omero.gateway.rnd

Class DataSink

java.lang.Object

omero.gateway.rnd.DataSink

All Implemented Interfaces:

AutoCloseable

public class DataSink
extends Object
implements AutoCloseable

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.

Constructor Summary

Constructors

Constructor and Description
DataSink(SecurityContext ctx, PixelsData source, Gateway gw) Creates a new instance.

Method Summary

Modifier and Type	Method and Description
void	close()
Map<Integer,int[]>	getHistogram(int[] channels, int binCount, boolean globalRange, omero.romio.PlaneDef plane) Get the histogram data for the given image.
Plane2D	getPlane(int z, int t, int c) Extracts a 2D plane from the pixels set this object is working for.
Plane2D	getTile(int z, int t, int c, int x, int y, int w, int h) 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.

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

Constructor Detail

DataSink

public DataSink(SecurityContext ctx,
                PixelsData source,
                Gateway gw)
         throws DSOutOfServiceException

Creates a new instance.

Parameters:

ctx - The SecurityContext

source - The pixels set.

gw - Reference to the gateway.

Throws:

DSOutOfServiceException - If the PixelsStore can't be accessed

Method Detail

getTile

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

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

Parameters:

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

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(int z,
                        int t,
                        int c)
                 throws DataSourceException

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

Parameters:

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.

getHistogram

public Map<Integer,int[]> getHistogram(int[] channels,
                                       int binCount,
                                       boolean globalRange,
                                       omero.romio.PlaneDef plane)
                                throws DataSourceException

Get the histogram data for the given image. Currently only non-tiled images are supported.

Parameters:

channels - The channel indices

binCount - The number of bins (optional, default: 256)

globalRange - Use the global minimum/maximum to determine the histogram range, otherwise use plane minimum/maximum value

plane - The plane to specify z/t and/or a certain region (optional, default: whole region of the first z/t plane)

Returns:

A Map of histogram data, where the key is the channel index

Throws:

DataSourceException - If an error occurred

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.

close

public void close()

Specified by:

close in interface AutoCloseable