A C D E F G H I M N O P R S T U V

A

accessFlags() - Method in class com.bitplane.xt.img.ImarisCachedCellImgOptions.Values

append(ImarisCachedCellImgOptions) - Method in class com.bitplane.xt.img.ImarisCachedCellImgOptions

asDataset() - Method in class com.bitplane.xt.ImarisDataset

Get a IJ2 net.imagej.Dataset wrapping the full resolution image (see ImarisDataset.asImg(), ImarisDataset.asImgPlus()).

asImg() - Method in class com.bitplane.xt.ImarisDataset

Get the full resolution image.

asImgPlus() - Method in class com.bitplane.xt.ImarisDataset

Get an ImgPlus wrapping the full resolution image (see ImarisDataset.asImg()).

AxisOrderUtils - Class in com.bitplane.xt.util

Get AxisOrder corresponding to CalibratedSpace.

C

cacheType(CacheOptions.CacheType) - Method in class com.bitplane.xt.ImarisDatasetOptions

Which in-memory cache type to use.

cellDimensions(int...) - Method in class com.bitplane.xt.ImarisDatasetOptions

Override the dimensions of a cell.

cellDimensions() - Method in class com.bitplane.xt.ImarisDatasetOptions.Values

cellDimensions() - Method in class com.bitplane.xt.img.ImarisCachedCellImgOptions.Values

CellGridUtils - Class in com.bitplane.xt.util

Create appropriate CellGrid for wrapping IDataSetPrx into CachedCellImg.

ColorTableUtils - Class in com.bitplane.xt.util

Convert Imaris color tables to imglib2.

com.bitplane.xt - package com.bitplane.xt

com.bitplane.xt.img - package com.bitplane.xt.img

com.bitplane.xt.options - package com.bitplane.xt.options

com.bitplane.xt.util - package com.bitplane.xt.util

computeCellDimensions(IDataSetPrx, int[], int[]) - Static method in class com.bitplane.xt.util.CellGridUtils

Compute the cell dimensions from block size of dataset, optionally overridden by user-defined optionalCellDimensions.

copyOrThis() - Method in class com.bitplane.xt.ImarisDatasetOptions

copyOrThis() - Method in class com.bitplane.xt.img.ImarisCachedCellImgOptions

create(long...) - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

create(Dimensions) - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

create(int[]) - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

create(long[], ImarisCachedCellImgOptions) - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

create(Dimensions, ImarisCachedCellImgOptions) - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

create(long[], CellLoader<T>) - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

create(Dimensions, CellLoader<T>) - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

create(long[], CellLoader<T>, ImarisCachedCellImgOptions) - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

create(Dimensions, CellLoader<T>, ImarisCachedCellImgOptions) - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

create(IDataSetPrx, long[], CellLoader<T>) - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

Create writable image around existing empty Imaris dataset.

create(IDataSetPrx, Dimensions, CellLoader<T>) - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

create(IDataSetPrx, long[], CellLoader<T>, ImarisCachedCellImgOptions) - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

create(IDataSetPrx, Dimensions, CellLoader<T>, ImarisCachedCellImgOptions) - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

create(IDataSetPrx, long...) - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

Create writable image around existing Imaris dataset.

create(IDataSetPrx, Dimensions) - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

create(IDataSetPrx, long[], ImarisCachedCellImgOptions) - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

create(IDataSetPrx, Dimensions, ImarisCachedCellImgOptions) - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

create(long[], T) - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

Deprecated.

create(long...) - Method in class com.bitplane.xt.img.ImarisCachedLabelImgFactory

create(Dimensions) - Method in class com.bitplane.xt.img.ImarisCachedLabelImgFactory

create(IDataSetPrx, long[], CellLoader<T>) - Method in class com.bitplane.xt.img.ImarisCachedLabelImgFactory

Create writable image around existing empty Imaris dataset.

create(IDataSetPrx, long[], CellLoader<T>, ImarisCachedCellImgOptions) - Method in class com.bitplane.xt.img.ImarisCachedLabelImgFactory

create(IDataSetPrx, long[]) - Method in class com.bitplane.xt.img.ImarisCachedLabelImgFactory

Create writable image around existing Imaris dataset.

create(IDataSetPrx, long[], ImarisCachedCellImgOptions) - Method in class com.bitplane.xt.img.ImarisCachedLabelImgFactory

create(long[], T) - Method in class com.bitplane.xt.img.ImarisCachedLabelImgFactory

Deprecated.

create(long...) - Method in class com.bitplane.xt.img.ImarisCachedProbabilitiesImgFactory

create(Dimensions) - Method in class com.bitplane.xt.img.ImarisCachedProbabilitiesImgFactory

create(IDataSetPrx, long[], CellLoader<T>) - Method in class com.bitplane.xt.img.ImarisCachedProbabilitiesImgFactory

Create writable image around existing empty Imaris dataset.

create(IDataSetPrx, long[], CellLoader<T>, ImarisCachedCellImgOptions) - Method in class com.bitplane.xt.img.ImarisCachedProbabilitiesImgFactory

create(IDataSetPrx, long[]) - Method in class com.bitplane.xt.img.ImarisCachedProbabilitiesImgFactory

