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More output

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More changes to Detections output.
This commit is contained in:
Douglas Gillespie 2023-09-13 17:28:47 +01:00
parent 85fd84d18a
commit db1cc75bc1
19 changed files with 631 additions and 235 deletions
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4
src/PamguardMVC/PamDataBlock.java
View File

@ -76,8 +76,10 @@ import PamguardMVC.background.BackgroundDataBlock;
import PamguardMVC.background.BackgroundManager;
import PamguardMVC.dataOffline.OfflineDataLoadInfo;
import PamguardMVC.dataOffline.OfflineDataLoading;
import PamguardMVC.dataSelector.DataSelectParams;
import PamguardMVC.dataSelector.DataSelector;
import PamguardMVC.dataSelector.DataSelectorCreator;
import PamguardMVC.dataSelector.DataSelectorSettings;
import PamguardMVC.dataSelector.NullDataSelectorCreator;
import PamguardMVC.datamenus.DataMenuParent;
import PamguardMVC.nanotime.NanoTimeCalculator;
@ -2840,7 +2842,7 @@ public class PamDataBlock<Tunit extends PamDataUnit> extends PamObservable {
* @return temporary copy of the data
*/
public ArrayList<Tunit> getDataCopy(long t1, long t2, boolean assumeOrder, DataSelector dataSelector) {
if (dataSelector == null) {
if (dataSelector == null || dataSelector.getParams().getCombinationFlag() == DataSelectParams.DATA_SELECT_DISABLE) {
return getDataCopy(t1, t2, assumeOrder);
}
else {

12
src/RightWhaleEdgeDetector/RWEDataBlock.java
View File

@ -7,7 +7,10 @@ import PamguardMVC.dataOffline.OfflineDataLoadInfo;
import PamguardMVC.dataSelector.DataSelectorCreator;
import RightWhaleEdgeDetector.datasel.RWDataSelCreator;
import RightWhaleEdgeDetector.species.RWSpeciesManager;
import RightWhaleEdgeDetector.species.RWTethysDataProvider;
import pamScrollSystem.ViewLoadObserver;
import tethys.TethysControl;
import tethys.pamdata.TethysDataProvider;
import tethys.species.DataBlockSpeciesManager;
import whistlesAndMoans.AbstractWhistleDataBlock;
@ -19,6 +22,7 @@ public class RWEDataBlock extends AbstractWhistleDataBlock<RWEDataUnit> implemen
private RWDataSelCreator dataSelCreator;
private RWSpeciesManager rwSpeciesManager;
private RWTethysDataProvider rwTethysDataProvider;
public RWEDataBlock(RWEControl rweControl, String dataName,
RWEProcess rweProcess, int channelMap) {
@ -65,4 +69,12 @@ public class RWEDataBlock extends AbstractWhistleDataBlock<RWEDataUnit> implemen
return rwSpeciesManager;
}
@Override
public TethysDataProvider getTethysDataProvider(TethysControl tethysControl) {
if (rwTethysDataProvider == null) {
rwTethysDataProvider = new RWTethysDataProvider(tethysControl, rweProcess.getRweDataBlock());
}
return rwTethysDataProvider;
}
}

37
src/RightWhaleEdgeDetector/species/RWTethysDataProvider.java Normal file
View File

@ -0,0 +1,37 @@
package RightWhaleEdgeDetector.species;
import PamguardMVC.PamDataBlock;
import PamguardMVC.PamDataUnit;
import RightWhaleEdgeDetector.RWEDataUnit;
import nilus.Detection;
import nilus.Detection.Parameters;
import tethys.TethysControl;
import tethys.output.StreamExportParams;
import tethys.output.TethysExportParams;
import tethys.pamdata.AutoTethysProvider;
public class RWTethysDataProvider extends AutoTethysProvider {
public RWTethysDataProvider(TethysControl tethysControl, PamDataBlock pamDataBlock) {
super(tethysControl, pamDataBlock);
}
@Override
public Detection createDetection(PamDataUnit dataUnit, TethysExportParams tethysExportParams,
StreamExportParams streamExportParams) {
Detection detection = super.createDetection(dataUnit, tethysExportParams, streamExportParams);
if (detection == null) {
return null;
}
RWEDataUnit rweDataUnit = (RWEDataUnit) dataUnit;
Parameters parameters = detection.getParameters();
parameters.setScore((double) rweDataUnit.rweSound.soundType);
double snr = 20.*Math.log10(rweDataUnit.rweSound.signal/rweDataUnit.rweSound.noise);
parameters.setSNRDB(snr);
return detection;
}
}

3
src/Spectrogram/SpectrogramDisplay.java
View File

@ -1639,6 +1639,9 @@ InternalFrameListener, DisplayPanelContainer, SpectrogramParametersUser, PamSett
return;
}
long t1 = dataUnit.getTimeMilliseconds()-viewerScroller.getValueMillis();
if (timeAxis == null) {
return;
}
int x1 = (int) Math.floor(timeAxis.getPosition(t1/1000));
int x2 = x1;
if (dataUnit.getDurationInMilliseconds() != null) {

11
src/dataMap/DataStreamPanel.java
View File

@ -751,7 +751,16 @@ public class DataStreamPanel extends JPanel implements DataMapObserver {
} else if (endTimeArrow != null && endTimeArrow.contains(me.getPoint())) {
tipText = "Data End: " + PamCalendar.formatDateTime(dataBlock.getCurrentViewDataEnd(), false);
} else {
tipText = "Cursor: " + PamCalendar.formatDateTime(tm, true);
OfflineDataMap dMap = dataBlock.getPrimaryDataMap();
if (dMap != null) {
tipText = String.format("%s Data from<p>%s to %s<p>Cursor: %s", dataBlock.getDataName(),
PamCalendar.formatDateTime(dMap.getFirstDataTime(), false),
PamCalendar.formatDateTime(dMap.getLastDataTime(), false),
PamCalendar.formatDateTime(tm, true));
}
else {
tipText = "Cursor: " + PamCalendar.formatDateTime(tm, true);
}
}
// tipText += "<br>Panel height = " + getHeight();

