From aa63d7175de759fc69aefcbc67fe76e6a39d9689 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Tue, 22 Oct 2019 14:02:50 -0400 Subject: [PATCH 01/23] trying regular old make --- configure.win | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/configure.win b/configure.win index e31e1f8b..aebdba2f 100755 --- a/configure.win +++ b/configure.win @@ -87,7 +87,8 @@ echo "all: \$(SHLIB)" >> Makevars.win echo "\$(SHLIB): libs" >> Makevars.win # MAKER=c:/Rtools/mingw_64/bin${R_ARCH_BIN}/mingw32-make.exe -MAKER=mingw32-make +# MAKER=mingw32-make +MAKER=make echo "libs: ; mkdir -p libs; cd antb && ls && ${MAKER} -j 4 && cd ANTS-build && ls && ${MAKER} all install && rm -rf ${R_PACKAGE_DIR}/libs/bin && cd ../../" >> Makevars.win echo "cleaner: ; cd ../libs/bin && rm -f antsRegistration antsApplyTransforms antsMotionCorr \ From 58ce75044c87b37722bbf58f1ba426e46d75a69e Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Thu, 24 Oct 2019 20:42:18 -0400 Subject: [PATCH 02/23] no v8 --- .travis.yml | 2 +- configure.win | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/.travis.yml b/.travis.yml index 444004f3..010ae387 100644 --- a/.travis.yml +++ b/.travis.yml @@ -59,7 +59,7 @@ before_install: then start_xvfb ; fi - - v8_install ; + # - v8_install ; - export rver=`r_version`; - export gh_user=`get_gh_user` ; echo $gh_user ; - cat DESCRIPTION diff --git a/configure.win b/configure.win index aebdba2f..e31e1f8b 100755 --- a/configure.win +++ b/configure.win @@ -87,8 +87,7 @@ echo "all: \$(SHLIB)" >> Makevars.win echo "\$(SHLIB): libs" >> Makevars.win # MAKER=c:/Rtools/mingw_64/bin${R_ARCH_BIN}/mingw32-make.exe -# MAKER=mingw32-make -MAKER=make +MAKER=mingw32-make echo "libs: ; mkdir -p libs; cd antb && ls && ${MAKER} -j 4 && cd ANTS-build && ls && ${MAKER} all install && rm -rf ${R_PACKAGE_DIR}/libs/bin && cd ../../" >> Makevars.win echo "cleaner: ; cd ../libs/bin && rm -f antsRegistration antsApplyTransforms antsMotionCorr \ From d219b96d3ef2f81c0432c57aa604680a9f619c46 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Thu, 24 Oct 2019 20:50:55 -0400 Subject: [PATCH 03/23] updated --- .travis.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 010ae387..29fba976 100644 --- a/.travis.yml +++ b/.travis.yml @@ -59,7 +59,6 @@ before_install: then start_xvfb ; fi - # - v8_install ; - export rver=`r_version`; - export gh_user=`get_gh_user` ; echo $gh_user ; - cat DESCRIPTION From a81db8eb27973e6c6a73a22a559f6874f129cd3d Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Thu, 24 Oct 2019 23:28:28 -0400 Subject: [PATCH 04/23] trying antpy typ ehting --- configure.win | 1 + 1 file changed, 1 insertion(+) diff --git a/configure.win b/configure.win index e31e1f8b..2c931009 100755 --- a/configure.win +++ b/configure.win @@ -170,6 +170,7 @@ ${cmaker} \ -DCMAKE_NEED_RESPONSE=1 \ -DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON \ -DCOPY_SCRIPT_FILES_TO_BIN_DIR=OFF \ + -DCMAKE_LIBRARY_OUTPUT_DIRECTORY_RELEASE="../ants/lib/" \ -DCMAKE_INSTALL_PREFIX:PATH="${R_PACKAGE_DIR}/libs/" \ -DCMAKE_BUILD_TYPE:STRING="${CMAKE_BUILD_TYPE}" \ -DVNL_CONFIG_ENABLE_SSE2_ROUNDING:BOOL=ON \ From 8d42b15e95b73e37125da0255af1c9a9d45ae238 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Thu, 24 Oct 2019 23:34:02 -0400 Subject: [PATCH 05/23] gcc 4.9 "allowed" --- configure.win | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/configure.win b/configure.win index 2c931009..708a0bc7 100755 --- a/configure.win +++ b/configure.win @@ -101,7 +101,7 @@ ThresholdImage LabelClustersUniquely SurfaceBasedSmoothing" >> Makevars # antsgit=https://github.com/ANTsX/ANTs.git # antstag=c60752a7a6eca0371b0f5ff5ffa13385a5f5ea4f # n4 bug antsgit=https://github.com/muschellij2/ANTs.git -antstag=c39585e656f7162cf74fd2d9b0438963671e03d2 +antstag=a400184125031566bd15fab0a6783bb9c4139731 git clone $antsgit ants mkdir -p ../data From 3fe8daa168b7311594188d56fa41ef14a23f7823 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Fri, 25 Oct 2019 15:26:48 -0400 Subject: [PATCH 06/23] no l_ dummy --- .travis.yml | 1 - configure.win | 12 ++++++------ 2 files changed, 6 insertions(+), 7 deletions(-) diff --git a/.travis.yml b/.travis.yml index 29fba976..bbf0974b 100644 --- a/.travis.yml +++ b/.travis.yml @@ -12,7 +12,6 @@ dist: xenial os: - linux - osx - - windows # as xenial services: diff --git a/configure.win b/configure.win index 708a0bc7..6455db54 100755 --- a/configure.win +++ b/configure.win @@ -67,12 +67,12 @@ echo "Running ${libitk}" # echo "Running libants" # libants="-L${myantslib} ${libants}" # echo "Running ${libants}" -libants="-L${myantslib} -lantsUtilities -ll_antsAffineInitializer -ll_antsApplyTransforms " -libants="${libants} -ll_antsApplyTransformsToPoints -ll_antsJointFusion -ll_antsMotionCorr " -libants="${libants} -ll_antsMotionCorrStats -ll_antsRegistration -ll_Atropos -ll_DenoiseImage " -libants="${libants} -ll_KellyKapowski -ll_LabelClustersUniquely -ll_LabelGeometryMeasures " -libants="${libants} -ll_N3BiasFieldCorrection -ll_N4BiasFieldCorrection -ll_ResampleImage " -libants="${libants} -ll_sccan -ll_SurfaceBasedSmoothing -ll_ThresholdImage " +libants="-L${myantslib} -lantsUtilities -lantsAffineInitializer -lantsApplyTransforms " +libants="${libants} -lantsApplyTransformsToPoints -lantsJointFusion -lantsMotionCorr " +libants="${libants} -lantsMotionCorrStats -lantsRegistration -lAtropos -lDenoiseImage " +libants="${libants} -lKellyKapowski -lLabelClustersUniquely -lLabelGeometryMeasures " +libants="${libants} -lN3BiasFieldCorrection -lN4BiasFieldCorrection -lResampleImage " +libants="${libants} -lsccan -lSurfaceBasedSmoothing -lThresholdImage " echo "PKG_LIBS=${PKG_LIBS} ${libitk} ${libants} ${libitk} ${libants} ${libitk} ${libants} ${libitk} \ ${libants} ${libitk} ${libants} ${libitk} ${libants} ${libitk} \ From e754a66f2d3873691f7177046041561aebd87561 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Fri, 25 Oct 2019 16:05:31 -0400 Subject: [PATCH 07/23] added --- .travis.yml | 1 - configure.win | 12 ++++++------ 2 files changed, 6 insertions(+), 7 deletions(-) diff --git a/.travis.yml b/.travis.yml index 29fba976..bbf0974b 100644 --- a/.travis.yml +++ b/.travis.yml @@ -12,7 +12,6 @@ dist: xenial os: - linux - osx - - windows # as xenial services: diff --git a/configure.win b/configure.win index 708a0bc7..6455db54 100755 --- a/configure.win +++ b/configure.win @@ -67,12 +67,12 @@ echo "Running ${libitk}" # echo "Running libants" # libants="-L${myantslib} ${libants}" # echo "Running ${libants}" -libants="-L${myantslib} -lantsUtilities -ll_antsAffineInitializer -ll_antsApplyTransforms " -libants="${libants} -ll_antsApplyTransformsToPoints -ll_antsJointFusion -ll_antsMotionCorr " -libants="${libants} -ll_antsMotionCorrStats -ll_antsRegistration -ll_Atropos -ll_DenoiseImage " -libants="${libants} -ll_KellyKapowski -ll_LabelClustersUniquely -ll_LabelGeometryMeasures " -libants="${libants} -ll_N3BiasFieldCorrection -ll_N4BiasFieldCorrection -ll_ResampleImage " -libants="${libants} -ll_sccan -ll_SurfaceBasedSmoothing -ll_ThresholdImage " +libants="-L${myantslib} -lantsUtilities -lantsAffineInitializer -lantsApplyTransforms " +libants="${libants} -lantsApplyTransformsToPoints -lantsJointFusion -lantsMotionCorr " +libants="${libants} -lantsMotionCorrStats -lantsRegistration -lAtropos -lDenoiseImage " +libants="${libants} -lKellyKapowski -lLabelClustersUniquely -lLabelGeometryMeasures " +libants="${libants} -lN3BiasFieldCorrection -lN4BiasFieldCorrection -lResampleImage " +libants="${libants} -lsccan -lSurfaceBasedSmoothing -lThresholdImage " echo "PKG_LIBS=${PKG_LIBS} ${libitk} ${libants} ${libitk} ${libants} ${libitk} ${libants} ${libitk} \ ${libants} ${libitk} ${libants} ${libitk} ${libants} ${libitk} \ From 7066966bc0cc1fcd4ccc5750926124b7cb274580 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Fri, 25 Oct 2019 16:07:52 -0400 Subject: [PATCH 08/23] added exdir now