Package ome.services.blitz.impl

Class RoiI

java.lang.Object

ome.services.blitz.impl.AbstractAmdServant

ome.services.blitz.impl.RoiI

All Implemented Interfaces:

BlitzOnly, ServiceFactoryAware, _IRoiOperations, _ServiceInterfaceOperations, org.springframework.beans.factory.Aware, org.springframework.context.ApplicationContextAware

public class RoiI
extends AbstractAmdServant
implements _IRoiOperations, ServiceFactoryAware, BlitzOnly

implementation of the IRoi service interface.

Since:

Beta4.1

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	RoiI.RoiResultMapper
static class	RoiI.RoiResultMapReturnMapper
static class	RoiI.RoiResultReturnMapper

Field Summary

Fields

Modifier and Type	Field	Description
protected ServiceFactoryI	factory
protected GeomTool	geomTool
protected ome.util.SqlAction	sql

Fields inherited from class ome.services.blitz.impl.AbstractAmdServant

be, ctx, holder, invoker, log, service

Constructor Summary

Constructors

Constructor	Description
RoiI(BlitzExecutor be, GeomTool geomTool, ome.util.SqlAction sql)

Method Summary

Modifier and Type	Method	Description
void	findByImage_async(AMD_IRoi_findByImage __cb, long imageId, RoiOptions opts, Ice.Current __current)	Returns all the Rois in an Image, indexed via Shape.
void	findByPlane_async(AMD_IRoi_findByPlane __cb, long imageId, int z, int t, RoiOptions opts, Ice.Current __current)	Returns all the Rois on the given plane, indexed via Shape.
void	findByRoi_async(AMD_IRoi_findByRoi __cb, long roiId, RoiOptions opts, Ice.Current __current)	Returns a RoiResult with a single Roi member.
void	getMeasuredRois_async(AMD_IRoi_getMeasuredRois __cb, long imageId, long annotationId, RoiOptions opts, Ice.Current __current)	Loads the ROIs which are linked to by the given FileAnnotation id for the given image.
void	getMeasuredRoisMap_async(AMD_IRoi_getMeasuredRoisMap __cb, long imageId, java.util.List<java.lang.Long> annotationIds, RoiOptions opts, Ice.Current __current)	Returns a map from FileAnnotation ids to RoiResult instances.
void	getPoints_async(AMD_IRoi_getPoints __cb, long shapeId, Ice.Current __current)	Calculate the points contained within a given shape
void	getRoiMeasurements_async(AMD_IRoi_getRoiMeasurements __cb, long imageId, RoiOptions opts, Ice.Current __current)	Returns a list of FileAnnotation instances with the namespace openmicroscopy.org/measurements which are attached to the Plate containing the given image AND which are attached to at least one Roi
void	getRoiStats_async(AMD_IRoi_getRoiStats __cb, long roiId, Ice.Current __current)	Calculate stats for all the shapes within the given Roi.
void	getShapeStats_async(AMD_IRoi_getShapeStats __cb, long shapeId, Ice.Current __current)	Calculate the stats for the points within the given Shape.
void	getShapeStatsList_async(AMD_IRoi_getShapeStatsList __cb, java.util.List<java.lang.Long> shapeIdList, Ice.Current __current)	Calculate the stats for the points within the given Shapes.
void	getShapeStatsRestricted_async(AMD_IRoi_getShapeStatsRestricted __cb, java.util.List<java.lang.Long> shapeIdList, int zForUnattached, int tForUnattached, int[] channels, Ice.Current __current)	Calculate the stats for the points within the given Shapes.
void	getTable_async(AMD_IRoi_getTable __cb, long annotationId, Ice.Current __current)	Returns the OMERO.tables service via the FileAnnotation id returned by getImageMeasurements.
protected java.util.List<ome.model.roi.Roi>	loadMeasuredRois(org.hibernate.Session session, long imageId, long annotationId)
void	setServiceFactory(ServiceFactoryI sf)
void	uploadMask_async(AMD_IRoi_uploadMask __cb, long imageId, int z, int t, byte[] bytes, Ice.Current __current)

