Package clickTrainDetector

Class CTDataUnit

java.lang.Object

PamguardMVC.PamDataUnit<T,SuperDetection>

PamguardMVC.superdet.SuperDetection<PamDataUnit>

detectiongrouplocaliser.DetectionGroupDataUnit

clickTrainDetector.CTDetectionGroupDataUnit

clickTrainDetector.CTDataUnit

All Implemented Interfaces:

Comparable<PamDataUnit>, PamDetection, AcousticDataUnit, RawDataHolder

public class CTDataUnit
extends CTDetectionGroupDataUnit
implements RawDataHolder, AcousticDataUnit

Data unit for a click train which holds a series of data units grouped into a click train.

Author:

Jamie Macaulay

Field Summary

Fields

Modifier and Type	Field	Description
AverageWaveform	averageWaveform	The average waveform.
Double	chi2	Chi^2 value for the click train.
ArrayList<CTClassification>	ctClassifications	The classifications for the click train.
static int	defaultFFTLen	The default FFT length for the average templates.

Constructor Summary

Constructors

Constructor	Description
CTDataUnit(long timeMilliseconds)

Method Summary

Modifier and Type	Method	Description
void	addCtClassification(CTClassification ctClassification)	Adds a classification for the click train.
int	addSubDetection(PamDataUnit subDetection)	Add a sub detection to the sub detection list.
int	addSubDetections(List<PamDataUnit> list)	Add multiple sub detections from a list.
void	addToAverageWaveform(PamDataUnit dataUnit)	Adds to the average waveform is the data unit contains raw info.
AverageWaveform	averageWaveform()
void	checkAverageWaveformInfo()
void	clearClassifiers()	Clear all classification results from the data unit
void	forceIDIUpdater()	Force an update of the IDI calculation.
double[]	getAverageSpectra()	Get an average spectrum for the data unit.
double[]	getAverageWaveform()	Get an average waveform for the data unit.
int	getClassificationIndex()	Get the the classification index (this is to set one classification as the "master" classifications).
CTAlgorithmInfo	getCTAlgorithmInfo()	Set the click train algorithm info class.
Double	getCTChi2()	Get the chi^2 value for the click train.
ArrayList<CTClassification>	getCtClassifications()	Get the click train's classification.
RawDataTransforms	getDataTransforms()	Get the raw data transforms class.
IDIInfo	getIDIInfo()	Get the IDI info for the data
String	getSummaryString()	Return an html formatted summary string describing the detection which can be used in tooltips anywhere in PAMGuard.
double[][]	getWaveData()	Get arrays of raw audio data, one per channel.
boolean	isJunkTrain()	Check whether a click train should be junked
void	removeAllSubDetections()	Remove all sub detection information.
void	setAverageWaveform(AverageWaveform averageWaveform2)	Set the average waveform.
void	setClassificationIndex(int i)	The index of the classification (this is to set one classification as the "master" classifications).
void	setCTAlgorithmInfo(CTAlgorithmInfo ctAlgorithmInfo)	Set the click train algorithm info class.
void	setCTChi2(Double chi2)	Set the chi^2 value for the click train.
void	setIDIInfo(IDIInfo idiInfo)	Set the current IDI info.
void	setJunkTrain(boolean junkTrain)	Set whther a click train should be junked.

Methods inherited from class clickTrainDetector.CTDetectionGroupDataUnit

calcMinMaxAng, calcStartSample, calcSummaryUnits, clearSummaryDataUnits, getAngleRange, getSummaryUnits

Methods inherited from class PamguardMVC.superdet.SuperDetection

addSubDetectionInfo, clearSubDetectionData, clearSubDetectionObjects, clearSubdetectionsRemoved, findSubDetection, findSubDetection, findSubDetection, findSubdetectionInfo, findSubDetectionInfo, getLoadedSubDetectionsCount, getPresentSubDetections, getSubDetection, getSubdetectionInfo, getSubDetectionInfo, getSubDetections, getSubDetectionsCount, getSubdetectionsRemoved, getSubDetectionSyncronisation, isAllowSubdetectionSharing, removeSubDetection, replaceSubDetection, sortSubDetections

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, getLocalisation, getMeasuredAmplitude, getMeasuredAmplitudeType, getNoiseBackground, getNumDataAnnotations, getOriginLatLong, 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, setTimeMilliseconds, setUID, setUniqueSuperDetection, sortOutputMaps, updateDataUnit

Methods inherited from class java.lang.Object

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

Field Details

chi2

public Double chi2

Chi^2 value for the click train.

ctClassifications

public ArrayList<CTClassification> ctClassifications

The classifications for the click train. This is a list of classifiers which have PASSED. i.e. which have an speciesID>0. Only the first classification gets loaded in from the database.

averageWaveform

public AverageWaveform averageWaveform

The average waveform.

defaultFFTLen

public static int defaultFFTLen

The default FFT length for the average templates. Made static because of the super constructor adding clicks in function addDetectionList

Constructor Details

CTDataUnit

public CTDataUnit(long timeMilliseconds)

Method Details

addSubDetections

public int addSubDetections(List<PamDataUnit> list)

Description copied from class: SuperDetection

Add multiple sub detections from a list.