10
src/dataMap/OfflineDataMap.java
View File

@ -84,6 +84,8 @@ abstract public class OfflineDataMap<TmapPoint extends OfflineDataMapPoint> {
public static final int POINT_END = 0x8; // 8
public static final int IN_DATA = 0x10; // 16
public static final int NO_DATA = 0x20; // 32
private static final long oneDayInMillis = 3600L*24L*1000L;
public OfflineDataMap(OfflineDataStore offlineDataStore, PamDataBlock parentDataBlock) {
super();
@ -145,10 +147,10 @@ abstract public class OfflineDataMap<TmapPoint extends OfflineDataMapPoint> {
*/
synchronized public void addDataPoint(TmapPoint mapPoint) {
boolean first = (mapPoints.size() == 0);
if (mapPoint.getStartTime() > 0) {
if (mapPoint.getStartTime() > oneDayInMillis) {
firstDataTime = Math.min(firstDataTime, mapPoint.getStartTime());
}
if (mapPoint.getEndTime() > 0) {
if (mapPoint.getEndTime() > oneDayInMillis) {
lastDataTime = Math.max(lastDataTime, mapPoint.getEndTime());
// if (mapPoint.getEndTime() > System.currentTimeMillis()) {
// System.out.println("Stupid large data time in " + mapPoint.getName());
@ -273,10 +275,10 @@ abstract public class OfflineDataMap<TmapPoint extends OfflineDataMapPoint> {
while (it.hasNext()) {
aPoint = it.next();
if (aPoint.getStartTime() > 0) {
if (aPoint.getStartTime() > oneDayInMillis) {
firstDataTime = Math.min(firstDataTime, aPoint.getStartTime());
}
if (aPoint.getEndTime() > 0) {
if (aPoint.getEndTime() > oneDayInMillis) {
lastDataTime = Math.max(lastDataTime, aPoint.getEndTime());
}
n = aPoint.getNDatas();

9
src/tethys/TethysControl.java
View File

@ -516,6 +516,15 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
count += dbxmlQueries.countData(synchInfo.getDataBlock(), pDepl.deployment.getId());
}
synchInfo.setDataCount(count);
// also count the actual number of Detectoin documents
ArrayList<String> someNames = getDbxmlQueries().getDetectionsDocuments(synchInfo.getDataBlock(), null);
if (someNames == null) {
synchInfo.setDetectionDocumentCount(0);
}
else {
synchInfo.setDetectionDocumentCount(someNames.size());
}
i++;
}
// int[] counts = dbxmlQueries.countDataForProject(deplData.getProject(), dataPrefixes);

