Merge pull request #784 from gadgetron/4.1

4.1
gadgetron · Nov 26, 2019 · 00b158c · 00b158c
2 parents edc0ca2 + 03ec874
commit 00b158c
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Showing 208 changed files with 2,604 additions and 11,426 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -6,22 +6,7 @@ else ()
     cmake_policy(VERSION 3.12)
 endif ()
 
-foreach (p
-        CMP0022
-        CMP0025 # CMake 3.0 Compiler id for Apple Clang is now ``AppleClang``.
-        CMP0042 # CMake 3.0 ``MACOSX_RPATH`` is enabled by default.
-        CMP0046 # CMake 3.0 Error on non-existent dependency in add_dependencies.
-        CMP0054 # CMake 3.1 Only interpret ``if()`` arguments as variables or keywords when unquoted.
-        CMP0056 # CMake 3.2 Honor link flags in ``try_compile()`` source-file signature.
-        CMP0058 # CMake 3.3 Ninja requires custom command byproducts to be explicit.
-        )
-    if (POLICY ${p})
-        cmake_policy(SET ${p} NEW)
-    endif ()
-endforeach ()
-
-project(GADGETRON
-        LANGUAGES CXX C)
+project(GADGETRON LANGUAGES CXX C)
 
 find_program(CCACHE_FOUND ccache)
 if (CCACHE_FOUND)
@@ -67,7 +52,7 @@ endif ()
 
 #VERSIONING AND INSTALL PATHS
 set(GADGETRON_VERSION_MAJOR 4)
-set(GADGETRON_VERSION_MINOR 0)
+set(GADGETRON_VERSION_MINOR 1)
 set(GADGETRON_VERSION_PATCH 0)
 set(GADGETRON_VERSION_STRING ${GADGETRON_VERSION_MAJOR}.${GADGETRON_VERSION_MINOR}.${GADGETRON_VERSION_PATCH})
 set(GADGETRON_SOVERSION ${GADGETRON_VERSION_MAJOR}.${GADGETRON_VERSION_MINOR})
@@ -86,7 +71,6 @@ else ()
 endif ()
 set(GADGETRON_INSTALL_CMAKE_PATH share/gadgetron/cmake)
 set(GADGETRON_INSTALL_CONFIG_PATH share/gadgetron/config)
-set(GADGETRON_INSTALL_MATLAB_PATH share/gadgetron/matlab)
 set(GADGETRON_INSTALL_PYTHON_MODULE_PATH share/gadgetron/python)
 set(GADGETRON_INSTALL_SCHEMA_PATH share/gadgetron/schema)
 set(GADGETRON_INSTALL_INCLUDE_PATH include/gadgetron)
@@ -193,21 +177,16 @@ else ()
     if (COMPILER_SUPPORT_WNON_VIRTUAL)
         set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Werror=non-virtual-dtor")
     endif ()
-
-#    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wl,--enable-new-dtags")
-
-
 endif ()
 
-
 # whether to suppress compilation warnings
 option(BUILD_SUPPRESS_WARNINGS "Build package while suppressing warnings" Off)
 if (BUILD_SUPPRESS_WARNINGS)
-if (WIN32)
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /W0")
-elseif (WIN32)
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -w")
-endif ()
+    if (WIN32)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /W0")
+    elseif (WIN32)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -w")
+    endif ()
 endif ()
 
 set(Boost_USE_STATIC_LIBS OFF)
@@ -216,9 +195,8 @@ set(Boost_USE_STATIC_RUNTIME OFF)
 # necessary for Windows and RHEL <=6 systems
 set(Boost_NO_BOOST_CMAKE ON)
 
-
 if(WIN32)
-add_definitions( -DHAVE_SNPRINTF) #Python decides to overwrite snprintf if this is not defined, because ofcourse it does. 
+add_definitions( -DHAVE_SNPRINTF) #Python decides to overwrite snprintf if this is not defined, because ofcourse it does.
 endif()
 # We actually only use system and thread explicitly, but they require linking in date_time and chrono
 if (WIN32)
@@ -278,33 +256,35 @@ endif ()
 
 find_package(GTest)
 