Methods inherited from class ome.services.blitz.impl.AbstractAmdServant

activate_async, applyHardWiredInterceptors, callInvokerOnMappedArgs, callInvokerOnRawArgs, executorWorkCall, getCurrentEventContext_async, onSetOmeroContext, passivate_async, runnableCall, safeRunnableCall, setApplicationContext, setHolder

Methods inherited from class java.lang.Object

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

Field Detail

factory

protected ServiceFactoryI factory

geomTool

protected final GeomTool geomTool

sql

protected final ome.util.SqlAction sql

Constructor Detail

RoiI

public RoiI(BlitzExecutor be,
            GeomTool geomTool,
            ome.util.SqlAction sql)

Method Detail

setServiceFactory

public void setServiceFactory(ServiceFactoryI sf)

Specified by:

setServiceFactory in interface ServiceFactoryAware

findByImage_async

public void findByImage_async(AMD_IRoi_findByImage __cb,
                              long imageId,
                              RoiOptions opts,
                              Ice.Current __current)
                       throws ServerError

Description copied from interface: _IRoiOperations

Returns all the Rois in an Image, indexed via Shape. Loads Rois as findByRoi.

Specified by:

findByImage_async in interface _IRoiOperations

Parameters:

__cb - The callback object for the operation.

__current - The Current object for the invocation.

Throws:

ServerError

findByRoi_async

public void findByRoi_async(AMD_IRoi_findByRoi __cb,
                            long roiId,
                            RoiOptions opts,
                            Ice.Current __current)
                     throws ServerError

Description copied from interface: _IRoiOperations

Returns a RoiResult with a single Roi member. Shape linkages are properly created. All Shapes are loaded, as is the Pixels and Image object. TODO: Annotations?

Specified by:

findByRoi_async in interface _IRoiOperations

Parameters:

__cb - The callback object for the operation.

__current - The Current object for the invocation.

Throws:

ServerError

findByPlane_async

public void findByPlane_async(AMD_IRoi_findByPlane __cb,
                              long imageId,
                              int z,
                              int t,
                              RoiOptions opts,
                              Ice.Current __current)
                       throws ServerError

Description copied from interface: _IRoiOperations

Returns all the Rois on the given plane, indexed via Shape. Loads Rois as findByRoi.

Specified by:

findByPlane_async in interface _IRoiOperations

Parameters:

__cb - The callback object for the operation.

__current - The Current object for the invocation.

Throws:

ServerError

getPoints_async

public void getPoints_async(AMD_IRoi_getPoints __cb,
                            long shapeId,
                            Ice.Current __current)
                     throws ServerError

Description copied from interface: _IRoiOperations

Calculate the points contained within a given shape

Specified by:

getPoints_async in interface _IRoiOperations

Parameters:

__cb - The callback object for the operation.

__current - The Current object for the invocation.

Throws:

ServerError

getShapeStats_async

public void getShapeStats_async(AMD_IRoi_getShapeStats __cb,
                                long shapeId,
                                Ice.Current __current)
                         throws ServerError

Description copied from interface: _IRoiOperations

Calculate the stats for the points within the given Shape.

Specified by:

getShapeStats_async in interface _IRoiOperations

Parameters:

__cb - The callback object for the operation.

__current - The Current object for the invocation.

Throws:

ServerError

getShapeStatsList_async

public void getShapeStatsList_async(AMD_IRoi_getShapeStatsList __cb,
                                    java.util.List<java.lang.Long> shapeIdList,
                                    Ice.Current __current)
                             throws ServerError

Description copied from interface: _IRoiOperations

Calculate the stats for the points within the given Shapes.

Specified by:

getShapeStatsList_async in interface _IRoiOperations

Parameters:

__cb - The callback object for the operation.

__current - The Current object for the invocation.

Throws:

ServerError

getRoiStats_async

public void getRoiStats_async(AMD_IRoi_getRoiStats __cb,
                              long roiId,
                              Ice.Current __current)
                       throws ServerError

Description copied from interface: _IRoiOperations

Calculate stats for all the shapes within the given Roi.

