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@ -1,6 +1,5 @@
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package tethys.deployment;
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import java.io.Serializable;
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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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@ -16,29 +15,32 @@ import Acquisition.DaqStatusDataUnit;
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import Acquisition.DaqSystem;
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import Array.ArrayManager;
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import Array.Hydrophone;
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import Array.HydrophoneLocator;
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import Array.PamArray;
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import Array.Streamer;
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import Array.ThreadingHydrophoneLocator;
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import PamController.PamControlledUnit;
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import PamController.PamController;
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import PamUtils.PamCalendar;
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import PamUtils.PamUtils;
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import PamguardMVC.PamDataBlock;
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import metadata.MetaDataContol;
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import metadata.deployment.DeploymentData;
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import nilus.Audio;
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import nilus.ChannelInfo;
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import nilus.ChannelInfo.Sampling;
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import nilus.ChannelInfo.Sampling.Regimen;
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import nilus.Deployment;
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import nilus.Deployment.Instrument;
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import nilus.Deployment.SamplingDetails;
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import nilus.Deployment.Sensors;
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import nilus.DeploymentRecoveryDetails;
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import nilus.GeometryTypeM;
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import nilus.Helper;
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import nilus.MarshalXML;
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import pamMaths.PamVector;
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import tethys.TethysLocationFuncs;
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import tethys.TethysTimeFuncs;
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/**
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* Functions to gather data for the deployment document from all around PAMGuard.
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* Functions to gather data for the deployment document from all around PAMGuard.
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* @author dg50
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*
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*/
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@ -46,42 +48,42 @@ public class DeploymentHandler {
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/**
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* Get an overview of all the deployments.
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* Get an overview of all the deployments.
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* @return
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*/
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public DeploymentOverview createOverview() {
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// first find an acquisition module.
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// first find an acquisition module.
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PamControlledUnit aModule = PamController.getInstance().findControlledUnit(AcquisitionControl.class, null);
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if (aModule instanceof AcquisitionControl == false) {
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// will return if it's null. Impossible for it to be the wrong type.
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// but it's good practice to check anyway before casting.
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if (!(aModule instanceof AcquisitionControl)) {
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// will return if it's null. Impossible for it to be the wrong type.
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// but it's good practice to check anyway before casting.
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return null;
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}
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// cast it to the right type.
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// cast it to the right type.
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AcquisitionControl daqControl = (AcquisitionControl) aModule;
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AcquisitionParameters daqParams = daqControl.getAcquisitionParameters();
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/**
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* The daqParams class has most of what we need about the set up in terms of sample rate,
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* number of channels, instrument type, ADC input range (part of calibration), etc.
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* It also has a hydrophone list, which maps the input channel numbers to the hydrophon numbers.
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* The daqParams class has most of what we need about the set up in terms of sample rate,
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* number of channels, instrument type, ADC input range (part of calibration), etc.
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* It also has a hydrophone list, which maps the input channel numbers to the hydrophon numbers.
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* Realistically, this list is always 0,1,2,etc or it goes horribly wrong !
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*/
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// so write functions here to get information from the daqParams.
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// so write functions here to get information from the daqParams.
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// System.out.printf("Sample regime: %s input with rate %3.1fHz, %d channels, gain %3.1fdB, ADCp-p %3.1fV\n", daqParams.getDaqSystemType(),
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// daqParams.getSampleRate(), daqParams.getNChannels(), daqParams.preamplifier.getGain(), daqParams.voltsPeak2Peak);
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/**
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* then there is the actual sampling. This is a bit harder to find. I thought it would be in the data map
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* but the datamap is a simple count of what's in the databasase which is not quite what we want.
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* we're going to have to query the database to get more detailed informatoin I think.
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* I'll do that here for now, but we may want to move this when we better organise the code.
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* but the datamap is a simple count of what's in the databasase which is not quite what we want.
