Index (omero-romio 5.8.0 API)

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

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 - Variable in class ome.io.nio.PixelsService: BackOff implementation for calculating MissingPyramidExceptions
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.
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(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
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.
bfReader - Variable in class ome.io.bioformats.BfPixelBuffer

C

calculate() - Method in class ome.io.nio.SimpleBackOff
calculate(Pixels) - 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
ConfiguredTileSizes(int, int, int, int, boolean) - 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, 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.
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.

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) - 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.
getCol(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
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>) - 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.
getHypercube(List<Integer>, List<Integer>, List<Integer>, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
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.
getMaxPlaneFloatOverride() - Method in class ome.io.nio.ConfiguredTileSizes
getMaxPlaneFloatOverride() - Method in interface ome.io.nio.TileSizes
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() - 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
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.
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) - 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.
getPlane(Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
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, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
getPlaneRegion(Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
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) - 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.
getRegion(Integer, Long, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
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) - 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.
getRow(Integer, Integer, Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
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) - 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.
getStack(Integer, Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
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(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.BfPixelBuffer
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) - 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.
getTimepoint(Integer, byte[]) - Method in class ome.io.bioformats.BfPixelsWrapper
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(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
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, boolean, 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
PixelsService(String, long, FilePathResolver, BackOff, TileSizes, IQuery) - Constructor for class ome.io.nio.PixelsService: Deprecated.
PixelsService(String, File, 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(String, boolean, File, long, FilePathResolver, BackOff, TileSizes, IQuery) with PixelsService.MEMOIZER_WAIT.
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.
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 - Variable in class ome.io.bioformats.BfPyramidPixelBuffer: Bio-Formats implementation the delegate uses to read the backing TIFF.
reader() - Method in class ome.io.bioformats.BfPixelBuffer: Do not call this method when looking to close the reader.
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(byte[], Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
setPlane(byte[], Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
setPlane(byte[], Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
setPlane(byte[], 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 class ome.io.nio.RomioPixelBuffer: Implemented as specified by PixelBuffer I/F.
setPlane(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
setPlane(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
setPlane(ByteBuffer, 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(ByteBuffer, 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, byte[]) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
setRegion(Integer, Long, byte[]) - 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, byte[]) - Method in class ome.io.nio.RomioPixelBuffer: Implemented as specified by PixelBuffer I/F.
setRegion(Integer, Long, ByteBuffer) - Method in class ome.io.bioformats.BfPixelBuffer
setRegion(Integer, Long, ByteBuffer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
setRegion(Integer, Long, ByteBuffer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
setRegion(Integer, Long, ByteBuffer) - Method in interface ome.io.nio.PixelBuffer: Sets a region in this pixel buffer.
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(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
setResolutionLevel(IFD) - Method in class ome.io.bioformats.OmeroPixelsPyramidReader
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(byte[], Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
setStack(byte[], Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
setStack(byte[], Integer, Integer, Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
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(byte[], Integer, Integer, Integer) - Method in class ome.io.nio.RomioPixelBuffer: Implemented as specified by PixelBuffer I/F.
setStack(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
setStack(ByteBuffer, Integer, Integer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
setStack(ByteBuffer, 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(ByteBuffer, 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(byte[], Integer) - Method in class ome.io.bioformats.BfPixelBuffer
setTimepoint(byte[], Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
setTimepoint(byte[], Integer) - Method in class ome.io.nio.InMemoryPlanarPixelBuffer
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(byte[], Integer) - Method in class ome.io.nio.RomioPixelBuffer: Implemented as specified by PixelBuffer I/F.
setTimepoint(ByteBuffer, Integer) - Method in class ome.io.bioformats.BfPixelBuffer
setTimepoint(ByteBuffer, Integer) - Method in class ome.io.bioformats.BfPyramidPixelBuffer
setTimepoint(ByteBuffer, 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(ByteBuffer, 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) - Method in class ome.io.nio.FileBuffer: Delegates to FileChannel
write(ByteBuffer, long) - 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 _
All Classes All Packages