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R/AllClass.R
In neuroim: Data Structures and Handling for Neuroimaging Data
Defines functions
NullSource
#' @include AllGeneric.R
#' @import methods
roxygen()
setOldClass("mesh3d")
setOldClass(c("file", "connection"))
setOldClass(c("gzfile", "connection"))
setOldClass("raster")
setOldClass("rastergrob")
setOldClass("gList")
.package_env <- new.env()
#' Base
#'
#' Generic S4 Base class
#'
#' @rdname Base-class
setClass("Base", contains=c("VIRTUAL"))
#' NamedAxis
#'
#' This class represents an axis with a name attribute
#' @rdname NamedAxis-class
#' @slot axis the name of the axis
#' @slot direction of axis (-1,+1)
#' @export
setClass("NamedAxis", representation=
representation(axis="character", direction="numeric"))
#' Base
#'
#' Virtual base class representing an ordered set of named axes.
#' @rdname AxisSet-class
#' @slot ndim the number of axes (or dimensions)
#' @export
setClass("AxisSet", representation=representation(ndim="integer"))
#' AxisSet1D
#'
#' A one-dimensional axis set
#' @rdname AxisSet1D-class
#' @slot i the first axis
#' @export
setClass("AxisSet1D", representation=representation(i="NamedAxis"), contains=c("AxisSet"))
#' AxisSet2D
#'
#' A two-dimensional axis set
#'
#' @rdname AxisSet2D-class
#' @slot j the second axis
#' @export
setClass("AxisSet2D", representation=representation(j="NamedAxis"),
contains=c("AxisSet1D"))
#' AxisSet3D
#'
#' A three-dimensional axis set
#'
#' @rdname AxisSet3D-class
#' @slot k the third axis
#' @export
setClass("AxisSet3D", representation=representation(k="NamedAxis"),
contains=c("AxisSet2D"))
#' AxisSet4D
#'
#' A four-dimensional axis set
#' @name AxisSet4D-class
#' @slot l the fourth axis
#' @export
setClass("AxisSet4D", representation=representation(l="NamedAxis"),
contains=c("AxisSet3D"))
#' AxisSet5D
#'
#' A five-dimensional axis set
#'
#' @name AxisSet5D-class
#' @slot m the fifth axis
#' @export
setClass("AxisSet5D", representation=representation(m="NamedAxis"),
contains=c("AxisSet4D"))
#' BrainFileDescriptor
#'
#' This class represents a neuroimaging file format
#'
#' @rdname BrainFileDescriptor-class
#' @slot fileFormat the name of the file format (e.g. NIfTI)
#' @slot headerEncoding the file encoding of the header file (e.g. 'raw' for binary, 'gzip' for gz compressed')
#' @slot headerExtension the file extension for the header file (e.g. 'nii' for NIfTI single files)
#' @slot dataEncoding the file encoding for the data file
#' @slot dataExtension the file extension for the data file (e.g. 'nii' for NIfTI single files)
#' @exportClass BrainFileDescriptor
setClass("BrainFileDescriptor",
representation=
representation(fileFormat="character",
headerEncoding="character",
headerExtension="character",
dataEncoding="character",
dataExtension="character"),
)
#' NIfTIFileDescriptor
#'
#' This class supports the NIfTI file format
#'
#' @rdname NIfTIFileDescriptor-class
#' @export
setClass("NIfTIFileDescriptor", contains=c("BrainFileDescriptor"))
#' AFNIFileDescriptor
#'
#' This class supports the AFNI file format
#' @rdname AFNIFileDescriptor-class
#' @export
setClass("AFNIFileDescriptor", contains=c("BrainFileDescriptor"))
#' NIMLSurfaceFileDescriptor
#'
#' This class supports the NIML file format for surface-based data
#' @rdname NIMLSurfaceFileDescriptor-class
#' @export
setClass("NIMLSurfaceFileDescriptor", contains=c("BrainFileDescriptor"))
#' FresurferAsciiSurfaceFileDescriptor
#'
#' This class supports the FreesurferAsciiSurfaceFileDescriptor file format for surface geometry
#' @rdname FreesurferAsciiSurfaceFileDescriptor-class
#' @export
setClass("FreesurferAsciiSurfaceFileDescriptor", contains=c("BrainFileDescriptor"))
#' BaseMetaInfo
#'
#' This is a base class to represent meta information
#' @rdname BaseMetaInfo-class
#' @exportClass BaseMetaInfo
setClass("BaseMetaInfo")
#' NullMetaInfo
#'
#' This is class is used to denote the absense of meta information
#' @rdname NullMetaInfo-class
setClass("NullMetaInfo", contains=c("BaseMetaInfo"))
#' show a \code{BaseMetaInfo}
#' @param object the object
#' @export
setMethod(f="show",
signature=signature(object="BaseMetaInfo"),
def=function(object) {
cat("an instance of class", class(object), "\n\n")
})
#' show a \code{NullMetaInfo}
#' @param object the object
#' @export
setMethod(f="show",
signature=signature(object="NullMetaInfo"),
def=function(object) {
cat("an instance of class", class(object), "\n\n")
cat("meta info is null \n")
})
#' SurfaceGeometryMetaInfo
#'
#' This class contains meta information for brain surface geometry
#'
#' @rdname SurfaceGeometryMetaInfo-class
#' @slot headerFile name of the file containing meta information
#' @slot dataFile name of the file containing data
#' @slot fileDescriptor descriptor of image file format
#' @slot vertices the number of surface vertices
#' @slot faces the number of faces
#' @slot embedDimension the dimensionality of the embedding
#' @slot label a label indicating the type of surface (e.g. white, pial, inflated, flat, spherical)
#' @export
setClass("SurfaceGeometryMetaInfo",
representation=
representation(
headerFile="character",
dataFile="character",
fileDescriptor="BrainFileDescriptor",
vertices="integer",
faces="integer",
label="character",
embedDimension="integer"),
contains=c("BaseMetaInfo"))
#' FreeSurferSurfaceGeometryMetaInfo
#'
#' This class contains meta information for brain surface geometry
#'
#' @rdname FreeSurferSurfaceGeometryMetaInfo-class
#' @export
setClass("FreesurferSurfaceGeometryMetaInfo", contains=c("SurfaceGeometryMetaInfo"))
#' SurfaceDataMetaInfo
#'
#' This class contains meta information for surface-based data (the values that map to a surface geometry)
#'
#' @rdname SurfaceDataMetaInfo-class
#' @slot headerFile name of the file containing meta information
#' @slot dataFile name of the file containing data
#' @slot fileDescriptor descriptor of image file format
#' @slot nodeCount the number of nodes for which surface data exists
#' @slot nels the number of data vectors (typically the number of columns in the surface data matrix; nels = 1 for a single surface data set)
#' @slot label a label indicating the type of surface (e.g. white, pial, inflated, flat, spherical)
#' @export
setClass("SurfaceDataMetaInfo",
representation=
representation(
headerFile="character",
dataFile="character",
fileDescriptor="BrainFileDescriptor",
nodeCount="integer",
nels="integer",
label="character"),
contains=c("BaseMetaInfo"))
#' NIMLSurfaceDataMetaInfo
#'
#' This class contains meta information for surface-based data for the NIML data format
#'
#' @rdname NIMLSurfaceDataMetaInfo-class
#' @slot data the numeric data matrix of surface values (rows = nodes, columns=surface vectors)
#' @slot nodeIndices the indices of the nodes for mapping to associated surface geometry.