-
 find_package(Armadillo REQUIRED )
-# check whether ILP64 MKL should is used
 add_library(armadillo INTERFACE)
 set_property(TARGET armadillo PROPERTY INTERFACE_INCLUDE_DIRECTORIES ${ARMADILLO_INCLUDE_DIR})
-add_definitions( -DARMA_DONT_USE_WRAPPER)
+add_definitions(-DARMA_DONT_USE_WRAPPER)
 
 find_package(PugiXML REQUIRED)
 find_package(ISMRMRD REQUIRED)
 
 link_directories(${ISMRMRD_LIBRARY_DIRS})
 if (CUDA_FOUND AND USE_CUDA)
 # bart needs cuda
-find_package(BART)
+    find_package(BART)
 endif()
+
+find_package(FFTW3 REQUIRED COMPONENTS single double)
 add_library(FFTW INTERFACE)
- find_package(FFTW3 REQUIRED COMPONENTS single double)
 target_link_libraries(FFTW INTERFACE ${FFTW3_LIBRARIES})
 set_property(TARGET FFTW PROPERTY INTERFACE_LINK_DIRECTORIES ${FFTW3_INCLUDE_DIR})
 
 option(USE_MKL OFF)
 if (USE_MKL)
-  find_package(MKL REQUIRED)
-  add_library(BLAS INTERFACE IMPORTED)
-  set_property(TARGET BLAS PROPERTY INTERFACE_INCLUDE_DIRECTORIES ${MKL_INCLUDE_DIR})
-  set_property(TARGET BLAS PROPERTY INTERFACE_LINK_DIRECTORIES ${MKL_LIB_DIR})
-  set_property(TARGET BLAS PROPERTY INTERFACE_LINK_LIBRARIES ${MKL_LIBRARIES})
+    find_package(MKL REQUIRED)
+    add_library(BLAS INTERFACE IMPORTED)
+    set_property(TARGET BLAS PROPERTY INTERFACE_INCLUDE_DIRECTORIES ${MKL_INCLUDE_DIR})
+    set_property(TARGET BLAS PROPERTY INTERFACE_LINK_DIRECTORIES ${MKL_LIB_DIR})
+    set_property(TARGET BLAS PROPERTY INTERFACE_LINK_LIBRARIES ${MKL_LIBRARIES})
+
+
+
 
   add_definitions(-DUSE_MKL)
   else()
@@ -321,22 +301,16 @@ if (USE_MKL)
 
 endif()
 
-if (MKL_FOUND)
-if ( MKL_VERSION_STRING VERSION_LESS 11.2.0 )
-message(FATAL_ERROR "Gadgetron requires Intel MKL version >= 11.2.0")
-endif ()
-endif ()
-
 if(EXISTS $ENV{TORCH_HOME})
-find_package(Torch)
-if (TORCH_FOUND)
-add_definitions(-DUSE_TORCH)
-message("Find Pytorch c++ library at ${TORCH_LIBRARIES}")
-else()
-message("Do not find Pytorch c++ library")
-endif ()
+    find_package(Torch)
+    if (TORCH_FOUND)
+        add_definitions(-DUSE_TORCH)
+        message("Find Pytorch c++ library at ${TORCH_LIBRARIES}")
+    else()
+        message("Do not find Pytorch c++ library")
+    endif ()
 else()
-message("Do not find TORCH_HOME")
+    message("Do not find TORCH_HOME")
 endif()
 
 option(BUILD_PYTHON_SUPPORT "Build Python gadgets etc" On)
@@ -367,20 +341,6 @@ target_link_libraries(boost INTERFACE python)
 
 endif()
 
-option(BUILD_MATLAB_SUPPORT "Build of MATLAB gadgets etc" On)
-if (BUILD_MATLAB_SUPPORT)
-find_package(GMatlab)
-if (MATLAB_FOUND)
-add_definitions(-DUSE_MATLAB)
-else()
-set(BUILD_MATLAB_SUPPORT OFF)
-endif ()
-else()
-# explicitly set it, just in case BUILD_MATLAB_SUPPORT was set to OFF
-# after Matlab was already found.
-set(MATLAB_FOUND OFF)
-endif ()
-
 message("Searching for OpenGL, GLEW, GLUT, and Qt. These libraries are only used in a single standalone application and are thus non-essential.")
 if(WIN32)
 message("For Windows users in particular, for ease of installation we do not reccomend installing these libraries.")
@@ -404,15 +364,14 @@ message("Adding gpertools to build.")
 find_package(Gperftools REQUIRED)
 endif()
 
-#add_subdirectory(test)
+add_subdirectory(test)
 add_subdirectory(cmake)
+add_subdirectory(chroot)
 
-
-option(BUILD_DOCUMENTATION "Build Gadgetron documentation" Off)
-if (BUILD_DOCUMENTATION)
-add_subdirectory(doc)
+option(BUILD_DOCUMENTATION "Build Gadgetron documentation." Off)
+if(BUILD_DOCUMENTATION)
+    add_subdirectory(doc)
 endif()
-add_subdirectory(chroot)
 
 # install dependencies for WIN32
 if (WIN32)

diff --git a/apps/CMakeLists.txt b/apps/CMakeLists.txt
@@ -3,6 +3,3 @@ add_subdirectory(gadgetron)
 add_subdirectory(clients)
 add_subdirectory(standalone)
 