Create writable image around existing Imaris dataset.

create(IDataSetPrx, long[], ImarisCachedCellImgOptions) - Method in class com.bitplane.xt.img.ImarisCachedProbabilitiesImgFactory

create(long[], T) - Method in class com.bitplane.xt.img.ImarisCachedProbabilitiesImgFactory

Deprecated.

createCellGrid(long[], int[], Fraction) - Static method in class com.bitplane.xt.util.CellGridUtils

Creates a CellGrid with the given dimensions and cellDimensions.

createChannelColorTable(IDataSetPrx, int) - Static method in class com.bitplane.xt.util.ColorTableUtils

Create an imglib2 ColorTable8 for the given channel of dataset.

createChannelConverterToARGB(T, IDataSetPrx, int) - Static method in class com.bitplane.xt.util.ColorTableUtils

Construct a converters for the specified channel with display range and color set up according to Imaris.

createDataset(T, int, int, int, int, int, ImarisDatasetOptions) - Method in class com.bitplane.xt.DefaultImarisApplication

createDataset(T, DatasetDimensions, ImarisDatasetOptions) - Method in class com.bitplane.xt.DefaultImarisApplication

createDataset(T, int, int, int, int, int, ImarisDatasetOptions) - Method in interface com.bitplane.xt.ImarisApplication

Create a new ImarisDataset of the specified type with the specified dimensions.

createDataset(T, int, int, int, int, int) - Method in interface com.bitplane.xt.ImarisApplication

Calls ImarisApplication.createDataset(NativeType, int, int, int, int, int, ImarisDatasetOptions) with default options.

createDataset(T, DatasetDimensions, ImarisDatasetOptions) - Method in interface com.bitplane.xt.ImarisApplication

TODO

createDataset(T, DatasetDimensions) - Method in interface com.bitplane.xt.ImarisApplication

TODO

createDataset(IApplicationPrx, tType, DatasetDimensions) - Static method in class com.bitplane.xt.util.ImarisUtils

Create an Imaris dataset.

createDataset(IApplicationPrx, tType, int...) - Static method in class com.bitplane.xt.util.ImarisUtils

Create an Imaris dataset.

createMapDimensions(int[], long[]) - Static method in class com.bitplane.xt.util.MapDimensions

Tries to derive a mapDimensions array matching the specified Imaris and imglib2 dimension arrays.

createWithCacheLoader(long[], CacheLoader<Long, Cell<A>>) - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

createWithCacheLoader(Dimensions, CacheLoader<Long, Cell<A>>) - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

createWithCacheLoader(long[], CacheLoader<Long, Cell<A>>, ImarisCachedCellImgOptions) - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

createWithCacheLoader(Dimensions, CacheLoader<Long, Cell<A>>, ImarisCachedCellImgOptions) - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

D

DatasetCalibration - Class in com.bitplane.xt

Calibration (voxel size and unit) and min coordinate for an ImarisDataset.

DatasetCalibration(String, double, double, double, double, double, double) - Constructor for class com.bitplane.xt.DatasetCalibration

DatasetDimensions - Class in com.bitplane.xt

Dimensions of an ImarisDataset.

DatasetDimensions(int, int, int, int, int) - Constructor for class com.bitplane.xt.DatasetDimensions

Create DatasetDimensions.

DatasetDimensions(IDataSetPrx, ImarisAxesOptions.Axis...) - Constructor for class com.bitplane.xt.DatasetDimensions

Create DatasetDimensions from the given Imaris IDataSetPrx.

DefaultImarisApplication - Class in com.bitplane.xt

Default implementation of ImarisApplication, which wraps IApplicationPrx and represents one particular Imaris instance.

DefaultImarisApplication(IApplicationPrx, int) - Constructor for class com.bitplane.xt.DefaultImarisApplication

DefaultImarisService - Class in com.bitplane.xt

Default implementation of ImarisService for connecting to the Imaris XT API, and providing access to the running Imaris instance(s).

DefaultImarisService() - Constructor for class com.bitplane.xt.DefaultImarisService

dimC() - Method in class com.bitplane.xt.DatasetDimensions

Get the index of the channel dimension in the ImgLib2 representation.

dimT() - Method in class com.bitplane.xt.DatasetDimensions

Get the index of the time dimension in the ImgLib2 representation.

dimX() - Method in class com.bitplane.xt.DatasetDimensions

Get the index of the X dimension in the ImgLib2 representation.

dimY() - Method in class com.bitplane.xt.DatasetDimensions

Get the index of the Y dimension in the ImgLib2 representation.

dimZ() - Method in class com.bitplane.xt.DatasetDimensions

Get the index of the Z dimension in the ImgLib2 representation.

dirtyAccesses(boolean) - Method in class com.bitplane.xt.img.ImarisCachedCellImgOptions

Specify whether the image should use Dirty accesses.

dirtyAccesses() - Method in class com.bitplane.xt.img.ImarisCachedCellImgOptions.Values

disconnect() - Method in class com.bitplane.xt.DefaultImarisService

disconnect() - Method in interface com.bitplane.xt.ImarisService

Disconnect from the ICE server.

