omero.gateway.rnd

Class DataSink

java.lang.Object

omero.gateway.rnd.DataSink

public class DataSink
extends Object

Encapsulates access to the image raw data. Contains the logic to interpret a linear byte array as a 5D array. Knows how to extract a 2D-plane from the 5D array, but delegates to the specified 2D-Plane the retrieval of pixel values.

Since:

OME3.0

Version:

3.0

Author:

Jean-Marie Burel j.burel@dundee.ac.uk, Donald MacDonald donald@lifesci.dundee.ac.uk

Field Summary

Fields

Modifier and Type	Field and Description
static String	DOUBLE Identifies the type used to store pixel values.
static String	FLOAT Identifies the type used to store pixel values.
static String	INT_16 Identifies the type used to store pixel values.
static String	INT_32 Identifies the type used to store pixel values.
static String	INT_8 Identifies the type used to store pixel values.
static String	UINT_16 Identifies the type used to store pixel values.
static String	UINT_32 Identifies the type used to store pixel values.
static String	UINT_8 Identifies the type used to store pixel values.

Method Summary

Modifier and Type	Method and Description
void	clearCache() Erases the cache.
Plane2D	getPlane(SecurityContext ctx, int z, int t, int c) Extracts a 2D plane from the pixels set this object is working for.
Plane2D	getPlane(SecurityContext ctx, int z, int t, int c, boolean close) Extracts a 2D plane from the pixels set this object is working for.
Plane2D	getTile(SecurityContext ctx, int z, int t, int c, int x, int y, int w, int h, boolean close) Extracts a 2D tile from the pixels set this object is working for.
boolean	isSame(long pixelsID) Returns true if a data source has already been created for the specified pixels set, false otherwise.
static DataSink	makeNew(PixelsData source, Gateway gw) Factory method to create a new DataSink to handle access to the metadata associated with the specified pixels set.
static DataSink	makeNew(PixelsData source, Gateway gw, int cacheSize) Factory method to create a new DataSink to handle access to the metadata associated with the specified pixels set.
void	setCacheInMemory(boolean cacheInMemory) Sets the size either to 1 or 0 depending on the passed value.

Methods inherited from class java.lang.Object

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

Field Detail

INT_8

public static final String INT_8

Identifies the type used to store pixel values.

See Also:

Constant Field Values

UINT_8

public static final String UINT_8

Identifies the type used to store pixel values.

See Also:

Constant Field Values

INT_16

public static final String INT_16

Identifies the type used to store pixel values.

See Also:

Constant Field Values

UINT_16

public static final String UINT_16

Identifies the type used to store pixel values.

See Also:

Constant Field Values

INT_32

public static final String INT_32

Identifies the type used to store pixel values.

See Also:

Constant Field Values

UINT_32

public static final String UINT_32

Identifies the type used to store pixel values.

See Also:

Constant Field Values

FLOAT

public static final String FLOAT

Identifies the type used to store pixel values.

See Also:

Constant Field Values

DOUBLE

public static final String DOUBLE

Identifies the type used to store pixel values.

See Also:

Constant Field Values

Method Detail

makeNew

public static DataSink makeNew(PixelsData source,
                               Gateway gw)

Factory method to create a new DataSink to handle access to the metadata associated with the specified pixels set.

Parameters:

source - The pixels set. Mustn't be null.

gw - Reference to the Gateway Mustn't be null.

Returns:

See above.

makeNew

public static DataSink makeNew(PixelsData source,
                               Gateway gw,
                               int cacheSize)

Factory method to create a new DataSink to handle access to the metadata associated with the specified pixels set.

Parameters:

source - The pixels set. Mustn't be null.

gw - Reference to the Gateway Mustn't be null.

cacheSize - The size of the cache to use. (Make sure the Gateway provides a CacheService)

Returns:

See above.

getTile

public Plane2D getTile(SecurityContext ctx,
                       int z,
                       int t,
                       int c,
                       int x,
                       int y,
                       int w,
                       int h,
                       boolean close)
                throws DataSourceException

Extracts a 2D tile from the pixels set this object is working for.

Parameters:

ctx - The security context.

z - The z-section at which data is to be fetched.

t - The timepoint at which data is to be fetched.

c - The channel at which data is to be fetched.

x - The x coordinate

y - The y coordinate

w - The width of the tile

h - The height of the tile

close - Indicates to close the service if true.

Returns:

A plane 2D object that encapsulates the actual plane pixels.

Throws:

DataSourceException - If an error occurs while retrieving the plane data from the pixels source.

getPlane

public Plane2D getPlane(SecurityContext ctx,
                        int z,
                        int t,
                        int c)
                 throws DataSourceException

Extracts a 2D plane from the pixels set this object is working for.

Parameters:

ctx - The security context.

z - The z-section at which data is to be fetched.

t - The timepoint at which data is to be fetched.

c - The channel at which data is to be fetched.

Returns:

A plane 2D object that encapsulates the actual plane pixels.

Throws:

DataSourceException - If an error occurs while retrieving the plane data from the pixels source.

getPlane

public Plane2D getPlane(SecurityContext ctx,
                        int z,
                        int t,
                        int c,
                        boolean close)
                 throws DataSourceException

Extracts a 2D plane from the pixels set this object is working for.

Parameters:

ctx - The security context.

z - The z-section at which data is to be fetched.

t - The timepoint at which data is to be fetched.

c - The channel at which data is to be fetched.

close - Indicate to close or not the service.

Returns:

A plane 2D object that encapsulates the actual plane pixels.

Throws:

DataSourceException - If an error occurs while retrieving the plane data from the pixels source.

isSame

public boolean isSame(long pixelsID)

Returns true if a data source has already been created for the specified pixels set, false otherwise.

Parameters:

pixelsID - The id of the pixels set.

Returns:

See above.

clearCache

public void clearCache()

Erases the cache.

setCacheInMemory

public void setCacheInMemory(boolean cacheInMemory)

Sets the size either to 1 or 0 depending on the passed value.

Parameters:

cacheInMemory - Passed true to set the size to 1, false to set to 0.