again --- configure.win | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/configure.win b/configure.win index 6455db54..430d24ed 100755 --- a/configure.win +++ b/configure.win @@ -44,7 +44,7 @@ echo "SHLIB_CXXLD=${CMAKE_EXE_LINKER_FLAGS}" # echo "myantslib=\"\${PWD}/antb/lib/\"" >> Makevars.win echo "myantslib=\${PWD}/antb/lib/">> Makevars.win - +echo "antsexdir=\${PWD}/antb/ANTS-build/Examples/">> Makevars.win # echo "libants=\`find \"\${myantslib}\" -name \"lib*.a\"\`" >> Makevars.win # echo "libitk=\`find \"${ITKRLIB}\" -name \"lib*.a\"\`" >> Makevars.win @@ -67,12 +67,12 @@ echo "Running ${libitk}" # echo "Running libants" # libants="-L${myantslib} ${libants}" # echo "Running ${libants}" -libants="-L${myantslib} -lantsUtilities -lantsAffineInitializer -lantsApplyTransforms " -libants="${libants} -lantsApplyTransformsToPoints -lantsJointFusion -lantsMotionCorr " -libants="${libants} -lantsMotionCorrStats -lantsRegistration -lAtropos -lDenoiseImage " -libants="${libants} -lKellyKapowski -lLabelClustersUniquely -lLabelGeometryMeasures " -libants="${libants} -lN3BiasFieldCorrection -lN4BiasFieldCorrection -lResampleImage " -libants="${libants} -lsccan -lSurfaceBasedSmoothing -lThresholdImage " +libants="-L${myantslib} -L${antsexdir} -lantsUtilities -ll_antsAffineInitializer -ll_antsApplyTransforms " +libants="${libants} -ll_antsApplyTransformsToPoints -ll_antsJointFusion -ll_antsMotionCorr " +libants="${libants} -ll_antsMotionCorrStats -ll_antsRegistration -ll_Atropos -ll_DenoiseImage " +libants="${libants} -ll_KellyKapowski -ll_LabelClustersUniquely -ll_LabelGeometryMeasures " +libants="${libants} -ll_N3BiasFieldCorrection -ll_N4BiasFieldCorrection -ll_ResampleImage " +libants="${libants} -ll_sccan -ll_SurfaceBasedSmoothing -ll_ThresholdImage " echo "PKG_LIBS=${PKG_LIBS} ${libitk} ${libants} ${libitk} ${libants} ${libitk} ${libants} ${libitk} \ ${libants} ${libitk} ${libants} ${libitk} ${libants} ${libitk} \ From 33c4533c8b083a4a4cb81073b967055513e76e4a Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Fri, 25 Oct 2019 16:55:05 -0400 Subject: [PATCH 09/23] added the merge with older gcc from ANTs --- configure.win | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/configure.win b/configure.win index 430d24ed..b69d8e78 100755 --- a/configure.win +++ b/configure.win @@ -101,7 +101,7 @@ ThresholdImage LabelClustersUniquely SurfaceBasedSmoothing" >> Makevars # antsgit=https://github.com/ANTsX/ANTs.git # antstag=c60752a7a6eca0371b0f5ff5ffa13385a5f5ea4f # n4 bug antsgit=https://github.com/muschellij2/ANTs.git -antstag=a400184125031566bd15fab0a6783bb9c4139731 +antstag=7ca882f532ae7fdf9b9a5ccb94810a39a98c9ef2 git clone $antsgit ants mkdir -p ../data From 8556f4ed49cd4dfa6c65b366be6105bb64c414e4 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Fri, 25 Oct 2019 17:43:20 -0400 Subject: [PATCH 10/23] fixing the exdir --- configure.win | 1 + 1 file changed, 1 insertion(+) diff --git a/configure.win b/configure.win index b69d8e78..e76794b2 100755 --- a/configure.win +++ b/configure.win @@ -29,6 +29,7 @@ PWD=`${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e 'cat(normalizePath(".", winslash= # platform-specific Makevars echo "PWD=${PWD}" > Makevars.win myantslib=${PWD}/antb/lib/ +antsexdir=${PWD}/antb/ANTS-build/Examples/ echo "myantssource=\${PWD}/ants" >> Makevars.win echo "ITK=\"${ITKRCMAKE}\"" >> Makevars.win From 90e8a931186e5c83c5c0980c02296090120e9ef1 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Mon, 28 Oct 2019 16:15:54 -0400 Subject: [PATCH 11/23] configure.win okwithout git --- configure.win | 42 +++++++++++++++++++++++++++++++++++++----- 1 file changed, 37 insertions(+), 5 deletions(-) diff --git a/configure.win b/configure.win index e76794b2..046b40bb 100755 --- a/configure.win +++ b/configure.win @@ -1,5 +1,14 @@ #!/bin/bash -antsrtag=`git log --pretty=format:'%H' -n 1` +git_exe=`${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "x=Sys.which('git'); cat(x)"` +if [ -z "${git_exe}" ]; then + ${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e 'if (!requireNamespace("git2r")) install.packages("git2r")' + str="repo = git2r::init();" + str="${str} x=git2r::sha(git2r::last_commit(repo));" + str="${str} cat(x)" + antsrtag=`${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "${str}"` +else + antsrtag=`git log --pretty=format:'%H' -n 1` +fi CXX_STD=CXX11 CC=`${R_HOME}/bin${R_ARCH_BIN}/R.exe CMD config CC` CXX=`${R_HOME}/bin${R_ARCH_BIN}/R.exe CMD config CXX` @@ -103,7 +112,15 @@ ThresholdImage LabelClustersUniquely SurfaceBasedSmoothing" >> Makevars # antstag=c60752a7a6eca0371b0f5ff5ffa13385a5f5ea4f # n4 bug antsgit=https://github.com/muschellij2/ANTs.git antstag=7ca882f532ae7fdf9b9a5ccb94810a39a98c9ef2 -git clone $antsgit ants +if [ -z "${git_exe}" ]; then + ${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e 'if (!requireNamespace("git2r")) install.packages("git2r")' + str="repo = git2r::clone(\"" + str="${str}${antsgit}" + str="${str}\", local_path = \"./ants\")" + ${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "${str}" +else + git clone $antsgit ants +fi mkdir -p ../data echo "Dependency;GitTag" > ../data/antsVersions.csv @@ -112,6 +129,23 @@ echo "ANTsRCore;${antsrtag}" >> ../data/antsVersions.csv echo "ANTsURL;${antsgit}" >> ../data/antsVersions.csv echo "ITK;${ITKTAG}" >> ../data/antsVersions.csv cd ants + +if [ -z "${git_exe}" ]; then + ${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e 'if (!requireNamespace("git2r")) install.packages("git2r")' + str="repo = git2r::init()" + if [ -n "${antstag}" ]; then + str="${str}; git2r::checkout(repo, branch = \"" + str="${str}${antstag}" + str="${str}\");" + fi + ${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "${str}" +else + git checkout master; + git pull; + git checkout $antstag +fi + +# windows workaround for warning if [[ -a "./CMake/ITKSetStandardCompilerFlags.cmake" ]]; then echo "working on ITKSetStandardCompilerFlags.cmake" @@ -121,9 +155,7 @@ then str=${str}'writeLines(x, fname)}' ${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "${str}" fi -git checkout master; -git pull; -git checkout $antstag + cd ../ mkdir -p antb cp ../inst/include/antscore.h ./ants/Examples/include/ants.h From 3688084eb39f5ed76c4281fb0b24983c91a30c1d Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Mon, 28 Oct 2019 16:22:38 -0400 Subject: [PATCH 12/23] trying to get the right zip --- configure.win | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/configure.win b/configure.win index 046b40bb..761d383e 100755 --- a/configure.win +++ b/configure.win @@ -3,7 +3,8 @@ git_exe=`${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "x=Sys.which('git'); cat(x)"` if [ -z "${git_exe}" ]; then ${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e 'if (!requireNamespace("git2r")) install.packages("git2r")' str="repo = git2r::init();" - str="${str} x=git2r::sha(git2r::last_commit(repo));" + str="${str} if (length(git2r::commits(repo)) > 0) {" + str="${str} x=git2r::sha(git2r::last_commit(repo)) } else {x = ''};" str="${str} cat(x)" antsrtag=`${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "${str}"` else @@ -142,7 +143,7 @@ if [ -z "${git_exe}" ]; then else git checkout master; git pull; - git checkout $antstag + git checkout $antstag ; fi # windows workaround for warning From 38405ac196f65aec53a06fbc2ccc1e6ff885a645 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Mon, 28 Oct 2019 16:25:56 -0400 Subject: [PATCH 13/23] ok make is added --- configure.win | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/configure.win b/configure.win index 761d383e..15548acf 100755 --- a/configure.win +++ b/configure.win @@ -98,7 +98,8 @@ echo "all: \$(SHLIB)" >> Makevars.win echo "\$(SHLIB): libs" >> Makevars.win # MAKER=c:/Rtools/mingw_64/bin${R_ARCH_BIN}/mingw32-make.exe -MAKER=mingw32-make +# MAKER=mingw32-make +MAKER=`${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "x=normalizePath(Sys.which('make'), winslash = '/''); cat(x)"` echo "libs: ; mkdir -p libs; cd antb && ls && ${MAKER} -j 4 && cd ANTS-build && ls && ${MAKER} all install && rm -rf ${R_PACKAGE_DIR}/libs/bin && cd ../../" >> Makevars.win echo "cleaner: ; cd ../libs/bin && rm -f antsRegistration antsApplyTransforms antsMotionCorr \ @@ -193,6 +194,7 @@ ${cmaker} \ -G "MinGW Makefiles" \ -DITK_DIR:PATH="${ITKDIR}" \ -DCMAKE_SH:BOOL=OFF \ + -DCMAKE_MAKE_PROGRAM="${MAKER}" \ -DCMAKE_C_FLAGS="${CMAKE_C_FLAGS} -Wa,-mbig-obj ${CMAKE_EXE_LINKER_FLAGS} ${compflags} -DNDEBUG -D_FILE_OFFSET_BITS=64"\ -DCMAKE_CXX_FLAGS="${CMAKE_CXX_FLAGS} -Wa,-mbig-obj ${compflags} -DNDEBUG "\ -DCMAKE_EXE_LINKER_FLAGS="${TRY_LINKER_FLAGS}" \ From 6f2ee68479d0d5da5b46e2fd142f592d2d56447f Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Mon, 28 Oct 2019 16:29:25 -0400 Subject: [PATCH 14/23] bad make --- configure.win | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/configure.win b/configure.win index 15548acf..2b2ac5de 100755 --- a/configure.win +++ b/configure.win @@ -99,7 +99,7 @@ echo "all: \$(SHLIB)" >> Makevars.win echo "\$(SHLIB): libs" >> Makevars.win # MAKER=c:/Rtools/mingw_64/bin${R_ARCH_BIN}/mingw32-make.exe # MAKER=mingw32-make -MAKER=`${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "x=normalizePath(Sys.which('make'), winslash = '/''); cat(x)"` +MAKER=`${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "x=normalizePath(Sys.which('make'), winslash = '/'); cat(x)"` echo "libs: ; mkdir -p libs; cd antb && ls && ${MAKER} -j 4 && cd ANTS-build && ls && ${MAKER} all install && rm -rf ${R_PACKAGE_DIR}/libs/bin && cd ../../" >> Makevars.win echo "cleaner: ; cd ../libs/bin && rm -f antsRegistration antsApplyTransforms antsMotionCorr \ @@ -194,7 +194,6 @@ ${cmaker} \ -G "MinGW Makefiles" \ -DITK_DIR:PATH="${ITKDIR}" \ -DCMAKE_SH:BOOL=OFF \ - -DCMAKE_MAKE_PROGRAM="${MAKER}" \ -DCMAKE_C_FLAGS="${CMAKE_C_FLAGS} -Wa,-mbig-obj ${CMAKE_EXE_LINKER_FLAGS} ${compflags} -DNDEBUG -D_FILE_OFFSET_BITS=64"\ -DCMAKE_CXX_FLAGS="${CMAKE_CXX_FLAGS} -Wa,-mbig-obj ${compflags} -DNDEBUG "\ -DCMAKE_EXE_LINKER_FLAGS="${TRY_LINKER_FLAGS}" \ From fd8929ecc8832d341b7de970db90608c6b9b79d5 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Mon, 28 Oct 2019 16:30:12 -0400 Subject: [PATCH 15/23] bad make --- configure.win | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/configure.win b/configure.win index 2b2ac5de..f81010eb 100755 --- a/configure.win +++ b/configure.win @@ -98,8 +98,10 @@ echo "all: \$(SHLIB)" >> Makevars.win echo "\$(SHLIB): libs" >> Makevars.win # MAKER=c:/Rtools/mingw_64/bin${R_ARCH_BIN}/mingw32-make.exe -# MAKER=mingw32-make -MAKER=`${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "x=normalizePath(Sys.which('make'), winslash = '/'); cat(x)"` +# MAKER=`${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "x=normalizePath(Sys.which('make'), winslash = '/'); cat(x)"` +MAKER=mingw32-make.exe +echo "MAKE IS" +echo "${MAKER}" echo "libs: ; mkdir -p libs; cd antb && ls && ${MAKER} -j 4 && cd ANTS-build && ls && ${MAKER} all install && rm -rf ${R_PACKAGE_DIR}/libs/bin && cd ../../" >> Makevars.win echo "cleaner: ; cd ../libs/bin && rm -f antsRegistration antsApplyTransforms antsMotionCorr \ From e56031ff2e4dde22380ec1aae4e12d07a4ebf8fc Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Tue, 29 Oct 2019 08:30:50 -0400 Subject: [PATCH 16/23] trying again --- configure.win | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/configure.win b/configure.win index f81010eb..516c09de 100755 --- a/configure.win +++ b/configure.win @@ -85,12 +85,10 @@ libants="${libants} -ll_KellyKapowski -ll_LabelClustersUniquely -ll_LabelGeometr libants="${libants} -ll_N3BiasFieldCorrection -ll_N4BiasFieldCorrection -ll_ResampleImage " libants="${libants} -ll_sccan -ll_SurfaceBasedSmoothing -ll_ThresholdImage " -echo "PKG_LIBS=${PKG_LIBS} ${libitk} ${libants} ${libitk} ${libants} ${libitk} ${libants} ${libitk} \ - ${libants} ${libitk} ${libants} ${libitk} ${libants} ${libitk} \ - ${libants}" >> Makevars.win -# echo "PKG_LIBS=${PKG_LIBS} -L${ITKRLIB} \${libants} \${libitk} \${libants} \${libitk} \ -# \${libants} \${libitk} \${libants} \${libitk} \${libants} \${libitk} \ -# \${libitk} \${libants}" >> Makevars.win +# echo "PKG_LIBS=${PKG_LIBS} ${libitk} ${libants} ${libitk} ${libants} ${libitk} ${libants} ${libitk} \ +# ${libants} ${libitk} ${libants} ${libitk} ${libants} ${libitk} \ +# ${libants}" >> Makevars.win +echo "PKG_LIBS=${PKG_LIBS} ${libitk} ${libants} ${libitk} ${libants} " >> Makevars.win echo ".PHONY: all libs" >> Makevars.win From 2b8c306d3babbe64a864026cb243783c07b9c538 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Tue, 29 Oct 2019 14:54:35 -0400 Subject: [PATCH 17/23] trying no dynamic for windows --- NAMESPACE | 2 +- src/init.c | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index 90d00a60..051c97cf 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -303,4 +303,4 @@ importFrom(utils,tail) importFrom(utils,txtProgressBar) importFrom(utils,unzip) importFrom(utils,write.csv) -useDynLib(ANTsRCore) +# useDynLib(ANTsRCore) diff --git a/src/init.c b/src/init.c index 870065b6..b888bd0b 100644 --- a/src/init.c +++ b/src/init.c @@ -214,5 +214,5 @@ static const R_CallMethodDef CallEntries[] = { void R_init_ANTsRCore(DllInfo *dll) { R_registerRoutines(dll, NULL, CallEntries, NULL, NULL); - R_useDynamicSymbols(dll, FALSE); + // R_useDynamicSymbols(dll, FALSE); } From 1400d2046c94de202246da1edd234e88a4d3a74c Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Tue, 29 Oct 2019 15:33:25 -0400 Subject: [PATCH 18/23] skip_ci windows --- NAMESPACE | 2 +- src/init.c | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index 051c97cf..90d00a60 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -303,4 +303,4 @@ importFrom(utils,tail) importFrom(utils,txtProgressBar) importFrom(utils,unzip) importFrom(utils,write.csv) -# useDynLib(ANTsRCore) +useDynLib(ANTsRCore) diff --git a/src/init.c b/src/init.c index b888bd0b..870065b6 100644 --- a/src/init.c +++ b/src/init.c @@ -214,5 +214,5 @@ static const R_CallMethodDef CallEntries[] = { void R_init_ANTsRCore(DllInfo *dll) { R_registerRoutines(dll, NULL, CallEntries, NULL, NULL); - // R_useDynamicSymbols(dll, FALSE); + R_useDynamicSymbols(dll, FALSE); } From e4b20de2a111b4dd395927f2f727647271738f12 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Tue, 29 Oct 2019 15:37:06 -0400 Subject: [PATCH 19/23] trying lower amount o fthings - will this link? --- src/init.c | 230 ++++++++++++++++++++++++++--------------------------- 1 file changed, 115 insertions(+), 115 deletions(-) diff --git a/src/init.c b/src/init.c index 870065b6..a0897214 100644 --- a/src/init.c +++ b/src/init.c @@ -17,8 +17,8 @@ */ /* .Call calls */ -extern SEXP antsApplyTransforms(SEXP); -extern SEXP antsApplyTransformsToPoints(SEXP); +// extern SEXP antsApplyTransforms(SEXP); +// extern SEXP antsApplyTransformsToPoints(SEXP); extern SEXP antsImage(SEXP, SEXP, SEXP); extern SEXP antsImage_asantsImage(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP); extern SEXP antsImage_asVector(SEXP, SEXP, SEXP); @@ -36,8 +36,8 @@ extern SEXP antsImage_SetOrigin(SEXP, SEXP); extern SEXP antsImage_SetPixels(SEXP, SEXP, SEXP); extern SEXP antsImage_SetRegion(SEXP, SEXP, SEXP, SEXP); extern SEXP antsImage_SetSpacing(SEXP, SEXP); -extern SEXP antsImage_TransformIndexToPhysicalPoint(SEXP, SEXP); -extern SEXP antsImage_TransformPhysicalPointToIndex(SEXP, SEXP); +// extern SEXP antsImage_TransformIndexToPhysicalPoint(SEXP, SEXP); +// extern SEXP antsImage_TransformPhysicalPointToIndex(SEXP, SEXP); extern SEXP antsImageArithImageImage(SEXP, SEXP, SEXP); extern SEXP antsImageArithImageNumeric(SEXP, SEXP, SEXP); extern SEXP antsImageArithNumericImage(SEXP, SEXP, SEXP); @@ -45,76 +45,76 @@ extern SEXP antsImageClone(SEXP, SEXP); extern SEXP