mirror of
https://github.com/PAMGuard/PAMGuard.git
synced 2024-11-21 22:52:22 +00:00
Added bin granularity
binned granularity in place. TODO Encounter granularity.
This commit is contained in:
Douglas Gillespie
parent
baca001ed8
commit
c221d78aa2
@ -581,10 +581,13 @@ public class PamguardXMLWriter implements PamSettings {
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return el;
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}
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private Element writeObjectData(Document doc, Element el, Object data, ArrayList<Object> objectHierarchy) {
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public Element writeObjectData(Document doc, Element el, Object data, ArrayList<Object> objectHierarchy) {
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if (data == null) {
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return null;
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}
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if (objectHierarchy == null) {
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objectHierarchy = new ArrayList<>();
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}
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if (objectHierarchy.contains(data)) {
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// just write the reference, but nothing else or we'll end up in an infinite loop of objects.
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Element e = doc.createElement("Object");
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@ -50,6 +50,7 @@ import org.w3c.dom.Element;
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import Acquisition.AcquisitionControl;
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import Acquisition.AcquisitionProcess;
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import pamScrollSystem.ViewLoadObserver;
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import tethys.TethysControl;
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import tethys.pamdata.AutoTethysProvider;
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import tethys.pamdata.TethysDataProvider;
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import tethys.species.DataBlockSpeciesManager;
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@ -3089,9 +3090,9 @@ public class PamDataBlock<Tunit extends PamDataUnit> extends PamObservable {
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* to be bespoke, but for now will autogenerate based on the SQLLogging information.
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* @return the tethysDataProvider
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*/
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public TethysDataProvider getTethysDataProvider() {
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public TethysDataProvider getTethysDataProvider(TethysControl tethysControl) {
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if (tethysDataProvider == null && PamDetection.class.isAssignableFrom(unitClass) && getLogging() != null) {
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tethysDataProvider = new AutoTethysProvider(this);
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tethysDataProvider = new AutoTethysProvider(tethysControl, this);
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}
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return tethysDataProvider;
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}
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@ -139,7 +139,7 @@ public abstract class DataSelector {
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}
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return null;
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}
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/**
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* Score a PAMDataUnit. this is used in preference
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* to a boolean select function so that the user can add different
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@ -211,7 +211,7 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
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ArrayList<PamDataBlock> sets = new ArrayList<>();
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ArrayList<PamDataBlock> allDataBlocks = PamController.getInstance().getDataBlocks();
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for (PamDataBlock aDataBlock : allDataBlocks) {
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if (aDataBlock.getTethysDataProvider() != null) {
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if (aDataBlock.getTethysDataProvider(this) != null) {
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sets.add(aDataBlock);
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}
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}
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@ -335,31 +335,31 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
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return tethysExportParams;
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}
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/**
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* We'll probably want to
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* @param parentFrame
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*/
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protected void tethysExport(JFrame parentFrame) {
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TethysExportParams newExportParams = TethysExportDialog.showDialog(parentFrame, this);
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if (newExportParams != null) {
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// dialog returns null if cancel was pressed.
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tethysExportParams = newExportParams;
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exportTethysData(tethysExportParams);
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}
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}
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/**
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* We'll arrive here if the dialog has been opened and we want to export Tethys data.
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* @param tethysExportParams2
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*/
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private void exportTethysData(TethysExportParams tethysExportParams) {
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TethysExporter tethysExporter = new TethysExporter(this, tethysExportParams);
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tethysExporter.doExport();
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sendStateUpdate(new TethysState(StateType.TRANSFERDATA));
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countProjectDetections();
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sendStateUpdate(new TethysState(StateType.NEWPAMGUARDSELECTION));
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}
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// /**
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// * We'll probably want to
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// * @param parentFrame
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// */
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// protected void tethysExport(JFrame parentFrame) {
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// TethysExportParams newExportParams = TethysExportDialog.showDialog(parentFrame, this);
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// if (newExportParams != null) {
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// // dialog returns null if cancel was pressed.
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// tethysExportParams = newExportParams;
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// exportTethysData(tethysExportParams);
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// }
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// }
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//
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// /**
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// * We'll arrive here if the dialog has been opened and we want to export Tethys data.
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// * @param tethysExportParams2
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// */
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// private void exportTethysData(TethysExportParams tethysExportParams) {
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// TethysExporter tethysExporter = new TethysExporter(this, tethysExportParams);
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// tethysExporter.doExport();
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//
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// sendStateUpdate(new TethysState(StateType.TRANSFERDATA));
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// countProjectDetections();
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// sendStateUpdate(new TethysState(StateType.NEWPAMGUARDSELECTION));
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// }
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/**
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* Get global deployment data. This is a bit of a mess, trying to use a separate module
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@ -644,4 +644,14 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
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return itisFunctions;
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}
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/**
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* Called when a detections document has been exported.
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* @param dataBlock
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*/
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public void exportedDetections(PamDataBlock dataBlock) {
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sendStateUpdate(new TethysState(StateType.TRANSFERDATA));
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countProjectDetections();
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sendStateUpdate(new TethysState(StateType.NEWPAMGUARDSELECTION));
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}
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}
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@ -541,6 +541,27 @@ public class DBXMLQueries {
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// String queryBase = "{\"return\":[\"Deployment/Project\"],\"select\":[],\"enclose\":1}";
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}
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/**
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* Find out if a document exists ?
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* @param collection
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* @param documentId
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* @return
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*/
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public boolean documentExists(String collection, String documentId) {
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Queries queries = dbXMLConnect.getTethysQueries();
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String result = null;
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try {
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result = queries.getDocument(collection, documentId);
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} catch (Exception e) {
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return false;
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}
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if (result == null || result.length() == 0) {
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return false;
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}
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return result.contains(documentId);
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}
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/**
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* Count on effort detections in a Detections document
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* @param docName
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161
src/tethys/detection/BinnedGranularityHandler.java
Normal file
161
src/tethys/detection/BinnedGranularityHandler.java
Normal file
@ -0,0 +1,161 @@
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package tethys.detection;
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import java.math.BigInteger;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.Set;
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import PamguardMVC.PamDataBlock;
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import PamguardMVC.PamDataUnit;
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import nilus.Detection;
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import nilus.SpeciesIDType;
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import tethys.TethysControl;
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import tethys.TethysTimeFuncs;
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import tethys.output.StreamExportParams;
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import tethys.output.TethysExportParams;
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import tethys.pamdata.TethysDataProvider;
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import tethys.species.DataBlockSpeciesCodes;
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import tethys.species.DataBlockSpeciesManager;
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import tethys.species.DataBlockSpeciesMap;
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import tethys.species.SpeciesMapItem;
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/**
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* Binned granularity
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* Will have to collect different counts for each type of call for each datablock (if there
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* are such things) so a little more complicated than might be expected.
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* @author dg50
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*
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*/
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public class BinnedGranularityHandler extends GranularityHandler {
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private double binDurationSeconds;
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private long binStartMillis, binEndMillis;
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private TethysDataProvider dataProvider;
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private DataBlockSpeciesManager speciesManager;
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private HashMap<String, Detection> currentDetections;
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public BinnedGranularityHandler(TethysControl tethysControl, PamDataBlock dataBlock,
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TethysExportParams tethysExportParams, StreamExportParams streamExportParams) {
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super(tethysControl, dataBlock, tethysExportParams, streamExportParams);
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binDurationSeconds = streamExportParams.binDurationS;
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dataProvider = dataBlock.getTethysDataProvider(tethysControl);
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speciesManager = dataBlock.getDatablockSpeciesManager();
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currentDetections = new HashMap<String, Detection>();
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}
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@Override
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public void prepare(long timeMillis) {
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long binStart = DetectionsHandler.roundDownBinStart(timeMillis, (long) (binDurationSeconds*1000));
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startBin(binStart);
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}
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private void startBin(long timeMillis) {
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binStartMillis = timeMillis;
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binEndMillis = binStartMillis + (long) (binDurationSeconds*1000.);
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/*
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* now make a Detection object for every possible species that
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* this might throw out.
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*/
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ArrayList<String> speciesCodes = speciesManager.getAllSpeciesCodes();
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String defaultCode = speciesManager.getDefaultSpeciesCode();
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Detection det;
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currentDetections.put(defaultCode, det = new Detection());
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det.setStart(TethysTimeFuncs.xmlGregCalFromMillis(binStartMillis));
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det.setEnd(TethysTimeFuncs.xmlGregCalFromMillis(binEndMillis));
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det.setCount(BigInteger.ZERO);
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det.setChannel(BigInteger.ZERO);
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// add codes at end, just before output.