#' @export
setClass("NIMLSurfaceDataMetaInfo",
representation=
representation(
data="matrix",
nodeIndices="integer"),
contains=c("SurfaceDataMetaInfo"))
#' BrainMetaInfo
#'
#' This class contains meta information from an image
#' @rdname BrainMetaInfo-class
#' @slot dataType the data type code, e.g. FLOAT
#' @slot Dim image dimensions
#' @slot spatialAxes image axes for spatial dimensions (x,y,z)
#' @slot additionalAxes axes for dimensions > 3 (e.g. time, color band, direction)
#' @slot spacing voxel dimensions
#' @slot origin coordinate origin
#' @slot label name(s) of images
#' @export
setClass("BrainMetaInfo",
representation=
representation(
dataType="character",
Dim="numeric",
spatialAxes="AxisSet3D",
additionalAxes="AxisSet",
spacing="numeric",
origin="numeric",
label="character"),
#prototype=prototype(),
contains=c("BaseMetaInfo"))
#' FileMetaInfo
#'
#' This class contains meta information from an image data file
#'
#' @rdname FileMetaInfo-class
#' @slot headerFile name of the file containing meta information
#' @slot dataFile name of the file containing data
#' @slot fileDescriptor descriptor of image file format
#' @slot endian byte order of data ('little' or 'big')
#' @slot dataOffset the number of bytes preceding the start of image data in data file
#' @slot bytesPerElement number of bytes per element
#' @slot intercept constant value added to image -- multiple values allowed (must equal numer of sub-images)
#' @slot slope image multiplier -- multiple values allowed (must equal numer of sub-images)
#' @slot header a list of format specific attributes
#' @export
setClass("FileMetaInfo",
representation=
representation(headerFile="character",
dataFile="character",
fileDescriptor="BrainFileDescriptor",
endian="character",
dataOffset="numeric",
bytesPerElement="integer",
intercept="numeric",
slope="numeric",
header="list"),
#prototype=prototype(),
contains=c("BrainMetaInfo"))
#' NifTIMetaInfo
#'
#' This class contains meta information for a NIfTI image file
#' @rdname FileMetaInfo-class
#' @slot nifti_header a \code{list} of attributes specific to the NIfTI file format
#' @export
setClass("NIfTIMetaInfo",
representation=(nifti_header="list"),
contains=c("FileMetaInfo"))
#' AFNIMetaInfo
#'
#' This class contains meta information for a AFNI image file
#' @rdname FileMetaInfo-class
#' @slot afni_header a list of attributes specific to the AFNI file format
#' @slot afni_header a \code{list} of attributes specific to the AFNI file format
#' @export
setClass("AFNIMetaInfo",
representation=(afni_header="list"),
contains=c("FileMetaInfo"))
#' BaseSource
#'
#' This is a base class to represent a data source
#' @rdname BaseSource-class
#' @slot metaInfo meta information for the data source
#' @exportClass BaseSource
setClass("BaseSource", representation=representation(metaInfo="BaseMetaInfo"))
NullSource <- function() {
ex <- exists(".NullSource", envir=.package_env)
if (!ex) {
ret <- new("BaseSource", metaInfo=new("NullMetaInfo"))
assign(".NullSource", ret, envir=.package_env)
ret
} else {
get(".NullSource", envir=.package_env)
}
}
#' BrainSource
#'
#' Base class for representing a data source for images. The purpose of this class is to provide a layer in between
#' low level IO and image loading functionality.
#' @rdname BrainSource-class
#' @slot metaInfo meta information for the data source
#' @exportClass BrainSource
setClass("BrainSource", representation=
representation(metaInfo="BrainMetaInfo"),
contains=c("BaseSource"))
#' BrainFileSource
#'
#' Base class for representing a data source for images. The purpose of this class is to provide a layer in between
#' low level IO and image loading functionality.
#' @rdname BrainFileSource-class
#' @slot metaInfo meta information for the data source
#' @exportClass BrainFileSource
setClass("BrainFileSource", representation=
representation(metaInfo="FileMetaInfo"),
contains=c("BrainSource"))
#' BrainVolume
#' BrainVolumeSource
#'
#' A class is used to produce a \code{\linkS4class{BrainVolume}} instance
#' @rdname BrainVolumeSource-class
#' @slot index the index of the volume to be read -- must be of length 1.
