUpdateReference().getValue();
PamTableDefinition tableDef = (PamTableDefinition) getTableDefinition();
int updateIndex = (Integer) tableDef.getUpdateReference().getValue();
if (updateIndex > 0) {
tcg = this.clickGroupDataBlock.findByDatabaseIndex(updateIndex);
}

2
src/clickDetector/dataSelector/ClickTrainDataSelector2.java
View File

@ -82,7 +82,7 @@ public class ClickTrainDataSelector2 extends DataSelector {
}
SQLLogging logging = getPamDataBlock().getLogging();
if (logging == null) return null; //cannot happen!
PamTableDefinition tableDef = logging.getTableDefinition();
EmptyTableDefinition tableDef = logging.getTableDefinition();
if (params.isIncludeUnclassified()) {
return null;
}

5
src/clickDetector/layoutFX/clickClassifiers/SweepClassifierSetPaneFX.java
View File

@ -1628,8 +1628,7 @@ public class SweepClassifierSetPaneFX extends SettingsPane<ClickTypeProperty> {
p.setLayout(new GridBagLayout());
GridBagConstraints c = new PamGridBagContraints();
// c.gridx = 0;
// addComponent(p, enableBearings, c);
// c.gridx += c.gridwidth;
@ -1737,7 +1736,7 @@ public class SweepClassifierSetPaneFX extends SettingsPane<ClickTypeProperty> {
// }
// }
// else multiChan = true;
// Debug.out.println("Check multi-channel: " + multiChan);
//// Debug.out.println("Check multi-channel: " + multiChan);
return multiChan;
}

7
src/clickDetector/offlineFuncs/DatabaseChecks.java
View File

@ -102,16 +102,17 @@ public class DatabaseChecks {
long resultTime;
long firstTime = Long.MAX_VALUE;
long lastTime = Long.MIN_VALUE;
PamTableDefinition pamTableDef = (PamTableDefinition) clickLogging.getTableDefinition();
try {
Statement stmt = con.getConnection().createStatement();
ResultSet result = stmt.executeQuery(sqlStr);
while (result.next()) {
nClicks++;
clickLogging.transferDataFromResult(sqlTypes, result);
ts = clickLogging.getTableDefinition().getTimeStampItem().getValue();
ts = pamTableDef.getTimeStampItem().getValue();
resultTime = sqlTypes.millisFromTimeStamp(ts);
if (resultTime%1000 == 0) {
resultTime += clickLogging.getTableDefinition().getTimeStampMillis().getIntegerValue();
resultTime += pamTableDef.getTimeStampMillis().getIntegerValue();
}
firstTime = Math.min(firstTime, resultTime);
lastTime = Math.max(lastTime, resultTime);
@ -188,7 +189,7 @@ public class DatabaseChecks {
eventDataBlock.addPamData(event);
PamConnection con = DBControlUnit.findConnection();
// now find a cursor and save it.
PamTableDefinition eventTableDef = eventDataBlock.getLogging().getTableDefinition();
PamTableDefinition eventTableDef = (PamTableDefinition) eventDataBlock.getLogging().getTableDefinition();
PamCursor cursor = eventDataBlock.getLogging().getViewerCursorFinder().getCursor(con, eventTableDef);
cursor.immediateInsert(con);
int newId = event.getDatabaseIndex();

5
src/clickDetector/offlineFuncs/OfflineClickLogging.java
View File

@ -277,13 +277,14 @@ public class OfflineClickLogging extends SQLLogging {
Integer millis;
Object ts;
SQLTypes sqlTypes = dbControl.getConnection().getSqlTypes();
PamTableDefinition tableDef = (PamTableDefinition) getTableDefinition();
try {
while (resultSet.next()) {
transferDataFromResult(sqlTypes, resultSet);
ts = getTableDefinition().getTimeStampItem().getValue();
ts = tableDef.getTimeStampItem().getValue();
long m = SQLTypes.millisFromTimeStamp(ts);
if (m%1000 == 0) {
millis = (Integer) getTableDefinition().getTimeStampMillis().getValue();
millis = (Integer) tableDef.getTimeStampMillis().getValue();
if (millis != null) {
m += millis;
}

4
src/clickDetector/offlineFuncs/rcImport/RainbowDatabseConverter.java
View File

@ -148,7 +148,7 @@ public class RainbowDatabseConverter {
ClickDataBlock clickDataBlock = clickControl.getClickDataBlock();
clickLogging = new ClickImportLogging(clickControl);
PamTableDefinition tableDef = clickLogging.getTableDefinition();
PamTableDefinition tableDef = (PamTableDefinition) clickLogging.getTableDefinition();
boolean ok = checkTable(pamConnection, tableDef);
if (!ok) {
System.out.println("Error in Pamguard clicks table");
@ -156,7 +156,7 @@ public class RainbowDatabseConverter {
}
eventLogging = new OfflineEventLogging(clickControl, clickControl.getClickDetector().getOfflineEventDataBlock());
tableDef = eventLogging.getTableDefinition();
tableDef = (PamTableDefinition) eventLogging.getTableDefinition();
ok = checkTable(pamConnection, tableDef);
if (!ok) {
System.out.println("Error in Pamguard events table");

2
src/difar/trackedGroups/TrackedGroupSqlLogging.java
View File

@ -125,7 +125,7 @@ public class TrackedGroupSqlLogging extends SQLLogging {
*/
protected void updateData(SQLTypes sqlTypes, PamDataUnit pamDataUnit) {
PamTableDefinition tableDef = getTableDefinition();
PamTableDefinition tableDef = (PamTableDefinition) getTableDefinition();
PamTableItem tableItem;
tableDef.getIndexItem().setValue(pamDataUnit.getDatabaseIndex());

10
src/fftManager/FFTDataBlock.java
View File

@ -4,6 +4,9 @@ import java.util.List;
import java.util.ListIterator;
import java.util.Vector;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import PamView.GeneralProjector.ParameterType;
import PamView.GeneralProjector.ParameterUnits;
import PamguardMVC.DataBlock2D;
@ -186,6 +189,13 @@ public class FFTDataBlock extends DataBlock2D<FFTDataUnit> {
public DataTypeInfo getScaleInfo() {
return dataTypeInfo;
}
@Override
public Element getDataBlockXML(Document doc) {
Element el = super.getDataBlockXML(doc);
el.setAttribute("FFTLength", String.format("%d", getFftLength()));
el.setAttribute("FFTHop", String.format("%d", getFftHop()));
return el;
}

8
src/generalDatabase/DBControl.java
View File

@ -577,10 +577,16 @@ PamSettingsSource {
*/
@Override
public boolean saveStartSettings(long timeNow) {
return dbProcess.saveStartSettings();
return dbProcess.saveStartSettings(timeNow);
}
@Override
public boolean saveEndSettings(long timeNow) {
// TODO Auto-generated method stub
return true;
}
@Override
public int getNumSettings() {
if (dbSettingsStore == null) {

15
src/generalDatabase/DBProcess.java
View File

@ -102,6 +102,8 @@ public class DBProcess extends PamProcess {
dbSpecials.add(logSettings = new LogSettings(databaseControll, "Pamguard Settings", false));
dbSpecials.add(logLastSettings = new LogSettings(databaseControll, "Pamguard Settings Last", true));
dbSpecials.add(logViewerSettings = new LogSettings(databaseControll, "Pamguard Settings Viewer", true));
dbSpecials.add(new LogXMLSettings(databaseControll));
}
@ -113,9 +115,13 @@ public class DBProcess extends PamProcess {
}
}
protected boolean saveStartSettings() {
protected boolean saveStartSettings(long timeNow) {
PamConnection con = databaseControll.getConnection();
if (con != null) {
/**
* This first one is the 'old' pre 2022 method which saves a serialised lump of all
* the settings in the database. It ain't broke, so not fixing it.
*/
for (int i = 0; i < dbSpecials.size(); i++) {
dbSpecials.get(i).pamStart(con);
}
@ -124,6 +130,11 @@ public class DBProcess extends PamProcess {
return false;
}
protected boolean saveEndSettings(long timeNow) {
return true;
}
@Override
public void pamStop() {
PamConnection con = databaseControll.getConnection();
@ -212,7 +223,7 @@ public class DBProcess extends PamProcess {
}
dataBlocks = PamController.getInstance().getDataBlocks();
PamTableDefinition tableDefinition;
EmptyTableDefinition tableDefinition;
SQLLogging logging;
// for each datablock, check that the process can log (ignoring GPS process)

30
src/generalDatabase/DBSchemaWriter.java
View File

@ -48,7 +48,7 @@ public class DBSchemaWriter {
}
PamTableDefinition tableDef = logging.getTableDefinition();
EmptyTableDefinition tableDef = logging.getTableDefinition();
tableDef = logging.getBaseTableDefinition();
if (tableDef instanceof PamTableDefinition) {
@ -63,13 +63,14 @@ public class DBSchemaWriter {
return true;
}
private void exportDatabaseSchema(File outputFolder, PamDataBlock dataBlock, SQLLogging logging, PamTableDefinition tableDef) {
/**
* write a parent item, e.g. if tableDef is a sub class of PamTableDefinition
*/
// String parentName = writeParentTableSchema(outputFolder, dataBlock, tableDef);
/**
* Generate an xml schema for a datablock.
* @param dataBlock
* @param logging
* @param tableDef
* @return
*/
public Document generateDatabaseSchema(PamDataBlock dataBlock, SQLLogging logging, EmptyTableDefinition tableDef) {
String tableName = tableDef.getTableName();
Document doc = PamUtils.XMLUtils.createBlankDoc();
Element schemaEl = doc.createElement("xs:schema");
@ -95,7 +96,20 @@ public class DBSchemaWriter {
}
}
}
return doc;
}
private void exportDatabaseSchema(File outputFolder, PamDataBlock dataBlock, SQLLogging logging, EmptyTableDefinition tableDef) {
/**
* write a parent item, e.g. if tableDef is a sub class of PamTableDefinition
*/
// String parentName = writeParentTableSchema(outputFolder, dataBlock, tableDef);
Document doc = generateDatabaseSchema(dataBlock, logging, tableDef);
String tableName = tableDef.getTableName();
try {
File outputFile = new File(outputFolder, tableName+".xsd");
XMLUtils.writeToFile(doc, outputFile);

