Merge branch 'main' of https://github.com/douggillespie/PAMGuardTethys

src/PamModel/PamModel.java

@@ -473,8 +473,7 @@ final public class PamModel implements PamModelInterface, PamSettings {
 			mi.setToolTipText("Interface to Tethys Database");
 			mi.setModulesMenuGroup(utilitiesGroup);
 			mi.setMaxNumber(1);
-		}
-		
+		}		
 		
 
 		/*

src/generalDatabase/SQLLogging.java

@@ -551,6 +551,71 @@ public abstract class SQLLogging {
 		//		}
 		return resultSet;
 	}
+	
+	/**
+	 * Find the data point which is closest in time to that given, or null 
+	 * returning whatever type of data unit this deals with. 
+	 * @param timeMillis
+	 * @return
+	 */
+	public PamDataUnit findClosestDataPoint(PamConnection con, long timeMillis) {
+
+		PamCursor pamCursor = loggingCursorFinder.getCursor(con, pamTableDefinition);
+
+		// can't really do any math with the string based dates, so will have to query from 
+		// a few s before the time we want. 
+		PamDataUnit[] beforeNafter = new PamDataUnit[2];
+		
+		SQLTypes sqlTypes = con.getSqlTypes();
+		
+		for (int i = 0; i < 2; i++) {
+			String clause;
+		
+			if (i == 0) {
+				clause = String.format("WHERE UTC <= %s ORDER BY UTC DESC", sqlTypes.formatDBDateTimeQueryString(timeMillis));
+			}
+			else {
+				clause = String.format("WHERE UTC >= %s ORDER BY UTC ASC", sqlTypes.formatDBDateTimeQueryString(timeMillis));
+			}
+
+			ResultSet result = pamCursor.openReadOnlyCursor(con, clause);
+			if (result==null) {
+				return null;
+			}
+
+			PamTableItem tableItem;
+			try {
+				if (result.next()) {
+					//				for (int i = 0; i < pamTableDefinition.getTableItemCount(); i++) {
+					//					tableItem = pamTableDefinition.getTableItem(i);
+					//					tableItem.setValue(result.getObject(i + 1));
+					//				}
+					//				return true;
+					boolean ok = transferDataFromResult(con.getSqlTypes(), result);
+					result.close();
+					beforeNafter[i] = createDataUnit(sqlTypes, lastTime, lastLoadIndex);
+				}
+			} catch (SQLException ex) {
+				ex.printStackTrace();
+				continue;
+			}
+		}
+		// now pick the closest
+		if (beforeNafter[0] == null) {
+			return beforeNafter[1];
+		}
+		if (beforeNafter[1] == null) {
+			return beforeNafter[0];
+		}
+		long t1 = timeMillis-beforeNafter[0].getTimeMilliseconds();
+		long t2 = beforeNafter[1].getTimeMilliseconds()-timeMillis;
+		if (t1 < t2) {
+			return beforeNafter[0];
+		}
+		else {
+			return beforeNafter[1];
+		}
+	}
 
