Package difar

Class DifarDataUnit

java.lang.Object

PamguardMVC.PamDataUnit<PamDataUnit,SuperDetection>

clipgenerator.ClipDataUnit

difar.DifarDataUnit

All Implemented Interfaces:

Comparable<PamDataUnit>, PamDetection, AcousticDataUnit, RawDataHolder

public class DifarDataUnit
extends ClipDataUnit

Field Summary

Fields inherited from class clipgenerator.ClipDataUnit

fileName, triggerMilliseconds, triggerName

Constructor Summary

Constructors

Constructor	Description
DifarDataUnit(long clipStartMillis, long triggerMilliseconds, long startSample, int durationSamples, int channelMap, String fileName, String triggerName, double[][] rawData, long signalStartMillis, PamDataUnit parentDetection, double[] frequencyRange, float sourceSampleRate, float displaySampleRate, double[] calFreqs, double[] calGains)	Constructor to use if storing data into the binary system.

Method Summary

Modifier and Type	Method	Description
Double	calculateDifarGain()	Now also work out the DIFAR gain for that angle.
Double	calculateDifarGain(Double selectedAngle, Double selectedFrequency)	Calculate teh DIFAR gain for a given angle and frequency
boolean	canAutoProcess()	Autoprocess everything except "Default" clips
boolean	canAutoSave()	//this is a bit pointless now as action performed doesn't attempt save if timer is stopped whether the difar unit has been interacted with causing autosave to be inapropriate
void	cancelAutoSave()	//this is a bit pointless now as action performed doesn't attempt save if timer is stopped
void	cleanUpData()	Gets called just before unit is added to processed data.
static double[]	decimateData(double[] ds, float origSmp, float displaySampRate)
static boolean[]	decimateLockArray(boolean[] lockInput, float origSmp, float displaySampRate)
double[][]	getCalibratedSpectrogramData(int channel, int fftLength, int fftHop)	Return a spectrogram clip that has calibrated intensity Intensity is "calibrated" using an arbitrary filter to correct for the DIFAR frequency response.
BufferedImage	getClipImage(int spectrogramImageChoice, int iChannel, int fftLen, int fftHop, double scaleMin, double scaleMax, Color[] colours)	Get a clip image for a particular wave type - decimated original, Om, EW, NS
long	getClipStartMillis()
double[][]	getDemuxedDecimatedData()
DIFARCrossingInfo	getDifarCrossing()
Double	getDifarGain()
float	getDisplaySampleRate()
double	getDurationInSeconds()	Used by some displays
boolean[][]	getLockDecimatedData()
LookupItem	getLutSpeciesItem()
Double	getMaximumAngle()
double[]	getMaximumAngleSummary()
Double	getMaximumFrequency()
double[]	getMultiplexedData()
GpsData	getOriginLatLong(boolean recalculate)	Get the latlong of the mean hydrophone position at the time of this detection.
PamDataUnit	getParentDetection()
double	getPreMarkSeconds()
Double	getRange()
Double	getSelectedAngle()	Get the angle selectedfrom the DIFARGram.
Double	getSelectedFrequency()
long	getSignalStart()	Signal start time in milliseconds relative to start of sound.
String	getSpeciesCode()	Get a species code - mostly used by the database.
String	getSpeciesName()
String	getSummaryString()	Return an html formatted summary string describing the detection which can be used in tooltips anywhere in PAMGuard.
double[][]	getSurfaceData()
double[]	getSurfaceSummary()
DIFARCrossingInfo	getTempCrossing()
String	getTempGroup()
String	getTrackedGroup()
Double	getTrueAngle()	Get the true bearing relative to the DIFAR buoy.
boolean	isVessel()
void	saveCrossing(boolean save)	Move the crossing info from it's temp position to a saved position.
void	saveGroup()
void	setDemuxedDecimatedData(double[][] demuxedDecimatedData)
void	setDifarCrossing(DIFARCrossingInfo difarCrossing)
void	setDifarGain(double difarGain)
void	setDisplaySampleRate(float displaySampleRate)
void	setFrequencyResponse(double[] f, double[] gain)
void	setLockDecimatedData(boolean[][] lockArrays)	Set the lock array iformation in the data unit.
void	setLutSpeciesItem(LookupItem lutSpeciesItem)
void	setMaximumAngle(Double maximumAngle)
void	setMaximumAngleSummary(double[] surfaceSummary)
void	setMaximumFrequency(Double maximumFrequency)
void	setParentDetection(PamDataUnit parentDetection)
void	setPreMarkSeconds(double preMarkSeconds)
void	setSelectedAngle(Double selectedAngle)	Set the selected angle from the DIFARGram.
void	setSelectedFrequency(Double selectedFrequency)
void	setSpeciesCode(LookupList speciesList, String speciesCode)	Called in viewer when data are read back from binary store to sort out the species luukup item.
void	setSpectrogramSensor(int spectrogramSensor)	Choice of data for spectrogram displays.
void	setSurfaceData(double[][] surfaceData)
void	setSurfaceSummary(double[] surfaceSummary)
void	setTempCrossing(DIFARCrossingInfo tempCrossing)
void	setTempGroup(String tempGroup)
void	setTrackedGroup(String newGroup)
void	setVessel(boolean isVessel)
String	toString()
void	updateDataUnit(long updateTime)

