whistlesAndMoans
Class ConnectedRegion

java.lang.Object
  whistlesAndMoans.ConnectedRegion

public class ConnectedRegion
extends java.lang.Object

Field Summary

private int	channel
private SliceData	currentSlice
private int	firstSlice
private int[]	freqRange
private boolean	growing
private int	maxPeaks
private int	nJoinedEnd After splitting of complex regions, these are Number of fragments connected to this at the start and at the end.
private int	nJoinedStart After splitting of complex regions, these are Number of fragments connected to this at the start and at the end.
private int[]	peakFreqsBins
private int	regionNumber
private java.util.List<SliceData>	sliceData
private int	sliceHeight
private int[]	timesBins list of time bins - there may be gaps in the whistle !
private int	totalPixels

Constructor Summary

ConnectedRegion(ConnectedRegion oldRegion, SliceData oldSlice, int peakNumber, int nJoinedStart)
Constructor to create a new connected region during fragmentation.

ConnectedRegion(int channel, int firstSlice, int regionNumber, int height)
Constructor used during initial region detection process.

Method Summary

void	addOfflineSlice(SliceData newSlice) Add in a slice during offline mode.
void	addPixel(int iCol, int iRow, FFTDataUnit fftDataUnit)
private SliceData	addSlice(int iSlice, int sliceLen, FFTDataUnit fftDataUnit)
private void	addSlicePeak(SliceData oldSlice, int peakNumber) Extend a region during fragmentation
protected void	breakShortBridges() Break short bridges in time.
double	calculateRMSAmplitude()
boolean	checkRepeatslices() Check for slices repeating twice.
void	cleanFragmentedFragment() similar to condenseInfo, but for refragmetned fragments.
void	condenseInfo() Go through the data and remove create triplets of into about each part of each slice in the region.
void	extendRegion(SliceData oldSlice, int peakNumber) Extend a region during fragmentation taking a single peak from a new slice.
private void	fillHoles(SliceData slice, int maxHeight, int nHoles) Fill in small holes in the slice.
protected void	fillSmallHoles()
protected void	fillSmallHoles(int maxHeight, int maxWidth) Fill small holes in the regions which will mess up later fragmentation
private SliceData	findSlice(int iSlice)
int	getChannel()
long	getDuration()
double	getEndGradient(int nBins) Gradient at the end of the shape for the first peak in pixels per pixel.
int	getFirstSlice()
SliceData	getFirstSliceData()
int[]	getFreqRange()
SliceData	getLastSliceData()
int	getMaxPeaks()
int	getNJoinedEnd()
int	getNJoinedStart()
int	getNumSlices()
int[]	getPeakFreqsBins()
int	getRegionNumber()
java.util.List<SliceData>	getSliceData()
int	getSliceHeight()
double	getStartGradient(int nBins) Gradient at the start of the shape for the first peak in pixels per pixel.
long	getStartMillis()
long	getStartSample()
int[]	getTimesBins()
int	getTotalPixels()
boolean	isCross(int maxCrossLength)
boolean	isGrowing()
boolean	isMerge(int maxCrossLength)
boolean	isRightMess()
boolean	isSplit(int maxCrossLength)
void	mergeFragmentedRegion(ConnectedRegion r2) for merging two regions during the fragmentation process.
void	mergeRegion(ConnectedRegion region) Merge another region into this region and then tell the array of regions that all references to that other region now refer to this one.
void	recycle()
void	resetRegion(int channel, int firstSlice, int regionNumber, int height) Prepare a region for re-use (saves some time reallocating the object if they were only used very briefly).
void	sayRegion()
void	setGrowing(boolean growing)
void	setNJoinedEnd(int nJoinedEnd)
void	setNJoinedStart(int nJoinedStart)

Methods inherited from class java.lang.Object

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

Field Detail

channel

private int channel

regionNumber

private int regionNumber

firstSlice

private int firstSlice

currentSlice

private SliceData currentSlice

sliceHeight

private int sliceHeight

sliceData

private java.util.List<SliceData> sliceData

totalPixels

private int totalPixels

growing

private boolean growing

freqRange

private int[] freqRange

peakFreqsBins

private int[] peakFreqsBins

timesBins

private int[] timesBins

list of time bins - there may be gaps in the whistle !

maxPeaks

private int maxPeaks

nJoinedStart

private int nJoinedStart

After splitting of complex regions, these are Number of fragments connected to this at the start and at the end. These are set in FragmentingFragmenter and used in RejoiningFragmenter.

nJoinedEnd

private int nJoinedEnd

After splitting of complex regions, these are Number of fragments connected to this at the start and at the end. These are set in FragmentingFragmenter and used in RejoiningFragmenter.

Constructor Detail

ConnectedRegion

public ConnectedRegion(int channel,
                       int firstSlice,
                       int regionNumber,
                       int height)

Constructor used during initial region detection process.

Parameters:

channel - channel number

firstSlice - first slice number

regionNumber - region number

height - fft length

ConnectedRegion

public ConnectedRegion(ConnectedRegion oldRegion,
                       SliceData oldSlice,
                       int peakNumber,
                       int nJoinedStart)

Constructor to create a new connected region during fragmentation. Constructor starts by making a single peak in a single slice.

