Histogram2D (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- sc.fiji.coloc.algorithms.Algorithm<T>
- - sc.fiji.coloc.algorithms.Histogram2D<T>

Type Parameters:

T - The source images value type

Direct Known Subclasses:

LiHistogram2D
```
public class Histogram2D<T extends RealType<T>>
extends Algorithm<T>
```
Represents the creation of a 2D histogram between two images. Channel 1 is set out in x direction, while channel 2 in y direction.

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class Histogram2D.DrawingFlags

Nested Classes
Modifier and Type	Class and Description
`static class`	`Histogram2D.DrawingFlags`

Field Summary

Fields
Modifier and Type	Field and Description
`protected String`	`ch1Label`
`protected String`	`ch2Label`
`protected boolean`	`swapChannels`
`protected String`	`title`
`protected int`	`xBins`
`protected int`	`yBins`

Fields inherited from class sc.fiji.coloc.algorithms.Algorithm
name

Constructor Summary

Constructors
Constructor and Description
`Histogram2D()`
`Histogram2D(String title)`
`Histogram2D(String title, boolean swapChannels)`
`Histogram2D(String title, boolean swapChannels, EnumSet<Histogram2D.DrawingFlags> drawingSettings)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`execute(DataContainer<T> container)` Executes the previously initialized `Algorithm`.
`protected void`	`generateHistogramData(DataContainer<T> container)`
`String`	`getData()` A table of x-values, y-values and the counts is generated and returned as a string.
`EnumSet<Histogram2D.DrawingFlags>`	`getDrawingSettings()`
`protected RandomAccessibleInterval<T>`	`getImageCh1(DataContainer<T> container)` Gets the image of channel one.
`protected RandomAccessibleInterval<T>`	`getImageCh2(DataContainer<T> container)` Gets the image of channel two.
`protected String`	`getLabelCh1()` Gets the label of channel one.
`protected String`	`getLabelCh2()` Gets the label of channel two.
`protected double`	`getMaxCh1(DataContainer<T> container)` Gets the maximum of channel one.
`protected double`	`getMaxCh2(DataContainer<T> container)` Gets the maximum of channel two.
`protected double`	`getMinCh1(DataContainer<T> container)` Gets the minimum of channel one.
`protected double`	`getMinCh2(DataContainer<T> container)` Gets the minimum of channel two.
`RandomAccessibleInterval<LongType>`	`getPlotImage()`
`String`	`getTitle()`
`double`	`getXBinWidth()`
`protected double`	`getXBinWidth(DataContainer<T> container)` Calculates the bin width of one bin in x/ch1 direction.
`String`	`getXLabel()`
`double`	`getXMax()`
`protected double`	`getXMax(DataContainer<T> container)`
`double`	`getXMin()`
`protected double`	`getXMin(DataContainer<T> container)`
`protected int`	`getXValue(double ch1Val, double ch1BinWidth, double ch2Val, double ch2BinWidth)` Calculates the locations x value.
`double`	`getYBinWidth()`
`protected double`	`getYBinWidth(DataContainer<T> container)` Calculates the bin width of one bin in y/ch2 direction.
`String`	`getYLabel()`
`double`	`getYMax()`
`protected double`	`getYMax(DataContainer<T> container)`
`double`	`getYMin()`
`protected double`	`getYMin(DataContainer<T> container)`
`protected int`	`getYValue(double ch1Val, double ch1BinWidth, double ch2Val, double ch2BinWidth)` Calculates the locations y value.
`void`	`processResults(ResultHandler<T> handler)` A method to give the algorithm the opportunity to let its results being processed by the passed handler.

Methods inherited from class sc.fiji.coloc.algorithms.Algorithm
addWarning, getName, getWarnings

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

- Field Detail
  - xBins
```
protected int xBins
```
  - yBins
```
protected int yBins
```
  - title
```
protected String title
```
  - swapChannels
```
protected boolean swapChannels
```
  - ch1Label
```
protected String ch1Label
```
  - ch2Label
```
protected String ch2Label
```
- Constructor Detail
  - Histogram2D
```
public Histogram2D()
```
  - Histogram2D
```
public Histogram2D(String title)
```
  - Histogram2D
```
public Histogram2D(String title,
                   boolean swapChannels)
```
  - Histogram2D
```
public Histogram2D(String title,
                   boolean swapChannels,
                   EnumSet<Histogram2D.DrawingFlags> drawingSettings)
```
- Method Detail
  - getMinCh1
```
protected double getMinCh1(DataContainer<T> container)
```
    Gets the minimum of channel one. Takes channel swapping into consideration and will return min of channel two if swapped.
    
    Returns:
    
    The minimum of what is seen as channel one.
  - getMinCh2
```
protected double getMinCh2(DataContainer<T> container)
```
    Gets the minimum of channel two. Takes channel swapping into consideration and will return min of channel one if swapped.
    
    Returns:
    
    The minimum of what is seen as channel two.
  - getMaxCh1
```
protected double getMaxCh1(DataContainer<T> container)
```
    Gets the maximum of channel one. Takes channel swapping into consideration and will return max of channel two if swapped.
    
    Returns:
    
    The maximum of what is seen as channel one.
  - getMaxCh2
```
protected double getMaxCh2(DataContainer<T> container)
```
    Gets the maximum of channel two. Takes channel swapping into consideration and will return max of channel one if swapped.
    
