com.bitplane.xt.img

Class ImarisCachedProbabilitiesImgFactory<T extends NativeType<T>>

java.lang.Object

net.imglib2.img.ImgFactory<T>

net.imglib2.img.NativeImgFactory<T>

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

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

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

At each pixel the image is assumed to represent a probability distribution over channels. For storing to Imaris IDataSetPrx backing cache, the first channel ("background") is removed (only the other channels are stored). If the dataset has UINT8 or UINT16 type, the [0, 1] range is scaled to the [0, 2^8-1] or [0, 2^16-1], respectively. For loading data back from the cache this operation is reversed.

Images can only be created with existing Imaris dataset. The number of channels in the Imaris dataset + 1 must be equal to the number of channels in the imglib dimensions. TODO: For now, tt is assumed that in the imglib dimensions, the last dimension represents the channel.

Author:

Tobias Pietzsch

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
ImarisCachedProbabilitiesImg<T,?>	create(Dimensions dimensions)
ImarisCachedProbabilitiesImg<T,?>	create(Imaris.IDataSetPrx dataset, long[] dimensions) Create writable image around existing Imaris dataset.
ImarisCachedProbabilitiesImg<T,?>	create(Imaris.IDataSetPrx dataset, long[] dimensions, CellLoader<T> loader) Create writable image around existing empty Imaris dataset.
ImarisCachedProbabilitiesImg<T,?>	create(Imaris.IDataSetPrx dataset, long[] dimensions, CellLoader<T> loader, ImarisCachedCellImgOptions additionalOptions)
ImarisCachedProbabilitiesImg<T,?>	create(Imaris.IDataSetPrx dataset, long[] dimensions, ImarisCachedCellImgOptions additionalOptions)
ImarisCachedProbabilitiesImg<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

ImarisCachedProbabilitiesImgFactory

public ImarisCachedProbabilitiesImgFactory(T type,
                                           ImarisApplication imaris)

Create a new ImarisCachedProbabilitiesImgFactory with default configuration.

ImarisCachedProbabilitiesImgFactory

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

Create a new ImarisCachedProbabilitiesImgFactory with the specified configuration.

Parameters:

optional - configuration options.

Method Detail

getApplication

public ImarisApplication getApplication()

create

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

Overrides:

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

create

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

Overrides:

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

create

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

create

public ImarisCachedProbabilitiesImg<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 ImarisCachedProbabilitiesImg<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>>