#' @exportClass BrainVolumeSource
setClass("BrainVolumeSource", representation=
representation(index="integer"),
contains=c("BrainSource"))
#' BrainVectorSource
#'
#' A class that is used to produce a \code{\linkS4class{BrainVectorSource}} instance
#' @rdname BrainVectorSource-class
#' @slot indices the index vector of the volumes to be loaded
#' @export
setClass("BrainVectorSource", representation=
representation(indices="integer"),
contains=c("BrainSource"))
#' BrainSurfaceVectorSource
#'
#' A class that is used to produce a \code{\linkS4class{BrainSurfaceVectorSource}} instance
#'
#' @rdname BrainSurfaceVectorSource-class
#' @slot indices the index vector of the volumes to be loaded
#' @export
setClass("BrainSurfaceVectorSource", representation=
representation(indices="integer"),
contains=c("BaseSource"))
#' BrainBucketSource
#'
#' A class that is used to produce a \code{\linkS4class{BrainBucket}} instance
#' @rdname BrainBucketSource-class
#' @slot sourceList a list of sources for the bucket sub-volumes
#' @slot cache a cache used to store data in memory
#' @export
setClass("BrainBucketSource",
representation=representation(sourceList="list", cache="environment"),
contains=c("BrainVectorSource"))
#' BrainSurfaceSource
#'
#' A class that is used to produce a \code{\linkS4class{BrainSurface}} instance
#' @rdname BrainSurfaceSource-class
#' @slot metaInfo a \code{\linkS4class{SurfaceGeometryMetaInfo}} instance
#' @slot dataMetaInfo a \code{\linkS4class{SurfaceDataMetaInfo}} instance
#' @slot index the index offset into the surface data matrix
#' @export
setClass("BrainSurfaceSource",
representation=representation(metaInfo="SurfaceGeometryMetaInfo", dataMetaInfo="SurfaceDataMetaInfo", index="integer"),
contains=c("BaseSource"))
#' BinaryReader
#'
#' This class supports reading of bulk binary data from a connection
#' @rdname BinaryReader-class
#' @slot input the binary input connection
#' @slot byteOffset the number of bytes to skip at the start of input
#' @slot dataType the dataType of the binary Elements
#' @slot bytesPerElement number of bytes in each data element (e.g. 4 or 8 for floating point numbers)
#' @slot endian endianness of binary input connection
#' @export
setClass("BinaryReader", representation=
representation(input="connection",
byteOffset="numeric",
dataType="character",
bytesPerElement="integer",
endian="character"))
#' ColumnReader
#'
#' This class supports reading of data froma matrix-like stroage format
#' @rdname ColumnReader-class
#' @slot nrow the number of rows
#' @slot ncol the number of columns
#' @slot reader a function that takes a set of column indices and returns a \code{matrix}
#' @export
setClass("ColumnReader", representation=
representation(nrow="integer", ncol="integer", reader="function"))
#' BinaryWriter
#'
#' This class supports writing of bulk binary data to a connection
#' @rdname BinaryWriter-class
#' @slot output the binary output connection
#' @slot byteOffset the number of bytes to skip at the start of input
#' @slot dataType the dataType of the binary Elements
#' @slot bytesPerElement number of bytes in each data element (e.g. 4 or 8 for floating point numbers)
#' @slot endian endianness of binary output connection
#' @export
setClass("BinaryWriter", representation=
representation(output="connection",
byteOffset="numeric",
dataType="character",
bytesPerElement="integer",
endian="character"))
#' BrainSpace
#'
#' This class represents the geometry of a brain image
#' @rdname BrainSpace-class
#' @slot Dim the grid dimensions of the image
#' @slot origin the coordinates of the spatial origin
#' @slot spacing the dimensions (in mm) of the grid units (voxels)
#' @slot axes the set of named spatial axes
#' @slot trans an affine transformation matrix that moves from grid -> real world coordinates
#' @slot inverseTrans an inverse matrix that moves from real world -> grid coordinates
#' @export
setClass("BrainSpace",
representation=
representation(Dim = "integer", origin = "numeric", spacing = "numeric",
axes="AxisSet", trans="matrix", inverseTrans="matrix"),
validity = function(object) {
Dim <- object@Dim
if (length(Dim) < length(object@spacing)) {
return("Dim slot must be of same length as spacing slot")
}
if (length(Dim) < length(object@origin)) {
return("Dim slot must be of same length as origin slot")
}
if (length(Dim) < ndim(object@axes)) {
return("Dim slot must be of same length as number of axes in AxisSet")
}
if (any(Dim) < 0) {
return("Dim slot must contain non-negative values")
}
})
#' BrainData
#'
#' Base class for brain image data
#'
#'
#' @rdname BrainData-class
#' @slot source an instance of class \code{\linkS4class{BaseSource}} to store the source of the data
#' @slot space an instance of class \code{\linkS4class{BrainSpace}} to represent the geometry of the data space
#' @export
setClass("BrainData",
representation=
representation(source="BaseSource",
space="BrainSpace"),
contains=c("VIRTUAL"))
#' BrainSlice
#'
#' Two-dimensional brain image
#' @rdname BrainSlice-class
#' @export
setClass("BrainSlice",
contains=c("BrainData", "array"))
#' Base class for image representing 3D volumetric data.
#' @rdname BrainVolume-class
#' @export
setClass("BrainVolume",
contains=c("BrainData"))
#' DenseBrainVolume
#'
#' Three-dimensional brain image, backed by an \code{array}
#' @rdname DenseBrainVolume-class
#' @export
setClass("DenseBrainVolume",
contains=c("BrainVolume", "array"))
#' SparseBrainVolume
#'
#' Three-dimensional brain image, backed by a \code{sparseVector} for \code{Matrix} package
#' @slot data a \code{sparseVector} instance
#' @rdname SparseBrainVolume-class
#' @export
setClass("SparseBrainVolume",
representation=representation(data="sparseVector"),
contains=c("BrainVolume"))
#' LogicalBrainVolume
#'
#' Three-dimensional brain image where all values are either TRUE or FALSE
#' @rdname LogicalBrainVolume-class
#' @export
setClass("LogicalBrainVolume",
contains=c("DenseBrainVolume"))
#' ClusteredBrainVolume
#'
#' Three-dimensional brain image that is divided into N disjoint partitions
#' @rdname ClusteredBrainVolume-class
#' @export
setClass("ClusteredBrainVolume",
representation=representation(mask="LogicalBrainVolume", clusters="integer", centers="matrix", labelMap="list", clusterMap="hash"),
contains=c("BrainVolume"))
#' IndexLookupVolume
#'
#' Three-dimensional brain image that can be used as a map between 1D grid indices and a table of values
#' Currently used in the \code{\linkS4class{SparseBrainVector}} class.
