Waves (Basic API)

java.lang.Object
- java.util.AbstractCollection<E>
- - java.util.AbstractList<E>
  - - java.util.Vector
    - - ij.wave.Waves

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable, java.util.Collection, java.util.List, java.util.RandomAccess

Direct Known Subclasses:

Bursts
```
public class Waves
extends java.util.Vector
implements java.io.Serializable
```
See Also:

Serialized Form

Field Summary
- Fields inherited from class java.util.Vector
  capacityIncrement, elementCount, elementData
- Fields inherited from class java.util.AbstractList
  modCount

Constructor Summary

Constructors
Constructor and Description
`Waves()` The default constructor
`Waves(double[][] matrix)` This loads a matrix were the first array is the columns that represent each Wave and the rows represent the timepoints.
`Waves(ImagePlus imp, Roi[] rois)` A utility constructor to build a set of Waves from a time-series image and the Rois on it.
`Waves(ImagePlus imp, Rois rois)` A utility constructor to build a set of Waves from a time-series image and the Rois on it.
`Waves(java.lang.String filename)` A constructor that immediately calls the load function with filename passed as argument.
`Waves(Wave[] waves)` Constructs a Waves object from an array of Wave objects.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`__delitem__(int i)`
`int`	`__len__()`
`void`	`__setitem__(int i, Wave wave)`
`void`	`addWave(Wave wave)` Adds the Wave to the end of the collection.
`void`	`addWaves(Waves waves)` Adds each Wave from the Waves to the current collection in the order they appear in the argument's collection.
`boolean`	`areEpisodic()` Returns true if ALL the Waves in this instance are EpisodicWaves
`Wave`	`averageWaves()` Returns a Wave named 'WaveAvg' by averaging each of the Waves at each sampling point.
`Waves`	`clone()` Returns a deep-copy of this Waves' instance.
`void`	`convolve(Wave firWave)` Convolves each Wave in this instance with the Wave passed as argument.
`void`	`differentiate()` Differentiates each Wave in this instance.
`void`	`exponentialFit()` Scales each Wave in this instance with respect to its own pattern by an exponential fit.
`Waves`	`filterOut(Waves waves2)` This instance of Waves should be the list of candidates to eliminate if they appear in waves2.
`protected int`	`findNextWave(java.util.ArrayList corrTimes, java.util.ArrayList corrValues)`
`Wave`	`get(int index)` A convenience method for calling getWave.
`Wave[]`	`getArray()` Returns this collection of Waves as an array.
`Waves`	`getCleanZscoredWaves()` Replaces the current instances of Waves with the clean zscored waves.
`Waves`	`getClusteredWaves(ViewFrame viewFrame)` Returns the Waves associated with the front ClusterFramePlugIn's selected cluster.
`java.lang.String`	`getFormattedString(java.lang.String prefix, int decimalPlaces, boolean withTimes)` Returns the Waves as a String in a tabular layout where each column is a Wave's data contents.
`double`	`getMaxValue()` Gets the maximum value across all the Waves in this instance.
`double`	`getMinValue()` Gets the minimum value across all the Waves in this instance.
`java.lang.String[]`	`getNames()`
`Roi[]`	`getRois()` Returns an array of Rois associated with each of the Waves in this instance.
`static Waves`	`getRoiWaves(ImagePlus imp)` Creates a new set of Waves from the selected ROIs in the RoiManager and the ImagePlus passed as argument.
`static Waves`	`getRoiWaves(ImagePlus imp, Roi[] rois, boolean trackThrough)` Creates a new set of Waves from Roi passed as argument the ImagePlus passed as argument by forwardly traversing through the next related Rois.
`static Waves`	`getRoiWaves(ImagePlus imp, Rois rois, boolean trackThrough)`
`Waves`	`getScrambledWaves()`
`Waves`	`getTruncatedZscoredWaves()` Replaces the current instances of Waves with the truncated zscored waves.
`Wave`	`getWave(int index)` Returns the Wave at the given index in the collection.
`Wave`	`getWave(java.lang.String waveName)`
`Waves`	`getWaveRanges(double startTime_s, double endTime_s)` Returns a new Waves object where each Wave encompasses the range of startTime_s up to endTime_s of the original Wave.
`Waves`	`getWavesByName(java.io.File file)`
`Waves`	`getWavesWithLengthAtLeast(int length)`
`void`	`integrate()` Integrates each Wave in this instance.
`Waves`	`intersection(Waves waves2)` Returns only the waves that are in both this instance's Waves and waves2 where the return Waves are from this list.
`void`	`invert()`
`void`	`linearFit()` Scales each Wave in this instance with respect to its own pattern by a linear fit.
`void`	`load(java.lang.String filename)` Loads either .txt, .zip, or individual .wave files into the current collection.
`void`	`normalize()` Normalizes each Wave in this instance with respect to itself on the range [0,1].
`void`	`normalize(double lowerBound, double upperBound)` Normalizes each Wave in this instance with respect to itself on the range given by arguments.
`ChartPlugIn`	`plot2D()`
`ChartPlugIn`	`plot2D(boolean overlay)`
`ChartPlugIn`	`plot3D()`
`ChartPlugIn`	`plot3D(double lowerZBound, double upperZBound)`
`Wave`	`pop()` Removes the last Wave from this Waves instance and returns it.
`void`	`reverse()`
`void`	`save(java.lang.String filename)`
`void`	`shuffle()`
`Waves`	`sort()`
`Waves`	`sort(boolean byZeroLagCorrelation)` Crosscorrelates each Wave with the average of all the Waves and returns them sorted by the highest correlation value at the earliest lag time or at the zero lag if indicated by the argument.
`java.lang.String`	`toString()` Returns a line-separated String containing the list of all the Wave names in this instance.

