rocca

Class RoccaParameters

java.lang.Object

rocca.RoccaParameters

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable

public class RoccaParameters
extends java.lang.Object
implements java.io.Serializable, java.lang.Cloneable

Parameters for Rocca modified contour calculations to better match original Matlab routine serialVersionUID = 2 2012/7/23 added whistle & moan as a potential data source for classifier serialVersionUID = 3 2012/8/12 corrected problem with not resetting inflection and sweep counts when reclassifying, resulting in doubling and tripling of the parameters serialVersionUID = 4 2012/8/16 corrected problem with freqmin=-1 when contour points dragged and end point reselected. serialVersionUID = 5 2012/10/12 added 'pick points' option to trace out contours serialVersionUID = 6 2012/11/11 fixed problem with single step being counted multiple times serialVersionUID = 7 2013/9/29 added 2nd stage classifier serialVersionUID = 8 2013/12/13 added error checking in RoccaProcess, to catch if a PamRawDataBlock is empty added error checking in RoccaContourDataBlock to catch if the filename for the source wav cannot be found serialVersionUID = 9 2014/01/18 added more error checking in RoccaProcess to catch if firstIndx or lastIndx cannot be determined from the data sent by the WMD serialVersionUID = 10 2014/02/04 in case numInflections <= 1, Rocca now writes a "0" to the following parameters instead of "999": INFLMAXDELTA INFLMINDELTA INFLMAXMINDELTA INFLMEANDELTA INFLSTDDEVDELTA INFLMEDIANDELTA serialVersionUID = 11 2014/04/09 added decimal places to the date/time output in column B of RoccaContourStats added End Date/Time column to RoccaContourStats serialVersionUID = 12 2014/05/07 integrated with click detector rev 12c 2014/07/26 released to Tina for beta testing serialVersionUID = 13 2014/09/09 added notes tab to Parameters dialog and added 4 string variables to params serialVersionUID = 14 2014/10/13 *changed version to 1_12_50 *allow multiple sources *changed click duration calculation in RoccaContourDataBlock.calculateClickStats(). Instead of calling clickDetection.clickLength, we now call SweepClassifier.getClickLength serialVersionUID = 15 2014/11/12 * add time calcs to school stats file

Author:

Michael Oswald

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static int	NO_CONTOUR_HERE constant used to define areas of spectrogram that do not contain whistle
static long	serialVersionUID for serialization

Constructor Summary

Constructors

Constructor and Description
RoccaParameters()

Method Summary

Methods

Modifier and Type	Method and Description
RoccaParameters	clone()
int	getChannelMap()
int	getClassificationThreshold()
java.lang.String	getClickDataSource()
java.lang.String	getClickNoiseDataSource()
int[]	getClickTypeList()
int	getEnergyBinSize()
int	getFftDataBlock()
java.lang.String	getFilenameTemplate()
double	getNoiseSensitivity()
java.lang.String	getNotesCruiseID()
java.lang.String	getNotesDataProvider()
java.lang.String	getNotesEncounterID()
java.lang.String	getNotesKnownSpecies()
java.io.File	getRoccaClassifier2ModelFilename()
java.io.File	getRoccaClassifierModelFilename()
java.io.File	getRoccaContourStatsOutputFilename()
java.io.File	getRoccaOutputDirectory()
java.io.File	getRoccaSightingStatsOutputFilename()
static long	getSerialVersionUID()
int	getSightingThreshold()
int	getStage1Link()
java.lang.String	getWmDataSource()
void	setChannelMap(int channelMap)
void	setClassificationThreshold(int classificationThreshold)
void	setClickDataSource(java.lang.String clickDataSource)
void	setClickNoiseDataSource(java.lang.String clickNoiseDataSource)
void	setClickTypeList(int[] clickTypeList)
void	setFilenameTemplate(java.lang.String filenameTemplate)
void	setNoiseSensitivity(double noiseSensitivity)
void	setNotesCruiseID(java.lang.String notesCruiseID)
void	setNotesDataProvider(java.lang.String notesDataProvider)
void	setNotesEncounterID(java.lang.String notesEncounterID)
void	setNotesKnownSpecies(java.lang.String notesKnownSpecies)
void	setRoccaClassifier2ModelFilename(java.io.File roccaClassifier2ModelFilename)
void	setRoccaClassifierModelFilename(java.io.File roccaClassifierModelFilename)
void	setSightingThreshold(int sightingThreshold)
void	setStage1Link(int stage1Link)
void	setUseClick(boolean useClick)
void	setUseFFT(boolean useFFT)
void	setUseWMD(boolean useWMD)
void	setWmDataSource(java.lang.String wmDataSource)
boolean	weAreUsingClick()
boolean	weAreUsingFFT()
boolean	weAreUsingWMD()

