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

A

AbstractBuffer - Class in ome.io.nio

AbstractFileSystemService - Class in ome.io.nio

AbstractFileSystemService(String) - Constructor for class ome.io.nio.AbstractFileSystemService

Deprecated.

AbstractFileSystemService(String, boolean) - Constructor for class ome.io.nio.AbstractFileSystemService

acquireLock() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

assertUsedFilesReadable(IFormatReader) - Method in interface ome.io.nio.ReaderSecurityCheck

Check that the used files reported by the reader are safe.

B

BackOff - Interface in ome.io.nio

Strategy interface which is used by PixelsService to calculate the appropriate backoff to report to users when pixel data is not available.

backOff - Variable in class ome.io.nio.PixelsService

BackOff implementation for calculating MissingPyramidExceptions

BfPixelBuffer - Class in ome.io.bioformats

PixelBuffer implementation which uses Bio-Formats to read pixels data directly from original files.

BfPixelBuffer(String, IFormatReader) - Constructor for class ome.io.bioformats.BfPixelBuffer

We may want a constructor that takes the id of an imported file or that takes a File object? There should ultimately be some sort of check here that the file is in a/the repository.

BfPixelsWrapper - Class in ome.io.bioformats

BfPixelsWrapper(String, IFormatReader) - Constructor for class ome.io.bioformats.BfPixelsWrapper

We may want a constructor that takes the id of an imported file or that takes a File object? There should ultimately be some sort of check here that the file is in a/the repository.

BfPyramidPixelBuffer - Class in ome.io.bioformats

PixelBuffer implementation which uses Bio-Formats to read pixels data directly from original files.

BfPyramidPixelBuffer(Pixels, String, boolean) - Constructor for class ome.io.bioformats.BfPyramidPixelBuffer

We may want a constructor that takes the id of an imported file or that takes a File object? There should ultimately be some sort of check here that the file is in a/the repository.

BfPyramidPixelBuffer(TileSizes, Pixels, String, boolean) - Constructor for class ome.io.bioformats.BfPyramidPixelBuffer

Full constructor taking a TileSizes implementation which defines how large the pyramid tiles will be.

BfPyramidPixelBuffer(TileSizes, Pixels, String, boolean, boolean) - Constructor for class ome.io.bioformats.BfPyramidPixelBuffer

bfReader - Variable in class ome.io.bioformats.BfPixelBuffer

C

calculate(Pixels) - Method in class ome.io.nio.SimpleBackOff

calculate() - Method in class ome.io.nio.SimpleBackOff

calculateMessageDigest() - Method in class ome.io.bioformats.BfPixelBuffer

calculateMessageDigest() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

calculateMessageDigest() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

calculateMessageDigest() - Method in interface ome.io.nio.PixelBuffer

Calculates a SHA-1 message digest for the entire pixel buffer.

calculateMessageDigest() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelsWrapper

checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Checks to ensure that no one particular axis has an offset out of bounds.

checkBounds(Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

close() - Method in class ome.io.bioformats.BfPixelBuffer

close() - Method in class ome.io.bioformats.BfPixelsWrapper

close() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

close() - Method in class ome.io.bioformats.OmeroPixelsPyramidReader

close() - Method in class ome.io.bioformats.OmeroPixelsPyramidWriter

close() - Method in class ome.io.nio.FileBuffer

Closes the buffer, cleaning up file state.

close() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

close() - Method in interface ome.io.nio.PixelBuffer

Closes the buffer, cleaning up file state.

close() - Method in class ome.io.nio.RomioPixelBuffer

Closes the buffer, cleaning up file state.

closeRaf() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

closeWriter() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

This method should never exit without releasing the lock.

ConfiguredTileSizes - Class in ome.io.nio

Implementation which has all values injected during configuration.

ConfiguredTileSizes() - Constructor for class ome.io.nio.ConfiguredTileSizes

ConfiguredTileSizes(int, int, int, int) - Constructor for class ome.io.nio.ConfiguredTileSizes

count - Variable in class ome.io.nio.SimpleBackOff

countTiles(Pixels) - Method in class ome.io.nio.SimpleBackOff

createBfPixelBuffer(String, int) - Method in class ome.io.nio.PixelsService

Helper method to properly log any exceptions raised by Bio-Formats.

createBfReader() - Method in class ome.io.nio.PixelsService

Create an IFormatReader with the appropriate ReaderWrapper instances and IFormatReader.setFlattenedResolutions(boolean) set to false.

createMinMaxBfPixelBuffer(String, int, IMinMaxStore) - Method in class ome.io.nio.PixelsService

Helper method to properly log any exceptions raised by Bio-Formats and add a min/max calculator wrapper to the reader stack.

createPixelBuffer(Pixels) - Method in class ome.io.nio.PixelsService

Creates a PixelBuffer for a given pixels set.

createPyramidPixelBuffer(Pixels, String, boolean) - Method in class ome.io.nio.PixelsService

Helper method to properly log any exceptions raised by Bio-Formats.

createRomioPixelBuffer(String, Pixels, boolean) - Method in class ome.io.nio.PixelsService