#' @rdname IndexLookupVolume-class
#' @export
setClass("IndexLookupVolume",
representation=
representation(space="BrainSpace", indices="integer", map="integer"),
contains=c("BrainVolume"))
#' BrainVector
#'
#' Four-dimensional brain image
#'
#' @rdname BrainVector-class
#' @export
setClass("BrainVector",
contains=c("BrainData"))
#' DenseBrainVector
#'
#' Four-dimensional brain image, backed by an array
#' @name DenseBrainVector-class
#' @export
setClass("DenseBrainVector",
contains=c("BrainVector", "array"))
# DenseMMapBrainVector
#
# Four-dimensional brain image, backed by a memory-mapped file
# @exportClass DenseMMapBrainVector
# setClass("DenseMMapBrainVector",
# representation=representation(data="mmap"),
# contains=c("BrainVector"))
#' SparseBrainVector
#'
#' a sparse four-dimensional brain image, backed by a \code{matrix}, where each column represents
#' a vector spanning the fourth dimension (e.g. time)
#' @rdname SparseBrainVector-class
#' @slot mask the mask defining the sparse domain
#' @slot data the matrix of series, where rows span across voxel space and columns span the fourth dimensions
#' @slot map instance of class \code{\linkS4class{IndexLookupVolume}} is used to map between spatial and index/row coordinates
#' @export
setClass("SparseBrainVector",
representation=representation(mask="LogicalBrainVolume",data="matrix", map="IndexLookupVolume"),
contains=c("BrainVector"))
#' SparseBrainVectorSource
#'
#' A class that is used to produce a \code{\linkS4class{SparseBrainVector}} instance
#' @rdname SparseBrainVectorSource-class
#' @slot mask the subset of voxels that will be stored in memory
#' @export
setClass("SparseBrainVectorSource", representation=
representation(mask="LogicalBrainVolume"),
contains=c("BrainVectorSource"))
#setClass("TiledBrainVector",
# representation=representation(cache="list", filename="character", indexList="list", mask="BrainVolume",capacity="numeric"),
# contains=c("BrainVector"))
#' ROIVolume
#'
#' A class that representing a volumetric region of interest (ROI).
#' @rdname ROIVolume-class
#' @slot data the \code{numeric} data stored in the ROI
#' @slot coords the voxel coordinates of the ROI
#' @exportClass ROIVolume
setClass("ROIVolume",
representation=representation(data="numeric", coords="matrix"), contains=c("BrainData"),
validity = function(object) {
if (ncol(object@coords) != 3) {
stop("coords slot must be a matrix with 3 columns")
}
})
#' Kernel
#'
#' A class representing an image kernel
#'
#' @rdname Kernel-class
#' @slot width the width in voxels of the kernel
#' @slot weights the kernel weights
#' @slot voxels the relative voxel coordinates of the kernel
#' @slot coords the relative real coordinates of the kernel
#' @export
setClass("Kernel",
representation=representation(width="numeric", weights="numeric", voxels="matrix", coords="matrix"))
## TODO add a LazyBrainBucket class
#' BrainSurface
#'
#' a three-dimensional surface consisting of a set of triangle vertices with one value per vertex.
#' @rdname BrainSurface-class
#' @slot source the data source for the surface
#' @slot mesh the underlying \code{mesh3d} object
#' @slot data the vector of data value at each vertex of the mesh
#' @export
setClass("BrainSurface",
representation=representation(source="BrainSource", mesh="mesh3d", data="numeric"))
#' BrainSurfaceVector
#'
#' a three-dimensional surface consisting of a set of triangle vertices with multiple values per vertex.
#'
#' @rdname BrainSurfaceVector-class
#' @slot source the data source for the surface
#' @slot mesh the underlying \code{mesh3d} object
#' @slot mat a matrix of values where each column contains a vector of values over the surface nodes.
#' @export
setClass("BrainSurfaceVector",
representation=representation(source="BrainSource", mesh="mesh3d", mat="numeric"))
#' BrainBucket
#'
#' a four-dimensional image that conists of a sequence of labeled image volumes backed by a list
#' @rdname BrainBucket-class
#' @slot source the data source for the bucket volumes
#' @slot labels the names of the sub-volumes contained in the bucket
#' @slot data a list of \code{\linkS4class{BrainVolume}} instances with names corresponding to volume labels
#' @export
setClass("BrainBucket",
representation=representation(source="BrainSource", labels="character", data="list"),
validity = function(object) {
if (any(sapply(object@data, function(obj) !is(obj, "BrainVolume")))) {
stop("all elements of data list must be of type `BrainVolume`")
} else {
TRUE
}
},
contains=c("BrainVector"))
#setClassUnion(name="index", members = c("numeric", "logical", "character"))
#' Layer
#'
#' A class used for displaying 2D images with color maps
#'
#' @rdname Layer-class
#' @slot vol the \code{BrainVolume} that provides the data for the layer.
#' @slot colorMap a character vector of colors in hexadecimal rgb format.
#' Can be generated by calls to \code{rainbow}, \code{heat.colors}, \code{topo.colors}, \code{terrain.colors} or similar functions.
#' @slot thresh cut-off value above which vlaues will be made transparent.
