SpectralTransform (LOCI Javadocs 0-SNAPSHOT API)

java.lang.Object
- loci.visbio.data.DataTransform
- - loci.visbio.data.ImageTransform
  - - loci.visbio.data.SpectralTransform

All Implemented Interfaces:

TransformListener, Dynamic, Saveable
```
public class SpectralTransform
extends ImageTransform
implements TransformListener
```
SpectralTransform is a mapping of spectral bands onto an RGB or grayscale color space, as specified by the user with weighted sliders.

Field Summary

Fields
Modifier and Type	Field and Description
`protected SpectralWidget`	`controls` Controls for this spectral mapping.
`protected RealType[]`	`range` Output range components.
`protected double[][]`	`weights` Spectral channel weights.

Fields inherited from class loci.visbio.data.ImageTransform
MICRON, micronHeight, micronStep, micronWidth, xType, yType, zType

Fields inherited from class loci.visbio.data.DataTransform
dims, font, labels, lengths, listeners, MU, name, nextId, parent, thumbs, transformId

Constructor Summary

Constructors
Constructor and Description
`SpectralTransform()` Creates an uninitialized spectral mapping.
`SpectralTransform(DataTransform parent, String name, int numRange)` Creates a spectral mapping from the given transform.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static FlatField`	`doWeightedMapping(FlatField field, RealType[] types, double[][] weights)` Applies a spectral mapping to the given field based on the given weights and range types.
`String`	`getCacheId(int[] pos, boolean global)` Gets a string id uniquely describing this data transform at the given dimensional position, for the purposes of thumbnail caching.
`JComponent`	`getControls()` Gets associated GUI controls for this transform.
`Data`	`getData(TransformLink link, int[] pos, int dim, DataCache cache)` Retrieves the data corresponding to the given dimensional position, for the given display dimensionality.
`int`	`getImageHeight()` Gets height of each image.
`int`	`getImageWidth()` Gets width of each image.
`int`	`getRangeCount()` Gets number of range components at each pixel.
`double[][]`	`getWeights()` Gets spectral channel weights.
`void`	`initState(Dynamic dyn)` Modifies this object's state to match that of the given object.
`boolean`	`isCompatible(Dynamic dyn)` Tests whether the given dynamic object can be used as an argument to initState, for initializing this dynamic object.
`static boolean`	`isParentRequired()` Indicates whether this transform type requires a parent transform.
`boolean`	`isValidDimension(int dim)` Gets whether this transform provides data of the given dimensionality.
`static boolean`	`isValidParent(DataTransform data)` Indicates whether this transform type would accept the given transform as its parent transform.
`static DataTransform`	`makeTransform(DataManager dm)` Creates a new spectral mapping, with user interaction.
`boolean`	`matches(Dynamic dyn)` Tests whether two dynamic objects are equivalent.
`void`	`restoreState(Element el)` Restores the current state from the given DOM element ("SpectralMapping").
`void`	`saveState(Element el)` Writes the current state to the given DOM element ("DataTransforms").
`void`	`setParameters(double[][] weights)` Assigns the parameters for this spectral mapping.
`void`	`transformChanged(TransformEvent e)` Called when parent data transform's parameters are updated.

Methods inherited from class loci.visbio.data.ImageTransform
canDisplay3D, getHTMLDescription, getImage, getImageUnits, getMicronHeight, getMicronStep, getMicronStep, getMicronWidth, getRangeTypes, getSuggestedMaps, getType, getXType, getYType, getZType, getZUnit, isImmediate

Methods inherited from class loci.visbio.data.DataTransform
addTransformListener, canDisplay2D, discard, displayChanged, getDimTypes, getFont, getLabels, getLengths, getName, getParent, getThumbHandler, getTransformId, getUnitDescription, makeLabels, notifyListeners, removeTransformListener, setFont, toString

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

- Field Detail
  - range
```
protected RealType[] range
```
    Output range components.
  - weights
```
protected double[][] weights
```
    Spectral channel weights.
  - controls
```
protected SpectralWidget controls
```
    Controls for this spectral mapping.
- Constructor Detail
  - SpectralTransform
```
public SpectralTransform()
```
    Creates an uninitialized spectral mapping.
  - SpectralTransform
```
public SpectralTransform(DataTransform parent,
                         String name,
                         int numRange)
```
    Creates a spectral mapping from the given transform.
- Method Detail
  - setParameters
```
public void setParameters(double[][] weights)
```
    Assigns the parameters for this spectral mapping.
  - getWeights
```
public double[][] getWeights()
```
    Gets spectral channel weights.
  - getImageWidth
```
public int getImageWidth()
```
    Gets width of each image.
    