Helper method to properlty create a RomioPixelBuffer.

createSubpath(String) - Method in class ome.io.nio.AbstractFileSystemService

Makes sure that for a given path, its subpath exists.

createThumbnail(Thumbnail, byte[]) - Method in class ome.io.nio.ThumbnailService

Creates thumbnail on disk using byte array

D

defaultValue - Variable in class ome.io.nio.SimpleBackOff

DimensionsOutOfBoundsException - Exception in ome.io.nio

DimensionsOutOfBoundsException(String) - Constructor for exception ome.io.nio.DimensionsOutOfBoundsException

E

exists(OriginalFile) - Method in class ome.io.nio.OriginalFilesService

Returns whether or not an OriginalFile exists on disk.

F

FailedTileLoopException() - Constructor for exception ome.io.nio.Utils.FailedTileLoopException

FileBuffer - Class in ome.io.nio

Raw file buffer which provides I/O operations within the OMERO file repository.

FileBuffer(String, String) - Constructor for class ome.io.nio.FileBuffer

Default constructor allowing to pass in a non-"rw" file mode.

filePath - Variable in class ome.io.bioformats.BfPixelBuffer

FilePathResolver - Interface in ome.io.nio

Resolver for file paths and related metadata.

FILES_PATH - Static variable in class ome.io.nio.AbstractFileSystemService

flush(boolean) - Method in class ome.io.nio.FileBuffer

Flush the buffer, writing any pending content to the underlying storage device, optionally also the file's metadata.

forEachTile(TileLoopIteration, PixelBuffer, int, int) - Static method in class ome.io.nio.Utils

Iterates over every tile in a given pixel buffer based on the over arching dimensions and a requested maximum tile width and height.

forEachTile(TileLoopIteration, int, int, int, int, int, int, int) - Static method in class ome.io.nio.Utils

Iterates over every tile in a given pixel buffer based on the over arching dimensions and a requested maximum tile width and height.

G

getBfReader(Pixels) - Method in class ome.io.nio.PixelsService

Short-cut in the FS case where we know that we are dealing with a FS-lite file, and want to retrieve the actual file as opposed to a pyramid or anything else.

getByteOrder() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

Returns the current pixel byte order.

getByteWidth() - Method in class ome.io.bioformats.BfPixelBuffer

getByteWidth() - Method in class ome.io.bioformats.BfPixelsWrapper

getByteWidth() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getByteWidth() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getByteWidth() - Method in interface ome.io.nio.PixelBuffer

Returns the byte width for the pixel buffer.

getByteWidth() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getCol(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

getCol(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper

getCol(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getCol(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getCol(Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Retrieves a particular column from this pixel buffer.

getCol(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer

getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer

Retrieves a particular column from this pixel buffer.

getColDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getColSize() - Method in class ome.io.bioformats.BfPixelBuffer

getColSize() - Method in class ome.io.bioformats.BfPixelsWrapper

getColSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getColSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getColSize() - Method in interface ome.io.nio.PixelBuffer

Retrieves the in memory size of a column of pixels in this pixel buffer.

getColSize() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getCount() - Method in class ome.io.nio.SimpleBackOff

getData() - Method in class ome.io.nio.ReorderedPixelData

Returns the backing buffer for the pixel data.

getFileBuffer(OriginalFile, String) - Method in class ome.io.nio.OriginalFilesService

Returns FileBuffer based on OriginalFile path

getFilesPath(Long) - Method in class ome.io.nio.AbstractFileSystemService

Returns a numbered path relative to the root of this service, but is ignorant of FS and similar constructs.

getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPixelBuffer

getHypercube(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper

getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in interface ome.io.nio.PixelBuffer

Retrieves a hypercube from this pixel buffer.

getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer

getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in interface ome.io.nio.PixelBuffer

Retrieves a hypercube from the given pixels directly.

getHypercubeDirect(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPixelBuffer

getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPixelsWrapper

getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in interface ome.io.nio.PixelBuffer

Retrieves a the size of a hypercube from this pixel buffer.

getHypercubeSize(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.io.nio.RomioPixelBuffer

getId() - Method in class ome.io.bioformats.BfPixelBuffer

getId() - Method in class ome.io.bioformats.BfPixelsWrapper

getId() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getId() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getId() - Method in interface ome.io.nio.PixelBuffer

Retrieves the identifier of this pixel buffer

getId() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getMaxPlaneHeight() - Method in class ome.io.nio.ConfiguredTileSizes

getMaxPlaneHeight() - Method in interface ome.io.nio.TileSizes

getMaxPlaneWidth() - Method in class ome.io.nio.ConfiguredTileSizes

getMaxPlaneWidth() - Method in interface ome.io.nio.TileSizes

getMemoizerDirectory() - Method in class ome.io.nio.PixelsService

getMemoizerWait() - Method in class ome.io.nio.PixelsService

getMessage() - Method in exception ome.io.nio.PixelBufferException

getMessageDigest() - Method in class ome.io.bioformats.BfPixelsWrapper

getMode() - Method in class ome.io.nio.FileBuffer

Retrieves the current file mode

getOrder() - Method in class ome.io.nio.ReorderedPixelData

Returns the byte order of the backing buffer.