401
src/tethys/dbxml/DBXMLQueries.java
View File

@ -47,7 +47,7 @@ public class DBXMLQueries {
private TethysControl tethysControl;
private DBXMLConnect dbXMLConnect;
private PamWarning queryWarning;
public DBXMLQueries(TethysControl tethysControl, DBXMLConnect dbXMLConnect) {
@ -119,7 +119,7 @@ public class DBXMLQueries {
queryWarning.setEndOfLife(t2+10000);
return result;
}
}
private DBQueryResult executeQueryT(String jsonQueryString) throws TethysQueryException {
@ -136,7 +136,7 @@ public class DBXMLQueries {
try {
JerseyClient jerseyClient = dbxmlConnect.getJerseyClient();
// Queries queries = new Queries(jerseyClient);
// Queries queries = new Queries(jerseyClient);
queryResult = jerseyClient.queryJSON(jsonQueryString, 0);
schemaPlan = jerseyClient.queryJSON(jsonQueryString, 1);
@ -148,7 +148,7 @@ public class DBXMLQueries {
}
return new DBQueryResult(System.currentTimeMillis()-t1, queryResult, schemaPlan);
}
/**
* Check whether or not to strip of the s of one of the collection names.
* This is caused by some daft thing whereby the Deployments colleciton is called Deployments
@ -169,7 +169,7 @@ public class DBXMLQueries {
}
return collection;
}
/**
* Get a list of all documents in a collection.
* @param collection
@ -180,18 +180,18 @@ public class DBXMLQueries {
return null;
}
collection = checkCollectionPlural(collection);
// if (collection.endsWith("s")) {
// collection = collection.substring(0, collection.length()-1);
// }
// if (collection.endsWith("s")) {
// collection = collection.substring(0, collection.length()-1);
// }
String baseQuery = "{\"return\":[\"COLLECTIONNAME/Id\"],\"select\":[],\"enclose\":1}";
baseQuery = baseQuery.replace("COLLECTIONNAME", collection);
String tagName = "Id";
if (collection.equals("SpeciesAbbreviations")) {
baseQuery = "{\"return\":[\"Abbreviations/Name\"],\"select\":[],\"enclose\":1}";
tagName = "Name";
}
DBQueryResult result;
try {
result = executeQuery(baseQuery);
@ -216,7 +216,7 @@ public class DBXMLQueries {
String docId = aNode.getTextContent();
docIds.add(docId);
}
return docIds;
}
@ -236,7 +236,7 @@ public class DBXMLQueries {
return null;
}
// System.out.println("Project query execution time millis = " + result.queryTimeMillis);
// System.out.println("Project query execution time millis = " + result.queryTimeMillis);
ArrayList<String> projectNames = new ArrayList<>();
// iterate through the document and make a list of names, then make them unique.
@ -264,22 +264,22 @@ public class DBXMLQueries {
projectNames.add(projName);
}
}
// }
// if (aNode instanceof Element) {
// Node depEl = ((Element) aNode).getFirstChild();
// if (depEl == null) {
// continue;
// }
// if (depEl instanceof Element) {
// Element projEl = (Element) ((Element) depEl).getFirstChild();
// String projName = projEl.getTextContent();
// if (projName != null) {
// if (!projectNames.contains(projName)) {
// projectNames.add(projName);
// }
// }
// }
// }
// }
// if (aNode instanceof Element) {
// Node depEl = ((Element) aNode).getFirstChild();
// if (depEl == null) {
// continue;
// }
// if (depEl instanceof Element) {
// Element projEl = (Element) ((Element) depEl).getFirstChild();
// String projName = projEl.getTextContent();
// if (projName != null) {
// if (!projectNames.contains(projName)) {
// projectNames.add(projName);
// }
// }
// }
// }
}
Collections.sort(projectNames);
@ -310,7 +310,7 @@ public class DBXMLQueries {
if (result == null) {
return null;
}
// System.out.println("Deployment query execution time millis = " + result.queryTimeMillis);
// System.out.println("Deployment query execution time millis = " + result.queryTimeMillis);
PamguardXMLWriter pamXMLWriter = PamguardXMLWriter.getXMLWriter();
@ -319,19 +319,19 @@ public class DBXMLQueries {
return null;
}
// System.out.println(pamXMLWriter.getAsString(doc));
// System.out.println(pamXMLWriter.getAsString(doc));
ArrayList<Deployment> deployments = new ArrayList<>();
NodeList returns = doc.getElementsByTagName("Deployment");
// if (returns.getLength() == 0) {
// // try REsult instead !
// returns = doc.getElementsByTagName("Result");
// }
// if (returns.getLength() == 0) {
// // try REsult instead !
// returns = doc.getElementsByTagName("Result");
// }
// System.out.println("N projects = " + returns.getLength());
int n = returns.getLength();
// Queries queries = new Queries(null)
// Queries queries = new Queries(null)
for (int i = 0; i < n; i++) {
Node aNode = returns.item(i);
if (aNode instanceof Element) {
@ -357,8 +357,8 @@ public class DBXMLQueries {
deployment.setDeploymentId(Integer.valueOf(DeploymentId));
XMLGregorianCalendar gcStart = TethysTimeFuncs.fromGregorianXML(audioStart);
XMLGregorianCalendar gcEnd = TethysTimeFuncs.fromGregorianXML(audioEnd);
// System.out.printf("Converted %s to %s\n", audioStart,
// PamCalendar.formatDBDateTime(TethysTimeFuncs.millisFromGregorianXML(gcStart), true));
// System.out.printf("Converted %s to %s\n", audioStart,
// PamCalendar.formatDBDateTime(TethysTimeFuncs.millisFromGregorianXML(gcStart), true));
deployment.getDeploymentDetails().setAudioTimeStamp(gcStart);
if (deployment.getRecoveryDetails() == null) {
deployment.setRecoveryDetails(new DeploymentRecoveryDetails());
@ -381,7 +381,7 @@ public class DBXMLQueries {
/**
* Get a list of Detections documents which associate with a datablock and a deploymentId.
* @param dataBlock
* @param deploymentId
* @param deploymentId can be null to get all docs for data block
* @return
*/
public ArrayList<String> getDetectionsDocuments(PamDataBlock dataBlock, String deploymentId) {
@ -422,9 +422,9 @@ public class DBXMLQueries {
ArrayList<String> detectionsNames = new ArrayList();
int count = 0;
NodeList returns = doc.getElementsByTagName("Detections");
// if (returns.getLength() == 0) {
// returns = doc.getElementsByTagName("Result");
// }
// if (returns.getLength() == 0) {
// returns = doc.getElementsByTagName("Result");
// }
for (int i = 0; i < returns.getLength(); i++) {
Node aNode = returns.item(i);
String docName = aNode.getTextContent();
@ -433,80 +433,81 @@ public class DBXMLQueries {
return detectionsNames;
}
/**
* Get the names of all detection documents for a given deployment for all data streams.
* @param deploymentId
* @return
*/
public ArrayList<String> getDetectionsDocuments(String deploymentId) {
String queryBase = "{\"species\":{\"query\":{\"op\":\"lib:abbrev2tsn\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]},\"return\":{\"op\":\"lib:tsn2abbrev\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]}},\"return\":[\"Detections/Id\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Detections/DataSource/DeploymentId\",\"SomeDeploymentId\"],\"optype\":\"binary\"}],\"enclose\":1}";
String queryStr = queryBase.replace("SomeDeploymentId", deploymentId);
DBQueryResult queryResult = null;
try {
queryResult = executeQuery(queryStr);
} catch (TethysQueryException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
if (queryResult == null || queryResult.queryException != null) {
return null;
}
// PamguardXMLWriter pamXMLWriter = PamguardXMLWriter.getXMLWriter();
Document doc = convertStringToXMLDocument(queryResult.queryResult);
if (doc == null) {
return null;
}
ArrayList<String> detectionDocs = new ArrayList<>();
NodeList returns = doc.getElementsByTagName("Return");
if (returns.getLength() == 0) {
returns = doc.getElementsByTagName("Result");
}
for (int i = 0; i < returns.getLength(); i++) {
Node aNode = returns.item(i);
detectionDocs.add(aNode.getTextContent());
