ome.api

Interface RawPixelsStore

All Superinterfaces:

ServiceInterface, StatefulServiceInterface

public interface RawPixelsStore
extends StatefulServiceInterface

Binary data provider. Initialized with the id of a Pixels instance, this interface can provide various slices, stacks, regions of the 5-dimensional (X-Y planes with multiple Z-sections and Channels over Time). The byte array returned by the getter methods and passed to the setter methods can and will be interpreted according to results of getByteWidth(), isFloat(), and isSigned().

Method Summary

Modifier and Type	Method and Description
byte[]	calculateMessageDigest()
java.util.Map<java.lang.Integer,double[]>	findMinMax(int[] channels)
int	getByteWidth()
byte[]	getCol(int x, int z, int c, int t)
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 z, int c, int t)
long	getPlaneOffset(int z, int c, int t)
byte[]	getPlaneRegion(int z, int c, int t, int count, int offset)
long	getPlaneSize() Returns the plane size
byte[]	getRegion(int size, long offset)
java.lang.Object	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 y, int z, int c, int t)
long	getRowOffset(int y, int z, int c, int t)
int	getRowSize()
byte[]	getStack(int c, int t)
long	getStackOffset(int c, int t)
long	getStackSize()
byte[]	getTile(int z, int c, int t, int x, int y, int w, int h)
int[]	getTileSize()
byte[]	getTimepoint(int t)
long	getTimepointOffset(int t)
long	getTimepointSize()
long	getTotalSize()
boolean	isFloat()
boolean	isSigned()
void	prepare(java.util.Set<java.lang.Long> pixelsIds) Prepares the stateful service with a cache of loaded Pixels objects.
boolean	requiresPixelsPyramid()
ome.model.core.Pixels	save()
void	setPixelsId(long pixelsId, boolean bypassOriginalFile) Initializes the stateful service for a given Pixels set.
void	setPlane(byte[] buffer, int z, int c, int t)
void	setRegion(int size, long offset, byte[] buffer)
void	setResolutionLevel(int resolutionLevel) Sets the active resolution level.
void	setRow(byte[] buffer, int y, int z, int c, int t)
void	setStack(byte[] buffer, int z, int c, int t)
void	setTile(byte[] buffer, int z, int c, int t, int x, int y, int w, int h)
void	setTimepoint(byte[] buffer, int t)

Methods inherited from interface ome.api.StatefulServiceInterface

activate, close, getCurrentEventContext, passivate

Method Detail

setPixelsId

void setPixelsId(long pixelsId,
                 boolean bypassOriginalFile)

Initializes the stateful service for a given Pixels set.

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.

getPixelsPath

java.lang.String getPixelsPath()

Returns the current Pixels path.

Returns:

See above.

getPixelsId

long getPixelsId()

Returns the current Pixels set identifier.

Returns:

See above.

prepare

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

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.

Parameters:

pixelsIds - Pixels IDs to cache.

getPlaneSize

long getPlaneSize()

Returns the plane size

Returns:

the plane size

getRowSize

int getRowSize()

getStackSize

long getStackSize()

getTimepointSize

long getTimepointSize()

getTotalSize

long getTotalSize()

getRowOffset

long getRowOffset(int y,
                  int z,
                  int c,
                  int t)

getPlaneOffset

long getPlaneOffset(int z,
                    int c,
                    int t)

getStackOffset

long getStackOffset(int c,
                    int t)

getTimepointOffset

long getTimepointOffset(int t)

getTile

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

getRegion

byte[] getRegion(int size,
                 long offset)

getRow

byte[] getRow(int y,
              int z,
              int c,
              int t)

getCol

byte[] getCol(int x,
              int z,
              int c,
              int t)

getHistogram

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

findMinMax

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

getHypercube

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

getPlaneRegion

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

getPlane

byte[] getPlane(int z,
                int c,
                int t)

getStack

byte[] getStack(int c,
                int t)

getTimepoint

byte[] getTimepoint(int t)

setTile

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

setRegion

void setRegion(int size,
               long offset,
               byte[] buffer)

setRow

void setRow(byte[] buffer,
            int y,
            int z,
            int c,
            int t)

setPlane

void setPlane(byte[] buffer,
              int z,
              int c,
              int t)

setStack

void setStack(byte[] buffer,
              int z,
              int c,
              int t)

setTimepoint

void setTimepoint(byte[] buffer,
                  int t)

getByteWidth

int getByteWidth()

isSigned

boolean isSigned()

isFloat

boolean isFloat()

calculateMessageDigest

byte[] calculateMessageDigest()

save

ome.model.core.Pixels save()

requiresPixelsPyramid

boolean requiresPixelsPyramid()

getResolutionDescriptions

java.lang.Object getResolutionDescriptions()

getResolutionLevels

int getResolutionLevels()

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

Returns:

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

getResolutionLevel

int getResolutionLevel()

Retrieves the active resolution level.

Returns:

The active resolution level. The level will be non-negative and less than 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

void setResolutionLevel(int resolutionLevel)

Sets the active resolution level.

Parameters:

resolutionLevel - The resolution level to be used. The level should be non-negative and less than 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.

getTileSize

int[] getTileSize()