#' @slot axis the axis index of perpendicular to the xy plane (option: 1,2,3; default is 3)
#' @slot zero.col the color pixels with intensity of zero. This value overrides the color from the slot \code{colorMap}
#' @slot alpha the transparency of the layer
#' @export
setClass("Layer",
representation=representation(vol="BrainVolume", colorMap="vector", thresh="numeric", axis="numeric", zero.col="character", alpha="numeric"))
setClass("Overlay",
representation(layers="list"))
setClass("RenderedSlice",
representation=representation(slice="BrainSlice",
width="numeric",
height="numeric",
raster="rastergrob"))
setClass("RenderedSliceStack",
representation=representation(slices="list",
width="numeric",
height="numeric",
grob="gList"))
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Defines functions NullSource
#' @include AllGeneric.R
#' @import methods
roxygen()
setOldClass("mesh3d")
setOldClass(c("file", "connection"))
setOldClass(c("gzfile", "connection"))
setOldClass("raster")
setOldClass("rastergrob")
setOldClass("gList")
.package_env <- new.env()
#' Base
#'
#' Generic S4 Base class
#'
#' @rdname Base-class
setClass("Base", contains=c("VIRTUAL"))
#' NamedAxis
#'
#' This class represents an axis with a name attribute
#' @rdname NamedAxis-class
#' @slot axis the name of the axis
#' @slot direction of axis (-1,+1)
#' @export
setClass("NamedAxis", representation=
representation(axis="character", direction="numeric"))
#' Base
#'
#' Virtual base class representing an ordered set of named axes.
#' @rdname AxisSet-class
#' @slot ndim the number of axes (or dimensions)
#' @export
setClass("AxisSet", representation=representation(ndim="integer"))
#' AxisSet1D
#'
#' A one-dimensional axis set
#' @rdname AxisSet1D-class
#' @slot i the first axis
#' @export
setClass("AxisSet1D", representation=representation(i="NamedAxis"), contains=c("AxisSet"))
#' AxisSet2D
#'
#' A two-dimensional axis set
#'
#' @rdname AxisSet2D-class
#' @slot j the second axis
#' @export
setClass("AxisSet2D", representation=representation(j="NamedAxis"),
contains=c("AxisSet1D"))
#' AxisSet3D
#'
#' A three-dimensional axis set
#'
#' @rdname AxisSet3D-class
#' @slot k the third axis
#' @export
setClass("AxisSet3D", representation=representation(k="NamedAxis"),
contains=c("AxisSet2D"))
#' AxisSet4D
#'
#' A four-dimensional axis set
#' @name AxisSet4D-class
#' @slot l the fourth axis
#' @export
setClass("AxisSet4D", representation=representation(l="NamedAxis"),
contains=c("AxisSet3D"))
#' AxisSet5D
#'
#' A five-dimensional axis set
#'
#' @name AxisSet5D-class
#' @slot m the fifth axis
#' @export
setClass("AxisSet5D", representation=representation(m="NamedAxis"),
contains=c("AxisSet4D"))
#' BrainFileDescriptor
#'
#' This class represents a neuroimaging file format
#'
#' @rdname BrainFileDescriptor-class
#' @slot fileFormat the name of the file format (e.g. NIfTI)
#' @slot headerEncoding the file encoding of the header file (e.g. 'raw' for binary, 'gzip' for gz compressed')
#' @slot headerExtension the file extension for the header file (e.g. 'nii' for NIfTI single files)
#' @slot dataEncoding the file encoding for the data file
#' @slot dataExtension the file extension for the data file (e.g. 'nii' for NIfTI single files)
#' @exportClass BrainFileDescriptor
setClass("BrainFileDescriptor",
representation=
representation(fileFormat="character",
headerEncoding="character",
headerExtension="character",
dataEncoding="character",
dataExtension="character"),
)
#' NIfTIFileDescriptor
#'
#' This class supports the NIfTI file format
#'
#' @rdname NIfTIFileDescriptor-class
#' @export
setClass("NIfTIFileDescriptor", contains=c("BrainFileDescriptor"))
#' AFNIFileDescriptor
#'
#' This class supports the AFNI file format
#' @rdname AFNIFileDescriptor-class
#' @export
setClass("AFNIFileDescriptor", contains=c("BrainFileDescriptor"))
#' NIMLSurfaceFileDescriptor
#'
#' This class supports the NIML file format for surface-based data
#' @rdname NIMLSurfaceFileDescriptor-class
#' @export
setClass("NIMLSurfaceFileDescriptor", contains=c("BrainFileDescriptor"))
#' FresurferAsciiSurfaceFileDescriptor
#'
#' This class supports the FreesurferAsciiSurfaceFileDescriptor file format for surface geometry
#' @rdname FreesurferAsciiSurfaceFileDescriptor-class
#' @export
setClass("FreesurferAsciiSurfaceFileDescriptor", contains=c("BrainFileDescriptor"))
#' BaseMetaInfo
#'
#' This is a base class to represent meta information
#' @rdname BaseMetaInfo-class
#' @exportClass BaseMetaInfo
setClass("BaseMetaInfo")
#' NullMetaInfo
#'
#' This is class is used to denote the absense of meta information
#' @rdname NullMetaInfo-class
setClass("NullMetaInfo", contains=c("BaseMetaInfo"))
#' show a \code{BaseMetaInfo}
#' @param object the object
#' @export
setMethod(f="show",
signature=signature(object="BaseMetaInfo"),
def=function(object) {
cat("an instance of class", class(object), "\n\n")
})
#' show a \code{NullMetaInfo}
#' @param object the object
#' @export
setMethod(f="show",
signature=signature(object="NullMetaInfo"),
def=function(object) {
cat("an instance of class", class(object), "\n\n")
cat("meta info is null \n")
})
#' SurfaceGeometryMetaInfo
#'
#' This class contains meta information for brain surface geometry
#'
#' @rdname SurfaceGeometryMetaInfo-class
#' @slot headerFile name of the file containing meta information
#' @slot dataFile name of the file containing data
#' @slot fileDescriptor descriptor of image file format
#' @slot vertices the number of surface vertices
#' @slot faces the number of faces
#' @slot embedDimension the dimensionality of the embedding
#' @slot label a label indicating the type of surface (e.g. white, pial, inflated, flat, spherical)
#' @export
setClass("SurfaceGeometryMetaInfo",
representation=
representation(
headerFile="character",
dataFile="character",
fileDescriptor="BrainFileDescriptor",
vertices="integer",
faces="integer",
label="character",
embedDimension="integer"),
contains=c("BaseMetaInfo"))
#' FreeSurferSurfaceGeometryMetaInfo
#'
#' This class contains meta information for brain surface geometry
#'
#' @rdname FreeSurferSurfaceGeometryMetaInfo-class
#' @export
setClass("FreesurferSurfaceGeometryMetaInfo", contains=c("SurfaceGeometryMetaInfo"))
#' SurfaceDataMetaInfo
#'
#' This class contains meta information for surface-based data (the values that map to a surface geometry)
#'
#' @rdname SurfaceDataMetaInfo-class
#' @slot headerFile name of the file containing meta information
#' @slot dataFile name of the file containing data
#' @slot fileDescriptor descriptor of image file format
#' @slot nodeCount the number of nodes for which surface data exists
#' @slot nels the number of data vectors (typically the number of columns in the surface data matrix; nels = 1 for a single surface data set)
#' @slot label a label indicating the type of surface (e.g. white, pial, inflated, flat, spherical)
#' @export
setClass("SurfaceDataMetaInfo",
representation=
representation(
headerFile="character",
dataFile="character",
fileDescriptor="BrainFileDescriptor",
nodeCount="integer",
nels="integer",
label="character"),
contains=c("BaseMetaInfo"))
#' NIMLSurfaceDataMetaInfo
#'
#' This class contains meta information for surface-based data for the NIML data format
#'
#' @rdname NIMLSurfaceDataMetaInfo-class
#' @slot data the numeric data matrix of surface values (rows = nodes, columns=surface vectors)
#' @slot nodeIndices the indices of the nodes for mapping to associated surface geometry.
