ImageTransform (LOCI Javadocs 0-SNAPSHOT API)

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

All Implemented Interfaces:

Dynamic, Saveable

Direct Known Subclasses:

CollapseTransform, DataSampling, Dataset, ExternalFunction, ProjectionTransform, SpectralTransform
```
public abstract class ImageTransform
extends DataTransform
```
ImageTransform is a DataTransform superclass that provides image data.

Field Summary

Fields
Modifier and Type	Field and Description
`static ScaledUnit`	`MICRON` Micron unit.
`protected double`	`micronHeight` Physical image dimensions in microns.
`protected double`	`micronStep` Physical image dimensions in microns.
`protected double`	`micronWidth` Physical image dimensions in microns.
`protected RealType`	`xType` X-axis type.
`protected RealType`	`yType` Y-axis type.
`protected RealType`	`zType` Z-axis type.

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
`ImageTransform()` Constructs an uninitialized image transform.
`ImageTransform(DataTransform parent, String name)` Creates an image transform with the given transform as its parent.
`ImageTransform(DataTransform parent, String name, double width, double height, double step)` Creates an image transform with the given transform as its parent, that is dimensioned according to the specified values in microns.

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`canDisplay3D()` Gets whether this data object can be displayed in 3D.
`Data`	`getData(TransformLink link, int[] pos, int dim, DataCache cache)` Retrieves the data corresponding to the given dimensional position, for the given display dimensionality.
`String`	`getHTMLDescription()` Gets a description of this transform, with HTML markup.
`BufferedImage`	`getImage(int[] pos)` Obtains an image from the source(s) at the given dimensional position.
`abstract int`	`getImageHeight()` Gets the height in pixels of each image.
`Unit[]`	`getImageUnits()` Gets X and Y units for use with image domain sets, computed from micron information.
`abstract int`	`getImageWidth()` Gets the width in pixels of each image.
`double`	`getMicronHeight()` Gets physical image height in microns.
`double`	`getMicronStep()` Gets physical distance between image slices in microns.
`double`	`getMicronStep(int axis)` Gets physical distance between image slices in microns for the given axis.
`double`	`getMicronWidth()` Gets physical image width in microns.
`abstract int`	`getRangeCount()` Gets number of range components at each pixel.
`RealType[]`	`getRangeTypes()` Gets the RealTypes used for the range components.
`ScalarMap[]`	`getSuggestedMaps()` Retrieves a set of mappings for displaying this transform effectively.
`FunctionType`	`getType()` Gets MathType of images generated by this image transform.
`RealType`	`getXType()` Gets the RealType used for the X-axis.
`RealType`	`getYType()` Gets the RealType used for the Y-axis.
`RealType`	`getZType()` Gets the RealType used for the Z-axis.
`Unit`	`getZUnit(int axis)` Gets Z unit for use with image stack domain sets, computed from micron information.
`boolean`	`isImmediate()` Most image transforms are not rendered immediately.
`void`	`restoreState(Element el)` Restores the current state from the given DOM element (a child of "DataTransforms").
`void`	`saveState(Element el)` Writes the current state to the given DOM element (a child of "DataTransforms").

