ome.services.projection

Class ProjectionBean

java.lang.Object

ome.logic.AbstractLevel2Service

ome.services.projection.ProjectionBean

All Implemented Interfaces:

IProjection, ServiceInterface, SelfConfigurableService

@Transactional(readOnly=true)
public class ProjectionBean
extends AbstractLevel2Service
implements IProjection

Implements projection functionality for Pixels sets as declared in IProjection.

Since:

OMERO-Beta3.1

Author:

Chris Allan callan@blackcat.ca

Field Summary

Fields

Modifier and Type	Field and Description
protected IPixels	iPixels Reference to the service used to retrieve the pixels metadata.
protected PixelsService	pixelsService Reference to the service used to retrieve the pixels data.

Fields inherited from class ome.logic.AbstractLevel2Service

iQuery, iUpdate, metadata, queryFactory, sec

Fields inherited from interface ome.api.IProjection

MAXIMUM_INTENSITY, MEAN_INTENSITY, METHODOLOGY_STRINGS, SUM_INTENSITY

Constructor Summary

Constructors

Constructor and Description
ProjectionBean()

Method Summary

Modifier and Type	Method and Description
Class<? extends ServiceInterface>	getServiceInterface() Returns the interface this implementation is for.
long	projectPixels(long pixelsId, PixelsType pixelsType, int algorithm, int tStart, int tEnd, List<Integer> channels, int stepping, int zStart, int zEnd, String name) Performs a projection through selected optical sections and optical sections for a given set of time points of a Pixels set.
byte[]	projectStack(long pixelsId, PixelsType pixelsType, int algorithm, int timepoint, int channelIndex, int stepping, int start, int end) Performs a projection through the optical sections of a particular wavelength at a given time point of a Pixels set.
void	setIPixels(IPixels iPixels) IPixels bean injector.
void	setPixelsService(PixelsService pixelsService) PixelsService bean injector.

Methods inherited from class ome.logic.AbstractLevel2Service

getBeanHelper, getExtendedMetadata, getQueryFactory, getSecuritySystem, selfConfigure, setExtendedMetadata, setQueryFactory, setQueryService, setSecuritySystem, setUpdateService

Methods inherited from class java.lang.Object

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

Field Detail

iPixels

protected transient IPixels iPixels

Reference to the service used to retrieve the pixels metadata.

pixelsService

protected transient PixelsService pixelsService

Reference to the service used to retrieve the pixels data.

Constructor Detail

ProjectionBean

public ProjectionBean()

Method Detail

getServiceInterface

public Class<? extends ServiceInterface> getServiceInterface()

Returns the interface this implementation is for.

Specified by:

getServiceInterface in interface SelfConfigurableService

See Also:

SelfConfigurableService.getServiceInterface()

setIPixels

public void setIPixels(IPixels iPixels)

IPixels bean injector. For use during configuration. Can only be called once.

setPixelsService

public void setPixelsService(PixelsService pixelsService)

PixelsService bean injector. For use during configuration. Can only be called once.

projectStack

public byte[] projectStack(long pixelsId,
                           PixelsType pixelsType,
                           int algorithm,
                           int timepoint,
                           int channelIndex,
                           int stepping,
                           int start,
                           int end)

Description copied from interface: IProjection

Performs a projection through the optical sections of a particular wavelength at a given time point of a Pixels set.

Specified by:

projectStack in interface IProjection

Parameters:

pixelsId - The source Pixels set Id.

pixelsType - The destination Pixels type. If null, the source Pixels set pixels type will be used.

algorithm - MAXIMUM_INTENSITY, MEAN_INTENSITY or SUM_INTENSITY. NOTE: When performing a SUM_INTENSITY projection, pixel values will be pinned to the maximum pixel value of the destination Pixels type.

timepoint - Timepoint to perform the projection.

channelIndex - Index of the channel to perform the projection.

stepping - Stepping value to use while calculating the projection. For example, stepping=1 will use every optical section from start to end where stepping=2 will use every other section from start to end to perform the projection.

start - Optical section to start projecting from.

end - Optical section to finish projecting.

Returns:

A byte array of projected pixel values whose length is equal to the Pixels set sizeX * sizeY * bytesPerPixel in big-endian format.

See Also:

IProjection.projectPixels(long, PixelsType, int, int, int, List, int, int, int, String)

projectPixels

@Transactional(readOnly=false)
public long projectPixels(long pixelsId,
                                                         PixelsType pixelsType,
                                                         int algorithm,
                                                         int tStart,
                                                         int tEnd,
                                                         List<Integer> channels,
                                                         int stepping,
                                                         int zStart,
                                                         int zEnd,
                                                         String name)

Description copied from interface: IProjection

Performs a projection through selected optical sections and optical sections for a given set of time points of a Pixels set. The Image which is linked to the Pixels set will be copied using IPixels.copyAndResizeImage(long, Integer, Integer, Integer, Integer, List, String, boolean).

Specified by:

projectPixels in interface IProjection

Parameters:

pixelsId - The source Pixels set Id.

pixelsType - The destination Pixels type. If null, the source Pixels set pixels type will be used.

algorithm - MAXIMUM_INTENSITY, MEAN_INTENSITY or SUM_INTENSITY. NOTE: When performing a SUM_INTENSITY projection, pixel values will be pinned to the maximum pixel value of the destination Pixels type.

tStart - Timepoint to start projecting from.

tEnd - Timepoint to finish projecting.

channels - List of the channel indexes to use while calculating the projection.

stepping - Stepping value to use while calculating the projection. For example, stepping=1 will use every optical section from start to end where stepping=2 will use every other section from start to end to perform the projection.

zStart - Optical section to start projecting from.

zEnd - Optical section to finish projecting.

name - Name for the newly created image. If null the name of the Image linked to the Pixels qualified by pixelsId will be used with a "Projection" suffix. For example, GFP-H2B Image of HeLa Cells will have an Image name of GFP-H2B Image of HeLa Cells Projection used for the projection.

Returns:

The Id of the newly created Image which has been projected.

See Also:

IProjection.projectStack(long, PixelsType, int, int, int, int, int start, int)