 	/**
 	 * Called when a new database is connected to read the last values back in

src/tethys/TethysLocationFuncs.java

@@ -0,0 +1,85 @@
+package tethys;
+
+import Array.ArrayManager;
+import Array.HydrophoneLocator;
+import Array.PamArray;
+import Array.Streamer;
+import GPS.GPSControl;
+import GPS.GpsData;
+import GPS.GpsDataUnit;
+import PamUtils.LatLong;
+import PamUtils.PamUtils;
+import PamguardMVC.PamDataUnit;
+import generalDatabase.DBControlUnit;
+import generalDatabase.PamConnection;
+import nilus.Deployment;
+import nilus.DeploymentRecoveryDetails;
+
+/**
+ * Function(s) to get location information for Tethys in the required format. 
+ * @author dg50
+ *
+ */
+public class TethysLocationFuncs {
+
+
+	/**
+	 * Get everything we need for a deployment document including the track #
+	 * and the deployment / recovery information. Basically this means we 
+	 * have to load the GPS data, then potentially filter it. Slight risk this 
+	 * may all be too much for memory, but give it a go by loading GPS data for 
+	 * the deployment times. 
+	 * @param deployment
+	 */
+	public static void getTrackAndPositionData(Deployment deployment) {
+		long start = TethysTimeFuncs.millisFromGregorianXML(deployment.getDeploymentDetails().getAudioTimeStamp());
+		long end = TethysTimeFuncs.millisFromGregorianXML(deployment.getRecoveryDetails().getAudioTimeStamp());
+		/*
+		 * Need to load data for GPS, Hydrophones and Streamers datablocks for this time period. Can then use
+		 * the snapshot geomentry classes to do the rest from the array manager ?
+		 */
+		boolean ok = true;
+		ok &= addPositionData(deployment.getDeploymentDetails());
+		ok &= addPositionData(deployment.getRecoveryDetails());
+		
+	}
+	
+	/**
+	 * Add position data to DeploymentRecoveryDetails. 
+	 * @param drd
+	 * @return
+	 */
+	public static boolean addPositionData(DeploymentRecoveryDetails drd) {
+		long timeMillis = TethysTimeFuncs.millisFromGregorianXML(drd.getAudioTimeStamp()); 
+		LatLong pos = getLatLongData(timeMillis);
+		if (pos == null) {
+			return false;
+		}
+		drd.setLongitude(PamUtils.constrainedAngle(pos.getLongitude(), 360));
+		drd.setLatitude(pos.getLatitude());
+		drd.setElevationInstrumentM(pos.getHeight());
+		drd.setDepthInstrumentM(-pos.getHeight());
+		return true;
+	}
+	
+	public static LatLong getLatLongData(long timeMillis) {
+		// check the array time. 
+		PamArray array = ArrayManager.getArrayManager().getCurrentArray();
+		Streamer aStreamer = array.getStreamer(0);
+		GPSControl gpsControl = GPSControl.getGpsControl();
+		PamConnection con = DBControlUnit.findConnection();
+		if (gpsControl != null) {
+//			check GPS data are loaded for times around this. 
+			GpsDataUnit gpsData = (GpsDataUnit) gpsControl.getGpsDataBlock().getLogging().findClosestDataPoint(con, timeMillis);
+			if (gpsData != null) {
+				return gpsData.getGpsData();
+			}
+		}
+		HydrophoneLocator hydrophoneLocator = aStreamer.getHydrophoneLocator();
+		if (hydrophoneLocator == null) {
+			return null;
+		}
+		return hydrophoneLocator.getStreamerLatLong(timeMillis);
+	}
+
+}

src/tethys/TethysTimeFuncs.java

@@ -0,0 +1,39 @@
+package tethys;
+
+import java.util.GregorianCalendar;
+
+import javax.xml.datatype.DatatypeConfigurationException;
+import javax.xml.datatype.DatatypeFactory;
+import javax.xml.datatype.XMLGregorianCalendar;
+
+public class TethysTimeFuncs {
+
+	/*
+	 * Copied from http://www.java2s.com/Code/Java/Development-Class/ConvertsagiventimeinmillisecondsintoaXMLGregorianCalendarobject.htm
+	 */
+	public static XMLGregorianCalendar xmlGregCalFromMillis(long millis) {
+		try {
+            final GregorianCalendar calendar = new GregorianCalendar();
+            calendar.setTimeInMillis(millis);
+            return DatatypeFactory.newInstance().newXMLGregorianCalendar(
+                calendar);
+        }
+        catch (final DatatypeConfigurationException ex) {
+            System.out.println("Unable to convert date '%s' to an XMLGregorianCalendar object");
+            return null;
+        }
+	}
+	
+	/**
+	 * Convert a Gregorian calendar value back to milliseconds. 
+	 * @param xmlGregorian
+	 * @return
+	 */
+	public static Long millisFromGregorianXML(XMLGregorianCalendar xmlGregorian) {
+		if (xmlGregorian == null) {
+			return null;
+		}
+	    GregorianCalendar gc2 = xmlGregorian.toGregorianCalendar();
+		return gc2.getTimeInMillis();
+	}
+}

src/tethys/output/TethysExporter.java

@@ -37,8 +37,11 @@ import generalDatabase.DBSchemaWriter;
 import generalDatabase.SQLLogging;
 import metadata.MetaDataContol;
 import metadata.deployment.DeploymentData;
+import nilus.Deployment;
 import nilus.DeploymentRecoveryDetails;
 import tethys.TethysControl;
+import tethys.TethysLocationFuncs;
+import tethys.TethysTimeFuncs;
 import tethys.dbxml.DBXMLConnect;
 import tethys.pamdata.TethysDataProvider;
 import tethys.pamdata.TethysSchema;
@@ -145,77 +148,83 @@ public class TethysExporter {
 		/*
 		 * A load of notes Katie put in ....654654654
 		 */
-		// 1. grab DeploymentRecoveryPair that has deployment details and recovery
-		// details
-		// a. this is based on start and end times
-		// Douglas calculates out dutycycles to only grab the
 
