Fixing check_nifti.

muschellij2 · Apr 24, 2015 · fb66b0a · fb66b0a
1 parent d695877
commit fb66b0a
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Showing 4 changed files with 25 additions and 4 deletions.
diff --git a/R/check_nifti.R b/R/check_nifti.R
@@ -32,7 +32,6 @@ setMethod("check_nifti", "nifti", function(x,
 
 #' @rdname check_nifti-methods
 #' @aliases check_nifti,character-method
-#' @importFrom R.utils gunzip
 #'  
 #' @export
 setMethod("check_nifti", "character", function(x, 
@@ -65,4 +64,17 @@ setMethod("check_nifti", "list", function(x,
 })
 
 
+#' @rdname check_nifti-methods
+#' @aliases check_nifti,array-method
+#' @export
+setMethod("check_nifti", "array", function(x,  
+                                          reorient=FALSE, 
+                                          allow.array=FALSE) { 
+  if (!allow.array){
+    stop("x is array but allow.array = FALSE")
+  }
+  return(x)
+})
+
+
 
diff --git a/R/dropEmptyImageDimensions.R b/R/dropEmptyImageDimensions.R
@@ -5,6 +5,8 @@
 #' @param value Value to check against.  If zero, then 
 #' \code{dropEmptyImageDimensions} will drop any dimension that has 
 #' all zeroes
+#' @param threshold Drop dimension if fewer than \code{threshold} voxels
+#' are in the slice
 #' @param other.imgs List of other nifti objects or filenames 
 #' to apply the same dropping as \code{img}.
 #' @param reorient Should image be reoriented if a filename?
@@ -13,6 +15,7 @@
 #' @export
 dropEmptyImageDimensions <- function(img, 
                                      value = 0, 
+                                     threshold = 0,
                                      other.imgs = NULL, 
                                      reorient = FALSE) {
 
@@ -28,8 +31,8 @@ dropEmptyImageDimensions <- function(img,
   for (i in 1:3){
     zero_x = apply(img, i, function(x) sum(x != value))
     dzero_x = !(
-      cumsum(zero_x) == 0 | 
-        rev( cumsum(rev(zero_x)) == 0 )
+      cumsum(zero_x) <= threshold | 
+        rev( cumsum(rev(zero_x)) <= threshold )
     )
     inds[[i]] = which(dzero_x)
     #     print(i)

diff --git a/man/check_nifti-methods.Rd b/man/check_nifti-methods.Rd
@@ -3,6 +3,7 @@
 \docType{methods}
 \name{check_nifti-methods}
 \alias{check_nifti}
+\alias{check_nifti,array-method}
 \alias{check_nifti,character-method}
 \alias{check_nifti,list-method}
 \alias{check_nifti,nifti-method}
@@ -16,6 +17,8 @@ check_nifti(x, reorient = FALSE, allow.array = FALSE)
 \S4method{check_nifti}{character}(x, reorient = FALSE, allow.array = FALSE)
 
 \S4method{check_nifti}{list}(x, reorient = FALSE, allow.array = FALSE)
+
+\S4method{check_nifti}{array}(x, reorient = FALSE, allow.array = FALSE)
 }
 \arguments{
 \item{x}{character path of image or

diff --git a/man/dropEmptyImageDimensions.Rd b/man/dropEmptyImageDimensions.Rd
@@ -4,7 +4,7 @@
 \alias{dropEmptyImageDimensions}
 \title{Drop Empty Image Dimensions}
 \usage{
-dropEmptyImageDimensions(img, value = 0, other.imgs = NULL,
+dropEmptyImageDimensions(img, value = 0, threshold = 0, other.imgs = NULL,
   reorient = FALSE)
 }
 \arguments{
@@ -14,6 +14,9 @@ dropEmptyImageDimensions(img, value = 0, other.imgs = NULL,
 \code{dropEmptyImageDimensions} will drop any dimension that has
 all zeroes}
 
+\item{threshold}{Drop dimension if fewer than \code{threshold} voxels
+are in the slice}
+
 \item{other.imgs}{List of other nifti objects or filenames
 to apply the same dropping as \code{img}.}