2
src/generalDatabase/DbSpecial.java
View File

@ -9,7 +9,7 @@ import PamguardMVC.PamDataUnit;
* @author Doug Gillespie
*
*/
abstract public class DbSpecial extends SQLLogging{
abstract public class DbSpecial extends SQLLogging {
private DBControl dbControl;

11
src/generalDatabase/EmptyTableDefinition.java
View File

@ -300,7 +300,7 @@ public class EmptyTableDefinition implements Cloneable {
* @param tableName
* @return reference to the database deinition if it exists, or null
*/
static PamTableDefinition findTableDefinition(String tableName) {
static EmptyTableDefinition findTableDefinition(String tableName) {
String searchName = EmptyTableDefinition.deblankString(tableName);
SQLLogging log = SQLLogging.findLogger(searchName);
if (log == null) return null;
@ -389,6 +389,15 @@ public class EmptyTableDefinition implements Cloneable {
this.updatePolicy = updatePolicy;
}
public PamConnection getCheckedConnection() {
return checkedConnection;
}
public void setCheckedConnection(PamConnection checkedConnection) {
this.checkedConnection = checkedConnection;
}
@Override
protected EmptyTableDefinition clone() {
try {

5
src/generalDatabase/LogSettings.java
View File

@ -23,7 +23,7 @@ import PamUtils.PamCalendar;
import PamguardMVC.PamDataUnit;
/**
* Functions for writing Pamguard Settings into any database as character data
* Functions for writing serialised Pamguard Settings into any database as character data
* Runs at DAQ start, goes through the settings manager list and for each
* set of settings, it serialises the settings data into a binary array, this
* is then converted from binary data to 6 bit ascii data (using the character set
@ -185,6 +185,7 @@ public class LogSettings extends DbSpecial {
DeserialisationWarning dsWarning = new DeserialisationWarning(getDbControl().getDatabaseName());
SQLTypes sqlTypes = con.getSqlTypes();
boolean haveData;
if (result != null) try {
haveData = result.next();
@ -193,7 +194,7 @@ public class LogSettings extends DbSpecial {
// transfer data back into the tableItems store.
transferDataFromResult(sqlTypes, result);
tableItem = getTableDefinition().getTimeStampItem();
tableItem = tableDef.getTimeStampItem();
// timestamp = (Timestamp) tableItem.getTimestampValue();
timeMillis = sqlTypes.millisFromTimeStamp(tableItem.getValue());

75
src/generalDatabase/LogXMLDataUnit.java Normal file
View File

@ -0,0 +1,75 @@
package generalDatabase;
import PamController.PamSettings;
import PamguardMVC.PamDataUnit;
/**
* simple data unit for use with the LogXMLSettings class
* @author dg50
*
*/
public class LogXMLDataUnit extends PamDataUnit {
private long processTime;
private PamSettings pamSettings;
private String xml;
private Long dataEnd, processEnd;
public LogXMLDataUnit(long timeMilliseconds, long processTime, PamSettings pamSettings, String xml) {
super(timeMilliseconds);
this.processTime = processTime;
this.pamSettings = pamSettings;
this.xml = xml;
}
/**
* @return the dataEnd
*/
public Long getDataEnd() {
return dataEnd;
}
/**
* @param dataEnd the dataEnd to set
*/
public void setDataEnd(Long dataEnd) {
this.dataEnd = dataEnd;
}
/**
* @return the processEnd
*/
public Long getProcessEnd() {
return processEnd;
}
/**
* @param processEnd the processEnd to set
*/
public void setProcessEnd(Long processEnd) {
this.processEnd = processEnd;
}
/**
* @return the processTime
*/
public long getProcessTime() {
return processTime;
}
/**
* @return the pamSettings
*/
public PamSettings getPamSettings() {
return pamSettings;
}
/**
* @return the xml
*/
public String getXml() {
return xml;
}
}

123
src/generalDatabase/LogXMLSettings.java Normal file
View File

@ -0,0 +1,123 @@
package generalDatabase;
import java.io.Serializable;
import java.util.HashMap;
import org.w3c.dom.Document;
import PamController.PamControlledUnit;
import PamController.PamController;
import PamController.PamSettings;
import PamController.PamguardVersionInfo;
import PamController.settings.output.xml.PamguardXMLWriter;
import PamUtils.PamCalendar;
import PamguardMVC.PamDataUnit;
/**
* 2022 Additional say of saving settings for each module into the database in more human readable
* XML format. <p>
* In other ways, similar to LogSettings which saves serialised Java. This will write a line
* per module. A main difference is that on pamStop it will update the end time for each line, so
* that we have a record of analysis effort for each module. Will therefore need to store the last
* index of the entry for each module, so that we can update the appropriate row.
* @author dg50
*
*/
public class LogXMLSettings extends DbSpecial {
private XMLSettingsTableDefinition xmlTableDef;
private HashMap<String, LogXMLDataUnit> moduleRows;
private PamguardXMLWriter xmlWriter;
public LogXMLSettings(DBControl dbControl) {
super(dbControl);
xmlTableDef = new XMLSettingsTableDefinition("Module Effort");
setTableDefinition(xmlTableDef);
moduleRows = new HashMap<>();
xmlWriter = PamguardXMLWriter.getXMLWriter();
}
@Override
public void pamStart(PamConnection con) {
long time = PamCalendar.getTimeInMillis();
saveModuleSettings(con, time);
}
@Override
public void pamStop(PamConnection con) {
long time = PamCalendar.getTimeInMillis();
updateModuleSettings(con, time);
}
private void saveModuleSettings(PamConnection con, long dataTime) {
int n = PamController.getInstance().getNumControlledUnits();
long now = System.currentTimeMillis();
for (int i = 0; i < n; i++) {
saveModuleSettings(con, dataTime, now, PamController.getInstance().getControlledUnit(i));
}
}
private void saveModuleSettings(PamConnection con, long dataTime, long now, PamControlledUnit controlledUnit) {
if (controlledUnit instanceof PamSettings == false) {
return;
}
PamSettings pamSettings = (PamSettings) controlledUnit;
Serializable settings = pamSettings.getSettingsReference();
Document doc = xmlWriter.writeOneModule(pamSettings, dataTime);
String xmlString = xmlWriter.getAsString(doc, true);
LogXMLDataUnit logXMLDataUnit = new LogXMLDataUnit(dataTime, now, pamSettings, xmlString);
logData(logXMLDataUnit);
int dbIndex = logXMLDataUnit.getDatabaseIndex();
moduleRows.put(getModuleHash(pamSettings), logXMLDataUnit);
}
private void updateModuleSettings(PamConnection con, long dataTime) {
int n = PamController.getInstance().getNumControlledUnits();
long now = System.currentTimeMillis();
for (int i = 0; i < n; i++) {
updateModuleSettings(con, dataTime, now, PamController.getInstance().getControlledUnit(i));
}
}
private void updateModuleSettings(PamConnection con, long dataTime, long now, PamControlledUnit controlledUnit) {
if (controlledUnit instanceof PamSettings == false) {
return;
}
PamSettings pamSettings = (PamSettings) controlledUnit;
LogXMLDataUnit logXMLDataUnit = moduleRows.get(getModuleHash(pamSettings));
if (logXMLDataUnit == null) {
return;
}
logXMLDataUnit.setDataEnd(dataTime);
logXMLDataUnit.setProcessEnd(now);
reLogData(con, logXMLDataUnit);
}
private String getModuleHash(PamSettings pamSettings) {
if (pamSettings == null) {
return null;
}
return pamSettings.getUnitName()+pamSettings.getUnitType();
}
@Override
public void setTableData(SQLTypes sqlTypes, PamDataUnit pamDataUnit) {
LogXMLDataUnit logXMLDataUnit = (LogXMLDataUnit) pamDataUnit;
PamSettings pamSettings = logXMLDataUnit.getPamSettings();
xmlTableDef.getDataStart().setValue(sqlTypes.getTimeStamp(pamDataUnit.getTimeMilliseconds()));
xmlTableDef.getDataEnd().setValue(sqlTypes.getTimeStamp(logXMLDataUnit.getDataEnd()));
xmlTableDef.getProcessStart().setValue(sqlTypes.getTimeStamp(logXMLDataUnit.getProcessTime()));
xmlTableDef.getProcessEnd().setValue(sqlTypes.getTimeStamp(logXMLDataUnit.getProcessEnd()));
xmlTableDef.getName().setValue(pamSettings.getUnitName());
xmlTableDef.getType().setValue(pamSettings.getUnitType());
xmlTableDef.getPamGuardVersion().setValue(PamguardVersionInfo.version);
xmlTableDef.getSettingsVersion().setValue(pamSettings.getSettingsVersion());
xmlTableDef.getXmlSettings().setValue(logXMLDataUnit.getXml());
}
}

9
src/generalDatabase/PamTableDefinition.java
View File

@ -192,14 +192,7 @@ public class PamTableDefinition extends EmptyTableDefinition implements Cloneabl
public PamTableItem getUidItem() {
return uid;
}
public PamConnection getCheckedConnection() {
return checkedConnection;
}
public void setCheckedConnection(PamConnection checkedConnection) {
this.checkedConnection = checkedConnection;
}
public PamTableItem getUpdateReference() {
return updateReference;
}

2
src/generalDatabase/PamTableItem.java
View File

@ -377,7 +377,7 @@ public class PamTableItem implements Cloneable {
* column for use in cross referencing.
*/
public static PamTableItem findTableItem(String tableName, String columnName) {
PamTableDefinition tableDef = EmptyTableDefinition.
EmptyTableDefinition tableDef = EmptyTableDefinition.
findTableDefinition(EmptyTableDefinition.deblankString(tableName));
if (tableDef == null) return null;
return tableDef.findTableItem(EmptyTableDefinition.deblankString(columnName));