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if (speciesCodes != null) {
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for (String code : speciesCodes) {
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currentDetections.put(code, det = new Detection());
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det.setStart(TethysTimeFuncs.xmlGregCalFromMillis(binStartMillis));
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det.setEnd(TethysTimeFuncs.xmlGregCalFromMillis(binEndMillis));
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det.setCount(BigInteger.ZERO);
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det.setChannel(BigInteger.ZERO);
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}
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}
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}
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@Override
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public Detection[] addDataUnit(PamDataUnit dataUnit) {
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Detection[] detections = null;
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if (dataUnit.getTimeMilliseconds() >= binEndMillis) {
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detections = closeBins(dataUnit.getTimeMilliseconds());
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}
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String speciesCode = speciesManager.getSpeciesCode(dataUnit);
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Detection det = currentDetections.get(speciesCode);
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if (det != null) {
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/*
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* Increase the detection count
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*/
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int count = det.getCount().intValue();
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count++;
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det.setCount(BigInteger.valueOf(count));
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/*
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* Add to the channel map too ...
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*/
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int channel = det.getChannel().intValue();
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channel |= dataUnit.getChannelBitmap();
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det.setChannel(BigInteger.valueOf(channel));
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}
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return detections;
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}
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/**
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* Called when units arrive after end of current bin, and also
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* at end of deployment output, to get that last bine.
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* @param timeMilliseconds
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* @return
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*/
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private Detection[] closeBins(long timeMilliseconds) {
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Set<String> speciesKeys = currentDetections.keySet();
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int n = speciesKeys.size();
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int nGood = 0;
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DataBlockSpeciesMap speciesMap = speciesManager.getDatablockSpeciesMap();
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Detection detections[] = new Detection[n];
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for (String key : speciesKeys) {
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Detection det = currentDetections.get(key);
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int callCount = det.getCount().intValue();
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if (callCount < Math.max(streamExportParams.minBinCount,1)) {
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continue;
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}
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SpeciesMapItem speciesStuff = speciesMap.getItem(key); // should be non null!
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if (speciesStuff == null) {
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continue;
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}
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SpeciesIDType species = new SpeciesIDType();
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species.setValue(BigInteger.valueOf(speciesStuff.getItisCode()));
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det.setSpeciesId(species);
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if (speciesStuff.getCallType() != null) {
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det.getCall().add(speciesStuff.getCallType());
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}
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detections[nGood++] = det;
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}
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// finally, start new bins (not really needed on last call, but do anyway).
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startBin(binEndMillis);
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/*
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* Clean up the end of the array and return detections that have enough calls.
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*/
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if (nGood == 0) {
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return null;
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}
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detections = Arrays.copyOf(detections, nGood);
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return detections;
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}
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@Override
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public Detection[] cleanup(long timeMillis) {
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return closeBins(timeMillis);
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}
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}
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40
src/tethys/detection/CallGranularityHandler.java
Normal file
40
src/tethys/detection/CallGranularityHandler.java
Normal file
@ -0,0 +1,40 @@
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package tethys.detection;
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import PamguardMVC.PamDataBlock;
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import PamguardMVC.PamDataUnit;
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import nilus.Detection;
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import tethys.TethysControl;
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import tethys.output.StreamExportParams;
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import tethys.output.TethysExportParams;
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import tethys.pamdata.TethysDataProvider;
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public class CallGranularityHandler extends GranularityHandler {
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private TethysDataProvider dataProvider;
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public CallGranularityHandler(TethysControl tethysControl, PamDataBlock dataBlock,
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TethysExportParams tethysExportParams, StreamExportParams streamExportParams) {
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super(tethysControl, dataBlock, tethysExportParams, streamExportParams);
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dataProvider = dataBlock.getTethysDataProvider(tethysControl);
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}
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@Override
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public void prepare(long timeMillis) {
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// never anything to do here for call level granularity.
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}
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@Override
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public Detection[] addDataUnit(PamDataUnit dataUnit) {
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Detection det = dataProvider.createDetection(dataUnit, tethysExportParams, streamExportParams);
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return toDetectionArray(det);
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}
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@Override
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public Detection[] cleanup(long timeMillis) {
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// never anything to do here for call level granularity.
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return null;
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}
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}
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@ -1,34 +0,0 @@
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package tethys.detection;
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/**
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* Class to help define what the granularity of exported detections
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* documents should be. The entire document will be in memory, so it
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* may be necessary to add many detections documents into the database
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* for a single Deployment.
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* @author dg50
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*
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*/
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public class DetectionGranularity {
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public enum GRANULARITY {NONE, BINARYFILE, TIME};
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/**
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* Type of granularity. Are data all in one lump, split by binary file or by time.
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*/
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GRANULARITY granularity = GRANULARITY.NONE;
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/**
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* Granularity interval in seconds. Output system will try to round these
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* to something with sensible boundaries.
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* This field is only needed when using the GRANULARITY.TIME option.
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*/
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public long granularityIntervalSeconds;
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public DetectionGranularity(GRANULARITY granularity, long granularityIntervalSeconds) {
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super();
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this.granularity = granularity;
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this.granularityIntervalSeconds = granularityIntervalSeconds;
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}
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}
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@ -1,33 +1,20 @@
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package tethys.detection;
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import java.math.BigInteger;
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import java.util.ArrayList;
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import java.util.List;
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import javax.swing.SwingWorker;
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import javax.xml.XMLConstants;
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import javax.xml.bind.JAXBException;
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import javax.xml.parsers.ParserConfigurationException;
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import org.pamguard.x3.sud.SUDClickDetectorInfo;
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import org.w3c.dom.Document;
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import org.w3c.dom.Element;
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import PamController.PamControlledUnit;
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import PamController.PamguardVersionInfo;
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import PamController.settings.output.xml.PamguardXMLWriter;
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import PamModel.PamPluginInterface;
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import PamUtils.PamCalendar;
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import PamUtils.XMLUtils;
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import PamguardMVC.PamDataBlock;
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import PamguardMVC.PamDataUnit;
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import PamguardMVC.PamProcess;
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import PamguardMVC.dataSelector.DataSelector;
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import dataMap.OfflineDataMap;
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import dataMap.OfflineDataMapPoint;
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import metadata.deployment.DeploymentData;
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import nilus.AlgorithmType;
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import nilus.AlgorithmType.Parameters;
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import nilus.AlgorithmType.SupportSoftware;
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import nilus.DataSourceType;
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import nilus.Deployment;
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@ -38,43 +25,38 @@ import nilus.DetectionGroup;
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import nilus.Detections;
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import nilus.Helper;
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import tethys.TethysControl;
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import tethys.TethysState;
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import tethys.TethysState.StateType;
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import tethys.deployment.DeploymentHandler;
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import tethys.TethysStateObserver;
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import tethys.TethysTimeFuncs;
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import tethys.dbxml.DBXMLConnect;
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import tethys.dbxml.TethysException;
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import tethys.detection.DetectionGranularity.GRANULARITY;
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import tethys.deployment.DeploymentHandler;
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import tethys.niluswraps.PDeployment;
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import tethys.niluswraps.PDetections;
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import tethys.niluswraps.TethysCollections;
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import tethys.output.StreamExportParams;
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import tethys.output.TethysExportParams;
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import tethys.pamdata.TethysDataPoint;
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import tethys.pamdata.TethysDataProvider;
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import tethys.swing.export.ExportWorkerCard;
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public class DetectionsHandler {
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private TethysControl tethysControl;
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public int uniqueDetectionsId=1;
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public int uniqueDetectionId;
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private volatile boolean activeExport;
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private ExportWorker exportWorker;
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public DetectionsHandler(TethysControl tethysControl) {
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super();
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this.tethysControl = tethysControl;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* Get a list of Detections documents associated with a particular data stream for
|
||||
* this data set (not the entire project).
|
||||
* Get a list of Detections documents associated with a particular data stream for
|
||||
* this data set (not the entire project).
|
||||
* @param dataBlock
|
||||
*/
|
||||
public StreamDetectionsSummary getStreamDetections(PamDataBlock dataBlock) {
|
||||
@ -84,21 +66,21 @@ public class DetectionsHandler {
|
||||
|
||||
/**
|
||||
* Get a list of Detections documents associated with a particular data block for the list of deployments
|
||||
* documents. Group them by abstract or something
|
||||
* documents. Group them by abstract or something
|
||||
* @param dataBlock
|
||||
* @param deployments
|
||||
* @return
|
||||
*/
|
||||
public StreamDetectionsSummary getStreamDetections(PamDataBlock dataBlock, ArrayList<PDeployment> deployments) {
|
||||
// get the basic data for each document including it's Description.
|
||||
|
||||
// get the basic data for each document including it's Description.
|
||||
|
||||
ArrayList<PDetections> detectionsDocs = new ArrayList<>();
|
||||
for (PDeployment aDep : deployments) {
|
||||
ArrayList<String> someNames = tethysControl.getDbxmlQueries().getDetectionsDocuments(dataBlock, aDep.deployment.getId());
|
||||
if (someNames == null) {
|
||||
continue;
|
||||
}
|
||||
// no have a list of all the Detections documents of interest for this datablock.
|
||||
// no have a list of all the Detections documents of interest for this datablock.
|
||||
for (String aDoc : someNames) {
|
||||
Detections detections = tethysControl.getDbxmlQueries().getDetectionsDocInfo(aDoc);
|
||||
int count = tethysControl.getDbxmlQueries().countDetections2(aDoc);
|
||||
@ -114,7 +96,7 @@ public class DetectionsHandler {
|
||||
// * Here is where we export data for a specific data stream to Tethys.
