Nothing
read_ima <- function(fraw, verbose = FALSE, extra) {
tags <- list(ascii_hdr = "0029,1120", spec_data = "7FE1,1010")
res <- dicom_reader(fraw, tags)
vars <- read_siemens_txt_hdr(res$ascii_hdr, "vd", verbose)
# works for CMRR MPRESS, but not CMRR sLASER
if (!vars$rm_oversampling) vars$N <- vars$N * 2
# calculate expected size of data points
data_size <- vars$x_pts * vars$y_pts * vars$z_pts * vars$N * 2
# note that for scans where oversampling is not removed there are actually
# twice the number of points in the DICOM tag. However these points seem to
# be garbage making this mode useless as half the time-domain data is lost.
raw_pts <- readBin(res$spec_data, what = "double", n = data_size, size = 4L)
# make complex
data <- raw_pts[c(TRUE, FALSE)] + 1i * raw_pts[c(FALSE, TRUE)]
data <- array(data, dim = c(vars$N, 1, 1, vars$z_pts, vars$y_pts, vars$x_pts,
1))
data <- aperm(data, c(7, 5, 6, 4, 3, 2, 1))
# freq domain vector vector
freq_domain <- rep(FALSE, 7)
# get the resolution and geom info
paras <- calc_siemens_paras(vars, TRUE)
meta <- list(EchoTime = vars$te,
FlipAngle = vars$flip_ang,
SequenceName = vars$seq_fname,
ChemicalShiftReference = 4.7 + vars$delta_freq,
NumberOfTransients = vars$averages,
Manufacturer = "Siemens")
if (toupper(vars$seq_fname) == "%SIEMENSSEQ%\\SVS_SE") {
meta <- append(meta, list(PulseSequenceType = "press"))
}
if (toupper(vars$seq_fname) == "%SIEMENSSEQ%\\SVS_ST") {
meta <- append(meta, list(PulseSequenceType = "steam"))
}
if (startsWith(toupper(vars$seq_fname), "%CUSTOMERSEQ%\\SVS_SLASER")) {
meta <- append(meta, list(PulseSequenceType = "slaser",
TE1 = vars$te1,
TE2 = vars$te2,
TE3 = vars$te3))
}
if (vars$rm_oversampling) meta <- append(meta, list(fid_filt_dist = TRUE))
mrs_data <- mrs_data(data = data, ft = vars$ft, resolution = paras$res,
ref = paras$ref, nuc = paras$nuc,
freq_domain = freq_domain, affine = paras$affine,
meta = meta, extra = extra)
return(mrs_data)
}
#' Read a directory containing Siemens MRS IMA files and combine along the coil
#' dimension. Note that the coil ID is inferred from the sorted file name and
#' should be checked when consistency is required between two directories.
#' @param dir data directory path.
#' @param extra an optional data frame to provide additional variables for use
#' in subsequent analysis steps, eg id or grouping variables.
#' @param verbose output extra information to the console.
#' @return mrs_data object.
#' @export
read_ima_coil_dir <- function(dir, extra = NULL, verbose = FALSE) {
# check the directory exists
if (!dir.exists(dir)) stop("Error read_ima_coil_dir directory was not found.")
# check it contains some files
files <- list.files(dir, full.names = TRUE)
if (length(files) == 0) stop("Error, read_ima_coil_dir files not found.")
#warning("coil ordering is based on file name only.")
files <- sort(files)
mrs_list <- lapply(files, read_mrs, format = "dicom", verbose = verbose,
extra = extra)
mrs_data <- append_coils(mrs_list)
return(mrs_data)
}
#' Read a directory containing Siemens MRS IMA files and combine along the
#' dynamic dimension. Note that the coil ID is inferred from the sorted file
#' name and should be checked when consistency is required.
#' @param dir data directory path.
#' @param extra an optional data frame to provide additional variables for use
#' in subsequent analysis steps, eg id or grouping variables.
#' @param verbose output extra information to the console.
#' @return mrs_data object.
#' @export
read_ima_dyn_dir <- function(dir, extra = NULL, verbose = FALSE) {
# check the directory exists
if (!dir.exists(dir)) stop("Error read_ima_dyn_dir directory was not found.")
# check it contains some files
files <- list.files(dir, full.names = TRUE)
if (length(files) == 0) stop("Error, read_ima_dyn_dir files not found.")
files <- sort(files)
mrs_list <- lapply(files, read_mrs, format = "dicom", verbose = verbose,
extra = extra)
mrs_data <- append_dyns(mrs_list)
# deal with CMRR reference scans if needed
seq_name_upper <- toupper(mrs_data$meta$SequenceName)
if (startsWith(seq_name_upper, "%CUSTOMERSEQ%\\SVS_SLASER")) {
if (mrs_data$meta$NumberOfTransients == Ndyns(mrs_data)) {
return(mrs_data)
} else {
return(extract_dkd_wref_scans(mrs_data))
}
} else {
return(mrs_data)
}
}
extract_dkd_wref_scans <- function(mrs_data) {
full_n <- Ndyns(mrs_data)
metab_n <- mrs_data$meta$NumberOfTransients
ref_n <- full_n - metab_n
metab_inds <- (ref_n / 2 + 1):(full_n - ref_n / 2)
metab <- get_dyns(mrs_data, metab_inds)
ref_inds_start <- 1:(ref_n / 2)
ref_inds_end <- ((full_n - ref_n / 2) + 1):full_n
# water ecc inds
ref_ecc_inds <- c(ref_inds_start[1:(ref_n / 4)],
ref_inds_end[1:(ref_n / 4)])
ref_ecc <- get_dyns(mrs_data, ref_ecc_inds)
ref_ecc <- set_Ntrans(ref_ecc, Ndyns(ref_ecc))
ref_ecc$meta$ChemicalShiftReference <- NULL
# water scaling inds
ref_inds <- c(ref_inds_start[((ref_n / 4) + 1):(ref_n / 2)],
ref_inds_end[((ref_n / 4) + 1):(ref_n / 2)])
ref <- get_dyns(mrs_data, ref_inds)
ref <- set_Ntrans(ref, Ndyns(ref))
ref$meta$ChemicalShiftReference <- NULL
out <- list(metab = metab, ref = ref, ref_ecc = ref_ecc)
class(out) <- c("list", "mrs_data")
return(out)
}
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