antsImageComparisonImageImage(SEXP, SEXP, SEXP); extern SEXP antsImageComparisonImageNumeric(SEXP, SEXP, SEXP); extern SEXP antsImageHeaderInfo(SEXP); -extern SEXP antsImageIterator(SEXP, SEXP, SEXP); -extern SEXP antsImageIterator_Get(SEXP); -extern SEXP antsImageIterator_GetIndex(SEXP); -extern SEXP antsImageIterator_GoToBegin(SEXP); -extern SEXP antsImageIterator_GoToReverseBegin(SEXP); -extern SEXP antsImageIterator_IsAtEnd(SEXP); -extern SEXP antsImageIterator_IsAtReverseEnd(SEXP); -extern SEXP antsImageIterator_Next(SEXP); -extern SEXP antsImageIterator_Previous(SEXP); -extern SEXP antsImageIterator_Remaining(SEXP); -extern SEXP antsImageIterator_Set(SEXP, SEXP); -extern SEXP antsImageIterator_SetIndex(SEXP, SEXP); +// extern SEXP antsImageIterator(SEXP, SEXP, SEXP); +// extern SEXP antsImageIterator_Get(SEXP); +// extern SEXP antsImageIterator_GetIndex(SEXP); +// extern SEXP antsImageIterator_GoToBegin(SEXP); +// extern SEXP antsImageIterator_GoToReverseBegin(SEXP); +// extern SEXP antsImageIterator_IsAtEnd(SEXP); +// extern SEXP antsImageIterator_IsAtReverseEnd(SEXP); +// extern SEXP antsImageIterator_Next(SEXP); +// extern SEXP antsImageIterator_Previous(SEXP); +// extern SEXP antsImageIterator_Remaining(SEXP); +// extern SEXP antsImageIterator_Set(SEXP, SEXP); +// extern SEXP antsImageIterator_SetIndex(SEXP, SEXP); extern SEXP antsImageLogicImageImage(SEXP, SEXP, SEXP); extern SEXP antsImageLogicImageNumeric(SEXP, SEXP, SEXP); extern SEXP antsImageMath(SEXP, SEXP); -extern SEXP antsImageMutualInformation(SEXP, SEXP); +// extern SEXP antsImageMutualInformation(SEXP, SEXP); extern SEXP antsImageRead(SEXP, SEXP, SEXP, SEXP); extern SEXP antsImageStats(SEXP,SEXP,SEXP); extern SEXP antsImageWrite(SEXP, SEXP, SEXP); -extern SEXP antsJointFusion(SEXP); -extern SEXP antsMatrix(SEXP); -extern SEXP antsMatrix_asantsMatrix(SEXP, SEXP); -extern SEXP antsMatrix_asList(SEXP); -extern SEXP antsRegistration(SEXP); +// extern SEXP antsJointFusion(SEXP); +// extern SEXP antsMatrix(SEXP); +// extern SEXP antsMatrix_asantsMatrix(SEXP, SEXP); +// extern SEXP antsMatrix_asList(SEXP); +// extern SEXP antsRegistration(SEXP); // extern SEXP antsrMetric(SEXP, SEXP, SEXP); -extern SEXP antsrMetric(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP); -extern SEXP antsrMetric_GetDerivative(SEXP); -extern SEXP antsrMetric_GetValue(SEXP); -extern SEXP antsrMetric_Initialize(SEXP); -extern SEXP antsrMetric_SetImage(SEXP, SEXP, SEXP, SEXP); -extern SEXP antsrMetric_SetNumberOfHistogramBins(SEXP, SEXP); -extern SEXP antsrMetric_SetRadius(SEXP, SEXP); -extern SEXP antsrMetric_SetSampling(SEXP, SEXP, SEXP); -extern SEXP antsrMetric_SetTransform(SEXP, SEXP, SEXP); -extern SEXP antsrTransform(SEXP, SEXP, SEXP); -extern SEXP antsrTransform_Compose(SEXP, SEXP, SEXP); -extern SEXP antsrTransform_FromDisplacementField(SEXP); -extern SEXP antsrTransform_GetFixedParameters(SEXP); -extern SEXP antsrTransform_GetParameters(SEXP); -extern SEXP antsrTransform_Inverse(SEXP); -extern SEXP antsrTransform_MatrixOffset(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP); -extern SEXP antsrTransform_Read(SEXP, SEXP, SEXP); -extern SEXP antsrTransform_SetFixedParameters(SEXP, SEXP); -extern SEXP antsrTransform_SetParameters(SEXP, SEXP); -extern SEXP antsrTransform_ToDisplacementField(SEXP,SEXP); -extern SEXP antsrTransform_TransformImage(SEXP, SEXP, SEXP, SEXP); -extern SEXP antsrTransform_TransformPoint(SEXP, SEXP); -extern SEXP antsrTransform_TransformVector(SEXP, SEXP); -extern SEXP antsrTransform_Write(SEXP, SEXP); -extern SEXP Atropos(SEXP); +// extern SEXP antsrMetric(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP); +// extern SEXP antsrMetric_GetDerivative(SEXP); +// extern SEXP antsrMetric_GetValue(SEXP); +// extern SEXP antsrMetric_Initialize(SEXP); +// extern SEXP antsrMetric_SetImage(SEXP, SEXP, SEXP, SEXP); +// extern SEXP antsrMetric_SetNumberOfHistogramBins(SEXP, SEXP); +// extern SEXP antsrMetric_SetRadius(SEXP, SEXP); +// extern SEXP antsrMetric_SetSampling(SEXP, SEXP, SEXP); +// extern SEXP antsrMetric_SetTransform(SEXP, SEXP, SEXP); +// extern SEXP antsrTransform(SEXP, SEXP, SEXP); +// extern SEXP antsrTransform_Compose(SEXP, SEXP, SEXP); +// extern SEXP antsrTransform_FromDisplacementField(SEXP); +// extern SEXP antsrTransform_GetFixedParameters(SEXP); +// extern SEXP antsrTransform_GetParameters(SEXP); +// extern SEXP antsrTransform_Inverse(SEXP); +// extern SEXP antsrTransform_MatrixOffset(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP); +// extern SEXP antsrTransform_Read(SEXP, SEXP, SEXP); +// extern SEXP antsrTransform_SetFixedParameters(SEXP, SEXP); +// extern SEXP antsrTransform_SetParameters(SEXP, SEXP); +// extern SEXP antsrTransform_ToDisplacementField(SEXP,SEXP); +// extern SEXP antsrTransform_TransformImage(SEXP, SEXP, SEXP, SEXP); +// extern SEXP antsrTransform_TransformPoint(SEXP, SEXP); +// extern SEXP antsrTransform_TransformVector(SEXP, SEXP); +// extern SEXP antsrTransform_Write(SEXP, SEXP); +// extern SEXP Atropos(SEXP); extern SEXP cropImage(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP); -extern SEXP DenoiseImage(SEXP); +// extern SEXP DenoiseImage(SEXP); extern SEXP extractSlice(SEXP, SEXP, SEXP); -extern SEXP imagesToMatrix(SEXP, SEXP, SEXP); +// extern SEXP imagesToMatrix(SEXP, SEXP, SEXP); extern SEXP iMathInterface(SEXP); extern SEXP iMathInterface1(SEXP); extern SEXP iMathInterface2(SEXP); -extern SEXP LabelClustersUniquely(SEXP); -extern SEXP labelStats(SEXP, SEXP); -extern SEXP mergeChannels(SEXP, SEXP); -extern SEXP N3BiasFieldCorrection(SEXP); -extern SEXP N4BiasFieldCorrection(SEXP); -extern SEXP patchAnalysis(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP); -extern SEXP smoothImage(SEXP, SEXP, SEXP, SEXP, SEXP); +// extern SEXP LabelClustersUniquely(SEXP); +// extern SEXP labelStats(SEXP, SEXP); +// extern SEXP mergeChannels(SEXP, SEXP); +// extern SEXP N3BiasFieldCorrection(SEXP); +// extern SEXP N4BiasFieldCorrection(SEXP); +// extern SEXP patchAnalysis(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP); +// extern SEXP smoothImage(SEXP, SEXP, SEXP, SEXP, SEXP); extern SEXP splitChannels(SEXP, SEXP); -extern SEXP ThresholdImage(SEXP); +// extern SEXP ThresholdImage(SEXP); static const R_CallMethodDef CallEntries[] = { - {"antsApplyTransforms", (DL_FUNC) &antsApplyTransforms, 1}, - {"antsApplyTransformsToPoints", (DL_FUNC) &antsApplyTransformsToPoints, 1}, + // {"antsApplyTransforms", (DL_FUNC) &antsApplyTransforms, 1}, + // {"antsApplyTransformsToPoints", (DL_FUNC) &antsApplyTransformsToPoints, 1}, {"antsImage", (DL_FUNC) &antsImage, 3}, {"antsImage_asantsImage", (DL_FUNC) &antsImage_asantsImage, 6}, {"antsImage_asVector", (DL_FUNC) &antsImage_asVector, 3}, @@ -132,8 +132,8 @@ static const R_CallMethodDef CallEntries[] = { {"antsImage_SetPixels", (DL_FUNC) &antsImage_SetPixels, 3}, {"antsImage_SetRegion", (DL_FUNC) &antsImage_SetRegion, 4}, {"antsImage_SetSpacing", (DL_FUNC) &antsImage_SetSpacing, 2}, - {"antsImage_TransformIndexToPhysicalPoint", (DL_FUNC) &antsImage_TransformIndexToPhysicalPoint, 2}, - {"antsImage_TransformPhysicalPointToIndex", (DL_FUNC) &antsImage_TransformPhysicalPointToIndex, 2}, + // {"antsImage_TransformIndexToPhysicalPoint", (DL_FUNC) &antsImage_TransformIndexToPhysicalPoint, 2}, + // {"antsImage_TransformPhysicalPointToIndex", (DL_FUNC) &antsImage_TransformPhysicalPointToIndex, 2}, {"antsImageArithImageImage", (DL_FUNC) &antsImageArithImageImage, 3}, {"antsImageArithImageNumeric", (DL_FUNC) &antsImageArithImageNumeric, 3}, {"antsImageArithNumericImage", (DL_FUNC) &antsImageArithNumericImage, 3}, @@ -141,73 +141,73 @@ static const R_CallMethodDef CallEntries[] = { {"antsImageComparisonImageImage", (DL_FUNC) &antsImageComparisonImageImage, 3}, {"antsImageComparisonImageNumeric", (DL_FUNC) &antsImageComparisonImageNumeric, 3}, {"antsImageHeaderInfo", (DL_FUNC) &antsImageHeaderInfo, 