getOriginalFilePath(AbstractFileSystemService, Pixels) - Method in interface ome.io.nio.FilePathResolver

Retrieves the original file path for a given set of pixels.

getOriginalFilePath(Pixels) - Method in class ome.io.nio.PixelsService

Retrieves the original file path for a given set of pixels.

getPath() - Method in class ome.io.bioformats.BfPixelBuffer

getPath() - Method in class ome.io.bioformats.BfPixelsWrapper

getPath() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getPath() - Method in class ome.io.nio.AbstractBuffer

getPath(String, Long) - Method in class ome.io.nio.AbstractFileSystemService

Returns a numbered path relative to the root of this service for a given prefix, but is ignorant of FS and similar constructs.

getPath() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getPath() - Method in interface ome.io.nio.PixelBuffer

Retrieves the full path to this pixel buffer on disk

getPixelBuffer(Pixels) - Method in class ome.io.nio.PixelsService

Deprecated.

In the future callers should use the more descriptive PixelsService.getPixelBuffer(Pixels, boolean).

getPixelBuffer(Pixels, boolean) - Method in class ome.io.nio.PixelsService

Returns a pixel buffer for a given set of pixels.

getPixelsDirectory() - Method in class ome.io.nio.AbstractFileSystemService

Returns a numbered path relative to the root of this service, but is ignorant of FS and similar constructs.

getPixelsPath(Long) - Method in class ome.io.nio.AbstractFileSystemService

Returns a numbered path relative to the root of this service, but is ignorant of FS and similar constructs.

getPixelsType() - Method in class ome.io.bioformats.BfPixelsWrapper

cgb - created from the methods below? Retrieves how many bytes per pixel the current plane or section has.

getPixelValueDirect(int) - Method in class ome.io.nio.ReorderedPixelData

Returns the pixel intensity value of the pixel at a given offset within the backing buffer.

getPlane(Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

getPlane(Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper

getPlane(Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getPlane(Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getPlane(Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Retrieves a particular 2D image plane from this pixel buffer.

getPlane(Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer

getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer

Retrieves a particular 2D image plane from this pixel buffer.

getPlaneDirect(Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getPlaneOffset(Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

getPlaneOffset(Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelsWrapper

getPlaneOffset(Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getPlaneOffset(Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getPlaneOffset(Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Retrieves the offset for a particular 2D image plane in this pixel buffer.

getPlaneOffset(Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getPlaneRegion(Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

getPlaneRegion(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper

getPlaneRegion(Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getPlaneRegion(Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getPlaneRegion(Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Retrieves a particular region of a 2D image plane from this pixel buffer.

getPlaneRegion(Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by ByteBuffer I/F.

getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer

getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer

Retrieves a region from a given plane directly.

getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getPlaneSize() - Method in class ome.io.bioformats.BfPixelBuffer

getPlaneSize() - Method in class ome.io.bioformats.BfPixelsWrapper

getPlaneSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getPlaneSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getPlaneSize() - Method in interface ome.io.nio.PixelBuffer

Retrieves the in memory size of a 2D image plane in this pixel buffer.

getPlaneSize() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getRegion(Integer, Long) - Method in class ome.io.bioformats.BfPixelBuffer

getRegion(Integer, Long, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper

getRegion(Integer, Long) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getRegion(Integer, Long) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getRegion(Integer, Long) - Method in interface ome.io.nio.PixelBuffer

Retrieves a region from this pixel buffer.

getRegion(Integer, Long) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getRegionDirect(Integer, Long, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer

getRegionDirect(Integer, Long, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getRegionDirect(Integer, Long, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getRegionDirect(Integer, Long, byte[]) - Method in interface ome.io.nio.PixelBuffer

Retrieves a region from this pixel buffer directly.

getRegionDirect(Integer, Long, byte[]) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getReorderedPixelOffset(int, int, int) - Static method in class ome.io.nio.ReorderedPixelData

Returns the re-ordered pixel offset.

getResolutionDescriptions() - Method in class ome.io.bioformats.BfPixelBuffer

getResolutionDescriptions() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getResolutionDescriptions() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getResolutionDescriptions() - Method in interface ome.io.nio.PixelBuffer

Return a list of lists each of which has sizeX, sizeY for the resolution level matching the index of the outer index.

getResolutionDescriptions() - Method in class ome.io.nio.RomioPixelBuffer

getResolutionLevel() - Method in class ome.io.bioformats.BfPixelBuffer

getResolutionLevel() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getResolutionLevel() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getResolutionLevel() - Method in interface ome.io.nio.PixelBuffer

Retrieves the active resolution level.

getResolutionLevel() - Method in class ome.io.nio.RomioPixelBuffer

getResolutionLevels() - Method in class ome.io.bioformats.BfPixelBuffer

getResolutionLevels() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getResolutionLevels() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getResolutionLevels() - Method in interface ome.io.nio.PixelBuffer

