omero.gateway.facility

Class RawDataFacility

java.lang.Object

omero.gateway.facility.Facility

omero.gateway.facility.RawDataFacility

All Implemented Interfaces:

AutoCloseable

public class RawDataFacility
extends Facility
implements AutoCloseable

A Facility for accessing raw data

Since:

5.1

Author:

Dominik Lindner d.lindner@dundee.ac.uk

Method Summary

Modifier and Type	Method and Description
void	close()
Map<Integer,int[]>	getHistogram(SecurityContext ctx, PixelsData pixels, int[] channels, int binCount, boolean globalRange, omero.romio.PlaneDef plane) Get the histogram data for the given image.
Map<Integer,int[]>	getHistogram(SecurityContext ctx, PixelsData pixels, int[] channels, int z, int t) Get the histogram data for the given image, using default 256 bins and the channels global min/max for the histogram range.
Plane2D	getPlane(SecurityContext ctx, PixelsData pixels, int z, int t, int c) Extracts a 2D plane from the pixels set.
Plane2D	getPlane(SecurityContext ctx, PixelsData pixels, int z, int t, int c, boolean close) Deprecated. Use getPlane(SecurityContext, PixelsData, z, t, c) instead
Plane2D	getTile(SecurityContext ctx, PixelsData pixels, int z, int t, int c, int x, int y, int w, int h) Extracts a 2D tile from the pixels set

Methods inherited from class omero.gateway.facility.Facility

addPropertyChangeListener, clear, firePropertyChanged, firePropertyChanged, getFacility, logDebug, logError, logInfo, logWarn, removePropertyChangeListener

Methods inherited from class java.lang.Object

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

Method Detail

getHistogram

public Map<Integer,int[]> getHistogram(SecurityContext ctx,
                                       PixelsData pixels,
                                       int[] channels,
                                       int z,
                                       int t)
                                throws DSOutOfServiceException,
                                       DSAccessException

Get the histogram data for the given image, using default 256 bins and the channels global min/max for the histogram range. Currently only non-tiled images are supported.

Parameters:

ctx - The SecurityContext

pixels - The PixelsData object

channels - The channel indices

z - The z plane index (optional; default: 0)

t - The t plane index (optional; default: 0)

Returns:

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

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

getHistogram

public Map<Integer,int[]> getHistogram(SecurityContext ctx,
                                       PixelsData pixels,
                                       int[] channels,
                                       int binCount,
                                       boolean globalRange,
                                       omero.romio.PlaneDef plane)
                                throws DSOutOfServiceException,
                                       DSAccessException

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

Parameters:

ctx - The SecurityContext

pixels - The PixelsData object

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:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

getPlane

public Plane2D getPlane(SecurityContext ctx,
                        PixelsData pixels,
                        int z,
                        int t,
                        int c)
                 throws DSOutOfServiceException,
                        DSAccessException

Extracts a 2D plane from the pixels set. Connection to the PixelsStore will be closed automatically.

Parameters:

ctx - The security context.

pixels - The PixelsData object to fetch the data from.

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:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

getPlane

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

Deprecated. Use getPlane(SecurityContext, PixelsData, z, t, c) instead

Extracts a 2D plane from the pixels set.

Parameters:

ctx - The security context.

pixels - The PixelsData object to fetch the data from.

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 - Pass true to close the connection to the Pixelstore, false to leave it open. (deprecated, the resources will be closed when the facility itself is closed, see close(), AutoCloseable)

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.

getTile

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

Extracts a 2D tile from the pixels set

Parameters:

ctx - The security context.

pixels - The PixelsData object to fetch the data from.

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 tile pixels.

Throws:

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

close

public void close()

Specified by:

close in interface AutoCloseable