Package rocca

Class RoccaProcess

java.lang.Object

PamguardMVC.PamProcess

rocca.RoccaProcess

All Implemented Interfaces:

PamObserver, ProcessAnnotator

public class RoccaProcess
extends PamProcess

Main Rocca process

Author:

Michael Oswald

Constructor Summary

Constructors

Constructor	Description
RoccaProcess(RoccaControl roccaControl)	Main constructor

Method Summary

Modifier and Type	Method	Description
NoiseDataBlock	getClickNoiseSourceData()
TrackedClickDataBlock	getClickSourceData()
File	getDataBlockFilename(RoccaContourDataBlock rcdb, String ext, int channel, int thisDetection, String sNum)	Generates a filename for the wav clip and the csv file containing the contour points, based on the filename template stored in RoccaParameters
GPSDataBlock	getGpsSourceData()
ClickDetection	getLatestClickNoise()
AbstractWhistleDataBlock	getWhistleSourceData()
boolean	isClassifierLoaded()	Checks to see if classifier has been loaded
RoccaContourDataBlock	newClickDetectorData(ClickDetection clickDetection)	Takes a ClickDetection created in the Click detector, and copies the data into a RoccaContourDataBlock for further analysis and classification.
void	newData(PamObservable o, PamDataUnit arg)	this method called when new data arrives
RoccaContourDataBlock	newWMDetectorData(ConnectedRegionDataUnit wmDataUnit)	Takes an AbstractWhistleDataUnit created in the Whistle and Moan detector, and copies the data into a RoccaContourDataBlock for further analysis and classification serialVersionUID = 9 if either firstIndx or lastIndx cannot be determined, return a null to the calling method
void	pamStart()	Called for each process to tell it to start (may not be necessary for processes which are listening for data anyway).
void	pamStop()	Stops the process.
void	prepareProcess()	Called for each process before any of them receive the PamStart command
boolean	saveContourPoints(RoccaContourDataBlock rcdb, int channel, int thisDetection, String sNum)	Saves the contour points in the datablock in a csv file.
boolean	saveContourStats(RoccaContourDataBlock rcdb, int channel, int thisDetection, String sNum)	Saves all contour stats to the contour stats summary file, as defined in the Rocca Parameters.
boolean	saveContourStats(RoccaContourDataBlock rcdb, int channel, int thisDetection, String sNum, String source)	Saves all contour stats to the contour stats summary file, as defined in the Rocca Parameters.
void	setClassifierLoaded(boolean classifierLoaded)	Sets the classifier loaded flag
void	setClickNoiseSourceData(NoiseDataBlock clickNoiseSourceData)
void	setClickSourceData(TrackedClickDataBlock clickSourceData)
void	setLatestClickNoise(ClickDetection latestClickNoise)
void	setupProcess()	Method run on startup
void	setWhistleSourceData(AbstractWhistleDataBlock whistleSourceData)
void	updateSidePanel(RoccaContourDataBlock rcdb, boolean isClick)

Methods inherited from class PamguardMVC.PamProcess

absMillisecondsToSamples, absSamplesToMilliseconds, addData, addMultiPlexDataBlock, addOutputDataBlock, changedThreading, clearOldData, createAnnotations, destroyProcess, dumpBufferStatus, flushDataBlockBuffers, getAncestorDataBlock, getAnnotation, getChainPosition, getCompatibleDataUnits, getCpuPercent, getFrequencyRange, getLastSourceNotificationObject, getLastSourceNotificationType, getMuiltiplexDataBlock, getNumAnnotations, getNumMuiltiplexDataBlocks, getNumOutputDataBlocks, getObserverName, getObserverObject, getOfflineData, getOfflineData, getOutputDataBlock, getOutputDataBlocks, getPamControlledUnit, getParentDataBlock, getParentDataBlocks, getParentProcess, getProcessCheck, getProcessName, getRawSourceDataBlock, getRawSourceDataBlock, getRequiredDataHistory, getSampleRate, getSourceDataBlock, getSourceProcess, hasOutputDatablock, isCanMultiThread, isExternalProcess, isMultiplex, makePamProcess, masterClockUpdate, noteNewSettings, notifyModelChanged, prepareProcessOK, processNewBuoyData, receiveSourceNotification, relMillisecondsToSamples, relSamplesToMilliseconds, removeAllDataBlocks, removeAllMultiPlexDataBlocks, removeMultiPlexDataBlock, removeObservable, removeOutputDatablock, resetDataBlocks, saveViewerData, setCanMultiThread, setExternalProcess, setMultiplex, setParentDataBlock, setParentDataBlock, setProcessCheck, setProcessName, setSampleRate, toString, updateData

Methods inherited from class java.lang.Object

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

Constructor Details

RoccaProcess

public RoccaProcess(RoccaControl roccaControl)

Main constructor

Parameters:

roccaControl -

Method Details

pamStart

public void pamStart()

Description copied from class: PamProcess

Called for each process to tell it to start (may not be necessary for processes which are listening for data anyway).

Specified by:

pamStart in class PamProcess

pamStop

public void pamStop()

Description copied from class: PamProcess

Stops the process.