84
src/generalDatabase/SQLLogging.java
View File

@ -92,7 +92,7 @@ public abstract class SQLLogging {
* Reference to the table definition object.
* This MUST be set from within the concrete logging class.
*/
private PamTableDefinition pamTableDefinition;
private EmptyTableDefinition pamTableDefinition;
/**
* More and more data blocks are starting to use annotations, which require
@ -102,7 +102,7 @@ public abstract class SQLLogging {
* table definition is set, so that it can be got and modified by the
* annotation handler shortly after the main table is created.
*/
private PamTableDefinition baseTableDefinition;
private EmptyTableDefinition baseTableDefinition;
// private long selectT1, selectT2;
private PamViewParameters currentViewParameters;
@ -190,7 +190,7 @@ public abstract class SQLLogging {
ArrayList<PamDataBlock> blockList = PamController.getInstance()
.getDataBlocks();
SQLLogging logger;
PamTableDefinition tableDef;
EmptyTableDefinition tableDef;
for (int i = 0; i < blockList.size(); i++) {
if ((logger = blockList.get(i).getLogging()) != null) {
tableDef = logger.getTableDefinition();
@ -234,7 +234,7 @@ public abstract class SQLLogging {
* @return a Pamguard database table definition object
* @see PamTableDefinition
*/
public final PamTableDefinition getTableDefinition() {
public final EmptyTableDefinition getTableDefinition() {
return pamTableDefinition;
}
@ -243,7 +243,7 @@ public abstract class SQLLogging {
*
* @param pamTableDefinition PamTableDefinition to set
*/
public void setTableDefinition(PamTableDefinition pamTableDefinition) {
public void setTableDefinition(EmptyTableDefinition pamTableDefinition) {
this.pamTableDefinition = pamTableDefinition;
if (baseTableDefinition == null && pamTableDefinition != null) {
baseTableDefinition = pamTableDefinition.clone();
@ -293,37 +293,42 @@ public abstract class SQLLogging {
* @param superDetection
*/
protected void fillTableData(SQLTypes sqlTypes, PamDataUnit pamDataUnit, PamDataUnit superDetection) {
EmptyTableDefinition emptyTableDef = getTableDefinition();
PamTableDefinition tableDef = getTableDefinition();
PamTableItem tableItem;
tableDef.getIndexItem().setValue(pamDataUnit.getDatabaseIndex());
/*
* All tables have a timestamp near the front of the table. And all data
* units have a time in milliseconds, so always fill this in !
*/
tableDef.getTimeStampItem().setValue(
sqlTypes.getTimeStamp(pamDataUnit.getTimeMilliseconds()));
emptyTableDef.getIndexItem().setValue(pamDataUnit.getDatabaseIndex());
if (emptyTableDef instanceof PamTableDefinition) {
PamTableDefinition tableDef = (PamTableDefinition) emptyTableDef;
/*
* All tables have a timestamp near the front of the table. And all data
* units have a time in milliseconds, so always fill this in !
*/
tableDef.getTimeStampItem().setValue(
sqlTypes.getTimeStamp(pamDataUnit.getTimeMilliseconds()));
tableDef.getTimeStampMillis().setValue((int) (pamDataUnit.getTimeMilliseconds()%1000));
tableDef.getTimeStampMillis().setValue((int) (pamDataUnit.getTimeMilliseconds()%1000));
tableDef.getLocalTimeItem().setValue(sqlTypes.getLocalTimeStamp(pamDataUnit.getTimeMilliseconds()));
tableDef.getLocalTimeItem().setValue(sqlTypes.getLocalTimeStamp(pamDataUnit.getTimeMilliseconds()));
tableDef.getPCTimeItem().setValue(sqlTypes.getTimeStamp(System.currentTimeMillis()));
tableDef.getPCTimeItem().setValue(sqlTypes.getTimeStamp(System.currentTimeMillis()));
tableDef.getUidItem().setValue(pamDataUnit.getUID());
tableDef.getUidItem().setValue(pamDataUnit.getUID());
tableDef.getChannelBitmap().setValue(pamDataUnit.getChannelBitmap());
tableDef.getChannelBitmap().setValue(pamDataUnit.getChannelBitmap());
tableDef.getSequenceBitmap().setValue(pamDataUnit.getSequenceBitmapObject());
tableDef.getSequenceBitmap().setValue(pamDataUnit.getSequenceBitmapObject());
if (tableDef.getUpdateReference() != null) {
tableDef.getUpdateReference().setValue(pamDataUnit.getDatabaseIndex());
if (tableDef.getUpdateReference() != null) {
tableDef.getUpdateReference().setValue(pamDataUnit.getDatabaseIndex());
}
}
for (int i = 0; i < tableDef.getTableItemCount(); i++) {
for (int i = 0; i < emptyTableDef.getTableItemCount(); i++) {
tableItem = tableDef.getTableItem(i);
tableItem = emptyTableDef.getTableItem(i);
// if (tableItem.isCounter()) {
// tableItem.setValue(1);
// }
@ -333,8 +338,8 @@ public abstract class SQLLogging {
}
}
if (tableDef instanceof PamSubtableDefinition) {
PamSubtableDefinition subTableDef = (PamSubtableDefinition) tableDef;
if (emptyTableDef instanceof PamSubtableDefinition) {
PamSubtableDefinition subTableDef = (PamSubtableDefinition) emptyTableDef;
fillSubTableData(subTableDef, pamDataUnit, superDetection);
}
@ -525,7 +530,7 @@ public abstract class SQLLogging {
}
// now put some sql into the statement
// if (resultSet == null) {
PamTableDefinition tableDef = getTableDefinition();
EmptyTableDefinition tableDef = getTableDefinition();
String sqlString = tableDef.getSQLSelectString(con.getSqlTypes());
// sqlString = "select \"comment\" from userinput";
try {
@ -1079,7 +1084,7 @@ public abstract class SQLLogging {
public boolean transferDataFromResult(SQLTypes sqlTypes, ResultSet resultSet) {
PamTableDefinition tableDef = getTableDefinition();
EmptyTableDefinition tableDef = getTableDefinition();
PamTableItem tableItem;
try {
for (int i = 0; i < tableDef.getTableItemCount(); i++) {
@ -1090,17 +1095,20 @@ public abstract class SQLLogging {
// Timestamp ts = (Timestamp) getTableDefinition().getTimeStampItem().getValue();
// Timestamp ts = getTableDefinition().getTimeStampItem().getTimestampValue();
// lastTime = sqlTypes.millisFromTimeStamp(ts);
lastTime = sqlTypes.millisFromTimeStamp(getTableDefinition().getTimeStampItem().getValue());
if (lastTime%1000 == 0) {
// some databases may have stored the milliseconds, in which
// case this next bit is redundant.
lastTime += getTableDefinition().getTimeStampMillis().getIntegerValue();
}
lastLoadIndex = getTableDefinition().getIndexItem().getIntegerValue();
lastLoadUID = getTableDefinition().getUidItem().getLongObject();
lastChannelBitmap = getTableDefinition().getChannelBitmap().getIntegerValue();
lastSequenceBitmap = getTableDefinition().getSequenceBitmap().getIntegerObject();
if (tableDef instanceof PamTableDefinition) {
PamTableDefinition pamTableDef = (PamTableDefinition) tableDef;
lastTime = sqlTypes.millisFromTimeStamp(pamTableDef.getTimeStampItem().getValue());
if (lastTime%1000 == 0) {
// some databases may have stored the milliseconds, in which
// case this next bit is redundant.
lastTime += pamTableDef.getTimeStampMillis().getIntegerValue();
}
lastLoadUID = pamTableDef.getUidItem().getLongObject();
lastChannelBitmap = pamTableDef.getChannelBitmap().getIntegerValue();
lastSequenceBitmap = pamTableDef.getSequenceBitmap().getIntegerObject();
}
return true;
} catch (SQLException ex) {
@ -1757,7 +1765,7 @@ public abstract class SQLLogging {
* annotation handler shortly after the main table is created.
* @return the baseTableDefinition
*/
public PamTableDefinition getBaseTableDefinition() {
public EmptyTableDefinition getBaseTableDefinition() {
return baseTableDefinition;
}

6
src/generalDatabase/SQLLoggingAddon.java
View File

@ -15,7 +15,7 @@ public interface SQLLoggingAddon {
* Add a load of columns to an existing table definition
* @param pamTableDefinition
*/
public void addTableItems(PamTableDefinition pamTableDefinition);
public void addTableItems(EmptyTableDefinition pamTableDefinition);
/**
* Save data - that is transfer data from the pamDataUnit to the data objects
@ -24,7 +24,7 @@ public interface SQLLoggingAddon {
* @param pamDataUnit data unit
* @return true if successful
*/
public boolean saveData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition, PamDataUnit pamDataUnit);
public boolean saveData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition, PamDataUnit pamDataUnit);
/**
* Load data - that is read data from the table definition and turn it into something sensible
@ -33,7 +33,7 @@ public interface SQLLoggingAddon {
* @param pamDataUnit data unit
* @return true if successful
*/
public boolean loadData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition, PamDataUnit pamDataUnit);
public boolean loadData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition, PamDataUnit pamDataUnit);
/**
* Get a name for the SQLLogging Addon. this is used