}
return detectionDocs;
* Get the names of all detection documents for a given deployment for all data streams.
* @param deploymentId
* @return
*/
public ArrayList<String> getDetectionsDocuments(String deploymentId) {
String queryBase = "{\"species\":{\"query\":{\"op\":\"lib:abbrev2tsn\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]},\"return\":{\"op\":\"lib:tsn2abbrev\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]}},\"return\":[\"Detections/Id\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Detections/DataSource/DeploymentId\",\"SomeDeploymentId\"],\"optype\":\"binary\"}],\"enclose\":1}";
String queryStr = queryBase.replace("SomeDeploymentId", deploymentId);
DBQueryResult queryResult = null;
try {
queryResult = executeQuery(queryStr);
} catch (TethysQueryException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
if (queryResult == null || queryResult.queryException != null) {
return null;
}
// PamguardXMLWriter pamXMLWriter = PamguardXMLWriter.getXMLWriter();
Document doc = convertStringToXMLDocument(queryResult.queryResult);
if (doc == null) {
return null;
}
ArrayList<String> detectionDocs = new ArrayList<>();
NodeList returns = doc.getElementsByTagName("Return");
if (returns.getLength() == 0) {
returns = doc.getElementsByTagName("Result");
}
for (int i = 0; i < returns.getLength(); i++) {
Node aNode = returns.item(i);
detectionDocs.add(aNode.getTextContent());
}
return detectionDocs;
}
public int countData(PamDataBlock dataBlock, String deploymentId) {
// /**
// * first query for Detections documents associated with this deployment and datablock.
// */
// String queryNoDepl = "{\"species\":{\"query\":{\"op\":\"lib:abbrev2tsn\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]},\"return\":{\"op\":\"lib:tsn2abbrev\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]}},\"return\":[\"Detections/Id\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Detections/Algorithm/Software\",\"LongDataName\"],\"optype\":\"binary\"}],\"enclose\":1}";
// String queryWithDepl = "{\"species\":{\"query\":{\"op\":\"lib:abbrev2tsn\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]},\"return\":{\"op\":\"lib:tsn2abbrev\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]}},\"return\":[\"Detections/Id\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Detections/Algorithm/Software\",\"LongDataName\"],\"optype\":\"binary\"},{\"op\":\"=\",\"operands\":[\"Detections/DataSource/DeploymentId\",\"TheDeploymentId\"],\"optype\":\"binary\"}],\"enclose\":1}";
// String query;
// if (deploymentId == null) {
// query = queryNoDepl;
// }
// else {
// query = queryWithDepl.replace("TheDeploymentId", deploymentId);
// }
// query = query.replace("LongDataName", dataBlock.getLongDataName());
// DBQueryResult queryResult = executeQuery(query);
// if (queryResult ==null) {
// return 0;
// }
// Document doc;
// try {
// doc = queryResult.getDocument();
// } catch (ParserConfigurationException | SAXException | IOException e) {
// e.printStackTrace();
// return 0;
// }
//
// int count = 0;
// NodeList returns = doc.getElementsByTagName("Return");
// /**
// * first query for Detections documents associated with this deployment and datablock.
// */
// String queryNoDepl = "{\"species\":{\"query\":{\"op\":\"lib:abbrev2tsn\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]},\"return\":{\"op\":\"lib:tsn2abbrev\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]}},\"return\":[\"Detections/Id\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Detections/Algorithm/Software\",\"LongDataName\"],\"optype\":\"binary\"}],\"enclose\":1}";
// String queryWithDepl = "{\"species\":{\"query\":{\"op\":\"lib:abbrev2tsn\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]},\"return\":{\"op\":\"lib:tsn2abbrev\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]}},\"return\":[\"Detections/Id\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Detections/Algorithm/Software\",\"LongDataName\"],\"optype\":\"binary\"},{\"op\":\"=\",\"operands\":[\"Detections/DataSource/DeploymentId\",\"TheDeploymentId\"],\"optype\":\"binary\"}],\"enclose\":1}";
// String query;
// if (deploymentId == null) {
// query = queryNoDepl;
// }
// else {
// query = queryWithDepl.replace("TheDeploymentId", deploymentId);
// }
// query = query.replace("LongDataName", dataBlock.getLongDataName());
// DBQueryResult queryResult = executeQuery(query);
// if (queryResult ==null) {
// return 0;
// }
// Document doc;
// try {
// doc = queryResult.getDocument();
// } catch (ParserConfigurationException | SAXException | IOException e) {
// e.printStackTrace();
// return 0;
// }
//
// int count = 0;
// NodeList returns = doc.getElementsByTagName("Return");
ArrayList<String> documentNames = getDetectionsDocuments(dataBlock, deploymentId);
if (documentNames == null) {
return 0;
}
int count = 0;
for (String docName : documentNames) {
// System.out.println(aNode.getTextContent());
// System.out.println(aNode.getTextContent());
int count2 = countDetections2(docName);
count += count2; //countDetecionsData(docName);
@ -515,22 +516,22 @@ public class DBXMLQueries {
}
public String getDocument(String collection, String documentId) {
// String queryBase = "return:(collection(\"replaceCollectionName\")/Detections[Id=\"ReplaceDocumentId\"])";
// queryBase = queryBase.replace("replaceCollectionName", collection);
// queryBase = queryBase.replace("ReplaceDocumentId", documentId);
//
// String result = null;
// try {
// Queries queries = dbXMLConnect.getTethysQueries();
// result = queries.QueryTethys(queryBase);
//// System.out.println(result);
// }
// catch (Exception e) {
// System.out.println("Error executing " + queryBase);
//// e.printStackTrace();
// return null;
// }
// return result;
// String queryBase = "return:(collection(\"replaceCollectionName\")/Detections[Id=\"ReplaceDocumentId\"])";
// queryBase = queryBase.replace("replaceCollectionName", collection);
// queryBase = queryBase.replace("ReplaceDocumentId", documentId);
//
// String result = null;
// try {
// Queries queries = dbXMLConnect.getTethysQueries();
// result = queries.QueryTethys(queryBase);
//// System.out.println(result);
// }
// catch (Exception e) {
// System.out.println("Error executing " + queryBase);
//// e.printStackTrace();
// return null;
// }
// return result;
Queries queries = dbXMLConnect.getTethysQueries();
String result = null;
@ -542,9 +543,9 @@ public class DBXMLQueries {
}
return result;
// String queryBase = "{\"return\":[\"Deployment/Project\"],\"select\":[],\"enclose\":1}";
// String queryBase = "{\"return\":[\"Deployment/Project\"],\"select\":[],\"enclose\":1}";
}
/**
* Find out if a document exists ?
* @param collection
@ -562,10 +563,10 @@ public class DBXMLQueries {
if (result == null || result.length() == 0) {
return false;
}
return result.contains(documentId);
}
/**
* Count on effort detections in a Detections document
* @param docName
@ -580,16 +581,16 @@ public class DBXMLQueries {
try {
Queries queries = dbXMLConnect.getTethysQueries();
result = queries.QueryTethys(query);
// System.out.println(result);
// System.out.println(result);
}
catch (Exception e) {
System.out.println("Error executing " + query);
// e.printStackTrace();
// e.printStackTrace();
return -1;
}
int count = 0;
try {
count = Integer.valueOf(result);
count = Integer.valueOf(result);
}
catch (NumberFormatException e) {
System.out.println("Unable to interpret count data " + result);
@ -598,67 +599,67 @@ public class DBXMLQueries {
return count;