Methods inherited from class java.util.Vector
add, add, addAll, addAll, addElement, capacity, clear, contains, containsAll, copyInto, elementAt, elements, ensureCapacity, equals, firstElement, forEach, hashCode, indexOf, indexOf, insertElementAt, isEmpty, iterator, lastElement, lastIndexOf, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, removeAllElements, removeElement, removeElementAt, removeIf, removeRange, replaceAll, retainAll, set, setElementAt, setSize, size, sort, spliterator, subList, toArray, toArray, trimToSize

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

Methods inherited from interface java.util.Collection
parallelStream, stream

- Constructor Detail
  - Waves
```
public Waves()
```
    The default constructor
  - Waves
```
public Waves(java.lang.String filename)
      throws java.io.IOException,
             java.lang.ClassNotFoundException
```
    A constructor that immediately calls the load function with filename passed as argument.
    
    Throws:
    
    java.io.IOException
    
    java.lang.ClassNotFoundException
  - Waves
```
public Waves(double[][] matrix)
```
    This loads a matrix were the first array is the columns that represent each Wave and the rows represent the timepoints. E.g., matrix.length should equal the number of Waves and matrix[0].length should be the length of the Waves. Also note that the first column is named '1'.
  - Waves
```
public Waves(Wave[] waves)
```
    Constructs a Waves object from an array of Wave objects. BEWARE: this is a shallow copy here.
  - Waves
```
public Waves(ImagePlus imp,
             Rois rois)
```
    A utility constructor to build a set of Waves from a time-series image and the Rois on it.
  - Waves
```
public Waves(ImagePlus imp,
             Roi[] rois)
```
    A utility constructor to build a set of Waves from a time-series image and the Rois on it.
- Method Detail
  - getArray
```
public Wave[] getArray()
```
    Returns this collection of Waves as an array.
  - getWaveRanges
```
public Waves getWaveRanges(double startTime_s,
                           double endTime_s)
```
    Returns a new Waves object where each Wave encompasses the range of startTime_s up to endTime_s of the original Wave.
  - pop
```
public Wave pop()
```
    Removes the last Wave from this Waves instance and returns it.
  - getFormattedString
```
public java.lang.String getFormattedString(java.lang.String prefix,
                                           int decimalPlaces,
                                           boolean withTimes)
```
    Returns the Waves as a String in a tabular layout where each column is a Wave's data contents.
  - areEpisodic
```
public boolean areEpisodic()
```
    Returns true if ALL the Waves in this instance are EpisodicWaves
  - save
```
public void save(java.lang.String filename)
```
  - load
```
public void load(java.lang.String filename)
          throws java.io.IOException,
                 java.lang.ClassNotFoundException
```
    Loads either .txt, .zip, or individual .wave files into the current collection. The .txt files should have the Wave name listed on the first line and the subsequent lines each sampling value. Each Wave is tab/space-limited. The sampling rate defaults to 10 Hz, so it should probably be set appropriately after calling this. The .wave files are simply serialized Java objects of the Wave class and should correctly contain all pertinent info to the Wave instance (like sampling rate, etc.).
    
    Throws:
    
    java.io.IOException
    
    java.lang.ClassNotFoundException
  - clone
```
public Waves clone()
```
    Returns a deep-copy of this Waves' instance.
    
    Overrides:
    