94
src/generalDatabase/XMLSettingsTableDefinition.java Normal file
View File

@ -0,0 +1,94 @@
package generalDatabase;
import java.sql.Types;
import PamguardMVC.PamConstants;
public class XMLSettingsTableDefinition extends EmptyTableDefinition {
private PamTableItem dataStart, dataEnd, processStart, processEnd, type, name, pamGuardVersion, settingsVersion, xmlSettings;
public XMLSettingsTableDefinition(String tableName) {
super(tableName, SQLLogging.UPDATE_POLICY_WRITENEW);
pamTableItems.add(dataStart = new PamTableItem("Data Start", Types.TIMESTAMP, "Data start time"));
pamTableItems.add(dataEnd = new PamTableItem("Data End", Types.TIMESTAMP, "Data end time"));
pamTableItems.add(processStart = new PamTableItem("Process Start", Types.TIMESTAMP, "Process start time"));
pamTableItems.add(processEnd = new PamTableItem("Process End", Types.TIMESTAMP, "Process end time"));
addTableItem(type = new PamTableItem("unitType", Types.CHAR, PamConstants.MAX_ITEM_NAME_LENGTH));
addTableItem(name = new PamTableItem("unitName", Types.CHAR, PamConstants.MAX_ITEM_NAME_LENGTH));
addTableItem(pamGuardVersion = new PamTableItem("PAMGuardVersion", Types.INTEGER));
addTableItem(settingsVersion = new PamTableItem("SettingsVersion", Types.INTEGER));
addTableItem(xmlSettings = new PamTableItem("XMLSettings", Types.VARCHAR));
setUseCheatIndexing(false);
}
/**
* @return the dataStart
*/
public PamTableItem getDataStart() {
return dataStart;
}
/**
* @return the dataEnd
*/
public PamTableItem getDataEnd() {
return dataEnd;
}
/**
* @return the processStart
*/
public PamTableItem getProcessStart() {
return processStart;
}
/**
* @return the processEnd
*/
public PamTableItem getProcessEnd() {
return processEnd;
}
/**
* @return the type
*/
public PamTableItem getType() {
return type;
}
/**
* @return the name
*/
public PamTableItem getName() {
return name;
}
/**
* @return the pamGuardVersion
*/
public PamTableItem getPamGuardVersion() {
return pamGuardVersion;
}
/**
* @return the settingsVersion
*/
public PamTableItem getSettingsVersion() {
return settingsVersion;
}
/**
* @return the xmlSettings
*/
public PamTableItem getXmlSettings() {
return xmlSettings;
}
}

187
src/generalDatabase/parameterstore/ParameterDatabaseStore.java Normal file
View File

@ -0,0 +1,187 @@
package generalDatabase.parameterstore;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.sql.Types;
import java.util.Arrays;
import java.util.Collection;
import PamModel.parametermanager.ManagedParameters;
import PamModel.parametermanager.PamParameterData;
import PamModel.parametermanager.PamParameterSet;
import generalDatabase.DBControlUnit;
import generalDatabase.EmptyTableDefinition;
import generalDatabase.PamConnection;
import generalDatabase.PamTableItem;
import generalDatabase.SQLTypes;
/**
* Store parameters from a managed parameter set in the PAMGuard database. These go into a dead simple table, which has
* two columns. The first is a name, the second a string value. Each parameter can only appear once.
* This works with ManagedParameters using the same names and field names that go into the xml output.
* @author dg50
*
*/
public class ParameterDatabaseStore {
private EmptyTableDefinition tableDef;
private PamTableItem nameItem, dataItem;
public ParameterDatabaseStore(String tableName) {
tableDef = new EmptyTableDefinition(tableName);
tableDef.addTableItem(nameItem = new PamTableItem("ParameterName", Types.VARCHAR));
tableDef.addTableItem(dataItem = new PamTableItem("Value", Types.VARCHAR));
}
public boolean saveParameterSet(ManagedParameters managedParameters) {
if (managedParameters == null) {
return false;
}
return saveParameterSet(managedParameters.getClass().getSimpleName(), managedParameters);
}
private boolean saveParameterSet(String name, ManagedParameters managedParameters) {
DBControlUnit dbControl = DBControlUnit.findDatabaseControl();
if (dbControl == null) {
return false;
}
PamConnection con = dbControl.getConnection();
if (checkTable(con) == false) {
return false;
}
String prefix;
if (name == null) {
prefix = "";
}
else {
prefix = name + ".";
}
PamParameterSet paramSet = managedParameters.getParameterSet();
Collection<PamParameterData> params = paramSet.getParameterCollection();
for (PamParameterData paramData : params) {
String paramName = paramData.getFieldName();
paramName = prefix + paramName;
Object data = null;
try {
data = paramData.getData();// .getField().get(managedParameters);
} catch (IllegalArgumentException | IllegalAccessException e) {
e.printStackTrace();
}
// System.out.printf("Store param \"%s\" as \"%s\"\n", paramName, data);
saveToDatabase(con, paramName, data);
}
dbControl.commitChanges();
return true;
}
private boolean saveToDatabase(PamConnection con, String name, Object data) {
int[] existing = findExistingRows(con, name);
boolean ok = true;
if (existing == null || existing.length == 0) {
ok |= newRecord(con, name, data);
}
else {
ok |= updateRecord(con, existing[0], name, data);
if (existing.length > 1) {
for (int i = 1; i < existing.length; i++) {
ok |= deleteDuplicateRow(con, existing[i]);
}
}
}
return true;
}
private int[] findExistingRows(PamConnection con, String name) {
/**
* Find existing rows with that name.
*/
int[] rows = new int[0];
if (con == null) {
return rows;
}
String qStr = String.format("SELECT Id FROM %s WHERE %s='%s'", tableDef.getTableName(), nameItem.getName(), name);
try {
Statement stmt = con.getConnection().createStatement();
ResultSet res = stmt.executeQuery(qStr);
while (res.next()) {
int rowId = res.getInt(1);
rows = Arrays.copyOf(rows, rows.length+1);
rows[rows.length-1] = rowId;
}
res.close();
stmt.close();
} catch (SQLException e) {
e.printStackTrace();
}
return rows;
}
private boolean newRecord(PamConnection con, String name, Object data) {
String insertStr = tableDef.getSQLInsertString(con.getSqlTypes());
try {
PreparedStatement stmt = con.getConnection().prepareStatement(insertStr);
stmt.setString(1, name);
if (data == null) {
stmt.setNull(2, Types.VARCHAR);
}
else {
stmt.setString(2, data.toString());
}
stmt.executeUpdate();
} catch (SQLException e) {
e.printStackTrace();
return false;
}
return true;
}
private boolean updateRecord(PamConnection con, int iRow, String name, Object data) {
SQLTypes st = con.getSqlTypes();
String updateString = String.format("UPDATE %s SET %s = '%s' WHERE Id = %d", tableDef.getTableName(),
st.formatColumnName(dataItem.getName()), data, iRow);
try {
PreparedStatement stmt = con.getConnection().prepareStatement(updateString);
stmt.executeUpdate();
} catch (SQLException e) {
e.printStackTrace();
return false;
}
return true;
}
private boolean deleteDuplicateRow(PamConnection con, int rowId) {
String delStr = String.format("DELETE FROM %s WHERE Id=%d", tableDef.getTableName(), rowId);
try {
PreparedStatement stmt = con.getConnection().prepareStatement(delStr);
stmt.executeUpdate();
} catch (SQLException e) {
e.printStackTrace();
return false;
}
return true;
}
private boolean checkTable(PamConnection con) {
DBControlUnit dbControl = DBControlUnit.findDatabaseControl();
if (dbControl == null) {
return false;
}
dbControl.commitChanges();
return dbControl.getDbProcess().checkTable(tableDef);
}
}

3
src/gpl/io/GPLLogging.java
View File

@ -5,6 +5,7 @@ import java.sql.Types;
import PamDetection.AcousticSQLLogging;
import PamguardMVC.PamDataBlock;
import PamguardMVC.PamDataUnit;
import generalDatabase.EmptyTableDefinition;
import generalDatabase.PamTableDefinition;
import generalDatabase.PamTableItem;
import generalDatabase.SQLTypes;
@ -22,7 +23,7 @@ public class GPLLogging extends AcousticSQLLogging {
super(gplDetectionBlock, gplControlledUnit.getUnitName() + " Detections");
this.gplControlledUnit = gplControlledUnit;
PamTableDefinition pamTable = getTableDefinition();
EmptyTableDefinition pamTable = getTableDefinition();
pamTable.addTableItem(peakValue = new PamTableItem("PeakValue", Types.REAL));
pamTable.addTableItem(contourArea = new PamTableItem("ContourArea", Types.REAL));
}

8
src/loc3d_Thode/TowedArray3DSQLLogging.java
View File

@ -1,5 +1,6 @@
package loc3d_Thode;
import generalDatabase.EmptyTableDefinition;
import generalDatabase.PamDetectionLogging;
import generalDatabase.PamTableDefinition;
import generalDatabase.PamTableItem;
@ -17,7 +18,6 @@ public class TowedArray3DSQLLogging extends PamDetectionLogging {
TowedArray3DController towedArray3DController;
PamTableDefinition tableDefinition;
PamTableItem dateItem, range_boat_Item, range_f_Item, range_r_Item, depthItem, azi_boat_Item,azi_f_Item, azi_r_Item, tdd_Item,
bearing_f_Item,bearing_r_Item, tds_f_Item, tds_r_Item, za_f_Item, za_r_Item;
@ -34,14 +34,14 @@ public class TowedArray3DSQLLogging extends PamDetectionLogging {
this.towedArray3DController = towedArray3DController;
// create the table definition.
tableDefinition = createTableDefinition();
EmptyTableDefinition tableDefinition = createTableDefinition();
}
public PamTableDefinition createTableDefinition() {
public EmptyTableDefinition createTableDefinition() {
// PamTableDefinition tableDef = new PamTableDefinition(towedArray3DController.getUnitName(), getUpdatePolicy());
PamTableDefinition tableDef = super.getTableDefinition();
EmptyTableDefinition tableDef = super.getTableDefinition();
tableDef.setUpdatePolicy(SQLLogging.UPDATE_POLICY_WRITENEW);
// PamTableItem tableItem;

7
src/matchedTemplateClassifer/annotation/MatchedClickAnnotationSQL.java
View File

@ -7,6 +7,7 @@ import java.util.List;
import PamUtils.PamArrayUtils;
import PamguardMVC.PamDataUnit;
import PamguardMVC.debug.Debug;
import generalDatabase.EmptyTableDefinition;
import generalDatabase.PamTableDefinition;
import generalDatabase.PamTableItem;
import generalDatabase.SQLLoggingAddon;
@ -49,7 +50,7 @@ public class MatchedClickAnnotationSQL implements SQLLoggingAddon {
}
@Override
public void addTableItems(PamTableDefinition pamTableDefinition) {
public void addTableItems(EmptyTableDefinition pamTableDefinition) {
pamTableDefinition.addTableItem(typeTable);
pamTableDefinition.addTableItem(mtThresholdsTable);
pamTableDefinition.addTableItem(mtMatchCorrsTable);
@ -58,7 +59,7 @@ public class MatchedClickAnnotationSQL implements SQLLoggingAddon {
}
@Override
public boolean saveData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
public boolean saveData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
MatchedClickAnnotation clickAnnotation =
(MatchedClickAnnotation) pamDataUnit.findDataAnnotation(MatchedClickAnnotation.class);
@ -95,7 +96,7 @@ public class MatchedClickAnnotationSQL implements SQLLoggingAddon {
}
@Override
public boolean loadData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
public boolean loadData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
String threshold = mtThresholdsTable.getDeblankedStringValue();
String mtMatchCorrs = mtMatchCorrsTable.getDeblankedStringValue();