E

extract(Cell<A>) - Method in class com.bitplane.xt.img.ImarisLabelCache

extract(Cell<A>) - Method in class com.bitplane.xt.img.ImarisProbabilitiesCache

extract(Cell<A>) - Method in class com.bitplane.xt.util.ImarisLoader

F

factory() - Method in class com.bitplane.xt.img.ImarisCachedCellImg

factory() - Method in class com.bitplane.xt.img.ImarisCachedLabelImg

factory() - Method in class com.bitplane.xt.img.ImarisCachedProbabilitiesImg

forDataSet(IDataSetPrx) - Static method in interface com.bitplane.xt.util.GetDataSubVolume

Get the appropriate GetDataSubVolume for the given dataset.

forDataSet(IDataSetPrx, tType) - Static method in interface com.bitplane.xt.util.GetDataSubVolume

Get the appropriate GetDataSubVolume for the given dataset.

forDataSet(IDataSetPrx) - Static method in interface com.bitplane.xt.util.SetDataSubVolume

Get the appropriate SetDataSubVolume for the given dataset.

forDataSet(IDataSetPrx, tType) - Static method in interface com.bitplane.xt.util.SetDataSubVolume

Get the appropriate GetDataSubVolume for the given dataset.

forEach(BiConsumer<String, Object>) - Method in class com.bitplane.xt.ImarisDatasetOptions.Values

forEach(BiConsumer<String, Object>) - Method in class com.bitplane.xt.img.ImarisCachedCellImgOptions.Values

forEach(BiConsumer<String, Object>) - Method in interface com.bitplane.xt.options.ImarisAxesOptions.Val

forEach(BiConsumer<String, Object>) - Method in interface com.bitplane.xt.options.ImarisCacheOptions.Val

forEach(BiConsumer<String, Object>) - Method in interface com.bitplane.xt.options.ReadOnlyOptions.Val

fromAxisOrder(AxisOrder) - Static method in class com.bitplane.xt.util.MapDimensions

G

get(Long) - Method in class com.bitplane.xt.img.ImarisLabelCache

get(Long) - Method in class com.bitplane.xt.img.ImarisProbabilitiesCache

get(int, int, int, int, int, int, int, int, int) - Method in interface com.bitplane.xt.util.GetDataSubVolume

Get sub-volume as flattened primitive array.

get(Long) - Method in class com.bitplane.xt.util.ImarisLoader

get(Long) - Method in class com.bitplane.xt.util.ImarisLoaderRemover

get(int, long[], int[]) - Method in interface com.bitplane.xt.util.PixelSource

Get sub-volume as flattened array.

getApplication() - Method in class com.bitplane.xt.DefaultImarisService

getApplication() - Method in interface com.bitplane.xt.ImarisService

Get the first running Imaris instance, or null if there are no running instances.

getApplication() - Method in class com.bitplane.xt.img.ImarisCachedCellImg

getApplication() - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

getApplication() - Method in class com.bitplane.xt.img.ImarisCachedLabelImg

getApplication() - Method in class com.bitplane.xt.img.ImarisCachedLabelImgFactory

getApplication() - Method in class com.bitplane.xt.img.ImarisCachedProbabilitiesImg

getApplication() - Method in class com.bitplane.xt.img.ImarisCachedProbabilitiesImgFactory

getApplication() - Method in interface com.bitplane.xt.img.ImarisImg

Get the ImarisApplication which holds (the backing cache for) this image.

getApplicationByID(int) - Method in class com.bitplane.xt.DefaultImarisService

getApplicationByID(int) - Method in interface com.bitplane.xt.ImarisService

Get the running Imaris instance with the specified ICE object ID.

getApplicationID() - Method in class com.bitplane.xt.DefaultImarisApplication

getApplicationID() - Method in interface com.bitplane.xt.ImarisApplication

Get the object ID of the underlying IApplication ICE proxy.

getApplications() - Method in class com.bitplane.xt.DefaultImarisService

getApplications() - Method in interface com.bitplane.xt.ImarisService

Get list of all running Imaris instances.

getAxisOrder() - Method in class com.bitplane.xt.DatasetDimensions

Returns the AxisOrder of the ImgLib2 representation.

getAxisOrder(CalibratedSpace<?>) - Static method in class com.bitplane.xt.util.AxisOrderUtils

Get the AxisOrder corresponding to space.

getCacheControl() - Method in class com.bitplane.xt.ImarisDataset

Get the SharedQueue used for asynchronous loading of blocks from Imaris.

getCalibration() - Method in class com.bitplane.xt.ImarisDataset

Get the physical calibration: unit, voxel size, and min in XYZ.

getChannelColor(int) - Method in class com.bitplane.xt.ImarisDataset

Get the base color of a channel.

getChannelColor(IDataSetPrx, int) - Static method in class com.bitplane.xt.util.ColorTableUtils

Get the base color of the given channel of dataset as an imglib2 ARGBType.

getDataset() - Method in interface com.bitplane.xt.ImarisApplication

Get the first Imaris image as an ImarisDataset.

getDataset(ImarisDatasetOptions) - Method in interface com.bitplane.xt.ImarisApplication

Get the first Imaris image as an ImarisDataset.

getDatasetDimensions() - Method in class com.bitplane.xt.ImarisDataset

Get the size of the underlying 5D Imaris dataset and the mapping to dimensions of the ImgLib2 representation.

