ome.api

Interface IPixels

All Superinterfaces:

ServiceInterface

public interface IPixels
extends ServiceInterface

Metadata gateway for the RenderingEngine and clients. This service provides all DB access that the rendering engine needs as well as Pixels services to a client. It also allows the rendering engine to also be run external to the server (e.g. client-side).

Since:

OME2.2

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, ome.model.enums.PixelsType pixelType, java.lang.String name, java.lang.String description) Creates the metadata, and only the metadata linked to an Image object.
<T extends ome.model.IObject> java.util.List<T>	getAllEnumerations(java.lang.Class<T> klass) Retrieves the exhaustive list of enumerations for a given enumeration class.
int	getBitDepth(ome.model.enums.PixelsType type) Bit depth for a given pixel type.
<T extends ome.model.IObject> T	getEnumeration(java.lang.Class<T> klass, java.lang.String value) Retrieves a particular enumeration for a given enumeration class.
ome.model.display.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<ome.model.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
ome.model.core.Pixels	retrievePixDescription(long pixelsId) 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
ome.model.display.RenderingDef	retrieveRndSettings(long pixelsId) Retrieves the rendering settings for a given pixels set and the currently logged in user.
ome.model.display.RenderingDef	retrieveRndSettingsFor(long pixelsId, 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(ome.model.display.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.

Method Detail

retrievePixDescription

ome.model.core.Pixels retrievePixDescription(long pixelsId)

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

Parameters:

pixelsId - Pixels id.

Returns:

Pixels object which matches id.

retrieveRndSettings

ome.model.display.RenderingDef retrieveRndSettings(long pixelsId)

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

Parameters:

pixelsId - Pixels id.

Returns:

Rendering definition.

retrieveRndSettingsFor

ome.model.display.RenderingDef retrieveRndSettingsFor(long pixelsId,
                                                      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

Parameters:

pixelsId - Pixels id.

userID - The id of the user.

Returns:

Rendering definition.

retrieveAllRndSettings

java.util.List<ome.model.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

Parameters:

pixId - Pixels id.

userId - The id of the user.

Returns:

Rendering definition.

loadRndSettings

ome.model.display.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

Parameters:

renderingDefId - Rendering definition id.

Returns:

Rendering definition.

Throws:

ValidationException - If no RenderingDef matches the ID renderingDefId.

copyAndResizePixels

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. 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.

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.

Throws:

ValidationException - If the X, Y, Z, T or channelList dimensions are out of bounds or the Pixels object corresponding to pixelsId is unlocatable.

copyAndResizeImage

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. 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.

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.

Throws:

ValidationException - If the X, Y, Z, T or channelList dimensions are out of bounds or the Pixels object corresponding to pixelsId is unlocatable.

createImage

java.lang.Long createImage(int sizeX,
                           int sizeY,
                           int sizeZ,
                           int sizeT,
                           java.util.List<java.lang.Integer> channelList,
                           ome.model.enums.PixelsType pixelType,
                           java.lang.String name,
                           java.lang.String description)

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.

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.

Throws:

ValidationException - If the channel list is null or of size == 0.

setChannelGlobalMinMax

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.

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

void saveRndSettings(ome.model.display.RenderingDef rndSettings)

Saves the specified rendering settings.

Parameters:

rndSettings - Rendering settings.

getBitDepth

int getBitDepth(ome.model.enums.PixelsType type)

Bit depth for a given pixel type.

Parameters:

type - Pixels type.

Returns:

Bit depth in bits.

getEnumeration

<T extends ome.model.IObject> T getEnumeration(java.lang.Class<T> klass,
                                               java.lang.String value)

Retrieves a particular enumeration for a given enumeration class.

Parameters:

klass - Enumeration class.

value - Enumeration string value.

Returns:

Enumeration object.

getAllEnumerations

<T extends ome.model.IObject> java.util.List<T> getAllEnumerations(java.lang.Class<T> klass)

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

Parameters:

klass - Enumeration class.

Returns:

List of all enumeration objects for the klass.