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

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

- Field Detail
  - MICRON
```
public static final ScaledUnit MICRON
```
    Micron unit.
  - micronWidth
```
protected double micronWidth
```
    Physical image dimensions in microns.
  - micronHeight
```
protected double micronHeight
```
    Physical image dimensions in microns.
  - micronStep
```
protected double micronStep
```
    Physical image dimensions in microns.
  - xType
```
protected RealType xType
```
    X-axis type.
  - yType
```
protected RealType yType
```
    Y-axis type.
  - zType
```
protected RealType zType
```
    Z-axis type.
- Constructor Detail
  - ImageTransform
```
public ImageTransform()
```
    Constructs an uninitialized image transform.
  - ImageTransform
```
public ImageTransform(DataTransform parent,
                      String name)
```
    Creates an image transform with the given transform as its parent.
  - ImageTransform
```
public ImageTransform(DataTransform parent,
                      String name,
                      double width,
                      double height,
                      double step)
```
    Creates an image transform with the given transform as its parent, that is dimensioned according to the specified values in microns.
- Method Detail
  - getImageWidth
```
public abstract int getImageWidth()
```
    Gets the width in pixels of each image.
  - getImageHeight
```
public abstract int getImageHeight()
```
    Gets the height in pixels of each image.
  - getRangeCount
```
public abstract int getRangeCount()
```
    Gets number of range components at each pixel.
  - getImage
```
public BufferedImage getImage(int[] pos)
```
    Obtains an image from the source(s) at the given dimensional position.
  - getMicronWidth
```
public double getMicronWidth()
```
    Gets physical image width in microns.
  - getMicronHeight
```
public double getMicronHeight()
```
    Gets physical image height in microns.
  - getMicronStep
```
public double getMicronStep()
```
    Gets physical distance between image slices in microns.
  - getMicronStep
```
public double getMicronStep(int axis)
```
    Gets physical distance between image slices in microns for the given axis. The default implementation simply returns the default step value. This method matters because derivative data objects such as DataSamplings could have a different distance between slices depending on the stack axis.
  - getXType
```
public RealType getXType()
```
    Gets the RealType used for the X-axis.
  - getYType
```
public RealType getYType()
```
    Gets the RealType used for the Y-axis.
  - getZType
```
public RealType getZType()
```
    Gets the RealType used for the Z-axis.
  - getRangeTypes
```
public RealType[] getRangeTypes()
```
    Gets the RealTypes used for the range components.
  - getType
```
public FunctionType getType()
```
    Gets MathType of images generated by this image transform.
  - getImageUnits
```
public Unit[] getImageUnits()
```
    Gets X and Y units for use with image domain sets, computed from micron information. Pixel range is assumed to be from 0 to width-1 (X) and 0 to height-1 (Y).
  - getZUnit
```
public Unit getZUnit(int axis)
```
    Gets Z unit for use with image stack domain sets, computed from micron information. Z range is assumed to be from 0 to numSlices-1.
  - 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.
    
    Specified by:
    
    getData in class DataTransform
    
    Returns:
    
    null if the transform does not provide data of that dimensionality
  - getSuggestedMaps
```
public ScalarMap[] getSuggestedMaps()
```
    Retrieves a set of mappings for displaying this transform effectively.
    
    Specified by:
    
    getSuggestedMaps in class DataTransform
  - isImmediate
```
public boolean isImmediate()
```
    Most image transforms are not rendered immediately.
    
    Specified by:
    
    isImmediate in class DataTransform
  - canDisplay3D
```
public boolean canDisplay3D()
```
    Gets whether this data object can be displayed in 3D.
    
    Overrides:
    
    canDisplay3D in class DataTransform
  - getHTMLDescription
```
public String getHTMLDescription()
```
    Gets a description of this transform, with HTML markup.
    
    Overrides:
    
    getHTMLDescription in class DataTransform
  - saveState
```
public void saveState(Element el)
               throws SaveException
```
    Writes the current state to the given DOM element (a child of "DataTransforms").
    
    Specified by:
    
    saveState in interface Saveable
    
    Overrides:
    
    saveState in class DataTransform
    
    Throws:
    
    SaveException
  - restoreState
```
public void restoreState(Element el)
                  throws SaveException
```
    Restores the current state from the given DOM element (a child of "DataTransforms").
    
    Specified by:
    
    restoreState in interface Saveable
    
    Overrides:
    
    restoreState in class DataTransform
    
    Throws:
    
    SaveException

Class ImageTransform

Field Summary

Fields inherited from class loci.visbio.data.DataTransform

Constructor Summary

Method Summary

Methods inherited from class loci.visbio.data.DataTransform

Methods inherited from class java.lang.Object

Field Detail

MICRON

micronWidth

micronHeight

micronStep

xType

yType

zType

Constructor Detail

ImageTransform

ImageTransform

ImageTransform

Method Detail

getImageWidth

getImageHeight

getRangeCount

getImage

getMicronWidth

getMicronHeight

getMicronStep

getMicronStep

getXType

getYType

getZType

getRangeTypes

getType

getImageUnits

getZUnit

getData

getSuggestedMaps

isImmediate

canDisplay3D

getHTMLDescription

saveState

restoreState