ome.services

Class RawPixelsBean

java.lang.Object

ome.services.AbstractStatefulBean

ome.services.RawPixelsBean

All Implemented Interfaces:

java.io.Serializable, RawPixelsStore, ServiceInterface, StatefulServiceInterface, SelfConfigurableService

Direct Known Subclasses:

RawPixelsBeanReadOnly

@Transactional(readOnly=true)
public class RawPixelsBean
extends AbstractStatefulBean
implements RawPixelsStore

Implementation of the RawPixelsStore stateful service.

Since:

OMERO3

Version:

3.0 (Internal version: $Revision$ $Date: 2005/07/05 16:13:52 $)

Author:

Josh Moore josh.moore@gmx.de

See Also:

Serialized Form

Field Summary

Fields inherited from class ome.services.AbstractStatefulBean

iQuery, iUpdate, modified, sec

Constructor Summary

Constructors

Constructor and Description
RawPixelsBean() default constructor
RawPixelsBean(boolean checking, java.lang.String omeroDataDir) overridden to allow Spring to set boolean

Method Summary

Modifier and Type	Method and Description
void	activate() Completely restore this service for active use from whatever passivation it has implemented.
byte[]	calculateMessageDigest()
void	clean()
void	close() signals the end of the service lifecycle.
java.util.Map<java.lang.Integer,double[]>	findMinMax(int[] channels)
int	getByteWidth()
byte[]	getCol(int arg0, int arg1, int arg2, int arg3)
java.util.Map<java.lang.Integer,int[]>	getHistogram(int[] channels, int binCount, boolean globalRange, PlaneDef plane)
byte[]	getHypercube(java.util.List<java.lang.Integer> offset, java.util.List<java.lang.Integer> size, java.util.List<java.lang.Integer> step)
long	getPixelsId() Returns the current Pixels set identifier.
java.lang.String	getPixelsPath() Returns the current Pixels path.
byte[]	getPlane(int arg0, int arg1, int arg2)
long	getPlaneOffset(int arg0, int arg1, int arg2)
byte[]	getPlaneRegion(int z, int c, int t, int count, int offset)
long	getPlaneSize() Returns the plane size
byte[]	getRegion(int arg0, long arg1)
java.util.List<java.util.List<java.lang.Integer>>	getResolutionDescriptions()
int	getResolutionLevel() Retrieves the active resolution level.
int	getResolutionLevels() Retrieves the number of resolution levels that the backing pixels pyramid contains.
byte[]	getRow(int arg0, int arg1, int arg2, int arg3)
long	getRowOffset(int arg0, int arg1, int arg2, int arg3)
int	getRowSize()
java.lang.Class<? extends ServiceInterface>	getServiceInterface()
byte[]	getStack(int arg0, int arg1)
long	getStackOffset(int arg0, int arg1)
long	getStackSize()
byte[]	getTile(int z, int c, int t, int x, int y, int w, int h)
int[]	getTileSize()
byte[]	getTimepoint(int arg0)
long	getTimepointOffset(int arg0)
long	getTimepointSize()
long	getTotalSize()
boolean	isDiskSpaceChecking()
boolean	isFloat()
boolean	isSigned()
void	passivate() Perform whatever passivation is possible or throw an exception.
void	prepare(java.util.Set<java.lang.Long> pixelsIds) Prepares the stateful service with a cache of loaded Pixels objects.
boolean	requiresPixelsPyramid()
Pixels	save()
void	setDiskSpaceChecking(boolean diskSpaceChecking)
void	setIRepositoryInfo(IRepositoryInfo iRepositoryInfo) Disk Space Usage service Bean injector
void	setPixelsData(PixelsService dataService)
void	setPixelsId(long pixelsId, boolean bypassOriginalFile) Initializes the stateful service for a given Pixels set.
void	setPixelsMetadata(IPixels metaService)
void	setPlane(byte[] arg0, int arg1, int arg2, int arg3)
void	setRegion(int arg0, long arg1, byte[] arg2)
void	setResolutionLevel(int resolutionLevel) Sets the active resolution level.
void	setRow(byte[] arg0, int arg1, int arg2, int arg3, int arg4)
void	setSqlAction(SqlAction sql) SQL action Bean injector
void	setStack(byte[] arg0, int arg1, int arg2, int arg3)
void	setTile(byte[] data, int z, int c, int t, int x, int y, int w, int h)
void	setTimepoint(byte[] arg0, int arg1)

Methods inherited from class ome.services.AbstractStatefulBean

getBeanHelper, getCurrentEventContext, isModified, modified, selfConfigure, setQueryService, setSecuritySystem, setUpdateService