-		// 2. loop through the pairs to populate the extra information
-		// one pair is one deployment
-		// see below for matching
-
-		// id => unique
-		// project => project in pamguard
-		// deploymentId == id
-		// deploymentAlias => blank
-		// site => UI addition in pamguard, not done, can be blank
-		// siteAlias => blank
-		// cruise => UI addition, optional
-		// Platform=> UI addition in pamguard
-		// region => UI addition
-		// Instrument/Type => UI, array manager details (hydrophone names area)
-		// Instrument/Id => UI, array manager details
-		// Instrument/Geometry => in pamguard array manager
-		// SamplingDetails/Channel
-		// ChannelNumber => in pamguard, hyrdrophone array
-		// SensorNumber => in pamguard,
-		// Start => same as timestamp deployment detail
-		// End => same as timestamp recovery detail
-		// Sampling/Regimen (change sample rate, pamgauard doesnt handle, only on, get
-		// channel info in that loop)
-		// TimeStamp => start time
-		// SampleRate_kHz =>
-		// SampleBits =>
-		// Gain (another func call to get gain info)
-		// DutyCycles => needs to be calculated, not fields in pamguard, have fun
-		// Douglas
-		// QualityAssurance => not in pamguard, UI, maybe deployment notes, optional
-		// Data/Audio (static)
-		// URI => folder where audio is saved
-		// Data/Tracks
-		// Track => GPS datatable (granularity filter)
-		// TrackId => not unique between deployments,
-		// TrackEffort
-		// OnPath => scattered throughout pamguard
-		// URI => option, check with Shannon on how they are doing deployments
-		// Sensors/Audio (per hydrophone not quad array) streamer info + individual
-		// hydrophone data together
-		// pamguard hydrophone data
-		// number => hydrophoneId
-		// sensorId => sensor serial number
-		// Geometry => array geometry field goes to
-		// Sensors/Depth
-		// optional
-		// Sensors/Sensor
-		// Number => hydrophoneId in pamguard
-		// SensorId => addition to UI
-		// Geometry => array geometry fields
-		// Type => Hydrophone Type
-
-		// get list of deployment recovery details (start, stop times and lat/long)
-		// deployment details and recovery details are same structure
-		// per pair, go through a loop to fill in each deployment
-//		ArrayList<DeploymentRecoveryPair> deployRecover = getSamplingDetails();
-//		if (deployRecover == null) {
-//			return false;
-//		}
-//	
-//		for (DeploymentRecoveryPair drd : deployRecover) {
-//			
-//			
-//			
-//			
-//		}
+		//1. grab DeploymentRecoveryPair that has deployment details and recovery details
+				//a. this is based on start and end times
+					//Douglas calculates out dutycycles to only grab the
+				
+		//2. loop through the pairs to populate the extra information
+			//one pair is one deployment
+			//see below for matching
+				
+		
+		//id => unique
+		//project => project in pamguard
+		//deploymentId == id
+		//deploymentAlias => blank
+		//site => UI addition in pamguard, not done, can be blank
+		//siteAlias => blank
+		//cruise => UI addition, optional
+		//Platform=> UI addition in pamguard
+		//region => UI addition
+		//Instrument/Type => UI, array manager details (hydrophone names area)
+		//Instrument/Id => UI, array manager details
+		//Instrument/Geometry => in pamguard array manager
+		//SamplingDetails/Channel
+			//ChannelNumber => in pamguard, hyrdrophone array  
+			//SensorNumber => in pamguard, 
+			//Start => same as timestamp deployment detail
+			//End => same as timestamp recovery detail
+			//Sampling/Regimen (change sample rate, pamgauard doesnt handle, only on, get channel info in that loop)
+				//TimeStamp => start time
+				//SampleRate_kHz => 
+				//SampleBits => 
+			//Gain (another func call to get gain info)
+			//DutyCycles => needs to be calculated, not fields in pamguard, have fun Douglas
+		//QualityAssurance => not in pamguard, UI, maybe deployment notes, optional
+		//Data/Audio (static)
+			//URI => folder where audio is saved
+		//Data/Tracks
+			//Track => GPS datatable (granularity filter)
+				//TrackId => not unique between deployments, 
+			//TrackEffort
+				//OnPath => scattered throughout pamguard
+			//URI => option, check with Shannon on how they are doing deployments
+		//Sensors/Audio (per hydrophone not quad array) streamer info + individual hydrophone data together
+			//pamguard hydrophone data
+			//number => hydrophoneId
+			//sensorId => sensor serial number
+			//Geometry => array geometry field goes to 
+		//Sensors/Depth
+			//optional 
+		//Sensors/Sensor 
+			//Number => hydrophoneId in pamguard
+			//SensorId => addition to UI
+			//Geometry => array geometry fields
+			//Type => Hydrophone Type
+		
+		
+		
+		
+		
+		//get list of deployment recovery details (start, stop times and lat/long)
+		//deployment details and recovery details are same structure
+		//per pair, go through a loop to fill in each deployment
+		ArrayList<DeploymentRecoveryPair> deployRecover = getSamplingDetails();
+		if (deployRecover == null) {
+			return false;
+		}
+	
+		/*
+		 * This will become the main loop over deployment documents
+		 */
+		int i = 0;
+		for (DeploymentRecoveryPair drd : deployRecover) {
+			
+			Deployment deployment = createDeploymentDocument(i++, drd);
+			
+			
+		}
 