Retrieves the number of resolution levels that the backing pixels pyramid contains.

getResolutionLevels() - Method in class ome.io.nio.RomioPixelBuffer

getRow(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

getRow(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper

getRow(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getRow(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getRow(Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Retrieves a particular row or scanline from this pixel buffer.

getRow(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer

getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer

Retrieves a particular row or scanline from this pixel buffer.

getRowDirect(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getRowOffset(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

getRowOffset(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelsWrapper

getRowOffset(Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getRowOffset(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getRowOffset(Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Retrieves the offset for a particular row or scanline in this pixel buffer.

getRowOffset(Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getRowSize() - Method in class ome.io.bioformats.BfPixelBuffer

getRowSize() - Method in class ome.io.bioformats.BfPixelsWrapper

getRowSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getRowSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getRowSize() - Method in interface ome.io.nio.PixelBuffer

Retrieves the in memory size of a row or scanline of pixels in this pixel buffer.

getRowSize() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getScalingFactor() - Method in class ome.io.nio.SimpleBackOff

getSeries() - Method in class ome.io.bioformats.BfPixelBuffer

Retrieves the current series of the underlying Bio-Formats reader.

getSeries(Pixels) - Method in class ome.io.nio.PixelsService

Retrieves the series for a given set of pixels.

getSha1() - Method in class ome.io.nio.RomioPixelBuffer

getSizeC() - Method in class ome.io.bioformats.BfPixelBuffer

getSizeC() - Method in class ome.io.bioformats.BfPixelsWrapper

getSizeC() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getSizeC() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getSizeC() - Method in interface ome.io.nio.PixelBuffer

Retrieves the size in C of this pixel buffer

getSizeC() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getSizeT() - Method in class ome.io.bioformats.BfPixelBuffer

getSizeT() - Method in class ome.io.bioformats.BfPixelsWrapper

getSizeT() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getSizeT() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getSizeT() - Method in interface ome.io.nio.PixelBuffer

Retrieves the size in T of this pixel buffer

getSizeT() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getSizeX() - Method in class ome.io.bioformats.BfPixelBuffer

getSizeX() - Method in class ome.io.bioformats.BfPixelsWrapper

getSizeX() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getSizeX() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getSizeX() - Method in interface ome.io.nio.PixelBuffer

Retrieves the size in X of this pixel buffer

getSizeX() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getSizeY() - Method in class ome.io.bioformats.BfPixelBuffer

getSizeY() - Method in class ome.io.bioformats.BfPixelsWrapper

getSizeY() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getSizeY() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getSizeY() - Method in interface ome.io.nio.PixelBuffer

Retrieves the size in Y of this pixel buffer

getSizeY() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getSizeZ() - Method in class ome.io.bioformats.BfPixelBuffer

getSizeZ() - Method in class ome.io.bioformats.BfPixelsWrapper

getSizeZ() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getSizeZ() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getSizeZ() - Method in interface ome.io.nio.PixelBuffer

Retrieves the size in Z of this pixel buffer

getSizeZ() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getStack(Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

getStack(Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper

getStack(Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getStack(Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getStack(Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Retrieves the the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.

getStack(Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getStackDirect(Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer

getStackDirect(Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getStackDirect(Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getStackDirect(Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer

Retrieves the the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.

getStackDirect(Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getStackOffset(Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

getStackOffset(Integer, Integer) - Method in class ome.io.bioformats.BfPixelsWrapper

getStackOffset(Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getStackOffset(Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getStackOffset(Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Retrieves the offset for the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.

getStackOffset(Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getStackSize() - Method in class ome.io.bioformats.BfPixelBuffer

getStackSize() - Method in class ome.io.bioformats.BfPixelsWrapper

getStackSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getStackSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getStackSize() - Method in interface ome.io.nio.PixelBuffer

Retrieves the in memory size of the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.

getStackSize() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getThumbnail(Thumbnail) - Method in class ome.io.nio.ThumbnailService

Return byte array of Thumbnail

getThumbnail(Thumbnail, byte[]) - Method in class ome.io.nio.ThumbnailService

Return byte array of Thumbnail, providing byte array

getThumbnailExists(Thumbnail) - Method in class ome.io.nio.ThumbnailService

Returns whether or not a thumbnail exists on disk.

getThumbnailLength(Thumbnail) - Method in class ome.io.nio.ThumbnailService

Returns length of Thumbnail on disk

getThumbnailOutputStream(Thumbnail) - Method in class ome.io.nio.ThumbnailService

Return FileOutputStream of Thumbnail

getThumbnailPath(Long) - Method in class ome.io.nio.AbstractFileSystemService

Returns a numbered path relative to the root of this service, but is ignorant of FS and similar constructs.

getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

getTile(int, int, int, int, int, int, int, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper

getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Retrieves a tile from this pixel buffer.

getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

getTileCount() - Method in exception ome.io.nio.Utils.FailedTileLoopException

getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer

getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer

Retrieves a tile from this pixel buffer.

getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer

getTileHeight() - Method in class ome.io.nio.ConfiguredTileSizes

getTileHeight() - Method in interface ome.io.nio.TileSizes

getTileSize() - Method in class ome.io.bioformats.BfPixelBuffer

getTileSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getTileSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getTileSize() - Method in interface ome.io.nio.PixelBuffer

Retrieves the tile size for the pixel store.

getTileSize() - Method in class ome.io.nio.RomioPixelBuffer

getTileWidth() - Method in class ome.io.nio.ConfiguredTileSizes

getTileWidth() - Method in interface ome.io.nio.TileSizes

getTimepoint(Integer) - Method in class ome.io.bioformats.BfPixelBuffer

getTimepoint(Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper

getTimepoint(Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getTimepoint(Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getTimepoint(Integer) - Method in interface ome.io.nio.PixelBuffer

Retrieves the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.

getTimepoint(Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getTimepointDirect(Integer, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer

getTimepointDirect(Integer, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getTimepointDirect(Integer, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getTimepointDirect(Integer, byte[]) - Method in interface ome.io.nio.PixelBuffer

Retrieves the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.

getTimepointDirect(Integer, byte[]) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getTimepointOffset(Integer) - Method in class ome.io.bioformats.BfPixelBuffer

getTimepointOffset(Integer) - Method in class ome.io.bioformats.BfPixelsWrapper

getTimepointOffset(Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getTimepointOffset(Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getTimepointOffset(Integer) - Method in interface ome.io.nio.PixelBuffer

Retrieves the in memory size of the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.

getTimepointOffset(Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getTimepointSize() - Method in class ome.io.bioformats.BfPixelBuffer

getTimepointSize() - Method in class ome.io.bioformats.BfPixelsWrapper

getTimepointSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getTimepointSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getTimepointSize() - Method in interface ome.io.nio.PixelBuffer

Retrieves the in memory size of the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.

getTimepointSize() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getTotalSize() - Method in class ome.io.bioformats.BfPixelBuffer

getTotalSize() - Method in class ome.io.bioformats.BfPixelsWrapper

getTotalSize() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

getTotalSize() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

getTotalSize() - Method in interface ome.io.nio.PixelBuffer

Retrieves the in memory size of the entire pixel buffer.

getTotalSize() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

getWarmUpFactor() - Method in class ome.io.nio.SimpleBackOff

H

handleMissingPyramid(Pixels, String) - Method in class ome.io.nio.PixelsService

If the outer loop should continue, this method returns successfully; otherwise it throws a MissingPyramidException.

handleMissingStatsInfo(Pixels) - Method in class ome.io.nio.PixelsService

If the outer loop should continue, this method returns successfully; otherwise it throws a MissingPyramidException.

I

IFD_TAG_PLANE_NUMBER - Static variable in class ome.io.bioformats.OmeroPixelsPyramidWriter

TIFF tag we're using to store the Bio-Formats plane number.

IFD_TAG_SERIES - Static variable in class ome.io.bioformats.OmeroPixelsPyramidWriter

TIFF tag we're using to store the Bio-Formats series.

IMAGE_DESCRIPTION - Static variable in class ome.io.bioformats.OmeroPixelsPyramidWriter

Current TIFF image comment for OMERO pixels pyramid TIFFs.

init(String, boolean) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

initializeReader() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

If the pyramid file exists (which the constructor guarantees) then we assume that even if a lock file is present, that it's no longer valid.

initializeWriter(String, String, boolean, int, int) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

Initializes the writer.

InMemoryPlanarPixelBuffer - Class in ome.io.nio

Class implementation of the PixelBuffer interface for in memory planar pixel data.

InMemoryPlanarPixelBuffer(Pixels, byte[][][][]) - Constructor for class ome.io.nio.InMemoryPlanarPixelBuffer

Constructs an in memory pixel buffer based on a defined dimensionality.

isFloat() - Method in class ome.io.bioformats.BfPixelBuffer

isFloat() - Method in class ome.io.bioformats.BfPixelsWrapper

isFloat() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

isFloat() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

isFloat() - Method in interface ome.io.nio.PixelBuffer

Returns whether or not the pixel buffer has floating point pixels.

isFloat() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

isLittleEndian() - Method in class ome.io.bioformats.BfPixelBuffer

Delegates to IFormatReader.isLittleEndian().

isLittleEndian() - Method in class ome.io.bioformats.BfPixelsWrapper

isLittleEndian() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

isLockedByOthers() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

isRetry() - Method in class ome.io.messages.MissingPyramidMessage

isSigned() - Method in class ome.io.bioformats.BfPixelBuffer

isSigned() - Method in class ome.io.bioformats.BfPixelsWrapper

isSigned() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

isSigned() - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

isSigned() - Method in interface ome.io.nio.PixelBuffer

Returns whether or not the pixel buffer has signed pixels.

isSigned() - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

isThisType(String, boolean) - Method in class ome.io.bioformats.OmeroPixelsPyramidReader

isWritableDirectory(File) - Method in class ome.io.bioformats.MemoizerReadOnly

n.b.: Overridden to test only read access, not write access.

isWrite() - Method in class ome.io.bioformats.BfPyramidPixelBuffer

Whether or not this instance is in writing-mode.