Overrides:

addSubDetections in class CTDetectionGroupDataUnit

Parameters:

list - List of new sub detections

Returns:

total number of sub detections now in the super detection

addSubDetection

public int addSubDetection(PamDataUnit subDetection)

Description copied from class: SuperDetection

Add a sub detection to the sub detection list.

Overrides:

addSubDetection in class SuperDetection<PamDataUnit>

Parameters:

subDetection - - the sub detection to add.

Returns:

- the total number of sub detections now in the list. .

checkAverageWaveformInfo

public void checkAverageWaveformInfo()

addToAverageWaveform

public void addToAverageWaveform(PamDataUnit dataUnit)

Adds to the average waveform is the data unit contains raw info.

Parameters:

dataUnit - - the data unit to add.

removeAllSubDetections

public void removeAllSubDetections()

Description copied from class: SuperDetection

Remove all sub detection information.

Overrides:

removeAllSubDetections in class SuperDetection<PamDataUnit>

getCTChi2

public Double getCTChi2()

Get the chi^2 value for the click train. Can be null if the click train algorithm does not calculate it.

Returns:

the chi2 algorithm.

setCTChi2

public void setCTChi2(Double chi2)

Set the chi^2 value for the click train.

Parameters:

chi - ^2 the chi^2 value to set.

getCtClassifications

public ArrayList<CTClassification> getCtClassifications()

Get the click train's classification.

Returns:

the ctClassification

averageWaveform

public AverageWaveform averageWaveform()

getAverageWaveform

public double[] getAverageWaveform()

Get an average waveform for the data unit.

Returns:

the average waveform

getAverageSpectra

public double[] getAverageSpectra()

Get an average spectrum for the data unit.

Returns:

the average spectrum

addCtClassification

public void addCtClassification(CTClassification ctClassification)

Adds a classification for the click train.

Parameters:

ctClassification - the ctClassification to set

clearClassifiers

public void clearClassifiers()

Clear all classification results from the data unit

getIDIInfo

public IDIInfo getIDIInfo()

Get the IDI info for the data

Returns:

the IDIInfo for the click train.

forceIDIUpdater

public void forceIDIUpdater()

Force an update of the IDI calculation. This should be used if data unit information changes. The IDI is automaticaly updated when new data units are added to the CTData unit.

isJunkTrain

public boolean isJunkTrain()

Check whether a click train should be junked

Returns:

true to junk train

setJunkTrain

public void setJunkTrain(boolean junkTrain)

Set whther a click train should be junked.

Parameters:

junkTrain - - true to junk train.

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 PamDataUnit<PamDataUnit,SuperDetection>

Returns:

summary string

setClassificationIndex

public void setClassificationIndex(int i)

The index of the classification (this is to set one classification as the "master" classifications). This is usually just for convenience, the index could be calculated by finding the first non zero species code in the classification list.

Parameters:

i - - the classification index.

getClassificationIndex

public int getClassificationIndex()

Get the the classification index (this is to set one classification as the "master" classifications). invalid input: '<'0 indicates that no classification was passed.

Parameters:

i - - the classification index.

setAverageWaveform

public void setAverageWaveform(AverageWaveform averageWaveform2)

Set the average waveform.

Parameters:

averageWaveform2 - - the average waveform to set.

getWaveData

public double[][] getWaveData()

Description copied from interface: RawDataHolder

Get arrays of raw audio data, one per channel. Assume that the array matches getChannelMap() !

Specified by:

getWaveData in interface RawDataHolder

Returns:

arrays of raw data by channel

setCTAlgorithmInfo

public void setCTAlgorithmInfo(CTAlgorithmInfo ctAlgorithmInfo)

Set the click train algorithm info class.

Parameters:

ctAlgorithmInfo -

getCTAlgorithmInfo

public CTAlgorithmInfo getCTAlgorithmInfo()

Set the click train algorithm info class. This provides extra information from the click, train algorithm used.

Parameters:

ctAlgorithmInfo - - the click train algorithm info.

getDataTransforms

public RawDataTransforms getDataTransforms()

Description copied from interface: RawDataHolder

Get the raw data transforms class. This handles standard data transforms that are often used in raw data units, e.g. calculating the spectrum, filtering waveforms, getting data as an int16 (short) array, etc.

Specified by:

getDataTransforms in interface RawDataHolder

Returns:

the data transforms object.

setIDIInfo

public void setIDIInfo(IDIInfo idiInfo)

Set the current IDI info.

Parameters:

idiInfo - - the IDI info.