Wave (Basic API)

java.lang.Object
- ij.wave.Wave

All Implemented Interfaces:

java.io.Serializable

Direct Known Subclasses:

Burst
```
public class Wave
extends java.lang.Object
implements java.io.Serializable
```
Represents an array of samples at a given sampling frequency.

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`BURST_TYPE`
`protected Comments`	`comments`
`protected ResizableDoubleArray`	`contents`
`static int`	`CROSSCORRELATION_TYPE`
`static int`	`ELECTROPHYS_TYPE`
`static int`	`EPISODIC_TYPE`
`static int`	`IMAGING_TYPE`
`protected java.util.Vector`	`listeners`
`protected static Max`	`max`
`protected static Mean`	`mean`
`protected static Median`	`median`
`protected static Min`	`min`
`protected Roi`	`roi`
`protected double`	`samplingRate_Hz`
`protected static StandardDeviation`	`stdev`
`protected int`	`type`
`protected java.lang.String`	`units`
`static int`	`UNKNOWN_TYPE`
`protected java.lang.String`	`waveName`
`protected int`	`xStartOffset`
`protected Wave`	`xwave`

Constructor Summary

Constructors
Constructor and Description

Wave()

Wave(double[] waveValues)

Wave(int initialCapacity)

Wave(java.lang.String filename)

Wave(Wave wave)