}
// /**
// * Get a count of the detections in a detections document.
// * Only looking in onEffort so far.
// * @param deploymentId
// * @param detectionDocId
// * @param dataBlock
// * @return
// */
// public int getDetectionsDetectionCount(String deploymentId, String detectionDocId, PamDataBlock dataBlock) {
// String queryBase = "{\"species\":{\"query\":{\"op\":\"lib:abbrev2tsn\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]},\"return\":{\"op\":\"lib:tsn2abbrev\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]}},\"return\":[\"Detections/OnEffort/Detection/Start\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Detections/Id\",\"SomeDetectionsId\"],\"optype\":\"binary\"},{\"op\":\"=\",\"operands\":[\"Detections/DataSource/DeploymentId\",\"SomeDeploymentId\"],\"optype\":\"binary\"}],\"enclose\":1}";
// String queryStr = queryBase.replace("SomeDetectionsId", detectionDocId);
// queryStr = queryStr.replace("SomeDeploymentId", deploymentId);
// DBQueryResult queryResult = executeQuery(queryStr);
// if (queryResult == null || queryResult.queryException != null) {
// return 0;
// }
//// System.out.println("Detections query time ms = " + queryResult.queryTimeMillis);
//
// PamguardXMLWriter pamXMLWriter = PamguardXMLWriter.getXMLWriter();
//
// Document doc = convertStringToXMLDocument(queryResult.queryResult);
// if (doc == null) {
// return 0;
// }
//
//// System.out.println(pamXMLWriter.getAsString(doc));
//
//// ArrayList<String> detectionDocs = new ArrayList<>();
//
// NodeList returns = doc.getElementsByTagName("Start");
// int n = returns.getLength();
// return n;
// }
// /**
// * Get a count of the detections in a detections document.
// * Only looking in onEffort so far.
// * @param deploymentId
// * @param detectionDocId
// * @param dataBlock
// * @return
// */
// public int getDetectionsDetectionCount(String deploymentId, String detectionDocId, PamDataBlock dataBlock) {
// String queryBase = "{\"species\":{\"query\":{\"op\":\"lib:abbrev2tsn\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]},\"return\":{\"op\":\"lib:tsn2abbrev\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]}},\"return\":[\"Detections/OnEffort/Detection/Start\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Detections/Id\",\"SomeDetectionsId\"],\"optype\":\"binary\"},{\"op\":\"=\",\"operands\":[\"Detections/DataSource/DeploymentId\",\"SomeDeploymentId\"],\"optype\":\"binary\"}],\"enclose\":1}";
// String queryStr = queryBase.replace("SomeDetectionsId", detectionDocId);
// queryStr = queryStr.replace("SomeDeploymentId", deploymentId);
// DBQueryResult queryResult = executeQuery(queryStr);
// if (queryResult == null || queryResult.queryException != null) {
// return 0;
// }
//// System.out.println("Detections query time ms = " + queryResult.queryTimeMillis);
//
// PamguardXMLWriter pamXMLWriter = PamguardXMLWriter.getXMLWriter();
//
// Document doc = convertStringToXMLDocument(queryResult.queryResult);
// if (doc == null) {
// return 0;
// }
//
//// System.out.println(pamXMLWriter.getAsString(doc));
//
//// ArrayList<String> detectionDocs = new ArrayList<>();
//
// NodeList returns = doc.getElementsByTagName("Start");
// int n = returns.getLength();
// return n;
// }
// /**
// * This is the quickest way of counting data in a project, but it will load the start
// * times for every detection in a project at once, so might use a lot of memory. Also
// * it wll probably get data for all deployments in a project, which may not be what we want.
// * @param projectName
// * @param dataPrefixes
// * @return
// */
// public int[] countDataForProject(String projectName, String[] dataPrefixes) {
// int[] n = new int[dataPrefixes.length];
// ArrayList<PDeployment> matchedDeployments = tethysControl.getDeploymentHandler().getMatchedDeployments();
//// ArrayList<nilus.Deployment> deployments = getProjectDeployments(projectName);
// if (matchedDeployments == null) {
// return null;
// }
// for (PDeployment aDeployment : matchedDeployments) {
//// ArrayList<String> detectionsIds = getDetectionsDocsIds(aDeployment.getId());
//// for (String detId : detectionsIds) {
//// n += getDetectionsDetectionCount(aDeployment.getId(), detId, dataBlock);
//// }
// int[] newN = countDataForDeployment(projectName, aDeployment.deployment.getId(), dataPrefixes);
// for (int i = 0; i < n.length; i++) {
// n[i] += newN[i];
// }
// }
// return n;
// }
// /**
// * This is the quickest way of counting data in a project, but it will load the start
// * times for every detection in a project at once, so might use a lot of memory. Also
// * it wll probably get data for all deployments in a project, which may not be what we want.
// * @param projectName
// * @param dataPrefixes
// * @return
// */
// public int[] countDataForProject(String projectName, String[] dataPrefixes) {
// int[] n = new int[dataPrefixes.length];
// ArrayList<PDeployment> matchedDeployments = tethysControl.getDeploymentHandler().getMatchedDeployments();
//// ArrayList<nilus.Deployment> deployments = getProjectDeployments(projectName);
// if (matchedDeployments == null) {
// return null;
// }
// for (PDeployment aDeployment : matchedDeployments) {
//// ArrayList<String> detectionsIds = getDetectionsDocsIds(aDeployment.getId());
//// for (String detId : detectionsIds) {
//// n += getDetectionsDetectionCount(aDeployment.getId(), detId, dataBlock);
//// }
// int[] newN = countDataForDeployment(projectName, aDeployment.deployment.getId(), dataPrefixes);
// for (int i = 0; i < n.length; i++) {
// n[i] += newN[i];
// }
// }
// return n;
// }
/**
* Count data within a deployment document which is associated with a set of datablocks
@ -688,14 +689,14 @@ public class DBXMLQueries {
return null;
}
// System.out.println(pamXMLWriter.getAsString(doc));
// System.out.println(pamXMLWriter.getAsString(doc));
NodeList detsDocs = doc.getElementsByTagName("Detections");
int[] blockCounts = new int[dataPrefixes.length];
// String detDocPrefix = projectId + "_" + dataBlock.getDataName();
// String detDocPrefix = projectId + "_" + dataBlock.getDataName();
// int totalCalls = 0;
// int totalCalls = 0;
int detCount = 0;
int dataIndex;
for (int i = 0; i < detsDocs.getLength(); i++) {
@ -716,17 +717,17 @@ public class DBXMLQueries {
dataIndex = j;
}
}
// if (id != null && id.startsWith(detDocPrefix) == false) {
// detCount = 0;
// break;
// }
// if (id != null && id.startsWith(detDocPrefix) == false) {
// detCount = 0;
// break;
// }
}
}
}
if (dataIndex >= 0) {
blockCounts[dataIndex] += detCount;
}
// System.out.printf("%d Added %d for new total %d\n",i, detCount, totalCalls);
// System.out.printf("%d Added %d for new total %d\n",i, detCount, totalCalls);
}
return blockCounts;
@ -818,7 +819,7 @@ public class DBXMLQueries {
e.printStackTrace();
return null;
}
// System.out.println(queryResult.queryResult);
// System.out.println(queryResult.queryResult);
Detections detections = new Detections();
try {
@ -844,7 +845,7 @@ public class DBXMLQueries {
description.setAbstract(getElementData(result, "Description.Abstract"));
description.setMethod(getElementData(result, "Description.Method"));
description.setObjectives(getElementData(result, "Description.Objectives"));
// try to find the granularity.
String granularityString = getElementData(result, "Effort.Kind.Granularity");
GranularityEnumType granularity = null;
@ -869,10 +870,10 @@ public class DBXMLQueries {
}
catch (NumberFormatException e) {
}
kinds.add(kind);
}
// String
// String