|
||||
// *
|
||||
// * @param aDataBlock
|
||||
// * @param aDeployment
|
||||
// * @param aDeployment
|
||||
// * @param tethysExportParams
|
||||
// * @param streamExportParams
|
||||
// */
|
||||
@ -135,7 +117,7 @@ public class DetectionsHandler {
|
||||
// }
|
||||
//
|
||||
// return false;
|
||||
//
|
||||
//
|
||||
//
|
||||
// }
|
||||
//
|
||||
@ -145,7 +127,7 @@ public class DetectionsHandler {
|
||||
// long deploymentStop = TethysTimeFuncs.millisFromGregorianXML(deployment.getRecoveryDetails().getAudioTimeStamp());
|
||||
// /*
|
||||
// * there should be a pretty good correspondence between the start of a binary file and the deploymentStart
|
||||
// * since they all derived from the same start clock.
|
||||
// * since they all derived from the same start clock.
|
||||
// */
|
||||
// OfflineDataMap dataMap = dataBlock.getPrimaryDataMap();
|
||||
// if (dataMap == null) {
|
||||
@ -160,11 +142,11 @@ public class DetectionsHandler {
|
||||
// if (mapPoint.getStartTime() >= deploymentStop) {
|
||||
// continue;
|
||||
// }
|
||||
// ok &= loadAndExport(dataBlock, deployment, Math.max(deploymentStart, mapPoint.getStartTime()),
|
||||
// ok &= loadAndExport(dataBlock, deployment, Math.max(deploymentStart, mapPoint.getStartTime()),
|
||||
// Math.min(deploymentStop, mapPoint.getEndTime()), tethysExportParams, streamExportParams);
|
||||
// }
|
||||
//
|
||||
//
|
||||
//
|
||||
//
|
||||
// return ok;
|
||||
// }
|
||||
//
|
||||
@ -185,11 +167,11 @@ public class DetectionsHandler {
|
||||
// exportStart *= chunkMillis;
|
||||
// boolean ok = true;
|
||||
// while (exportStart < deploymentStop) {
|
||||
// ok &= loadAndExport(dataBlock, deployment, Math.max(deploymentStart, exportStart),
|
||||
// ok &= loadAndExport(dataBlock, deployment, Math.max(deploymentStart, exportStart),
|
||||
// Math.min(deploymentStop, exportStart + chunkMillis), tethysExportParams, streamExportParams);
|
||||
// exportStart += chunkMillis;
|
||||
// }
|
||||
//
|
||||
//
|
||||
// return ok;
|
||||
// }
|
||||
//
|
||||
@ -210,11 +192,11 @@ public class DetectionsHandler {
|
||||
// DataSelector dataSelector = dataBlock.getDataSelector(tethysControl.getDataSelectName(), false);
|
||||
// /*
|
||||
// * for easier synching, get a copy of the data and also apply the data selector right away so that
|
||||
// * we've a list of exactly the right data.
|
||||
// * we've a list of exactly the right data.
|
||||
// */
|
||||
// ArrayList<PamDataUnit> data = dataBlock.getDataCopy(startTimeMillis, endTimeMillis, true, dataSelector);
|
||||
// /*
|
||||
// * Here, make Detection object and add the DetectionEffort data.
|
||||
// * Here, make Detection object and add the DetectionEffort data.
|
||||
// */
|
||||
// DeploymentData globalDeplData = tethysControl.getGlobalDeplopymentData();
|
||||
// TethysDataProvider dataProvider = dataBlock.getTethysDataProvider();
|
||||
@ -235,25 +217,25 @@ public class DetectionsHandler {
|
||||
// List<Detection> detectionList = detectionGroup.getDetection();
|
||||
// for (int i = 0; i < data.size(); i++) {
|
||||
// PamDataUnit dataUnit = data.get(i);
|
||||
// Detection detection = dataProvider.createDetection(dataUnit, tethysExportParams, streamExportParams);
|
||||
// Detection detection = dataProvider.createDetection(dataUnit, tethysExportParams, streamExportParams);
|
||||
// if (detection != null) {
|
||||
// detectionList.add(detection);
|
||||
// }
|
||||
// }
|
||||
// System.out.printf("Exporting %d %s detections for time period %s to %s\n", detectionList.size(), dataBlock.getDataName(),
|
||||
// System.out.printf("Exporting %d %s detections for time period %s to %s\n", detectionList.size(), dataBlock.getDataName(),
|
||||
// detections.getEffort().getStart().toString(), detections.getEffort().getEnd().toString());
|
||||
// /*
|
||||
// * We should now have a fully populated Detections object, so write it to the database
|
||||
// * using functions in DBXMLConnect
|
||||
// * using functions in DBXMLConnect
|
||||
// */
|
||||
// ArrayList<Detections> detectionDocuments = new ArrayList();
|
||||
// detectionDocuments.add(detections);
|
||||
//
|
||||
//// tethysControl.getDbxmlConnect().postToTethys(detectionDocuments); // call whatever you need to call in here to write the Detections.
|
||||
//
|
||||
//
|
||||
//
|
||||
//// tethysControl.getDbxmlConnect().postToTethys(detectionDocuments); // call whatever you need to call in here to write the Detections.
|
||||
//
|
||||
//
|
||||
// return true;
|
||||
//
|
||||
//
|
||||
// }
|
||||
|
||||
// private boolean exportByTimeChunk(PamDataBlock aDataBlock, Deployment deployment, long granularityIntervalSeconds,
|
||||
@ -272,15 +254,15 @@ public class DetectionsHandler {
|
||||
// effort.set // no setter for DetectionEffortKind
|
||||
List<DetectionEffortKind> effortKinds = effort.getKind();
|
||||
|
||||
TethysDataProvider dataProvider = dataBlock.getTethysDataProvider();
|
||||
TethysDataProvider dataProvider = dataBlock.getTethysDataProvider(tethysControl);
|
||||
dataProvider.getEffortKinds(pDeployment, effortKinds, exportParams);
|
||||
|
||||
|
||||
|
||||
|
||||
return effort;
|
||||
}
|
||||
|
||||
/**
|
||||
* Method string for Detections Algorithm documents.
|
||||
* Method string for Detections Algorithm documents.
|
||||
* @param dataBlock
|
||||
* @return
|
||||
*/
|
||||
@ -290,11 +272,11 @@ public class DetectionsHandler {
|
||||
}
|
||||
PamProcess process = dataBlock.getParentProcess();
|
||||
return "PAMGuard " + process.getProcessName();
|
||||
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* Software string for Detections Algorithm documents.
|
||||
* Software string for Detections Algorithm documents.
|
||||
* @param dataBlock
|
||||
* @return
|
||||
*/
|
||||
@ -306,7 +288,7 @@ public class DetectionsHandler {
|
||||
}
|
||||
|
||||
/**
|
||||
* Software string for Detections Algorithm documents.
|
||||
* Software string for Detections Algorithm documents.
|
||||
* @param dataBlock
|
||||
* @return
|
||||
*/
|
||||
@ -324,31 +306,31 @@ public class DetectionsHandler {
|
||||
return plugin.getVersion();
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
public String getSupportSoftware(PamDataBlock dataBlock) {
|
||||
return "PAMGuard";
|
||||
}
|
||||
|
||||
|
||||
public String getSupportSoftwareVersion(PamDataBlock dataBlock) {
|
||||
// should try to dig into the binary store and get the version from there.
|
||||
// should try to dig into the binary store and get the version from there.
|
||||
return PamguardVersionInfo.version;
|
||||
}
|
||||
// /**
|
||||
// * Get a prefix for a id for a Detections document. This is just the project name
|
||||
// * Get a prefix for a id for a Detections document. This is just the project name
|
||||
// * and the datablock name. Something may need to be added to allow for multiple
|
||||
// * analysis going into one database.
|
||||
// * analysis going into one database.
|
||||
// * @param project
|
||||
// * @param dataBlock
|
||||
// * @return Detections document prefix.
|
||||
// * @return Detections document prefix.
|
||||
// */
|
||||
// public static final String getDetectionsDocIdPrefix(String project, PamDataBlock dataBlock) {
|
||||
// return project + "_" + dataBlock.getDataName();
|
||||
// }
|
||||
|
||||
/**
|
||||
* Detections will be exported in a separate worker thread since export may take some time and
|
||||
* the user should be given ample opportunity to cancel it.
|
||||
* @param pamDataBlock
|
||||
* Detections will be exported in a separate worker thread since export may take some time and
|
||||
* the user should be given ample opportunity to cancel it.
|
||||
* @param pamDataBlock
|
||||
* @param streamExportParams
|
||||
* @param exportWorkerCard
|
||||
*/
|
||||
@ -358,13 +340,25 @@ public class DetectionsHandler {
|
||||
exportWorker = new ExportWorker(pamDataBlock, streamExportParams, exportObserver);
|
||||
exportWorker.execute();
|
||||
}
|
||||
|
||||
|
||||
public void cancelExport() {
|
||||
activeExport = false;
|
||||
}
|
||||
|
||||
/**
|
||||
* Export detections in all deployments for this PAMGuard dataset.
