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Added code to find acquisition settings

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This is most of the data needed for TEthys
This commit is contained in:
Douglas Gillespie 2023-02-22 10:51:04 +00:00
parent f12be978aa
commit 9c10af43bc
1 changed files with 110 additions and 2 deletions
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112
src/tethys/output/TethysExporter.java
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@ -1,22 +1,29 @@
package tethys.output;
import java.util.ArrayList;
import java.util.List;
import org.w3c.dom.Document;
import Acquisition.AcquisitionControl;
import Acquisition.AcquisitionParameters;
import Acquisition.AcquisitionProcess;
import Acquisition.DaqStatusDataUnit;
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 dataMap.OfflineDataMap;
import dataMap.OfflineDataMapPoint;
import generalDatabase.DBControlUnit;
import generalDatabase.DBSchemaWriter;
import generalDatabase.SQLLogging;
import metadata.MetaDataContol;
@ -66,6 +73,29 @@ public class TethysExporter {
SnapshotGeometry arrayGeometry = findArrayGeometrey();
/**
* 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 to the PAMGuard Array dialog and can
* then be extraced from there. We had some useful discussion about what constitutes
* an instrumnet in Tinas dataset where there was a deployment of 10 MARU's, but the
* files from all of them were merged into a single 10 channel wav file dataset and
* processed together for detection and localisation. Clearly this goes into a single
* Tethys database, but do we put 'MARU Array' as the instrument and then include
* serial numbers of individual MARU's with the hydrophone data, or what ?
*/
/**
* Doug write something here to get most of the 'samplingdetails' schema.
* This all comes out of the Sound Acquisition module. Code below shows how
* to find this and iterate through various bits of information ...
* (I've put it in a separate function. Currently returning void,but could
* presumably return a Tethys samplingdetails document?)
*/
getSamplingDetails();
/*
* Call some general export function
*/
@ -151,6 +181,84 @@ public class TethysExporter {
return currentGeometry;
}
private void getSamplingDetails() {
// first find an acquisition module.
PamControlledUnit aModule = PamController.getInstance().findControlledUnit(AcquisitionControl.class, null);
if (aModule instanceof AcquisitionControl == false) {
// will return if it's null. Impossible for it to be the wrong type.
// but it's good practice to check anyway before casting.
return;
}
// cast it to the right type.
AcquisitionControl daqControl = (AcquisitionControl) aModule;
AcquisitionParameters daqParams = daqControl.getAcquisitionParameters();
/**
* The daqParams class has most of what we need about the set up in terms of sample rate,
* number of channels, instrument type, ADC input range (part of calibration), etc.
* It also has a hydrophone list, which maps the input channel numbers to the hydrophon numbers.
* Realistically, this list is always 0,1,2,etc or it goes horribly wrong !
*/
// so write functions here to get information from the daqParams.
System.out.printf("Sample regime: %s input with rate %3.1fHz, %d channels, gain %3.1fdB, ADCp-p %3.1fV\n", daqParams.getDaqSystemType(),
daqParams.getSampleRate(), daqParams.getNChannels(), daqParams.preamplifier.getGain(), daqParams.voltsPeak2Peak);
/**
* then there is the actual sampling. This is a bit harder to find. I thought it would be in the data map
* but the datamap is a simple count of what's in the databasase which is not quite what we want.
* we're going to have to query the database to get more detailed informatoin I think.
* I'll do that here for now, but we may want to move this when we better organise the code.
* It also seems that there are 'bad' dates in the database when it starts new files, which are the date
* data were analysed at. So we really need to check the start and stop records only.
*/
PamDataBlock<DaqStatusDataUnit> daqInfoDataBlock = daqControl.getAcquisitionProcess().getDaqStatusDataBlock();
// just load everything. Probably OK for the acqusition, but will bring down
daqInfoDataBlock.loadViewerData(0, Long.MAX_VALUE, null);
ArrayList<DaqStatusDataUnit> allStatusData = daqInfoDataBlock.getDataCopy();
if (allStatusData != null && allStatusData.size() > 0) {
long dataStart = Long.MAX_VALUE;
long dataEnd = Long.MIN_VALUE;
// find the number of times it started and stopped ....
int nStart = 0, nStop = 0, nFile=0;
for (DaqStatusDataUnit daqStatus : allStatusData) {
switch (daqStatus.getStatus()) {
case "Start":
nStart++;
dataStart = Math.min(dataStart, daqStatus.getTimeMilliseconds());
break;
case "Stop":
nStop++;
dataEnd = Math.max(dataEnd, daqStatus.getEndTimeInMilliseconds());
break;
case "NextFile":
nFile++;
break;
}
}
System.out.printf("Input map of sound data indicates data from %s to %s with %d starts and %d stops over %d files\n",
PamCalendar.formatDateTime(dataStart), PamCalendar.formatDateTime(dataEnd), nStart, nStop, nFile+1);
}
// // and we find the datamap within that ...
// OfflineDataMap daqMap = daqInfoDataBlock.getOfflineDataMap(DBControlUnit.findDatabaseControl());
// if (daqMap != null) {
// // iterate through it.
// long dataStart = daqMap.getFirstDataTime();
// long dataEnd = daqMap.getLastDataTime();
// List<OfflineDataMapPoint> mapPoints = daqMap.getMapPoints();
// System.out.printf("Input map of sound data indicates data from %s to %s with %d individual files\n",
// PamCalendar.formatDateTime(dataStart), PamCalendar.formatDateTime(dataEnd), mapPoints.size());
// /*
// * clearly in the first database I've been looking at of Tinas data, this is NOT getting sensible start and
// * end times. Print them out to see what's going on.
// */
//// for ()
// }
}
/**
@ -201,7 +309,7 @@ public class TethysExporter {
* (though I'd assume that having the Document is more useful)
*/
String schemaXMLString = pamXMLWriter.getAsString(tethysSchema.getXsd(), false);
// System.out.printf("Schema for %s is %s\n", aDataBlock.getDataName(), schemaXMLString);
System.out.printf("Schema for %s is %s\n", aDataBlock.getDataName(), schemaXMLString);
/*
@ -209,7 +317,7 @@ public class TethysExporter {
* the parameters that were controlling that module, with adequate data about
* upstream modules). I think this has to go somewhere into the Detections document.
*/
Document doc = pamXMLWriter.writeOneModule(pamXMLWriter, System.currentTimeMillis());
Document doc = pamXMLWriter.writeOneModule((PamSettings) pamControlledUnit, System.currentTimeMillis());
String moduleXML = null;
if (doc != null) {
// this string should be XML of all the settings for the module controlling this datablock.