Nothing
#' @include AllClass.R
roxygen()
#' @include AllGeneric.R
roxygen()
#' @include BrainFileDescriptor.R
roxygen()
#' @include Axis.R
roxygen()
#' @include NIFTI_IO.R
roxygen()
#' Generic function to create data reader
#' @param x an object specifying the infromation required to produce the reader
#' @param offset the byte offset (number of bytes to skip before reading)
#' @export dataReader
#' @rdname dataReader-methods
setGeneric(name="dataReader", def=function(x, offset) standardGeneric("dataReader"))
#' dim of \code{FileMetaInfo}
#' @param x the object
#' @export
setMethod(f="dim", signature=signature("FileMetaInfo"),
def=function(x) {
x@Dim
})
# @rdname loadData-methods
# setMethod(f="loadData", signature=signature(""))
#' @rdname dataReader-methods
setMethod(f="dataReader", signature=signature("NIfTIMetaInfo"),
def=function(x, offset=0) {
if (x@fileDescriptor@dataEncoding == "gzip") {
BinaryReader(gzfile(x@dataFile, "rb"), x@dataOffset+offset, .getRStorage(x@dataType), x@bytesPerElement, x@endian)
} else {
BinaryReader(x@dataFile, x@dataOffset+offset, .getRStorage(x@dataType), x@bytesPerElement, x@endian)
}
})
#' @rdname dataReader-methods
setMethod(f="dataReader", signature=signature("AFNIMetaInfo"),
def=function(x, offset=0) {
if (x@fileDescriptor@dataEncoding == "gzip") {
BinaryReader(gzfile(x@dataFile, "rb"), x@dataOffset+offset, .getRStorage(x@dataType), x@bytesPerElement, x@endian)
} else {
BinaryReader(x@dataFile, x@dataOffset+offset, .getRStorage(x@dataType), x@bytesPerElement, x@endian)
}
})
#' @rdname dataReader-methods
setMethod(f="dataReader", signature=signature("NIMLSurfaceDataMetaInfo"),
def=function(x) {
reader <- function(i) {
if (length(i) == 1 && i == 0) {
x@nodeIndices
} else {
x@data[,i,drop=FALSE]
}
}
new("ColumnReader", nrow=as.integer(nrow(x@data)), ncol=as.integer(ncol(x@data)), reader=reader)
})
#' @rdname readColumns-methods
setMethod(f="readColumns", signature=signature(x="ColumnReader", columnIndices="numeric"),
def=function(x,columnIndices) {
x@reader(columnIndices)
})
#' @rdname trans-methods
setMethod(f="trans", signature=signature("BrainMetaInfo"),
def=function(x) {
D <- min(length(x@Dim), 3)
trans <- diag(c(x@spacing,1))
trans[1:D,D+1] <- x@origin
trans
})
#' @rdname trans-methods
setMethod(f="trans", signature=signature("NIfTIMetaInfo"),
def=function(x) {
x@header$qform
})
niftiDim <- function(nifti_header) {
dimarray <- nifti_header$dimensions
lastidx <- min(which(dimarray == 1)) - 1
dimarray[2:lastidx]
}
#' This class contains meta information for an image
#'
#' @param Dim image dimensions
#' @param spacing voxel dimensions
#' @param origin coordinate origin
#' @param dataType the type of the data (e.g. "FLOAT")
#' @param label name(s) of images
#' @param spatialAxes image axes for spatial dimensions (x,y,z)
#' @param additionalAxes axes for dimensions > 3 (e.g. time, color band, direction)
#' @return an instance of class \code{\linkS4class{BrainMetaInfo}}
#' @export BrainMetaInfo
#' @rdname BrainMetaInfo-class
BrainMetaInfo <- function(Dim, spacing, origin=rep(0, length(spacing)), dataType="FLOAT", label="", spatialAxes=OrientationList3D$AXIAL_LPI, additionalAxes=NullAxis) {
new("BrainMetaInfo",
Dim=Dim,
spacing=spacing,
origin=origin,
dataType=dataType,
label=label,
spatialAxes=spatialAxes,
additionalAxes=additionalAxes)
}