    Specified by:
    
    getImageWidth in class ImageTransform
  - getImageHeight
```
public int getImageHeight()
```
    Gets height of each image.
    
    Specified by:
    
    getImageHeight in class ImageTransform
  - getRangeCount
```
public int getRangeCount()
```
    Gets number of range components at each pixel.
    
    Specified by:
    
    getRangeCount in class ImageTransform
  - makeTransform
```
public static DataTransform makeTransform(DataManager dm)
```
    Creates a new spectral mapping, with user interaction.
  - isValidParent
```
public static boolean isValidParent(DataTransform data)
```
    Indicates whether this transform type would accept the given transform as its parent transform.
  - isParentRequired
```
public static boolean isParentRequired()
```
    Indicates whether this transform type requires a parent transform.
  - getData
```
public Data getData(TransformLink link,
                    int[] pos,
                    int dim,
                    DataCache cache)
```
    Retrieves the data corresponding to the given dimensional position, for the given display dimensionality.
    
    Overrides:
    
    getData in class ImageTransform
    
    Returns:
    
    null if the transform does not provide data of that dimensionality
  - isValidDimension
```
public boolean isValidDimension(int dim)
```
    Gets whether this transform provides data of the given dimensionality.
    
    Specified by:
    
    isValidDimension in class DataTransform
  - getCacheId
```
public String getCacheId(int[] pos,
                         boolean global)
```
    Gets a string id uniquely describing this data transform at the given dimensional position, for the purposes of thumbnail caching. If global flag is true, the id is suitable for use in the default, global cache file.
    
    Specified by:
    
    getCacheId in class DataTransform
  - getControls
```
public JComponent getControls()
```
    Gets associated GUI controls for this transform.
    
    Overrides:
    
    getControls in class DataTransform
  - matches
```
public boolean matches(Dynamic dyn)
```
    Tests whether two dynamic objects are equivalent.
    
    Specified by:
    
    matches in interface Dynamic
    
    Overrides:
    
    matches in class DataTransform
  - isCompatible
```
public boolean isCompatible(Dynamic dyn)
```
    Tests whether the given dynamic object can be used as an argument to initState, for initializing this dynamic object.
    
    Specified by:
    
    isCompatible in interface Dynamic
    
    Overrides:
    
    isCompatible in class DataTransform
  - initState
```
public void initState(Dynamic dyn)
```
    Modifies this object's state to match that of the given object. If the argument is null, the object is initialized according to its current state instead.
    
    Specified by:
    
    initState in interface Dynamic
    
    Overrides:
    
    initState in class DataTransform
  - saveState
```
public void saveState(Element el)
               throws SaveException
```
    Writes the current state to the given DOM element ("DataTransforms").
    
    Specified by:
    
    saveState in interface Saveable
    
    Overrides:
    
    saveState in class ImageTransform
    
    Throws:
    
    SaveException
  - restoreState
```
public void restoreState(Element el)
                  throws SaveException
```
    Restores the current state from the given DOM element ("SpectralMapping").
    
    Specified by:
    
    restoreState in interface Saveable
    
    Overrides:
    
    restoreState in class ImageTransform
    
    Throws:
    
    SaveException
  - transformChanged
```
public void transformChanged(TransformEvent e)
```
    Called when parent data transform's parameters are updated.
    
    Specified by:
    
    transformChanged in interface TransformListener
  - doWeightedMapping
```
public static FlatField doWeightedMapping(FlatField field,
                                          RealType[] types,
                                          double[][] weights)
```
    Applies a spectral mapping to the given field based on the given weights and range types.

Class SpectralTransform

Field Summary

Fields inherited from class loci.visbio.data.ImageTransform

Fields inherited from class loci.visbio.data.DataTransform

Constructor Summary

Method Summary

Methods inherited from class loci.visbio.data.ImageTransform

Methods inherited from class loci.visbio.data.DataTransform

Methods inherited from class java.lang.Object

Field Detail

range

weights

controls

Constructor Detail

SpectralTransform

SpectralTransform

Method Detail

setParameters

getWeights

getImageWidth

getImageHeight

getRangeCount

makeTransform

isValidParent

isParentRequired

getData

isValidDimension

getCacheId

getControls

matches

isCompatible

initState

saveState

restoreState

transformChanged

doWeightedMapping