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COMP: Deal with recent ANTsR/ANTsRCore changes.
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ntustison committed Apr 7, 2024
1 parent ddd3d76 commit 6414c63
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30 changes: 0 additions & 30 deletions NAMESPACE
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Expand Up @@ -204,36 +204,6 @@ export(weighted_categorical_crossentropy)
export(wholeHeadInpainting)
export(wmhSegmentation)
import(keras)
importFrom(ANTsR,composeTransformsToField)
importFrom(ANTsR,getCenterOfMass)
importFrom(ANTsR,simulateDisplacementField)
importFrom(ANTsRCore,antsAverageImages)
importFrom(ANTsRCore,antsCopyImageInfo)
importFrom(ANTsRCore,antsGetDirection)
importFrom(ANTsRCore,antsGetOrigin)
importFrom(ANTsRCore,antsGetSpacing)
importFrom(ANTsRCore,antsImagePhysicalSpaceConsistency)
importFrom(ANTsRCore,antsSetSpacing)
importFrom(ANTsRCore,antsTransformIndexToPhysicalPoint)
importFrom(ANTsRCore,antsrTransformFromDisplacementField)
importFrom(ANTsRCore,applyAntsrTransform)
importFrom(ANTsRCore,as.antsImage)
importFrom(ANTsRCore,composeAntsrTransforms)
importFrom(ANTsRCore,createAntsrTransform)
importFrom(ANTsRCore,getAntsrTransformFixedParameters)
importFrom(ANTsRCore,getAntsrTransformParameters)
importFrom(ANTsRCore,iMath)
importFrom(ANTsRCore,labelStats)
importFrom(ANTsRCore,makeImage)
importFrom(ANTsRCore,mergeChannels)
importFrom(ANTsRCore,randomMask)
importFrom(ANTsRCore,readAntsrTransform)
importFrom(ANTsRCore,resampleImage)
importFrom(ANTsRCore,resampleImageToTarget)
importFrom(ANTsRCore,setAntsrTransformFixedParameters)
importFrom(ANTsRCore,setAntsrTransformParameters)
importFrom(ANTsRCore,smoothImage)
importFrom(ANTsRCore,splitChannels)
importFrom(R6,R6Class)
importFrom(Rcpp,cppFunction)
importFrom(Rcpp,sourceCpp)
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4 changes: 0 additions & 4 deletions R/applyDBPN4x.R
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Expand Up @@ -73,10 +73,6 @@ linMatchIntensity <- function( fromImg, toImg, polyOrder = 1, truncate = TRUE, m
#' plot(img)
#' plot(simg)
#' }
#' @importFrom ANTsRCore antsCopyImageInfo antsSetSpacing
#' @importFrom ANTsRCore splitChannels antsAverageImages
#' @importFrom ANTsRCore antsTransformIndexToPhysicalPoint
#' @importFrom ANTsRCore antsTransformIndexToPhysicalPoint
#' @export applySuperResolutionModel
applySuperResolutionModel <- function(
image,
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3 changes: 0 additions & 3 deletions R/randomImageTransformAugmentation.R
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Expand Up @@ -34,9 +34,6 @@
#' @seealso \code{\link{randomImageTransformBatchGenerator}}
#' @importFrom mvtnorm rmvnorm
#' @importFrom stats sd
#' @importFrom ANTsR getCenterOfMass
#' @importFrom ANTsRCore getAntsrTransformFixedParameters iMath resampleImageToTarget composeAntsrTransforms applyAntsrTransform antsGetSpacing antsImagePhysicalSpaceConsistency antsrTransformFromDisplacementField makeImage smoothImage setAntsrTransformFixedParameters getAntsrTransformParameters setAntsrTransformParameters readAntsrTransform createAntsrTransform randomMask mergeChannels
#' @importFrom ANTsR composeTransformsToField
#' @importFrom stats rnorm
#' @examples
#'
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2 changes: 0 additions & 2 deletions R/randomlyTransformImageData.R
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Expand Up @@ -41,8 +41,6 @@
#' \"nearestNeighbor\".
#' @return list (if no directory set) or boolean for success, failure
#' @author Avants BB, Tustison NJ
#' @importFrom ANTsRCore getAntsrTransformFixedParameters iMath resampleImageToTarget applyAntsrTransform antsImagePhysicalSpaceConsistency antsrTransformFromDisplacementField makeImage smoothImage setAntsrTransformFixedParameters getAntsrTransformParameters setAntsrTransformParameters readAntsrTransform createAntsrTransform randomMask mergeChannels
#' @importFrom ANTsR composeTransformsToField simulateDisplacementField
#' @importFrom stats rnorm
#' @examples
#'
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1 change: 0 additions & 1 deletion R/reconstructImageFromPatches.R
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Expand Up @@ -24,7 +24,6 @@
#' rm(image); gc()
#' rm(patchSet); gc()
#' rm(imageReconstructed); gc()
#' @importFrom ANTsRCore as.antsImage
#' @export
reconstructImageFromPatches <- function( patches, domainImage,
strideLength = 1, domainImageIsMask = FALSE )
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1 change: 0 additions & 1 deletion R/unetUtilities.R
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Expand Up @@ -65,7 +65,6 @@ encodeUnet <- function( segmentationsArray, segmentationLabels = NULL )
#' @importFrom stats predict
#' @importFrom stats kmeans
#' @importFrom magrittr %>%
#' @importFrom ANTsRCore as.antsImage
#' @export
decodeUnet <- function( yPredicted, domainImage )
{
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1 change: 0 additions & 1 deletion R/uvaSeg.R
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Expand Up @@ -307,7 +307,6 @@ uvaSegTrain <- function( patches,
#' @export uvaSeg
#' @importFrom Rcpp cppFunction sourceCpp
#' @importFrom utils download.file
#' @importFrom ANTsRCore antsGetDirection antsGetOrigin resampleImage labelStats
uvaSeg <- function(
image,
model,
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