GetDataSubVolume - Interface in com.bitplane.xt.util

Common generic interface for IDataSetPrx.GetPyramidDataBytes(int, int, int, int, int, int, int, int, int), IDataSetPrx.GetPyramidDataShorts(int, int, int, int, int, int, int, int, int), IDataSetPrx.GetPyramidDataFloats(int, int, int, int, int, int, int, int, int).

getFilename() - Method in class com.bitplane.xt.ImarisDataset

Get the "Image > Filename" parameter of the dataset.

getIApplicationPrx() - Method in class com.bitplane.xt.DefaultImarisApplication

getIApplicationPrx() - Method in interface com.bitplane.xt.ImarisApplication

Get the underlying IApplication ICE proxy.

getIDataSetPrx() - Method in class com.bitplane.xt.ImarisDataset

Get the underlying IDataSet ICE proxy.

getIDataSetPrx() - Method in class com.bitplane.xt.img.ImarisCachedCellImg

getIDataSetPrx() - Method in class com.bitplane.xt.img.ImarisCachedLabelImg

getIDataSetPrx() - Method in class com.bitplane.xt.img.ImarisCachedProbabilitiesImg

getIDataSetPrx() - Method in interface com.bitplane.xt.img.ImarisImg

Get the underlying IDataSet ICE proxy.

getImage(int, ImarisDatasetOptions) - Method in class com.bitplane.xt.DefaultImarisApplication

getImage(int, ImarisDatasetOptions) - Method in interface com.bitplane.xt.ImarisApplication

Get the Imaris image at imageIndex as an ImarisDataset.

getImage(int) - Method in interface com.bitplane.xt.ImarisApplication

Get the Imaris image at imageIndex as an ImarisDataset.

getImarisDimensions() - Method in class com.bitplane.xt.DatasetDimensions

Returns the 5D dimensions of the dataset on the imaris side.

getMapDimensions() - Method in class com.bitplane.xt.DatasetDimensions

Get the mapping between dimension indices in the Imaris and in the ImgLib2 representation.

getName() - Method in class com.bitplane.xt.ImarisDataset

Get the "Image > Name" parameter of the dataset.

getNumberOfImages() - Method in class com.bitplane.xt.DefaultImarisApplication

getNumberOfImages() - Method in interface com.bitplane.xt.ImarisApplication

Get the number of images loaded in the application.

getSources() - Method in class com.bitplane.xt.ImarisDataset

Get a list of BigDataViewer sources, one for each channel of the dataset.

getType() - Method in class com.bitplane.xt.ImarisDataset

Get an instance of the pixel type.

getVoxelDimensions(CalibratedSpace<?>) - Static method in class com.bitplane.xt.util.AxisOrderUtils

Get XYZ calibration of space as VoxelDimensions.

grid - Variable in class com.bitplane.xt.util.ImarisLoader

H

hasC() - Method in class com.bitplane.xt.DatasetDimensions

Returns true if the ImgLib2 representation has a channel dimension.

hasT() - Method in class com.bitplane.xt.DatasetDimensions

Returns true if the ImgLib2 representation has a time dimension.

hasZ() - Method in class com.bitplane.xt.DatasetDimensions

Returns true if the ImgLib2 representation has a Z dimension.

I

ImarisApplication - Interface in com.bitplane.xt

ImarisApplication wraps IApplicationPrx and represents one particular Imaris instance.

ImarisAxesOptions<T> - Interface in com.bitplane.xt.options

Option to specify which axes should be included (at least) when mapping an Imaris dataset to a ImgLib2 image.

ImarisAxesOptions.Axis - Enum in com.bitplane.xt.options

ImarisAxesOptions.Val - Interface in com.bitplane.xt.options

ImarisCachedCellImg<T extends NativeType<T>,A> - Class in com.bitplane.xt.img

A LazyCellImg that creates empty Cells lazily when they are accessed and sends (modified) Cells to Imaris when memory runs full.

ImarisCachedCellImg(ImarisCachedCellImgFactory<T>, IDataSetPrx, CellGrid, Fraction, Cache<Long, Cell<A>>, IoSync<?, ?, ?>, A) - Constructor for class com.bitplane.xt.img.ImarisCachedCellImg

ImarisCachedCellImgFactory<T extends NativeType<T>> - Class in com.bitplane.xt.img

Factory for creating ImarisCachedCellImgs.

ImarisCachedCellImgFactory(T, ImarisApplication) - Constructor for class com.bitplane.xt.img.ImarisCachedCellImgFactory

Create a new ImarisCachedCellImgFactory with default configuration.

ImarisCachedCellImgFactory(T, ImarisApplication, ImarisCachedCellImgOptions) - Constructor for class com.bitplane.xt.img.ImarisCachedCellImgFactory

Create a new ImarisCachedCellImgFactory with the specified configuration.

