Merge branch 'master' into TransformMultiChannel

NAMESPACE

@@ -102,6 +102,7 @@ export(cropIndices)
 export(decropImage)
 export(denoiseImage)
 export(direction)
+export(displacementFieldFromAntsrTransform)
 export(error_not_antsImage)
 export(extractSlice)
 export(getANTsRData)

R/antsAverageImages.R

@@ -1,9 +1,10 @@
-#' @title Computes average of image list 
+#' @title Computes average of image list
 #'
-#' @description Calculate the mean of a list of antsImages 
+#' @description Calculate the mean of a list of antsImages
 #' @param imageList list of antsImages or a character vector of filenames
 #' @param normalize boolean determines if image is divided by mean before
 #' averaging
+#' @param weights a vector of weights of length equal to imageList
 #' @author Avants BB, Pustina D
 #' @examples
 #' f1 = getANTsRData('r16')
@@ -19,11 +20,11 @@
 #' testthat::expect_error(antsAverageImages(list(r64, bad)))
 #' diff_size = as.antsImage(r64[1:10, 1:10], ref = r64)
 #' testthat::expect_error(antsAverageImages(list(r64, diff_size)))
-#' 
+#'
 #' @export
-antsAverageImages <- function( imageList, normalize = FALSE)
+antsAverageImages <- function( imageList, normalize = FALSE, weights )
   {
-  
+
   # determine if input is list of images or filenames
   isfile = FALSE
   if (class(imageList) == 'character') {
@@ -32,18 +33,23 @@ antsAverageImages <- function( imageList, normalize = FALSE)
     }
     isfile = TRUE
   }
-  
+
   # create empty average image
   if (isfile) {
     avg = antsImageRead(imageList[1])*0
     masterdim = dim(avg)
-  } else {  
+  } else {
     avg <- imageList[[1]] * 0
   }
-  
+
   # average them
+  if ( missing( "weights") )
+    weights = rep( 1.0 / length( imageList ), length( imageList ) )
+  if ( length( weights ) != length( imageList ) )
+    stop( "length( weights ) != length( imageList )" )
+  ct = 1
   for ( i in imageList ) {
-    
+
     if (isfile) {
       img = antsImageRead(i)
       if ( any(dim(img) != masterdim) ) {
@@ -53,12 +59,12 @@ antsAverageImages <- function( imageList, normalize = FALSE)
     } else {
       img = i
     }
-    
+
     if ( normalize ) {
       img <- img / mean( img )
     }
-    avg <- avg + img
+    avg <- avg + img * weights[ ct ]
+    ct = ct + 1
   }
-  avg <- avg / length(imageList)
   return( avg )
 }

R/antsRegistration.R

@@ -87,6 +87,8 @@
 #'   \item{"TVMSQ": }{time-varying diffeomorphism with mean square metric}
 #'   \item{"TVMSQC": }{time-varying diffeomorphism with mean square metric
 #'   for very large deformation}
+#'   \item{"Elastic": }{simple elastic deformation.  one might want to run an
+#' affine transformation before this.  may not produce diffeomorphic transformations.  user may need to explore gradient and sigma parameters.  this will not produce a valid inverse deformation.  \code{totalSigma} should be greater than zero.}
 #' }
 #' @return outputs a list containing:
 #' \itemize{
@@ -296,7 +298,7 @@ antsRegistration <- function(
       # change this to a match.arg
       allowableTx <- c("Translation","Rigid", "Similarity", "Affine", "TRSAA",
                        "SyN","SyNRA","SyNOnly","SyNCC","SyNabp", "SyNBold", "SyNBoldAff",
-                       "SyNAggro", "SyNLessAggro", "TVMSQ","TVMSQC","ElasticSyN")
+                       "SyNAggro", "SyNLessAggro", "TVMSQ","TVMSQC","ElasticSyN","Elastic")
       ttexists <- typeofTransform %in% allowableTx
       if (ttexists) {
         initx = initialTransform
@@ -614,6 +616,24 @@ antsRegistration <- function(
           if ( !is.na(maskopt)  )
             args=lappend(  args, list( "-x", maskopt ) ) else args=lappend( args, list( "-x", "[NA,NA]" ) )
         }
+
+        if ( typeofTransform == "Elastic" ) {
+          if ( is.na(gradStep) ) gradStep=0.25
+          tvtx=paste("GaussianDisplacementField[",
+                     gradStep,",",flowSigma,",",totalSigma,"]",sep='')
+          args <- list("-d", as.character(fixed@dimension), "-r", initx,
+                       "-m", paste(synMetric,"[", f, ",", m, ",1,",synSampling,"]", sep = ""),
+                       "-t", tvtx,
+                       "-c", paste("[",synits,",1e-7,8]",collapse=''),
+                       "-s", smoothingsigmas,
+                       "-f", shrinkfactors,
+                       "-u", "0", "-z", "1", "-l", myl,
+                       "-o", paste("[", outprefix, ",", wmo, ",", wfo, "]", sep = ""))
+          if ( !is.na(maskopt)  )
+            args=lappend(  args, list( "-x", maskopt ) ) else args=lappend( args, list( "-x", "[NA,NA]" ) )
+        }
+
+
         if ( typeofTransform == "Rigid" |
              typeofTransform == "Similarity" |
              typeofTransform == "Translation" |

