OmeroBlitz API

omero::api::IPixels

Overview

[ "ami", "amd" ] 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).

Operation Index

retrievePixDescription: Retrieves the pixels metadata.
retrieveRndSettings: Retrieves the rendering settings for a given pixels set and the currently logged in user.
retrieveRndSettingsFor: Retrieves the rendering settings for a given pixels set and the passed user.
retrieveAllRndSettings: Retrieves all the rendering settings for a given pixels set and the passed user.
loadRndSettings: Loads a specific set of rendering settings.
saveRndSettings: Saves the specified rendering settings.
getBitDepth: Bit depth for a given pixel type.
getEnumeration: Retrieves a particular enumeration for a given enumeration class.
Deprecated.
getAllEnumerations: Retrieves the exhaustive list of enumerations for a given enumeration class.
Deprecated.
copyAndResizePixels: 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.
copyAndResizeImage: 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.
createImage: Creates the metadata, and only the metadata linked to an Image object.
setChannelGlobalMinMax: Sets the channel global (all 2D optical sections corresponding to a particular channel) minimum and maximum for a Pixels set.

Operations

model::Pixels retrievePixDescription(long pixId) throws ServerError

Retrieves the pixels metadata. The following objects are pre-linked:

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

Parameters

pixId: Pixels id.

Return Value

Pixels object which matches id.

model::RenderingDef retrieveRndSettings(long pixId) throws ServerError

Retrieves the rendering settings for a given pixels set and the currently logged in user. If the current user has no model::RenderingDef, and the user is an administrator, then a model::RenderingDef may be returned for the owner of the model::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

pixId: Pixels id.

Return Value

Rendering definition.

model::RenderingDef retrieveRndSettingsFor(long pixId, long userId) throws ServerError

Retrieves the rendering settings for a given pixels set and the passed user. The following objects are 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.

Return Value

Rendering definition.

IObjectList retrieveAllRndSettings(long pixId, long userId) throws ServerError

Retrieves all the rendering settings for a given pixels set and the passed user. The following objects are 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.

Return Value

Rendering definition.

model::RenderingDef loadRndSettings(long renderingSettingsId) throws ServerError

Loads a specific set of rendering settings. The following objects are pre-linked:

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

Parameters

renderingSettingsId: Rendering definition id.

Return Value

Rendering definition.

Exceptions

ValidationException: If no RenderingDef matches the ID renderingDefId.

void saveRndSettings(model::RenderingDef rndSettings) throws ServerError

Saves the specified rendering settings.

Parameters

rndSettings: Rendering settings.

int getBitDepth(model::PixelsType type) throws ServerError

Bit depth for a given pixel type.

Parameters

type: Pixels type.

Return Value

Bit depth in bits.

model::IObject getEnumeration(string enumClass, string value) throws ServerError

Retrieves a particular enumeration for a given enumeration class.

Use ITypes#getEnumeration(string, string) instead.

Parameters

enumClass: Enumeration class.
value: Enumeration string value.

Return Value

Enumeration object.

IObjectList getAllEnumerations(string enumClass) throws ServerError

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

Use ITypes#allEnumerations(string) instead.

Parameters

enumClass: Enumeration class.

Return Value

List of all enumeration objects for the enumClass.

RLong copyAndResizePixels(long pixelsId, RInt sizeX, RInt sizeY, RInt sizeZ, RInt sizeT, sys::IntList channelList, string methodology, bool copyStats) throws ServerError

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 model::PlaneInfo and/or other Pixels set specific metadata. It is also assumed that the caller wishes the pixels dimensions and model::PixelsType to remain the same; changing these is outside the scope of this method. NOTE: As model::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 model::StatsInfo for each channel.

Return Value

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

Exceptions

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

RLong copyAndResizeImage(long imageId, RInt sizeX, RInt sizeY, RInt sizeZ, RInt sizeT, sys::IntList channelList, string methodology, bool copyStats) throws ServerError

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 model::PlaneInfo and/or other Pixels set specific metadata. It is also assumed that the caller wishes the pixels dimensions and model::PixelsType to remain the same; changing these is outside the scope of this method. NOTE: As model::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.
methodology: The name of the new Image.
copyStats: Whether or not to copy the model::StatsInfo for each channel.

Return Value

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

Exceptions

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

RLong createImage(int sizeX, int sizeY, int sizeZ, int sizeT, sys::IntList channelList, model::PixelsType pixelsType, string name, string description) throws ServerError

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 model::PlaneInfo or model::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.
pixelsType: The pixelsType
name: The name of the new Image.
description: The description of the new Image.

Return Value

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

Exceptions

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

void setChannelGlobalMinMax(long pixelsId, int channelIndex, double min, double max) throws ServerError

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.

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