1}, - {"antsImageIterator", (DL_FUNC) &antsImageIterator, 1}, - {"antsImageIterator", (DL_FUNC) &antsImageIterator, 3}, - {"antsImageIterator_Get", (DL_FUNC) &antsImageIterator_Get, 1}, - {"antsImageIterator_GetIndex", (DL_FUNC) &antsImageIterator_GetIndex, 1}, - {"antsImageIterator_GoToBegin", (DL_FUNC) &antsImageIterator_GoToBegin, 1}, - {"antsImageIterator_GoToReverseBegin", (DL_FUNC) &antsImageIterator_GoToReverseBegin, 1}, - {"antsImageIterator_IsAtEnd", (DL_FUNC) &antsImageIterator_IsAtEnd, 1}, - {"antsImageIterator_IsAtReverseEnd", (DL_FUNC) &antsImageIterator_IsAtReverseEnd, 1}, - {"antsImageIterator_Next", (DL_FUNC) &antsImageIterator_Next, 1}, - {"antsImageIterator_Previous", (DL_FUNC) &antsImageIterator_Previous, 1}, - {"antsImageIterator_Remaining", (DL_FUNC) &antsImageIterator_Remaining, 1}, - {"antsImageIterator_Set", (DL_FUNC) &antsImageIterator_Set, 2}, - {"antsImageIterator_SetIndex", (DL_FUNC) &antsImageIterator_SetIndex, 2}, + // {"antsImageIterator", (DL_FUNC) &antsImageIterator, 1}, + // {"antsImageIterator", (DL_FUNC) &antsImageIterator, 3}, + // {"antsImageIterator_Get", (DL_FUNC) &antsImageIterator_Get, 1}, + // {"antsImageIterator_GetIndex", (DL_FUNC) &antsImageIterator_GetIndex, 1}, + // {"antsImageIterator_GoToBegin", (DL_FUNC) &antsImageIterator_GoToBegin, 1}, + // {"antsImageIterator_GoToReverseBegin", (DL_FUNC) &antsImageIterator_GoToReverseBegin, 1}, + // {"antsImageIterator_IsAtEnd", (DL_FUNC) &antsImageIterator_IsAtEnd, 1}, + // {"antsImageIterator_IsAtReverseEnd", (DL_FUNC) &antsImageIterator_IsAtReverseEnd, 1}, + // {"antsImageIterator_Next", (DL_FUNC) &antsImageIterator_Next, 1}, + // {"antsImageIterator_Previous", (DL_FUNC) &antsImageIterator_Previous, 1}, + // {"antsImageIterator_Remaining", (DL_FUNC) &antsImageIterator_Remaining, 1}, + // {"antsImageIterator_Set", (DL_FUNC) &antsImageIterator_Set, 2}, + // {"antsImageIterator_SetIndex", (DL_FUNC) &antsImageIterator_SetIndex, 2}, {"antsImageLogicImageImage", (DL_FUNC) &antsImageLogicImageImage, 3}, {"antsImageLogicImageNumeric", (DL_FUNC) &antsImageLogicImageNumeric, 3}, {"antsImageMath", (DL_FUNC) &antsImageMath, 2}, - {"antsImageMutualInformation", (DL_FUNC) &antsImageMutualInformation, 2}, + // {"antsImageMutualInformation", (DL_FUNC) &antsImageMutualInformation, 2}, {"antsImageRead", (DL_FUNC) &antsImageRead, 4}, {"antsImageStats", (DL_FUNC) &antsImageStats, 3}, {"antsImageWrite", (DL_FUNC) &antsImageWrite, 3}, - {"antsJointFusion", (DL_FUNC) &antsJointFusion, 1}, - {"antsMatrix", (DL_FUNC) &antsMatrix, 1}, - {"antsMatrix_asantsMatrix", (DL_FUNC) &antsMatrix_asantsMatrix, 2}, - {"antsMatrix_asList", (DL_FUNC) &antsMatrix_asList, 1}, - {"antsRegistration", (DL_FUNC) &antsRegistration, 1}, + // {"antsJointFusion", (DL_FUNC) &antsJointFusion, 1}, + // {"antsMatrix", (DL_FUNC) &antsMatrix, 1}, + // {"antsMatrix_asantsMatrix", (DL_FUNC) &antsMatrix_asantsMatrix, 2}, + // {"antsMatrix_asList", (DL_FUNC) &antsMatrix_asList, 1}, + // {"antsRegistration", (DL_FUNC) &antsRegistration, 1}, // {"antsrMetric", (DL_FUNC) &antsrMetric, 3}, - {"antsrMetric", (DL_FUNC) &antsrMetric, 6}, - {"antsrMetric_GetDerivative", (DL_FUNC) &antsrMetric_GetDerivative, 1}, - {"antsrMetric_GetValue", (DL_FUNC) &antsrMetric_GetValue, 1}, - {"antsrMetric_Initialize", (DL_FUNC) &antsrMetric_Initialize, 1}, - {"antsrMetric_SetImage", (DL_FUNC) &antsrMetric_SetImage, 4}, - {"antsrMetric_SetNumberOfHistogramBins", (DL_FUNC) &antsrMetric_SetNumberOfHistogramBins, 2}, - {"antsrMetric_SetRadius", (DL_FUNC) &antsrMetric_SetRadius, 2}, - {"antsrMetric_SetSampling", (DL_FUNC) &antsrMetric_SetSampling, 3}, - {"antsrMetric_SetTransform", (DL_FUNC) &antsrMetric_SetTransform, 3}, - {"antsrTransform", (DL_FUNC) &antsrTransform, 3}, - {"antsrTransform_Compose", (DL_FUNC) &antsrTransform_Compose, 3}, - {"antsrTransform_FromDisplacementField", (DL_FUNC) &antsrTransform_FromDisplacementField, 1}, - {"antsrTransform_GetFixedParameters", (DL_FUNC) &antsrTransform_GetFixedParameters, 1}, - {"antsrTransform_GetParameters", (DL_FUNC) &antsrTransform_GetParameters, 1}, - {"antsrTransform_Inverse", (DL_FUNC) &antsrTransform_Inverse, 1}, - {"antsrTransform_MatrixOffset", (DL_FUNC) &antsrTransform_MatrixOffset, 9}, - {"antsrTransform_Read", (DL_FUNC) &antsrTransform_Read, 3}, - {"antsrTransform_SetFixedParameters", (DL_FUNC) &antsrTransform_SetFixedParameters, 2}, - {"antsrTransform_SetParameters", (DL_FUNC) &antsrTransform_SetParameters, 2}, - {"antsrTransform_ToDisplacementField", (DL_FUNC) &antsrTransform_ToDisplacementField, 2}, - {"antsrTransform_TransformImage", (DL_FUNC) &antsrTransform_TransformImage, 4}, - {"antsrTransform_TransformPoint", (DL_FUNC) &antsrTransform_TransformPoint, 2}, - {"antsrTransform_TransformVector", (DL_FUNC) &antsrTransform_TransformVector, 2}, - {"antsrTransform_Write", (DL_FUNC) &antsrTransform_Write, 2}, - {"Atropos", (DL_FUNC) &Atropos, 1}, + // {"antsrMetric", (DL_FUNC) &antsrMetric, 6}, + // {"antsrMetric_GetDerivative", (DL_FUNC) &antsrMetric_GetDerivative, 1}, + // {"antsrMetric_GetValue", (DL_FUNC) &antsrMetric_GetValue, 1}, + // {"antsrMetric_Initialize", (DL_FUNC) &antsrMetric_Initialize, 1}, + // {"antsrMetric_SetImage", (DL_FUNC) &antsrMetric_SetImage, 4}, + // {"antsrMetric_SetNumberOfHistogramBins", (DL_FUNC) &antsrMetric_SetNumberOfHistogramBins, 2}, + // {"antsrMetric_SetRadius", (DL_FUNC) &antsrMetric_SetRadius, 2}, + // {"antsrMetric_SetSampling", (DL_FUNC) &antsrMetric_SetSampling, 3}, + // {"antsrMetric_SetTransform", (DL_FUNC) &antsrMetric_SetTransform, 3}, + // {"antsrTransform", (DL_FUNC) &antsrTransform, 3}, + // {"antsrTransform_Compose", (DL_FUNC) &antsrTransform_Compose, 3}, + // {"antsrTransform_FromDisplacementField", (DL_FUNC) &antsrTransform_FromDisplacementField, 1}, + // {"antsrTransform_GetFixedParameters", (DL_FUNC) &antsrTransform_GetFixedParameters, 1}, + // {"antsrTransform_GetParameters", (DL_FUNC) &antsrTransform_GetParameters, 1}, + // {"antsrTransform_Inverse", (DL_FUNC) &antsrTransform_Inverse, 1}, + // {"antsrTransform_MatrixOffset", (DL_FUNC) &antsrTransform_MatrixOffset, 9}, + // {"antsrTransform_Read", (DL_FUNC) &antsrTransform_Read, 3}, + // {"antsrTransform_SetFixedParameters", (DL_FUNC) &antsrTransform_SetFixedParameters, 2}, + // {"antsrTransform_SetParameters", (DL_FUNC) &antsrTransform_SetParameters, 2}, + // {"antsrTransform_ToDisplacementField", (DL_FUNC) &antsrTransform_ToDisplacementField, 2}, + // {"antsrTransform_TransformImage", (DL_FUNC) &antsrTransform_TransformImage, 4}, + // {"antsrTransform_TransformPoint", (DL_FUNC) &antsrTransform_TransformPoint, 2}, + // {"antsrTransform_TransformVector", (DL_FUNC) &antsrTransform_TransformVector, 2}, + // {"antsrTransform_Write", (DL_FUNC) &antsrTransform_Write, 2}, + // {"Atropos", (DL_FUNC) &Atropos, 1}, {"cropImage", (DL_FUNC) &cropImage, 6}, - {"DenoiseImage", (DL_FUNC) &DenoiseImage, 1}, + // {"DenoiseImage", (DL_FUNC) &DenoiseImage, 1}, {"extractSlice", (DL_FUNC) &extractSlice, 3}, - {"imagesToMatrix", (DL_FUNC) &imagesToMatrix, 3}, + // {"imagesToMatrix", (DL_FUNC) &imagesToMatrix, 3}, {"iMathInterface", (DL_FUNC) &iMathInterface, 1}, {"iMathInterface1", (DL_FUNC) &iMathInterface1, 1}, {"iMathInterface2", (DL_FUNC) &iMathInterface2, 1}, - {"LabelClustersUniquely", (DL_FUNC) &LabelClustersUniquely, 1}, - {"labelStats", (DL_FUNC) &labelStats, 2}, - {"mergeChannels", (DL_FUNC) &mergeChannels, 2}, - {"N3BiasFieldCorrection", (DL_FUNC) &N3BiasFieldCorrection, 1}, - {"N4BiasFieldCorrection", (DL_FUNC) &N4BiasFieldCorrection, 1}, - {"patchAnalysis", (DL_FUNC) &patchAnalysis, 12}, - {"smoothImage", (DL_FUNC) &smoothImage, 5}, + // {"LabelClustersUniquely", (DL_FUNC) &LabelClustersUniquely, 1}, + // {"labelStats", (DL_FUNC) &labelStats, 2}, + // {"mergeChannels", (DL_FUNC) &mergeChannels, 2}, + // {"N3BiasFieldCorrection", (DL_FUNC) &N3BiasFieldCorrection, 