103
src/tethys/detection/DetectionsHandler.java
View File

@ -8,6 +8,7 @@ import javax.swing.SwingWorker;
import PamController.PamControlledUnit;
import PamController.PamguardVersionInfo;
import PamModel.PamPluginInterface;
import PamView.dialog.warn.WarnOnce;
import PamguardMVC.PamDataBlock;
import PamguardMVC.PamDataUnit;
import PamguardMVC.PamProcess;
@ -84,7 +85,7 @@ public class DetectionsHandler {
for (String aDoc : someNames) {
Detections detections = tethysControl.getDbxmlQueries().getDetectionsDocInfo(aDoc);
int count = tethysControl.getDbxmlQueries().countDetections2(aDoc);
PDetections pDetections = new PDetections(detections, null, count);
PDetections pDetections = new PDetections(detections, dataBlock, aDep, count);
detectionsDocs.add(pDetections);
}
}
@ -364,6 +365,98 @@ public class DetectionsHandler {
* @param exportObserver
* @return
*/
private int countDetections(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.
*/
TethysExportParams exportParams = tethysControl.getTethysExportParams();
DBXMLConnect dbxmlConnect = tethysControl.getDbxmlConnect();
DeploymentHandler depHandler = tethysControl.getDeploymentHandler();
ArrayList<PDeployment> deployments = depHandler.getMatchedDeployments();
// Detections currentDetections = null;
OfflineDataMap dataMap = dataBlock.getPrimaryDataMap();
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,
lastUnitTime, totalCount, exportCount, skipCount, DetectionExportProgress.STATE_GATHERING);
exportObserver.update(prog);
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) {
prog = new DetectionExportProgress(deployment, null,
lastUnitTime, totalCount, exportCount, skipCount, DetectionExportProgress.STATE_CANCELED);
exportObserver.update(prog);
}
if (mapPoint.getEndTime() < deployment.getAudioStart()) {
continue;
}
if (mapPoint.getStartTime() >= deployment.getAudioEnd()) {
break;
}
dataBlock.loadViewerData(mapPoint.getStartTime(), mapPoint.getEndTime(), null);
ArrayList<PamDataUnit> dataCopy = dataBlock.getDataCopy(deployment.getAudioStart(), deployment.getAudioEnd(), true, dataSelector);
skipCount += dataBlock.getUnitsCount() - dataCopy.size();
for (PamDataUnit dataUnit : dataCopy) {
/*
* Here is where we need to handle the different granularities.
*/
Detection dets[] = granularityHandler.addDataUnit(dataUnit);
if (dets != null) {
exportCount+=dets.length;
documentCount+=dets.length;
}
// Detection det = dataProvider.createDetection(dataUnit, exportParams, streamExportParams);
// exportCount++;
// documentCount++;
// onEffort.getDetection().add(det);
lastUnitTime = dataUnit.getTimeMilliseconds();
}
prog = new DetectionExportProgress(deployment, null,
lastUnitTime, totalCount, exportCount, skipCount, DetectionExportProgress.STATE_GATHERING);
exportObserver.update(prog);
// if (documentCount > 500000 && mapPoint != dataMap.getLastMapPoint()) {
// prog = new DetectionExportProgress(deployment, currentDetections,
// lastUnitTime, totalCount, exportCount, skipCount, DetectionExportProgress.STATE_WRITING);
// exportObserver.update(prog);
// closeDetectionsDocument(currentDetections, mapPoint.getEndTime());
// try {
// dbxmlConnect.postToTethys(currentDetections);
// } catch (TethysException e) {
// tethysControl.showException(e);
// }
// currentDetections = null;
// }
}
}
prog = new DetectionExportProgress(null, null,
lastUnitTime, totalCount, exportCount, skipCount, DetectionExportProgress.STATE_COMPLETE);
exportObserver.update(prog);
return exportCount;
}/**
* Export detections in all deployments for this PAMGuard dataset.
* @param dataBlock
* @param streamExportParams
* @param exportObserver
* @return
*/
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
@ -559,7 +652,13 @@ public class DetectionsHandler {
protected Integer doInBackground() throws Exception {
Integer ans = null;
try {
ans = exportDetections(dataBlock, exportParams, this);
int count = countDetections(dataBlock, exportParams, exportObserver);
String msg = String.format("Do you want to go ahead and output %d %s detections to Tethys?",
count, exportParams.granularity);
int doit = WarnOnce.showWarning("Tethys Detections Export", msg, WarnOnce.OK_CANCEL_OPTION);
if (doit == WarnOnce.OK_OPTION) {
ans = exportDetections(dataBlock, exportParams, this);
}
}
catch (Exception e) {
e.printStackTrace();

130
src/tethys/detection/EncounterGranularityHandler.java
View File

@ -1,36 +1,152 @@
package tethys.detection;
import java.math.BigInteger;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.Set;
import PamguardMVC.PamDataBlock;
import PamguardMVC.PamDataUnit;
import nilus.Detection;
import nilus.SpeciesIDType;
import tethys.TethysControl;
import tethys.TethysTimeFuncs;
import tethys.output.StreamExportParams;
import tethys.output.TethysExportParams;
import tethys.pamdata.TethysDataProvider;
import tethys.species.DataBlockSpeciesManager;
import tethys.species.SpeciesMapItem;
/**
* As with the binned Detections, this may generate multiple encounters
* at the same time for different types of sounds.
* @author dg50
*
*/
public class EncounterGranularityHandler extends GranularityHandler {
private HashMap<String, Detection> currentDetections;
private TethysDataProvider dataProvider;
private DataBlockSpeciesManager speciesManager;
private long maxGapMillis;
public EncounterGranularityHandler(TethysControl tethysControl, PamDataBlock dataBlock,
TethysExportParams tethysExportParams, StreamExportParams streamExportParams) {
super(tethysControl, dataBlock, tethysExportParams, streamExportParams);
// TODO Auto-generated constructor stub
dataProvider = dataBlock.getTethysDataProvider(tethysControl);
speciesManager = dataBlock.getDatablockSpeciesManager();
maxGapMillis = (long) (streamExportParams.encounterGapS*1000);
currentDetections = new HashMap<String, Detection>();
}
@Override
public void prepare(long timeMillis) {
// TODO Auto-generated method stub
}
@Override
public Detection[] addDataUnit(PamDataUnit dataUnit) {
// TODO Auto-generated method stub
return null;
Detection[] completeDetections = checkCurrentEncounters(dataUnit.getTimeMilliseconds());
// now look for new ones. First get the species of the dataUnit and find it in the hashmap
String speciesCode = speciesManager.getSpeciesCode(dataUnit);
Detection det = currentDetections.get(speciesCode);
if (det == null) {
// need to make a new one.
det = new Detection();
det.setStart(TethysTimeFuncs.xmlGregCalFromMillis(dataUnit.getTimeMilliseconds()));
det.setEnd(TethysTimeFuncs.xmlGregCalFromMillis(dataUnit.getEndTimeInMilliseconds()));
det.setCount(BigInteger.ONE);
det.setChannel(BigInteger.valueOf(dataUnit.getChannelBitmap()));
// this should always return something, so am going to crash if it doesn't.
// may revisit this later on if we've unassigned things we don't want to label
// in which case they should be rejected earlier than this.
SpeciesMapItem speciesStuff = speciesManager.getSpeciesItem(dataUnit);
SpeciesIDType species = new SpeciesIDType();
species.setValue(BigInteger.valueOf(speciesStuff.getItisCode()));
det.setSpeciesId(species);
if (speciesStuff.getCallType() != null) {
det.getCall().add(speciesStuff.getCallType());
}
currentDetections.put(speciesCode, det);
}
else {
// add to current detection. Set new end time and increment count
det.setEnd(TethysTimeFuncs.xmlGregCalFromMillis(dataUnit.getEndTimeInMilliseconds()));
int count = det.getCount().intValue() + 1;
det.setCount(BigInteger.valueOf(count));
int chan = det.getChannel().intValue();
chan |= dataUnit.getChannelBitmap();
det.setChannel(BigInteger.valueOf(chan));
}
return completeDetections;
}
/**
* See if it's time to close off any encounters.
* @param timeMilliseconds current time
* @return list of complete encounters.
*/
private Detection[] checkCurrentEncounters(long timeMilliseconds) {
Set<String> keys = currentDetections.keySet();
int nGood = 0;
Detection[] newDetections = new Detection[currentDetections.size()];
for (String aKey : keys) {
Detection aDet = currentDetections.get(aKey);
Long detEnd = TethysTimeFuncs.millisFromGregorianXML(aDet.getEnd());
if (timeMilliseconds-detEnd > maxGapMillis) {
// only keep if it's got a min number of calls.
if (aDet.getCount().intValue() >= streamExportParams.minBinCount) {
newDetections[nGood++] = aDet;
}
// remove from set. A new one will be created only when required.
currentDetections.remove(aKey);
}
}
if (nGood == 0) {
return null;
}
else {
return Arrays.copyOf(newDetections, nGood);
}
}
// private Detection[] checkCurrentEncounters(long timeMilliseconds) {
// if (currentDetections == null || currentDetections.size() == 0) {
// return null;
// }
// int nGood = 0;
// Detection[] newDetections = new Detection[currentDetections.size()];
// Iterator<Detection> detIt = currentDetections.iterator();
// while (detIt.hasNext()) {
// Detection aDet = detIt.next();
// Long detEnd = TethysTimeFuncs.millisFromGregorianXML(aDet.getEnd());
// if (timeMilliseconds-detEnd > maxGapMillis) {
// detIt.remove();
// newDetections[nGood++] = aDet;
// }
// }
//
// if (nGood == 0) {
// return null;
// }
// else {
// return Arrays.copyOf(newDetections, nGood);
// }
// }
@Override
public Detection[] cleanup(long timeMillis) {
// TODO Auto-generated method stub
return null;
// get everything still on the go.
return checkCurrentEncounters(timeMillis + maxGapMillis);
}
}