#' Constructor for \code{\linkS4class{SurfaceGeometryMetaInfo}} class
#' @param descriptor the file descriptor
#' @param header a \code{list} containing header information
SurfaceGeometryMetaInfo <- function(descriptor, header) {
stopifnot(is.numeric(header$vertices))
stopifnot(is.numeric(header$faces))
new("SurfaceGeometryMetaInfo",
headerFile=header$headerFile,
dataFile=header$dataFile,
fileDescriptor=descriptor,
vertices=as.integer(header$vertices),
faces=as.integer(header$faces),
label=as.character(header$label),
embedDimension=as.integer(header$embedDimension))
}
#' Constructor for \code{\linkS4class{SurfaceDataMetaInfo}} class
#' @param descriptor the file descriptor
#' @param header a \code{list} containing header information
SurfaceDataMetaInfo <- function(descriptor, header) {
stopifnot(is.numeric(header$nodes))
new("SurfaceDataMetaInfo",
headerFile=header$headerFile,
dataFile=header$dataFile,
fileDescriptor=descriptor,
nodeCount=as.integer(header$nodes),
nels=as.integer(header$nels),
label=as.character(header$label))
}
#' Constructor for \code{\linkS4class{NIMLSurfaceDataMetaInfo}} class
#' @param descriptor the file descriptor
#' @param header a \code{list} containing header information
#'
NIMLSurfaceDataMetaInfo <- function(descriptor, header) {
stopifnot(is.numeric(header$nodes))
new("NIMLSurfaceDataMetaInfo",
headerFile=header$headerFile,
dataFile=header$dateFile,
fileDescriptor=descriptor,
nodeCount=as.integer(header$nodeCount),
nels=as.integer(header$nels),
label=as.character(header$label),
data=header$data,
nodeIndices=header$nodes)
}
#' Constructor for \code{\linkS4class{NIfTIMetaInfo}} class
#' @param descriptor an instance of class \code{\linkS4class{NIfTIFileDescriptor}}
#' @param nifti_header a \code{list} returned by \code{readNIftiHeader}
#' @return an instance of class \code{\linkS4class{NIfTIMetaInfo}}
#' @export NIfTIMetaInfo
#' @rdname NIfTIMetaInfo-class
NIfTIMetaInfo <- function(descriptor, nifti_header) {
stopifnot(!is.null(nifti_header$fileType) || (nifti_header$fileType == "NIfTI"))
new("NIfTIMetaInfo",
headerFile=headerFile(descriptor, nifti_header$fileName),
dataFile=dataFile(descriptor, nifti_header$fileName),
fileDescriptor=descriptor,
endian=nifti_header$endian,
dataOffset=nifti_header$voxOffset,
dataType=nifti_header$dataStorage,
bytesPerElement=as.integer(.getDataSize(nifti_header$dataStorage)),
Dim=niftiDim(nifti_header),
spatialAxes=.nearestAnatomy(nifti_header$qform),
additionalAxes=NullAxis,
spacing=nifti_header$pixdim[2:4],
origin=nifti_header$qoffset,
label=stripExtension(descriptor, basename(nifti_header$fileName)),
intercept=nifti_header$sclIntercept,
slope=nifti_header$sclSlope,
header=nifti_header)
}
#' show an \code{SurfaceGeometryMetaInfo}
#' @param object the object
#' @export
setMethod(f="show", signature=signature("SurfaceGeometryMetaInfo"),
def=function(object) {
cat("an instance of class", class(object), "\n\n")
cat("number of vertices:", "\t", object@vertices, "\n")
cat("number of faces:", "\t", object@faces, "\n")
cat("label:", "\t", object@label, "\n")
cat("embed dimension:", "\t", object@embedDimension, "\n")
})
#' show an \code{SurfaceDataMetaInfo}
#' @param object the object
#' @export
setMethod(f="show", signature=signature("SurfaceDataMetaInfo"),
def=function(object) {
cat("an instance of class", class(object), "\n\n")