Constructors
Constructor and Description
`Wave()`
`Wave(double[] waveValues)`
`Wave(int initialCapacity)`
`Wave(java.lang.String filename)`
`Wave(Wave wave)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`Wave`	`__add__(java.lang.Double other)`
`Wave`	`__add__(Wave other)`
`void`	`__delitem__(int i)`
`Wave`	`__div__(java.lang.Double other)`
`java.lang.Double`	`__getitem__(double d)`
`java.lang.Double`	`__getitem__(int i)`
`int`	`__len__()`
`Wave`	`__mul__(java.lang.Double other)`
`void`	`__setitem__(int i, double value)`
`Wave`	`__sub__(java.lang.Double other)`
`Wave`	`__sub__(Wave other)`
`void`	`abs()`
`void`	`add(double value)` Adds each element within this Wave by the value passed as argument and fires a waveChanged event.
`void`	`addElement(double value)` Appends a value to the end of this array and fires a waveChanged event.
`void`	`addElement(double value, boolean fireWaveChanged)` Appends a value to this array with the option of firing a waveChanged event.
`void`	`addWave(Wave wave2)` Adds the contents of the Wave passed as argument, to this Wave instance index-by-index.
`void`	`addWaveListener(WaveListener listener)`
`void`	`append(Wave wave2)` Appends the contents of the Wave passed as argument to the end of this Wave instance.
`void`	`applyWindowFunction()`
`protected double`	`averageWindow(double[] values, int index, int length)`
`double`	`calculateArea()` Duplicates the Wave, integrates it, and returns the sum between the time values passed as argument.
`double`	`calculateArea(double startTime_s, double endTime_s)` Duplicates the Wave, integrates it, and returns the sum between the time values passed as argument.
`double`	`calculateResiduals(Wave modelWave)`
`void`	`centerAboutZero()` Centers the amplitudes of this Wave about zero and fires a waveChanged event.
`void`	`clear()` Removes all elements from this Wave.
`Wave`	`clone()`
`protected void`	`cloneMetadata(Wave wave2)`
`void`	`convolve(double[] fir)`
`void`	`convolve(Wave firWave)`
`protected void`	`createContentsBufferIfNecessary()`
`ij.measure.CurveFitter`	`curveFit(int fitType, boolean showOptions)`
`FitWave`	`curveFitExponential()`
`void`	`decimate(int decimateFactor)`
`void`	`differentiate()` Replaces the values at each index with the delta y compared to the previous index but does not scale based on the sampling rate.
`void`	`divide(double value)` Divides each element within this Wave by the value passed as argument and fires a waveChanged event.
`void`	`exponentialFit()` Applies an exponential fit to the contents of this Wave, subtracts it, and fires a waveChanged event.
`double`	`findNextTimeAbove(double startTime_s, double threshold)`
`double`	`findNextTimeBelow(double startTime_s, double threshold)`
`double`	`get(int i)`
`Bursts`	`getBursts(double absThreshold)` Identifies bursts based on an absolute threshold crossing algorithm.
`Bursts`	`getBursts(double absThreshold, boolean showBurstCycleIndices)` Identifies bursts based on an absolute threshold crossing algorithm.
`Bursts`	`getBursts(java.lang.String prefix, double absThreshold, double thresholdMax, double tailingOffset, double tailingOffsetMax, boolean showBurstCycleIndices)` Identifies bursts based on an absolute threshold crossing algorithm.
`Bursts`	`getBursts(java.lang.String prefix, java.util.Vector indiceVectors)`
`Bursts`	`getBurstsFromLocalMaxima(double minimumBurstDur_s, double ampThresholdFactor, Wave amplitudeWave)` Uses the median value of the amplitudeWave as the zero-reference amplitude and assumes 'this' wave is a central finite difference of the amplitude wave to find the relative peak amplitude constrained by the other parameters.
`Bursts`	`getBurstsFromLocalMinima(double minimumBurstDur_s, double ampThresholdFactor, Wave amplitudeWave)` Uses the median value of the amplitudeWave as the zero-reference amplitude and assumes 'this' wave is a central finite difference of the amplitude wave to find the relative trough amplitude constrained by the other parameters.
`Bursts`	`getBurstsFromPeakDetector(double smoothDegree_s, double minimumBurstDur_s, double ampThresholdFactor)`
`Wave`	`getCleanZscore()`
`Wave`	`getCleanZscore(double smooth_s)` This reduces low-frequency oscillations in the truncated zscore -- this can take a while.
`Wave`	`getCleanZscoredWave()`
`Wave`	`getCleanZscoredWave(double smooth_s)` This reduces low-frequency oscillations in the truncated zscore -- this can take a while.
`Comments`	`getComments()`
`double`	`getCorrelationTime()`
`double`	`getCorrelationValue()`
`Waves`	`getDifferenceWavesExcludingBursts(Bursts bursts)` Returns a list of Waves that are not represented by the Bursts passed as argument; this assumes the Bursts are arrayed in the order they appear in this wave.
`double`	`getEndTime()`
`protected Wave`	`getExponentialWave(double[] paramVals, double samplingRate_Hz, int length)`
`int`	`getIndex(double time_s)` Returns the index in the list of values for the time passed as argument.
`java.lang.String`	`getInfo()`
`double`	`getLength_s()` Returns the length of this Wave in seconds.
`int`	`getLength()` Returns the number of elements in this Wave.
`double`	`getMaxValue()`
`double`	`getMaxValue(double startTime, double endTime)`
`double`	`getMaxValue(int startIndex, int length)`
`double`	`getMaxValueTime()`
`double`	`getMaxValueTime(double startTime, double endTime)` Returns the time that the max value of the Wave is achieved (in seconds).
`double`	`getMaxValueTime(int startIndex, int endIndex)`
`double`	`getMeanValue()`
`double`	`getMeanValue(double startTime, double endTime)`
`double`	`getMedianValue()`
`double`	`getMedianValue(double startTime, double endTime)`
`double`	`getMinValue()`
`double`	`getMinValue(double startTime, double endTime)`
`double`	`getMinValue(int startIndex, int length)`
`double`	`getMinValueTime()`
`double`	`getMinValueTime(double startTime, double endTime)` Returns the time that the min value of the Wave is achieved (in seconds).
`double`	`getMinValueTime(int startIndex, int endIndex)`
`java.lang.String`	`getName()` Sets the name of this wave