1}, + // {"N4BiasFieldCorrection", (DL_FUNC) &N4BiasFieldCorrection, 1}, + // {"patchAnalysis", (DL_FUNC) &patchAnalysis, 12}, + // {"smoothImage", (DL_FUNC) &smoothImage, 5}, {"splitChannels", (DL_FUNC) &splitChannels, 2}, - {"ThresholdImage", (DL_FUNC) &ThresholdImage, 1}, + // {"ThresholdImage", (DL_FUNC) &ThresholdImage, 1}, {NULL, NULL, 0} }; From 0d3c153eb80e56a04332cd2d28ed9e3389d388f1 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Tue, 29 Oct 2019 15:38:14 -0400 Subject: [PATCH 20/23] fixing it back --- src/init.c | 230 ++++++++++++++++++++++++++--------------------------- 1 file changed, 115 insertions(+), 115 deletions(-) diff --git a/src/init.c b/src/init.c index a0897214..870065b6 100644 --- a/src/init.c +++ b/src/init.c @@ -17,8 +17,8 @@ */ /* .Call calls */ -// extern SEXP antsApplyTransforms(SEXP); -// extern SEXP antsApplyTransformsToPoints(SEXP); +extern SEXP antsApplyTransforms(SEXP); +extern SEXP antsApplyTransformsToPoints(SEXP); extern SEXP antsImage(SEXP, SEXP, SEXP); extern SEXP antsImage_asantsImage(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP); extern SEXP antsImage_asVector(SEXP, SEXP, SEXP); @@ -36,8 +36,8 @@ extern SEXP antsImage_SetOrigin(SEXP, SEXP); extern SEXP antsImage_SetPixels(SEXP, SEXP, SEXP); extern SEXP antsImage_SetRegion(SEXP, SEXP, SEXP, SEXP); extern SEXP antsImage_SetSpacing(SEXP, SEXP); -// extern SEXP antsImage_TransformIndexToPhysicalPoint(SEXP, SEXP); -// extern SEXP antsImage_TransformPhysicalPointToIndex(SEXP, SEXP); +extern SEXP antsImage_TransformIndexToPhysicalPoint(SEXP, SEXP); +extern SEXP antsImage_TransformPhysicalPointToIndex(SEXP, SEXP); extern SEXP antsImageArithImageImage(SEXP, SEXP, SEXP); extern SEXP antsImageArithImageNumeric(SEXP, SEXP, SEXP); extern SEXP antsImageArithNumericImage(SEXP, SEXP, SEXP); @@ -45,76 +45,76 @@ extern SEXP antsImageClone(SEXP, SEXP); extern SEXP antsImageComparisonImageImage(SEXP, SEXP, SEXP); extern SEXP antsImageComparisonImageNumeric(SEXP, SEXP, SEXP); extern SEXP antsImageHeaderInfo(SEXP); -// extern SEXP antsImageIterator(SEXP, SEXP, SEXP); -// extern SEXP antsImageIterator_Get(SEXP); -// extern SEXP antsImageIterator_GetIndex(SEXP); -// extern SEXP antsImageIterator_GoToBegin(SEXP); -// extern SEXP antsImageIterator_GoToReverseBegin(SEXP); -// extern SEXP antsImageIterator_IsAtEnd(SEXP); -// extern SEXP antsImageIterator_IsAtReverseEnd(SEXP); -// extern SEXP antsImageIterator_Next(SEXP); -// extern SEXP antsImageIterator_Previous(SEXP); -// extern SEXP antsImageIterator_Remaining(SEXP); -// extern SEXP antsImageIterator_Set(SEXP, SEXP); -// extern SEXP antsImageIterator_SetIndex(SEXP, SEXP); +extern SEXP antsImageIterator(SEXP, SEXP, SEXP); +extern SEXP antsImageIterator_Get(SEXP); +extern SEXP antsImageIterator_GetIndex(SEXP); +extern SEXP antsImageIterator_GoToBegin(SEXP); +extern SEXP antsImageIterator_GoToReverseBegin(SEXP); +extern SEXP antsImageIterator_IsAtEnd(SEXP); +extern SEXP antsImageIterator_IsAtReverseEnd(SEXP); +extern SEXP antsImageIterator_Next(SEXP); +extern SEXP antsImageIterator_Previous(SEXP); +extern SEXP antsImageIterator_Remaining(SEXP); +extern SEXP antsImageIterator_Set(SEXP, SEXP); +extern SEXP antsImageIterator_SetIndex(SEXP, SEXP); extern SEXP antsImageLogicImageImage(SEXP, SEXP, SEXP); extern SEXP antsImageLogicImageNumeric(SEXP, SEXP, SEXP); extern SEXP antsImageMath(SEXP, SEXP); -// extern SEXP antsImageMutualInformation(SEXP, SEXP); +extern SEXP antsImageMutualInformation(SEXP, SEXP); extern SEXP antsImageRead(SEXP, SEXP, SEXP, SEXP); extern SEXP antsImageStats(SEXP,SEXP,SEXP); extern SEXP antsImageWrite(SEXP, SEXP, SEXP); -// extern SEXP antsJointFusion(SEXP); -// extern SEXP antsMatrix(SEXP); -// extern SEXP antsMatrix_asantsMatrix(SEXP, SEXP); -// extern SEXP antsMatrix_asList(SEXP); -// extern SEXP antsRegistration(SEXP); +extern SEXP antsJointFusion(SEXP); +extern SEXP antsMatrix(SEXP); +extern SEXP antsMatrix_asantsMatrix(SEXP, SEXP); +extern SEXP antsMatrix_asList(SEXP); +extern SEXP antsRegistration(SEXP); // extern SEXP antsrMetric(SEXP, SEXP, SEXP); -// extern SEXP antsrMetric(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP); -// extern SEXP antsrMetric_GetDerivative(SEXP); -// extern SEXP antsrMetric_GetValue(SEXP); -// extern SEXP antsrMetric_Initialize(SEXP); -// extern SEXP antsrMetric_SetImage(SEXP, SEXP, SEXP, SEXP); -// extern SEXP antsrMetric_SetNumberOfHistogramBins(SEXP, SEXP); -// extern SEXP antsrMetric_SetRadius(SEXP, SEXP); -// extern SEXP antsrMetric_SetSampling(SEXP, SEXP, SEXP); -// extern SEXP antsrMetric_SetTransform(SEXP, SEXP, SEXP); -// extern SEXP antsrTransform(SEXP, SEXP, SEXP); -// extern SEXP antsrTransform_Compose(SEXP, SEXP, SEXP); -// extern SEXP antsrTransform_FromDisplacementField(SEXP); -// extern SEXP antsrTransform_GetFixedParameters(SEXP); -// extern SEXP antsrTransform_GetParameters(SEXP); -// extern SEXP antsrTransform_Inverse(SEXP); -// extern SEXP antsrTransform_MatrixOffset(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP); -// extern SEXP antsrTransform_Read(SEXP, SEXP, SEXP); -// extern SEXP antsrTransform_SetFixedParameters(SEXP, SEXP); -// extern SEXP antsrTransform_SetParameters(SEXP, SEXP); -// extern SEXP antsrTransform_ToDisplacementField(SEXP,SEXP); -// extern SEXP antsrTransform_TransformImage(SEXP, SEXP, SEXP, SEXP); -// extern SEXP antsrTransform_TransformPoint(SEXP, SEXP); -// extern SEXP antsrTransform_TransformVector(SEXP, SEXP); -// extern SEXP antsrTransform_Write(SEXP, SEXP); -// extern SEXP Atropos(SEXP); +extern SEXP antsrMetric(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP); +extern SEXP antsrMetric_GetDerivative(SEXP); +extern SEXP antsrMetric_GetValue(SEXP); +extern SEXP antsrMetric_Initialize(SEXP); +extern SEXP antsrMetric_SetImage(SEXP, SEXP, SEXP, SEXP); +extern SEXP antsrMetric_SetNumberOfHistogramBins(SEXP, SEXP); +extern SEXP antsrMetric_SetRadius(SEXP, SEXP); +extern SEXP antsrMetric_SetSampling(SEXP, SEXP, SEXP); +extern SEXP antsrMetric_SetTransform(SEXP, SEXP, SEXP); +extern SEXP antsrTransform(SEXP, SEXP, SEXP); +extern SEXP antsrTransform_Compose(SEXP, SEXP, SEXP); +extern SEXP antsrTransform_FromDisplacementField(SEXP); +extern SEXP antsrTransform_GetFixedParameters(SEXP); +extern SEXP antsrTransform_GetParameters(SEXP); +extern SEXP antsrTransform_Inverse(SEXP); +extern SEXP antsrTransform_MatrixOffset(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP); +extern SEXP antsrTransform_Read(SEXP, SEXP, SEXP); +extern SEXP antsrTransform_SetFixedParameters(SEXP, SEXP); +extern SEXP antsrTransform_SetParameters(SEXP, SEXP); +extern SEXP antsrTransform_ToDisplacementField(SEXP,SEXP); +extern SEXP antsrTransform_TransformImage(SEXP, SEXP, SEXP, SEXP); +extern SEXP antsrTransform_TransformPoint(SEXP, SEXP); +extern SEXP antsrTransform_TransformVector(SEXP, SEXP); +extern SEXP antsrTransform_Write(SEXP, SEXP); +extern SEXP Atropos(SEXP); extern SEXP cropImage(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP); -// extern SEXP DenoiseImage(SEXP); +extern SEXP DenoiseImage(SEXP); extern SEXP extractSlice(SEXP, SEXP, SEXP); -// extern SEXP imagesToMatrix(SEXP, SEXP, SEXP); +extern SEXP imagesToMatrix(SEXP, SEXP, SEXP); extern SEXP iMathInterface(SEXP); extern SEXP iMathInterface1(SEXP); extern SEXP iMathInterface2(SEXP); -// extern SEXP LabelClustersUniquely(SEXP); -// extern SEXP labelStats(SEXP, SEXP); -// extern SEXP mergeChannels(SEXP, SEXP); -// extern SEXP N3BiasFieldCorrection(SEXP); -// extern SEXP N4BiasFieldCorrection(SEXP); -// extern SEXP patchAnalysis(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP); -// extern SEXP smoothImage(SEXP, SEXP, SEXP, SEXP, SEXP); +extern SEXP LabelClustersUniquely(SEXP); +extern SEXP labelStats(SEXP, SEXP); +extern SEXP mergeChannels(SEXP, SEXP); +extern SEXP N3BiasFieldCorrection(SEXP); +extern SEXP N4BiasFieldCorrection(SEXP); +extern SEXP