ImarisCachedCellImgOptions - Class in com.bitplane.xt.img

Optional parameters for constructing a ImarisCachedCellImgFactory.

ImarisCachedCellImgOptions() - Constructor for class com.bitplane.xt.img.ImarisCachedCellImgOptions

ImarisCachedCellImgOptions.Values - Class in com.bitplane.xt.img

ImarisCachedLabelImg<T extends NativeType<T>,A> - Class in com.bitplane.xt.img

A LazyCellImg that creates empty Cells lazily when they are accessed and sends (modified) Cells to Imaris when memory runs full.

ImarisCachedLabelImg(ImarisCachedLabelImgFactory<T>, IDataSetPrx, CellGrid, Fraction, Cache<Long, Cell<A>>, IoSync<?, ?, ?>, A) - Constructor for class com.bitplane.xt.img.ImarisCachedLabelImg

ImarisCachedLabelImgFactory<T extends NativeType<T>> - Class in com.bitplane.xt.img

Factory for creating ImarisCachedLabelImgs.

ImarisCachedLabelImgFactory(T, ImarisApplication) - Constructor for class com.bitplane.xt.img.ImarisCachedLabelImgFactory

Create a new ImarisCachedLabelImgFactory with default configuration.

ImarisCachedLabelImgFactory(T, ImarisApplication, ImarisCachedCellImgOptions) - Constructor for class com.bitplane.xt.img.ImarisCachedLabelImgFactory

Create a new ImarisCachedLabelImgFactory with the specified configuration.

ImarisCachedProbabilitiesImg<T extends NativeType<T>,A> - Class in com.bitplane.xt.img

A LazyCellImg that creates empty Cells lazily when they are accessed and sends (modified) Cells to Imaris when memory runs full.

ImarisCachedProbabilitiesImg(ImarisCachedProbabilitiesImgFactory<T>, IDataSetPrx, CellGrid, Fraction, Cache<Long, Cell<A>>, IoSync<?, ?, ?>, A) - Constructor for class com.bitplane.xt.img.ImarisCachedProbabilitiesImg

ImarisCachedProbabilitiesImgFactory<T extends NativeType<T>> - Class in com.bitplane.xt.img

Factory for creating ImarisCachedProbabilitiesImgs.

ImarisCachedProbabilitiesImgFactory(T, ImarisApplication) - Constructor for class com.bitplane.xt.img.ImarisCachedProbabilitiesImgFactory

Create a new ImarisCachedProbabilitiesImgFactory with default configuration.

ImarisCachedProbabilitiesImgFactory(T, ImarisApplication, ImarisCachedCellImgOptions) - Constructor for class com.bitplane.xt.img.ImarisCachedProbabilitiesImgFactory

Create a new ImarisCachedProbabilitiesImgFactory with the specified configuration.

ImarisCacheOptions<T> - Interface in com.bitplane.xt.options

Optional arguments that specify the cache behaviour of ImarisCachedCellImg or ImarisDataset.

ImarisCacheOptions.Val - Interface in com.bitplane.xt.options

ImarisDataset<T extends NativeType<T> & RealType<T>> - Class in com.bitplane.xt

ImarisDataset wraps an Imaris IDataSetPrx into a lazy-loaded ImgLib2 CachedCellImg.

ImarisDataset(Context, IDataSetPrx) - Constructor for class com.bitplane.xt.ImarisDataset

Wrap an existing IDataSetPrx.

ImarisDataset(Context, IDataSetPrx, ImarisDatasetOptions) - Constructor for class com.bitplane.xt.ImarisDataset

Wrap an existing IDataSetPrx.

ImarisDatasetOptions - Class in com.bitplane.xt

Optional parameters for creating ImarisDataset.

ImarisDatasetOptions() - Constructor for class com.bitplane.xt.ImarisDatasetOptions

ImarisDatasetOptions.Values - Class in com.bitplane.xt

ImarisDirtyLabelCache<A extends Dirty> - Class in com.bitplane.xt.img

Variant of ImarisLabelCache, which writes cells to Imaris IDataset, but only if they were modified.

ImarisDirtyLabelCache(IDataSetPrx, PrimitiveType, int[], CellGrid, CacheLoader<Long, Cell<A>>, boolean) - Constructor for class com.bitplane.xt.img.ImarisDirtyLabelCache

ImarisDirtyLoaderRemover<A extends Dirty> - Class in com.bitplane.xt.util

Variant of ImarisLoaderRemover, which writes cells to Imaris IDataset, but only if they were modified.

ImarisDirtyLoaderRemover(IDataSetPrx, int[], CellGrid, CacheLoader<Long, Cell<A>>, boolean) - Constructor for class com.bitplane.xt.util.ImarisDirtyLoaderRemover

ImarisDirtyProbabilitiesCache<A extends Dirty> - Class in com.bitplane.xt.img

Variant of ImarisProbabilitiesCache, which writes cells to Imaris IDataset, but only if they were modified.

ImarisDirtyProbabilitiesCache(IDataSetPrx, PrimitiveType, int[], CellGrid, CacheLoader<Long, Cell<A>>, boolean) - Constructor for class com.bitplane.xt.img.ImarisDirtyProbabilitiesCache

ImarisImg - Interface in com.bitplane.xt.img

Implemented by the various ImarisCachedImgs.