Methods inherited from class java.lang.Object

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

Field Detail

serialVersionUID

public static final long serialVersionUID

for serialization

See Also:

Constant Field Values

NO_CONTOUR_HERE

public static final int NO_CONTOUR_HERE

constant used to define areas of spectrogram that do not contain whistle

See Also:

Constant Field Values

Constructor Detail

RoccaParameters

public RoccaParameters()

Method Detail

clone

public RoccaParameters clone()

Overrides:

clone in class java.lang.Object

getSerialVersionUID

public static long getSerialVersionUID()

getChannelMap

public int getChannelMap()

setChannelMap

public void setChannelMap(int channelMap)

getEnergyBinSize

public int getEnergyBinSize()

getFftDataBlock

public int getFftDataBlock()

getNoiseSensitivity

public double getNoiseSensitivity()

setNoiseSensitivity

public void setNoiseSensitivity(double noiseSensitivity)

getRoccaClassifierModelFilename

public java.io.File getRoccaClassifierModelFilename()

getRoccaClassifier2ModelFilename

public java.io.File getRoccaClassifier2ModelFilename()

setRoccaClassifierModelFilename

public void setRoccaClassifierModelFilename(java.io.File roccaClassifierModelFilename)

Parameters:

roccaClassifierModelFilename - the roccaClassifierModelFilename to set

setRoccaClassifier2ModelFilename

public void setRoccaClassifier2ModelFilename(java.io.File roccaClassifier2ModelFilename)

Parameters:

roccaClassifier2ModelFilename - the roccaClassifier2ModelFilename to set

getRoccaContourStatsOutputFilename

public java.io.File getRoccaContourStatsOutputFilename()

getStage1Link

public int getStage1Link()

Returns:

the stage1Link

setStage1Link

public void setStage1Link(int stage1Link)

Parameters:

stage1Link - the stage1Link to set

getRoccaOutputDirectory

public java.io.File getRoccaOutputDirectory()

getClassificationThreshold

public int getClassificationThreshold()

setClassificationThreshold

public void setClassificationThreshold(int classificationThreshold)

getSightingThreshold

public int getSightingThreshold()

setSightingThreshold

public void setSightingThreshold(int sightingThreshold)

getRoccaSightingStatsOutputFilename

public java.io.File getRoccaSightingStatsOutputFilename()

getFilenameTemplate

public java.lang.String getFilenameTemplate()

setFilenameTemplate

public void setFilenameTemplate(java.lang.String filenameTemplate)

getWmDataSource

public java.lang.String getWmDataSource()

setWmDataSource

public void setWmDataSource(java.lang.String wmDataSource)

getClickDataSource

public java.lang.String getClickDataSource()

Returns:

the clickDataSource

setClickDataSource

public void setClickDataSource(java.lang.String clickDataSource)

Parameters:

clickDataSource - the clickDataSource to set

getClickNoiseDataSource

public java.lang.String getClickNoiseDataSource()

Returns:

the clickNoiseDataSource

setClickNoiseDataSource

public void setClickNoiseDataSource(java.lang.String clickNoiseDataSource)

Parameters:

clickNoiseDataSource - the clickNoiseDataSource to set

weAreUsingFFT

public boolean weAreUsingFFT()

setUseFFT

public void setUseFFT(boolean useFFT)

weAreUsingClick

public boolean weAreUsingClick()

setUseClick

public void setUseClick(boolean useClick)

weAreUsingWMD

public boolean weAreUsingWMD()

setUseWMD

public void setUseWMD(boolean useWMD)

getClickTypeList

public int[] getClickTypeList()

Returns:

the clickTypeList

setClickTypeList

public void setClickTypeList(int[] clickTypeList)

Parameters:

clickTypeList - the clickTypeList to set

getNotesEncounterID

public java.lang.String getNotesEncounterID()

Returns:

the notesEncounterID

setNotesEncounterID

public void setNotesEncounterID(java.lang.String notesEncounterID)

Parameters:

notesEncounterID - the notesEncounterID to set

getNotesCruiseID

public java.lang.String getNotesCruiseID()

Returns:

the notesCruiseID

setNotesCruiseID

public void setNotesCruiseID(java.lang.String notesCruiseID)

Parameters:

notesCruiseID - the notesCruiseID to set

getNotesDataProvider

public java.lang.String getNotesDataProvider()

Returns:

the notesDataProvider

setNotesDataProvider

public void setNotesDataProvider(java.lang.String notesDataProvider)

Parameters:

notesDataProvider - the notesDataProvider to set

getNotesKnownSpecies

public java.lang.String getNotesKnownSpecies()

Returns:

the notesKnownSpecies

setNotesKnownSpecies

public void setNotesKnownSpecies(java.lang.String notesKnownSpecies)

Parameters:

notesKnownSpecies - the notesKnownSpecies to set