`Roi`	`getRoi()` Returns an Roi associated with this Wave.
`static Wave`	`getRoiWave(ImagePlus imp, Roi roi)` Creates a new Wave from Roi passed as argument the ImagePlus passed as argument.
`static Wave`	`getRoiWave(ImagePlus imp, Roi[] rois)`
`double`	`getSamplingRateHz()` Returns the sampling rate of this wave in Hz
`Wave`	`getScrambledWave()` Returns the same Wave but with an new start location within the waveform depending on the value of a uniformly random number -- the new Wave wraps to maintain the same length as the original instance.
`Wave`	`getSpikeUnits()` Returns the spike units as a new wave -- this is defined as an absolute (value-median) > thresholdFactor*stdev where the stdevFactorAsThreshold defaults to 3.0.
`Wave`	`getSpikeUnits(double thresholdFactor)` Returns the spike units as a new wave -- this is defined as an absolute (value-median) > thresholdFactor*stdev.
`double`	`getStartTime()`
`double`	`getStdevValue()`
`double`	`getStdevValue(double startTime, double endTime)`
`Wave`	`getTemporalHistogram(double binSize_s)`
`Wave`	`getTruncatedZscoredWave()`
`Wave`	`getTruncatedZscoredWave(boolean clone)` This returns the wave from "getZscoredWave" truncated below 0.0 and clones the wave if specified by the argument, otherwise replaces the current Wave.
`int`	`getType()`
`java.lang.String`	`getTypeAsString()`
`java.lang.String`	`getUnits()`
`double`	`getValueAt(double time_s)` Returns the value of the wave at the specified time (in seconds).
`double[]`	`getValues()` Returns the values of this Wave.
`double[]`	`getValues(double startTime_s, double endTime_s)` Returns just the values of the current Wave between the times passed as argument.
`double[]`	`getValues(int subsampleReduction)` Returns a decimated array corresponding to the waveform and picks out the max/min values for the decimation.
`double[]`	`getValues(int startIndex, int endIndex)`
`Wave`	`getWaveForBurstAnalysisFromLocalMaxima(double smoothDegree_s)` Returns a new Wave that has a moving average filter applied to it and then a central finite difference applied.
`Wave`	`getWaveRange(double startTime_s, double endTime_s)` Returns a duplicate Wave from the startTime_s up to endTime_s.
`Wave`	`getWaveRange(int startIndex, int length)` Returns a duplicate Wave from the startIndex to the startIndex+length index.
`int`	`getXStartOffset()` An offset for the first element in the wave.
`double[]`	`getXValues()` Returns the time (i.e., 'x') values associated with this Wave.
`Wave`	`getXWave()`
`double[]`	`getYValues()` Returns the same values as the getValues function.
`Wave`	`getZscoredWave()`
`Wave`	`getZscoredWave(boolean clone)` Returns a clone copy of this wave but where each value in the series has the z-scored value (i.e., the mean of the Wave will be 0 and the stdev=1).
`void`	`integrate()` Converts the current Wave to an integrated Wave by approximating the Rectangle Method (http://en.wikipedia.org/wiki/Rectangle_method).
`void`	`invert()` Inverts the sign of the wave.
`boolean`	`isElectrophysType()`
`boolean`	`isImagingType()`
`boolean`	`isProxy()` Returns false unless a class extends WaveProxy.
`boolean`	`isUnknownType()`
`void`	`linearFit()` Applies a linear fit to the contents of this Wave, subtracts it, and fires a waveChanged event.
`void`	`load(java.lang.String filename)`
`void`	`loadFromText(java.lang.String filename, int iterateBy)`
`void`	`movingAverageFilter(double time_s)`
`void`	`movingAverageFilter2(double time_s)`
`void`	`multiply(double value)` Multiplies each element within this Wave by the value passed as argument and fires a waveChanged event.
`void`	`normalize()` Normalize the waveform to the range [-1, 1]
`void`	`normalize(double newMinValue, double newMaxValue)` according to this: http://en.wikipedia.org/wiki/Normalization_%28image_processing%29
`static Wave`	`open(java.lang.String filename)` Returns a new Wave instance loaded from the .wave binary file passed as input.
`ChartPlugIn`	`plot2D()`
`void`	`readObject(java.io.ObjectInputStream in)`
`static void`	`recalcExponentialWave(Wave expWave, double[] paramVals)`
`void`	`removeWaveListener(WaveListener listener)`
`void`	`save(java.lang.String filename)`
`void`	`saveAsText(java.lang.String filename)` Saves the waveform to the text file with a default of 3 decimal places.
`void`	`saveAsText(java.lang.String filename, int decimalPlaces)` Saves the waveform to the text file with the number of decimal places passed as argument.
`void`	`set(int i, double value)`
`void`	`setBlankValues(double blankValue, java.lang.String choice, double thresholdValue)`
`void`	`setComments(Comments newComments)`
`void`	`setCorrelationTime(double newTime)`
`void`	`setCorrelationValue(double newCorr)`
`void`	`setName(java.lang.String name)` Returns the name of this wave
`void`	`setRoi(Roi newRoi)` Sets an Roi associated with this Wave.
`void`	`setSamplingRateHz(double newSamplingRate_Hz)` Sets the sampling rate of this wave in Hz
`void`	`setType(int waveType)`
`void`	`setUnits(java.lang.String units)`
`void`	`setValues(double[] values)` Sets the contents of this Wave to the values passed as argument.
`void`	`setXStartOffset(int newValue)` An offset for the first element in the wave.
`void`	`setXStartOffsetTime(double newValue)` An offset for the first element in the wave.
`void`	`setXWave(Wave xwave)`
`Waves`	`split(double timeToSplit)` Splits the Wave instance into two Waves at the time passed as argument (in seconds).
`void`	`subtract(double value)` Subtracts each element within this Wave by the value passed as argument and fires a waveChanged event.
`void`	`subtractWave(Wave wave2)` Subtracts the contents of the Wave passed as argument, to this Wave instance index-by-index.
`double`	`sum(double startTime_s, double endTime_s)` Sums all the values within the Wave inclusively between the times passed as argument.
`void`	`waveChanged()`
`void`	`writeAudioFile(java.lang.String outputFilename)` Writes the amplitude-scaled waveform to a .wav audio file passed as argument.
`void`	`writeObject(java.io.ObjectOutputStream out)`