Methods inherited from class clipgenerator.ClipDataUnit

clearClipSpecData, findTriggerDataUnit, generateComplexSpectrogram, generateSpectrogramArrays, getClipImage, getDataTransforms, getLocalisation, getRawData, getSourceSampleRate, getSpectrogramData, getTriggerDataUnit, getTriggerMilliseconds, getTriggerUID, getWaveData, getWindowType, setRawData, setTimeMilliseconds, setTriggerDataUnit, setTriggerUID, setWindowType

Methods inherited from class PamguardMVC.PamDataUnit

addDataAnnotation, addSuperDetection, amplifyMeasuredAmplitudeByDB, amplifyMeasuredAmplitudeByLinear, calcSnapshotGeometry, clearOandAngles, clearUpdateCount, compareTo, findDataAnnotation, findDataAnnotation, freeData, getAbsBlockIndex, getAmplitudeDB, getAnnotationsSummaryString, getBasicData, getCalculatedAmlitudeDB, getChannelBitmap, getColourIndex, getDataAnnotation, getDatabaseIndex, getDatabaseUpdateOf, getDataUnitFileInformation, getDataUnitPopupMenu, getDurationInMilliseconds, getEndTimeInMilliseconds, getFrequency, getFrequencyOverlap, getHydrophoneBitmap, getHydrophoneHeading, getLastChangeTime, getLastSample, getLastUpdateTime, getMeasuredAmplitude, getMeasuredAmplitudeType, getNoiseBackground, getNumDataAnnotations, getParentDataBlock, getSampleDuration, getSampleDurationAsInt, getSeconds, getSequenceBitmap, getSequenceBitmapObject, getSignalExcess, getSignalSPL, getSnapshotGeometry, getStartSample, getSuperDetection, getSuperDetection, getSuperDetection, getSuperDetection, getSuperDetection, getSuperDetectionsCount, getSuperDetectionSyncronisation, getSuperId, getTimeDelaysSeconds, getTimeMilliseconds, getTimeNanoseconds, getTimeOverlap, getUID, getUpdateCount, isEmbryonic, isForceAmpRecalc, linAmplitudeToDB, removeDataAnnotation, removeDataAnnotation, removeSuperDetection, setAbsBlockIndex, setCalculatedAmlitudeDB, setChannelBitmap, setDatabaseIndex, setDatabaseUpdateOf, setDataUnitFileInformation, setDurationInMilliseconds, setEmbryonic, setForceAmpRecalc, setFrequency, setInfo, setLastUpdateTime, setLocalisation, setMeasuredAmpAndType, setMeasuredAmplitude, setMeasuredAmplitudeType, setNoiseBackground, setParentDataBlock, setSampleDuration, setSequenceBitmap, setSignalExcess, setSignalSPL, setSnapshotGeometry, setStartSample, setTimeDelaysSeconds, setUID, setUniqueSuperDetection, sortOutputMaps

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details

DifarDataUnit

public DifarDataUnit(long clipStartMillis,
 long triggerMilliseconds,
 long startSample,
 int durationSamples,
 int channelMap,
 String fileName,
 String triggerName,
 double[][] rawData,
 long signalStartMillis,
 PamDataUnit parentDetection,
 double[] frequencyRange,
 float sourceSampleRate,
 float displaySampleRate,
 double[] calFreqs,
 double[] calGains)

Constructor to use if storing data into the binary system.

Parameters:

triggerMilliseconds -

startSample -

durationSamples -

channelMap -

fileName -

triggerName -

rawData -

timeMilliseconds -

upperFreq -

Method Details

decimateData

public static double[] decimateData(double[] ds,
 float origSmp,
 float displaySampRate)

setFrequencyResponse

public void setFrequencyResponse(double[] f,
 double[] gain)

getParentDetection

public PamDataUnit getParentDetection()

setParentDetection

public void setParentDetection(PamDataUnit parentDetection)

getMultiplexedData

public double[] getMultiplexedData()

getSignalStart

public long getSignalStart()

Signal start time in milliseconds relative to start of sound.

