remove dependency on boost::thread

instances of boost::thread and boost::mutex are all replaced by std versions.
This means we don't need to link with boost::thread anymore.

This should reduce boost version conflicts, such as those in #429 and #241.

CMakeLists.txt

@@ -73,7 +73,7 @@ endif(APPLE)
 
 #### we need the boost library from boost.org
 set(BOOST_ROOT CACHE PATH "root of Boost")
-find_package(Boost 1.36.0 COMPONENTS system filesystem thread date_time chrono REQUIRED)
+find_package(Boost 1.36.0 COMPONENTS system filesystem REQUIRED)
 # For Visual Studio we have to disable the auto-linking feature of boost
 # where just including a boost file automatically adds it to the linker path.
 # Although this sounds great, it sadly breaks because of conflicting file-paths when linking etc etc.

src/xGadgetron/cGadgetron/CMakeLists.txt

@@ -17,7 +17,7 @@
 #
 #=========================================================================
 # Commented out, as this is now done at the top-level
-#find_package(Boost COMPONENTS system filesystem thread date_time chrono REQUIRED)
+#find_package(Boost COMPONENTS system filesystem REQUIRED)
 # For Visual Studio we have to disable the auto-linking feature of boost
 # where just including a boost file automatically adds it to the linker path.
 # Although this sounds great, it sadly breaks because of conflicting file-paths when linking etc etc.
@@ -28,7 +28,7 @@
 if (SIRF_INSTALL_DEPENDENCIES AND WIN32)
     set(Boost_DLL_DIR ${Boost_LIBRARY_DIR_RELEASE})
     message(STATUS "Install boost shared libraries from ${Boost_DLL_DIR} ")
-	foreach (__boost_lib system filesystem thread date_time chrono)
+	foreach (__boost_lib system filesystem)
 	   file(GLOB Boost_DLL "${Boost_DLL_DIR}/boost_${__boost_lib}*.dll")
        install( FILES ${Boost_DLL} DESTINATION bin )
 	endforeach()
@@ -50,13 +50,13 @@ target_link_libraries(cgadgetron iutilities csirf)
 if((CMAKE_VERSION VERSION_LESS 3.5.0) OR (NOT _Boost_IMPORTED_TARGETS))
   # This is harder than it should be on older CMake versions to be able to cope with
   # spaces in filenames.
-  foreach(C SYSTEM FILESYSTEM THREAD DATE_TIME CHRONO)
+  foreach(C SYSTEM FILESYSTEM)
     target_link_libraries(cgadgetron optimized "${Boost_${C}_LIBRARY_RELEASE}")
     target_link_libraries(cgadgetron debug  "${Boost_${C}_LIBRARY_DEBUG}")
   endforeach()
 else()
   # Nice and simple for recent CMake (which knows about your Boost version)
-  target_link_libraries(cgadgetron Boost::system Boost::filesystem Boost::thread Boost::date_time Boost::chrono)
+  target_link_libraries(cgadgetron Boost::system Boost::filesystem)
 endif()
 
 # Note: cannot use ISMRMRD_LIBRARIES on Windows as it generally contains 

src/xGadgetron/cGadgetron/cgadgetron.cpp

@@ -47,7 +47,7 @@ return NEW_OBJECT_HANDLE(G)
 #define NEW_GADGET_CHAIN(C) if (boost::iequals(name, C::class_name())) \
 return NEW_OBJECT_HANDLE(C)
 
-shared_ptr<boost::mutex> Mutex::sptr_mutex_;
+shared_ptr<std::mutex> Mutex::sptr_mutex_;
 
 static void*
 unknownObject(const char* obj, const char* name, const char* file, int line)
@@ -1237,7 +1237,7 @@ cGT_sendAcquisitions(void* ptr_con, void* ptr_dat)
 		GTConnector& conn = objectFromHandle<GTConnector>(h_con);
 		GadgetronClientConnector& con = conn();
 		Mutex mutex;
-		boost::mutex& mtx = mutex();
+		std::mutex& mtx = mutex();
 		ISMRMRD::Dataset& ismrmrd_dataset = 
 			objectFromHandle<ISMRMRD::Dataset>(h_dat);
 