44
src/metadata/MetaDataContol.java Normal file
View File

@ -0,0 +1,44 @@
package metadata;
import javax.swing.JFrame;
import javax.swing.JMenuItem;
import PamController.PamControlledUnit;
import PamModel.parametermanager.ParameterSetManager;
import generalDatabase.parameterstore.ParameterDatabaseStore;
import metadata.deployment.DeploymentData;
public class MetaDataContol extends PamControlledUnit {
public static final String unitType = "Meta Data";
private DeploymentData deploymentData = new DeploymentData();
private ParameterSetManager<DeploymentData> deploymentSetManager;
public MetaDataContol(String unitName) {
super(unitType, unitName);
deploymentSetManager = new ParameterSetManager<DeploymentData>(deploymentData, "Deployment Data");
}
@Override
public JMenuItem createFileMenu(JFrame parentFrame) {
return deploymentSetManager.getMenuItem(parentFrame);
}
/**
* @return the deploymentData
*/
public DeploymentData getDeploymentData() {
return deploymentData;
}
/**
* @param deploymentData the deploymentData to set
*/
public void setDeploymentData(DeploymentData deploymentData) {
this.deploymentData = deploymentData;
}
}

266
src/metadata/deployment/DeploymentData.java Normal file
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@ -0,0 +1,266 @@
package metadata.deployment;
import java.io.Serializable;
import PamModel.parametermanager.FieldNotFoundException;
import PamModel.parametermanager.ManagedParameters;
import PamModel.parametermanager.PamParameterSet;
/**
* Class to hold Deployment data in a form consistent with the ANSI PAM
* Standard. This has been keep separate from the Tethys Interface to keep it
* easy to benefit from these data without using Tethys itself.
*
* @author dg50
*
*/
public class DeploymentData implements Serializable, Cloneable, ManagedParameters {
public static final long serialVersionUID = 1L;
/**
* String that uniquely identifies this deployment.
*/
private String id;
/**
* Name of project associated with this deployment. Can be related to a
* geographic region, funding source, etc
*/
private String project;
/**
* Deployment identifier, a number related to either the Nth deployment
* operation in a series of deployments or the Nth deployment at a specific
* site. This is different from Id which is unique across all deployments
*/
private int deploymentId;
/**
* Alternative deployment description.
*/
private String deploymentAlias;
/**
* Name for current location.
*/
private String site;
/**
* Alternative names for the deployment location
*/
private String siteAliases;
/**
* Name of deployment cruise.
*/
private String cruise;
/**
* On what platform is the instrument deployed? (e.g. mooring, tag)
*/
private String platform = "Unknown";
/**
* Name of geographic region.
*/
private String region;
/**
* Instrument type, e.g. HARP, EAR, Popup, DMON, etc.
*/
private String instrumentType;
/**
* Instrument identifier, e.g. serial number
*/
private String instrumentId;
public DeploymentData() {
}
@Override
protected DeploymentData clone() {
try {
return (DeploymentData) super.clone();
} catch (CloneNotSupportedException e) {
e.printStackTrace();
return null;
}
}
@Override
public PamParameterSet getParameterSet() {
PamParameterSet ps = PamParameterSet.autoGenerate(this);
try {
ps.findParameterData("id").setInfo("Unique Id", null, "String that uniquely identifies this deployment", 128);
// ps.setOrder("id", 0);
ps.findParameterData("project").setInfo("Project Name", null, "Name of project associated with this deployment. Can be related to a geographic region, funding source, etc", 200);
ps.findParameterData("deploymentId").setInfo("Deployment Identifier", null, "Deployment identifier, a number related to either the Nth deployment operation in a series of deployments or the Nth deployment at a specific site. This is different from Id which is unique across all deployments");
ps.findParameterData("deploymentAlias").setInfo("Alternative deployment description", null, "Alternative deployment description", 20);
ps.findParameterData("site").setInfo("Site name", null, "Name for current location", 40);
ps.findParameterData("siteAliases").setInfo("Alternative site name", null, "Alternative site description", 40);
ps.findParameterData("cruise").setInfo("Deployment cruise", null, "Name of deployment cruise");
ps.findParameterData("platform").setInfo("Platform type", null, "On what platform is the instrument deployed? (e.g. mooring, tag)", 20);
ps.findParameterData("region").setInfo("Geographic Region", "", "Name of geographic region", 40);
} catch (FieldNotFoundException e) {
e.printStackTrace();
}
return ps;
}
/**
* @return the id
*/
public String getId() {
return id;
}
/**
* @param id the id to set
*/
public void setId(String id) {
this.id = id;
}
/**
* @return the project
*/
public String getProject() {
return project;
}
/**
* @param project the project to set
*/
public void setProject(String project) {
this.project = project;
}
/**
* @return the deploymentId
*/
public int getDeploymentId() {
return deploymentId;
}
/**
* @param deploymentId the deploymentId to set
*/
public void setDeploymentId(int deploymentId) {
this.deploymentId = deploymentId;
}
/**
* @return the deplomentAlias
*/
public String getDeploymentAlias() {
return deploymentAlias;
}
/**
* @param deplomentAlias the deplomentAlias to set
*/
public void setDeploymentAlias(String deplomentAlias) {
this.deploymentAlias = deplomentAlias;
}
/**
* @return the site
*/
public String getSite() {
return site;
}
/**
* @param site the site to set
*/
public void setSite(String site) {
this.site = site;
}
/**
* @return the siteAliases
*/
public String getSiteAliases() {
return siteAliases;
}
/**
* @param siteAliases the siteAliases to set
*/
public void setSiteAliases(String siteAliases) {
this.siteAliases = siteAliases;
}
/**
* @return the cruise
*/
public String getCruise() {
return cruise;
}
/**
* @param cruise the cruise to set
*/
public void setCruise(String cruise) {
this.cruise = cruise;
}
/**
* @return the platform
*/
public String getPlatform() {
return platform;
}
/**
* @param platform the platform to set
*/
public void setPlatform(String platform) {
this.platform = platform;
}
/**
* @return the region
*/
public String getRegion() {
return region;
}
/**
* @param region the region to set
*/
public void setRegion(String region) {
this.region = region;
}
/**
* @return the instrumentType
*/
public String getInstrumentType() {
return instrumentType;
}
/**
* @param instrumentType the instrumentType to set
*/
public void setInstrumentType(String instrumentType) {
this.instrumentType = instrumentType;
}
/**
* @return the instrumentId
*/
public String getInstrumentId() {
return instrumentId;
}
/**
* @param instrumentId the instrumentId to set
*/
public void setInstrumentId(String instrumentId) {
this.instrumentId = instrumentId;
}
}

40
src/metadata/deployment/QAData.java Normal file
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@ -0,0 +1,40 @@
package metadata.deployment;
import java.io.Serializable;
import PamModel.parametermanager.ManagedParameters;
import PamModel.parametermanager.PamParameterSet;
/**
* Largely the content of the Tethys QualityAssurance schema
* @author dg50
*
*/
public class QAData implements Serializable, Cloneable, ManagedParameters {
public static final long serialVersionUID = 1L;
private String objectives;
private String qaAbstract;
private String method;
private String responsibleName;
private String responsibleOrganisation;
private String responsiblePosition;
private String responsiblePhone;
private String responsibleAddress;
private String responsibleEmail;
public QAData() {
// TODO Auto-generated constructor stub
}
@Override
public PamParameterSet getParameterSet() {
PamParameterSet ps = PamParameterSet.autoGenerate(this);
return ps;
}
}

7
src/nidaqdev/networkdaq/NIDaqLogging.java
View File

@ -3,6 +3,7 @@ package nidaqdev.networkdaq;
import java.sql.Types;
import PamguardMVC.PamDataUnit;
import generalDatabase.EmptyTableDefinition;
import generalDatabase.PamTableDefinition;
import generalDatabase.PamTableItem;
import generalDatabase.SQLLoggingAddon;
@ -20,12 +21,12 @@ public class NIDaqLogging implements SQLLoggingAddon {
}
@Override
public void addTableItems(PamTableDefinition pamTableDefinition) {
public void addTableItems(EmptyTableDefinition pamTableDefinition) {
pamTableDefinition.addTableItem(crioTemperature);
}
@Override
public boolean saveData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
public boolean saveData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
Double lastTemp = niNetworkDaq.getLastTemperature();
if (lastTemp == null) {
crioTemperature.setValue(null);
@ -38,7 +39,7 @@ public class NIDaqLogging implements SQLLoggingAddon {
}
@Override
public boolean loadData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
public boolean loadData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
// TODO Auto-generated method stub
return false;
}

7
src/rawDeepLearningClassifier/logging/DLAnnotationSQL.java
View File

@ -1,6 +1,7 @@
package rawDeepLearningClassifier.logging;
import PamguardMVC.PamDataUnit;
import generalDatabase.EmptyTableDefinition;
import generalDatabase.PamTableDefinition;
import generalDatabase.SQLLoggingAddon;
import generalDatabase.SQLTypes;
@ -12,19 +13,19 @@ public class DLAnnotationSQL implements SQLLoggingAddon {
}
@Override
public void addTableItems(PamTableDefinition pamTableDefinition) {
public void addTableItems(EmptyTableDefinition pamTableDefinition) {
// TODO Auto-generated method stub
}
@Override
public boolean saveData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
public boolean saveData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
// TODO Auto-generated method stub
return false;
}
@Override
public boolean loadData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
public boolean loadData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition, PamDataUnit pamDataUnit) {
// TODO Auto-generated method stub
return false;
}