|
||||
* Round a bin start so that it's aligned correctly with
|
||||
* day starts.
|
||||
* @param binStart
|
||||
* @param binInterval
|
||||
* @return
|
||||
*/
|
||||
public static long roundDownBinStart(long binStart, long binInterval) {
|
||||
binStart/=binInterval;
|
||||
return binStart*binInterval;
|
||||
}
|
||||
|
||||
/**
|
||||
* Export detections in all deployments for this PAMGuard dataset.
|
||||
* @param dataBlock
|
||||
* @param streamExportParams
|
||||
* @param exportObserver
|
||||
@ -372,8 +366,8 @@ public class DetectionsHandler {
|
||||
*/
|
||||
private int exportDetections(PamDataBlock dataBlock, StreamExportParams streamExportParams, DetectionExportObserver exportObserver) {
|
||||
/*
|
||||
* This is currently called for the entire dataset, but we will need to loop over specific Deployment documents
|
||||
* and export the content of each separately.
|
||||
* This is currently called for the entire dataset, but we will need to loop over specific Deployment documents
|
||||
* and export the content of each separately.
|
||||
*/
|
||||
TethysExportParams exportParams = tethysControl.getTethysExportParams();
|
||||
DBXMLConnect dbxmlConnect = tethysControl.getDbxmlConnect();
|
||||
@ -381,28 +375,29 @@ public class DetectionsHandler {
|
||||
ArrayList<PDeployment> deployments = depHandler.getMatchedDeployments();
|
||||
Detections currentDetections = null;
|
||||
OfflineDataMap dataMap = dataBlock.getPrimaryDataMap();
|
||||
TethysDataProvider dataProvider = dataBlock.getTethysDataProvider();
|
||||
DataSelector dataSelector = dataBlock.getDataSelector(tethysControl.getDataSelectName(), false);
|
||||
int totalCount = dataMap.getDataCount();
|
||||
int skipCount = 0;
|
||||
int exportCount = 0;
|
||||
long lastUnitTime = 0;
|
||||
DetectionExportProgress prog;
|
||||
GranularityHandler granularityHandler = GranularityHandler.getHandler(streamExportParams.granularity, tethysControl, dataBlock, exportParams, streamExportParams);
|
||||
for (PDeployment deployment : deployments) {
|
||||
int documentCount = 0;
|
||||
prog = new DetectionExportProgress(deployment, null,
|
||||
prog = new DetectionExportProgress(deployment, null,
|
||||
lastUnitTime, totalCount, exportCount, skipCount, DetectionExportProgress.STATE_GATHERING);
|
||||
exportObserver.update(prog);
|
||||
// export everything in that deployment.
|
||||
// need to loop through all map points in this interval.
|
||||
granularityHandler.prepare(deployment.getAudioStart());
|
||||
// export everything in that deployment.
|
||||
// need to loop through all map points in this interval.
|
||||
List<OfflineDataMapPoint> mapPoints = dataMap.getMapPoints();
|
||||
for (OfflineDataMapPoint mapPoint : mapPoints) {
|
||||
if (activeExport == false) {
|
||||
prog = new DetectionExportProgress(deployment, currentDetections,
|
||||
if (!activeExport) {
|
||||
prog = new DetectionExportProgress(deployment, currentDetections,
|
||||
lastUnitTime, totalCount, exportCount, skipCount, DetectionExportProgress.STATE_CANCELED);
|
||||
exportObserver.update(prog);
|
||||
}
|
||||
|
||||
|
||||
if (currentDetections == null) {
|
||||
currentDetections = startDetectionsDocument(deployment, dataBlock, streamExportParams);
|
||||
currentDetections.getEffort().setStart(TethysTimeFuncs.xmlGregCalFromMillis(mapPoint.getStartTime()));
|
||||
@ -418,19 +413,30 @@ public class DetectionsHandler {
|
||||
skipCount += dataBlock.getUnitsCount() - dataCopy.size();
|
||||
DetectionGroup onEffort = currentDetections.getOnEffort();
|
||||
for (PamDataUnit dataUnit : dataCopy) {
|
||||
Detection det = dataProvider.createDetection(dataUnit, exportParams, streamExportParams);
|
||||
exportCount++;
|
||||
documentCount++;
|
||||
onEffort.getDetection().add(det);
|
||||
/*
|
||||
* Here is where we need to handle the different granularities.
|
||||
*/
|
||||
Detection dets[] = granularityHandler.addDataUnit(dataUnit);
|
||||
if (dets != null) {
|
||||
for (int dd = 0; dd < dets.length; dd++) {
|
||||
exportCount++;
|
||||
documentCount++;
|
||||
onEffort.getDetection().add(dets[dd]);
|
||||
}
|
||||
}
|
||||
// Detection det = dataProvider.createDetection(dataUnit, exportParams, streamExportParams);
|
||||
// exportCount++;
|
||||
// documentCount++;
|
||||
// onEffort.getDetection().add(det);
|
||||
lastUnitTime = dataUnit.getTimeMilliseconds();
|
||||
}
|
||||
|
||||
prog = new DetectionExportProgress(deployment, currentDetections,
|
||||
|
||||
prog = new DetectionExportProgress(deployment, currentDetections,
|
||||
lastUnitTime, totalCount, exportCount, skipCount, DetectionExportProgress.STATE_GATHERING);
|
||||
exportObserver.update(prog);
|
||||
|
||||
|
||||
if (documentCount > 500000 && mapPoint != dataMap.getLastMapPoint()) {
|
||||
prog = new DetectionExportProgress(deployment, currentDetections,
|
||||
prog = new DetectionExportProgress(deployment, currentDetections,
|
||||
lastUnitTime, totalCount, exportCount, skipCount, DetectionExportProgress.STATE_WRITING);
|
||||
exportObserver.update(prog);
|
||||
closeDetectionsDocument(currentDetections, mapPoint.getEndTime());
|
||||
@ -443,8 +449,17 @@ public class DetectionsHandler {
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
if (currentDetections != null) {
|
||||
prog = new DetectionExportProgress(deployment, currentDetections,
|
||||
Detection dets[] = granularityHandler.cleanup(deployment.getAudioEnd());
|
||||
if (dets != null) {
|
||||
for (int dd = 0; dd < dets.length; dd++) {
|
||||
exportCount++;
|
||||
documentCount++;
|
||||
currentDetections.getOnEffort().getDetection().add(dets[dd]);
|
||||
}
|
||||
}
|
||||
prog = new DetectionExportProgress(deployment, currentDetections,
|
||||
lastUnitTime, totalCount, exportCount, skipCount, DetectionExportProgress.STATE_WRITING);
|
||||
closeDetectionsDocument(currentDetections, deployment.getAudioEnd());
|
||||
try {
|
||||
@ -456,7 +471,7 @@ public class DetectionsHandler {
|
||||
}
|
||||
}
|
||||
|
||||
prog = new DetectionExportProgress(null, null,
|
||||
prog = new DetectionExportProgress(null, null,
|
||||
lastUnitTime, totalCount, exportCount, skipCount, DetectionExportProgress.STATE_COMPLETE);
|
||||
exportObserver.update(prog);
|
||||
return DetectionExportProgress.STATE_COMPLETE;
|
||||
@ -472,7 +487,17 @@ public class DetectionsHandler {
|
||||
}
|
||||
|
||||
String prefix = deployment.deployment.getId();
|
||||
detections.setId(String.format("%s_%d", prefix, uniqueDetectionsId++));
|
||||
String fullId = "";
|
||||
/*
|
||||
* Check the document name isn't already used and increment id as necessary.
|
||||
*/
|
||||
while (true) {
|
||||
fullId = String.format("%s_%d", prefix, uniqueDetectionsId++);
|
||||
if (!tethysControl.getDbxmlQueries().documentExists(TethysCollections.Detections.toString(), fullId)) {
|
||||
break;
|
||||
}
|
||||
}
|
||||
detections.setId(fullId);
|
||||
// detections.setDescription(dataProvider.getDescription(deployment, tethysExportParams));
|
||||
detections.setDescription(exportParams.getNilusDetectionDescription());
|
||||
DataSourceType dataSource = new DataSourceType();
|
||||
@ -480,8 +505,8 @@ public class DetectionsHandler {
|
||||
// dataSource.setEnsembleId(""); ToDo
|
||||
detections.setDataSource(dataSource);
|
||||
AlgorithmType algorithm = detections.getAlgorithm();
|
||||
|
||||
TethysDataProvider dataProvider = dataBlock.getTethysDataProvider();
|
||||
|
||||
TethysDataProvider dataProvider = dataBlock.getTethysDataProvider(tethysControl);
|
||||
if (dataProvider != null) {
|
||||
algorithm = dataProvider.getAlgorithm();
|
||||
// detections.setAlgorithm(algorithm);
|
||||
@ -489,7 +514,7 @@ public class DetectionsHandler {
|
||||
algorithm.setMethod(getMethodString(dataBlock));
|
||||
algorithm.setSoftware(getSoftwareString(dataBlock));
|
||||
algorithm.setVersion(getVersionString(dataBlock));
|
||||
|
||||
|
||||
List<SupportSoftware> supSoft = algorithm.getSupportSoftware();
|
||||
SupportSoftware supportSoft = new SupportSoftware();
|
||||
supportSoft.setSoftware(getSupportSoftware(dataBlock));
|
||||
@ -498,13 +523,13 @@ public class DetectionsHandler {
|
||||
detections.setAlgorithm(algorithm);
|
||||
detections.setUserId("Unknown user");
|
||||
detections.setEffort(getDetectorEffort(deployment, dataBlock, exportParams));
|
||||
|
||||
|
||||
return detections;
|
||||
}
|
||||
|
||||
/**
|
||||
* Close a detections document. This basically just means rewriting the end time and it's only
|
||||
* important in the event that a document got too big and has to be restarted.