ImarisLabelCache<A> - Class in com.bitplane.xt.img

A CacheRemover/CacheLoader for writing/reading cells to an Imaris IDataset.

ImarisLabelCache(IDataSetPrx, PrimitiveType, int[], CellGrid, CacheLoader<Long, Cell<A>>, boolean) - Constructor for class com.bitplane.xt.img.ImarisLabelCache

ImarisLabelCache(IDataSetPrx, PrimitiveType, int[], CellGrid, CacheLoader<Long, Cell<A>>, boolean, boolean) - Constructor for class com.bitplane.xt.img.ImarisLabelCache

ImarisLoader<A> - Class in com.bitplane.xt.util

A CacheLoader/CacheRemover for reading cells from an Imaris IDataset.

ImarisLoader(IDataSetPrx, int[], CellGrid, int) - Constructor for class com.bitplane.xt.util.ImarisLoader

TODO

ImarisLoader(IDataSetPrx, int[], CellGrid, int, boolean) - Constructor for class com.bitplane.xt.util.ImarisLoader

ImarisLoaderRemover<A> - Class in com.bitplane.xt.util

Basic CacheLoader/CacheRemover for writing/reading cells to an Imaris IDataset.

ImarisLoaderRemover(IDataSetPrx, int[], CellGrid, CacheLoader<Long, Cell<A>>, boolean) - Constructor for class com.bitplane.xt.util.ImarisLoaderRemover

TODO

ImarisLoaderRemover(IDataSetPrx, int[], CellGrid, CacheLoader<Long, Cell<A>>, boolean, boolean) - Constructor for class com.bitplane.xt.util.ImarisLoaderRemover

ImarisProbabilitiesCache<A> - Class in com.bitplane.xt.img

A CacheRemover/CacheLoader for writing/reading cells to an Imaris IDataset.

ImarisProbabilitiesCache(IDataSetPrx, PrimitiveType, int[], CellGrid, CacheLoader<Long, Cell<A>>, boolean) - Constructor for class com.bitplane.xt.img.ImarisProbabilitiesCache

ImarisProbabilitiesCache(IDataSetPrx, PrimitiveType, int[], CellGrid, CacheLoader<Long, Cell<A>>, boolean, boolean) - Constructor for class com.bitplane.xt.img.ImarisProbabilitiesCache

ImarisService - Interface in com.bitplane.xt

ImarisService connects to the Imaris XT API, providing access to the running Imaris instance(s).

imarisTypeFor(Object) - Static method in class com.bitplane.xt.util.TypeUtils

Get the Imaris tType corresponding to the given imglib2 type

ImarisUtils - Class in com.bitplane.xt.util

Helper functions for creating DataSets.

ImarisUtils() - Constructor for class com.bitplane.xt.util.ImarisUtils

imgFactory(S) - Method in class com.bitplane.xt.img.ImarisCachedCellImgFactory

imgFactory(S) - Method in class com.bitplane.xt.img.ImarisCachedLabelImgFactory

imgFactory(S) - Method in class com.bitplane.xt.img.ImarisCachedProbabilitiesImgFactory

imglibTypeFor(tType) - Static method in class com.bitplane.xt.util.TypeUtils

Get the ImgLib2 Type corresponding to the given Imaris type

includeAxes(ImarisAxesOptions.Axis...) - Method in class com.bitplane.xt.ImarisDatasetOptions

Specify which axes should be included (at least) when mapping an Imaris dataset to a ImgLib2 image.

includeAxes(ImarisAxesOptions.Axis...) - Method in interface com.bitplane.xt.options.ImarisAxesOptions

Specify which axes should be included (at least) when mapping an Imaris dataset to a ImgLib2 image.

includeAxes() - Method in interface com.bitplane.xt.options.ImarisAxesOptions.Val

initializeCellsAsDirty(boolean) - Method in interface com.bitplane.xt.options.ImarisCacheOptions

Specify whether cells initialized by a CellLoader should be marked as dirty.

initializeCellsAsDirty() - Method in interface com.bitplane.xt.options.ImarisCacheOptions.Val

invalidate(Long) - Method in class com.bitplane.xt.img.ImarisLabelCache

invalidate(Long) - Method in class com.bitplane.xt.img.ImarisProbabilitiesCache

invalidateAll(long) - Method in class com.bitplane.xt.img.ImarisLabelCache

invalidateAll(long) - Method in class com.bitplane.xt.img.ImarisProbabilitiesCache

invalidateIf(long, Predicate<Long>) - Method in class com.bitplane.xt.img.ImarisLabelCache

invalidateIf(long, Predicate<Long>) - Method in class com.bitplane.xt.img.ImarisProbabilitiesCache

invalidatePyramid() - Method in class com.bitplane.xt.ImarisDataset

Invalidate cache for all levels of the resolution pyramid, except the full resolution.

invertMapDimensions(int[]) - Static method in class com.bitplane.xt.util.MapDimensions

Return the reverse mapping for the given mapDimensions, such that mapDimensions[inv[i]] == i for all i.

