Add cmake file

CMakeLists.txt

@@ -0,0 +1,76 @@
+cmake_minimum_required(VERSION 2.7)
+
+add_executable(asl_file asl_file.cc readoptions.cc asl_functions.cc)
+
+if(APPLE)
+  # Force use of libstdc++ on Mac as FSL uses this and we cannot link otherwise
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -stdlib=libstdc++")
+  # Get rid of CMake warning
+  set(CMAKE_MACOSX_RPATH ON)
+endif(APPLE)
+
+find_path(NEWMAT_INCLUDE_DIR newmat.h
+            HINTS $ENV{FSLDIR}/extras/include/newmat REQUIRED)
+find_path(FSL_INCLUDE_DIR newimage/newimage.h
+            HINTS $ENV{FSLDIR}/include REQUIRED)
+find_path(FSL_EXT_INCLUDE_DIR libprob/libprob.h
+            HINTS $ENV{FSLDIR}/extras/include REQUIRED)
+
+Message("-- FSL headers in ${FSL_INCLUDE_DIR} ${NEWMAT_INCLUDE_DIR} ${FSL_EXT_INCLUDE_DIR}")
+
+find_library(NEWMAT_LIBRARY NAMES newmat libnewmat
+             HINTS $ENV{FSLDIR}/extras/lib REQUIRED )
+find_library(UTILS_LIBRARY NAMES utils libutils
+             HINTS $ENV{FSLDIR}/lib REQUIRED )
+find_library(MISCMATHS_LIBRARY NAMES miscmaths libmiscmaths
+             HINTS $ENV{FSLDIR}/lib REQUIRED )
+find_library(NEWIMAGE_LIBRARY NAMES newimage libnewimage
+             HINTS $ENV{FSLDIR}/lib REQUIRED )
+find_library(FSLIO_LIBRARY NAMES fslio libfslio
+             HINTS $ENV{FSLDIR}/lib REQUIRED )
+find_library(NIFTIIO_LIBRARY NAMES niftiio libniftiio
+             HINTS $ENV{FSLDIR}/lib REQUIRED )
+find_library(ZNZ_LIBRARY NAMES znz libznz
+             HINTS $ENV{FSLDIR}/lib REQUIRED )
+find_library(Z_LIBRARY NAMES z libz zlib zlibd 
+               HINTS $ENV{FSLDIR}/lib REQUIRED )
+
+set(LIBS ${UTILS_LIBRARY} ${NEWIMAGE_LIBRARY} ${FSLIO_LIBRARY} ${MISCMATHS_LIBRARY} ${NIFTIIO_LIBRARY} ${ZNZ_LIBRARY} ${Z_LIBRARY} ${NEWMAT_LIBRARY})
+
+Message("-- Using libznz: ${ZNZ_LIBRARY}")
+Message("-- Using miscmaths: ${MISCMATHS_LIBRARY}")
+Message("-- Using fslio: ${FSLIO_LIBRARY}")
+Message("-- Using newimage: ${NEWIMAGE_LIBRARY}")
+Message("-- Using niftiio: ${NIFTIIO_LIBRARY}")
+Message("-- Using newmat: ${NEWMAT_LIBRARY} ${NEWMAT_INCLUDE_DIR}")
+Message("-- Using newimage: ${NEWIMAGE_LIBRARY}")
+Message("-- Using zlib: ${Z_LIBRARY}")
+
+target_link_libraries(asl_file ${LIBS})
+include_directories(AFTER ${NEWMAT_INCLUDE_DIR} ${FSL_INCLUDE_DIR} ${FSL_EXT_INCLUDE_DIR})
+
+# Extract GIT revision for versioning
+execute_process(COMMAND
+  git describe --dirty
+  WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
+  OUTPUT_VARIABLE GIT_SHA1
+  ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+execute_process(COMMAND
+  git log -1 --format=%ad --date=local
+  WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
+  OUTPUT_VARIABLE GIT_DATE
+  ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+configure_file(oxford_asl.in oxford_asl @ONLY)
+configure_file(asl_calib.in asl_calib @ONLY)
+configure_file(asl_reg.in asl_reg @ONLY)
+configure_file(quasil.in quasil @ONLY)
+
+INSTALL(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/oxford_asl 
+        ${CMAKE_CURRENT_BINARY_DIR}/asl_calib
+	${CMAKE_CURRENT_BINARY_DIR}/asl_reg
+	${CMAKE_CURRENT_BINARY_DIR}/quasil
+	${CMAKE_CURRENT_BINARY_DIR}/asl_file
+	DESTINATION bin)
+