ome.io.nio

Class PixelsService

java.lang.Object

ome.io.nio.AbstractFileSystemService

ome.io.nio.PixelsService

All Implemented Interfaces:

org.springframework.beans.factory.Aware, org.springframework.context.ApplicationEventPublisherAware

public class PixelsService
extends AbstractFileSystemService
implements org.springframework.context.ApplicationEventPublisherAware

Since:

OMERO-Beta1.0

Field Summary

Fields

Modifier and Type	Field and Description
protected BackOff	backOff BackOff implementation for calculating MissingPyramidExceptions
static long	MEMOIZER_WAIT Default of 100 ms for memoizerWait
protected java.io.File	memoizerDirectory Location where cached data from the Memoizer should be stored.
protected java.io.File	memoizerDirectoryLocalRW For read-only servers, this directory is a local read-write directory for storing memo files.
protected long	memoizerWait Time in ms.
static byte[]	NULL_PLANE Null plane byte array.
static int	NULL_PLANE_SIZE Null plane size constant.
static byte[]	nullPlane Deprecated. in favor of NULL_PLANE
static java.lang.String	PYRAMID_SUFFIX Suffix for an the image pyramid of a given pixels set.
protected FilePathResolver	resolver Resolver of archived original file paths for pixels sets.
protected TileSizes	sizes TileSizes implementation for default values

Fields inherited from class ome.io.nio.AbstractFileSystemService

FILES_PATH, PIXELS_PATH, ROOT_DEFAULT, THUMBNAILS_PATH

Constructor Summary

Constructors

Constructor and Description
PixelsService(java.lang.String path) Constructor.
PixelsService(java.lang.String path, boolean isReadOnlyRepo, java.io.File memoizerDirectory, long memoizerWait, FilePathResolver resolver, BackOff backOff, TileSizes sizes, ome.api.IQuery iQuery)
PixelsService(java.lang.String path, boolean isReadOnlyRepo, long memoizerWait, FilePathResolver resolver, BackOff backOff, TileSizes sizes, ome.api.IQuery iQuery) Deprecated.
PixelsService(java.lang.String path, java.io.File memoizerDirectory, FilePathResolver resolver, BackOff backOff, TileSizes sizes, ome.api.IQuery iQuery) Call PixelsService(String, boolean, File, long, FilePathResolver, BackOff, TileSizes, IQuery) with MEMOIZER_WAIT.
PixelsService(java.lang.String path, java.io.File memoizerDirectory, long memoizerWait, FilePathResolver resolver, BackOff backOff, TileSizes sizes, ome.api.IQuery iQuery) Deprecated.
PixelsService(java.lang.String path, FilePathResolver resolver) Deprecated.
PixelsService(java.lang.String path, FilePathResolver resolver, BackOff backOff, TileSizes sizes, ome.api.IQuery iQuery) Constructor.
PixelsService(java.lang.String path, long memoizerWait, FilePathResolver resolver, BackOff backOff, TileSizes sizes, ome.api.IQuery iQuery) Deprecated.