|
||||
* important in the event that a document got too big and has to be restarted.
|
||||
* @param detections
|
||||
* @param audioEnd
|
||||
*/
|
||||
@ -517,7 +542,7 @@ public class DetectionsHandler {
|
||||
private PamDataBlock dataBlock;
|
||||
private StreamExportParams exportParams;
|
||||
private DetectionExportObserver exportObserver;
|
||||
|
||||
|
||||
public ExportWorker(PamDataBlock dataBlock, StreamExportParams exportParams,
|
||||
DetectionExportObserver exportObserver) {
|
||||
super();
|
||||
@ -525,21 +550,28 @@ public class DetectionsHandler {
|
||||
this.exportParams = exportParams;
|
||||
this.exportObserver = exportObserver;
|
||||
}
|
||||
|
||||
|
||||
public void publish(DetectionExportProgress exportProgress) {
|
||||
super.publish(exportProgress);
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
protected Integer doInBackground() throws Exception {
|
||||
// eventually need to switch over the four granularity options here.
|
||||
return exportDetections(dataBlock, exportParams, this);
|
||||
Integer ans = null;
|
||||
try {
|
||||
ans = exportDetections(dataBlock, exportParams, this);
|
||||
}
|
||||
catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
return ans;
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void done() {
|
||||
// this.
|
||||
DetectionExportProgress prog = new DetectionExportProgress(null, null, 0, 0, 0, 0, DetectionExportProgress.STATE_COMPLETE);
|
||||
tethysControl.exportedDetections(dataBlock);
|
||||
exportObserver.update(prog);
|
||||
}
|
||||
|
||||
@ -554,6 +586,6 @@ public class DetectionsHandler {
|
||||
public void update(DetectionExportProgress progress) {
|
||||
publish(progress);
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
36
src/tethys/detection/EncounterGranularityHandler.java
Normal file
36
src/tethys/detection/EncounterGranularityHandler.java
Normal file
@ -0,0 +1,36 @@
|
||||
package tethys.detection;
|
||||
|
||||
import PamguardMVC.PamDataBlock;
|
||||
import PamguardMVC.PamDataUnit;
|
||||
import nilus.Detection;
|
||||
import tethys.TethysControl;
|
||||
import tethys.output.StreamExportParams;
|
||||
import tethys.output.TethysExportParams;
|
||||
|
||||
public class EncounterGranularityHandler extends GranularityHandler {
|
||||
|
||||
public EncounterGranularityHandler(TethysControl tethysControl, PamDataBlock dataBlock,
|
||||
TethysExportParams tethysExportParams, StreamExportParams streamExportParams) {
|
||||
super(tethysControl, dataBlock, tethysExportParams, streamExportParams);
|
||||
// TODO Auto-generated constructor stub
|
||||
}
|
||||
|
||||
@Override
|
||||
public void prepare(long timeMillis) {
|
||||
// TODO Auto-generated method stub
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public Detection[] addDataUnit(PamDataUnit dataUnit) {
|
||||
// TODO Auto-generated method stub
|
||||
return null;
|
||||
}
|
||||
|
||||
@Override
|
||||
public Detection[] cleanup(long timeMillis) {
|
||||
// TODO Auto-generated method stub
|
||||
return null;
|
||||
}
|
||||
|
||||
}
|
||||
100
src/tethys/detection/GranularityHandler.java
Normal file
100
src/tethys/detection/GranularityHandler.java
Normal file
@ -0,0 +1,100 @@
|
||||
package tethys.detection;
|
||||
|
||||
import PamguardMVC.PamDataBlock;
|
||||
import PamguardMVC.PamDataUnit;
|
||||
import nilus.Detection;
|
||||
import nilus.GranularityEnumType;
|
||||
import tethys.TethysControl;
|
||||
import tethys.output.StreamExportParams;
|
||||
import tethys.output.TethysExportParams;
|
||||
|
||||
public abstract class GranularityHandler {
|
||||
|
||||
protected TethysControl tethysControl;
|
||||
|
||||
protected PamDataBlock dataBlock;
|
||||
|
||||
protected TethysExportParams tethysExportParams;
|
||||
|
||||
protected StreamExportParams streamExportParams;
|
||||
|
||||
/**
|
||||
* @param tethysControl
|
||||
* @param dataBlock
|
||||
* @param tethysExportParams
|
||||
* @param streamExportParams
|
||||
*/
|
||||
public GranularityHandler(TethysControl tethysControl, PamDataBlock dataBlock,
|
||||
TethysExportParams tethysExportParams, StreamExportParams streamExportParams) {
|
||||
this.tethysControl = tethysControl;
|
||||
this.dataBlock = dataBlock;
|
||||
this.tethysExportParams = tethysExportParams;
|
||||
this.streamExportParams = streamExportParams;
|
||||
}
|
||||
|
||||
/**
|
||||
* Prepare to start, passing the start time of the effort
|
||||
* or of the first time bin for binned granularity types.
|
||||
* @param timeMillis
|
||||
*/
|
||||
public abstract void prepare(long timeMillis);
|
||||
|
||||
/**
|
||||
* Put a data unit into a Detection object. for Call granularity
|
||||
* this will probably return every time. For binned and encounter
|
||||
* types this will only return at the end of a bin / encounter
|
||||
* @param dataUnit
|
||||
* @return Detection object, but only when ready to be added to Detections
|
||||
*/
|
||||
public abstract Detection[] addDataUnit(PamDataUnit dataUnit);
|
||||
|
||||
/**
|
||||
* Called after end end of all data units to get the last bin / encounter. <p>
|
||||
*
|
||||
* @param timeMillis end time of effort or last bin in milliseconds.
|
||||
* @return null for Call granularity, otherwise may be non null for binned or encounter.
|
||||
*/
|
||||
public abstract Detection[] cleanup(long timeMillis);
|
||||
|
||||
/**
|
||||
* Convert a single detection to a one element array since that's what'
|
||||
* most functions need to return.
|
||||
* @param det
|
||||
* @return
|
||||
*/
|
||||
protected Detection[] toDetectionArray(Detection det) {
|
||||
if (det == null) {
|
||||
return null;
|
||||
}
|
||||
Detection[] dets = new Detection[1];
|
||||
dets[0] = det;
|
||||
return dets;
|
||||
}
|
||||
|
||||
/**
|
||||
* Create the correct type of granularity handler to put individual data units into
|
||||
* Detection objects.
|
||||
* @param granularity
|
||||
* @param tethysControl
|
||||
* @param dataBlock
|
||||
* @param tethysExportParams
|
||||
* @param streamExportParams
|
||||
* @return
|
||||
*/
|
||||
public static GranularityHandler getHandler(GranularityEnumType granularity, TethysControl tethysControl, PamDataBlock dataBlock,
|
||||
TethysExportParams tethysExportParams, StreamExportParams streamExportParams) {
|
||||
switch (granularity) {
|
||||
case BINNED:
|
||||
return new BinnedGranularityHandler(tethysControl, dataBlock, tethysExportParams, streamExportParams);
|
||||
case CALL:
|
||||
return new CallGranularityHandler(tethysControl, dataBlock, tethysExportParams, streamExportParams);
|
||||
case ENCOUNTER:
|
||||
new EncounterGranularityHandler(tethysControl, dataBlock, tethysExportParams, streamExportParams);
|
||||
case GROUPED:
|
||||
return new GroupedGranularityHandler(tethysControl, dataBlock, tethysExportParams, streamExportParams);
|
||||
default:
|
||||
break;
|
||||
}
|
||||
return null;
|
||||
}
|
||||
}
|
||||
36
src/tethys/detection/GroupedGranularityHandler.java
Normal file
36
src/tethys/detection/GroupedGranularityHandler.java
Normal file
@ -0,0 +1,36 @@
|
||||
package tethys.detection;
|
||||
|
||||
import PamguardMVC.PamDataBlock;
|
||||
import PamguardMVC.PamDataUnit;
|
||||
import nilus.Detection;
|
||||
import tethys.TethysControl;
|
||||
import tethys.output.StreamExportParams;
|
||||
import tethys.output.TethysExportParams;
|
||||
|
||||
public class GroupedGranularityHandler extends GranularityHandler {
|
||||
|
||||
public GroupedGranularityHandler(TethysControl tethysControl, PamDataBlock dataBlock,
|
||||
TethysExportParams tethysExportParams, StreamExportParams streamExportParams) {
|
||||
super(tethysControl, dataBlock, tethysExportParams, streamExportParams);
|
||||
// TODO Auto-generated constructor stub
|
||||
}
|
||||
|
||||
@Override
|
||||
public void prepare(long timeMillis) {
|
||||
// TODO Auto-generated method stub
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public Detection[] addDataUnit(PamDataUnit dataUnit) {
|
||||
// TODO Auto-generated method stub
|
||||
return null;
|
||||
}
|
||||
|
||||
@Override
|
||||
public Detection[] cleanup(long timeMillis) {
|
||||
// TODO Auto-generated method stub
|
||||
return null;
|
||||
}
|
||||
|
||||
}
|
||||
@ -8,7 +8,7 @@ import tethys.TethysControl;
|
||||
* All the information needed to populate a table row in the synchronisation table.
