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file_format.R
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file_format.R
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#' @include all_class.R
NULL
#' @include all_generic.R
#' @rdname file_matches-methods
setMethod(f="file_matches", signature=signature(x= "FileFormat", file_name="character"),
def=function(x, file_name) {
if (header_file_matches(x,file_name)) {
file.exists(paste(strip_extension(x, file_name), ".", x@data_extension, sep=""))
} else if (data_file_matches(x,file_name)) {
file.exists(paste(strip_extension(x, file_name), ".", x@header_extension, sep=""))
} else {
FALSE
}
})
#' @rdname header_file_matches-methods
setMethod(f="header_file_matches", signature=signature(x= "FileFormat", file_name="character"),
def=function(x, file_name) {
regexpr(paste(".*", x@header_extension, "$", sep=""), file_name) > 0
})
#' @rdname data_file_matches-methods
setMethod(f="data_file_matches", signature=signature(x= "FileFormat", file_name="character"),
def=function(x, file_name) {
regexpr(paste(".*", x@data_extension, "$", sep=""), file_name) > 0
})
#' @rdname header_file-methods
setMethod(f="header_file",signature=signature(x= "FileFormat", file_name="character"),
def=function(x, file_name) {
if (header_file_matches(x, file_name)) {
file_name
} else if (data_file_matches(x, file_name)) {
paste(strip_extension(x, file_name), x@header_extension, sep=".")
} else {
stop(paste("could not derive header file name from: ", file_name))
}
})
#' @rdname data_file-methods
setMethod(f="data_file",signature=signature(x= "FileFormat", file_name="character"),
def=function(x, file_name) {
if (data_file_matches(x, file_name)) {
file_name
} else if (header_file_matches(x, file_name)) {
paste(strip_extension(x, file_name), x@data_extension, sep=".")
} else {
stop(paste("could not derive data file name from: ", file_name))
}
})
#' @rdname strip_extension-methods
setMethod(f="strip_extension",signature=signature(x= "FileFormat", file_name="character"),
def=function(x, file_name) {
if (header_file_matches(x, file_name)) {
ret <- strsplit(file_name, paste(x@header_extension, "$", sep=""))[[1]][1]
substr(ret, 1, nchar(ret)-1)
} else if (data_file_matches(x, file_name)) {
ret <- strsplit(file_name, paste(x@data_extension, "$", sep=""))[[1]][1]
substr(ret, 1, nchar(ret)-1)
} else {
stop("file does not match descriptor: " + x)
}
})
#' @keywords internal
#' @noRd
.read_meta_info <- function(desc, file_name, read_func, constructor) {
hfile <- header_file(desc, file_name)
header <- read_func(hfile)
header$file_name <- hfile
constructor(desc, header)
}
#' @rdname read_meta_info-methods
setMethod(f="read_meta_info",signature=signature(x= "NIFTIFormat"),
def=function(x, file_name) {
.read_meta_info(x, file_name, read_nifti_header, NIFTIMetaInfo)
})
#' @rdname read_meta_info-methods
setMethod(f="read_meta_info",signature=signature(x= "AFNIFormat"),
def=function(x, file_name) {
.read_meta_info(x, file_name, read_afni_header, AFNIMetaInfo)
})
#' @keywords internal
#' @noRd
find_descriptor <- function(file_name) {
if (file_matches(NIFTI, file_name)) NIFTI
else if (file_matches(NIFTI_GZ, file_name)) NIFTI_GZ
else if (file_matches(NIFTI_PAIR, file_name)) NIFTI_PAIR
else if (file_matches(NIFTI_PAIR_GZ, file_name)) NIFTI_PAIR_GZ
else if (file_matches(AFNI, file_name)) AFNI
else if (file_matches(AFNI_GZ, file_name)) AFNI_GZ
else NULL
}
#' @keywords internal
#' @noRd
AFNI <- new("AFNIFormat",
file_format="AFNI",
header_encoding="raw",
header_extension="HEAD",
data_encoding="raw",
data_extension="BRIK")
#' @keywords internal
#' @noRd
AFNI_GZ <- new("AFNIFormat",
file_format="AFNI",
header_encoding="gzip",
header_extension="HEAD",
data_encoding="gzip",
data_extension="BRIK.gz")
#' @keywords internal
#' @noRd
NIFTI <- new("NIFTIFormat",
file_format="NIFTI",
header_encoding="raw",
header_extension="nii",
data_encoding="raw",
data_extension="nii")
#' @keywords internal
#' @noRd
NIFTI_GZ <- new("NIFTIFormat",
file_format="NIFTI",
header_encoding="gzip",
header_extension="nii.gz",
data_encoding="gzip",
data_extension="nii.gz")
#' @keywords internal
#' @noRd
NIFTI_PAIR <- new("NIFTIFormat",
file_format="NIFTI",
header_encoding="raw",
header_extension="hdr",
data_encoding="raw",
data_extension="img")
#' @keywords internal
NIFTI_PAIR_GZ <- new("NIFTIFormat",
file_format="NIFTI",
header_encoding="gzip",
header_extension="hdr.gz",
data_encoding="gzip",
data_extension="img.gz")