M

makePyramid(Pixels) - Method in class ome.io.nio.PixelsService

Creates a pixels pyramid for a given set of pixels.

MAXIMUM_BUFFER_SIZE - Static variable in class ome.io.nio.RomioPixelBuffer

Default maximum buffer size for planar data transfer.

maxPixels - Variable in class ome.io.nio.SimpleBackOff

MEMOIZER_WAIT - Static variable in class ome.io.nio.PixelsService

Default of 100 ms for PixelsService.memoizerWait

memoizerDirectory - Variable in class ome.io.nio.PixelsService

Location where cached data from the Memoizer should be stored.

memoizerDirectoryLocalRW - Variable in class ome.io.nio.PixelsService

For read-only servers, this directory is a local read-write directory for storing memo files.

MemoizerFallback - Class in ome.io.bioformats

While appearing to be a Memoizer this class actually wraps multiple memoizers.

MemoizerFallback(IFormatReader, long, File, Collection<MemoizerReadOnly>) - Constructor for class ome.io.bioformats.MemoizerFallback

As Memoizer.Memoizer(IFormatReader, long, File) with an additional fallbacks argument that provides other memoizers from which this instance may copy a memo.

MemoizerReadOnly - Class in ome.io.bioformats

Adapts Memoizer to tolerate cache directories that it may not write.

MemoizerReadOnly(IFormatReader, long, File) - Constructor for class ome.io.bioformats.MemoizerReadOnly

memoizerWait - Variable in class ome.io.nio.PixelsService

Time in ms.

message - Variable in exception ome.io.nio.PixelBufferException

MissingPyramidMessage - Class in ome.io.messages

Published when an request is made for a pixels pyramid when the file does not yet exist.

MissingPyramidMessage(Object, long) - Constructor for class ome.io.messages.MissingPyramidMessage

MissingStatsInfoMessage - Class in ome.io.messages

Published when an request is made for a pixels pyramid when the file does not yet contain channel statistics.

MissingStatsInfoMessage(Object, long) - Constructor for class ome.io.messages.MissingStatsInfoMessage

N

NULL_PLANE - Static variable in class ome.io.nio.PixelsService

Null plane byte array.

NULL_PLANE_SIZE - Static variable in class ome.io.nio.PixelsService

Null plane size constant.

nullPlane - Static variable in class ome.io.nio.PixelsService

Deprecated.

in favor of PixelsService.NULL_PLANE

O

ome.io.bioformats - package ome.io.bioformats

ome.io.messages - package ome.io.messages

ome.io.nio - package ome.io.nio

New Input/Output handling for the OMERO server

OmeroPixelsPyramidReader - Class in ome.io.bioformats

File format reader for OMERO pixels pyramid files.

OmeroPixelsPyramidReader() - Constructor for class ome.io.bioformats.OmeroPixelsPyramidReader

OmeroPixelsPyramidWriter - Class in ome.io.bioformats

File format writer for OMERO pixels pyramid files.

OmeroPixelsPyramidWriter() - Constructor for class ome.io.bioformats.OmeroPixelsPyramidWriter

OriginalFilesService - Class in ome.io.nio

Raw file service which provides access to FileBuffers.

OriginalFilesService(String) - Constructor for class ome.io.nio.OriginalFilesService

Deprecated.

OriginalFilesService(String, boolean) - Constructor for class ome.io.nio.OriginalFilesService

P

PixelBuffer - Interface in ome.io.nio

This interface declares the I/O responsibilities of a buffer, file or otherwise, that contains a 5-dimensional Pixel array (XYZCT).

PixelBufferException - Exception in ome.io.nio

PixelBufferException(String) - Constructor for exception ome.io.nio.PixelBufferException

PIXELS_PATH - Static variable in class ome.io.nio.AbstractFileSystemService

pixelsID - Variable in class ome.io.messages.MissingPyramidMessage

PixelsService - Class in ome.io.nio

PixelsService(String) - Constructor for class ome.io.nio.PixelsService

Constructor.

PixelsService(String, FilePathResolver) - Constructor for class ome.io.nio.PixelsService

Deprecated.

PixelsService(String, FilePathResolver, BackOff, TileSizes, IQuery) - Constructor for class ome.io.nio.PixelsService

Constructor.

PixelsService(String, long, FilePathResolver, BackOff, TileSizes, IQuery) - Constructor for class ome.io.nio.PixelsService

Deprecated.

PixelsService(String, boolean, long, FilePathResolver, BackOff, TileSizes, IQuery) - Constructor for class ome.io.nio.PixelsService

Deprecated.

PixelsService(String, File, FilePathResolver, BackOff, TileSizes, IQuery) - Constructor for class ome.io.nio.PixelsService

Call PixelsService.PixelsService(String, boolean, File, long, FilePathResolver, BackOff, TileSizes, IQuery) with PixelsService.MEMOIZER_WAIT.

PixelsService(String, File, long, FilePathResolver, BackOff, TileSizes, IQuery) - Constructor for class ome.io.nio.PixelsService

Deprecated.