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* we're going to have to query the database to get more detailed informatoin I think.
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* I'll do that here for now, but we may want to move this when we better organise the code.
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* It also seems that there are 'bad' dates in the database when it starts new files, which are the date
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* data were analysed at. So we really need to check the start and stop records only.
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* data were analysed at. So we really need to check the start and stop records only.
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*/
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PamDataBlock<DaqStatusDataUnit> daqInfoDataBlock = daqControl.getAcquisitionProcess().getDaqStatusDataBlock();
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// just load everything. Probably OK for the acqusition, but will bring down
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// just load everything. Probably OK for the acqusition, but will bring down
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daqInfoDataBlock.loadViewerData(0, Long.MAX_VALUE, null);
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ArrayList<DaqStatusDataUnit> allStatusData = daqInfoDataBlock.getDataCopy();
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ArrayList<RecordingPeriod> tempPeriods = null;
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if (allStatusData == null || allStatusData.size() == 0) {
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@ -95,7 +97,7 @@ public class DeploymentHandler {
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System.out.println("Data appear to have no logged recording periods available either from the database or the raw recordings.");
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}
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int nPeriods = tempPeriods.size();
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// now go through those and merge into longer periods where there is no gap between files.
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// now go through those and merge into longer periods where there is no gap between files.
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ListIterator<RecordingPeriod> iterator = tempPeriods.listIterator();
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RecordingPeriod prevPeriod = null;
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while (iterator.hasNext()) {
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@ -108,7 +110,7 @@ public class DeploymentHandler {
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long gap = nextPeriod.getRecordStart() - prevPeriod.getRecordStop();
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long prevDur = prevPeriod.getRecordStop()-prevPeriod.getRecordStart();
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if (gap < 3 || gap < prevDur/50) {
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// ignoring up to 3s gap or a sample error < 2%.Dunno if this is sensible or not.
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// ignoring up to 3s gap or a sample error < 2%.Dunno if this is sensible or not.
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prevPeriod.setRecordStop(nextPeriod.getRecordStop());
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iterator.remove();
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nextPeriod = prevPeriod;
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@ -121,16 +123,16 @@ public class DeploymentHandler {
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DeploymentOverview deploymentOverview = new DeploymentOverview(false, tempPeriods);
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return deploymentOverview;
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// find the number of times it started and stopped ....
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// System.out.printf("Input map of sound data indicates data from %s to %s with %d starts and %d stops over %d files\n",
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// System.out.printf("Input map of sound data indicates data from %s to %s with %d starts and %d stops over %d files\n",
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// PamCalendar.formatDateTime(dataStart), PamCalendar.formatDateTime(dataEnd), nStart, nStop, nFile+1);
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// now work out where there are genuine gaps and make up a revised list of recording periods.
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// now work out where there are genuine gaps and make up a revised list of recording periods.
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}
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/**
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* Work out whether or not the data are evenly duty cycled by testing the
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* distributions of on and off times.
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* Work out whether or not the data are evenly duty cycled by testing the
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* distributions of on and off times.
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* @param tempPeriods
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* @return
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*/
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@ -187,38 +189,38 @@ public class DeploymentHandler {
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//in each channel
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public ArrayList<DeploymentRecoveryPair> getDeployments() {
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DeploymentOverview recordingOverview = createOverview();
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// first find an acquisition module.
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// first find an acquisition module.
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PamControlledUnit aModule = PamController.getInstance().findControlledUnit(AcquisitionControl.class, null);
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if (aModule instanceof AcquisitionControl == false) {
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// will return if it's null. Impossible for it to be the wrong type.
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// but it's good practice to check anyway before casting.
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if (!(aModule instanceof AcquisitionControl)) {
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// will return if it's null. Impossible for it to be the wrong type.
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// but it's good practice to check anyway before casting.
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return null;
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}
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// cast it to the right type.
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// cast it to the right type.