cat("nodeCount:", "\t", object@nodeCount, "\n")
cat("nels:", "\t", object@nels, "\n")
cat("label:", "\t", object@label, "\n")
})
#' show a \code{FileMetaInfo}
#' @param object the object
#' @export
setMethod(f="show", signature=signature("FileMetaInfo"),
def=function(object) {
cat("an instance of class", class(object), "\n\n")
cat("headerFile:", "\t", object@headerFile, "\n")
cat("dataFile:", "\t", object@dataFile, "\n")
cat("endian:", "\t", object@endian, "\n")
cat("dataOffset:", "\t", object@dataOffset, "\n")
cat("dataType:", "\t", object@dataType, "\n")
cat("dimensions:", "\t", object@Dim, "\n")
cat("voxel size:", "\t", object@spacing, "\n")
cat("origin:", "\t", object@origin, "\n")
cat("label(s):", "\t", object@label, "\n")
cat("intercept:", "\t", object@intercept, "\n")
cat("slope:", "\t\t", object@slope, "\n\n")
cat("additional format-specific info may be contained in @header slot", "\n")
})
#' AFNIMetaInfo
#'
#' Constructor for \code{\linkS4class{AFNIMetaInfo}} class
#' @param descriptor an instance of class \code{\linkS4class{AFNIFileDescriptor}}
#' @param afni_header a \code{list} returned by \code{readAFNIHeader}
#' @return an instance of class \code{\linkS4class{AFNIMetaInfo}}
#' @export AFNIMetaInfo
#' @rdname AFNIMetaInfo-class
AFNIMetaInfo <- function(descriptor, afni_header) {
.Dim <- afni_header$DATASET_DIMENSIONS$content[afni_header$DATASET_DIMENSIONS$content > 0]
if (afni_header$DATASET_RANK$content[2] > 1) {
.Dim <- c(.Dim, afni_header$DATASET_RANK$content[2])
}
labs <- if (is.null(afni_header$BRICK_LABS$content)) {
labs <- paste("#", seq(0, afni_header$DATASET_RANK$content[2]), sep="")
} else {
afni_header$BRICK_LABS$content
}
## AFNI contains a transform from IJK to dicom (RAI) space.
## We want the transform to go from IJK to nifti (LPI) space
Tdicom <- matrix(afni_header$IJK_TO_DICOM$content, 3,4, byrow=TRUE)
Tdicom <- rbind(Tdicom, c(0,0,0,1))
TLPI <- diag(c(-1,-1,1,1)) %*% Tdicom
new("AFNIMetaInfo",
headerFile=headerFile(descriptor, afni_header$fileName),
dataFile=dataFile(descriptor, afni_header$fileName),
fileDescriptor=descriptor,
endian=ifelse(afni_header[["BYTEORDER_STRING"]]$content == "MSB_FIRST", "big", "little"),
dataOffset=0,
dataType=switch(afni_header$BRICK_TYPES$content[1], "0"="BYTE", "1"="SHORT", "3"="FLOAT"),
bytesPerElement=as.integer(switch(afni_header$BRICK_TYPES$content[1], "0"=1, "1"=2, "3"=4)),
Dim=.Dim,
spatialAxes=OrientationList3D$AXIAL_LPI, # incorrect
additionalAxes=NullAxis, # incorrect
spacing=abs(afni_header$DELTA$content),
origin=afni_header$ORIGIN$content,
label=labs,
intercept=0,
slope=ifelse(afni_header$BRICK_FLOAT_FACS$content == 0, 1, afni_header$BRICK_FLOAT_FACS$content),
header=afni_header)
}
#' read header information of an image file
#'
#'
#' @param fileName the name of the file to read
#' @return an instance of class \code{\linkS4class{FileMetaInfo}}
#' @export readHeader
readHeader <- function(fileName) {
desc <- findDescriptor(fileName)
if (is.null(desc)) {
stop(paste("could not find reader for file: ", fileName))
}
readMetaInfo(desc, fileName)
}
setAs(from="BrainMetaInfo", to="NIfTIMetaInfo", def=function(from) {
if (inherits(from, "NIfTIMetaInfo")) {
from
} else {
hdr <- as.nifti.header(from)
desc <- findDescriptor(hdr$fileName)
NIfTIMetaInfo(desc, hdr)
}
})
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