R/antsrTransform_class.R

@@ -201,7 +201,7 @@ getAntsrTransformParameters <- function(transform) {
   return(.Call("antsrTransform_GetParameters", transform, PACKAGE = "ANTsRCore"))
 }
 
-#' @title setAntsrTransformParameters
+#' @title setAntsrTransformFixedParameters
 #' @description Set parameters of transform
 #' @param transform antsrTransform
 #' @param parameters array of parameters'
@@ -215,10 +215,10 @@ setAntsrTransformFixedParameters <- function(transform, parameters) {
   invisible(.Call("antsrTransform_SetFixedParameters", transform, parameters, PACKAGE = "ANTsRCore"))
 }
 
-#' @title getAntsrTransformParameters
-#' @description Get parameters of transform
+#' @title getAntsrTransformFixedParameters
+#' @description Get fixed parameters of transform
 #' @param transform antsrTransform
-#' @return array of parameters'
+#' @return array of fixed parameters
 #' @examples
 #' tx = new("antsrTransform")
 #' params = getAntsrTransformFixedParameters(tx)
@@ -227,7 +227,7 @@ getAntsrTransformFixedParameters <- function(transform) {
   return(.Call("antsrTransform_GetFixedParameters", transform, PACKAGE = "ANTsRCore"))
 }
 
-#' @title getAntsrTransformParameters
+#' @title antsrTransformFromDisplacementField
 #' @description Convert deformation field (multiChannel image) to antsrTransform
 #' @param field deformation field (multiChannel image)
 #' @return antsrTransform'
@@ -236,6 +236,16 @@ antsrTransformFromDisplacementField <- function( field ) {
   return(.Call("antsrTransform_FromDisplacementField", field, PACKAGE="ANTsRCore"))
 }
 
+#' @title displacementFieldFromAntsrTransform
+#' @description Conver antsrTransform to displacement field
+#' @param tx antsrTransform
+#' @param reference reference antsImage if converting linear transform
+#' @return antsImage
+#' @export
+displacementFieldFromAntsrTransform <- function( tx, reference=NA ) {
+  return(.Call("antsrTransform_ToDisplacementField", tx, ref, PACKAGE="ANTsRCore"))
+}
+
 #' @title applyAntsrTransform
 #' @description Apply transform to point, vector or antsImage data
 #' @param transform antsrTransform

data/antsVersions.csv

@@ -1,3 +1,3 @@
 Dependency;GitTag
-ANTs;23e88fe16fde013909f601438f5407079eb0ad57
-ANTsRCore;811354209d079d146cbb30c55821817f5d421cf5
+ANTs;680942c1628c8ed142c6b25a4c8b9e47aadf3e01
+ANTsRCore;a1b732bae6716713407a14b3fcce3b5d81b12fe7