ome.logic

Class PixelsImpl

java.lang.Object

ome.logic.AbstractLevel2Service

ome.logic.PixelsImpl

All Implemented Interfaces:

IPixels, ServiceInterface, SelfConfigurableService

@Transactional(readOnly=true)
public class PixelsImpl
extends AbstractLevel2Service
implements IPixels

implementation of the Pixels service interface.

Since:

OME2.2

Version:

2.2 (Internal version: $Revision$ $Date: 2005/06/12 23:27:31 $)

Author:

Jean-Marie Burel j.burel@dundee.ac.uk,
Andrea Falconi a.falconi@dundee.ac.uk

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	RENDERING_DEF_QUERY_PREFIX Standard rendering definition HQL query prefix

Fields inherited from class ome.logic.AbstractLevel2Service

iQuery, iUpdate, metadata, queryFactory, sec

Constructor Summary

Constructors

Constructor and Description
PixelsImpl()

Method Summary

Modifier and Type	Method and Description
java.lang.Long	copyAndResizeImage(long imageId, java.lang.Integer sizeX, java.lang.Integer sizeY, java.lang.Integer sizeZ, java.lang.Integer sizeT, java.util.List<java.lang.Integer> channelList, java.lang.String name, boolean copyStats) Copies the metadata, and only the metadata linked to a Image object into a new Image object of equal or differing size across one or many of its three physical dimensions or temporal dimension.
java.lang.Long	copyAndResizePixels(long pixelsId, java.lang.Integer sizeX, java.lang.Integer sizeY, java.lang.Integer sizeZ, java.lang.Integer sizeT, java.util.List<java.lang.Integer> channelList, java.lang.String methodology, boolean copyStats) Copies the metadata, and only the metadata linked to a Pixels object into a new Pixels object of equal or differing size across one or many of its three physical dimensions or temporal dimension.
java.lang.Long	createImage(int sizeX, int sizeY, int sizeZ, int sizeT, java.util.List<java.lang.Integer> channelList, PixelsType pixelsType, java.lang.String name, java.lang.String description) Creates the metadata, and only the metadata linked to an Image object.
<T extends IObject> java.util.List<T>	getAllEnumerations(java.lang.Class<T> klass) Deprecated.
int	getBitDepth(PixelsType pixelsType) Bit depth for a given pixel type.
<T extends IObject> T	getEnumeration(java.lang.Class<T> klass, java.lang.String value) Deprecated.
java.lang.Class<? extends ServiceInterface>	getServiceInterface() Returns the interface this implementation is for.
RenderingDef	loadRndSettings(long renderingDefId) Loads a specific set of rendering settings with the following objects pre-linked: renderingDef.quantization renderingDef.model renderingDef.waveRendering renderingDef.waveRendering.color renderingDef.waveRendering.family renderingDef.spatialDomainEnhancement
java.util.List<IObject>	retrieveAllRndSettings(long pixId, long userId) Retrieves all the rendering settings for a given pixels set and the passed user with the following objects pre-linked: renderingDef.quantization renderingDef.model renderingDef.waveRendering renderingDef.waveRendering.color renderingDef.waveRendering.family renderingDef.spatialDomainEnhancement
Pixels	retrievePixDescription(long pixId) Retrieves the pixels metadata with the following objects pre-linked: pixels.pixelsType pixels.pixelsDimensions pixels.channels pixels.channnels.statsInfo pixels.channnels.colorComponent pixels.channnels.logicalChannel pixels.channnels.logicalChannel.photometricInterpretation
RenderingDef	retrieveRndSettings(long pixId) Retrieves the rendering settings for a given pixels set and the currently logged in user.
RenderingDef	retrieveRndSettingsFor(long pixId, long userId) Retrieves the rendering settings for a given pixels set and the passed user with the following objects pre-linked: renderingDef.quantization renderingDef.model renderingDef.waveRendering renderingDef.waveRendering.color renderingDef.waveRendering.family renderingDef.spatialDomainEnhancement
void	saveRndSettings(RenderingDef rndSettings) Saves the specified rendering settings.
void	setChannelGlobalMinMax(long pixelsId, int channelIndex, double min, double max) Sets the channel global (all 2D optical sections corresponding to a particular channel) minimum and maximum for a Pixels set.

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

RENDERING_DEF_QUERY_PREFIX

public static final java.lang.String RENDERING_DEF_QUERY_PREFIX

Standard rendering definition HQL query prefix

See Also:

Constant Field Values

Constructor Detail

PixelsImpl

public PixelsImpl()

Method Detail

getServiceInterface

public java.lang.Class<? extends ServiceInterface> getServiceInterface()

Returns the interface this implementation is for.