#' @export
setClass("NIMLSurfaceDataMetaInfo",
representation=
representation(
data="matrix",
nodeIndices="integer"),
contains=c("SurfaceDataMetaInfo"))
#' BrainMetaInfo
#'
#' This class contains meta information from an image
#' @rdname BrainMetaInfo-class
#' @slot dataType the data type code, e.g. FLOAT
#' @slot Dim image dimensions
#' @slot spatialAxes image axes for spatial dimensions (x,y,z)
#' @slot additionalAxes axes for dimensions > 3 (e.g. time, color band, direction)
#' @slot spacing voxel dimensions
#' @slot origin coordinate origin
#' @slot label name(s) of images
#' @export
setClass("BrainMetaInfo",
representation=
representation(
dataType="character",
Dim="numeric",
spatialAxes="AxisSet3D",
additionalAxes="AxisSet",
spacing="numeric",
origin="numeric",
label="character"),
#prototype=prototype(),
contains=c("BaseMetaInfo"))
#' FileMetaInfo
#'
#' This class contains meta information from an image data file
#'
#' @rdname FileMetaInfo-class
#' @slot headerFile name of the file containing meta information
#' @slot dataFile name of the file containing data
#' @slot fileDescriptor descriptor of image file format
#' @slot endian byte order of data ('little' or 'big')
#' @slot dataOffset the number of bytes preceding the start of image data in data file
#' @slot bytesPerElement number of bytes per element
#' @slot intercept constant value added to image -- multiple values allowed (must equal numer of sub-images)
#' @slot slope image multiplier -- multiple values allowed (must equal numer of sub-images)
#' @slot header a list of format specific attributes
#' @export
setClass("FileMetaInfo",
representation=
representation(headerFile="character",
dataFile="character",
fileDescriptor="BrainFileDescriptor",
endian="character",
dataOffset="numeric",
bytesPerElement="integer",
intercept="numeric",
slope="numeric",
header="list"),
#prototype=prototype(),
contains=c("BrainMetaInfo"))
#' NifTIMetaInfo
#'
#' This class contains meta information for a NIfTI image file
#' @rdname FileMetaInfo-class
#' @slot nifti_header a \code{list} of attributes specific to the NIfTI file format
#' @export
setClass("NIfTIMetaInfo",
representation=(nifti_header="list"),
contains=c("FileMetaInfo"))
#' AFNIMetaInfo
#'
#' This class contains meta information for a AFNI image file
#' @rdname FileMetaInfo-class
#' @slot afni_header a list of attributes specific to the AFNI file format
#' @slot afni_header a \code{list} of attributes specific to the AFNI file format
#' @export
setClass("AFNIMetaInfo",
representation=(afni_header="list"),
contains=c("FileMetaInfo"))
#' BaseSource
#'
#' This is a base class to represent a data source
#' @rdname BaseSource-class
#' @slot metaInfo meta information for the data source
#' @exportClass BaseSource
setClass("BaseSource", representation=representation(metaInfo="BaseMetaInfo"))
NullSource <- function() {
ex <- exists(".NullSource", envir=.package_env)
if (!ex) {
ret <- new("BaseSource", metaInfo=new("NullMetaInfo"))
assign(".NullSource", ret, envir=.package_env)
ret
} else {
get(".NullSource", envir=.package_env)
}
}
#' BrainSource
#'
#' Base class for representing a data source for images. The purpose of this class is to provide a layer in between
#' low level IO and image loading functionality.
#' @rdname BrainSource-class
#' @slot metaInfo meta information for the data source
#' @exportClass BrainSource
setClass("BrainSource", representation=
representation(metaInfo="BrainMetaInfo"),
contains=c("BaseSource"))
#' BrainFileSource
#'
#' Base class for representing a data source for images. The purpose of this class is to provide a layer in between
#' low level IO and image loading functionality.
#' @rdname BrainFileSource-class
#' @slot metaInfo meta information for the data source
#' @exportClass BrainFileSource
setClass("BrainFileSource", representation=
representation(metaInfo="FileMetaInfo"),
contains=c("BrainSource"))
#' BrainVolume
#' BrainVolumeSource
#'
#' A class is used to produce a \code{\linkS4class{BrainVolume}} instance
#' @rdname BrainVolumeSource-class
#' @slot index the index of the volume to be read -- must be of length 1.