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AcquisitionControl daqControl = (AcquisitionControl) aModule;
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AcquisitionParameters daqParams = daqControl.getAcquisitionParameters();
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/**
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* The daqParams class has most of what we need about the set up in terms of sample rate,
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|
* number of channels, instrument type, ADC input range (part of calibration), etc.
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* It also has a hydrophone list, which maps the input channel numbers to the hydrophon numbers.
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* The daqParams class has most of what we need about the set up in terms of sample rate,
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* number of channels, instrument type, ADC input range (part of calibration), etc.
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* It also has a hydrophone list, which maps the input channel numbers to the hydrophon numbers.
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* Realistically, this list is always 0,1,2,etc or it goes horribly wrong !
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*/
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// so write functions here to get information from the daqParams.
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// so write functions here to get information from the daqParams.
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// System.out.printf("Sample regime: %s input with rate %3.1fHz, %d channels, gain %3.1fdB, ADCp-p %3.1fV\n", daqParams.getDaqSystemType(),
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// daqParams.getSampleRate(), daqParams.getNChannels(), daqParams.preamplifier.getGain(), daqParams.voltsPeak2Peak);
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/**
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* then there is the actual sampling. This is a bit harder to find. I thought it would be in the data map
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* but the datamap is a simple count of what's in the databasase which is not quite what we want.
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* we're going to have to query the database to get more detailed informatoin I think.
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* I'll do that here for now, but we may want to move this when we better organise the code.
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* but the datamap is a simple count of what's in the databasase which is not quite what we want.
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* we're going to have to query the database to get more detailed informatoin I think.
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* I'll do that here for now, but we may want to move this when we better organise the code.
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* It also seems that there are 'bad' dates in the database when it starts new files, which are the date
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* data were analysed at. So we really need to check the start and stop records only.
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* data were analysed at. So we really need to check the start and stop records only.
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*/
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PamDataBlock<DaqStatusDataUnit> daqInfoDataBlock = daqControl.getAcquisitionProcess().getDaqStatusDataBlock();
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// just load everything. Probably OK for the acqusition, but will bring down
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// just load everything. Probably OK for the acqusition, but will bring down
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daqInfoDataBlock.loadViewerData(0, Long.MAX_VALUE, null);
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ArrayList<DaqStatusDataUnit> allStatusData = daqInfoDataBlock.getDataCopy();
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long dataStart = Long.MAX_VALUE;
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@ -241,24 +243,24 @@ public class DeploymentHandler {
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break;
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}
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}
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// System.out.printf("Input map of sound data indicates data from %s to %s with %d starts and %d stops over %d files\n",
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// System.out.printf("Input map of sound data indicates data from %s to %s with %d starts and %d stops over %d files\n",
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// PamCalendar.formatDateTime(dataStart), PamCalendar.formatDateTime(dataEnd), nStart, nStop, nFile+1);
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}
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// // and we find the datamap within that ...
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// OfflineDataMap daqMap = daqInfoDataBlock.getOfflineDataMap(DBControlUnit.findDatabaseControl());
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// if (daqMap != null) {
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// // iterate through it.
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// // iterate through it.
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// long dataStart = daqMap.getFirstDataTime();
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// long dataEnd = daqMap.getLastDataTime();
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// List<OfflineDataMapPoint> mapPoints = daqMap.getMapPoints();
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// System.out.printf("Input map of sound data indicates data from %s to %s with %d individual files\n",
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// System.out.printf("Input map of sound data indicates data from %s to %s with %d individual files\n",
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// PamCalendar.formatDateTime(dataStart), PamCalendar.formatDateTime(dataEnd), mapPoints.size());
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// /*
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// * clearly in the first database I've been looking at of Tinas data, this is NOT getting sensible start and
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// * end times. Print them out to see what's going on.
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// * end times. Print them out to see what's going on.