13
src/targetMotionOld/TargetMotionSQLLogging.java
View File

@ -15,6 +15,7 @@ import PamDetection.AbstractLocalisation;
import PamDetection.LocContents;
import PamUtils.LatLong;
import PamguardMVC.PamDataUnit;
import generalDatabase.EmptyTableDefinition;
import generalDatabase.PamTableDefinition;
import generalDatabase.PamTableItem;
import generalDatabase.SQLLoggingAddon;
@ -119,7 +120,7 @@ public class TargetMotionSQLLogging implements SQLLoggingAddon {
}
@Override
public void addTableItems(PamTableDefinition pamTableDefinition) {
public void addTableItems(EmptyTableDefinition pamTableDefinition) {
pamTableDefinition.addTableItem(modelName);
@ -146,7 +147,7 @@ public class TargetMotionSQLLogging implements SQLLoggingAddon {
}
@Override
public boolean saveData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition,
public boolean saveData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition,
PamDataUnit pamDataUnit) {
AbstractLocalisation tmResult = pamDataUnit.getLocalisation();
clearEverything();
@ -218,7 +219,7 @@ public class TargetMotionSQLLogging implements SQLLoggingAddon {
return true;
}
private boolean saveGroupLocalisation(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition,
private boolean saveGroupLocalisation(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition,
PamDataUnit pamDataUnit, GroupLocalisation groupLocalisation) {
int nAmbiguities = groupLocalisation.getAmbiguityCount();
@ -239,7 +240,7 @@ public class TargetMotionSQLLogging implements SQLLoggingAddon {
return true;
}
private boolean saveGroupLocalisation(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition,
private boolean saveGroupLocalisation(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition,
PamDataUnit pamDataUnit, int resultIndex, GroupLocResult tmResult) {
@ -323,7 +324,7 @@ public class TargetMotionSQLLogging implements SQLLoggingAddon {
}
@Override
public boolean loadData(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition,
public boolean loadData(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition,
PamDataUnit pamDataUnit) {
GroupLocalisation tml = new GroupLocalisation(pamDataUnit, null);
@ -341,7 +342,7 @@ public class TargetMotionSQLLogging implements SQLLoggingAddon {
return true;
}
private GroupLocResult loadLocResult(SQLTypes sqlTypes, PamTableDefinition pamTableDefinition,
private GroupLocResult loadLocResult(SQLTypes sqlTypes, EmptyTableDefinition pamTableDefinition,
PamDataUnit pamDataUnit, GroupLocalisation tml, int resultIndex) {
double latVal, longVal;

93
src/tethys/TethysControl.java Normal file
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@ -0,0 +1,93 @@
package tethys;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.ArrayList;
import javax.swing.JFrame;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import PamController.PamControlledUnit;
import PamController.PamController;
import PamguardMVC.PamDataBlock;
import nilus.Deployment;
import nilus.Deployment.Instrument;
import tethys.output.StreamExportParams;
import tethys.output.TethysExportParams;
import tethys.output.TethysExporter;
import tethys.output.swing.TethysExportDialog;
/**
* Quick play with a simple system for outputting data to Tethys. At it's start
* this is simply going to offer a dialog and have a few functions which show how
* to access data within PAMGuard.
* @author dg50
*
*/
public class TethysControl extends PamControlledUnit {
public static final String unitType = "Tethys Interface";
public static String defaultName = "Tethys";
private TethysExportParams tethysExportParams = new TethysExportParams();
public TethysControl(String unitName) {
super(unitType, unitName);
}
@Override
public JMenuItem createFileMenu(JFrame parentFrame) {
JMenu tethysMenu = new JMenu("Tethys");
JMenuItem tethysExport = new JMenuItem("Export ...");
tethysMenu.add(tethysExport);
tethysExport.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
tethysExport(parentFrame);
}
});
return tethysMenu;
}
/**
* @return the tethysExportParams
*/
public TethysExportParams getTethysExportParams() {
return tethysExportParams;
}
/**
* We'll probably want to
* @param parentFrame
*/
protected void tethysExport(JFrame parentFrame) {
TethysExportParams newExportParams = TethysExportDialog.showDialog(parentFrame, this);
if (newExportParams != null) {
// dialog returns null if cancel was pressed.
tethysExportParams = newExportParams;
exportTethysData(tethysExportParams);
}
}
/**
* We'll arrive here if the dialog has been opened and we want to export Tethys data.
* @param tethysExportParams2
*/
private void exportTethysData(TethysExportParams tethysExportParams) {
TethysExporter tethysExporter = new TethysExporter(this, tethysExportParams);
tethysExporter.doExport();
}
/**
* A name for any deta selectors.
* @return
*/
public String getDataSelectName() {
return getUnitName();
}
}

24
src/tethys/dbxml/DBXMLConnect.java Normal file
View File

@ -0,0 +1,24 @@
package tethys.dbxml;
import tethys.TethysControl;
public class DBXMLConnect {
private TethysControl tethysControl;
public DBXMLConnect(TethysControl tethysControl) {
this.tethysControl = tethysControl;
}
public boolean openDatabase() {
return true;
}
public void closeDatabase() {
}
// add whatever calls are necessary to set up schema's etc.
}

85
src/tethys/deployment/DeploymentWrapper.java Normal file
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@ -0,0 +1,85 @@
package tethys.deployment;
import java.io.ByteArrayOutputStream;
import java.io.Serializable;
import java.lang.annotation.Annotation;
import java.lang.reflect.AnnotatedType;
import java.util.List;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBElement;
import javax.xml.bind.Marshaller;
import javax.xml.namespace.QName;
import javax.xml.validation.Schema;
import nilus.Deployment.Data.Audio;
import nilus.Deployment;
import nilus.Deployment.Data;
import nilus.Deployment.Instrument;
public class DeploymentWrapper<T extends Serializable> {
public DeploymentWrapper(T tethysObject) {
}
public List<String> getFieldNames() {
return null;
}
public List<Serializable> getComplexObjects() {
return null;
}
public static void main(String[] args) {
// quick play with some JAXB objects to see what they can do.
Deployment deployment = new Deployment();
Class<? extends Deployment> deploymentClass = deployment.getClass();
Annotation[] annots = deploymentClass.getAnnotations();
AnnotatedType[] annotInterfaces = deploymentClass.getAnnotatedInterfaces();
Annotation[] declAnnots = deploymentClass.getDeclaredAnnotations();
Instrument instrument = new Instrument();
instrument.setID("22");
instrument.setType("SoundTrap");
QName qName = new QName("Instrument");
JAXBElement<Instrument> jInst = new JAXBElement<Deployment.Instrument>(qName, Instrument.class, instrument);
deployment.getContent().add(jInst);
Deployment.Data data = new Data();
Audio audio = new Audio();
audio.setProcessed("??");
data.setAudio(audio);
JAXBElement jData = new JAXBElement<Deployment.Data>(new QName("Data"), Data.class, data);
deployment.getContent().add(jData);
String project = "Project Name";
JAXBElement<String> jProj = new JAXBElement<String>(new QName("Project"), String.class, project);
deployment.getContent().add(jProj);
String aaa = "Project Something else";
JAXBElement<String> jProj2 = new JAXBElement<String>(new QName("Region"), String.class, aaa);
deployment.getContent().add(jProj2);
try {
JAXBContext jContext = JAXBContext.newInstance(Deployment.class);
Marshaller mar = (Marshaller) jContext.createMarshaller();
mar.setProperty(javax.xml.bind.Marshaller.JAXB_FORMATTED_OUTPUT, true);
ByteArrayOutputStream bos = new ByteArrayOutputStream();
mar.marshal(deployment, bos);
String xml = new String(bos.toByteArray());
System.out.println(xml);
// Schema schema = mar.getSchema(); // is null. Can't generate it's own it seems.
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
}

64
src/tethys/deployment/PamDeployment.java Normal file
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@ -0,0 +1,64 @@
package tethys.deployment;
import java.io.Serializable;
import nilus.DeploymentRecoveryDetails;
/**
* Wrapper and functions associated with the Tethys Deployment object which can
* exchange these with the PAMGuard database and display Everything is just held
* within a list, in no particular order, which getContent public
*
* This is from the Deployment JavaDoc. TBH it's pretty horrible, since it's possible to have
* more than one of each type of object in the list, so not sure what to do about that. Would be nicer
* as a HashTable. however we are where we're are for now. Start by focussing on getting the
* content saved for each type
*
* List<Serializable> getContent()
*
* Gets the value of the content property. This accessor method returns a
* reference to the live list,not a snapshot. Therefore any modification you
* make to the returned list will be present inside the JAXB object.This is why
* there is not a set method for the content property.
*
* For example, to add a new item, do as follows: getContent().add(newItem);
*
*
* Objects of the following type(s) are allowed in the list JAXBElement<String>
* JAXBElement<String>
* JAXBElement<Integer>
* JAXBElement<DeploymentRecoveryDetails>
* JAXBElement<String>
* JAXBElement<Deployment.SamplingDetails>
* JAXBElement<Deployment.Sensors>
* JAXBElement<Deployment.Instrument>
* JAXBElement<String>
* JAXBElement<Deployment.Data>
* JAXBElement<String> String
* JAXBElement<AcousticDataQAType>
* JAXBElement<Deployment.SiteAliases>
* JAXBElement<String>
* JAXBElement<DeploymentRecoveryDetails>
*
*
* @author dg50
*
*/
public class PamDeployment {
public PamDeployment() {
}
public DeploymentRecoveryDetails getDeploymentRecoveryDetails() {
DeploymentRecoveryDetails drd = new DeploymentRecoveryDetails();
return null;
}
private void ripApart(Serializable object) {
Class cls = object.getClass();
// cls.get
}
}

27
src/tethys/output/StreamExportParams.java Normal file
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package tethys.output;
import java.io.Serializable;
/**
* Parameters controlling export of a single stream.
* Starts just with a boolean 'selected', but may grow.
* These all contain data names rather than references to a Datablock so that
* they can be serialised.
* @author dg50
*
*/
public class StreamExportParams implements Serializable {
public static final long serialVersionUID = 1L;
public StreamExportParams(String longDataName, boolean selected) {
super();
this.longDataName = longDataName;
this.selected = selected;
}
public String longDataName;
public boolean selected;
}