#' @exportClass BrainVolumeSource
setClass("BrainVolumeSource", representation=
representation(index="integer"),
contains=c("BrainSource"))
#' BrainVectorSource
#'
#' A class that is used to produce a \code{\linkS4class{BrainVectorSource}} instance
#' @rdname BrainVectorSource-class
#' @slot indices the index vector of the volumes to be loaded
#' @export
setClass("BrainVectorSource", representation=
representation(indices="integer"),
contains=c("BrainSource"))
#' BrainSurfaceVectorSource
#'
#' A class that is used to produce a \code{\linkS4class{BrainSurfaceVectorSource}} instance
#'
#' @rdname BrainSurfaceVectorSource-class
#' @slot indices the index vector of the volumes to be loaded
#' @export
setClass("BrainSurfaceVectorSource", representation=
representation(indices="integer"),
contains=c("BaseSource"))
#' BrainBucketSource
#'
#' A class that is used to produce a \code{\linkS4class{BrainBucket}} instance
#' @rdname BrainBucketSource-class
#' @slot sourceList a list of sources for the bucket sub-volumes
#' @slot cache a cache used to store data in memory
#' @export
setClass("BrainBucketSource",
representation=representation(sourceList="list", cache="environment"),
contains=c("BrainVectorSource"))
#' BrainSurfaceSource
#'
#' A class that is used to produce a \code{\linkS4class{BrainSurface}} instance
#' @rdname BrainSurfaceSource-class
#' @slot metaInfo a \code{\linkS4class{SurfaceGeometryMetaInfo}} instance
#' @slot dataMetaInfo a \code{\linkS4class{SurfaceDataMetaInfo}} instance
#' @slot index the index offset into the surface data matrix
#' @export
setClass("BrainSurfaceSource",
representation=representation(metaInfo="SurfaceGeometryMetaInfo", dataMetaInfo="SurfaceDataMetaInfo", index="integer"),
contains=c("BaseSource"))
#' BinaryReader
#'
#' This class supports reading of bulk binary data from a connection
#' @rdname BinaryReader-class
#' @slot input the binary input connection
#' @slot byteOffset the number of bytes to skip at the start of input
#' @slot dataType the dataType of the binary Elements
#' @slot bytesPerElement number of bytes in each data element (e.g. 4 or 8 for floating point numbers)
#' @slot endian endianness of binary input connection
#' @export
setClass("BinaryReader", representation=
representation(input="connection",
byteOffset="numeric",
dataType="character",
bytesPerElement="integer",
endian="character"))
#' ColumnReader
#'
#' This class supports reading of data froma matrix-like stroage format
#' @rdname ColumnReader-class
#' @slot nrow the number of rows
#' @slot ncol the number of columns
#' @slot reader a function that takes a set of column indices and returns a \code{matrix}
#' @export
setClass("ColumnReader", representation=
representation(nrow="integer", ncol="integer", reader="function"))
#' BinaryWriter
#'
#' This class supports writing of bulk binary data to a connection
#' @rdname BinaryWriter-class
#' @slot output the binary output connection
#' @slot byteOffset the number of bytes to skip at the start of input
#' @slot dataType the dataType of the binary Elements
#' @slot bytesPerElement number of bytes in each data element (e.g. 4 or 8 for floating point numbers)
#' @slot endian endianness of binary output connection
#' @export
setClass("BinaryWriter", representation=
representation(output="connection",
byteOffset="numeric",
dataType="character",
bytesPerElement="integer",
endian="character"))
#' BrainSpace
#'
#' This class represents the geometry of a brain image
#' @rdname BrainSpace-class
#' @slot Dim the grid dimensions of the image
#' @slot origin the coordinates of the spatial origin
#' @slot spacing the dimensions (in mm) of the grid units (voxels)
#' @slot axes the set of named spatial axes
#' @slot trans an affine transformation matrix that moves from grid -> real world coordinates
#' @slot inverseTrans an inverse matrix that moves from real world -> grid coordinates
#' @export
setClass("BrainSpace",
representation=
representation(Dim = "integer", origin = "numeric", spacing = "numeric",
axes="AxisSet", trans="matrix", inverseTrans="matrix"),
validity = function(object) {
Dim <- object@Dim
if (length(Dim) < length(object@spacing)) {
return("Dim slot must be of same length as spacing slot")
}
if (length(Dim) < length(object@origin)) {
return("Dim slot must be of same length as origin slot")
}
if (length(Dim) < ndim(object@axes)) {
return("Dim slot must be of same length as number of axes in AxisSet")
}
if (any(Dim) < 0) {
return("Dim slot must contain non-negative values")
}
})
#' BrainData
#'
#' Base class for brain image data
#'
#'
#' @rdname BrainData-class
#' @slot source an instance of class \code{\linkS4class{BaseSource}} to store the source of the data
#' @slot space an instance of class \code{\linkS4class{BrainSpace}} to represent the geometry of the data space
#' @export
setClass("BrainData",
representation=
representation(source="BaseSource",
space="BrainSpace"),
contains=c("VIRTUAL"))
#' BrainSlice
#'
#' Two-dimensional brain image
#' @rdname BrainSlice-class
#' @export
setClass("BrainSlice",
contains=c("BrainData", "array"))
#' Base class for image representing 3D volumetric data.
#' @rdname BrainVolume-class
#' @export
setClass("BrainVolume",
contains=c("BrainData"))
#' DenseBrainVolume
#'
#' Three-dimensional brain image, backed by an \code{array}
#' @rdname DenseBrainVolume-class
#' @export
setClass("DenseBrainVolume",
contains=c("BrainVolume", "array"))
#' SparseBrainVolume
#'
#' Three-dimensional brain image, backed by a \code{sparseVector} for \code{Matrix} package
#' @slot data a \code{sparseVector} instance
#' @rdname SparseBrainVolume-class
#' @export
setClass("SparseBrainVolume",
representation=representation(data="sparseVector"),
contains=c("BrainVolume"))
#' LogicalBrainVolume
#'
#' Three-dimensional brain image where all values are either TRUE or FALSE
#' @rdname LogicalBrainVolume-class
#' @export
setClass("LogicalBrainVolume",
contains=c("DenseBrainVolume"))
#' ClusteredBrainVolume
#'
#' Three-dimensional brain image that is divided into N disjoint partitions
#' @rdname ClusteredBrainVolume-class
#' @export
setClass("ClusteredBrainVolume",
representation=representation(mask="LogicalBrainVolume", clusters="integer", centers="matrix", labelMap="list", clusterMap="hash"),
contains=c("BrainVolume"))
#' IndexLookupVolume
#'
#' Three-dimensional brain image that can be used as a map between 1D grid indices and a table of values
#' Currently used in the \code{\linkS4class{SparseBrainVector}} class.