M

MapDimensions - Class in com.bitplane.xt.util

Utilities for mapping between Imaris and ImgLib2 dimension arrays.

MapDimensions.SelectIntervalDimension - Interface in com.bitplane.xt.util

Selects a particular element of the min and size vectors of an interval.

maxCacheSize(long) - Method in class com.bitplane.xt.ImarisDatasetOptions

Set the maximum number of values (cells) to keep in the cache.

maxIoQueueSize(int) - Method in class com.bitplane.xt.ImarisDatasetOptions

Set the maximum size of the disk write queue.

maxIoQueueSize(int) - Method in interface com.bitplane.xt.options.ImarisCacheOptions

Set the maximum size of the disk write queue.

maxIoQueueSize() - Method in interface com.bitplane.xt.options.ImarisCacheOptions.Val

min(int) - Method in class com.bitplane.xt.DatasetCalibration

Get the coordinate (in dimension d) of the min corner of the dataset, where 0 ≤ d < 3.

min(long[]) - Method in interface com.bitplane.xt.util.MapDimensions.SelectIntervalDimension

N

n - Variable in class com.bitplane.xt.util.ImarisLoader

numDimensions() - Method in class com.bitplane.xt.ImarisDataset

numIoThreads(int) - Method in class com.bitplane.xt.ImarisDatasetOptions

The specified number of threads is started to handle asynchronous writing of values that are evicted from the memory cache.

numIoThreads(int) - Method in interface com.bitplane.xt.options.ImarisCacheOptions

The specified number of threads is started to handle asynchronous writing of values that are evicted from the memory cache.

numIoThreads() - Method in interface com.bitplane.xt.options.ImarisCacheOptions.Val

numResolutions() - Method in class com.bitplane.xt.ImarisDataset

Get the number of levels in the resolution pyramid.

numTimepoints() - Method in class com.bitplane.xt.ImarisDataset

Get the number timepoints.

O

onRemoval(Long, A) - Method in class com.bitplane.xt.img.ImarisDirtyLabelCache

onRemoval(Long, A) - Method in class com.bitplane.xt.img.ImarisDirtyProbabilitiesCache

onRemoval(Long, A) - Method in class com.bitplane.xt.img.ImarisLabelCache

onRemoval(Long, A) - Method in class com.bitplane.xt.img.ImarisProbabilitiesCache

onRemoval(Long, A) - Method in class com.bitplane.xt.util.ImarisDirtyLoaderRemover

onRemoval(Long, A) - Method in class com.bitplane.xt.util.ImarisLoader

onRemoval(Long, A) - Method in class com.bitplane.xt.util.ImarisLoaderRemover

options() - Static method in class com.bitplane.xt.ImarisDatasetOptions

Create default ImarisDatasetOptions.

options() - Static method in class com.bitplane.xt.img.ImarisCachedCellImgOptions

Create default ImarisCachedCellImgOptions.

P

persist() - Method in class com.bitplane.xt.ImarisDataset

Persist all modifications back to Imaris.

persist() - Method in class com.bitplane.xt.img.ImarisCachedCellImg

Persist all changes back to Imaris

persist() - Method in class com.bitplane.xt.img.ImarisCachedLabelImg

Persist all changes back to Imaris

persist() - Method in class com.bitplane.xt.img.ImarisCachedProbabilitiesImg

Persist all changes back to Imaris

persist(Long, A) - Method in class com.bitplane.xt.img.ImarisDirtyLabelCache

persist(Long, A) - Method in class com.bitplane.xt.img.ImarisDirtyProbabilitiesCache

persist() - Method in interface com.bitplane.xt.img.ImarisImg

Persist all changes back to Imaris

persist(Long, A) - Method in class com.bitplane.xt.img.ImarisLabelCache

persist(Long, A) - Method in class com.bitplane.xt.img.ImarisProbabilitiesCache

persist(Long, A) - Method in class com.bitplane.xt.util.ImarisDirtyLoaderRemover

persist(Long, A) - Method in class com.bitplane.xt.util.ImarisLoader

persist(Long, A) - Method in class com.bitplane.xt.util.ImarisLoaderRemover

persistOnLoad(boolean) - Method in interface com.bitplane.xt.options.ImarisCacheOptions

Specify whether cells initialized by a CellLoader should be immediately persisted to Imaris.

persistOnLoad() - Method in interface com.bitplane.xt.options.ImarisCacheOptions.Val

PixelSink<A> - Interface in com.bitplane.xt.util

Writing ArrayDataAccess as Imaris blocks

PixelSource<A> - Interface in com.bitplane.xt.util

Reading Imaris blocks as primitive arrays

primitiveArraySource(IDataSetPrx, tType, int[]) - Static method in interface com.bitplane.xt.util.PixelSource

TODO

put(A, long[], int[]) - Method in interface com.bitplane.xt.util.PixelSink

Set sub-volume as flattened primitive array.