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// */
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//// for ()
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// }
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@ -267,18 +269,18 @@ public class DeploymentHandler {
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DeploymentRecoveryDetails recovery = new DeploymentRecoveryDetails();
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pair.deploymentDetails = deployment;
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pair.recoveryDetails = recovery;
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deployment.setTimeStamp(TethysTimeFuncs.xmlGregCalFromMillis(dataStart));
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deployment.setAudioTimeStamp(TethysTimeFuncs.xmlGregCalFromMillis(dataStart));
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recovery.setTimeStamp(TethysTimeFuncs.xmlGregCalFromMillis(dataEnd));
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recovery.setAudioTimeStamp(TethysTimeFuncs.xmlGregCalFromMillis(dataEnd));
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ArrayList<DeploymentRecoveryPair> drPairs = new ArrayList<>();
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drPairs.add(pair);
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return drPairs;
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}
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public Deployment createDeploymentDocument(int i, DeploymentRecoveryPair drd) {
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Deployment deployment = new Deployment();
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String id = String.format("%d", i);
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@ -286,25 +288,79 @@ public class DeploymentHandler {
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deployment.setDeploymentId(i);
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deployment.setDeploymentDetails(drd.deploymentDetails);
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deployment.setRecoveryDetails(drd.recoveryDetails);
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TethysLocationFuncs.getTrackAndPositionData(deployment);
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getProjectData(deployment);
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getSamplingDetails(deployment);
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getSensorDetails(deployment);
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/**
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* Stuff that may need to be put into the UI:
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* Audio: can easily get current loc of raw and binary data, but may need to override these. I think
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* this may be for the export UI ?
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* Tracks: trackline information. General problem in PAMGUard.
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* Audio: can easily get current loc of raw and binary data, but may need to override these. I think
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* this may be for the export UI ?
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* Tracks: trackline information. General problem in PAMGUard.
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*/
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return deployment;
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}
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/**
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* Add project Metadata to a Deploymnet document. This is currently being
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* made available in the MetaDataControl module which should be added to PAMGuard
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* as well as the Tethys output module.
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* @param deployment
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*/
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private boolean getProjectData(Deployment deployment) {
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PamControlledUnit aUnit = PamController.getInstance().findControlledUnit(MetaDataContol.class, null);
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if (aUnit instanceof MetaDataContol == false) {
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return false;
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}
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MetaDataContol metaControl = (MetaDataContol) aUnit;
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DeploymentData deploymentData = metaControl.getDeploymentData();
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deployment.setProject(deploymentData.getProject());
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deployment.setDeploymentAlias(deploymentData.getDeploymentAlias());
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deployment.setSite(deploymentData.getSite());
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deployment.setCruise(deploymentData.getCruise());
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deployment.setPlatform(deploymentData.getPlatform());
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deployment.setRegion(deploymentData.getRegion());
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Instrument instrument = new Instrument();
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instrument.setType(deploymentData.getInstrumentType());
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instrument.setInstrumentId(deploymentData.getInstrumentId());
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// get the geometry type from the array manager.
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String geomType = getGeometryType();
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instrument.setGeometryType(geomType);
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deployment.setInstrument(instrument);
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return true;
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}
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/**
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* Get a geometry type string for Tethys based on information in the array manager.
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* @return
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*/
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private String getGeometryType() {
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PamArray array = ArrayManager.getArrayManager().getCurrentArray();
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int nStreamer = array.getStreamerCount();
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for (int i = 0; i < nStreamer; i++) {
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Streamer streamer = array.getStreamer(i);
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HydrophoneLocator locator = streamer.getHydrophoneLocator();
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if (locator == null) {
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continue;
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}
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if (locator instanceof ThreadingHydrophoneLocator) {
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return "cabled";
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}
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else {
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return "rigid";
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}
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}
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return "unknown";
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}
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private boolean getSensorDetails(Deployment deployment) {
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PamArray array = ArrayManager.getArrayManager().getCurrentArray();
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Sensors sensors = new Sensors();
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@ -322,7 +378,7 @@ public class DeploymentHandler {
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PamVector hydLocs = array.getAbsHydrophoneVector(iPhone, timeMillis);
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Audio audio = new Audio();
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audio.setNumber(BigInteger.valueOf(iPhone));
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audio.setSensorId(String.format("Hydrophone %d", iPhone)); // shold replace with serial number if it exists.