Method Summary

Modifier and Type	Method and Description
PixelBuffer	_getPixelBuffer(ome.model.core.Pixels pixels, boolean write)
protected BfPixelBuffer	createBfPixelBuffer(java.lang.String filePath, int series) Helper method to properly log any exceptions raised by Bio-Formats.
protected loci.formats.IFormatReader	createBfReader() Create an IFormatReader with the appropriate ReaderWrapper instances and IFormatReader.setFlattenedResolutions(boolean) set to false.
protected BfPixelBuffer	createMinMaxBfPixelBuffer(java.lang.String filePath, int series, loci.formats.meta.IMinMaxStore store) Helper method to properly log any exceptions raised by Bio-Formats and add a min/max calculator wrapper to the reader stack.
PixelBuffer	createPixelBuffer(ome.model.core.Pixels pixels) Creates a PixelBuffer for a given pixels set.
protected BfPyramidPixelBuffer	createPyramidPixelBuffer(ome.model.core.Pixels pixels, java.lang.String filePath, boolean write) Helper method to properly log any exceptions raised by Bio-Formats.
protected PixelBuffer	createRomioPixelBuffer(java.lang.String pixelsFilePath, ome.model.core.Pixels pixels, boolean allowModification) Helper method to properlty create a RomioPixelBuffer.
loci.formats.IFormatReader	getBfReader(ome.model.core.Pixels pixels) 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.
java.io.File	getMemoizerDirectory()
long	getMemoizerWait()
protected java.lang.String	getOriginalFilePath(ome.model.core.Pixels pixels) Retrieves the original file path for a given set of pixels.
PixelBuffer	getPixelBuffer(ome.model.core.Pixels pixels) Deprecated. In the future callers should use the more descriptive getPixelBuffer(Pixels, boolean).
PixelBuffer	getPixelBuffer(ome.model.core.Pixels pixels, boolean write) Returns a pixel buffer for a given set of pixels.
protected int	getSeries(ome.model.core.Pixels pixels) Retrieves the series for a given set of pixels.
protected void	handleMissingPyramid(ome.model.core.Pixels pixels, java.lang.String pixelsPyramidFilePath) If the outer loop should continue, this method returns successfully; otherwise it throws a MissingPyramidException.
protected void	handleMissingStatsInfo(ome.model.core.Pixels pixels) If the outer loop should continue, this method returns successfully; otherwise it throws a MissingPyramidException.
ome.model.stats.StatsInfo[]	makePyramid(ome.model.core.Pixels pixels) Creates a pixels pyramid for a given set of pixels.
void	removePixels(java.util.List<java.lang.Long> pixelIds) Removes files from data repository based on a parameterized List of Long pixels ids
boolean	requiresPixelsPyramid(ome.model.core.Pixels pixels) Returns whether a pyramid should be used for the given Pixels.
void	setApplicationEventPublisher(org.springframework.context.ApplicationEventPublisher pub)
void	setFilePathResolver(FilePathResolver resolver)
void	setMemoizerDirectoryLocal(java.lang.String path)
void	setMetrics(ome.system.metrics.Metrics metrics)
void	setReaderSecurityCheck(ReaderSecurityCheck check)

Methods inherited from class ome.io.nio.AbstractFileSystemService

createSubpath, getFilesPath, getPixelsDirectory, getPixelsPath, getThumbnailPath

Methods inherited from class java.lang.Object

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

Field Detail

PYRAMID_SUFFIX

public static final java.lang.String PYRAMID_SUFFIX

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

See Also:

Constant Field Values

NULL_PLANE_SIZE

public static final int NULL_PLANE_SIZE

Null plane size constant.

See Also:

Constant Field Values

NULL_PLANE

public static final byte[] NULL_PLANE

Null plane byte array.

MEMOIZER_WAIT

public static final long MEMOIZER_WAIT

Default of 100 ms for memoizerWait

See Also:

Constant Field Values

resolver

protected FilePathResolver resolver

Resolver of archived original file paths for pixels sets.

backOff

protected final BackOff backOff

BackOff implementation for calculating MissingPyramidExceptions

sizes

protected final TileSizes sizes

TileSizes implementation for default values

memoizerDirectory

protected final java.io.File memoizerDirectory

Location where cached data from the Memoizer should be stored.

memoizerDirectoryLocalRW

protected java.io.File memoizerDirectoryLocalRW

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

memoizerWait

protected final long memoizerWait

Time in ms. which setId must take before a file is memoized

nullPlane

@Deprecated
public static final byte[] nullPlane

Deprecated. in favor of NULL_PLANE

Null plane byte array.

Constructor Detail

PixelsService

public PixelsService(java.lang.String path)

Constructor.

Parameters:

path - The root of the ROMIO proprietary pixels store. (usually /OMERO/Pixels).

