R/BrainFileDescriptor.R

In neuroim: Data Structures and Handling for Neuroimaging Data

#' @include AllClass.R
roxygen()
#' @include NIFTI_IO.R
roxygen()
#' @include AFNI_IO.R
roxygen()




#' @rdname fileMatches-methods
setMethod(f="fileMatches", signature=signature(x= "BrainFileDescriptor", fileName="character"),
		def=function(x, fileName) {
			if (headerFileMatches(x,fileName)) {
				file.exists(paste(stripExtension(x, fileName), ".", x@dataExtension, sep=""))				
			} else if (dataFileMatches(x,fileName)) {
				file.exists(paste(stripExtension(x, fileName), ".", x@headerExtension, sep=""))				
			} else {
				FALSE
			}	
		})

#' @rdname headerFileMatches-methods
setMethod(f="headerFileMatches", signature=signature(x= "BrainFileDescriptor", fileName="character"),
		def=function(x, fileName) {
			regexpr(paste(".*", x@headerExtension, "$", sep=""), fileName) > 0
					
		})

#' @rdname dataFileMatches-methods
setMethod(f="dataFileMatches", signature=signature(x= "BrainFileDescriptor", fileName="character"),
		def=function(x, fileName) {
			regexpr(paste(".*", x@dataExtension, "$", sep=""), fileName) > 0
		})

#' @rdname headerFile-methods
setMethod(f="headerFile",signature=signature(x= "BrainFileDescriptor", fileName="character"),
		def=function(x, fileName) {
			if (headerFileMatches(x, fileName)) {
				fileName
			} else if (dataFileMatches(x, fileName)) {
				paste(stripExtension(x, fileName), x@headerExtension, sep=".")				
			} else {
				stop(paste("could not derive header file name from: ", fileName))
			}		
		})

#' @rdname dataFile-methods
setMethod(f="dataFile",signature=signature(x= "BrainFileDescriptor", fileName="character"),
		def=function(x, fileName) {
			if (dataFileMatches(x, fileName)) {
				fileName
			} else if (headerFileMatches(x, fileName)) {
				paste(stripExtension(x, fileName), x@dataExtension, sep=".")
			} else {
				stop(paste("could not derive data file name from: ", fileName))
			}				
		})

#' @rdname stripExtension-methods
setMethod(f="stripExtension",signature=signature(x= "BrainFileDescriptor", fileName="character"),
		def=function(x, fileName) {
			if (headerFileMatches(x, fileName)) {
				ret <- strsplit(fileName, paste(x@headerExtension, "$", sep=""))[[1]][1]	
				substr(ret, 1, nchar(ret)-1)
			} else if (dataFileMatches(x, fileName)) {
				ret <- strsplit(fileName, paste(x@dataExtension, "$", sep=""))[[1]][1]		
				substr(ret, 1, nchar(ret)-1)
			} else {
				stop("file does not match descriptor: " + x)
			}		
		})


.readMetaInfo <- function(desc, fileName, readFunc, constructor) {
	
	hfile <- headerFile(desc, fileName)
	header <- readFunc(hfile)		
	header$fileName <- hfile
	constructor(desc, header)	
}

#' @rdname readMetaInfo-methods
#' @export
setMethod(f="readMetaInfo",signature=signature(x= "NIfTIFileDescriptor"),
		def=function(x, fileName) {
			.readMetaInfo(x, fileName, readNIfTIHeader, NIfTIMetaInfo)
		})

#' @rdname readMetaInfo-methods
#' @export
setMethod(f="readMetaInfo",signature=signature(x= "AFNIFileDescriptor"),
		def=function(x, fileName) {
			.readMetaInfo(x, fileName, readAFNIHeader, AFNIMetaInfo)
			
		})


#' @rdname readMetaInfo-methods
#' @export
setMethod(f="readMetaInfo",signature=signature(x= "NIMLSurfaceFileDescriptor"),
    def=function(x, fileName) {
      .readMetaInfo(x, fileName, readNIMLSurfaceHeader, NIMLSurfaceDataMetaInfo)
    })

#' @rdname readMetaInfo-methods
#' @export
setMethod(f="readMetaInfo",signature=signature(x= "FreesurferAsciiSurfaceFileDescriptor"),
    def=function(x, fileName) {
      .readMetaInfo(x, fileName, readFreesurferAsciiHeader, SurfaceGeometryMetaInfo)
    })


findDescriptor <- function(fileName) {
	if (fileMatches(NIFTI, fileName)) NIFTI
	else if (fileMatches(NIFTI_GZ, fileName)) NIFTI_GZ
	else if (fileMatches(NIFTI_PAIR, fileName)) NIFTI_PAIR
	else if (fileMatches(NIFTI_PAIR_GZ, fileName)) NIFTI_PAIR_GZ
	else if (fileMatches(AFNI, fileName)) AFNI
	else if (fileMatches(AFNI_GZ, fileName)) AFNI_GZ
  else if (fileMatches(NIML_SURFACE_DSET, fileName)) NIML_SURFACE_DSET
  else if (fileMatches(FREESURFER_ASCII_SURFACE_DSET, fileName)) FREESURFER_ASCII_SURFACE_DSET
	else NULL
}

AFNI <- new("AFNIFileDescriptor",
		fileFormat="AFNI",
		headerEncoding="raw",
		headerExtension="HEAD",
		dataEncoding="raw",
		dataExtension="BRIK")

AFNI_GZ <- new("AFNIFileDescriptor",
		fileFormat="AFNI",
		headerEncoding="gzip",
		headerExtension="HEAD",
		dataEncoding="gzip",
		dataExtension="BRIK.gz")

NIFTI <- new("NIfTIFileDescriptor",
		fileFormat="NIfTI",
		headerEncoding="raw",
		headerExtension="nii",
		dataEncoding="raw",
		dataExtension="nii")

NIFTI_GZ <- new("NIfTIFileDescriptor",
		fileFormat="NIfTI",
		headerEncoding="gzip",
		headerExtension="nii.gz",
		dataEncoding="gzip",
		dataExtension="nii.gz")

NIFTI_PAIR <- new("NIfTIFileDescriptor",
		fileFormat="NIfTI",
		headerEncoding="raw",
		headerExtension="hdr",
		dataEncoding="raw",
		dataExtension="img")

NIFTI_PAIR_GZ <- new("NIfTIFileDescriptor",
		fileFormat="NIfTI",
		headerEncoding="gzip",
		headerExtension="hdr.gz",
		dataEncoding="gzip",
		dataExtension="img.gz")

NIML_SURFACE_DSET <- new("NIMLSurfaceFileDescriptor",
                     fileFormat="NIML",
                     headerEncoding="raw",
                     headerExtension="niml.dset",
                     dataEncoding="raw",
                     dataExtension="niml.dset")

FREESURFER_ASCII_SURFACE_DSET <- new("FreesurferAsciiSurfaceFileDescriptor",
                         fileFormat="Freesurfer_ASCII",
                         headerEncoding="text",
                         headerExtension="asc",
                         dataEncoding="raw",
                         dataExtension="asc")