Specified by:

getRoiStats_async in interface _IRoiOperations

Parameters:

__cb - The callback object for the operation.

__current - The Current object for the invocation.

Throws:

ServerError

getShapeStatsRestricted_async

public void getShapeStatsRestricted_async(AMD_IRoi_getShapeStatsRestricted __cb,
                                          java.util.List<java.lang.Long> shapeIdList,
                                          int zForUnattached,
                                          int tForUnattached,
                                          int[] channels,
                                          Ice.Current __current)
                                   throws ServerError

Description copied from interface: _IRoiOperations

Calculate the stats for the points within the given Shapes. Varies to the above in the following ways: - does not allow tiled images - shapes have to be all belonging to the same image - unattached z/t use the fallback parameters zForUnattached/tForUnattached that is to say there is never more than 1 z/t combination queried - if channel list is given, only the channels in that list are iterated over - does not request data from reader on each iteration

Specified by:

getShapeStatsRestricted_async in interface _IRoiOperations

Parameters:

__cb - The callback object for the operation.

__current - The Current object for the invocation.

Throws:

ServerError

getRoiMeasurements_async

public void getRoiMeasurements_async(AMD_IRoi_getRoiMeasurements __cb,
                                     long imageId,
                                     RoiOptions opts,
                                     Ice.Current __current)
                              throws ServerError

Description copied from interface: _IRoiOperations

Returns a list of FileAnnotation instances with the namespace openmicroscopy.org/measurements which are attached to the Plate containing the given image AND which are attached to at least one Roi

Specified by:

getRoiMeasurements_async in interface _IRoiOperations

Parameters:

__cb - The callback object for the operation.

__current - The Current object for the invocation.

Throws:

ServerError

loadMeasuredRois

protected java.util.List<ome.model.roi.Roi> loadMeasuredRois(org.hibernate.Session session,
                                                             long imageId,
                                                             long annotationId)

getMeasuredRoisMap_async

public void getMeasuredRoisMap_async(AMD_IRoi_getMeasuredRoisMap __cb,
                                     long imageId,
                                     java.util.List<java.lang.Long> annotationIds,
                                     RoiOptions opts,
                                     Ice.Current __current)
                              throws ServerError

Description copied from interface: _IRoiOperations

Returns a map from FileAnnotation ids to RoiResult instances. Logic is identical to getMeasuredRois, but Roi data will not be duplicated. (i.e. the objects are referentially identical)

Specified by:

getMeasuredRoisMap_async in interface _IRoiOperations

Parameters:

__cb - The callback object for the operation.

__current - The Current object for the invocation.

Throws:

ServerError

getMeasuredRois_async

public void getMeasuredRois_async(AMD_IRoi_getMeasuredRois __cb,
                                  long imageId,
                                  long annotationId,
                                  RoiOptions opts,
                                  Ice.Current __current)
                           throws ServerError

Description copied from interface: _IRoiOperations

Loads the ROIs which are linked to by the given FileAnnotation id for the given image.

Specified by:

getMeasuredRois_async in interface _IRoiOperations

Parameters:

__cb - The callback object for the operation.

annotationId - if -1, logic is identical to findByImage(imageId, opts)

__current - The Current object for the invocation.

Throws:

ServerError

getTable_async

public void getTable_async(AMD_IRoi_getTable __cb,
                           long annotationId,
                           Ice.Current __current)
                    throws ServerError

Description copied from interface: _IRoiOperations

Returns the OMERO.tables service via the FileAnnotation id returned by getImageMeasurements.

Specified by:

getTable_async in interface _IRoiOperations

Parameters:

__cb - The callback object for the operation.

__current - The Current object for the invocation.

Throws:

ServerError

uploadMask_async

public void uploadMask_async(AMD_IRoi_uploadMask __cb,
                             long imageId,
                             int z,
                             int t,
                             byte[] bytes,
                             Ice.Current __current)
                      throws ServerError

Specified by:

uploadMask_async in interface _IRoiOperations

Parameters:

__cb - The callback object for the operation.

__current - The Current object for the invocation.

Throws:

ServerError