com.bitplane.xt.img

Class ImarisCachedLabelImgFactory<T extends NativeType<T>>

java.lang.Object

net.imglib2.img.ImgFactory<T>

net.imglib2.img.NativeImgFactory<T>

com.bitplane.xt.img.ImarisCachedLabelImgFactory<T>

public class ImarisCachedLabelImgFactory<T extends NativeType<T>>
extends NativeImgFactory<T>

Factory for creating ImarisCachedLabelImgs. See ImarisCachedCellImgOptions for available configuration options and defaults.

Integer labels on the ImgLib2 side are translated into channels on the Imaris side. Therefore, because the channel dimension is used to decompose the labels (values), this factory can create at most 4D images.

Images can only be created with existing Imaris dataset.

Author:

Tobias Pietzsch

Constructor Summary

Constructors

Constructor and Description
ImarisCachedLabelImgFactory(T type, ImarisApplication imaris) Create a new ImarisCachedLabelImgFactory with default configuration.
ImarisCachedLabelImgFactory(T type, ImarisApplication imaris, ImarisCachedCellImgOptions optional) Create a new ImarisCachedLabelImgFactory with the specified configuration.

Method Summary

Modifier and Type	Method and Description
ImarisCachedLabelImg<T,?>	create(Dimensions dimensions)
ImarisCachedLabelImg<T,?>	create(Imaris.IDataSetPrx dataset, long[] dimensions) Create writable image around existing Imaris dataset.
ImarisCachedLabelImg<T,?>	create(Imaris.IDataSetPrx dataset, long[] dimensions, CellLoader<T> loader) Create writable image around existing empty Imaris dataset.
ImarisCachedLabelImg<T,?>	create(Imaris.IDataSetPrx dataset, long[] dimensions, CellLoader<T> loader, ImarisCachedCellImgOptions additionalOptions)
ImarisCachedLabelImg<T,?>	create(Imaris.IDataSetPrx dataset, long[] dimensions, ImarisCachedCellImgOptions additionalOptions)
ImarisCachedLabelImg<T,?>	create(long... dimensions)
NativeImg<T,?>	create(long[] dimension, T type) Deprecated.
ImarisApplication	getApplication()
<S> ImgFactory<S>	imgFactory(S type)

Methods inherited from class net.imglib2.img.NativeImgFactory

create

Methods inherited from class net.imglib2.img.ImgFactory

cache, create, create, create, create, create, imgFactory, type

Methods inherited from class java.lang.Object

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

Constructor Detail

ImarisCachedLabelImgFactory

public ImarisCachedLabelImgFactory(T type,
                                   ImarisApplication imaris)

Create a new ImarisCachedLabelImgFactory with default configuration.

ImarisCachedLabelImgFactory

public ImarisCachedLabelImgFactory(T type,
                                   ImarisApplication imaris,
                                   ImarisCachedCellImgOptions optional)

Create a new ImarisCachedLabelImgFactory with the specified configuration.

Parameters:

optional - configuration options.

Method Detail

getApplication

public ImarisApplication getApplication()

create

public ImarisCachedLabelImg<T,?> create(long... dimensions)

Overrides:

create in class NativeImgFactory<T extends NativeType<T>>

create

public ImarisCachedLabelImg<T,?> create(Dimensions dimensions)

Overrides:

create in class NativeImgFactory<T extends NativeType<T>>

create

public ImarisCachedLabelImg<T,?> create(Imaris.IDataSetPrx dataset,
                                        long[] dimensions,
                                        CellLoader<T> loader)

Create writable image around existing empty Imaris dataset.

dataset dimensions and dimensions must match. (But dimensions is allowed to strip dimensions with extent 1.)

It is assumed that dataset is empty and cells will be populated from the given loader. Existing data in dataset will thus be potentially overwritten!

create

public ImarisCachedLabelImg<T,?> create(Imaris.IDataSetPrx dataset,
                                        long[] dimensions,
                                        CellLoader<T> loader,
                                        ImarisCachedCellImgOptions additionalOptions)

create

public ImarisCachedLabelImg<T,?> create(Imaris.IDataSetPrx dataset,
                                        long[] dimensions)

Create writable image around existing Imaris dataset.

dataset dimensions and dimensions + 1 must match. (But dimensions is allowed to strip dimensions with extent 1.)

Note that this creates a writable image, and modifying the image will result in modifying the Imaris dataset! (eventually, when writing back modified data from the cache).

create

public ImarisCachedLabelImg<T,?> create(Imaris.IDataSetPrx dataset,
                                        long[] dimensions,
                                        ImarisCachedCellImgOptions additionalOptions)

See Also:

create(IDataSetPrx, long...)

imgFactory

public <S> ImgFactory<S> imgFactory(S type)
                             throws IncompatibleTypeException

Specified by:

imgFactory in class ImgFactory<T extends NativeType<T>>

Throws:

IncompatibleTypeException

create

@Deprecated
public NativeImg<T,?> create(long[] dimension,
                                         T type)

Deprecated.

Specified by:

create in class NativeImgFactory<T extends NativeType<T>>