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

protected ResizableDoubleArray contents

max
```
protected static Max max
```

min
```
protected static Min min
```

mean
```
protected static Mean mean
```

median
```
protected static Median median
```

stdev

protected static StandardDeviation stdev

comments
```
protected Comments comments
```

units
```
protected java.lang.String units
```

waveName
```
protected java.lang.String waveName
```

samplingRate_Hz
```
protected double samplingRate_Hz
```

listeners
```
protected java.util.Vector listeners
```

xStartOffset
```
protected int xStartOffset
```

UNKNOWN_TYPE
```
public static final int UNKNOWN_TYPE
```
See Also:

Constant Field Values

IMAGING_TYPE
```
public static final int IMAGING_TYPE
```
See Also:

Constant Field Values

ELECTROPHYS_TYPE
```
public static final int ELECTROPHYS_TYPE
```
See Also:

Constant Field Values

EPISODIC_TYPE
```
public static final int EPISODIC_TYPE
```
See Also:

Constant Field Values

CROSSCORRELATION_TYPE
```
public static final int CROSSCORRELATION_TYPE
```
See Also:

Constant Field Values

BURST_TYPE
```
public static final int BURST_TYPE
```
See Also:

Constant Field Values

type
```
protected int type
```

roi
```
protected Roi roi
```

xwave
```
protected Wave xwave
```

Constructor Detail

Wave
```
public Wave()
```

Wave
```
public Wave(double[] waveValues)
```

Wave

public Wave(java.lang.String filename)
     throws java.io.IOException,
            java.lang.ClassNotFoundException

Throws:: java.io.IOException; java.lang.ClassNotFoundException

Wave
```
public Wave(Wave wave)
```

Wave
```
public Wave(int initialCapacity)
```

Method Detail

getComments
```
public Comments getComments()
```

setComments

public void setComments(Comments newComments)

getStartTime
```
public double getStartTime()
```

getEndTime
```
public double getEndTime()
```

getInfo
```
public java.lang.String getInfo()
```

open

public static Wave open(java.lang.String filename)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Returns a new Wave instance loaded from the .wave binary file passed as input.

