ExternalFunction (LOCI Javadocs 0-SNAPSHOT API)

java.lang.Object
- loci.visbio.data.DataTransform
- - loci.visbio.data.ImageTransform
  - - loci.visbio.ext.ExternalFunction

All Implemented Interfaces:

Dynamic, Saveable

Direct Known Subclasses:

ExternalProgram, MatlabFunction
```
public abstract class ExternalFunction
extends ImageTransform
```
ExternalFunction is an abstract transform that calls some form of external function. Examples include system calls to an external program using stdin and stdout for binary data transfer, or calls to a MATLAB function.

Field Summary

Fields
Modifier and Type	Field and Description
`protected FunctionWidget`	`controls` Controls for this external function transform.
`protected String`	`function` The name of the external function to execute.
`protected int`	`numRange` Range component count for each image.
`protected FunctionParam[]`	`paramList` List of parameters and associated default values.
`protected String[]`	`params` Parameter values for passing to the function.
`protected int`	`resX` Width of each image.
`protected int`	`resY` Height of each image.

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
`ExternalFunction()` Creates an uninitialized external function transform.
`ExternalFunction(DataTransform parent, String name, String function)` Creates an external function transform from the given transform.

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`abstract FlatField`	`evaluate(FlatField input, String[] params)` Evaluates the function for the given input data and parameter values.
`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.
`String[]`	`getParameterDefaults()` Gets the default parameter values for this external function transform.
`String[]`	`getParameterNames()` Gets the name of each parameter for this external function transform.
`String[]`	`getParameters()` Gets the current parameter values for this external function transform.
`int`	`getRangeCount()` Gets number of range components at each pixel.
`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.
`boolean`	`isValidDimension(int dim)` Gets whether this transform provides data of the given dimensionality.
`boolean`	`matches(Dynamic dyn)` Tests whether two dynamic objects are equivalent.
`abstract FunctionParam[]`	`params()` Gets the input parameter names and corresponding default values.
`abstract int[]`	`predict(int width, int height, int num, String[] params)` Predicts the width, height and number of output planes, given the width, height and number of input planes, and parameter values.
`void`	`restoreState(Element el)` Restores the current state from the given DOM element ("ExternalFunction").
`void`	`saveState(Element el)` Writes the current state to the given DOM element ("DataTransforms").
`void`	`setParameters(String[] params)` Assigns the parameters for this external function transform.
`protected void`	`setParameters(String[] params, boolean notify)` Assigns the parameters for this external function transform.

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
  - function
```
protected String function
```
    The name of the external function to execute.
  - paramList
```
protected FunctionParam[] paramList
```
    List of parameters and associated default values.
  - params
```
protected String[] params
```
    Parameter values for passing to the function.
  - numRange
```
protected int numRange
```
    Range component count for each image.
  - resX
```
protected int resX
```
    Width of each image.
  - resY
```
protected int resY
```
    Height of each image.
  - controls
```
protected FunctionWidget controls
```
    Controls for this external function transform.
- Constructor Detail
  - ExternalFunction
```
public ExternalFunction()
```
    Creates an uninitialized external function transform.
  - ExternalFunction
```
public ExternalFunction(DataTransform parent,
                        String name,
                        String function)
```
    Creates an external function transform from the given transform.
- Method Detail
  - predict
```
public abstract int[] predict(int width,
                              int height,
                              int num,
                              String[] params)
```
    Predicts the width, height and number of output planes, given the width, height and number of input planes, and parameter values.
    
    Returns:
    
    An int[3] array representing output width, height and num values.
  - params
```
public abstract FunctionParam[] params()
```
    Gets the input parameter names and corresponding default values.
  - evaluate
```
public abstract FlatField evaluate(FlatField input,
                                   String[] params)
```
    Evaluates the function for the given input data and parameter values.
  - setParameters
```
public void setParameters(String[] params)
```
    Assigns the parameters for this external function transform.
  - setParameters
```
protected void setParameters(String[] params,
                             boolean notify)
```
    Assigns the parameters for this external function transform.
  - getParameterNames
```
public String[] getParameterNames()
```
    Gets the name of each parameter for this external function transform.
  - getParameterDefaults
```
public String[] getParameterDefaults()
```
    Gets the default parameter values for this external function transform.
  - getParameters
```
public String[] getParameters()
```
    Gets the current parameter values for this external function transform.
  - 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
  - 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 ("ExternalFunction").
    
    Specified by:
    
    restoreState in interface Saveable
    
    Overrides:
    
    restoreState in class ImageTransform
    
    Throws:
    
    SaveException

Class ExternalFunction

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

function

paramList

params

numRange

resX

resY

controls

Constructor Detail

ExternalFunction

ExternalFunction

Method Detail

predict

params

evaluate

setParameters

setParameters

getParameterNames

getParameterDefaults

getParameters

getImageWidth

getImageHeight

getRangeCount

getData

isValidDimension

getCacheId

getControls

matches

isCompatible

initState

saveState

restoreState