patchAnalysis(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP); +extern SEXP smoothImage(SEXP, SEXP, SEXP, SEXP, SEXP); extern SEXP splitChannels(SEXP, SEXP); -// extern SEXP ThresholdImage(SEXP); +extern SEXP ThresholdImage(SEXP); static const R_CallMethodDef CallEntries[] = { - // {"antsApplyTransforms", (DL_FUNC) &antsApplyTransforms, 1}, - // {"antsApplyTransformsToPoints", (DL_FUNC) &antsApplyTransformsToPoints, 1}, + {"antsApplyTransforms", (DL_FUNC) &antsApplyTransforms, 1}, + {"antsApplyTransformsToPoints", (DL_FUNC) &antsApplyTransformsToPoints, 1}, {"antsImage", (DL_FUNC) &antsImage, 3}, {"antsImage_asantsImage", (DL_FUNC) &antsImage_asantsImage, 6}, {"antsImage_asVector", (DL_FUNC) &antsImage_asVector, 3}, @@ -132,8 +132,8 @@ static const R_CallMethodDef CallEntries[] = { {"antsImage_SetPixels", (DL_FUNC) &antsImage_SetPixels, 3}, {"antsImage_SetRegion", (DL_FUNC) &antsImage_SetRegion, 4}, {"antsImage_SetSpacing", (DL_FUNC) &antsImage_SetSpacing, 2}, - // {"antsImage_TransformIndexToPhysicalPoint", (DL_FUNC) &antsImage_TransformIndexToPhysicalPoint, 2}, - // {"antsImage_TransformPhysicalPointToIndex", (DL_FUNC) &antsImage_TransformPhysicalPointToIndex, 2}, + {"antsImage_TransformIndexToPhysicalPoint", (DL_FUNC) &antsImage_TransformIndexToPhysicalPoint, 2}, + {"antsImage_TransformPhysicalPointToIndex", (DL_FUNC) &antsImage_TransformPhysicalPointToIndex, 2}, {"antsImageArithImageImage", (DL_FUNC) &antsImageArithImageImage, 3}, {"antsImageArithImageNumeric", (DL_FUNC) &antsImageArithImageNumeric, 3}, {"antsImageArithNumericImage", (DL_FUNC) &antsImageArithNumericImage, 3}, @@ -141,73 +141,73 @@ static const R_CallMethodDef CallEntries[] = { {"antsImageComparisonImageImage", (DL_FUNC) &antsImageComparisonImageImage, 3}, {"antsImageComparisonImageNumeric", (DL_FUNC) &antsImageComparisonImageNumeric, 3}, {"antsImageHeaderInfo", (DL_FUNC) &antsImageHeaderInfo, 1}, - // {"antsImageIterator", (DL_FUNC) &antsImageIterator, 1}, - // {"antsImageIterator", (DL_FUNC) &antsImageIterator, 3}, - // {"antsImageIterator_Get", (DL_FUNC) &antsImageIterator_Get, 1}, - // {"antsImageIterator_GetIndex", (DL_FUNC) &antsImageIterator_GetIndex, 1}, - // {"antsImageIterator_GoToBegin", (DL_FUNC) &antsImageIterator_GoToBegin, 1}, - // {"antsImageIterator_GoToReverseBegin", (DL_FUNC) &antsImageIterator_GoToReverseBegin, 1}, - // {"antsImageIterator_IsAtEnd", (DL_FUNC) &antsImageIterator_IsAtEnd, 1}, - // {"antsImageIterator_IsAtReverseEnd", (DL_FUNC) &antsImageIterator_IsAtReverseEnd, 1}, - // {"antsImageIterator_Next", (DL_FUNC) &antsImageIterator_Next, 1}, - // {"antsImageIterator_Previous", (DL_FUNC) &antsImageIterator_Previous, 1}, - // {"antsImageIterator_Remaining", (DL_FUNC) &antsImageIterator_Remaining, 1}, - // {"antsImageIterator_Set", (DL_FUNC) &antsImageIterator_Set, 2}, - // {"antsImageIterator_SetIndex", (DL_FUNC) &antsImageIterator_SetIndex, 2}, + {"antsImageIterator", (DL_FUNC) &antsImageIterator, 1}, + {"antsImageIterator", (DL_FUNC) &antsImageIterator, 3}, + {"antsImageIterator_Get", (DL_FUNC) &antsImageIterator_Get, 1}, + {"antsImageIterator_GetIndex", (DL_FUNC) &antsImageIterator_GetIndex, 1}, + {"antsImageIterator_GoToBegin", (DL_FUNC) &antsImageIterator_GoToBegin, 1}, + {"antsImageIterator_GoToReverseBegin", (DL_FUNC) &antsImageIterator_GoToReverseBegin, 1}, + {"antsImageIterator_IsAtEnd", (DL_FUNC) &antsImageIterator_IsAtEnd, 1}, + {"antsImageIterator_IsAtReverseEnd", (DL_FUNC) &antsImageIterator_IsAtReverseEnd, 1}, + {"antsImageIterator_Next", (DL_FUNC) &antsImageIterator_Next, 1}, + {"antsImageIterator_Previous", (DL_FUNC) &antsImageIterator_Previous, 1}, + {"antsImageIterator_Remaining", (DL_FUNC) &antsImageIterator_Remaining, 1}, + {"antsImageIterator_Set", (DL_FUNC) &antsImageIterator_Set, 2}, + {"antsImageIterator_SetIndex", (DL_FUNC) &antsImageIterator_SetIndex, 2}, {"antsImageLogicImageImage", (DL_FUNC) &antsImageLogicImageImage, 3}, {"antsImageLogicImageNumeric", (DL_FUNC) &antsImageLogicImageNumeric, 3}, {"antsImageMath", (DL_FUNC) &antsImageMath, 2}, - // {"antsImageMutualInformation", (DL_FUNC) &antsImageMutualInformation, 2}, + {"antsImageMutualInformation", (DL_FUNC) &antsImageMutualInformation, 2}, {"antsImageRead", (DL_FUNC) &antsImageRead, 4}, {"antsImageStats", (DL_FUNC) &antsImageStats, 3}, {"antsImageWrite", (DL_FUNC) &antsImageWrite, 3}, - // {"antsJointFusion", (DL_FUNC) &antsJointFusion, 1}, - // {"antsMatrix", (DL_FUNC) &antsMatrix, 1}, - // {"antsMatrix_asantsMatrix", (DL_FUNC) &antsMatrix_asantsMatrix, 2}, - // {"antsMatrix_asList", (DL_FUNC) &antsMatrix_asList, 1}, - // {"antsRegistration", (DL_FUNC) &antsRegistration, 1}, + {"antsJointFusion", (DL_FUNC) &antsJointFusion, 1}, + {"antsMatrix", (DL_FUNC) &antsMatrix, 1}, + {"antsMatrix_asantsMatrix", (DL_FUNC) &antsMatrix_asantsMatrix, 2}, + {"antsMatrix_asList", (DL_FUNC) &antsMatrix_asList, 1}, + {"antsRegistration", (DL_FUNC) &antsRegistration, 1}, // {"antsrMetric", (DL_FUNC) &antsrMetric, 3}, - // {"antsrMetric", (DL_FUNC) &antsrMetric, 6}, - // {"antsrMetric_GetDerivative", (DL_FUNC) &antsrMetric_GetDerivative, 1}, - // {"antsrMetric_GetValue", (DL_FUNC) &antsrMetric_GetValue, 1}, - // {"antsrMetric_Initialize", (DL_FUNC) &antsrMetric_Initialize, 1}, - // {"antsrMetric_SetImage", (DL_FUNC) &antsrMetric_SetImage, 4}, - // {"antsrMetric_SetNumberOfHistogramBins", (DL_FUNC) &antsrMetric_SetNumberOfHistogramBins, 2}, - // {"antsrMetric_SetRadius", (DL_FUNC) &antsrMetric_SetRadius, 2}, - // {"antsrMetric_SetSampling", (DL_FUNC) &antsrMetric_SetSampling, 3}, - // {"antsrMetric_SetTransform", (DL_FUNC) &antsrMetric_SetTransform, 3}, - // {"antsrTransform", (DL_FUNC) &antsrTransform, 3}, - // {"antsrTransform_Compose", (DL_FUNC) &antsrTransform_Compose, 3}, - // {"antsrTransform_FromDisplacementField", (DL_FUNC) &antsrTransform_FromDisplacementField, 1}, - // {"antsrTransform_GetFixedParameters", (DL_FUNC) &antsrTransform_GetFixedParameters, 1}, - // {"antsrTransform_GetParameters", (DL_FUNC) &antsrTransform_GetParameters, 1}, - // {"antsrTransform_Inverse", (DL_FUNC) &antsrTransform_Inverse, 1}, - // {"antsrTransform_MatrixOffset", (DL_FUNC) &antsrTransform_MatrixOffset, 9}, - // {"antsrTransform_Read", (DL_FUNC) &antsrTransform_Read, 3}, - // {"antsrTransform_SetFixedParameters", (DL_FUNC) &antsrTransform_SetFixedParameters, 2}, - // {"antsrTransform_SetParameters", (DL_FUNC) &antsrTransform_SetParameters, 2}, - // {"antsrTransform_ToDisplacementField", (DL_FUNC) &antsrTransform_ToDisplacementField, 2}, - // {"antsrTransform_TransformImage", (DL_FUNC) &antsrTransform_TransformImage, 4}, - // {"antsrTransform_TransformPoint", (DL_FUNC) &antsrTransform_TransformPoint, 2}, - // {"antsrTransform_TransformVector", (DL_FUNC) &antsrTransform_TransformVector, 2}, - // {"antsrTransform_Write", (DL_FUNC) &antsrTransform_Write, 2}, - // {"Atropos", (DL_FUNC) &Atropos, 1}, + {"antsrMetric", (DL_FUNC) &antsrMetric, 6}, + {"antsrMetric_GetDerivative", (DL_FUNC) &antsrMetric_GetDerivative, 1}, + {"antsrMetric_GetValue", (DL_FUNC) &antsrMetric_GetValue, 1}, + {"antsrMetric_Initialize", (DL_FUNC) &antsrMetric_Initialize, 1}, + {"antsrMetric_SetImage", (DL_FUNC) &antsrMetric_SetImage, 4}, + {"antsrMetric_SetNumberOfHistogramBins", (DL_FUNC) &antsrMetric_SetNumberOfHistogramBins, 2}, + {"antsrMetric_SetRadius", (DL_FUNC) &antsrMetric_SetRadius, 2}, + {"antsrMetric_SetSampling", (DL_FUNC) &antsrMetric_SetSampling, 3}, + {"antsrMetric_SetTransform", (DL_FUNC) &antsrMetric_SetTransform, 3}, + {"antsrTransform", (DL_FUNC) &antsrTransform, 3}, + {"antsrTransform_Compose", (DL_FUNC) &antsrTransform_Compose, 3}, + {"antsrTransform_FromDisplacementField", (DL_FUNC) &antsrTransform_FromDisplacementField, 1}, + {"antsrTransform_GetFixedParameters", (DL_FUNC) &antsrTransform_GetFixedParameters, 1}, + {"antsrTransform_GetParameters", (DL_FUNC) &antsrTransform_GetParameters, 1}, + {"antsrTransform_Inverse", (DL_FUNC) &antsrTransform_Inverse, 