Throws:: java.io.IOException; java.lang.ClassNotFoundException

load

public void load(java.lang.String filename)
          throws java.io.IOException,
                 java.lang.ClassNotFoundException

Throws:: java.io.IOException; java.lang.ClassNotFoundException

setName

public void setName(java.lang.String name)

Returns the name of this wave

getName
```
public java.lang.String getName()
```
Sets the name of this wave

setUnits

public void setUnits(java.lang.String units)

getUnits
```
public java.lang.String getUnits()
```

getSamplingRateHz
```
public double getSamplingRateHz()
```
Returns the sampling rate of this wave in Hz

setSamplingRateHz

public void setSamplingRateHz(double newSamplingRate_Hz)

Sets the sampling rate of this wave in Hz

setRoi
```
public void setRoi(Roi newRoi)
```
Sets an Roi associated with this Wave.

getRoi
```
public Roi getRoi()
```
Returns an Roi associated with this Wave.

findNextTimeAbove

public double findNextTimeAbove(double startTime_s,
                                double threshold)

findNextTimeBelow

public double findNextTimeBelow(double startTime_s,
                                double threshold)

decimate

public void decimate(int decimateFactor)

setBlankValues

public void setBlankValues(double blankValue,
                           java.lang.String choice,
                           double thresholdValue)

add
```
public void add(double value)
```
Adds each element within this Wave by the value passed as argument and fires a waveChanged event.

addWave
```
public void addWave(Wave wave2)
```
Adds the contents of the Wave passed as argument, to this Wave instance index-by-index.

subtractWave
```
public void subtractWave(Wave wave2)
```
Subtracts the contents of the Wave passed as argument, to this Wave instance index-by-index.

invert
```
public void invert()
```
Inverts the sign of the wave.

subtract
```
public void subtract(double value)
```
Subtracts each element within this Wave by the value passed as argument and fires a waveChanged event.

multiply
```
public void multiply(double value)
```
Multiplies each element within this Wave by the value passed as argument and fires a waveChanged event.

divide
```
public void divide(double value)
```
Divides each element within this Wave by the value passed as argument and fires a waveChanged event.

getMaxValue
```
public double getMaxValue()
```

getMaxValue

public double getMaxValue(double startTime,
                          double endTime)

getMaxValue

public double getMaxValue(int startIndex,
                          int length)

getMinValue
```
public double getMinValue()
```

getMinValue

public double getMinValue(double startTime,
                          double endTime)

getMinValue

public double getMinValue(int startIndex,
                          int length)

getMinValueTime
```
public double getMinValueTime()
```

getMinValueTime

public double getMinValueTime(double startTime,
                              double endTime)

Returns the time that the min value of the Wave is achieved (in seconds).

getMinValueTime

public double getMinValueTime(int startIndex,
                              int endIndex)

getMaxValueTime
```
public double getMaxValueTime()
```

getMaxValueTime

public double getMaxValueTime(double startTime,
                              double endTime)

Returns the time that the max value of the Wave is achieved (in seconds).

getMaxValueTime

public double getMaxValueTime(int startIndex,
                              int endIndex)

getTemporalHistogram

public Wave getTemporalHistogram(double binSize_s)

getSpikeUnits
```
public Wave getSpikeUnits()
```
Returns the spike units as a new wave -- this is defined as an absolute (value-median) > thresholdFactor*stdev where the stdevFactorAsThreshold defaults to 3.0.

getSpikeUnits
```
public Wave getSpikeUnits(double thresholdFactor)
```
Returns the spike units as a new wave -- this is defined as an absolute (value-median) > thresholdFactor*stdev.

getScrambledWave
```
public Wave getScrambledWave()
```
Returns the same Wave but with an new start location within the waveform depending on the value of a uniformly random number -- the new Wave wraps to maintain the same length as the original instance.

getMeanValue

public double getMeanValue(double startTime,
                           double endTime)

getMeanValue
```
public double getMeanValue()
```

getMedianValue

public double getMedianValue(double startTime,
                             double endTime)

getMedianValue
```
public double getMedianValue()
```

getStdevValue

public double getStdevValue(double startTime,
                            double endTime)

getStdevValue
```
public double getStdevValue()
```

normalize
```
public void normalize()
```
Normalize the waveform to the range [-1, 1]

normalize
```
public void normalize(double newMinValue,
                      double newMaxValue)
```
according to this: http://en.wikipedia.org/wiki/Normalization_%28image_processing%29

getValueAt
```
public double getValueAt(double time_s)
```
Returns the value of the wave at the specified time (in seconds).