59
src/tethys/output/TethysExportParams.java Normal file
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package tethys.output;
import java.io.Serializable;
import java.util.HashMap;
import PamguardMVC.PamDataBlock;
/**
* Parameters for controlling export of Tethys data.
* @author dg50
*
*/
public class TethysExportParams implements Serializable, Cloneable{
public static final long serialVersionUID = 1L;
/*
* Need to add lots of other parameters here, such as the connection detils
* for the tethys database.
*/
private HashMap<String, StreamExportParams> streamParamsMap = new HashMap();
@Override
public TethysExportParams clone() {
try {
return (TethysExportParams) super.clone();
} catch (CloneNotSupportedException e) {
e.printStackTrace();
return null;
}
}
/**
* Set stream export parameters for a given datablock.
* @param dataBlock
* @param exportParams
*/
public void setStreamParams(PamDataBlock dataBlock, StreamExportParams exportParams) {
setStreamParams(dataBlock.getLongDataName(), exportParams);
}
/**
* Set stream export parameters for a given data name.
* @param dataBlock
* @param exportParams
*/
public void setStreamParams(String longDataName, StreamExportParams exportParams) {
streamParamsMap.put(longDataName, exportParams);
}
public StreamExportParams getStreamParams(PamDataBlock dataBlock) {
return getStreamParams(dataBlock.getLongDataName());
}
private StreamExportParams getStreamParams(String longDataName) {
return streamParamsMap.get(longDataName);
}
}

272
src/tethys/output/TethysExporter.java Normal file
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package tethys.output;
import java.util.ArrayList;
import org.w3c.dom.Document;
import Acquisition.AcquisitionControl;
import Acquisition.AcquisitionProcess;
import Array.ArrayManager;
import Array.Hydrophone;
import Array.PamArray;
import Array.SnapshotGeometry;
import PamController.PamControlledUnit;
import PamController.PamController;
import PamController.settings.output.xml.PamguardXMLWriter;
import PamUtils.PamCalendar;
import PamguardMVC.PamDataBlock;
import PamguardMVC.PamDataUnit;
import PamguardMVC.dataSelector.DataSelector;
import generalDatabase.DBSchemaWriter;
import generalDatabase.SQLLogging;
import metadata.MetaDataContol;
import metadata.deployment.DeploymentData;
import tethys.TethysControl;
import tethys.dbxml.DBXMLConnect;
import tethys.pamdata.TethysDataProvider;
import tethys.pamdata.TethysSchema;
/**
* Class sitting at the centre of all operations. It will talk to PAMGuard objects to get schemas and data
* and talk to the database connection to move data out (and possibly in). Eventually, a lot of the functionality
* in here will be moved to worker threads (SwingWorker?) so that it's easy to keep dialogs alive, show
* progress for big export jobs, etc. For now though, it's a relatively simple set of function which
* we can use to a) open the database, b) check everything such as schemas, etc. c) export data and d) clean up.
* @author dg50
*
*/
public class TethysExporter {
private TethysControl tethysControl;
private TethysExportParams tethysExportParams;
private DBXMLConnect dbxmlConnect;
public TethysExporter(TethysControl tethysControl, TethysExportParams tethysExportParams) {
this.tethysControl = tethysControl;
this.tethysExportParams = tethysExportParams;
dbxmlConnect = new DBXMLConnect(tethysControl);
}
/**
* Does the work. In reality this will need an awful lot of changing, for instance
* to provide feedback to an observer class to show progress on the display.
* @return OK if success.
*/
public boolean doExport() {
boolean dbOK = dbxmlConnect.openDatabase();
if (!dbOK) {
/*
* should we set up some exceptions to throw ? Can be a lot
* more informative than a simple 'false'
*/
return false;
}
SnapshotGeometry arrayGeometry = findArrayGeometrey();
/*
* Call some general export function
*/
exportGeneralData(tethysExportParams);
/*
* go through the export params and call something for every
* data block that's enabled.
*/
ArrayList<PamDataBlock> allDataBlocks = PamController.getInstance().getDataBlocks();
for (PamDataBlock aDataBlock : allDataBlocks) {
StreamExportParams streamExportParams = tethysExportParams.getStreamParams(aDataBlock);
if (streamExportParams == null || streamExportParams.selected == false) {
continue; // not interested in this one.
}
exportDataStream(aDataBlock, tethysExportParams, streamExportParams);
}
/*
* Then do whatever else is needed to complete the document.
*/
dbxmlConnect.closeDatabase();
return true;
}
/**
* find Deployment data. This is stored in a separate PAMGuard module, which may not
* be present.
* @return
*/
public DeploymentData findDeploymentData() {
/**
* What to do if this isn't present or is incomplete ? Should we be showing this in the
* main export dialog at some point ? More a Q for when we make a nicer UI later in the project.
*/
MetaDataContol metaControl = (MetaDataContol) PamController.getInstance().findControlledUnit(MetaDataContol.unitType);
if (metaControl == null) {
return null;
}
else {
return metaControl.getDeploymentData();
}
}
public SnapshotGeometry findArrayGeometrey() {
/*
* this should never be null, but again, we might want to put some warnings
* and exception handlers in here anyway. Really just an example to show how
* to find this. We'll need to dig a bit elsewhere to get more detailed
* hydrophone information.
*/
/*
* In PAMGuard hydrophones are assigned to streamers, which can have different methods for estimating
* their positions from GPS. The geometry is a sum of xyz in the streamer and xyz in the hydrophone object
* Within a streamer, hydrophones are considered rigid relative to each other. The stremer will floow
* a choice of modesl (rigid, threading, etc) to estimate it's position relative to the GPS track. Different
* errors are used when estimating localisation errors within and between streamers.
* The Snapshot geometry sorts a lot of this out for a point in time and will give back a single object
* which is most of what we'll be wanting.
*/
PamArray currentArray = ArrayManager.getArrayManager().getCurrentArray();
SnapshotGeometry currentGeometry = currentArray.getSnapshotGeometry(PamCalendar.getTimeInMillis());
/*
* The following lines of code show how to get more detailed calibration info for each
* hydrophone, but we'll have to think about the easiest way to repackage this for Tethys.
* e.g. this function could be modified to return the correct Tethys object in one go.
*/
ArrayList<Hydrophone> hydrophones = currentArray.getHydrophoneArray();
/*
* each object in the list will have more detailed cal information for each phone. But
* for the full system calibration we'd need to go to the Acquisition module.
*/
AcquisitionControl daqControl = (AcquisitionControl) PamController.getInstance().findControlledUnit(AcquisitionControl.unitType);
if (daqControl != null) {
AcquisitionProcess daqProcess = daqControl.getAcquisitionProcess();
for (int iPhone = 0; iPhone < hydrophones.size(); iPhone++) {
Hydrophone aPhone = hydrophones.get(iPhone);
double totalCal = -daqProcess.rawAmplitude2dB(1, iPhone, false);
System.out.printf("hydrophone %d has sensitivity %3.1fdB + gain %3.1fdB. Total calibration is %3.1fdB re1U/uPa\n",
iPhone, aPhone.getSensitivity(), aPhone.getPreampGain(), totalCal);
}
}
return currentGeometry;
}
/**
* No idea if we need this or not. May want to return something different to void, e.g.
* a reference to the main object for a tethys export. I've no idea !
* @param tethysExportParams2
*/
private void exportGeneralData(TethysExportParams tethysExportParams) {
// TODO Auto-generated method stub
}
/**
* Here is where we export data for a specific data stream to Tethys.
*
* @param aDataBlock
* @param tethysExportParams
* @param streamExportParams
*/
private void exportDataStream(PamDataBlock aDataBlock, TethysExportParams tethysExportParams,
StreamExportParams streamExportParams) {
/**
* This will probably need to be passed additional parameters and may also want to return something
* other than void in order to build a bigger Tethys document.
*/
/*
* Some examples of how to do whatever is needed to get schema and data out of PAMGuard.
*/
/*
* first we'll probably want a reference to the module containing the data.
* in principle this can't get null, since the datablock was found be searching in
* the other direction.
*/
PamControlledUnit pamControlledUnit = aDataBlock.getParentProcess().getPamControlledUnit();
TethysDataProvider dataProvider = aDataBlock.getTethysDataProvider();
PamguardXMLWriter pamXMLWriter = PamguardXMLWriter.getXMLWriter();
if (dataProvider == null) {
return;
}
TethysSchema tethysSchema = dataProvider.getSchema();
/*
* the schema should have a Document object in it. If we wanted to turn
* that into an XML string we can ...
* (though I'd assume that having the Document is more useful)
*/
String schemaXMLString = pamXMLWriter.getAsString(tethysSchema.getXsd(), false);
// System.out.printf("Schema for %s is %s\n", aDataBlock.getDataName(), schemaXMLString);
/*
* Get the XML settings for that datablock. This is (or should be
* the parameters that were controlling that module, with adequate data about
* upstream modules). I think this has to go somewhere into the Detections document.
*/
Document doc = pamXMLWriter.writeOneModule(pamXMLWriter, System.currentTimeMillis());
String moduleXML = null;
if (doc != null) {
// this string should be XML of all the settings for the module controlling this datablock.
moduleXML = pamXMLWriter.getAsString(doc, true); // change to false to get smaller xml
System.out.printf("Module settings for datablock %s are:\n", moduleXML);
System.out.println(moduleXML);
}
/**
* Now can go through the data. Probably, we'll want to go through all the data in
* the project, but we can hold off on that for now and just go for data that
* are in memory. We'll also have to think a lot about updating parts of the
* database which have been reprocessed - what we want to do, should eventually all
* be options set in the dialog and available within TethysExportParams
* For now though, we're just going to export data that are in memory.
* Once basic export is working, I can easily enough write something which will go
* through an entire data set, go through between two times, etc.
*/
// so this is a way of iterating through the data that are in memory, which will do for now ..
// do it with a data copy which can avoid synchronising the entire block for what may be a long time
// the copy function is itself synched, and is quite fast, so easier and safe this way
ArrayList<PamDataUnit> dataCopy = aDataBlock.getDataCopy();
DataSelector dataSelector = aDataBlock.getDataSelector(tethysControl.getDataSelectName(), false);
int nSkipped = 0;
int nExport = 0;
for (PamDataUnit aData : dataCopy) {
/*
* see if we want this data unit. PAMGuard has a complicated system of data selectors specific to
* each data type. These are centrally managed so you don't need to worry too much about them. They
* are identified by name for each data stream and the behaviour here should follow the selections you
* made in the dialog.
* the data selection system allows different displays to show different data, so a stream can have many differently
* named selectors active at any one time, all doing different things in different parts of PAMGuard.
*/
if (dataSelector != null) {
if (dataSelector.scoreData(aData) <= 0) {
nSkipped++;
continue; // don't want this one.
}
}
/*
* then we do whatever we need to do to convert this into something for Tethys
* this might happen in the tethysSchema object for each data stream ????
*/
nExport ++;
}
System.out.printf("Exported %d data units and skipped %d in %s", nExport, nSkipped, aDataBlock.getLongDataName());
}
}