1}, + {"antsrTransform_MatrixOffset", (DL_FUNC) &antsrTransform_MatrixOffset, 9}, + {"antsrTransform_Read", (DL_FUNC) &antsrTransform_Read, 3}, + {"antsrTransform_SetFixedParameters", (DL_FUNC) &antsrTransform_SetFixedParameters, 2}, + {"antsrTransform_SetParameters", (DL_FUNC) &antsrTransform_SetParameters, 2}, + {"antsrTransform_ToDisplacementField", (DL_FUNC) &antsrTransform_ToDisplacementField, 2}, + {"antsrTransform_TransformImage", (DL_FUNC) &antsrTransform_TransformImage, 4}, + {"antsrTransform_TransformPoint", (DL_FUNC) &antsrTransform_TransformPoint, 2}, + {"antsrTransform_TransformVector", (DL_FUNC) &antsrTransform_TransformVector, 2}, + {"antsrTransform_Write", (DL_FUNC) &antsrTransform_Write, 2}, + {"Atropos", (DL_FUNC) &Atropos, 1}, {"cropImage", (DL_FUNC) &cropImage, 6}, - // {"DenoiseImage", (DL_FUNC) &DenoiseImage, 1}, + {"DenoiseImage", (DL_FUNC) &DenoiseImage, 1}, {"extractSlice", (DL_FUNC) &extractSlice, 3}, - // {"imagesToMatrix", (DL_FUNC) &imagesToMatrix, 3}, + {"imagesToMatrix", (DL_FUNC) &imagesToMatrix, 3}, {"iMathInterface", (DL_FUNC) &iMathInterface, 1}, {"iMathInterface1", (DL_FUNC) &iMathInterface1, 1}, {"iMathInterface2", (DL_FUNC) &iMathInterface2, 1}, - // {"LabelClustersUniquely", (DL_FUNC) &LabelClustersUniquely, 1}, - // {"labelStats", (DL_FUNC) &labelStats, 2}, - // {"mergeChannels", (DL_FUNC) &mergeChannels, 2}, - // {"N3BiasFieldCorrection", (DL_FUNC) &N3BiasFieldCorrection, 1}, - // {"N4BiasFieldCorrection", (DL_FUNC) &N4BiasFieldCorrection, 1}, - // {"patchAnalysis", (DL_FUNC) &patchAnalysis, 12}, - // {"smoothImage", (DL_FUNC) &smoothImage, 5}, + {"LabelClustersUniquely", (DL_FUNC) &LabelClustersUniquely, 1}, + {"labelStats", (DL_FUNC) &labelStats, 2}, + {"mergeChannels", (DL_FUNC) &mergeChannels, 2}, + {"N3BiasFieldCorrection", (DL_FUNC) &N3BiasFieldCorrection, 1}, + {"N4BiasFieldCorrection", (DL_FUNC) &N4BiasFieldCorrection, 1}, + {"patchAnalysis", (DL_FUNC) &patchAnalysis, 12}, + {"smoothImage", (DL_FUNC) &smoothImage, 5}, {"splitChannels", (DL_FUNC) &splitChannels, 2}, - // {"ThresholdImage", (DL_FUNC) &ThresholdImage, 1}, + {"ThresholdImage", (DL_FUNC) &ThresholdImage, 1}, {NULL, NULL, 0} }; From a9494040ce1c6fd69a50888e32e6f92e9436da8f Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Wed, 30 Oct 2019 13:27:46 -0400 Subject: [PATCH 21/23] updated the .call problems --- R/imagesToMatrix.R | 2 +- R/mergeChannels.R | 2 +- R/n4BiasFieldCorrection.R | 3 ++- R/splitChannels.R | 2 +- data/antsVersions.csv | 6 ++++-- man/plot.antsImage.Rd | 13 ++++++------- 6 files changed, 15 insertions(+), 13 deletions(-) diff --git a/R/imagesToMatrix.R b/R/imagesToMatrix.R index 5ecb2920..faa5595c 100644 --- a/R/imagesToMatrix.R +++ b/R/imagesToMatrix.R @@ -40,5 +40,5 @@ imagesToMatrix <- function(imageList, mask) { print("Must pass a list of filenames") return(NA) } - return(.Call("imagesToMatrix", imageList, mask, n)) + return(.Call("imagesToMatrix", imageList, mask, n, PACKAGE = "ANTsRCore")) } diff --git a/R/mergeChannels.R b/R/mergeChannels.R index 93c06fc0..a550f1f7 100644 --- a/R/mergeChannels.R +++ b/R/mergeChannels.R @@ -33,6 +33,6 @@ mergeChannels <- function(imageList) { } } - img = .Call("mergeChannels", imageList, package="ANTsR") + img = .Call("mergeChannels", imageList, package="ANTsRCore") return(img) } diff --git a/R/n4BiasFieldCorrection.R b/R/n4BiasFieldCorrection.R index a8861c66..bbe446e2 100644 --- a/R/n4BiasFieldCorrection.R +++ b/R/n4BiasFieldCorrection.R @@ -91,5 +91,6 @@ n4BiasFieldCorrection <- function( img, return(outimg) } .helpn4BiasFieldCorrection <- function(...) { - .Call("N4BiasFieldCorrection", .int_antsProcessArguments(c(...))) + .Call("N4BiasFieldCorrection", .int_antsProcessArguments(c(...)), + PACKAGE = "ANTsRCore") } diff --git a/R/splitChannels.R b/R/splitChannels.R index 76abcfdc..ddab0e56 100644 --- a/R/splitChannels.R +++ b/R/splitChannels.R @@ -32,6 +32,6 @@ splitChannels <- function(image) { stop( "input must have more than 1 components") } - img = .Call("splitChannels", image, package="ANTsR") + img = .Call("splitChannels", image, package="ANTsRCore") return(img) } diff --git a/data/antsVersions.csv b/data/antsVersions.csv index 3d460dad..bdd8daf9 100644 --- a/data/antsVersions.csv +++ b/data/antsVersions.csv @@ -1,3 +1,5 @@ Dependency;GitTag -ANTs;554b696927351c0de998fa6cde346c16630212fb -ANTsRCore;44880fce95158ba5cc77e2b6b0df0cfc9b1d6d33 +ANTs;1c421a5853f343a020aaae861a751545112e0807 +ANTsRCore;0d3c153eb80e56a04332cd2d28ed9e3389d388f1 +ANTsURL;https://github.com/ANTsX/ANTs.git +ITK; diff --git a/man/plot.antsImage.Rd b/man/plot.antsImage.Rd index c01ec21b..c7d266b6 100644 --- a/man/plot.antsImage.Rd +++ b/man/plot.antsImage.Rd @@ -6,13 +6,12 @@ \usage{ \method{plot}{antsImage}(x, y = NULL, color.img = "white", color.overlay = c("jet", "red", "blue", "green", "yellow", "viridis", - "magma", "plasma", "inferno"), axis = 2, slices, - colorbar = is.null(y), title.colorbar, title.img, title.line = NA, - color.colorbar, window.img, window.overlay, quality = 2, - outname = NA, alpha = 1, direction = 1, begin = 0, end = 1, - newwindow = FALSE, nslices = 10, domainImageMap = NULL, - ncolumns = 4, useAbsoluteScale = FALSE, doCropping = TRUE, text, - ...) + "magma", "plasma", "inferno"), axis = 2, slices, colorbar = FALSE, + title.colorbar, title.img, title.line = NA, color.colorbar, window.img, + window.overlay, quality = 2, outname = NA, alpha = 1, + direction = 1, begin = 0, end = 1, newwindow = FALSE, + nslices = 10, domainImageMap = NULL, ncolumns = 4, + useAbsoluteScale = FALSE, doCropping = TRUE, text, ...) } \arguments{ \item{x}{the reference image on which to overlay.} From dbeb60967f22427876eabadcab5af3171f9af740 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Wed, 30 Oct 2019 13:30:05 -0400 Subject: [PATCH 22/23] updated description --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 640897ab..5cd940fc 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: ANTsRCore Type: Package Title: Core Software Infrastructure for 'ANTsR' -Version: 0.7.1 -Date: 2019-09-19 +Version: 0.7.1.9000 +Date: 2019-10-30 Authors@R: c( person(given = "Brian B.", family = "Avants", role = "cre", email = "stnava@gmail.com"), From 2580b27fa289b1b1422ba99e7a847fa5a103cdd3 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Wed, 30 Oct 2019 14:23:14 -0400 Subject: [PATCH 23/23] added expect_equal instead of sum --- tests/testthat/test-antsImage.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/testthat/test-antsImage.R b/tests/testthat/test-antsImage.R index dbe7298a..2fd2c4b7 100644 --- a/tests/testthat/test-antsImage.R +++ b/tests/testthat/test-antsImage.R @@ -271,7 +271,7 @@ test_that("antsImage %% antsImage, preserves header", { test_that("antsImage %% antsImage", { expect_true(is.antsImage(img1 %% img2)) - expect_true(sum(img1 %% img2) == sum(valuesm %% values2)) + expect_equal(sum(img1 %% img2), sum(valuesm %% values2)) }) test_that("antsImage %% antsImage, preserves header", { expect_true(antsImagePhysicalSpaceConsistency(data.type = TRUE, img, img %% img)) @@ -279,7 +279,7 @@ test_that("antsImage %% antsImage, preserves header", { test_that("antsImage %/% scalar", { expect_true(is.antsImage(img1 %/% 2)) - expect_true(sum(img1 %/% 2) == sum(valuesm %/% 2)) + expect_equal(sum(img1 %/% 2), sum(valuesm %/% 2)) }) test_that("antsImage %/% scalar, preserves header", { expect_true(antsImagePhysicalSpaceConsistency(data.type = TRUE, img, img %/% 2)) @@ -295,7 +295,7 @@ test_that("antsImage %% antsImage, preserves header", { test_that("antsImage %/% antsImage", { expect_true(is.antsImage(img1 %% img2)) - expect_true(sum(img1 %/% img2) == sum(valuesm %/% values2)) + expect_equal(sum(img1 %/% img2), sum(valuesm %/% values2)) }) test_that("antsImage %/% antsImage, preserves header", { expect_true(antsImagePhysicalSpaceConsistency(data.type = TRUE, img1, img1 %/% img2))