|
||||
* some will need to be set as rarely as possible since it may
|
||||
* be slow to update. <br>
|
||||
* This needs to sit alongside the StreamExportParams objects since those others are serialisable wheras
|
||||
* This needs to sit alongside the StreamExportParams objects since those others are serialisable whereas
|
||||
* there is a lot of stuff in here which isn't.
|
||||
* @author dg50
|
||||
*
|
||||
|
||||
@ -31,6 +31,12 @@ public class StreamExportParams implements Serializable {
|
||||
|
||||
public GranularityEnumType granularity = GranularityEnumType.CALL;
|
||||
|
||||
public double binDurationS = 60;
|
||||
|
||||
public double encounterGapS = 60;
|
||||
|
||||
public int minBinCount = 1;
|
||||
|
||||
/*
|
||||
* Can't have this here since it isn't serializable.
|
||||
*/
|
||||
|
||||
@ -1,32 +1,16 @@
|
||||
package tethys.output;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.io.PrintWriter;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
import java.util.ArrayList;
|
||||
|
||||
import javax.xml.bind.JAXBContext;
|
||||
import javax.xml.bind.JAXBException;
|
||||
import javax.xml.bind.Marshaller;
|
||||
|
||||
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.PamSettings;
|
||||
import PamController.settings.output.xml.PamguardXMLWriter;
|
||||
import PamUtils.PamCalendar;
|
||||
import PamguardMVC.PamDataBlock;
|
||||
import PamguardMVC.PamDataUnit;
|
||||
import PamguardMVC.dataSelector.DataSelector;
|
||||
import dbxml.uploader.Importer;
|
||||
import metadata.MetaDataContol;
|
||||
import metadata.deployment.DeploymentData;
|
||||
import nilus.Deployment;
|
||||
@ -35,15 +19,13 @@ import tethys.dbxml.DBXMLConnect;
|
||||
import tethys.dbxml.TethysException;
|
||||
import tethys.deployment.DeploymentHandler;
|
||||
import tethys.deployment.DeploymentOverview;
|
||||
import tethys.deployment.DeploymentRecoveryPair;
|
||||
import tethys.deployment.RecordingPeriod;
|
||||
import tethys.detection.DetectionGranularity;
|
||||
import tethys.detection.DetectionGranularity.GRANULARITY;
|
||||
import tethys.detection.DetectionsHandler;
|
||||
import tethys.pamdata.TethysDataProvider;
|
||||
import tethys.pamdata.TethysSchema;
|
||||
|
||||
/**
|
||||
* No longer used. This was purely a test class used for making the first couple
|
||||
* of test connections and exports to Tethys. Can probably delete.
|
||||
*
|
||||
* 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
|
||||
@ -55,6 +37,7 @@ import tethys.pamdata.TethysSchema;
|
||||
* @author dg50
|
||||
*
|
||||
*/
|
||||
@Deprecated
|
||||
public class TethysExporter {
|
||||
|
||||
private TethysControl tethysControl;
|
||||
@ -62,7 +45,7 @@ public class TethysExporter {
|
||||
|
||||
private DBXMLConnect dbxmlConnect;
|
||||
|
||||
public TethysExporter(TethysControl tethysControl, TethysExportParams tethysExportParams) {
|
||||
private TethysExporter(TethysControl tethysControl, TethysExportParams tethysExportParams) {
|
||||
this.tethysControl = tethysControl;
|
||||
this.tethysExportParams = tethysExportParams;
|
||||
dbxmlConnect = new DBXMLConnect(tethysControl);
|
||||
@ -85,7 +68,7 @@ public class TethysExporter {
|
||||
*/
|
||||
// return false;
|
||||
// }
|
||||
|
||||
|
||||
/**
|
||||
* Doug populate instrument fields - may need to add a few things. Marie to
|
||||
* define what we mean by instrument. Instrument names probably need to be added
|
||||
@ -206,7 +189,7 @@ public class TethysExporter {
|
||||
DetectionsHandler detectionsHandler = new DetectionsHandler(tethysControl);
|
||||
ArrayList<PamDataBlock> allDataBlocks = PamController.getInstance().getDataBlocks();
|
||||
// /**
|
||||
// * Outer loop is through deployemnt documents. Will then export detections within each
|
||||
// * Outer loop is through deployemnt documents. Will then export detections within each
|
||||
// * deployment detector by detector
|
||||
// */
|
||||
// for (Deployment aDeployment : deploymentDocs) {
|
||||
@ -215,7 +198,7 @@ public class TethysExporter {
|
||||
// if (streamExportParams == null || !streamExportParams.selected) {
|
||||
// continue; // not interested in this one.
|
||||
// }
|
||||
// detectionsHandler.exportDetections(aDataBlock, aDeployment,
|
||||
// detectionsHandler.exportDetections(aDataBlock, aDeployment,
|
||||
// new DetectionGranularity(GRANULARITY.TIME, 3600*12), tethysExportParams, streamExportParams);
|
||||
// }
|
||||
// }
|
||||
|
||||
@ -112,7 +112,7 @@ public class TethysExportDialog extends PamDialog {
|
||||
ArrayList<DataStreamSet> sets = new ArrayList<>();
|
||||
ArrayList<PamDataBlock> allDataBlocks = PamController.getInstance().getDataBlocks();
|
||||
for (PamDataBlock aDataBlock : allDataBlocks) {
|
||||
if (aDataBlock.getTethysDataProvider() != null) {
|
||||
if (aDataBlock.getTethysDataProvider(tethysControl) != null) {
|
||||
sets.add(new DataStreamSet(aDataBlock));
|
||||
}
|
||||
}
|
||||
|
||||
@ -31,6 +31,7 @@ import nilus.DetectionEffortKind;
|
||||
import nilus.SpeciesIDType;
|
||||
import tethys.TethysControl;
|
||||
import tethys.TethysTimeFuncs;
|
||||
import tethys.detection.DetectionsHandler;
|
||||
import tethys.niluswraps.PDeployment;
|
||||
import tethys.output.StreamExportParams;
|
||||
import tethys.output.TethysExportParams;
|
||||
@ -62,8 +63,10 @@ public class AutoTethysProvider implements TethysDataProvider {
|
||||
private PamDataBlock pamDataBlock;
|
||||
private PamProcess pamProcess;
|
||||
private PamControlledUnit pamControlledUnit;
|
||||
private TethysControl tethysControl;
|
||||
|
||||
public AutoTethysProvider(PamDataBlock pamDataBlock) {
|
||||
public AutoTethysProvider(TethysControl tethysControl, PamDataBlock pamDataBlock) {
|
||||
this.tethysControl = tethysControl;
|
||||
this.pamDataBlock = pamDataBlock;
|
||||
pamProcess = pamDataBlock.getParentProcess();
|
||||
pamControlledUnit = pamProcess.getPamControlledUnit();
|
||||
@ -135,7 +138,7 @@ public class AutoTethysProvider implements TethysDataProvider {
|
||||
Object settings = pamSettings.getSettingsReference();
|
||||
TethysParameterPacker paramPacker = null;
|
||||
try {
|
||||
paramPacker = new TethysParameterPacker();
|
||||
paramPacker = new TethysParameterPacker(tethysControl);
|
||||
} catch (JAXBException e) {
|
||||
// TODO Auto-generated catch block
|
||||
e.printStackTrace();
|
||||
@ -425,6 +428,22 @@ public class AutoTethysProvider implements TethysDataProvider {
|
||||
|
||||
kind.getSpeciesId().setValue(BigInteger.valueOf(mapItem.getItisCode()));
|
||||
kind.getGranularity().setValue(exportParams.granularity);
|
||||
// nilus.DetectionEffortKind.Parameters granularityParams = kind.getParameters();
|
||||
switch (exportParams.granularity) {
|
||||
case BINNED:
|
||||
kind.getGranularity().setBinSizeM(exportParams.binDurationS/60.);
|
||||
long firstBin = DetectionsHandler.roundDownBinStart(pDeployment.getAudioStart(), (long) (exportParams.binDurationS*1000));
|
||||
kind.getGranularity().setFirstBinStart(TethysTimeFuncs.xmlGregCalFromMillis(firstBin));
|
||||
break;
|
||||
case CALL:
|
||||
break;
|
||||
case ENCOUNTER:
|
||||
kind.getGranularity().setEncounterGapM(exportParams.encounterGapS/60.);
|
||||
break;
|
||||
case GROUPED:
|
||||
break;
|
||||
|
||||
}
|
||||
kind.setCall(mapItem.getCallType());
|
||||
|
||||
|
||||
|
||||
@ -14,6 +14,7 @@ import javax.xml.parsers.DocumentBuilderFactory;
|
||||
import javax.xml.parsers.ParserConfigurationException;
|
||||
import javax.xml.transform.dom.DOMResult;
|
||||
|
||||
import org.docx4j.model.listnumbering.NumberFormatLowerLetter;
|
||||
import org.w3c.dom.Document;
|
||||
import org.w3c.dom.Element;
|
||||
|
||||
@ -25,7 +26,10 @@ import PamModel.parametermanager.PamParameterData;
|
||||
import PamModel.parametermanager.PamParameterSet;
|
||||
import PamguardMVC.PamDataBlock;
|
||||
import PamguardMVC.PamProcess;
|
||||
import PamguardMVC.dataSelector.DataSelectParams;
|
||||
import PamguardMVC.dataSelector.DataSelector;
|
||||
import nilus.MarshalXML;
|
||||
import tethys.TethysControl;
|
||||
|
||||
/**
|
||||
* Functions to pack up a PAMGuard parameters object into the correct format
|
||||
@ -74,12 +78,15 @@ public class TethysParameterPacker {
|
||||
|
||||
private PamguardXMLWriter xmlWriter;
|
||||
|
||||
private TethysControl tethysControl;
|
||||
|
||||
/**
|
||||
* @throws JAXBException
|
||||
*
|
||||
*/
|
||||
public TethysParameterPacker() throws JAXBException {
|
||||
public TethysParameterPacker(TethysControl tethysControl) throws JAXBException {
|
||||
super();
|
||||
this.tethysControl = tethysControl;
|
||||
try {
|
||||
marshaller = new MarshalXML();
|
||||
} catch (JAXBException e) {
|
||||
@ -117,12 +124,43 @@ public class TethysParameterPacker {
|
||||
if (parameterSet == null) {
|
||||
return null;
|
||||
}
|
||||
// Document document = null;
|
||||
// try {
|
||||
// document = DocumentBuilderFactory.newInstance().newDocumentBuilder().newDocument();
|
||||
// } catch (ParserConfigurationException e1) {
|
||||
// e1.printStackTrace();
|
||||
// }
|
||||
// get the XML writer ready for a new export ...