R

readOnly() - Method in class com.bitplane.xt.ImarisDatasetOptions

Open the dataset as read-only (vs modifiable).

readOnly() - Method in interface com.bitplane.xt.options.ReadOnlyOptions

Open the dataset as read-only (vs modifiable).

readOnly() - Method in interface com.bitplane.xt.options.ReadOnlyOptions.Val

ReadOnlyOptions<T> - Interface in com.bitplane.xt.options

Specify whether ImarisDataset should be opened as read-only (vs modifiable).

ReadOnlyOptions.Val - Interface in com.bitplane.xt.options

reconstruct(Long, A) - Method in class com.bitplane.xt.img.ImarisLabelCache

reconstruct(Long, A) - Method in class com.bitplane.xt.img.ImarisProbabilitiesCache

reconstruct(Long, A) - Method in class com.bitplane.xt.util.ImarisLoader

S

selectIntervalDimension(int) - Static method in class com.bitplane.xt.util.MapDimensions

Create a MapIntervalDimension that selects the d-th element of any min or size vectors.

set(Object, int, int, int, int, int, int, int, int) - Method in interface com.bitplane.xt.util.SetDataSubVolume

Set sub-volume as flattened primitive array.

setCalibration(String, float, float, float, float, float, float) - Method in class com.bitplane.xt.ImarisDataset

Sets unit, voxel size, and min coordinate from Imaris extents.

setCalibration(VoxelDimensions) - Method in class com.bitplane.xt.ImarisDataset

Set unit and voxel size.

setCalibration(VoxelDimensions, double, double, double) - Method in class com.bitplane.xt.ImarisDataset

Sets unit, voxel size, and min coordinate.

setCalibration(DatasetCalibration) - Method in class com.bitplane.xt.ImarisDataset

Sets unit, voxel size, and min coordinate.

setDataset(ImarisDataset<?>) - Method in interface com.bitplane.xt.ImarisApplication

Equivalent to setImage(0,dataset).

SetDataSubVolume - Interface in com.bitplane.xt.util

Common generic interface for IDataSetPrx.SetDataSubVolumeAs1DArrayBytes(byte[], int, int, int, int, int, int, int, int), IDataSetPrx.SetDataSubVolumeAs1DArrayShorts(short[], int, int, int, int, int, int, int, int), IDataSetPrx.SetDataSubVolumeAs1DArrayFloats(float[], int, int, int, int, int, int, int, int).

setImage(int, ImarisDataset<?>) - Method in class com.bitplane.xt.DefaultImarisApplication

setImage(int, ImarisDataset<?>) - Method in interface com.bitplane.xt.ImarisApplication

Set an image to the application.

setModified(boolean) - Method in class com.bitplane.xt.ImarisDataset

Set the modification flag of the Imaris dataset.

shutdown() - Method in class com.bitplane.xt.img.ImarisCachedCellImg

Shutdown the internal IoSync to free resources via IoSync.shutdown().

shutdown() - Method in class com.bitplane.xt.img.ImarisCachedLabelImg

Shutdown the internal IoSync to free resources via IoSync.shutdown().

shutdown() - Method in class com.bitplane.xt.img.ImarisCachedProbabilitiesImg

Shutdown the internal IoSync to free resources via IoSync.shutdown().

size(int[]) - Method in interface com.bitplane.xt.util.MapDimensions.SelectIntervalDimension

sizeC() - Method in class com.bitplane.xt.DatasetDimensions

Returns the number of channels.

sizeT() - Method in class com.bitplane.xt.DatasetDimensions

Returns the number of timepoints.

sizeX() - Method in class com.bitplane.xt.DatasetDimensions

Returns the size along X.

sizeY() - Method in class com.bitplane.xt.DatasetDimensions

Returns the size along Y.

sizeZ() - Method in class com.bitplane.xt.DatasetDimensions

Returns the size along Z.

T

toString() - Method in class com.bitplane.xt.DatasetCalibration

toString() - Method in class com.bitplane.xt.DatasetDimensions

TypeUtils - Class in com.bitplane.xt.util

ImgLib2 Type for Imaris tType, and vice versa.

U

unit() - Method in class com.bitplane.xt.DatasetCalibration

Get units for DatasetCalibration.voxelSize(int)

V

valueOf(String) - Static method in enum com.bitplane.xt.options.ImarisAxesOptions.Axis

Returns the enum constant of this type with the specified name.

values - Variable in class com.bitplane.xt.ImarisDatasetOptions

Values() - Constructor for class com.bitplane.xt.ImarisDatasetOptions.Values

values - Variable in class com.bitplane.xt.img.ImarisCachedCellImgOptions

Values() - Constructor for class com.bitplane.xt.img.ImarisCachedCellImgOptions.Values

values() - Static method in enum com.bitplane.xt.options.ImarisAxesOptions.Axis

Returns an array containing the constants of this enum type, in the order they are declared.

volatileArraySink(IDataSetPrx, tType, int[]) - Static method in interface com.bitplane.xt.util.PixelSink

TODO

volatileArraySource(IDataSetPrx, tType, int[], boolean) - Static method in interface com.bitplane.xt.util.PixelSource

TODO

voxelSize(int) - Method in class com.bitplane.xt.DatasetCalibration

Get size of a voxel in dimension d, where 0 ≤ d < 3.

A C D E F G H I M N O P R S T U V