Returns:

signal start time in milliseconds

getSurfaceData

public double[][] getSurfaceData()

setSurfaceData

public void setSurfaceData(double[][] surfaceData)

isVessel

public boolean isVessel()

Returns:

the isVessel

setVessel

public void setVessel(boolean isVessel)

Parameters:

isVessel - the isVessel to set

getLutSpeciesItem

public LookupItem getLutSpeciesItem()

Returns:

the lutSpeciesItem

setLutSpeciesItem

public void setLutSpeciesItem(LookupItem lutSpeciesItem)

Parameters:

lutSpeciesItem - the lutSpeciesItem to set

getDisplaySampleRate

public float getDisplaySampleRate()

Overrides:

getDisplaySampleRate in class ClipDataUnit

Returns:

the displaySampleRate

setDisplaySampleRate

public void setDisplaySampleRate(float displaySampleRate)

Parameters:

displaySampleRate - the displaySampleRate to set

getSelectedAngle

public Double getSelectedAngle()

Get the angle selectedfrom the DIFARGram. Note that this is the angle relative to the DIFAR buoy and is therefore a MAGNETIC angle. If you want an angle corrected for magnetic deviation, use getTrueAngle();

Returns:

the selectedAngle

getRange

public Double getRange()

getTrueAngle

public Double getTrueAngle()

Get the true bearing relative to the DIFAR buoy. This is the selected angle (see getSelectedAngle() + the local magnetic deviation calulcated from the World Magnetic Model. For map display, this bearing may be further corrected for any offset in the buoy heading in the array manager. If there is no offset in the arraymanager, then return the magnetic bearing since returning null for the trueBearing may cause problems down the line.

Returns:

true angle (if the buoy is orientated right !)

getTrackedGroup

public String getTrackedGroup()

setTrackedGroup

public void setTrackedGroup(String newGroup)

setSelectedAngle

public void setSelectedAngle(Double selectedAngle)

Set the selected angle from the DIFARGram. Note that this is the angle relative to the DIFAR buoy and is therefore a MAGNETIC angle.

Parameters:

selectedAngle - the selectedAngle to set

calculateDifarGain

public Double calculateDifarGain()

Now also work out the DIFAR gain for that angle. This means taking the closest point in the summary line and seeing what it's value is for that angle

Returns:

gain.

calculateDifarGain

public Double calculateDifarGain(Double selectedAngle,
 Double selectedFrequency)

Calculate teh DIFAR gain for a given angle and frequency

Parameters:

selectedAngle - angle 0 - 360

selectedFrequency - Frequency Hz

Returns:

gain

getSelectedFrequency

public Double getSelectedFrequency()

Returns:

the selectedFrequency

setSelectedFrequency

public void setSelectedFrequency(Double selectedFrequency)

Parameters:

selectedFrequency - the selectedFrequency to set

getSurfaceSummary

public double[] getSurfaceSummary()

Returns:

the surfaceSummary

setSurfaceSummary

public void setSurfaceSummary(double[] surfaceSummary)

Parameters:

surfaceSummary - the surfaceSummary to set

getMaximumAngleSummary

public double[] getMaximumAngleSummary()

Returns:

the maximumAngleSummary

setMaximumAngleSummary

public void setMaximumAngleSummary(double[] surfaceSummary)

Parameters:

surfaceSummary - the surfaceSummary to set

getMaximumAngle

public Double getMaximumAngle()

Returns:

the maximumAngle

setMaximumAngle

public void setMaximumAngle(Double maximumAngle)

Parameters:

maximumAngle - the maximumAngle to set

getMaximumFrequency

public Double getMaximumFrequency()

Returns:

the maximumFrequency

setMaximumFrequency

public void setMaximumFrequency(Double maximumFrequency)

Parameters:

maximumFrequency - the maximumFrequency to set

setSpectrogramSensor

public void setSpectrogramSensor(int spectrogramSensor)

Choice of data for spectrogram displays.
0 = decimated original data.
1 = Omni demuxed
2 = EW demuxed
3 = NS demuxed

Parameters:

spectrogramSensor - the spectrogramSensor to set

getDemuxedDecimatedData

public double[][] getDemuxedDecimatedData()

Returns:

the demuxedDecimatedData

setDemuxedDecimatedData

public void setDemuxedDecimatedData(double[][] demuxedDecimatedData)

Parameters:

demuxedDecimatedData - the demuxedDecimatedData to set

getClipImage

public BufferedImage getClipImage(int spectrogramImageChoice,
 int iChannel,
 int fftLen,
 int fftHop,
 double scaleMin,
 double scaleMax,
 Color[] colours)

Get a clip image for a particular wave type - decimated original, Om, EW, NS

Parameters:

spectrogramImageChoice -

iChannel -

fftLen -

fftHop -

scaleMin -

scaleMax -

colours -

Returns:

getSpeciesName

public String getSpeciesName()

Returns:

null, Vessel or the long name from the lookup

getSpeciesCode

public String getSpeciesCode()

Get a species code - mostly used by the database.

