Cardinal (version 1.4.0)

ImageData-class: Class Containing Arrays of Imaging Data

Description

A container class for holding imaging data, designed to contain one or more arrays in an immutable environment. It is assumed that the first dimension of each array corresponds to the features.

Note that only visible objects (names not beginning with '.') are checked for validity; however, all objects are copied if any elements in the data slot are modified when data is an "immutableEnvironment".

Usage

## Instance creation
ImageData(..., data = new.env(parent=emptyenv()), storageMode = c("immutableEnvironment", "lockedEnvironment", "environment"))
## Additional methods documented below

Arguments

...

Named arguments that are passed to the initialize method for instantiating the object. These must be arrays or array-like objects with an equal number of dimensions. They will be assigned into the environment in the data slot.

data

An environment in which to assign the previously named variables.

storageMode

The storage mode to use for the ImageData object for the environment in the data slot. This must be one of "immutableEnvironment", "lockedEnvironment", or "environment". See documentation on the storageMode slot below for more details.

Slots

data:

An environment which may contain one or more arrays with an equal number of dimensions. It is assumed that the first dimension corresponds to the features.

storageMode:

A character which is one of "immutableEnvironment", "lockedEnvironment", or "environment". The values "lockedEnvironment" and "environment" behave as described in the documentation of AssayData. An "immutableEnvironment" uses a locked environment while retaining R's typical copy-on-write behavior. Whenever an object in an immutable environment is modified, a new environment is created for the data slot, and all objects copied into it. This allows usual R functional semantics while avoiding copying of large objects when other slots are modified.

.__classVersion__:

A Versions object describing the version of the class used to created the instance. Intended for developer use.

Extends

Versioned

Creating Objects

ImageData instances are usually created through ImageData().

Methods

Class-specific methods:

storageMode(object), storageMode(object)<-:

Return or set the storage mode. See documentation on the storageMode slot above for more details.

Standard generic methods:

initialize:

Initialize an ImageData object. Called by new. Not to be used by the user.

validObject:

Validity-check that the arrays in the data slot environment are all of equal number of dimensions, and the storage mode is a valid value.

combine(x, y, ...):

Combine two or more ImageData objects. All elements must have matching names, and are combined with calls to combine. Higher dimensional arrays are combined using the same rules as for matrices. (See combine for more details.)

annotatedDataFrameFrom(object):

Returns an IAnnotatedDataFrame with columns for the dimensions of the elements of data. All dimensions must be named (determined by the rownames(dims(object))). It is assumed that the first dimension corresponds to the features, and is not used as a dimension in the returned IAnnotatedDataFrame. Additional arguments (byrow, ...) are ignored.

dims:

A matrix with each column corresponding to the dimensions of an element in the data slot.

names(x), names(x)<-:

Access or replace the array names of the elements contained in the data slot environment.

ImageData[[name]], ImageData[[name]] <- value:

Access or replace an element named "name" in the environment in the data slot.

See Also

AssayData, SImageData, SImageSet, MSImageSet

Examples

## Create an ImageData object
ImageData()

idata <- ImageData(data0=matrix(1:4, nrow=2))
idata[["data0"]]

# Immutable environments in ImageData objects
storageMode(idata) <- "lockedEnvironment"
try(idata[["data0"]][,1] <- c(10,11)) # Fails

storageMode(idata) <- "immutableEnvironment"
try(idata[["data0"]][,1] <- c(10,11)) # Succeeds

# Test copy-on-write for immutable environments
idata2 <- idata
idata2[["data0"]] <- matrix(5:8, nrow=2)
idata[["data0"]] == idata2[["data0"]] # False