setXWave
```
public void setXWave(Wave xwave)
```

getXWave
```
public Wave getXWave()
```

getXValues
```
public double[] getXValues()
```
Returns the time (i.e., 'x') values associated with this Wave.

getYValues
```
public double[] getYValues()
```
Returns the same values as the getValues function.

getValues
```
public double[] getValues()
```
Returns the values of this Wave.

getLength
```
public int getLength()
```
Returns the number of elements in this Wave.

getLength_s
```
public double getLength_s()
```
Returns the length of this Wave in seconds.

setValues
```
public void setValues(double[] values)
```
Sets the contents of this Wave to the values passed as argument.

centerAboutZero
```
public void centerAboutZero()
```
Centers the amplitudes of this Wave about zero and fires a waveChanged event.

applyWindowFunction
```
public void applyWindowFunction()
```

getExponentialWave

protected Wave getExponentialWave(double[] paramVals,
                                  double samplingRate_Hz,
                                  int length)

recalcExponentialWave

public static void recalcExponentialWave(Wave expWave,
                                         double[] paramVals)

curveFit

public ij.measure.CurveFitter curveFit(int fitType,
                                       boolean showOptions)

curveFitExponential
```
public FitWave curveFitExponential()
```

calculateResiduals

public double calculateResiduals(Wave modelWave)

exponentialFit
```
public void exponentialFit()
```
Applies an exponential fit to the contents of this Wave, subtracts it, and fires a waveChanged event.

linearFit
```
public void linearFit()
```
Applies a linear fit to the contents of this Wave, subtracts it, and fires a waveChanged event.

getValues
```
public double[] getValues(int subsampleReduction)
```
Returns a decimated array corresponding to the waveform and picks out the max/min values for the decimation.

setCorrelationTime

public void setCorrelationTime(double newTime)

getCorrelationTime
```
public double getCorrelationTime()
```

setCorrelationValue

public void setCorrelationValue(double newCorr)

getCorrelationValue
```
public double getCorrelationValue()
```

getBursts
```
public Bursts getBursts(double absThreshold)
```
Identifies bursts based on an absolute threshold crossing algorithm.

getBursts

public Bursts getBursts(double absThreshold,
                        boolean showBurstCycleIndices)

Identifies bursts based on an absolute threshold crossing algorithm.

getBursts

public Bursts getBursts(java.lang.String prefix,
                        double absThreshold,
                        double thresholdMax,
                        double tailingOffset,
                        double tailingOffsetMax,
                        boolean showBurstCycleIndices)

Identifies bursts based on an absolute threshold crossing algorithm.

getWaveForBurstAnalysisFromLocalMaxima
```
public Wave getWaveForBurstAnalysisFromLocalMaxima(double smoothDegree_s)
```
Returns a new Wave that has a moving average filter applied to it and then a central finite difference applied.

getBurstsFromPeakDetector

public Bursts getBurstsFromPeakDetector(double smoothDegree_s,
                                        double minimumBurstDur_s,
                                        double ampThresholdFactor)

getBurstsFromLocalMaxima
```
public Bursts getBurstsFromLocalMaxima(double minimumBurstDur_s,
                                       double ampThresholdFactor,
                                       Wave amplitudeWave)
```
Uses the median value of the amplitudeWave as the zero-reference amplitude and assumes 'this' wave is a central finite difference of the amplitude wave to find the relative peak amplitude constrained by the other parameters.

getBurstsFromLocalMinima
```
public Bursts getBurstsFromLocalMinima(double minimumBurstDur_s,
                                       double ampThresholdFactor,
                                       Wave amplitudeWave)
```
Uses the median value of the amplitudeWave as the zero-reference amplitude and assumes 'this' wave is a central finite difference of the amplitude wave to find the relative trough amplitude constrained by the other parameters.

getDifferenceWavesExcludingBursts
```
public Waves getDifferenceWavesExcludingBursts(Bursts bursts)
```
Returns a list of Waves that are not represented by the Bursts passed as argument; this assumes the Bursts are arrayed in the order they appear in this wave.

getBursts

public Bursts getBursts(java.lang.String prefix,
                        java.util.Vector indiceVectors)

writeAudioFile
```
public void writeAudioFile(java.lang.String outputFilename)
                    throws java.io.IOException
```
Writes the amplitude-scaled waveform to a .wav audio file passed as argument.