Returns:

a species code (the shorter bit from the lookup table) TODO: Store species parameters with each data unit

setSpeciesCode

public void setSpeciesCode(LookupList speciesList,
 String speciesCode)

Called in viewer when data are read back from binary store to sort out the species luukup item.

Parameters:

speciesList - list of programmed species codes

speciesCode - data units code or "Vessel"

decimateLockArray

public static boolean[] decimateLockArray(boolean[] lockInput,
 float origSmp,
 float displaySampRate)

Parameters:

lock_15 -

sampleRate -

displaySampleRate2 -

getDifarGain

public Double getDifarGain()

Returns:

the difarGain

setDifarGain

public void setDifarGain(double difarGain)

Parameters:

difarGain - the difarGain to set

setLockDecimatedData

public void setLockDecimatedData(boolean[][] lockArrays)

Set the lock array iformation in the data unit. This is a 2xn boolean array of the 7.5 and 15kHz locks, decimated to the same freqeuncy as the demuxed audio data.

Parameters:

lockArrays - TODO: Move all lock related code into the Greeneridge demux

getLockDecimatedData

public boolean[][] getLockDecimatedData()

cleanUpData

public void cleanUpData()

Gets called just before unit is added to processed data. Some things are no longer needed at this point, so can clean them up.

getDurationInSeconds

public double getDurationInSeconds()

Used by some displays

Returns:

getSummaryString

public String getSummaryString()

Description copied from class: PamDataUnit

Return an html formatted summary string describing the detection which can be used in tooltips anywhere in PAMGuard.

Overrides:

getSummaryString in class ClipDataUnit

Returns:

summary string

getPreMarkSeconds

public double getPreMarkSeconds()

Returns:

the Number of seconds added to the sound prior to the specrogram mark or detection.

setPreMarkSeconds

public void setPreMarkSeconds(double preMarkSeconds)

Parameters:

the - Number of seconds added to the sound prior to the specrogram mark or detection

getClipStartMillis

public long getClipStartMillis()

Returns:

the clipStartMillis. This is the start of the clip - which will generally have been put afew secs before the actual sound.

canAutoProcess

public boolean canAutoProcess()

Autoprocess everything except "Default" clips

Returns:

cancelAutoSave

public void cancelAutoSave()

//this is a bit pointless now as action performed doesn't attempt save if timer is stopped

Parameters:

sets - canAutoSave false

canAutoSave

public boolean canAutoSave()

//this is a bit pointless now as action performed doesn't attempt save if timer is stopped whether the difar unit has been interacted with causing autosave to be inapropriate

toString

public String toString()

Overrides:

toString in class Object

saveCrossing

public void saveCrossing(boolean save)

Move the crossing info from it's temp position to a saved position. Called just at the point when the difar unit is saved and moved from the queue to the output data block.

Parameters:

save - - save it, or discard it (also from other units associated with this crossing

getDifarCrossing

public DIFARCrossingInfo getDifarCrossing()

Returns:

the crossing point when multiple matching DIFAR bearings are crossed.

setDifarCrossing

public void setDifarCrossing(DIFARCrossingInfo difarCrossing)

Parameters:

difarCrossing - the difarCrossing to set

getTempCrossing

public DIFARCrossingInfo getTempCrossing()

Returns:

the tempCrossing

setTempCrossing

public void setTempCrossing(DIFARCrossingInfo tempCrossing)

Parameters:

tempCrossing - the tempCrossing to set

getTempGroup

public String getTempGroup()

Returns:

the tempCrossing

setTempGroup

public void setTempGroup(String tempGroup)

Parameters:

tempCrossing - the tempCrossing to set

getOriginLatLong

public GpsData getOriginLatLong(boolean recalculate)

Description copied from class: PamDataUnit

Get the latlong of the mean hydrophone position at the time of this detection. If the data unit has a channel bitmap of zero, then get the GPS position of the vessel at that time.

Overrides:

getOriginLatLong in class PamDataUnit<PamDataUnit,SuperDetection>

Returns:

Lat long of detection origin (usually the position of the reference hydrophone at time of detection)

saveGroup

public void saveGroup()

getCalibratedSpectrogramData

public double[][] getCalibratedSpectrogramData(int channel,
 int fftLength,
 int fftHop)

Return a spectrogram clip that has calibrated intensity Intensity is "calibrated" using an arbitrary filter to correct for the DIFAR frequency response.

Parameters:

fftLength -

fftHop -

i -

Returns:

updateDataUnit

public void updateDataUnit(long updateTime)

Overrides:

updateDataUnit in class PamDataUnit<PamDataUnit,SuperDetection>