 		/*
 		 * Call some general export function
@@ -241,6 +250,18 @@ public class TethysExporter {
 
 		return true;
 	}
+	
+	private Deployment createDeploymentDocument(int i, DeploymentRecoveryPair drd) {
+		Deployment deployment = new Deployment();
+		deployment.setDeploymentDetails(drd.deploymentDetails);
+		deployment.setRecoveryDetails(drd.recoveryDetails);
+		
+		TethysLocationFuncs.getTrackAndPositionData(deployment);
+		
+		
+		
+		return deployment;
+	}
 
 	/**
 	 * find Deployment data. This is stored in a separate PAMGuard module, which may
@@ -348,9 +369,9 @@ public class TethysExporter {
 		// just load everything. Probably OK for the acqusition, but will bring down
 		daqInfoDataBlock.loadViewerData(0, Long.MAX_VALUE, null);
 		ArrayList<DaqStatusDataUnit> allStatusData = daqInfoDataBlock.getDataCopy();
+		long dataStart = Long.MAX_VALUE;
+		long dataEnd = Long.MIN_VALUE;
 		if (allStatusData != null && allStatusData.size() > 0) {
-			long dataStart = Long.MAX_VALUE;
-			long dataEnd = Long.MIN_VALUE;
 			// find the number of times it started and stopped ....
 			int nStart = 0, nStop = 0, nFile = 0;
 			for (DaqStatusDataUnit daqStatus : allStatusData) {
@@ -392,8 +413,22 @@ public class TethysExporter {
 ////			for ()
 //		}
 
-		return null;
 
+		DeploymentRecoveryPair pair = new DeploymentRecoveryPair();
+		DeploymentRecoveryDetails deployment = new DeploymentRecoveryDetails();
+		DeploymentRecoveryDetails recovery = new DeploymentRecoveryDetails();
+		pair.deploymentDetails = deployment;
+		pair.recoveryDetails = recovery;
+		
+		deployment.setTimeStamp(TethysTimeFuncs.xmlGregCalFromMillis(dataStart));
+		deployment.setAudioTimeStamp(TethysTimeFuncs.xmlGregCalFromMillis(dataStart));
+		recovery.setTimeStamp(TethysTimeFuncs.xmlGregCalFromMillis(dataEnd));
+		recovery.setAudioTimeStamp(TethysTimeFuncs.xmlGregCalFromMillis(dataEnd));
+		
+		ArrayList<DeploymentRecoveryPair> drPairs = new ArrayList<>();
+		drPairs.add(pair);
+		return drPairs;
+		
 	}
 
 	/**