Throws:

java.io.IOException

save

public void save(java.lang.String filename)
          throws java.io.IOException

Throws:: java.io.IOException

saveAsText
```
public void saveAsText(java.lang.String filename)
                throws java.io.IOException
```
Saves the waveform to the text file with a default of 3 decimal places.

Throws:

java.io.IOException

saveAsText

public void saveAsText(java.lang.String filename,
                       int decimalPlaces)
                throws java.io.IOException

Saves the waveform to the text file with the number of decimal places passed as argument.

Throws:: java.io.IOException

setType
```
public void setType(int waveType)
```

getType
```
public int getType()
```

getTypeAsString

public java.lang.String getTypeAsString()

isImagingType
```
public boolean isImagingType()
```

isElectrophysType
```
public boolean isElectrophysType()
```

isUnknownType
```
public boolean isUnknownType()
```

getRoiWave

public static Wave getRoiWave(ImagePlus imp,
                              Roi[] rois)

getRoiWave

public static Wave getRoiWave(ImagePlus imp,
                              Roi roi)

Creates a new Wave from Roi passed as argument the ImagePlus passed as argument.

createContentsBufferIfNecessary

protected void createContentsBufferIfNecessary()

clear
```
public void clear()
```
Removes all elements from this Wave.

addElement
```
public void addElement(double value)
```
Appends a value to the end of this array and fires a waveChanged event.

addElement

public void addElement(double value,
                       boolean fireWaveChanged)

Appends a value to this array with the option of firing a waveChanged event.

setXStartOffset
```
public void setXStartOffset(int newValue)
```
An offset for the first element in the wave. This is useful for displaying correlograms correctly for example.

setXStartOffsetTime
```
public void setXStartOffsetTime(double newValue)
```
An offset for the first element in the wave. This is useful for displaying correlograms correctly for example.

getXStartOffset
```
public int getXStartOffset()
```
An offset for the first element in the wave. This is useful for displaying correlograms correctly for example.

loadFromText

public void loadFromText(java.lang.String filename,
                         int iterateBy)
                  throws java.io.IOException

Throws:: java.io.IOException

add

public Wave __add__(java.lang.Double other)

__add__
```
public Wave __add__(Wave other)
```

sub

public Wave __sub__(java.lang.Double other)

__sub__
```
public Wave __sub__(Wave other)
```

mul

public Wave __mul__(java.lang.Double other)

div

public Wave __div__(java.lang.Double other)

get
```
public double get(int i)
```

getitem

public java.lang.Double __getitem__(int i)

getitem

public java.lang.Double __getitem__(double d)

setitem

public void __setitem__(int i,
                        double value)

set

public void set(int i,
                double value)

__delitem__
```
public void __delitem__(int i)
```

__len__
```
public int __len__()
```

differentiate
```
public void differentiate()
```
Replaces the values at each index with the delta y compared to the previous index but does not scale based on the sampling rate.

calculateArea
```
public double calculateArea(double startTime_s,
                            double endTime_s)
```
Duplicates the Wave, integrates it, and returns the sum between the time values passed as argument.

calculateArea
```
public double calculateArea()
```
Duplicates the Wave, integrates it, and returns the sum between the time values passed as argument.

sum
```
public double sum(double startTime_s,
                  double endTime_s)
```
Sums all the values within the Wave inclusively between the times passed as argument.

getIndex
```
public int getIndex(double time_s)
```
Returns the index in the list of values for the time passed as argument.

getValues

public double[] getValues(int startIndex,
                          int endIndex)

getValues

public double[] getValues(double startTime_s,
                          double endTime_s)

Returns just the values of the current Wave between the times passed as argument.

integrate
```
public void integrate()
```
Converts the current Wave to an integrated Wave by approximating the Rectangle Method (http://en.wikipedia.org/wiki/Rectangle_method). This simply multiplies the Wave values at each time point by the inverse of the sampling rate.

