fixing .motion_correction

NAMESPACE

@@ -12,6 +12,7 @@ S3method(unique,antsImage)
 S3method(var,antsImage)
 S3method(var,default)
 export("%>%")
+export(.motion_correction)
 export(abpBrainExtraction)
 export(abpN4)
 export(affineInitializer)

R/ants_motion_estimation.R

@@ -16,6 +16,7 @@
 #' testimg<-makeImage( c(10,10,10,5),  rnorm(  5000  ) )
 #' testimg<-iMath(testimg,"PadImage",5)
 #' mocorr<-.motion_correction( testimg )
+#' @export
 .motion_correction <- function( img, fixed = NA, moreaccurate = 1,
                                 txtype = "Affine", verbose=FALSE )
 {

configure.win

@@ -0,0 +1,54 @@
+#!/bin/bash
+CXX_STD=CXX11
+ITKRCMAKE=`${R_HOME}/bin/Rscript.exe -e 'a<-ITKR:::itkIncludes(); cat(a)'`
+ITKRLIB=`${R_HOME}/bin/Rscript.exe -e 'a<-ITKR:::itkLibs(); cat(a)'`
+compflags=`${R_HOME}/bin/Rscript.exe -e 'a<-ITKR:::itkCompileFlags(); cat(a)'`
+ITKDIR=`${R_HOME}/bin/Rscript.exe -e 'a<-ITKR:::itkDir(); cat(a)'`
+
+CMAKE_BUILD_TYPE=Release
+# get a version of cmake
+# cmaker=`which cmake`
+# if [[ ! -x $cmaker ]] ; then # try r version
+#   cmaker=`${R_HOME}/bin/Rscript -e 'a<-cmaker::cmake()'`
+# fi
+cd ./src
+# platform-specific Makevars
+echo "myantssource=\${PWD}/ants/" > Makevars
+# echo "ITK = \`\$(R_HOME)/bin/Rscript -e 'ITKR:::itkIncludes()'\`" >> Makevars
+echo "ITK=${ITKRCMAKE}" >> Makevars
+
+needVCL_CAN_STATIC_CONST_INIT_FLOAT=0
+echo $OSTYPE $needVCL_CAN_STATIC_CONST_INIT_FLOAT
+
+aincludes=`${R_HOME}/bin/Rscript.exe -e 'a<-ANTsRCore:::antsIncludes(); cat(a)'`
+
+# echo "PKG_CPPFLAGS = -I\${ITK} -I\${PWD}  \
+#   -I`\${R_HOME}/bin/Rscript -e 'ANTsRCore:::antsIncludes()'` \
+#   -I../inst/include/ " >> Makevars
+echo "PKG_CPPFLAGS = -I\${ITK} -I\${PWD}  \
+  -I${aincludes} \
+  -I../inst/include/ " >> Makevars
+
+echo "CXX_STD = CXX11" >> Makevars
+
+myantslib=`${R_HOME}/bin/Rscript.exe -e 'a<-ANTsRCore:::antsLibs(); cat(a)'`
+
+# echo "myantslib=`\${R_HOME}/bin/Rscript -e 'ANTsRCore:::antsLibs()'` " >> Makevars
+echo "myantslib=${myantslib}" >> Makevars
+
+echo "libants=\`find ${myantslib} -name \"lib*.a\"\`" >> Makevars
+
+echo "libitk=\`find ${ITKRLIB} -name \"lib*.a\"\`" >> Makevars
+
+echo "PKG_LIBS=\${libitk} \${libants} \${libitk} \${libants} \${libitk} \
+                 \${libants} \${libitk} \${libants} \${itklib} \${libants} \
+                 \${libitk} \${libants} \${itklib} \${libants} \${itklib} \
+                 \${libants} \${libitk} \${libants} \${itklib}" >> Makevars
+
+echo ".PHONY: all libs" >> Makevars
+
+echo "all: \$(SHLIB)" >> Makevars
+
+echo "\$(SHLIB): libs" >> Makevars
+
+echo "libs: ; cd \${PWD}" >> Makevars