PixelsService(String, boolean, File, long, FilePathResolver, BackOff, TileSizes, IQuery) - Constructor for class ome.io.nio.PixelsService

postProcess() - Method in class ome.io.bioformats.OmeroPixelsPyramidWriter

Performs re-compression post processing on the pixel pyramid.

PYR_LOCK_EXT - Static variable in class ome.io.bioformats.BfPyramidPixelBuffer

PYRAMID_SUFFIX - Static variable in class ome.io.nio.PixelsService

Suffix for an the image pyramid of a given pixels set.

R

read(ByteBuffer) - Method in class ome.io.nio.FileBuffer

Delegates to FileChannel

read(ByteBuffer, long) - Method in class ome.io.nio.FileBuffer

Delegates to FileChannel

reader - Variable in class ome.io.bioformats.BfPixelBuffer

reader() - Method in class ome.io.bioformats.BfPixelBuffer

Do not call this method when looking to close the reader.

reader - Variable in class ome.io.bioformats.BfPyramidPixelBuffer

Bio-Formats implementation the delegate uses to read the backing TIFF.

ReaderSecurityCheck - Interface in ome.io.nio

Check that OMERO permissions violations are not being attempted by means of a Bio-Formats readers' I/O.

recompressSeries(TiffReader, int) - Method in class ome.io.bioformats.OmeroPixelsPyramidWriter

Re-compresses a source series, that is JPEG 2000 compressed, via its resolution level.

removeFiles(List<Long>) - Method in class ome.io.nio.OriginalFilesService

Removes files from data repository based on a parameterized List of Long file ids

removePixels(List<Long>) - Method in class ome.io.nio.PixelsService

Removes files from data repository based on a parameterized List of Long pixels ids

removeThumbnails(List<Long>) - Method in class ome.io.nio.ThumbnailService

Removes files from data repository based on a parameterized List of Long thumbnail ids

ReorderedPixelData - Class in ome.io.nio

Represents a block of pixel data that needs to be re-ordered in accordance with a DeltaVision file.

ReorderedPixelData(String, ByteBuffer, int) - Constructor for class ome.io.nio.ReorderedPixelData

Default constructor.

requiresPixelsPyramid(Pixels) - Method in class ome.io.nio.PixelsService

Returns whether a pyramid should be used for the given Pixels.

resolver - Variable in class ome.io.nio.PixelsService

Resolver of archived original file paths for pixels sets.

RomioPixelBuffer - Class in ome.io.nio

Class implementation of the PixelBuffer interface for standard "proprietary" ROMIO/OMEIS data format.

RomioPixelBuffer(String, Pixels) - Constructor for class ome.io.nio.RomioPixelBuffer

Creates a new instance.

RomioPixelBuffer(String, Pixels, boolean) - Constructor for class ome.io.nio.RomioPixelBuffer

Creates a new instance, with manual setting of RomioPixelBuffer.permitModification.

ROOT_DEFAULT - Static variable in class ome.io.nio.AbstractFileSystemService

run(int, int, int, int, int, int, int, int) - Method in interface ome.io.nio.TileLoopIteration

Invoke a single loop iteration.

S

safeLongToInteger(Long) - Static method in class ome.io.nio.RomioPixelBuffer

Converts a Long value to an Integer safely.

scalingFactor - Variable in class ome.io.nio.SimpleBackOff

setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.io.nio.PixelsService

setByteOrder(ByteOrder) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

Sets the pixel byte order.

setFilePathResolver(FilePathResolver) - Method in class ome.io.nio.PixelsService

setId(String) - Method in class ome.io.bioformats.MemoizerFallback

setId(String) - Method in class ome.io.bioformats.OmeroPixelsPyramidReader

setId(String) - Method in class ome.io.bioformats.OmeroPixelsPyramidWriter

setMemoizerDirectoryLocal(String) - Method in class ome.io.nio.PixelsService

setMetrics(Metrics) - Method in class ome.io.nio.PixelsService

setOrder(ByteOrder) - Method in class ome.io.nio.ReorderedPixelData

Set the byte order of the backing buffer.

setPlane(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

setPlane(byte[], Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

setPlane(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

setPlane(byte[], Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

setPlane(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

setPlane(byte[], Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

setPlane(ByteBuffer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Sets a particular 2D image plane in this pixel buffer.

setPlane(byte[], Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Sets a particular 2D image plane in this pixel buffer.

setPlane(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

setPlane(byte[], Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

setReaderSecurityCheck(ReaderSecurityCheck) - Method in class ome.io.nio.PixelsService

setRegion(Integer, Long, byte[]) - Method in class ome.io.bioformats.BfPixelBuffer

setRegion(Integer, Long, ByteBuffer) - Method in class ome.io.bioformats.BfPixelBuffer

setRegion(Integer, Long, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

setRegion(Integer, Long, ByteBuffer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

setRegion(Integer, Long, byte[]) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

setRegion(Integer, Long, ByteBuffer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

setRegion(Integer, Long, byte[]) - Method in interface ome.io.nio.PixelBuffer

Sets a region in this pixel buffer.