Methods inherited from class java.lang.Object

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

Methods inherited from interface ome.api.StatefulServiceInterface

getCurrentEventContext

Constructor Detail

RawPixelsBean

public RawPixelsBean()

default constructor

RawPixelsBean

public RawPixelsBean(boolean checking,
                     java.lang.String omeroDataDir)

overridden to allow Spring to set boolean

Parameters:

checking -

Method Detail

getServiceInterface

public java.lang.Class<? extends ServiceInterface> getServiceInterface()

Specified by:

getServiceInterface in interface SelfConfigurableService

setPixelsMetadata

public final void setPixelsMetadata(IPixels metaService)

setPixelsData

public final void setPixelsData(PixelsService dataService)

setIRepositoryInfo

public final void setIRepositoryInfo(IRepositoryInfo iRepositoryInfo)

Disk Space Usage service Bean injector

Parameters:

iRepositoryInfo - an IRepositoryInfo

setSqlAction

public final void setSqlAction(SqlAction sql)

SQL action Bean injector

Parameters:

sql - a SqlAction

passivate

@Transactional(readOnly=true)
public void passivate()

Description copied from interface: StatefulServiceInterface

Perform whatever passivation is possible or throw an exception. A good passivation method will free up as much memory as possible, most likely by storing it to disk. A call to passivate should be safe even if the service is already passivated.

Specified by:

passivate in interface StatefulServiceInterface

activate

@Transactional(readOnly=true)
public void activate()

Description copied from interface: StatefulServiceInterface

Completely restore this service for active use from whatever passivation it has implemented. A call to activate should be safe even if the service is already activated.

Specified by:

activate in interface StatefulServiceInterface

save

@Transactional(readOnly=false)
public Pixels save()

Specified by:

save in interface RawPixelsStore

close

@Transactional(readOnly=false)
public void close()

Description copied from interface: StatefulServiceInterface

signals the end of the service lifecycle. Resources such as Sessions can be released. All further calls will throw an exception.

Specified by:

close in interface StatefulServiceInterface

clean

public void clean()

setPixelsId

public void setPixelsId(long pixelsId,
                        boolean bypassOriginalFile)

Description copied from interface: RawPixelsStore

Initializes the stateful service for a given Pixels set.

Specified by:

setPixelsId in interface RawPixelsStore

Parameters:

pixelsId - Pixels set identifier.

bypassOriginalFile - Whether or not to bypass checking for an original file to back the pixel buffer used by this service. If requests are predominantly write-only or involve the population of a brand new pixel buffer using true here is a safe optimization otherwise false is expected.

getPixelsId

public long getPixelsId()

Description copied from interface: RawPixelsStore

Returns the current Pixels set identifier.

Specified by:

getPixelsId in interface RawPixelsStore

Returns:

See above.

getPixelsPath

public java.lang.String getPixelsPath()

Description copied from interface: RawPixelsStore

Returns the current Pixels path.

Specified by:

getPixelsPath in interface RawPixelsStore

Returns:

See above.

prepare

public void prepare(java.util.Set<java.lang.Long> pixelsIds)

Description copied from interface: RawPixelsStore

Prepares the stateful service with a cache of loaded Pixels objects. This method is designed to combat query overhead, where many sets of Pixels are to be read from or written to, by loading all the Pixels sets at once. Multiple calls will result in the existing cache being overwritten.

Specified by:

prepare in interface RawPixelsStore

Parameters:

pixelsIds - Pixels IDs to cache.

calculateMessageDigest

public byte[] calculateMessageDigest()

Specified by:

calculateMessageDigest in interface RawPixelsStore

getHypercube

public byte[] getHypercube(java.util.List<java.lang.Integer> offset,
                           java.util.List<java.lang.Integer> size,
                           java.util.List<java.lang.Integer> step)

Specified by:

getHypercube in interface RawPixelsStore

getPlaneRegion

public byte[] getPlaneRegion(int z,
                             int c,
                             int t,
                             int count,
                             int offset)

Specified by:

getPlaneRegion in interface RawPixelsStore

getPlane

public byte[] getPlane(int arg0,
                       int arg1,
                       int arg2)

Specified by:

getPlane in interface RawPixelsStore

getPlaneOffset

public long getPlaneOffset(int arg0,
                           int arg1,
                           int arg2)

Specified by:

getPlaneOffset in interface RawPixelsStore

getPlaneSize

public long getPlaneSize()

Description copied from interface: RawPixelsStore

Returns the plane size

Specified by:

getPlaneSize in interface RawPixelsStore

Returns:

the plane size

getRegion

public byte[] getRegion(int arg0,
                        long arg1)

Specified by:

getRegion in interface RawPixelsStore

getRow

public byte[] getRow(int arg0,
                     int arg1,
                     int arg2,
                     int arg3)

Specified by:

getRow in interface RawPixelsStore

getCol

public byte[] getCol(int arg0,
                     int arg1,
                     int arg2,
                     int arg3)

