Dataset (LOCI Javadocs 0-SNAPSHOT API)

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

All Implemented Interfaces:

Dynamic, Saveable
```
public class Dataset
extends ImageTransform
```
A Dataset object encompasses a multidimensional biological image series. Such an object is typically between two and six dimensions as follows:
- 2D: a single image
- 3D: an image stack, or a time series of images
- 4D: a time series of image stacks, a multispectral image stack, or an image stack with lifetime data at each pixel
- 5D: an image stack with spectral lifetime data at each pixel
- 6D: a time series of image stacks with spectral lifetime data at each pixel
Other configurations are certainly possible, and Dataset provides an interface for multidimensional image data of any organization.

Dataset keeps no data in memory itself, leaving that management to the application, and just loads data as necessary to return whatever the application requests, according to the DataTransform API.

Field Summary

Fields
Modifier and Type	Field and Description
`protected RealType[]`	`color` Types mapped to color components (RGBA).
`protected DatasetWidget`	`controls` Controls for this dataset.
`protected loci.common.StatusListener`	`listener` Optional listener for constructor progress.
`protected String`	`pattern` A string pattern describing this dataset.
`protected BufferedImageReader`	`reader` Data reader.
`protected RealType[]`	`spatial` Types mapped to spatial components (X, Y).

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
`Dataset()` Constructs an uninitialized multidimensional data object.
`Dataset(String name, String pattern)` Constructs a multidimensional data object.
`Dataset(String name, String pattern, loci.common.StatusListener listener)` Constructs a new multidimensional data object from the given file pattern.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`close()` Close all open ids.
`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.
`String`	`getFileFormat()` Gets a description of the source files' file format.
`String[]`	`getFilenames()` Gets filenames of all files in dataset.
`String`	`getHTMLDescription()` Gets a description of this dataset, with HTML markup.
`BufferedImage`	`getImage(int[] pos)` Obtains an image from the source(s) at the given dimensional position.
`int`	`getImageHeight()` Gets height of each image.
`int`	`getImageWidth()` Gets width of each image.
`Hashtable`	`getMetadata()` Gets metadata associated with the dataset.
`String`	`getOMEXML()` Gets an OME-XML string for the dataset.
`ome.xml.model.OME`	`getOMEXMLRoot()` Gets an OME-XML root for the dataset.
`String`	`getPattern()` Gets the string pattern describing this dataset.
`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.
`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 dataset, with user interaction.
`static DataTransform`	`makeTransform(DataManager dm, File file, Component parent)` Creates a new dataset, with user interaction, with the given default file.
`boolean`	`matches(Dynamic dyn)` Tests whether two dynamic objects have matching states.
`void`	`restoreState(Element el)` Restores the current state from the given DOM element ("Dataset").
`void`	`saveState(Element el)` Writes the current state to the given DOM element ("DataTransforms").

Methods inherited from class loci.visbio.data.ImageTransform
canDisplay3D, getData, 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
  - pattern
```
protected String pattern
```
    A string pattern describing this dataset.
  - listener
```
protected loci.common.StatusListener listener
```
    Optional listener for constructor progress.
  - reader
```
protected BufferedImageReader reader
```
    Data reader.
  - controls
```
protected DatasetWidget controls
```
    Controls for this dataset.
  - spatial
```
protected RealType[] spatial
```
    Types mapped to spatial components (X, Y).
  - color
```
protected RealType[] color
```
    Types mapped to color components (RGBA).
- Constructor Detail
  - Dataset
```
public Dataset()
```
    Constructs an uninitialized multidimensional data object.
  - Dataset
```
public Dataset(String name,
               String pattern)
```
    Constructs a multidimensional data object. See the complete constructor for more information.
  - Dataset
```
public Dataset(String name,
               String pattern,
               loci.common.StatusListener listener)
```
    Constructs a new multidimensional data object from the given file pattern.
    
    Parameters:
    
    name - Label for the dataset.
    
    pattern - File pattern identifying the dataset.
    
    listener - Listener object to be informed of construction progress.
- Method Detail
  - close
```
public void close()
           throws FormatException,
                  IOException
```
    Close all open ids.
    
    Throws:
    
    FormatException
    
    IOException
  - getPattern
```
public String getPattern()
```
    Gets the string pattern describing this dataset.
  - getFilenames
```
public String[] getFilenames()
```
    Gets filenames of all files in dataset.
  - getFileFormat
```
public String getFileFormat()
```
    Gets a description of the source files' file format.
  - getMetadata
```
public Hashtable getMetadata()
```
    Gets metadata associated with the dataset.
  - getOMEXMLRoot
```
public ome.xml.model.OME getOMEXMLRoot()
```
    Gets an OME-XML root for the dataset.
  - getOMEXML
```
public String getOMEXML()
```
    Gets an OME-XML string for the dataset.
  - getImage
```
public BufferedImage getImage(int[] pos)
```
    Obtains an image from the source(s) at the given dimensional position.
    
    Overrides:
    
    getImage in class ImageTransform
  - 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 dataset, with user interaction.
  - makeTransform
```
public static DataTransform makeTransform(DataManager dm,
                                          File file,
                                          Component parent)
```
    Creates a new dataset, with user interaction, with the given default file.
  - 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.
  - 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
  - getHTMLDescription
```
public String getHTMLDescription()
```
    Gets a description of this dataset, with HTML markup.
    
    Overrides:
    
    getHTMLDescription in class ImageTransform
  - 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 have matching states.
    
    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.
    
    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 ("Dataset").
    
    Specified by:
    
    restoreState in interface Saveable
    
    Overrides:
    
    restoreState in class ImageTransform
    
    Throws:
    
    SaveException

Class Dataset

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

pattern

listener

reader

controls

spatial

color

Constructor Detail

Dataset

Dataset

Dataset

Method Detail

close

getPattern

getFilenames

getFileFormat

getMetadata

getOMEXMLRoot

getOMEXML

getImage

getImageWidth

getImageHeight

getRangeCount

makeTransform

makeTransform

isValidParent

isParentRequired

isValidDimension

getCacheId

getHTMLDescription

getControls

matches

isCompatible

initState

saveState

restoreState