    Returns:
    
    The maximum of what is seen as channel two.
  - getImageCh1
```
protected RandomAccessibleInterval<T> getImageCh1(DataContainer<T> container)
```
    Gets the image of channel one. Takes channel swapping into consideration and will return image of channel two if swapped.
    
    Returns:
    
    The image of what is seen as channel one.
  - getImageCh2
```
protected RandomAccessibleInterval<T> getImageCh2(DataContainer<T> container)
```
    Gets the image of channel two. Takes channel swapping into consideration and will return image of channel one if swapped.
    
    Returns:
    
    The image of what is seen as channel two.
  - getLabelCh1
```
protected String getLabelCh1()
```
    Gets the label of channel one. Takes channel swapping into consideration and will return label of channel two if swapped.
    
    Returns:
    
    The label of what is seen as channel one.
  - getLabelCh2
```
protected String getLabelCh2()
```
    Gets the label of channel two. Takes channel swapping into consideration and will return label of channel one if swapped.
    
    Returns:
    
    The label of what is seen as channel two.
  - execute
```
public void execute(DataContainer<T> container)
             throws MissingPreconditionException
```
    Description copied from class: Algorithm
    
    Executes the previously initialized Algorithm.
    
    Specified by:
    
    execute in class Algorithm<T extends RealType<T>>
    
    Throws:
    
    MissingPreconditionException
  - generateHistogramData
```
protected void generateHistogramData(DataContainer<T> container)
```
  - getData
```
public String getData()
```
    A table of x-values, y-values and the counts is generated and returned as a string. The single fields in one row (X Y Count) are separated by tabs.
    
    Returns:
    
    A String representation of the histogram data.
  - processResults
```
public void processResults(ResultHandler<T> handler)
```
    Description copied from class: Algorithm
    
    A method to give the algorithm the opportunity to let its results being processed by the passed handler. By default this methods passes the collected warnings to the handler and sub-classes should make use of this by adding custom behavior and call the super class.
    
    Overrides:
    
    processResults in class Algorithm<T extends RealType<T>>
    
    Parameters:
    
    handler - The ResultHandler to process the results.
  - getXBinWidth
```
protected double getXBinWidth(DataContainer<T> container)
```
    Calculates the bin width of one bin in x/ch1 direction.
    
    Parameters:
    
    container - The container with images to work on
    
    Returns:
    
    The width of one bin in x direction
  - getYBinWidth
```
protected double getYBinWidth(DataContainer<T> container)
```
    Calculates the bin width of one bin in y/ch2 direction.
    
    Parameters:
    
    container - The container with images to work on
    
    Returns:
    
    The width of one bin in y direction
  - getXValue
```
protected int getXValue(double ch1Val,
                        double ch1BinWidth,
                        double ch2Val,
                        double ch2BinWidth)
```
    Calculates the locations x value.
    
    Parameters:
    
    ch1Val - The intensity of channel one
    
    ch1BinWidth - The bin width for channel one
    
    Returns:
    
    The x value of the data point location
  - getYValue
```
protected int getYValue(double ch1Val,
                        double ch1BinWidth,
                        double ch2Val,
                        double ch2BinWidth)
```
    Calculates the locations y value.
    
    Parameters:
    
    ch2Val - The intensity of channel one
    
    ch2BinWidth - The bin width for channel one
    
    Returns:
    
    The x value of the data point location
  - getXMin
```
protected double getXMin(DataContainer<T> container)
```
  - getXMax
```
protected double getXMax(DataContainer<T> container)
```
  - getYMin
```
protected double getYMin(DataContainer<T> container)
```
  - getYMax
```
protected double getYMax(DataContainer<T> container)
```
  - getPlotImage
```
public RandomAccessibleInterval<LongType> getPlotImage()
```
  - getXBinWidth
```
public double getXBinWidth()
```
  - getYBinWidth
```
public double getYBinWidth()
```
  - getXLabel
```
public String getXLabel()
```
  - getYLabel
```
public String getYLabel()
```
  - getXMin
```
public double getXMin()
```
  - getXMax
```
public double getXMax()
```
  - getYMin
```
public double getYMin()
```
  - getYMax
```
public double getYMax()
```
  - getTitle
```
public String getTitle()
```
  - getDrawingSettings
```
public EnumSet<Histogram2D.DrawingFlags> getDrawingSettings()
```

Class Histogram2D<T extends RealType<T>>

Nested Class Summary

Field Summary

Fields inherited from class sc.fiji.coloc.algorithms.Algorithm

Constructor Summary

Method Summary

Methods inherited from class sc.fiji.coloc.algorithms.Algorithm

Methods inherited from class java.lang.Object

Field Detail

xBins

yBins

title

swapChannels

ch1Label

ch2Label

Constructor Detail

Histogram2D

Histogram2D

Histogram2D

Histogram2D

Method Detail

getMinCh1

getMinCh2

getMaxCh1

getMaxCh2

getImageCh1

getImageCh2

getLabelCh1

getLabelCh2

execute

generateHistogramData

getData

processResults

getXBinWidth

getYBinWidth

getXValue

getYValue

getXMin

getXMax

getYMin

getYMax

getPlotImage

getXBinWidth

getYBinWidth

getXLabel

getYLabel

getXMin

getXMax

getYMin

getYMax

getTitle

getDrawingSettings