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audio.setSensorId(String.format("Hydrophone %d", iPhone)); // shold replace with serial number if it exists.
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GeometryTypeM geom = new GeometryTypeM();
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geom.setXM(hydLocs.getCoordinate(0));
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geom.setYM(hydLocs.getCoordinate(1));
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@ -342,7 +398,7 @@ public class DeploymentHandler {
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// e.printStackTrace();
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// }
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/**
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* Need to be able to add the values from hydLocs to the geometry object, but can't.
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* Need to be able to add the values from hydLocs to the geometry object, but can't.
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*/
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audioList.add(audio);
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iPhone++;
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@ -354,18 +410,18 @@ public class DeploymentHandler {
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// // TODO Auto-generated catch block
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// e.printStackTrace();
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// }
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deployment.setSensors(sensors);
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deployment.setSensors(sensors);
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return true;
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}
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/**
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* Fill in the sampling details in a Deployment document.
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* Fill in the sampling details in a Deployment document.
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* @param deployment
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*/
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private boolean getSamplingDetails(Deployment deployment) {
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SamplingDetails samplingDetails = new SamplingDetails();
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// this is basically going to be a list of almost identical channel information
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// currently just for the first acquisition. May extend to more.
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// currently just for the first acquisition. May extend to more.
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AcquisitionControl daq = (AcquisitionControl) PamController.getInstance().findControlledUnit(AcquisitionControl.class, null);
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if (daq == null) {
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return false;
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@ -377,15 +433,15 @@ public class DeploymentHandler {
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int[] hydroMap = daqParams.getHydrophoneList();
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int[] inputMap = daqParams.getHardwareChannelList();
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double vp2p = daqParams.getVoltsPeak2Peak();
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List<ChannelInfo> channelInfos = samplingDetails.getChannel();
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for (int i = 0; i < nChan; i++) {
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ChannelInfo channelInfo = new ChannelInfo();
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channelInfo.setStart(deployment.getDeploymentDetails().getAudioTimeStamp());
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channelInfo.setEnd(deployment.getRecoveryDetails().getAudioTimeStamp());
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BigIntegerConverter biCon = new BigIntegerConverter();
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BigInteger chanNum = BigInteger.valueOf((long) i);
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BigInteger chanNum = BigInteger.valueOf(i);
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channelInfo.setChannelNumber(chanNum);
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if (hydroMap != null) {
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channelInfo.setSensorNumber(hydroMap[i]);
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@ -402,7 +458,7 @@ public class DeploymentHandler {
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nilus.ChannelInfo.Gain.Regimen aGain = new nilus.ChannelInfo.Gain.Regimen();
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aGain.setGainDB(daqParams.getPreamplifier().getGain());
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channelInfo.setGain(gain);
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Sampling sampling = new Sampling();
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List<Regimen> regimens = sampling.getRegimen();
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Sampling.Regimen regimen = new Sampling.Regimen();
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@ -412,14 +468,14 @@ public class DeploymentHandler {
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regimen.setSampleBits(system.getSampleBits());
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}
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regimens.add(regimen);
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channelInfo.setSampling(sampling);
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channelInfos.add(channelInfo);
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/**
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* Need something about duty cycling. this is probably something that will have to be added
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* earlier to a wrapper around the Deployment class.
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* Need something about duty cycling. this is probably something that will have to be added
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* earlier to a wrapper around the Deployment class.
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*/
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}
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deployment.setSamplingDetails(samplingDetails);
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Douglas Gillespie