2
src/tethys/detection/GranularityHandler.java
View File

@ -89,7 +89,7 @@ public abstract class GranularityHandler {
case CALL:
return new CallGranularityHandler(tethysControl, dataBlock, tethysExportParams, streamExportParams);
case ENCOUNTER:
new EncounterGranularityHandler(tethysControl, dataBlock, tethysExportParams, streamExportParams);
return new EncounterGranularityHandler(tethysControl, dataBlock, tethysExportParams, streamExportParams);
case GROUPED:
return new GroupedGranularityHandler(tethysControl, dataBlock, tethysExportParams, streamExportParams);
default:

2
src/tethys/niluswraps/PDeployment.java
View File

@ -73,7 +73,7 @@ public class PDeployment {
}
Double gap = granularity.getEncounterGapM();
if (gap != null) {
str += String.format( " (%3.1f s)", gap);
str += String.format( " (%3.1f s)", gap*60.);
}
return str;
}

6
src/tethys/niluswraps/PDetections.java
View File

@ -1,5 +1,6 @@
package tethys.niluswraps;
import PamguardMVC.PamDataBlock;
import nilus.Detections;
public class PDetections {
@ -10,8 +11,11 @@ public class PDetections {
public PDeployment deployment;
public PDetections(Detections detections, PDeployment deployment, Integer count) {
public PamDataBlock dataBlock;
public PDetections(Detections detections, PamDataBlock dataBlock, PDeployment deployment, Integer count) {
super();
this.dataBlock = dataBlock;
this.detections = detections;
this.deployment = deployment;
this.count = count;

30
src/tethys/output/DatablockSynchInfo.java
View File

@ -16,18 +16,28 @@ import tethys.TethysControl;
public class DatablockSynchInfo {
private PamDataBlock dataBlock;
public PamDataBlock getDataBlock() {
return dataBlock;
}
private TethysControl tethysControl;
/**
* Count of individual datas in all Detections documents
*/
private int setDataCount;
/**
* Count of the number of Detections documents
*/
private int detectionDocumentCount;
public DatablockSynchInfo(TethysControl tethysControl, PamDataBlock dataBlock) {
super();
this.tethysControl = tethysControl;
this.dataBlock = dataBlock;
}
public PamDataBlock getDataBlock() {
return dataBlock;
}
/**
* Get the stored export params for this data block
@ -44,5 +54,19 @@ public class DatablockSynchInfo {
public int getDataCount() {
return setDataCount;
}
/**
* @return the detectionDocumentCount
*/
public int getDetectionDocumentCount() {
return detectionDocumentCount;
}
/**
* @param detectionDocumentCount the detectionDocumentCount to set
*/
public void setDetectionDocumentCount(int detectionDocumentCount) {
this.detectionDocumentCount = detectionDocumentCount;
}
}

45
src/tethys/pamdata/AutoTethysProvider.java
View File

@ -20,14 +20,17 @@ import PamguardMVC.PamDataUnit;
import PamguardMVC.PamProcess;
import PamguardMVC.TFContourData;
import PamguardMVC.TFContourProvider;
import binaryFileStorage.DataUnitFileInformation;
import generalDatabase.DBSchemaWriter;
import generalDatabase.SQLLogging;
import nilus.AlgorithmType;
import nilus.AlgorithmType.Parameters;
import nilus.Deployment;
import nilus.DescriptionType;
import nilus.Detection;
import nilus.Detection.Parameters;
import nilus.Detection.Parameters.UserDefined;
import nilus.DetectionEffortKind;
import nilus.Helper;
import nilus.SpeciesIDType;
import tethys.TethysControl;
import tethys.TethysTimeFuncs;
@ -42,6 +45,7 @@ import tethys.species.SpeciesMapItem;
import whistleClassifier.WhistleContour;
import javax.xml.bind.JAXBException;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.*;
import javax.xml.transform.dom.DOMResult;
import javax.xml.transform.dom.DOMSource;
@ -54,7 +58,9 @@ import java.net.URISyntaxException;
/**
* Automatically provides Tethys data based on the SQL database interface
* for a data block.
* for a data block. does most of what needs to be done, though individual modules
* may want to override this, call the base createDetection function and then add a
* few more bespoke elements.
* @author dg50
*
*/
@ -119,7 +125,7 @@ public class AutoTethysProvider implements TethysDataProvider {
// algorithm.setMethod(this.getAlgorithmMethod());
// algorithm.setSoftware("PAMGuard");
// algorithm.setVersion(PamguardVersionInfo.version);
Parameters algoParameters = this.getAlgorithmParameters();
nilus.AlgorithmType.Parameters algoParameters = this.getAlgorithmParameters();
if (algoParameters != null) {
algorithm.setParameters(algoParameters);
}
@ -128,12 +134,12 @@ public class AutoTethysProvider implements TethysDataProvider {
}
@Override
public Parameters getAlgorithmParameters() {
public nilus.AlgorithmType.Parameters getAlgorithmParameters() {
if (pamControlledUnit instanceof PamSettings == false) {
return null;
}
PamSettings pamSettings = (PamSettings) pamControlledUnit;
Parameters parameters = new Parameters();
nilus.AlgorithmType.Parameters parameters = new nilus.AlgorithmType.Parameters();
List<Element> paramList = parameters.getAny();
Object settings = pamSettings.getSettingsReference();
TethysParameterPacker paramPacker = null;
@ -343,9 +349,38 @@ public class AutoTethysProvider implements TethysDataProvider {
detParams.setReceivedLevelDB(ampli);
// DataUnitBaseData basicData = dataUnit.getBasicData();
gotTonalContour(dataUnit, detParams);
String uid = BigInteger.valueOf(dataUnit.getUID()).toString();
Element el = addUserDefined(detParams,"PAMGuardUID", uid);
DataUnitFileInformation fileInf = dataUnit.getDataUnitFileInformation();
if (fileInf != null) {
el.setAttribute("BinaryFile", fileInf.getShortFileName(2048));
el.setAttribute("FileIndex", Long.valueOf(fileInf.getIndexInFile()).toString());
}
return detection;
}
private Element addUserDefined(Parameters parameters, String parameterName, String parameterValue) {
UserDefined userDefined = parameters.getUserDefined();
if (userDefined == null) {
userDefined = new UserDefined();
parameters.setUserDefined(userDefined);
}
Helper helper;
Element el = null;
try {
helper = new Helper();
el = helper.AddAnyElement(userDefined.getAny(), parameterName, parameterValue);
} catch (JAXBException e) {
e.printStackTrace();
return null;
} catch (ParserConfigurationException e) {
e.printStackTrace();
return null;
}
return el;
}
/**
* Get tonal sounds contour. Sadly there are two slightly different interfaces in use