#' @rdname IndexLookupVolume-class
#' @export
setClass("IndexLookupVolume",
representation=
representation(space="BrainSpace", indices="integer", map="integer"),
contains=c("BrainVolume"))
#' BrainVector
#'
#' Four-dimensional brain image
#'
#' @rdname BrainVector-class
#' @export
setClass("BrainVector",
contains=c("BrainData"))
#' DenseBrainVector
#'
#' Four-dimensional brain image, backed by an array
#' @name DenseBrainVector-class
#' @export
setClass("DenseBrainVector",
contains=c("BrainVector", "array"))
# DenseMMapBrainVector
#
# Four-dimensional brain image, backed by a memory-mapped file
# @exportClass DenseMMapBrainVector
# setClass("DenseMMapBrainVector",
# representation=representation(data="mmap"),
# contains=c("BrainVector"))
#' SparseBrainVector
#'
#' a sparse four-dimensional brain image, backed by a \code{matrix}, where each column represents
#' a vector spanning the fourth dimension (e.g. time)
#' @rdname SparseBrainVector-class
#' @slot mask the mask defining the sparse domain
#' @slot data the matrix of series, where rows span across voxel space and columns span the fourth dimensions
#' @slot map instance of class \code{\linkS4class{IndexLookupVolume}} is used to map between spatial and index/row coordinates
#' @export
setClass("SparseBrainVector",
representation=representation(mask="LogicalBrainVolume",data="matrix", map="IndexLookupVolume"),
contains=c("BrainVector"))
#' SparseBrainVectorSource
#'
#' A class that is used to produce a \code{\linkS4class{SparseBrainVector}} instance
#' @rdname SparseBrainVectorSource-class
#' @slot mask the subset of voxels that will be stored in memory
#' @export
setClass("SparseBrainVectorSource", representation=
representation(mask="LogicalBrainVolume"),
contains=c("BrainVectorSource"))
#setClass("TiledBrainVector",
# representation=representation(cache="list", filename="character", indexList="list", mask="BrainVolume",capacity="numeric"),
# contains=c("BrainVector"))
#' ROIVolume
#'
#' A class that representing a volumetric region of interest (ROI).
#' @rdname ROIVolume-class
#' @slot data the \code{numeric} data stored in the ROI
#' @slot coords the voxel coordinates of the ROI
#' @exportClass ROIVolume
setClass("ROIVolume",
representation=representation(data="numeric", coords="matrix"), contains=c("BrainData"),
validity = function(object) {
if (ncol(object@coords) != 3) {
stop("coords slot must be a matrix with 3 columns")
}
})
#' Kernel
#'
#' A class representing an image kernel
#'
#' @rdname Kernel-class
#' @slot width the width in voxels of the kernel
#' @slot weights the kernel weights
#' @slot voxels the relative voxel coordinates of the kernel
#' @slot coords the relative real coordinates of the kernel
#' @export
setClass("Kernel",
representation=representation(width="numeric", weights="numeric", voxels="matrix", coords="matrix"))
## TODO add a LazyBrainBucket class
#' BrainSurface
#'
#' a three-dimensional surface consisting of a set of triangle vertices with one value per vertex.
#' @rdname BrainSurface-class
#' @slot source the data source for the surface
#' @slot mesh the underlying \code{mesh3d} object
#' @slot data the vector of data value at each vertex of the mesh
#' @export
setClass("BrainSurface",
representation=representation(source="BrainSource", mesh="mesh3d", data="numeric"))
#' BrainSurfaceVector
#'
#' a three-dimensional surface consisting of a set of triangle vertices with multiple values per vertex.
#'
#' @rdname BrainSurfaceVector-class
#' @slot source the data source for the surface
#' @slot mesh the underlying \code{mesh3d} object
#' @slot mat a matrix of values where each column contains a vector of values over the surface nodes.
#' @export
setClass("BrainSurfaceVector",
representation=representation(source="BrainSource", mesh="mesh3d", mat="numeric"))
#' BrainBucket
#'
#' a four-dimensional image that conists of a sequence of labeled image volumes backed by a list
#' @rdname BrainBucket-class
#' @slot source the data source for the bucket volumes
#' @slot labels the names of the sub-volumes contained in the bucket
#' @slot data a list of \code{\linkS4class{BrainVolume}} instances with names corresponding to volume labels
#' @export
setClass("BrainBucket",
representation=representation(source="BrainSource", labels="character", data="list"),
validity = function(object) {
if (any(sapply(object@data, function(obj) !is(obj, "BrainVolume")))) {
stop("all elements of data list must be of type `BrainVolume`")
} else {
TRUE
}
},
contains=c("BrainVector"))
#setClassUnion(name="index", members = c("numeric", "logical", "character"))
#' Layer
#'
#' A class used for displaying 2D images with color maps
#'
#' @rdname Layer-class
#' @slot vol the \code{BrainVolume} that provides the data for the layer.
#' @slot colorMap a character vector of colors in hexadecimal rgb format.
#' Can be generated by calls to \code{rainbow}, \code{heat.colors}, \code{topo.colors}, \code{terrain.colors} or similar functions.
#' @slot thresh cut-off value above which vlaues will be made transparent.
#' @slot axis the axis index of perpendicular to the xy plane (option: 1,2,3; default is 3)
#' @slot zero.col the color pixels with intensity of zero. This value overrides the color from the slot \code{colorMap}
#' @slot alpha the transparency of the layer
#' @export
setClass("Layer",
representation=representation(vol="BrainVolume", colorMap="vector", thresh="numeric", axis="numeric", zero.col="character", alpha="numeric"))
setClass("Overlay",
representation(layers="list"))
setClass("RenderedSlice",
representation=representation(slice="BrainSlice",
width="numeric",
height="numeric",
raster="rastergrob"))
setClass("RenderedSliceStack",
representation=representation(slices="list",
width="numeric",
height="numeric",
grob="gList"))
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