|
||||
xmlWriter.setExcludeDisplaySettings(true);
|
||||
xmlWriter.makeSettingsList();
|
||||
|
||||
/**
|
||||
* first do the data filter. I can't see any way of doing this
|
||||
* without creating a doc as was in the helper example.
|
||||
*/
|
||||
QName qnamef = new QName(MarshalXML.schema, "datafilter", "ty");
|
||||
JAXBElement<String> jaxelf = new JAXBElement<String>(
|
||||
qnamef, String.class, parameterSet.getParentObject().getClass().getCanonicalName());
|
||||
Document docf = null;
|
||||
try {
|
||||
docf = marshaller.marshalToDOM(jaxelf);
|
||||
} catch (JAXBException | ParserConfigurationException e1) {
|
||||
e1.printStackTrace();
|
||||
}
|
||||
Element elf = docf.getDocumentElement();
|
||||
elList.add(elf);/**
|
||||
* Is there a data filter ? If so, write it's
|
||||
* XML parameters out here.
|
||||
*/
|
||||
DataSelector dataSelector = pamDataBlock.getDataSelector(tethysControl.getDataSelectName(), false);
|
||||
if (dataSelector != null) {
|
||||
DataSelectParams filterParams = dataSelector.getParams();
|
||||
if (filterParams != null) {
|
||||
Element pEl = xmlWriter.writeObjectData(docf, elf, filterParams, null);
|
||||
// if (pEl != null) {
|
||||
//// filterEl.appendChild(pEl);
|
||||
// elf.appendChild(filterEl);
|
||||
// }
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
QName qname = new QName(MarshalXML.schema, "parameters", "ty");
|
||||
JAXBElement<String> jaxel = new JAXBElement<String>(
|
||||
qname, String.class, parameterSet.getParentObject().getClass().getCanonicalName());
|
||||
@ -133,18 +171,14 @@ public class TethysParameterPacker {
|
||||
e1.printStackTrace();
|
||||
}
|
||||
Element el = doc.getDocumentElement();
|
||||
|
||||
for (PamParameterData pamParam : parameterSet.getParameterCollection()) {
|
||||
try {
|
||||
Object paramData = pamParam.getData();
|
||||
boolean ok = createElement(doc, el, paramData, pamParam, objectHierarchy);
|
||||
} catch (IllegalArgumentException | IllegalAccessException e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
}
|
||||
elList.add(el);
|
||||
xmlWriter.setExcludeDisplaySettings(true);
|
||||
xmlWriter.makeSettingsList();
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* Now get the chain of PAMGuard modules for the current detector and for
|
||||
* all upstream modules.
|
||||
*/
|
||||
ArrayList<PamControlledUnit> moduleChain = getParentChain(pamDataBlock);
|
||||
for (PamControlledUnit pcu : moduleChain) {
|
||||
if (pcu instanceof PamSettings == false) {
|
||||
|
||||
@ -20,6 +20,8 @@ import PamView.tables.SwingTableColumnWidths;
|
||||
import PamguardMVC.PamDataBlock;
|
||||
import nilus.Detections;
|
||||
import tethys.TethysControl;
|
||||
import tethys.TethysState;
|
||||
import tethys.TethysState.StateType;
|
||||
import tethys.dbxml.TethysException;
|
||||
import tethys.detection.StreamDetectionsSummary;
|
||||
import tethys.niluswraps.PDetections;
|
||||
@ -75,6 +77,13 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
|
||||
tableModel.fireTableDataChanged();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void updateState(TethysState tethysState) {
|
||||
if (dataBlock != null) {
|
||||
selectDataBlock(dataBlock);
|
||||
}
|
||||
}
|
||||
|
||||
private class MouseActions extends MouseAdapter {
|
||||
|
||||
@Override
|
||||
@ -137,6 +146,7 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
|
||||
} catch (TethysException e) {
|
||||
getTethysControl().showException(e);
|
||||
}
|
||||
getTethysControl().exportedDetections(dataBlock);
|
||||
selectDataBlock(dataBlock); // force table update.
