version bump

Merge branch 'devel' # Conflicts: # docs/404.html # docs/CONTRIBUTING.html # docs/LICENSE-text.html # docs/articles/abfit-baseline-opts.html # docs/articles/abfit-baseline-opts_files/figure-html/abfit_aic-1.png # docs/articles/abfit-baseline-opts_files/figure-html/abfit_bspline-1.png # docs/articles/abfit-baseline-opts_files/figure-html/abfit_bspline_more-1.png # docs/articles/abfit-baseline-opts_files/figure-html/abfit_default-1.png # docs/articles/abfit-baseline-opts_files/figure-html/abfit_flex-1.png # docs/articles/abfit-baseline-opts_files/figure-html/abfit_stiff-1.png # docs/articles/index.html # docs/articles/spant-basis-simulation.html # docs/articles/spant-intro.html # docs/articles/spant-intro_files/figure-html/unnamed-chunk-10-1.png # docs/articles/spant-metabolite-simulation.html # docs/articles/spant-preprocessing.html # docs/authors.html # docs/index.html # docs/news/index.html # docs/pkgdown.yml # docs/reference/Arg.mrs_data.html # docs/reference/Conj.mrs_data.html # docs/reference/Im.mrs_data.html # 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martin3141 · Aug 27, 2024 · 33f5ccb · 33f5ccb
2 parents 2158ea3 + f49480b
commit 33f5ccb
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Showing 400 changed files with 9,532 additions and 4,426 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: spant
 Type: Package
 Title: MR Spectroscopy Analysis Tools
-Version: 2.22.0
-Date: 2024-07-11
+Version: 2.23.0
+Date: 2024-08-27
 Authors@R: c(
     person("Martin", "Wilson", email = "martin@pipegrep.co.uk",
            role = c("cre", "aut"), comment = c(ORCID = "0000-0002-2089-3956")),
@@ -14,7 +14,7 @@ Description: Tools for reading, visualising and processing Magnetic Resonance
     <DOI:10.1002/mrm.27605>. 
 BugReports: https://github.com/martin3141/spant/issues/
 License: GPL-3
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE, roclets = c("rd", "namespace", "collate"))
 NeedsCompilation: yes
 LazyData: yes
@@ -50,6 +50,7 @@ Suggests:
     testthat,
     ragg,
     doParallel,
+    parallel,
     car
 VignetteBuilder:
     knitr

diff --git a/NAMESPACE b/NAMESPACE
@@ -78,6 +78,8 @@ export(bc_poly)
 export(bc_spline)
 export(beta2lw)
 export(bin_spec)
+export(calc_basis_corr_mat)
+export(calc_basis_crlbs)
 export(calc_coil_noise_cor)
 export(calc_coil_noise_sd)
 export(calc_design_efficiency)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# spant 2.23.0
+* abfit options for lipid and MM maximum broadening and maximum frequency shift
+now default to be the same as the metabolite values unless explicitly changed.
+* Added function to calculate the correlation matrix from a basis_set.
+* Fix for RDA files where a comma is sometimes used as a decimal point.
+
 # spant 2.22.0
 * Added find_bids_mrs and mrs_data2bids helper functions.
 * Improved handling of CMRR semi-LASER SVS water reference scans.

diff --git a/R/abfit.R b/R/abfit.R
diff --git a/R/basis_set.R b/R/basis_set.R
@@ -246,11 +246,13 @@ write_basis <- function(basis, basis_file, fwhmba = 0.1) {
 #' @param amps a vector of scaling factors to apply to each basis element.
 #' @param shifts a vector of frequency shifts (in ppm) to apply to each basis
 #' element.
+#' @param lbs a vector of Lorentzian line broadening terms (in Hz) to apply to
+#' each basis element.
 #' @return an mrs_data object with basis signals spread across the dynamic 
 #' dimension or summed.
 #' @export
 basis2mrs_data <- function(basis, sum_elements = FALSE, amps = NULL,
-                           shifts = NULL) {
+                           shifts = NULL, lbs = NULL) {
 
   # TODO nuc is just the default for now 
   res <- mat2mrs_data(t(basis$data), fs = basis$fs, ft = basis$ft,
@@ -277,9 +279,17 @@ basis2mrs_data <- function(basis, sum_elements = FALSE, amps = NULL,
     res <- shift(res, shifts)
   }
 
+  # Lorentzian line broaden basis elements
+  if (!is.null(lbs)) {
+    if (n_sigs != length(lbs)) {
+      stop(paste("Error, length of amps does not match the number of basis elements :", dim(basis$data)[2]))
+    }
+    res <- lb(res, lbs, 0)
+  }
+
   if (sum_elements) res <- sum_dyns(res)
 