setRegion(Integer, Long, ByteBuffer) - Method in interface ome.io.nio.PixelBuffer

Sets a region in this pixel buffer.

setRegion(Integer, Long, byte[]) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

setRegion(Integer, Long, ByteBuffer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

setResolutionLevel(int) - Method in class ome.io.bioformats.BfPixelBuffer

setResolutionLevel(int) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

setResolutionLevel(IFD) - Method in class ome.io.bioformats.OmeroPixelsPyramidReader

setResolutionLevel(int) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

setResolutionLevel(int) - Method in interface ome.io.nio.PixelBuffer

Sets the active resolution level.

setResolutionLevel(int) - Method in class ome.io.nio.RomioPixelBuffer

setRetry() - Method in class ome.io.messages.MissingPyramidMessage

setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Sets a particular row or scanline in this pixel buffer.

setRow(ByteBuffer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

setSeries(int) - Method in class ome.io.bioformats.BfPixelBuffer

Sets the current series in the underlying Bio-Formats reader.

setStack(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

setStack(byte[], Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

setStack(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

setStack(byte[], Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

setStack(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

setStack(byte[], Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

setStack(ByteBuffer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Sets the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.

setStack(byte[], Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Sets the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.

setStack(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

setStack(byte[], Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

setTile(byte[], Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

setTile(byte[], Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

setTile(byte[], Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

setTile(byte[], Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in interface ome.io.nio.PixelBuffer

Sets a tile in this pixel buffer.

setTile(byte[], Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

setTileCount(Integer) - Method in exception ome.io.nio.Utils.FailedTileLoopException

setTimepoint(ByteBuffer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer

setTimepoint(byte[], Integer) - Method in class ome.io.bioformats.BfPixelBuffer

setTimepoint(ByteBuffer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

setTimepoint(byte[], Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer

setTimepoint(ByteBuffer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

setTimepoint(byte[], Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer

setTimepoint(ByteBuffer, Integer) - Method in interface ome.io.nio.PixelBuffer

Sets the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.

setTimepoint(byte[], Integer) - Method in interface ome.io.nio.PixelBuffer

Sets the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.

setTimepoint(ByteBuffer, Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

setTimepoint(byte[], Integer) - Method in class ome.io.nio.RomioPixelBuffer

Implemented as specified by PixelBuffer I/F.

SimpleBackOff - Class in ome.io.nio

Basic BackOff implementation which attempts several writes of the default block size on startup, and uses that as a scaling factor for all subsequent calculations.

SimpleBackOff() - Constructor for class ome.io.nio.SimpleBackOff

SimpleBackOff(TileSizes) - Constructor for class ome.io.nio.SimpleBackOff

SimpleBackOff(TileSizes, long, long) - Constructor for class ome.io.nio.SimpleBackOff

size() - Method in class ome.io.nio.FileBuffer

sizes - Variable in class ome.io.nio.PixelsService

TileSizes implementation for default values

sizes - Variable in class ome.io.nio.SimpleBackOff

swapIfRequired(byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper

cgb - stolen from ImportLibrary - slightly modified Examines a byte array to see if it needs to be byte swapped and modifies the byte array directly.

T

throwMissingPyramidException(String, Pixels) - Method in interface ome.io.nio.BackOff

throwMissingPyramidException(String, Pixels) - Method in class ome.io.nio.SimpleBackOff

THUMBNAILS_PATH - Static variable in class ome.io.nio.AbstractFileSystemService

ThumbnailService - Class in ome.io.nio

ThumbnailService(String) - Constructor for class ome.io.nio.ThumbnailService

Deprecated.

ThumbnailService(String, boolean) - Constructor for class ome.io.nio.ThumbnailService

TileLoopIteration - Interface in ome.io.nio

A single iteration of a tile for each loop.

TileSizes - Interface in ome.io.nio

Strategy interface which is used by PixelsService to specify the default tile sizes as well as when tiling is necessary.

toString() - Method in class ome.io.nio.AbstractBuffer

toString() - Method in class ome.io.nio.ConfiguredTileSizes

toString() - Method in class ome.io.nio.SimpleBackOff

truncate(long) - Method in class ome.io.nio.FileBuffer

truncateIfSmaller(long) - Method in class ome.io.nio.FileBuffer

Only truncate if the size of the file is less than the size argument.

U

Utils - Class in ome.io.nio

General utility methods for working with ROMIO classes.

Utils() - Constructor for class ome.io.nio.Utils

Utils.FailedTileLoopException - Exception in ome.io.nio

The processing of a tile failed so abort the loop.

W

warmUpFactor - Variable in class ome.io.nio.SimpleBackOff

write(ByteBuffer, long) - Method in class ome.io.nio.FileBuffer

Delegates to FileChannel

write(ByteBuffer) - Method in class ome.io.nio.FileBuffer

Delegates to FileChannel

writer - Variable in class ome.io.bioformats.BfPyramidPixelBuffer

Bio-Formats implementation used to write to the backing TIFF.

_

_getPixelBuffer(Pixels, boolean) - Method in class ome.io.nio.PixelsService

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