    clone in class java.util.Vector
  - getClusteredWaves
```
public Waves getClusteredWaves(ViewFrame viewFrame)
```
    Returns the Waves associated with the front ClusterFramePlugIn's selected cluster.
  - getRoiWaves
```
public static Waves getRoiWaves(ImagePlus imp)
```
    Creates a new set of Waves from the selected ROIs in the RoiManager and the ImagePlus passed as argument.
  - getWavesWithLengthAtLeast
```
public Waves getWavesWithLengthAtLeast(int length)
```
  - getRoiWaves
```
public static Waves getRoiWaves(ImagePlus imp,
                                Rois rois,
                                boolean trackThrough)
```
  - getRoiWaves
```
public static Waves getRoiWaves(ImagePlus imp,
                                Roi[] rois,
                                boolean trackThrough)
```
    Creates a new set of Waves from Roi passed as argument the ImagePlus passed as argument by forwardly traversing through the next related Rois.
  - normalize
```
public void normalize(double lowerBound,
                      double upperBound)
```
    Normalizes each Wave in this instance with respect to itself on the range given by arguments.
  - normalize
```
public void normalize()
```
    Normalizes each Wave in this instance with respect to itself on the range [0,1].
  - linearFit
```
public void linearFit()
```
    Scales each Wave in this instance with respect to its own pattern by a linear fit.
  - exponentialFit
```
public void exponentialFit()
```
    Scales each Wave in this instance with respect to its own pattern by an exponential fit.
  - differentiate
```
public void differentiate()
```
    Differentiates each Wave in this instance.
  - integrate
```
public void integrate()
```
    Integrates each Wave in this instance.
  - convolve
```
public void convolve(Wave firWave)
```
    Convolves each Wave in this instance with the Wave passed as argument.
  - getMinValue
```
public double getMinValue()
```
    Gets the minimum value across all the Waves in this instance.
  - getMaxValue
```
public double getMaxValue()
```
    Gets the maximum value across all the Waves in this instance.
  - getRois
```
public Roi[] getRois()
```
    Returns an array of Rois associated with each of the Waves in this instance.
  - get
```
public Wave get(int index)
```
    A convenience method for calling getWave.
    
    Specified by:
    
    get in interface java.util.List
    
    Overrides:
    
    get in class java.util.Vector
  - getWave
```
public Wave getWave(int index)
```
    Returns the Wave at the given index in the collection.
  - getWave
```
public Wave getWave(java.lang.String waveName)
```
  - getNames
```
public java.lang.String[] getNames()
```
  - addWave
```
public void addWave(Wave wave)
```
    Adds the Wave to the end of the collection.
  - addWaves
```
public void addWaves(Waves waves)
```
    Adds each Wave from the Waves to the current collection in the order they appear in the argument's collection.
  - averageWaves
```
public Wave averageWaves()
```
    Returns a Wave named 'WaveAvg' by averaging each of the Waves at each sampling point. So, the length of the return Wave will be the length of Waves in this instance.
  - __setitem__
```
public void __setitem__(int i,
                        Wave wave)
```
  - __delitem__
```
public void __delitem__(int i)
```
  - __len__
```
public int __len__()
```
  - findNextWave
```
protected int findNextWave(java.util.ArrayList corrTimes,
                           java.util.ArrayList corrValues)
```
  - reverse
```
public void reverse()
```
  - shuffle
```
public void shuffle()
```
  - sort
```
public Waves sort()
```
  - invert
```
public void invert()
```
  - getScrambledWaves
```
public Waves getScrambledWaves()
```
  - sort
```
public Waves sort(boolean byZeroLagCorrelation)
```
    Crosscorrelates each Wave with the average of all the Waves and returns them sorted by the highest correlation value at the earliest lag time or at the zero lag if indicated by the argument.
  - toString
```
public java.lang.String toString()
```
    Returns a line-separated String containing the list of all the Wave names in this instance.
    
    Overrides:
    
    toString in class java.util.Vector
  - getWavesByName
```
public Waves getWavesByName(java.io.File file)
```
  - getCleanZscoredWaves
```
public Waves getCleanZscoredWaves()
```
    Replaces the current instances of Waves with the clean zscored waves.
  - getTruncatedZscoredWaves
```
public Waves getTruncatedZscoredWaves()
```
    Replaces the current instances of Waves with the truncated zscored waves.
  - plot2D
```
public ChartPlugIn plot2D()
```
  - plot2D
```
public ChartPlugIn plot2D(boolean overlay)
```
  - plot3D
```
public ChartPlugIn plot3D()
```
  - plot3D
```
public ChartPlugIn plot3D(double lowerZBound,
                          double upperZBound)
```
  - intersection
```
public Waves intersection(Waves waves2)
```
    Returns only the waves that are in both this instance's Waves and waves2 where the return Waves are from this list.
  - filterOut
```
public Waves filterOut(Waves waves2)
```
    This instance of Waves should be the list of candidates to eliminate if they appear in waves2. In other words, the return waves should only include Waves from 'this' if they are NOT already in waves2.

Class Waves

Field Summary

Fields inherited from class java.util.Vector

Fields inherited from class java.util.AbstractList

Constructor Summary

Method Summary

Methods inherited from class java.util.Vector

Methods inherited from class java.lang.Object

Methods inherited from interface java.util.Collection

Constructor Detail

Waves

Waves

Waves

Waves

Waves

Waves

Method Detail

getArray

getWaveRanges

pop

getFormattedString

areEpisodic

save

load

clone

getClusteredWaves

getRoiWaves

getWavesWithLengthAtLeast

getRoiWaves

getRoiWaves

normalize

normalize

linearFit

exponentialFit

differentiate

integrate

convolve

getMinValue

getMaxValue

getRois

get

getWave

getWave

getNames

addWave

addWaves

averageWaves

__setitem__

__delitem__

__len__

findNextWave

reverse

shuffle

sort

invert

getScrambledWaves

sort

toString

getWavesByName

getCleanZscoredWaves

getTruncatedZscoredWaves

plot2D

plot2D

plot3D

plot3D

intersection

filterOut

setitem

delitem

len