Specified by:

getServiceInterface in interface SelfConfigurableService

See Also:

SelfConfigurableService.getServiceInterface()

retrievePixDescription

public Pixels retrievePixDescription(long pixId)

Description copied from interface: IPixels

Retrieves the pixels metadata with the following objects pre-linked:

• pixels.pixelsType
• pixels.pixelsDimensions
• pixels.channels
• pixels.channnels.statsInfo
• pixels.channnels.colorComponent
• pixels.channnels.logicalChannel
• pixels.channnels.logicalChannel.photometricInterpretation

Specified by:

retrievePixDescription in interface IPixels

Parameters:

pixId - Pixels id.

Returns:

Pixels object which matches id.

retrieveRndSettingsFor

public RenderingDef retrieveRndSettingsFor(long pixId,
                                           long userId)

Description copied from interface: IPixels

Retrieves the rendering settings for a given pixels set and the passed user with the following objects pre-linked:

• renderingDef.quantization
• renderingDef.model
• renderingDef.waveRendering
• renderingDef.waveRendering.color
• renderingDef.waveRendering.family
• renderingDef.spatialDomainEnhancement

Specified by:

retrieveRndSettingsFor in interface IPixels

Parameters:

pixId - Pixels id.

userId - The id of the user.

Returns:

Rendering definition.

retrieveAllRndSettings

public java.util.List<IObject> retrieveAllRndSettings(long pixId,
                                                      long userId)

Description copied from interface: IPixels

Retrieves all the rendering settings for a given pixels set and the passed user with the following objects pre-linked:

• renderingDef.quantization
• renderingDef.model
• renderingDef.waveRendering
• renderingDef.waveRendering.color
• renderingDef.waveRendering.family
• renderingDef.spatialDomainEnhancement

Specified by:

retrieveAllRndSettings in interface IPixels

Parameters:

pixId - Pixels id.

userId - The id of the user.

Returns:

Rendering definition.

retrieveRndSettings

public RenderingDef retrieveRndSettings(long pixId)

Description copied from interface: IPixels

Retrieves the rendering settings for a given pixels set and the currently logged in user. If the current user has no RenderingDef, and the user is an administrator, then a RenderingDef may be returned for the owner of the Pixels. This matches the behavior of the Rendering service. The following objects will be pre-linked:

• renderingDef.quantization
• renderingDef.model
• renderingDef.waveRendering
• renderingDef.waveRendering.color
• renderingDef.waveRendering.family
• renderingDef.spatialDomainEnhancement

Specified by:

retrieveRndSettings in interface IPixels

Parameters:

pixId - Pixels id.

Returns:

Rendering definition.

loadRndSettings

public RenderingDef loadRndSettings(long renderingDefId)

Description copied from interface: IPixels

Loads a specific set of rendering settings with the following objects pre-linked:

• renderingDef.quantization
• renderingDef.model
• renderingDef.waveRendering
• renderingDef.waveRendering.color
• renderingDef.waveRendering.family
• renderingDef.spatialDomainEnhancement

Specified by:

loadRndSettings in interface IPixels

Parameters:

renderingDefId - Rendering definition id.

Returns:

Rendering definition.

copyAndResizePixels

@Transactional(readOnly=false)
public java.lang.Long copyAndResizePixels(long pixelsId,
                                                                         java.lang.Integer sizeX,
                                                                         java.lang.Integer sizeY,
                                                                         java.lang.Integer sizeZ,
                                                                         java.lang.Integer sizeT,
                                                                         java.util.List<java.lang.Integer> channelList,
                                                                         java.lang.String methodology,
                                                                         boolean copyStats)

Description copied from interface: IPixels

Copies the metadata, and only the metadata linked to a Pixels object into a new Pixels object of equal or differing size across one or many of its three physical dimensions or temporal dimension. It is beyond the scope of this method to handle updates or changes to the raw pixel data available through RawPixelsStore or to add and link PlaneInfo and/or other Pixels set specific metadata. It is also assumed that the caller wishes the pixels dimensions and PixelsType to remain the same; changing these is outside the scope of this method. NOTE: As Channel objects are only able to apply to a single set of Pixels any annotations or linkage to these objects will be lost.

Specified by:

copyAndResizePixels in interface IPixels

Parameters:

pixelsId - The source Pixels set id.

sizeX - The new size across the X-axis. null if the copy should maintain the same size.

sizeY - The new size across the Y-axis. null if the copy should maintain the same size.

sizeZ - The new size across the Z-axis. null if the copy should maintain the same size.

sizeT - The new number of timepoints. null if the copy should maintain the same number.

channelList - The channels that should be copied into the new Pixels set.

methodology - An optional string signifying the methodology that will be used to produce this new Pixels set.

copyStats - Whether or not to copy the StatsInfo for each channel.