averageWindow

protected double averageWindow(double[] values,
                               int index,
                               int length)

getCleanZscoredWave
```
public Wave getCleanZscoredWave()
```

getCleanZscore
```
public Wave getCleanZscore()
```

getCleanZscoredWave
```
public Wave getCleanZscoredWave(double smooth_s)
```
This reduces low-frequency oscillations in the truncated zscore -- this can take a while.

getCleanZscore
```
public Wave getCleanZscore(double smooth_s)
```
This reduces low-frequency oscillations in the truncated zscore -- this can take a while.

movingAverageFilter2

public void movingAverageFilter2(double time_s)

movingAverageFilter

public void movingAverageFilter(double time_s)

convolve
```
public void convolve(Wave firWave)
```

convolve
```
public void convolve(double[] fir)
```

abs
```
public void abs()
```

clone
```
public Wave clone()
```
Overrides:

clone in class java.lang.Object

waveChanged
```
public void waveChanged()
```

addWaveListener

public void addWaveListener(WaveListener listener)

removeWaveListener

public void removeWaveListener(WaveListener listener)

writeObject

public void writeObject(java.io.ObjectOutputStream out)
                 throws java.io.IOException

Throws:: java.io.IOException

readObject

public void readObject(java.io.ObjectInputStream in)
                throws java.io.IOException,
                       java.lang.ClassNotFoundException

Throws:: java.io.IOException; java.lang.ClassNotFoundException

isProxy
```
public boolean isProxy()
```
Returns false unless a class extends WaveProxy.

append
```
public void append(Wave wave2)
```
Appends the contents of the Wave passed as argument to the end of this Wave instance.

cloneMetadata

protected void cloneMetadata(Wave wave2)

getZscoredWave
```
public Wave getZscoredWave(boolean clone)
```
Returns a clone copy of this wave but where each value in the series has the z-scored value (i.e., the mean of the Wave will be 0 and the stdev=1).

getZscoredWave
```
public Wave getZscoredWave()
```

getTruncatedZscoredWave
```
public Wave getTruncatedZscoredWave(boolean clone)
```
This returns the wave from "getZscoredWave" truncated below 0.0 and clones the wave if specified by the argument, otherwise replaces the current Wave.

getTruncatedZscoredWave
```
public Wave getTruncatedZscoredWave()
```

getWaveRange
```
public Wave getWaveRange(int startIndex,
                         int length)
```
Returns a duplicate Wave from the startIndex to the startIndex+length index.

getWaveRange

public Wave getWaveRange(double startTime_s,
                         double endTime_s)

Returns a duplicate Wave from the startTime_s up to endTime_s.

split
```
public Waves split(double timeToSplit)
```
Splits the Wave instance into two Waves at the time passed as argument (in seconds).

plot2D
```
public ChartPlugIn plot2D()
```

Class Wave

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

contents

max

min

mean

median

stdev

comments

units

waveName

samplingRate_Hz

listeners

xStartOffset

UNKNOWN_TYPE

IMAGING_TYPE

ELECTROPHYS_TYPE

EPISODIC_TYPE

CROSSCORRELATION_TYPE

BURST_TYPE

type

roi

xwave

Constructor Detail

Wave

Wave

Wave

Wave

Wave

Method Detail

getComments

setComments

getStartTime

getEndTime

getInfo

open

load

setName

getName

setUnits

getUnits

getSamplingRateHz

setSamplingRateHz

setRoi

getRoi

findNextTimeAbove

findNextTimeBelow

decimate

setBlankValues

add

addWave

subtractWave

invert

subtract

multiply

divide

getMaxValue

getMaxValue

getMaxValue

getMinValue

getMinValue

getMinValue

getMinValueTime

getMinValueTime

getMinValueTime

getMaxValueTime

getMaxValueTime

getMaxValueTime

getTemporalHistogram

getSpikeUnits

getSpikeUnits

getScrambledWave

getMeanValue

getMeanValue

getMedianValue

getMedianValue

add

add

sub

sub

mul

div

getitem

getitem

setitem

delitem

len