Added all the functions from fslstats for simple wrappers

.Rbuildignore

@@ -9,6 +9,9 @@ Generic_Function.R
 Generic_Function2.R
 fslr_Generic_Maker.R
 fslr_Generic_Function.R
+fslr_Generic_fslstats.R
+fslr_Generic_fslstats_nonzero.R
+fslr_Generic_fslstats_Maker.R
 fslr_Generic_fslmaths.R
 fslr_Generic_fslmaths_onefile.R
 fslr_Generic_fslmaths_Maker.R

NAMESPACE

@@ -58,6 +58,7 @@ export(fsldiv)
 export(fsldiv.help)
 export(fsledge)
 export(fsledge.help)
+export(fslentropy)
 export(fslerode)
 export(fslerode.help)
 export(fslexp)
@@ -77,6 +78,7 @@ export(fslmask)
 export(fslmask.help)
 export(fslmaths)
 export(fslmaths.help)
+export(fslmean)
 export(fslmerge)
 export(fslmerge.help)
 export(fslmul)
@@ -98,6 +100,7 @@ export(fslrem)
 export(fslrem.help)
 export(fslreorient2std)
 export(fslreorient2std.help)
+export(fslsd)
 export(fslsin)
 export(fslsin.help)
 export(fslsmooth)

R/fslentropy.R

@@ -0,0 +1,23 @@
+#' @title Image Mean Entropy
+#' @description Estimates Mean Entropy of Image from FSL
+#' @param img Object of class nifti, or path of file
+#' @param nonzero (logical) Should the statistic be taken over non-zero voxels
+#' @param verbose (logical) print out command before running 
+#' @param ts (logical) is the series a timeseries (4D), invoking \code{-t} 
+#' option  
+#' @note This uses option -e or -E in \code{\link{fslstats}}
+#' @return Vector of unless ts option invoked, then matrix
+#' @export
+fslentropy = function(img, nonzero = FALSE, verbose = TRUE, ts = FALSE){
+  opts = "-e"
+  opts = ifelse(nonzero, toupper(opts), opts)
+
+  val = fslstats(img, opts = opts, verbose = verbose, ts = ts)
+  val = strsplit(val, " ")
+  if (length(val) == 1) {
+    val = as.numeric(val[[1]])
+  } else {
+    val = sapply(val, as.numeric)
+  }
+  val
+}

R/fslhd.R

@@ -118,7 +118,7 @@ fslmaths.help = function(){
 #' @title FSL Stats Help
 #' @description This function calls \code{fslstats}'s help
 #' @return Prints help output and returns output as character vector
-#' @aliases fslrange.help
+#' @aliases fslrange.help fslmean.help fslentropy.help fslsd.help
 #' @export
 #' @examples
 #' if (have.fsl()){
@@ -659,8 +659,10 @@ check_sform_file <- function(file, value=0, ...){
 
 
 #' @title Get range of an image
-#' @description This function calls \code{fslstats -R} to get the range of an image
+#' @description This function calls \code{fslstats -R} to get the range of an image or \code{fslstats -r} to 
+#' get the robust range
 #' @param file (character) filename of image to be checked
+#' @param robust (logical) Should the range be robust (\code{-r})
 #' @param verbose (logical) print out command before running
 #' @param ts (logical) is the series a timeseries (4D), invoking \code{-t} 
 #' option
@@ -674,22 +676,18 @@ check_sform_file <- function(file, value=0, ...){
 #'    "MNI152_T1_2mm.nii.gz")
 #'  fslrange(mnifile)
 #' }  
-fslrange <- function(file, verbose =TRUE, ts = FALSE, ...){
-  cmd <- get.fsl()
-  file = checkimg(file, ...)
-  cmd <- paste0(cmd, 
-                sprintf('fslstats %s "%s" -R', ifelse(ts, "-t", ""), file))
-  if (verbose){
-    cat(cmd, "\n")
-  }
-  x = str_trim(system(cmd, intern = TRUE))
-  x = strsplit(x, " ")
-  if (length(x) == 1) {
-    x = as.numeric(x[[1]])
+fslrange <- function(file, robust = FALSE, verbose = TRUE, ts = FALSE, ...){
+  opts = "-R"
+  opts = ifelse(robust, tolower(opts), opts)
+
+  val = fslstats(file, opts = opts, verbose = verbose, ts = ts)
+  val = strsplit(val, " ")
+  if (length(val) == 1) {
+    val = as.numeric(val[[1]])
   } else {
-    x = t(sapply(x, as.numeric))
+    val = t(sapply(val, as.numeric))
   }
-  x
+  val
 }
 
 #' @title Fill image holes

R/fslmean.R

@@ -0,0 +1,23 @@
+#' @title Image Mean
+#' @description Estimates Mean of Image from FSL
+#' @param img Object of class nifti, or path of file
+#' @param nonzero (logical) Should the statistic be taken over non-zero voxels
+#' @param verbose (logical) print out command before running 
+#' @param ts (logical) is the series a timeseries (4D), invoking \code{-t} 
+#' option  
+#' @note This uses option -m or -M in \code{\link{fslstats}}
+#' @return Vector of unless ts option invoked, then matrix
+#' @export
+fslmean = function(img, nonzero = FALSE, verbose = TRUE, ts = FALSE){
+  opts = "-m"
+  opts = ifelse(nonzero, toupper(opts), opts)
+
+  val = fslstats(img, opts = opts, verbose = verbose, ts = ts)
+  val = strsplit(val, " ")
+  if (length(val) == 1) {
+    val = as.numeric(val[[1]])
+  } else {
+    val = sapply(val, as.numeric)
+  }
+  val
+}