Specified by:

getCol in interface RawPixelsStore

getRowOffset

public long getRowOffset(int arg0,
                         int arg1,
                         int arg2,
                         int arg3)

Specified by:

getRowOffset in interface RawPixelsStore

getRowSize

public int getRowSize()

Specified by:

getRowSize in interface RawPixelsStore

getStack

public byte[] getStack(int arg0,
                       int arg1)

Specified by:

getStack in interface RawPixelsStore

getStackOffset

public long getStackOffset(int arg0,
                           int arg1)

Specified by:

getStackOffset in interface RawPixelsStore

getStackSize

public long getStackSize()

Specified by:

getStackSize in interface RawPixelsStore

getTimepoint

public byte[] getTimepoint(int arg0)

Specified by:

getTimepoint in interface RawPixelsStore

getTimepointOffset

public long getTimepointOffset(int arg0)

Specified by:

getTimepointOffset in interface RawPixelsStore

getTimepointSize

public long getTimepointSize()

Specified by:

getTimepointSize in interface RawPixelsStore

getTotalSize

public long getTotalSize()

Specified by:

getTotalSize in interface RawPixelsStore

getByteWidth

public int getByteWidth()

Specified by:

getByteWidth in interface RawPixelsStore

isSigned

public boolean isSigned()

Specified by:

isSigned in interface RawPixelsStore

isFloat

public boolean isFloat()

Specified by:

isFloat in interface RawPixelsStore

setPlane

public void setPlane(byte[] arg0,
                     int arg1,
                     int arg2,
                     int arg3)

Specified by:

setPlane in interface RawPixelsStore

setRegion

public void setRegion(int arg0,
                      long arg1,
                      byte[] arg2)

Specified by:

setRegion in interface RawPixelsStore

setRow

public void setRow(byte[] arg0,
                   int arg1,
                   int arg2,
                   int arg3,
                   int arg4)

Specified by:

setRow in interface RawPixelsStore

setStack

public void setStack(byte[] arg0,
                     int arg1,
                     int arg2,
                     int arg3)

Specified by:

setStack in interface RawPixelsStore

setTimepoint

public void setTimepoint(byte[] arg0,
                         int arg1)

Specified by:

setTimepoint in interface RawPixelsStore

getHistogram

public java.util.Map<java.lang.Integer,int[]> getHistogram(int[] channels,
                                                           int binCount,
                                                           boolean globalRange,
                                                           PlaneDef plane)

Specified by:

getHistogram in interface RawPixelsStore

findMinMax

public java.util.Map<java.lang.Integer,double[]> findMinMax(int[] channels)

Specified by:

findMinMax in interface RawPixelsStore

isDiskSpaceChecking

public boolean isDiskSpaceChecking()

setDiskSpaceChecking

public void setDiskSpaceChecking(boolean diskSpaceChecking)

getResolutionLevels

public int getResolutionLevels()

Description copied from interface: RawPixelsStore

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

Specified by:

getResolutionLevels in interface RawPixelsStore

Returns:

The number of resolution levels. This value does not necessarily indicate either the presence or absence of a pixels pyramid.

getResolutionDescriptions

public java.util.List<java.util.List<java.lang.Integer>> getResolutionDescriptions()

Specified by:

getResolutionDescriptions in interface RawPixelsStore

getTileSize

public int[] getTileSize()

Specified by:

getTileSize in interface RawPixelsStore

requiresPixelsPyramid

public boolean requiresPixelsPyramid()

Specified by:

requiresPixelsPyramid in interface RawPixelsStore

getResolutionLevel

public int getResolutionLevel()

Description copied from interface: RawPixelsStore

Retrieves the active resolution level.

Specified by:

getResolutionLevel in interface RawPixelsStore

Returns:

The active resolution level. The level will be non-negative and less than RawPixelsStore.getResolutionLevels(). Resolution level 0 is the smallest resolution and resolution level getResolutionLevels() - 1 is the largest resolution. This is the inverse of how Bio-Formats indexes resolutions.

setResolutionLevel

public void setResolutionLevel(int resolutionLevel)

Description copied from interface: RawPixelsStore

Sets the active resolution level.

Specified by:

setResolutionLevel in interface RawPixelsStore

Parameters:

resolutionLevel - The resolution level to be used. The level should be non-negative and less than RawPixelsStore.getResolutionLevels(). * Resolution level 0 is the smallest resolution and resolution level getResolutionLevels() - 1 is the largest resolution. This is the inverse of how Bio-Formats indexes resolutions.

getTile

public byte[] getTile(int z,
                      int c,
                      int t,
                      int x,
                      int y,
                      int w,
                      int h)

Specified by:

getTile in interface RawPixelsStore

setTile

public void setTile(byte[] data,
                    int z,
                    int c,
                    int t,
                    int x,
                    int y,
                    int w,
                    int h)

Specified by:

setTile in interface RawPixelsStore