-  res
+  return(res)
 }
 
 #' Convert a basis object to a dynamic mrs_data object.
@@ -478,3 +488,86 @@ make_basis_from_raw <- function(dir_path, ft, fs, ref) {
   basis <- mrs_data2basis(mrs_data_dynamic, names = names)
   return(basis)
 }
+
+#' Estimate the CRLB for each element in a basis set.
+#' @param basis basis_set object.
+#' @param xlim spectral range to use in ppm.
+#' @param zf zero-fill the basis set.
+#' @param sd standard deviation of the noise.
+#' @param bl_comp_pppm number spline baseline components to append per-ppm.
+#' @return a vector of predicted errors.
+#' @export
+calc_basis_crlbs <- function(basis, xlim = c(4, 0.2), zf = TRUE, sd = 1,
+                             bl_comp_pppm = NULL) {
+
+  basis_mrs <- basis2mrs_data(basis)
+
+  if (zf) basis_mrs <- zf(basis_mrs)
+
+  if (is.null(xlim)) {
+    ppm_sc <- ppm(basis_mrs)
+    xlim <- c(ppm_sc[1], ppm_sc[length(ppm_sc)])
+    basis_mrs <- td2fd(basis_mrs)
+  } else {
+    basis_mrs <- crop_spec(basis_mrs, xlim = xlim)
+  }
+
+  if (is.null(bl_comp_pppm)) {
+    D <- t(Re(mrs_data2mat(basis_mrs)))
+  } else {
+    D <- t(Re(mrs_data2mat(basis_mrs)))
+    comps <- diff(sort(xlim)) * bl_comp_pppm
+    sp_basis <- bbase(dim(D)[1], round(comps))
+    D <- cbind(D, sp_basis)
+  }
+
+  F <- (t(D) %*% D) / (sd ^ 2)
+
+  F_inv <- pracma::pinv(F)
+
+  errors <- diag(F_inv) ^ 0.5
+
+  if (is.null(bl_comp_pppm)) {
+    names(errors) <- basis$names
+  } else {
+    spline_names  <- paste("SPLINE", as.character(1:dim(sp_basis)[2]),
+                           sep = "_")
+
+    names(errors) <- c(basis$names, spline_names)
+  }
+
+  return(errors) 
+}
+
+#' Estimate the correlation matrix for a basis set.
+#' @param basis basis_set object.
+#' @param xlim spectral range to use in ppm.
+#' @param zf zero-fill the basis set.
+#' @return correlation matrix.
+#' @export
+calc_basis_corr_mat <- function(basis, xlim = c(4, 0.2), zf = TRUE) {
+
+  basis_mrs <- basis2mrs_data(basis)
+
+  if (zf) basis_mrs <- zf(basis_mrs)
+
+  basis_mrs <- crop_spec(basis_mrs, xlim = xlim)
+
+  D <- t(Re(mrs_data2mat(basis_mrs)))
+
+  F     <- (t(D) %*% D)
+  F_inv <- pracma::pinv(F)
+
+  corr_mat <- matrix(nrow = nrow(F_inv), ncol = ncol(F_inv))
+
+  for (x in 1:nrow(corr_mat)) {
+    for (y in 1:ncol(corr_mat)) {
+      corr_mat[x, y] <- F_inv[x, y] / ((F_inv[x, x] * F_inv[y, y]) ^ 0.5)
+    }
+  }
+
+  rownames(corr_mat) <- basis$names
+  colnames(corr_mat) <- basis$names
+
+  return(corr_mat)
+}
diff --git a/R/fitting.R b/R/fitting.R
@@ -31,6 +31,8 @@
 #' @param w_ref water reference data for concentration scaling (optional).
 #' @param opts options to pass to the analysis method.
 #' @param parallel perform analyses in parallel (TRUE or FALSE).
+#' @param cl a parallel socket cluster required to run analyses in parallel.
+#' Eg, cl <- parallel::makeCluster(4).
 #' @param time measure the time taken for the analysis to complete
 #' (TRUE or FALSE).
 #' @param progress option is passed to plyr::alply function to display a
@@ -49,13 +51,12 @@
 #' }
 #' @export
 fit_mrs <- function(metab, basis = NULL, method = 'ABFIT', w_ref = NULL,
-                    opts = NULL, parallel = FALSE, time = TRUE,
+                    opts = NULL, parallel = FALSE, cl = NULL, time = TRUE,
                     progress = "text", extra = NULL) {
 
   if (inherits(metab, "list")) {
 
     if (!is.null(w_ref)) {
-      # if (class(w_ref) != "list") stop("w_ref is not a list but metab is")
       if (!inherits(w_ref, "list")) stop("w_ref is not a list but metab is")
 
       if (length(metab) != length(w_ref)) {
@@ -137,23 +138,31 @@ fit_mrs <- function(metab, basis = NULL, method = 'ABFIT', w_ref = NULL,
 
     acq_paras <- get_acq_paras(metab)
 