Parameters:

oldRegion - old mother region which is being fragmented

sliceData - start slice in the old region

peakNumber - peak number in the slice

nJoinedStart - number of contours that joined this one before the were fragmented.

Method Detail

extendRegion

public void extendRegion(SliceData oldSlice,
                         int peakNumber)

Extend a region during fragmentation taking a single peak from a new slice.

Parameters:

oldSlice - reference to slice in old unit

peakNumber - number of peak to copy

addOfflineSlice

public void addOfflineSlice(SliceData newSlice)

Add in a slice during offline mode.

Parameters:

i - slice number (or slice index as it's read back !

peakInfo -

checkRepeatslices

public boolean checkRepeatslices()

Check for slices repeating twice.

Returns:

addSlicePeak

private void addSlicePeak(SliceData oldSlice,
                          int peakNumber)

Extend a region during fragmentation

Parameters:

oldSlice - old slice

peakNumber - peak to steal.

resetRegion

public void resetRegion(int channel,
                        int firstSlice,
                        int regionNumber,
                        int height)

Prepare a region for re-use (saves some time reallocating the object if they were only used very briefly).

Parameters:

channel -

firstSlice -

regionNumber -

height -

addPixel

public void addPixel(int iCol,
                     int iRow,
                     FFTDataUnit fftDataUnit)

addSlice

private SliceData addSlice(int iSlice,
                           int sliceLen,
                           FFTDataUnit fftDataUnit)

findSlice

private SliceData findSlice(int iSlice)

fillSmallHoles

protected void fillSmallHoles(int maxHeight,
                              int maxWidth)

Fill small holes in the regions which will mess up later fragmentation

Parameters:

maxHeight - max height of hole in pixels

maxWidth - max width of hole in pixels

fillHoles

private void fillHoles(SliceData slice,
                       int maxHeight,
                       int nHoles)

Fill in small holes in the slice.

Parameters:

slice - slice to fill

maxHeight - max hole height.

mergeRegion

public void mergeRegion(ConnectedRegion region)

Merge another region into this region and then tell the array of regions that all references to that other region now refer to this one.

Parameters:

region - other region

regionArray - array of region references to update.

mergeFragmentedRegion

public void mergeFragmentedRegion(ConnectedRegion r2)

for merging two regions during the fragmentation process. Can be assumed that all slices in r2 come AFTER those in this.

Parameters:

r2 -

recycle

public void recycle()

condenseInfo

public void condenseInfo()

Go through the data and remove create triplets of into about each part of each slice in the region. Called durign initial detection, not after refragmentation of complex shapes.

cleanFragmentedFragment

public void cleanFragmentedFragment()

similar to condenseInfo, but for refragmetned fragments.

breakShortBridges

protected void breakShortBridges()

Break short bridges in time.

fillSmallHoles

protected void fillSmallHoles()

isGrowing

public boolean isGrowing()

setGrowing

public void setGrowing(boolean growing)

getChannel

public int getChannel()

getRegionNumber

public int getRegionNumber()

getFirstSlice

public int getFirstSlice()

getSliceHeight

public int getSliceHeight()

getSliceData

public java.util.List<SliceData> getSliceData()

getNumSlices

public int getNumSlices()

getTotalPixels

public int getTotalPixels()

getStartMillis

public long getStartMillis()

getDuration

public long getDuration()

getStartSample

public long getStartSample()

sayRegion

public void sayRegion()

calculateRMSAmplitude

public double calculateRMSAmplitude()

getFreqRange

public int[] getFreqRange()

getMaxPeaks

public int getMaxPeaks()

getPeakFreqsBins

public int[] getPeakFreqsBins()

getTimesBins

public int[] getTimesBins()

getFirstSliceData

public SliceData getFirstSliceData()

getLastSliceData

public SliceData getLastSliceData()

setNJoinedStart

public void setNJoinedStart(int nJoinedStart)

Parameters:

nJoinedStart - the nJoinedStart to set

getNJoinedStart

public int getNJoinedStart()

Returns:

the nJoinedStart

setNJoinedEnd

public void setNJoinedEnd(int nJoinedEnd)

Parameters:

nJoinedEnd - the nJoinedEnd to set

getNJoinedEnd

public int getNJoinedEnd()

Returns:

the nJoinedEnd

getStartGradient

public double getStartGradient(int nBins)

Gradient at the start of the shape for the first peak in pixels per pixel.
Used for rapid region matching in RejoiningFragmenter

Parameters:

nBins - number of bins to measure over.

Returns:

gradient.

getEndGradient

public double getEndGradient(int nBins)

Gradient at the end of the shape for the first peak in pixels per pixel.
Used for rapid region matching in RejoiningFragmenter

Parameters:

nBins - number of bins to measure over.

Returns:

gradient.

isCross

public boolean isCross(int maxCrossLength)

Returns:

true if two or more whistles cross in this region

isMerge

public boolean isMerge(int maxCrossLength)

Returns:

true if two or more whistles merged into this Region

isSplit

public boolean isSplit(int maxCrossLength)

Returns:

true if this region splits into two or more parts

isRightMess

public boolean isRightMess()

Returns:

true if > 2 sounds joined this region at the start and > 2 left at the end, but they were not the same number of sounds.