From 6414c633ee92d8200cad8df3f41e269eda8769fa Mon Sep 17 00:00:00 2001
From: Nick Tustison <ntustison@gmail.com>
Date: Sat, 6 Apr 2024 17:52:52 -0700
Subject: [PATCH] COMP:  Deal with recent ANTsR/ANTsRCore changes.

---
 NAMESPACE                            | 30 ----------------------------
 R/applyDBPN4x.R                      |  4 ----
 R/randomImageTransformAugmentation.R |  3 ---
 R/randomlyTransformImageData.R       |  2 --
 R/reconstructImageFromPatches.R      |  1 -
 R/unetUtilities.R                    |  1 -
 R/uvaSeg.R                           |  1 -
 7 files changed, 42 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index f3841ccf..20d66369 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -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)
diff --git a/R/applyDBPN4x.R b/R/applyDBPN4x.R
index cb4dd5ba..b7a57466 100644
--- a/R/applyDBPN4x.R
+++ b/R/applyDBPN4x.R
@@ -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,
diff --git a/R/randomImageTransformAugmentation.R b/R/randomImageTransformAugmentation.R
index 72495b5c..4870229b 100644
--- a/R/randomImageTransformAugmentation.R
+++ b/R/randomImageTransformAugmentation.R
@@ -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
 #'
diff --git a/R/randomlyTransformImageData.R b/R/randomlyTransformImageData.R
index b8fc1d3a..65834755 100644
--- a/R/randomlyTransformImageData.R
+++ b/R/randomlyTransformImageData.R
@@ -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
 #'
diff --git a/R/reconstructImageFromPatches.R b/R/reconstructImageFromPatches.R
index e6a18ce7..abc36a7f 100644
--- a/R/reconstructImageFromPatches.R
+++ b/R/reconstructImageFromPatches.R
@@ -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 )
diff --git a/R/unetUtilities.R b/R/unetUtilities.R
index 658cd7d3..8e7e418b 100644
--- a/R/unetUtilities.R
+++ b/R/unetUtilities.R
@@ -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 )
 {
diff --git a/R/uvaSeg.R b/R/uvaSeg.R
index c6b98546..b573731d 100644
--- a/R/uvaSeg.R
+++ b/R/uvaSeg.R
@@ -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,