R/fslsd.R

@@ -0,0 +1,23 @@
+#' @title Image Standard Deviation
+#' @description Estimates Standard Deviation of Image from FSL
+#' @param img Object of class nifti, or path of file
+#' @param nonzero (logical) Should the statistic be taken over non-zero voxels
+#' @param verbose (logical) print out command before running 
+#' @param ts (logical) is the series a timeseries (4D), invoking \code{-t} 
+#' option  
+#' @note This uses option -s or -S in \code{\link{fslstats}}
+#' @return Vector of unless ts option invoked, then matrix
+#' @export
+fslsd = function(img, nonzero = FALSE, verbose = TRUE, ts = FALSE){
+  opts = "-s"
+  opts = ifelse(nonzero, toupper(opts), opts)
+
+  val = fslstats(img, opts = opts, verbose = verbose, ts = ts)
+  val = strsplit(val, " ")
+  if (length(val) == 1) {
+    val = as.numeric(val[[1]])
+  } else {
+    val = sapply(val, as.numeric)
+  }
+  val
+}

fslr_Generic_fslstats.R

@@ -0,0 +1,21 @@
+#' @title Image %FUNC%
+#' @description Estimates %FUNC% of Image from FSL
+#' @param img Object of class nifti, or path of file
+#' @param verbose (logical) print out command before running 
+#' @param ts (logical) is the series a timeseries (4D), invoking \code{-t} 
+#' option  
+#' @note This uses option -%opt% in \code{\link{fslstats}}
+#' @return Vector of length 1 unless ts option invoked, then vector of with length the number of timepoints.
+#' @export
+fsl%func% = function(img, verbose = TRUE, ts = FALSE){
+  opts = "-%opt%"
+
+  val = fslstats(img, opts = opts, verbose = verbose, ts = ts)
+  val = strsplit(val, " ")
+  if (length(val) == 1) {
+    val = as.numeric(val[[1]])
+  } else {
+    val = t(sapply(val, as.numeric))
+  }
+  val
+}

fslr_Generic_fslstats_Maker.R

@@ -0,0 +1,62 @@
+
+proper = function(x){
+  paste0(toupper(substr(x, 1,1)), substr(x, 2, nchar(x)))
+}
+
+#############################################
+# Function maker that involves 1 file
+#############################################
+makefunc = function(opt, FUNC, func,
+                    remove = TRUE){
+
+  x = readLines('fslr_Generic_fslstats.R')
+  x = gsub("%opt%", opt, x)
+  x = gsub("%FUNC%", FUNC, x)
+  x = gsub("%func%", func, x)
+  funcname = paste0("fsl", opt)
+
+  writeLines(text = x, con = paste0("R/", funcname, ".R"))
+  if (remove) file.remove(paste0("R/", funcname, ".R"))
+  return(TRUE)
+}
+
+#############################################
+# Function maker that involves non-zero entries
+#############################################
+makefunc = function(opt, 
+                    FUNC, 
+                    func,
+                    remove = TRUE){
+
+  x = readLines('fslr_Generic_fslstats_nonzero.R')
+  x = gsub("%opt%", opt, x)
+  x = gsub("%OPT%", toupper(opt), x)
+  x = gsub("%FUNC%", FUNC, x)
+  x = gsub("%func%", func, x)
+  funcname = paste0("fsl", func)
+
+  writeLines(text = x, con = paste0("R/", funcname, ".R"))
+  if (remove) file.remove(paste0("R/", funcname, ".R"))
+  return(TRUE)
+}
+
+
+remove = FALSE
+################################################################
+# Make Functions that take in 1 file
+################################################################
+# makefunc("r", FUNC = "Robust Range", func = "rrange",
+#          remove = TRUE)
+
+
+makefunc("m", FUNC = "Mean", func = "mean",
+         remove = remove)
+makefunc("s", FUNC = "Standard Deviation", func = "sd",
+         remove = remove)
+makefunc("e", FUNC = "Mean Entropy", func = "entropy",
+         remove = remove)
+
+
+
+
+

fslr_Generic_fslstats_nonzero.R

@@ -0,0 +1,23 @@
+#' @title Image %FUNC%
+#' @description Estimates %FUNC% of Image from FSL
+#' @param img Object of class nifti, or path of file
+#' @param nonzero (logical) Should the statistic be taken over non-zero voxels
+#' @param verbose (logical) print out command before running 
+#' @param ts (logical) is the series a timeseries (4D), invoking \code{-t} 
+#' option  
+#' @note This uses option -%opt% or -%OPT% in \code{\link{fslstats}}
+#' @return Vector of unless ts option invoked, then matrix
+#' @export
+fsl%func% = function(img, nonzero = FALSE, verbose = TRUE, ts = FALSE){
+  opts = "-%opt%"
+  opts = ifelse(nonzero, toupper(opts), opts)
+
+  val = fslstats(img, opts = opts, verbose = verbose, ts = ts)
+  val = strsplit(val, " ")
+  if (length(val) == 1) {
+    val = as.numeric(val[[1]])
+  } else {
+    val = sapply(val, as.numeric)
+  }
+  val
+}