@@ -1253,7 +1253,7 @@ cGT_sendAcquisitions(void* ptr_con, void* ptr_dat)
 		ISMRMRD::Acquisition acq_tmp;
 		for (uint32_t i = 0; i < acquisitions; i++) {
 			{
-				boost::mutex::scoped_lock scoped_lock(mtx);
+				std::unique_lock<std::mutex> scoped_lock(mtx);
 				ismrmrd_dataset.readAcquisition(i, acq_tmp);
 			}
 			con.send_ismrmrd_acquisition(acq_tmp);

src/xGadgetron/cGadgetron/gadgetron_client.cpp

@@ -160,7 +160,7 @@ GadgetronClientConnector::connect(std::string hostname, std::string port)
 		throw GadgetronClientException("Error connecting using socket.");
 
 	reader_thread_ =
-		boost::thread(boost::bind(&GadgetronClientConnector::read_task, this));
+		std::thread(&GadgetronClientConnector::read_task, this);
 }
 
 void 

src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadgetron_client.h

@@ -39,7 +39,6 @@ limitations under the License.
 #include <thread>
 
 #include <boost/asio.hpp>
-#include <boost/thread/thread.hpp>
 
 #include <ismrmrd/dataset.h>
 #include <ismrmrd/ismrmrd.h>
@@ -260,7 +259,7 @@ namespace sirf {
 
 		boost::asio::io_service io_service;
 		boost::asio::ip::tcp::socket* socket_;
-		boost::thread reader_thread_;
+		std::thread reader_thread_;
 		maptype readers_;
 		unsigned int timeout_ms_;
 	};

src/xGadgetron/cGadgetron/include/sirf/Gadgetron/xgadgetron_utilities.h

@@ -33,7 +33,7 @@ limitations under the License.
 #include <chrono>
 #include <complex>
 
-#include <boost/thread/mutex.hpp>
+#include <mutex>
 
 #include "sirf/Gadgetron/cgadgetron_shared_ptr.h"
 
@@ -106,11 +106,11 @@ namespace sirf {
 		{
 			init_();
 		}
-		boost::mutex& operator()()
+		std::mutex& operator()()
 		{
 			return *sptr_mutex_.get();
 		}
-		gadgetron::shared_ptr<boost::mutex> sptr()
+		gadgetron::shared_ptr<std::mutex> sptr()
 		{
 			return sptr_mutex_;
 		}
@@ -123,17 +123,17 @@ namespace sirf {
 			sptr_mutex_->unlock();
 		}
 	private:
-		static gadgetron::shared_ptr<boost::mutex> sptr_mutex_;
+		static gadgetron::shared_ptr<std::mutex> sptr_mutex_;
 		static void init_()
 		{
 			static bool initialized = false;
 			if (!initialized) {
-				sptr_mutex_ = gadgetron::shared_ptr<boost::mutex>(new boost::mutex);
+				sptr_mutex_ = gadgetron::shared_ptr<std::mutex>(new std::mutex);
 				initialized = true;
 			}
 		}
 	};
 
 }
 
-#endif
+#endif

src/xGadgetron/mGadgetron/CMakeLists.txt

@@ -18,7 +18,7 @@
 
 if(BUILD_MATLAB)
   #commented out as done at top-level
-  #find_package(Boost COMPONENTS system thread filesystem REQUIRED)
+  #find_package(Boost COMPONENTS system filesystem REQUIRED)
 
   set(CMAKE_POSITION_INDEPENDENT_CODE True)
 

src/xSTIR/cSTIR/CMakeLists.txt

@@ -29,17 +29,5 @@ target_include_directories(cstir PUBLIC "${STIR_INCLUDE_DIRS}")
 
 target_link_libraries(cstir csirf iutilities)
 target_link_libraries(cstir "${STIR_LIBRARIES}")
-# Add boost library dependencies
-if((CMAKE_VERSION VERSION_LESS 3.5.0) OR (NOT _Boost_IMPORTED_TARGETS))
-  # This is harder than it should be on older CMake versions to be able to cope with
-  # spaces in filenames.
-  foreach(C SYSTEM FILESYSTEM THREAD DATE_TIME CHRONO)
-    target_link_libraries(cstir optimized "${Boost_${C}_LIBRARY_RELEASE}")
-    target_link_libraries(cstir debug  "${Boost_${C}_LIBRARY_DEBUG}")
-  endforeach()
-else()
-  # Nice and simple for recent CMake (which knows about your Boost version)
-  target_link_libraries(cstir Boost::system Boost::filesystem Boost::thread Boost::date_time Boost::chrono)
-endif()
 
 ADD_SUBDIRECTORY(tests)