PixelsService

@Deprecated
public PixelsService(java.lang.String path,
                                 FilePathResolver resolver)

Deprecated.

Constructor.

Parameters:

path - The root of the ROMIO proprietary pixels store. (usually /OMERO/Pixels).

PixelsService

public PixelsService(java.lang.String path,
                     FilePathResolver resolver,
                     BackOff backOff,
                     TileSizes sizes,
                     ome.api.IQuery iQuery)

Constructor.

Parameters:

path - The root of the ROMIO proprietary pixels store. (usually /OMERO/Pixels).

resolver - Original file path resolver for pixels sets.

PixelsService

@Deprecated
public PixelsService(java.lang.String path,
                                 long memoizerWait,
                                 FilePathResolver resolver,
                                 BackOff backOff,
                                 TileSizes sizes,
                                 ome.api.IQuery iQuery)

Deprecated.

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

PixelsService

@Deprecated
public PixelsService(java.lang.String path,
                                 boolean isReadOnlyRepo,
                                 long memoizerWait,
                                 FilePathResolver resolver,
                                 BackOff backOff,
                                 TileSizes sizes,
                                 ome.api.IQuery iQuery)

Deprecated.

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

PixelsService

public PixelsService(java.lang.String path,
                     java.io.File memoizerDirectory,
                     FilePathResolver resolver,
                     BackOff backOff,
                     TileSizes sizes,
                     ome.api.IQuery iQuery)

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

PixelsService

@Deprecated
public PixelsService(java.lang.String path,
                                 java.io.File memoizerDirectory,
                                 long memoizerWait,
                                 FilePathResolver resolver,
                                 BackOff backOff,
                                 TileSizes sizes,
                                 ome.api.IQuery iQuery)

Deprecated.

PixelsService

public PixelsService(java.lang.String path,
                     boolean isReadOnlyRepo,
                     java.io.File memoizerDirectory,
                     long memoizerWait,
                     FilePathResolver resolver,
                     BackOff backOff,
                     TileSizes sizes,
                     ome.api.IQuery iQuery)

Method Detail

setMetrics

public void setMetrics(ome.system.metrics.Metrics metrics)

setReaderSecurityCheck

public void setReaderSecurityCheck(ReaderSecurityCheck check)

Parameters:

check - the used files check to apply after subsequent IFormatHandler.setId(String)

getMemoizerWait

public long getMemoizerWait()

getMemoizerDirectory

public java.io.File getMemoizerDirectory()

setApplicationEventPublisher

public void setApplicationEventPublisher(org.springframework.context.ApplicationEventPublisher pub)

Specified by:

setApplicationEventPublisher in interface org.springframework.context.ApplicationEventPublisherAware

setFilePathResolver

public void setFilePathResolver(FilePathResolver resolver)

setMemoizerDirectoryLocal

public void setMemoizerDirectoryLocal(java.lang.String path)

createPixelBuffer

public PixelBuffer createPixelBuffer(ome.model.core.Pixels pixels)
                              throws java.io.IOException

Creates a PixelBuffer for a given pixels set.

Parameters:

pixels - Pixels set to create a pixel buffer for.

Returns:

Allocated pixel buffer ready to be used.

Throws:

java.io.IOException - If there is an I/O error creating the pixel buffer backing file.

makePyramid

public ome.model.stats.StatsInfo[] makePyramid(ome.model.core.Pixels pixels)

Creates a pixels pyramid for a given set of pixels. If the pyramid file already exists, then a DEBUG message is logged and this method returns.

Parameters:

pixels - Pixels set to retrieve a pixel buffer for.

Since:

OMERO-Beta4.3

getPixelBuffer

@Deprecated
public PixelBuffer getPixelBuffer(ome.model.core.Pixels pixels)

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

Returns a pixel buffer for a given set of pixels. Either a proprietary ROMIO pixel buffer or a specific pixel buffer implementation.