187
src/tethys/output/swing/TethysExportDialog.java Normal file
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package tethys.output.swing;
import java.awt.BorderLayout;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Window;
import java.util.ArrayList;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.border.TitledBorder;
import PamController.PamController;
import PamView.dialog.PamDialog;
import PamView.dialog.PamGridBagContraints;
import PamguardMVC.PamDataBlock;
import PamguardMVC.dataSelector.DataSelector;
import tethys.TethysControl;
import tethys.output.StreamExportParams;
import tethys.output.TethysExportParams;
/**
* Start of a dialog for controlling the export of Tethys data. For first iteration
* this will just be a list of output streams (PamDataBlocks) which have a database
* connection. Each will have a checkbox. On OK it will return back a class listing
* what to output and the calling function can do as it will. Future versions will
* probably want to push the functionality into a SwingWorker to show progress, etc.
* but that can come later.
*
* Normally, I use single instance dialogs for this sort of thing.
* @author dg50
*
*/
public class TethysExportDialog extends PamDialog {
private static TethysExportDialog singleInstance;
private TethysControl tethysControl;
private TethysExportParams exportParams;
private JPanel streamsPanel;
private ArrayList<DataStreamSet> dataStreamSets = new ArrayList<>();
private TethysExportDialog(Window parentFrame, TethysControl tethysControl) {
super(parentFrame, "Tethys Export", false);
this.tethysControl = tethysControl;
JPanel mainPanel = new JPanel(new BorderLayout());
/*
* Expect to add at least one more panel at the top of this to have options
* for things like connection details to the database. If not another panel,
* then they can be arranged on tabs, as a wizard, etc.
*/
streamsPanel = new JPanel();
streamsPanel.setBorder(new TitledBorder("Data Streams"));
mainPanel.add(BorderLayout.CENTER, streamsPanel);
setDialogComponent(mainPanel);
setResizable(true);
}
public static TethysExportParams showDialog(Window parentFrame, TethysControl tethysControl) {
if (singleInstance == null || singleInstance.getOwner() != parentFrame || singleInstance.tethysControl != tethysControl) {
singleInstance = new TethysExportDialog(parentFrame, tethysControl);
}
singleInstance.makeStreamsPanel();
singleInstance.setParams();
singleInstance.setVisible(true);
return singleInstance.exportParams;
}
/**
* remake the panel. Gets rebuilt whenever dialog opens in case
* the list of available data has changed.
*/
private void makeStreamsPanel() {
streamsPanel.removeAll();
streamsPanel.setLayout(new GridBagLayout());
GridBagConstraints c = new PamGridBagContraints();
dataStreamSets = findDataStreams();
streamsPanel.add(new JLabel(" Data Stream ", JLabel.CENTER), c);
c.gridx++;
streamsPanel.add(new JLabel(" Data Select ", JLabel.CENTER), c);
for (DataStreamSet aSet : dataStreamSets) {
c.gridx = 0;
c.gridy++;
streamsPanel.add(aSet.checkBox, c);
// try to add a data selector
DataSelector dataSelector = aSet.dataBlock.getDataSelector(tethysControl.getDataSelectName(), false);
if (dataSelector != null) {
c.gridx++;
JButton button = dataSelector.getDialogButton(this);
if (button != null) {
streamsPanel.add(button, c);
}
}
}
pack();
}
/**
* Get a set of data blocks that can provide Tethys data.
* @return datablocks which can provide Tethys data
*/
private ArrayList<DataStreamSet> findDataStreams() {
ArrayList<DataStreamSet> sets = new ArrayList<>();
ArrayList<PamDataBlock> allDataBlocks = PamController.getInstance().getDataBlocks();
for (PamDataBlock aDataBlock : allDataBlocks) {
if (aDataBlock.getTethysDataProvider() != null) {
sets.add(new DataStreamSet(aDataBlock));
}
}
return sets;
}
private void setParams() {
this.exportParams = tethysControl.getTethysExportParams();
if (exportParams == null) {
exportParams = new TethysExportParams();
}
else {
exportParams = exportParams.clone();
}
setParams(exportParams);
}
private void setParams(TethysExportParams exportParams) {
if (exportParams == null || dataStreamSets == null) {
return;
}
for (DataStreamSet streamSet : dataStreamSets) {
StreamExportParams streamOpts = exportParams.getStreamParams(streamSet.dataBlock);
if (streamOpts == null) {
continue;
}
streamSet.checkBox.setSelected(streamOpts.selected);
}
}
@Override
public boolean getParams() {
if (exportParams == null || dataStreamSets == null) {
return false;
}
int nSel = 0;
for (DataStreamSet streamSet : dataStreamSets) {
StreamExportParams streamOpts = new StreamExportParams(streamSet.dataBlock.getLongDataName(), streamSet.checkBox.isSelected());
exportParams.setStreamParams(streamSet.dataBlock, streamOpts);
nSel++;
}
return nSel > 0;
}
@Override
public void cancelButtonPressed() {
exportParams = null;
}
@Override
public void restoreDefaultSettings() {
// TODO Auto-generated method stub
}
private class DataStreamSet {
private PamDataBlock dataBlock;
private JCheckBox checkBox;
public DataStreamSet(PamDataBlock dataBlock) {
super();
this.dataBlock = dataBlock;
checkBox = new JCheckBox(dataBlock.getDataName());
checkBox.setToolTipText(dataBlock.getLongDataName());
}
}
}

42
src/tethys/pamdata/AutoTethysProvider.java Normal file
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package tethys.pamdata;
import org.w3c.dom.Document;
import PamguardMVC.PamDataBlock;
import PamguardMVC.PamDataUnit;
import generalDatabase.DBSchemaWriter;
import generalDatabase.SQLLogging;
/**
* Automatically provides Tethys data based on the SQL database interface
* for a data block.
* @author dg50
*
*/
public class AutoTethysProvider implements TethysDataProvider {
private PamDataBlock pamDataBlock;
public AutoTethysProvider(PamDataBlock pamDataBlock) {
this.pamDataBlock = pamDataBlock;
}
@Override
public TethysSchema getSchema() {
SQLLogging logging = pamDataBlock.getLogging();
if (logging == null) {
return null;
}
DBSchemaWriter schemaWriter = new DBSchemaWriter();
Document doc = schemaWriter.generateDatabaseSchema(pamDataBlock, logging, logging.getTableDefinition());
TethysSchema schema = new TethysSchema(doc);
return schema;
}
@Override
public TethysDataPoint getDataPoint(PamDataUnit pamDataUnit) {
// TODO Auto-generated method stub
return null;
}
}

18
src/tethys/pamdata/TethysDataPoint.java Normal file
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@ -0,0 +1,18 @@
package tethys.pamdata;
import PamguardMVC.PamDataUnit;
/**
* This will be a unit of Tethys Data, e.g. a Detection.
* Can it also be used for things like GPS data ?
* @author dg50
*
*/
public class TethysDataPoint {
public TethysDataPoint(PamDataUnit dataUnit) {
// TODO Auto-generated constructor stub
}
}

32
src/tethys/pamdata/TethysDataProvider.java Normal file
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@ -0,0 +1,32 @@
package tethys.pamdata;
import PamguardMVC.PamDataUnit;
/**
* Any PAMGuard data stream which can provide Detection data to PAMGuard will
* be able to return one of these. It will provide a schema and a function which
* can turn individual data units into data formatted for Tethys. The nature of how these
* work TBD.
* @author dg50
*
*/
public interface TethysDataProvider {
/**
* This gets the Tethys schema for this type of data in whatever
* form we decide it's best stored in, an XML string, or what ?
* @return
*/
public TethysSchema getSchema();
/**
* This will convert a data unit for this provider into whatever format we need the
* data to be in for Tethys. Some base function but also bespoke stuff depending on the
* data type. Will probably need writing for every module individually?
* @param pamDataUnit
* @return
*/
public TethysDataPoint getDataPoint(PamDataUnit pamDataUnit);
}

32
src/tethys/pamdata/TethysSchema.java Normal file
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package tethys.pamdata;
import org.w3c.dom.Document;
/**
* object for a Tethys Schema. This may just be a very simple
* wrapper around an XML string, or a JAXB object or something,
* but may get more sophisticated. TBD in discussions with SDSU
*/
public class TethysSchema {
private Document schemaDoc;
public TethysSchema(Document doc) {
this.setXsd(doc);
}
/**
* @return the xsd
*/
public Document getXsd() {
return schemaDoc;
}
/**
* @param xsd the xsd to set
*/
public void setXsd(Document xsd) {
this.schemaDoc = xsd;
}
}

3
src/whistleDetector/WhistleLogger.java
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@ -1,5 +1,6 @@
package whistleDetector;
import generalDatabase.EmptyTableDefinition;
import generalDatabase.PamDetectionLogging;
import generalDatabase.PamTableDefinition;
import generalDatabase.PamTableItem;
@ -24,7 +25,7 @@ public class WhistleLogger extends PamDetectionLogging {
this.whistleControl = whistleControl;
PamTableDefinition tableDefinition = getTableDefinition();
EmptyTableDefinition tableDefinition = getTableDefinition();
tableDefinition.addTableItem(sliceCount = new PamTableItem("SliceCount", Types.INTEGER));
tableDefinition.addTableItem(length = new PamTableItem("WhistleLength", Types.DOUBLE));
tableDefinition.addTableItem(minFreq = new PamTableItem("MinFreq", Types.DOUBLE));