io.scif

Class AbstractPlane<T,P extends DataPlane<T>>

java.lang.Object

io.scif.AbstractPlane<T,P>

Type Parameters:

T - - The underlying data type used by this Plane

P - - A recursive reference to this concrete class

All Implemented Interfaces:

DataPlane<T>, Plane

Direct Known Subclasses:

BufferedImagePlane, ByteArrayPlane

public abstract class AbstractPlane<T,P extends DataPlane<T>>
extends Object
implements DataPlane<T>

Abstract superclass for Plane implementations in SCIFIO.

Author:

Mark Hiner

See Also:

Plane, DataPlane

Constructor Summary

Constructors

Constructor and Description
AbstractPlane()
AbstractPlane(ImageMetadata meta, net.imglib2.Interval bounds)

Method Summary

Modifier and Type	Method and Description
protected abstract T	blankPlane(net.imglib2.Interval bounds)
net.imglib2.Interval	getBounds()
net.imglib2.display.ColorTable	getColorTable() Gets this plane's ColorTable.
T	getData() Gets this plane's type-specific pixel data.
ImageMetadata	getImageMetadata() Gets the ImageMetadata associated with this plane.
P	populate(DataPlane<T> plane) Populate this plane by copying the provided plane.
P	populate(ImageMetadata meta, net.imglib2.Interval bounds) Populates this planes offsets, dimensions and Metadata.
P	populate(ImageMetadata meta, T data, net.imglib2.Interval bounds) As DataPlane.populate(Object, Interval), but also sets the ImageMetadata of the source from which this Plane was read.
P	populate(Plane p) Populates this plane by copying the fields of the provided plane
P	populate(T data, net.imglib2.Interval bounds) Populate this plane using the specified lengths and offsets, with the provided data representation of the pixels in that region.
void	setBounds(net.imglib2.Interval bounds) Sets this plane's bounds relative to the underlying image.
void	setColorTable(net.imglib2.display.ColorTable lut) Sets the ColorTable for this plane.
void	setData(T data) Sets the native pixel data for this plane.
void	setImageMetadata(ImageMetadata meta) Sets the ImageMetadata representation of the underlying image.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface io.scif.Plane

getBytes, getLengths, getMax, getMin

Constructor Detail

AbstractPlane

public AbstractPlane()

AbstractPlane

public AbstractPlane(ImageMetadata meta,
                     net.imglib2.Interval bounds)

Method Detail

setData

public void setData(T data)

Description copied from interface: DataPlane

Sets the native pixel data for this plane. If Plane.getColorTable() returns null, then this is the pixel data. Otherwise, this data should be used as an index into the associated ColorTable.

Specified by:

setData in interface DataPlane<T>

Parameters:

data - - an object matching the native data type of this plane.

getData

public T getData()

Description copied from interface: DataPlane

Gets this plane's type-specific pixel data.

Specified by:

getData in interface DataPlane<T>

Returns:

The native representation for this plane's data.

setColorTable

public void setColorTable(net.imglib2.display.ColorTable lut)

Description copied from interface: Plane

Sets the ColorTable for this plane. ColorTables are used for indexed color planes, where the underlying pixel data is an index into the associated color (lookup) table.

Specified by:

setColorTable in interface Plane

Parameters:

lut - - a ColorTable implementation.

getColorTable

public net.imglib2.display.ColorTable getColorTable()

Description copied from interface: Plane

Gets this plane's ColorTable.

Specified by:

getColorTable in interface Plane

Returns:

A reference to the ColorTable instance associated with this plane.

getImageMetadata

public ImageMetadata getImageMetadata()

Description copied from interface: Plane

Gets the ImageMetadata associated with this plane. The ImageMetadata returned by this method can then be used to answer questions about this plane.

Specified by:

getImageMetadata in interface Plane

Returns:

An ImageMetadata instance describing the image associated with this plane.

populate

public P populate(Plane p)

Description copied from interface: Plane

Populates this plane by copying the fields of the provided plane

Specified by:

populate in interface Plane

Parameters:

p - - A Plane to copy

Returns:

A reference to this Plane

populate

public P populate(DataPlane<T> plane)

Description copied from interface: DataPlane

Populate this plane by copying the provided plane.

Specified by:

populate in interface DataPlane<T>

Parameters:

plane - the plane to copy

Returns:

A reference to this plane

populate

public P populate(ImageMetadata meta,
                  net.imglib2.Interval bounds)

Description copied from interface: Plane

Populates this planes offsets, dimensions and Metadata.

Specified by:

populate in interface Plane

Parameters:

meta - - ImageMetadata to associate with this Plane

bounds - bounds of the planar axes.

Returns:

A reference to this Plane

populate

public P populate(T data,
                  net.imglib2.Interval bounds)

Description copied from interface: DataPlane

Populate this plane using the specified lengths and offsets, with the provided data representation of the pixels in that region.

Specified by:

populate in interface DataPlane<T>

Parameters:

data - Pixel information for the region of this plane.

bounds - bounds of the planar axes.

Returns:

A reference to this plane

populate

public P populate(ImageMetadata meta,
                  T data,
                  net.imglib2.Interval bounds)

Description copied from interface: DataPlane

As DataPlane.populate(Object, Interval), but also sets the ImageMetadata of the source from which this Plane was read.

Specified by:

populate in interface DataPlane<T>

Parameters:

meta - ImageMetadata of the source associated with this Plane

data - Pixel information for the region of this plane.

bounds - bounds of the planar axes.

Returns:

A reference to this plane

setImageMetadata

public void setImageMetadata(ImageMetadata meta)

Description copied from interface: Plane

Sets the ImageMetadata representation of the underlying image.

Specified by:

setImageMetadata in interface Plane

Parameters:

meta - - an initialized ImageMetadata instance.

getBounds

public net.imglib2.Interval getBounds()

Specified by:

getBounds in interface Plane

Returns:

The bounds of this plane relative to the origin image

setBounds

public void setBounds(net.imglib2.Interval bounds)

Description copied from interface: Plane

Sets this plane's bounds relative to the underlying image.

Specified by:

setBounds in interface Plane

blankPlane

protected abstract T blankPlane(net.imglib2.Interval bounds)

Returns:

an empty data conforming to the given planar bounds.