|
||||
}
|
||||
|
||||
|
||||
@ -28,10 +28,11 @@ import PamguardMVC.PamDataBlock;
|
||||
import dataMap.OfflineDataMap;
|
||||
import tethys.TethysControl;
|
||||
import tethys.TethysState;
|
||||
import tethys.TethysStateObserver;
|
||||
import tethys.output.DatablockSynchInfo;
|
||||
import tethys.species.DataBlockSpeciesManager;
|
||||
|
||||
public class DatablockSynchPanel extends TethysGUIPanel {
|
||||
public class DatablockSynchPanel extends TethysGUIPanel {
|
||||
|
||||
public JPanel mainPanel;
|
||||
|
||||
@ -133,6 +134,7 @@ public class DatablockSynchPanel extends TethysGUIPanel {
|
||||
@Override
|
||||
public void updateState(TethysState tethysState) {
|
||||
synchTableModel.fireTableDataChanged();
|
||||
selectRow();
|
||||
}
|
||||
|
||||
public void addTableObserver(StreamTableObserver observer) {
|
||||
|
||||
@ -20,7 +20,7 @@ public class AlgorithmCard extends ExportWizardCard {
|
||||
|
||||
private JTextField method, software, version, supportSoftware;
|
||||
|
||||
public AlgorithmCard(TethysControl tethysControl, PamDataBlock dataBlock) {
|
||||
public AlgorithmCard(DetectionsExportWizard detectionsExportWizard, TethysControl tethysControl, PamDataBlock dataBlock) {
|
||||
super(tethysControl, "Algorithm", dataBlock);
|
||||
setBorder(new TitledBorder("Algorithm details"));
|
||||
method = new JTextField(40);
|
||||
|
||||
@ -10,7 +10,7 @@ public class DescriptionCard extends ExportWizardCard {
|
||||
|
||||
private DescriptionTypePanel descriptionPanel;
|
||||
|
||||
public DescriptionCard(TethysControl tethysControl, PamDataBlock dataBlock) {
|
||||
public DescriptionCard(DetectionsExportWizard detectionsExportWizard, TethysControl tethysControl, PamDataBlock dataBlock) {
|
||||
super(tethysControl, "Description", dataBlock);
|
||||
this.setLayout(new BorderLayout());
|
||||
descriptionPanel = new DescriptionTypePanel("Description data", true, true, true);
|
||||
|
||||
@ -48,10 +48,10 @@ public class DetectionsExportWizard extends PamDialog {
|
||||
cardPanel = new JPanel(cardLayout);
|
||||
mainPanel.add(BorderLayout.CENTER, cardPanel);
|
||||
|
||||
addCard(algorithmCard = new AlgorithmCard(tethysControl, dataBlock));
|
||||
addCard(granularityCard = new GranularityCard(tethysControl, dataBlock));
|
||||
addCard(descriptionCard = new DescriptionCard(tethysControl, dataBlock));
|
||||
addCard(exportWorkerCard = new ExportWorkerCard(tethysControl, dataBlock));
|
||||
addCard(algorithmCard = new AlgorithmCard(this, tethysControl, dataBlock));
|
||||
addCard(granularityCard = new GranularityCard(this, tethysControl, dataBlock));
|
||||
addCard(descriptionCard = new DescriptionCard(this, tethysControl, dataBlock));
|
||||
addCard(exportWorkerCard = new ExportWorkerCard(this, tethysControl, dataBlock));
|
||||
|
||||
cardLayout.first(cardPanel);
|
||||
|
||||
@ -98,6 +98,10 @@ public class DetectionsExportWizard extends PamDialog {
|
||||
cardLayout.previous(cardPanel);
|
||||
enableControls();
|
||||
}
|
||||
|
||||
public JButton getPreviousButton() {
|
||||
return prevButton;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean getParams() {
|
||||
|
||||
@ -36,8 +36,11 @@ public class ExportWorkerCard extends ExportWizardCard implements DetectionExpor
|
||||
|
||||
private StreamExportParams streamExportParams;
|
||||
|
||||
public ExportWorkerCard(TethysControl tethysControl, PamDataBlock dataBlock) {
|
||||
private DetectionsExportWizard detectionsExportWizard;
|
||||
|
||||
public ExportWorkerCard(DetectionsExportWizard detectionsExportWizard, TethysControl tethysControl, PamDataBlock dataBlock) {
|
||||
super(tethysControl, "Export", dataBlock);
|
||||
this.detectionsExportWizard = detectionsExportWizard;
|
||||
setLayout(new BorderLayout());
|
||||
setBorder(new TitledBorder("Export data"));
|
||||
JPanel exPanel = new PamNorthPanel(new GridBagLayout());
|
||||
@ -146,6 +149,8 @@ public class ExportWorkerCard extends ExportWizardCard implements DetectionExpor
|
||||
break;
|
||||
case DetectionExportProgress.STATE_COMPLETE:
|
||||
progressText.setText("Export complete");
|
||||
detectionsExportWizard.getCancelButton().setText("Close");
|
||||
detectionsExportWizard.getPreviousButton().setEnabled(false);
|
||||
break;
|
||||
case DetectionExportProgress.STATE_WRITING:
|
||||
progressText.setText("Writing to Tethys: " + progress.currentDetections.getId());
|
||||
|
||||
@ -34,17 +34,22 @@ import tethys.output.StreamExportParams;
|
||||
public class GranularityCard extends ExportWizardCard {
|
||||
|
||||
private JRadioButton[] granularities;
|
||||
|
||||
|
||||
private JTextArea dataSelectionText;
|
||||
|
||||
private JTextField binLength, encounterGap;
|
||||
|
||||
private JTextField binLength, minCalls, encounterGap;
|
||||
|
||||
private DataSelector dataSelector;
|
||||
|
||||
public GranularityCard(TethysControl tethysControl, PamDataBlock dataBlock) {
|
||||
|
||||
private DetectionsExportWizard detectionsExportWizard;
|
||||
|
||||
private int encounterIndex, binnedIndex;
|
||||
|
||||
public GranularityCard(DetectionsExportWizard detectionsExportWizard, TethysControl tethysControl, PamDataBlock dataBlock) {
|
||||
super(tethysControl, "Granularity", dataBlock);
|
||||
this.detectionsExportWizard = detectionsExportWizard;
|
||||
setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
|
||||
|
||||
|
||||
// granularity
|
||||
GranularityEnumType[] grans = GranularityEnumType.values();
|
||||
granularities = new JRadioButton[grans.length];
|
||||
@ -52,34 +57,41 @@ public class GranularityCard extends ExportWizardCard {
|
||||
GridBagConstraints c = new PamGridBagContraints();
|
||||
granPanel.setBorder(new TitledBorder("Granularity"));
|
||||
ButtonGroup granGroup = new ButtonGroup();
|
||||
GranularityChange gc = new GranularityChange();
|
||||
for (int i = 0; i < grans.length; i++) {
|
||||
c.gridx = 0;
|
||||
granularities[i] = new JRadioButton(PGranularityType.prettyString(grans[i]));
|
||||
granularities[i].setToolTipText(PGranularityType.toolTip(grans[i]));
|
||||
granularities[i].addActionListener(gc);
|
||||
granPanel.add(granularities[i], c);
|
||||
granGroup.add(granularities[i]);
|
||||
if (grans[i] == GranularityEnumType.BINNED) {
|
||||
binnedIndex = i;
|
||||
c.gridx++;
|
||||
granPanel.add(new JLabel(" bin duration ", JLabel.RIGHT), c);
|
||||
c.gridx++;
|
||||
granPanel.add(binLength = new JTextField(5), c);
|
||||
c.gridx++;
|
||||
granPanel.add(new JLabel(" (s) ", JLabel.LEFT), c);
|
||||
|
||||
granPanel.add(new JLabel("(s), min Calls", JLabel.LEFT), c);
|
||||
c.gridx++;
|
||||
granPanel.add(minCalls = new JTextField(5), c);
|
||||
binLength.setToolTipText("Time bin duration in seconds");
|
||||
minCalls.setToolTipText("Minimum number of calls for a bin to be output");
|
||||
}
|
||||
if (grans[i] == GranularityEnumType.ENCOUNTER) {
|
||||
encounterIndex = i;
|
||||
c.gridx++;
|
||||
granPanel.add(new JLabel(" min gap ", JLabel.RIGHT), c);
|
||||
c.gridx++;
|
||||
granPanel.add(encounterGap = new JTextField(5), c);
|
||||
c.gridx++;
|
||||
granPanel.add(new JLabel(" (s) ", JLabel.LEFT), c);
|
||||
|
||||
granPanel.add(new JLabel("(s) ", JLabel.LEFT), c);
|
||||
encounterGap.setToolTipText("Minimum gap between separate encounters");
|
||||
}
|
||||
c.gridy++;
|
||||
}
|
||||
this.add(granPanel);
|
||||
|
||||
|
||||
// data selection
|
||||
dataSelector = dataBlock.getDataSelector(tethysControl.getDataSelectName(), false);
|
||||
if (dataSelector != null) {
|
||||
@ -101,7 +113,22 @@ public class GranularityCard extends ExportWizardCard {
|
||||
dataPanel.add(BorderLayout.CENTER, sp);
|
||||
this.add(dataPanel);
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
private class GranularityChange implements ActionListener {
|
||||
|
||||
@Override
|
||||
public void actionPerformed(ActionEvent e) {
|
||||
enableControls();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private void enableControls() {
|
||||
binLength.setEnabled(granularities[binnedIndex].isSelected());
|
||||
minCalls.setEnabled(granularities[binnedIndex].isSelected());
|
||||
encounterGap.setEnabled(granularities[encounterIndex].isSelected());
|
||||
}
|
||||
|
||||
protected void newDataSelection() {
|
||||
@ -129,7 +156,29 @@ public class GranularityCard extends ExportWizardCard {
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
if (streamExportParams.granularity == GranularityEnumType.BINNED) {
|
||||
try {
|
||||
streamExportParams.binDurationS = Double.valueOf(binLength.getText());
|
||||
}
|
||||
catch (NumberFormatException e) {
|
||||
return detectionsExportWizard.showWarning("Invalid bin duration parameter");
|
||||
}
|
||||
try {
|
||||
streamExportParams.minBinCount = Integer.valueOf(minCalls.getText());
|
||||
}
|
||||
catch (NumberFormatException e) {
|
||||
return detectionsExportWizard.showWarning("Invalid minimum call count");
|
||||
}
|
||||
}
|
||||
if (streamExportParams.granularity == GranularityEnumType.ENCOUNTER) {
|
||||
try {
|
||||
streamExportParams.encounterGapS = Double.valueOf(encounterGap.getText());
|
||||
}
|
||||
catch (NumberFormatException e) {
|
||||
return detectionsExportWizard.showWarning("Invalid encounter gap parameter");
|
||||
}
|
||||
}
|
||||
|
||||
return streamExportParams.granularity != null;
|
||||
}
|
||||
|
||||
@ -139,7 +188,11 @@ public class GranularityCard extends ExportWizardCard {
|
||||
for (int i = 0; i < grans.length; i++) {
|
||||
granularities[i].setSelected(streamExportParams.granularity == grans[i]);
|
||||
}
|
||||
binLength.setText(String.format("%3.1f", streamExportParams.binDurationS));
|
||||
minCalls.setText(String.format("%d", streamExportParams.minBinCount));
|
||||
encounterGap.setText(String.format("%3.1f", streamExportParams.encounterGapS));
|
||||
newDataSelection();
|
||||
enableControls();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
Loading…
Reference in New Issue
Block a user