-    plyr <- TRUE
-    if (plyr) {
+    if (!parallel) {
       result_list <- plyr::alply(metab$data, c(2, 3, 4, 5, 6), abfit,
                                  acq_paras, basis, opts,
                                  .parallel = parallel,
                                  .paropts = list(.inorder = TRUE,
                                                  .packages = "spant"),
                                  .progress = progress, .inform = FALSE)
     } else {
-      result_list <- apply(metab$data, c(2, 3, 4, 5, 6), abfit, acq_paras,
-                           basis, opts)
+      if (is.null(cl)) stop("pass cl argument to fit_mrs for parallel analyses")
+      result_list <- parallel::parApply(cl, metab$data, c(2, 3, 4, 5, 6), abfit,
+                                        acq_paras, basis, opts)
       labs <- which(array(TRUE, dim(result_list)), arr.ind = TRUE)
       result_list <- result_list[,,,,]
       attr(result_list, "split_labels") <- labs
       names(result_list) <- seq_len(nrow(labs))
     }
 
+    # method using base apply
+    # result_list <- apply(metab$data, c(2, 3, 4, 5, 6), abfit, acq_paras,
+    #                      basis, opts)
+    # labs <- which(array(TRUE, dim(result_list)), arr.ind = TRUE)
+    # result_list <- result_list[,,,,]
+    # attr(result_list, "split_labels") <- labs
+    # names(result_list) <- seq_len(nrow(labs))
+
   } else if (METHOD == "VARPRO") {
     # read basis into memory if a file
     if (is.character(basis)) {
@@ -266,12 +275,30 @@ fit_mrs <- function(metab, basis = NULL, method = 'ABFIT', w_ref = NULL,
     temp_mrs$data = temp_mrs$data[1, 1, 1, 1, 1, 1,]
     dim(temp_mrs$data) <- c(1, 1, 1, 1, 1, 1, length(temp_mrs$data))
 
-    result_list <- plyr::alply(metab$data, c(2,3,4,5,6), lcmodel_fit, 
-                               temp_mrs, basis_file, opts,
-                               .parallel = parallel, 
-                               .paropts = list(.inorder = TRUE,
-                                               .packages = "spant"),
-                               .progress = progress, .inform = FALSE)
+    if (!parallel) {
+      result_list <- plyr::alply(metab$data, c(2, 3, 4, 5, 6), lcmodel_fit,
+                                 temp_mrs, basis_file, opts,
+                                 .parallel = parallel,
+                                 .paropts = list(.inorder = TRUE,
+                                                 .packages = "spant"),
+                                 .progress = progress, .inform = FALSE)
+    } else {
+      if (is.null(cl)) stop("pass cl argument to fit_mrs for parallel analyses")
+      result_list <- parallel::parApply(cl, metab$data, c(2, 3, 4, 5, 6),
+                                        lcmodel_fit, temp_mrs, basis_file, opts)
+      labs <- which(array(TRUE, dim(result_list)), arr.ind = TRUE)
+      result_list <- result_list[,,,,]
+      attr(result_list, "split_labels") <- labs
+      names(result_list) <- seq_len(nrow(labs))
+    }
+
+    # result_list <- plyr::alply(metab$data, c(2,3,4,5,6), lcmodel_fit, 
+    #                            temp_mrs, basis_file, opts,
+    #                            .parallel = parallel, 
+    #                            .paropts = list(.inorder = TRUE,
+    #                                            .packages = "spant"),
+    #                            .progress = progress, .inform = FALSE)
+
   } else if (exists(method)) {
     message(paste("Using external fit method :", method))
 

diff --git a/R/mrs_read_rda.R b/R/mrs_read_rda.R
@@ -25,6 +25,9 @@ read_rda <- function(fname, extra) {
   col_ori <- rep(NA, 3)
   pos_vec <- rep(NA, 3)
 
+  # a fix for when commas are used as decimal points
+  txt$V2 <- gsub(",", ".", txt$V2)
+
   N <- as.integer(txt$V2[which(txt$V1 == "VectorSize")])
   fs <- 1e6 / as.numeric(txt$V2[which(txt$V1 == "DwellTime")])
   ft <- 1e6 * as.numeric(txt$V2[which(txt$V1 == "MRFrequency")])

diff --git a/docs/404.html b/docs/404.html