Specified by:

pamStop in class PamProcess

prepareProcess

public void prepareProcess()

Description copied from class: PamProcess

Called for each process before any of them receive the PamStart command

Overrides:

prepareProcess in class PamProcess

newData

public void newData(PamObservable o,
 PamDataUnit arg)

this method called when new data arrives

Overrides:

newData in class PamProcess

updateSidePanel

public void updateSidePanel(RoccaContourDataBlock rcdb,
 boolean isClick)

isClassifierLoaded

public boolean isClassifierLoaded()

Checks to see if classifier has been loaded

Returns:

boolean indicating whether classifier has been loaded

setClassifierLoaded

public void setClassifierLoaded(boolean classifierLoaded)

Sets the classifier loaded flag

Parameters:

classifierLoaded - true=loaded, false=not loaded

setupProcess

public void setupProcess()

Method run on startup

Overrides:

setupProcess in class PamProcess

newWMDetectorData

public RoccaContourDataBlock newWMDetectorData(ConnectedRegionDataUnit wmDataUnit)

Takes an AbstractWhistleDataUnit created in the Whistle and Moan detector, and copies the data into a RoccaContourDataBlock for further analysis and classification serialVersionUID = 9 if either firstIndx or lastIndx cannot be determined, return a null to the calling method

Parameters:

wmDataUnit - the ConnectedRegionDataUnit containing the whistle

Returns:

a RoccaContourDataBlock containing the whistle's time/freq pairs

newClickDetectorData

public RoccaContourDataBlock newClickDetectorData(ClickDetection clickDetection)

Takes a ClickDetection created in the Click detector, and copies the data into a RoccaContourDataBlock for further analysis and classification. Create a RoccaContourDataUnit and populate it with information from the clickDetection

Parameters:

clickDetection - a ClickDetection object

Returns:

saveContourStats

public boolean saveContourStats(RoccaContourDataBlock rcdb,
 int channel,
 int thisDetection,
 String sNum)

Saves all contour stats to the contour stats summary file, as defined in the Rocca Parameters. If the file does not exist, it is created and a header line is written. If it does exist, data is appended to the end. Each contour is 1 row. Note that the last few columns contain the random forest votes, and so the number of columns depends on how many species are in the classifier. This won't be a problem if the same classifier is always used, but if a different classifier with a different number of species is tried out the number of columns from one row to the next will not match. More importantly, the order of the species from one row to the next might not match and you would never know unless you remember. For this reason, instead of saving the species names as the column headers (which would only be accurate for the classifier selected when the file had been created), the species names are written in the row AFTER the tree votes. The classifier name is also saved, for reference. While this is awkward, at least results from different classifiers can be interpreted properly without having to guess which vote is for which species

Returns:

boolean indicating whether or not the save was successful

saveContourStats

public boolean saveContourStats(RoccaContourDataBlock rcdb,
 int channel,
 int thisDetection,
 String sNum,
 String source)

Saves all contour stats to the contour stats summary file, as defined in the Rocca Parameters. If the file does not exist, it is created and a header line is written. If it does exist, data is appended to the end. Each contour is 1 row. Note that the last few columns contain the random forest votes, and so the number of columns depends on how many species are in the classifier. This won't be a problem if the same classifier is always used, but if a different classifier with a different number of species is tried out the number of columns from one row to the next will not match. More importantly, the order of the species from one row to the next might not match and you would never know unless you remember. For this reason, instead of saving the species names as the column headers (which would only be accurate for the classifier selected when the file had been created), the species names are written in the row AFTER the tree votes. The classifier name is also saved, for reference. While this is awkward, at least results from different classifiers can be interpreted properly without having to guess which vote is for which species

Returns:

boolean indicating whether or not the save was successful

saveContourPoints

public boolean saveContourPoints(RoccaContourDataBlock rcdb,
 int channel,
 int thisDetection,
 String sNum)

Saves the contour points in the datablock in a csv file. Saves the time and peak frequency of each point, along with the duty cycle, energy, and windows RMS

Parameters:

rcdb - the datablock containing the selected whistle contour

Returns:

saveContourPoints boolean indicating success or failure

getDataBlockFilename

public File getDataBlockFilename(RoccaContourDataBlock rcdb,
 String ext,
 int channel,
 int thisDetection,
 String sNum)

Generates a filename for the wav clip and the csv file containing the contour points, based on the filename template stored in RoccaParameters

Parameters:

rcdb - The RoccaContourDataBlock containing the data to save

ext - The filename extension (wav or csv)

Returns:

A File

getWhistleSourceData

public AbstractWhistleDataBlock getWhistleSourceData()

Returns:

the whistleSourceData

setWhistleSourceData

public void setWhistleSourceData(AbstractWhistleDataBlock whistleSourceData)

Parameters:

whistleSourceData - the whistleSourceData to set

getClickSourceData

public TrackedClickDataBlock getClickSourceData()

Returns:

the clickSourceData

setClickSourceData

public void setClickSourceData(TrackedClickDataBlock clickSourceData)

Parameters:

clickSourceData - the clickSourceData to set

getClickNoiseSourceData

public NoiseDataBlock getClickNoiseSourceData()

Returns:

the clickNoiseSourceData

setClickNoiseSourceData

public void setClickNoiseSourceData(NoiseDataBlock clickNoiseSourceData)

Parameters:

clickNoiseSourceData - the clickNoiseSourceData to set

getLatestClickNoise

public ClickDetection getLatestClickNoise()

Returns:

the latestClickNoise

setLatestClickNoise

public void setLatestClickNoise(ClickDetection latestClickNoise)

Parameters:

latestClickNoise - the latestClickNoise to set

getGpsSourceData

public GPSDataBlock getGpsSourceData()