Parameters:

pixels - Pixels set to retrieve a pixel buffer for.

Returns:

A pixel buffer instance. NOTE: The pixel buffer is initialized as read-write.

Since:

OMERO-Beta4.3

See Also:

getPixelBuffer(Pixels, boolean)

getPixelBuffer

public PixelBuffer getPixelBuffer(ome.model.core.Pixels pixels,
                                  boolean write)

Returns a pixel buffer for a given set of pixels. Either a proprietary ROMIO pixel buffer or a specific pixel buffer implementation.

Parameters:

pixels - Pixels set to retrieve a pixel buffer for.

write - Whether or not to open the pixel buffer as read-write. true opens as read-write, false opens as read-only.

Returns:

A pixel buffer instance.

Since:

OMERO-Beta4.3

_getPixelBuffer

public PixelBuffer _getPixelBuffer(ome.model.core.Pixels pixels,
                                   boolean write)

requiresPixelsPyramid

public boolean requiresPixelsPyramid(ome.model.core.Pixels pixels)

Returns whether a pyramid should be used for the given Pixels. This usually implies that this is a "Big image" and therefore will need tiling.

Parameters:

pixels -

Returns:

true if a pyramid should be used, false otherwise

getOriginalFilePath

protected java.lang.String getOriginalFilePath(ome.model.core.Pixels pixels)

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

Parameters:

pixels - Set of pixels to return an orignal file path for.

Returns:

The original file path or null if the original file path could not be located or the resolver has not been set.

getSeries

protected int getSeries(ome.model.core.Pixels pixels)

Retrieves the series for a given set of pixels.

Parameters:

pixels - Set of pixels to return the series for.

Returns:

The series as specified by the pixels parameters or 0 (the first series).

handleMissingStatsInfo

protected void handleMissingStatsInfo(ome.model.core.Pixels pixels)

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

Parameters:

pixels -

handleMissingPyramid

protected void handleMissingPyramid(ome.model.core.Pixels pixels,
                                    java.lang.String pixelsPyramidFilePath)

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

Parameters:

pixels -

pixelsPyramidFilePath -

Throws:

ome.conditions.MissingPyramidException

createMinMaxBfPixelBuffer

protected BfPixelBuffer createMinMaxBfPixelBuffer(java.lang.String filePath,
                                                  int series,
                                                  loci.formats.meta.IMinMaxStore store)

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

Parameters:

filePath - Non-null.

series - series to use

store - Min/max store to use with the min/max calculator.

getBfReader

public loci.formats.IFormatReader getBfReader(ome.model.core.Pixels pixels)
                                       throws loci.formats.FormatException,
                                              java.io.IOException

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. This may be used to access the original metadata.

Throws:

loci.formats.FormatException

java.io.IOException

createBfReader

protected loci.formats.IFormatReader createBfReader()

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

createBfPixelBuffer

protected BfPixelBuffer createBfPixelBuffer(java.lang.String filePath,
                                            int series)

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

Parameters:

filePath - Non-null.

series - series to use

Returns:

the initialized BfPixelBuffer

createPyramidPixelBuffer

protected BfPyramidPixelBuffer createPyramidPixelBuffer(ome.model.core.Pixels pixels,
                                                        java.lang.String filePath,
                                                        boolean write)

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

Parameters:

pixels - passed to BfPixelBuffer

filePath - Non-null.

Returns:

the initialized BfPyramidPixelBuffer

createRomioPixelBuffer

protected PixelBuffer createRomioPixelBuffer(java.lang.String pixelsFilePath,
                                             ome.model.core.Pixels pixels,
                                             boolean allowModification)

Helper method to properlty create a RomioPixelBuffer.

Parameters:

pixelsFilePath -

pixels -

allowModification -

removePixels

public void removePixels(java.util.List<java.lang.Long> pixelIds)

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

Parameters:

pixelIds - Long file keys to be deleted

Throws:

ome.conditions.ResourceError - If deletion fails.