52
src/tethys/swing/DatablockDetectionsPanel.java
View File

@ -16,6 +16,7 @@ import javax.swing.JScrollPane;
import javax.swing.JTable;
import javax.swing.border.TitledBorder;
import javax.swing.table.AbstractTableModel;
import javax.swing.table.JTableHeader;
import PamView.PamGui;
import PamView.dialog.warn.WarnOnce;
@ -26,7 +27,6 @@ import nilus.Detections;
import nilus.GranularityType;
import tethys.TethysControl;
import tethys.TethysState;
import tethys.TethysState.StateType;
import tethys.dbxml.TethysException;
import tethys.detection.StreamDetectionsSummary;
import tethys.niluswraps.PDeployment;
@ -61,7 +61,21 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
mainPanel.setBorder(new TitledBorder("Data stream Tethys Detections documents"));
tableModel = new TableModel();
table = new JTable(tableModel);
table = new JTable(tableModel) {
@Override
public String getToolTipText(MouseEvent event) {
return getToolTip(event);
}
protected JTableHeader createDefaultTableHeader() {
return new JTableHeader(columnModel) {
public String getToolTipText(MouseEvent e) {
return getToolTip(e);
}
};
}
};
JScrollPane scrollPane = new JScrollPane(table);
mainPanel.add(BorderLayout.CENTER, scrollPane);
@ -70,6 +84,29 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
table.addMouseListener(new MouseActions());
}
protected String getToolTip(MouseEvent event) {
java.awt.Point p = event.getPoint();
int rowIndex = table.rowAtPoint(p);
// if (rowIndex < 0) {
// return null;
// }
int colIndex = table.columnAtPoint(p);
switch (colIndex) {
case 0:
return "Tethys Detections document name";
case 1:
return "Name of PAMGuard data stream";
case 2:
return "Output granularity";
case 3:
return "Number of detection elements in document";
case 4:
return "Document abstract";
}
return "No tip";
}
@Override
public JComponent getComponent() {
return mainPanel;
@ -192,7 +229,7 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
private class TableModel extends AbstractTableModel {
private String[] colNames = {"Document", "Granularity", "Count", "Abstract"};
private String[] colNames = {"Document", "Detector", "Granularity", "Count", "Abstract"};
@Override
public int getRowCount() {
@ -230,6 +267,11 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
case 0:
return dets.getId();
case 1:
if (pDets.dataBlock == null) {
return null;
}
return pDets.dataBlock.getDataName();
case 2:
List<DetectionEffortKind> kinds = dets.getEffort().getKind();
if (kinds == null) {
return null;
@ -244,9 +286,9 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
}
}
break;
case 2:
return pDets.count;
case 3:
return pDets.count;
case 4:
return dets.getDescription().getAbstract();
}
return null;

4
src/tethys/swing/DatablockSynchPanel.java
View File

@ -156,7 +156,7 @@ public class DatablockSynchPanel extends TethysGUIPanel {
private class SynchTableModel extends AbstractTableModel {
String[] columnNames = {"Data Stream", "N PAM Datas", "PAMGuard Time", "N Tethys Datas", "Tethys Time", "Options"};
String[] columnNames = {"Data Stream", "N PAM Datas", "PAMGuard Time", "Tethys Documents", "Tethys Time", "Options"};
@Override
public int getRowCount() {
@ -200,7 +200,7 @@ public class DatablockSynchPanel extends TethysGUIPanel {
long stop = synchInfo.getDataBlock().getPrimaryDataMap().getLastDataTime();
return String.format("%s - %s", PamCalendar.formatDBDateTime(start), PamCalendar.formatDBDateTime(stop));
case 3:
return synchInfo.getDataCount();
return synchInfo.getDetectionDocumentCount();
}
return null;
}

3
src/tethys/swing/DetectionsExportPanel.java
View File

@ -30,7 +30,7 @@ public class DetectionsExportPanel extends TethysGUIPanel implements StreamTable
mainPanel = new PamAlignmentPanel(BorderLayout.NORTH);
mainPanel.setLayout(new GridBagLayout());
mainPanel.setBorder(new TitledBorder("Export"));
exportButton = new JButton("Export");
exportButton = new JButton("<html>Export<p>>>>></html>");
exportButton.setToolTipText("Export PAMGaurd data to Tethys");
exportButton.addActionListener(new ActionListener() {
@Override
@ -38,6 +38,7 @@ public class DetectionsExportPanel extends TethysGUIPanel implements StreamTable
doExport();
}
});
exportButton.setToolTipText("Select a Data Block on the left to enable export");
exportButton.setEnabled(false);
GridBagConstraints c = new PamGridBagContraints();
mainPanel.add(exportButton, c);

2
src/tethys/swing/TethysMainPanel.java
View File

@ -52,7 +52,7 @@ public class TethysMainPanel extends TethysGUIPanel {
southwestSplit.add(datablockSynchPanel.getComponent());
southwestSplit.add(southEastPanel);
southEastPanel.add(datablockDetectionsPanel.getComponent(), BorderLayout.CENTER);
southEastPanel.add(detectionsExportPanel.getComponent(), BorderLayout.EAST);
southEastPanel.add(detectionsExportPanel.getComponent(), BorderLayout.WEST);
splitPane.add(southwestSplit);
SwingUtilities.invokeLater(new Runnable() {
// these only work if called after display is visible