Returns:

Id of the new Pixels object on success or null on failure.

copyAndResizeImage

@Transactional(readOnly=false)
public java.lang.Long copyAndResizeImage(long imageId,
                                                                        java.lang.Integer sizeX,
                                                                        java.lang.Integer sizeY,
                                                                        java.lang.Integer sizeZ,
                                                                        java.lang.Integer sizeT,
                                                                        java.util.List<java.lang.Integer> channelList,
                                                                        java.lang.String name,
                                                                        boolean copyStats)

Description copied from interface: IPixels

Copies the metadata, and only the metadata linked to a Image object into a new Image object of equal or differing size across one or many of its three physical dimensions or temporal dimension. It is beyond the scope of this method to handle updates or changes to the raw pixel data available through RawPixelsStore or to add and link PlaneInfo and/or other Pixels set specific metadata. It is also assumed that the caller wishes the pixels dimensions and PixelsType to remain the same; changing these is outside the scope of this method. NOTE: As Channel objects are only able to apply to a single set of Pixels any annotations or linkage to these objects will be lost.

Specified by:

copyAndResizeImage in interface IPixels

Parameters:

imageId - The source Image id.

sizeX - The new size across the X-axis. null if the copy should maintain the same size.

sizeY - The new size across the Y-axis. null if the copy should maintain the same size.

sizeZ - The new size across the Z-axis. null if the copy should maintain the same size.

sizeT - The new number of timepoints. null if the copy should maintain the same number.

channelList - The channels that should be copied into the new Pixels set.

name - The name of the new Image.

copyStats - Whether or not to copy the StatsInfo for each channel.

Returns:

Id of the new Pixels object on success or null on failure.

createImage

@Transactional(readOnly=false)
public java.lang.Long createImage(int sizeX,
                                                                 int sizeY,
                                                                 int sizeZ,
                                                                 int sizeT,
                                                                 java.util.List<java.lang.Integer> channelList,
                                                                 PixelsType pixelsType,
                                                                 java.lang.String name,
                                                                 java.lang.String description)

Description copied from interface: IPixels

Creates the metadata, and only the metadata linked to an Image object. It is beyond the scope of this method to handle updates or changes to the raw pixel data available through RawPixelsStore or to add and link PlaneInfo or StatsInfo objects and/or other Pixels set specific metadata. It is also up to the caller to update the pixels dimensions.

Specified by:

createImage in interface IPixels

Parameters:

sizeX - The new size across the X-axis.

sizeY - The new size across the Y-axis.

sizeZ - The new size across the Z-axis.

sizeT - The new number of timepoints.

channelList - The channels (emission wavelength in nanometers) that should be added to the new Pixels set.

name - The name of the new Image.

description - The description of the new Image.

Returns:

Id of the new Image object on success or null on failure.

setChannelGlobalMinMax

@Transactional(readOnly=false)
public void setChannelGlobalMinMax(long pixelsId,
                                                                  int channelIndex,
                                                                  double min,
                                                                  double max)

Description copied from interface: IPixels

Sets the channel global (all 2D optical sections corresponding to a particular channel) minimum and maximum for a Pixels set.

Specified by:

setChannelGlobalMinMax in interface IPixels

Parameters:

pixelsId - The source Pixels set id.

channelIndex - The channel index within the Pixels set.

min - The channel global minimum.

max - The channel global maximum.

saveRndSettings

@Transactional(readOnly=false)
public void saveRndSettings(RenderingDef rndSettings)

Description copied from interface: IPixels

Saves the specified rendering settings.

Specified by:

saveRndSettings in interface IPixels

Parameters:

rndSettings - Rendering settings.

getBitDepth

public int getBitDepth(PixelsType pixelsType)

Description copied from interface: IPixels

Bit depth for a given pixel type.

Specified by:

getBitDepth in interface IPixels

Parameters:

pixelsType - Pixels type.

Returns:

Bit depth in bits.

getEnumeration

@Deprecated
public <T extends IObject> T getEnumeration(java.lang.Class<T> klass,
                                                        java.lang.String value)

Deprecated.

Description copied from interface: IPixels

Retrieves a particular enumeration for a given enumeration class.

Specified by:

getEnumeration in interface IPixels

Parameters:

klass - Enumeration class.

value - Enumeration string value.

Returns:

Enumeration object.

getAllEnumerations

@Deprecated
public <T extends IObject> java.util.List<T> getAllEnumerations(java.lang.Class<T> klass)

Deprecated.

Description copied from interface: IPixels

Retrieves the exhaustive list of enumerations for a given enumeration class.

Specified by:

getAllEnumerations in interface IPixels

Parameters:

klass - Enumeration class.

Returns:

List of all enumeration objects for the klass.