-if (MATLAB_FOUND )
-  add_subdirectory(matlab)
-endif ()
diff --git a/apps/clients/gadgetron_ismrmrd_client/gadgetron_ismrmrd_client.cpp b/apps/clients/gadgetron_ismrmrd_client/gadgetron_ismrmrd_client.cpp
@@ -1246,7 +1246,7 @@ class GadgetronClientConnector
         id.id = GADGET_MESSAGE_CONFIG_SCRIPT;
 
         GadgetMessageScript conf;
-        conf.script_length = (uint32_t)xml_string.size()+1;
+        conf.script_length = (uint32_t)xml_string.size();
 
         boost::asio::write(*socket_, boost::asio::buffer(&id, sizeof(GadgetMessageIdentifier)));
         boost::asio::write(*socket_, boost::asio::buffer(&conf, sizeof(GadgetMessageScript)));
@@ -1264,7 +1264,7 @@ class GadgetronClientConnector
         id.id = GADGET_MESSAGE_PARAMETER_SCRIPT;
 
         GadgetMessageScript conf;
-        conf.script_length = (uint32_t)xml_string.size()+1;
+        conf.script_length = (uint32_t)xml_string.size();
 
         boost::asio::write(*socket_, boost::asio::buffer(&id, sizeof(GadgetMessageIdentifier)));
         boost::asio::write(*socket_, boost::asio::buffer(&conf, sizeof(GadgetMessageScript)));

diff --git a/apps/gadgetron/Connection.cpp b/apps/gadgetron/Connection.cpp
@@ -18,8 +18,8 @@ namespace Gadgetron::Server::Connection {
 #if _WIN32 || !NDEBUG || GADGETRON_DISABLE_FORK
 
     void handle(
-            const Gadgetron::Core::Context::Paths& paths,
-            const Gadgetron::Core::Context::Args& args,
+            const Gadgetron::Core::StreamContext::Paths& paths,
+            const Gadgetron::Core::StreamContext::Args& args,
             std::unique_ptr<std::iostream> stream
     ) {
         auto thread = std::thread(handle_connection, std::move(stream), paths, args);
@@ -29,8 +29,8 @@ namespace Gadgetron::Server::Connection {
 #else
 
     void handle(
-            const Gadgetron::Core::Context::Paths& paths,
-            const Gadgetron::Core::Context::Args& args,
+            const Gadgetron::Core::StreamContext::Paths& paths,
+            const Gadgetron::Core::StreamContext::Args& args,
             std::unique_ptr<std::iostream> stream
     ) {
         auto pid = fork();

diff --git a/apps/gadgetron/Connection.h b/apps/gadgetron/Connection.h
@@ -7,8 +7,8 @@
 
 namespace Gadgetron::Server::Connection {
     void handle(
-            const Gadgetron::Core::Context::Paths &paths,
-            const Gadgetron::Core::Context::Args &args,
+            const Gadgetron::Core::StreamContext::Paths &paths,
+            const Gadgetron::Core::StreamContext::Args &args,
             std::unique_ptr<std::iostream> stream
     );
 }
diff --git a/apps/gadgetron/Server.cpp b/apps/gadgetron/Server.cpp
@@ -23,13 +23,18 @@ void Server::serve() {
 
     Gadgetron::Core::Context::Paths paths{args["home"].as<path>(), args["dir"].as<path>()};
 
-    boost::asio::io_service service;
+#if(BOOST_VERSION >= 107000)
+    boost::asio::io_context executor;
+#else
+    boost::asio::io_service executor;
+#endif
     boost::asio::ip::tcp::endpoint local(boost::asio::ip::tcp::v6(), args["port"].as<unsigned short>());
-    boost::asio::ip::tcp::acceptor acceptor(service, local);
+    boost::asio::ip::tcp::acceptor acceptor(executor, local);
+
     acceptor.set_option(boost::asio::socket_base::reuse_address(true));
 
     while(true) {
-        auto socket = std::make_unique<boost::asio::ip::tcp::socket>(service);
+        auto socket = std::make_unique<boost::asio::ip::tcp::socket>(executor);
         acceptor.accept(*socket);
 
         GINFO_STREAM("Accepted connection from: " << socket->remote_endpoint().address());

diff --git a/apps/gadgetron/connection/Config.cpp b/apps/gadgetron/connection/Config.cpp
@@ -6,11 +6,9 @@
 #include <memory>
 #include <string>
 
-#include <boost/parameter/name.hpp>
 #include <boost/range/algorithm/transform.hpp>
 #include <boost/range/algorithm/count_if.hpp>
 #include <boost/range/algorithm/find_if.hpp>
-#include <numeric>
 
 #include "log.h"
 
@@ -399,15 +397,6 @@ namespace {
         };
     }
 
-    bool is_legacy_matlab_gadget(const Config::Gadget &gadget) {
-        return gadget.dll == "gadgetron_matlab" && gadget.classname == "MatlabBufferGadget";
-    }
-
-    Config::Node transform_legacy_matlab_gadget(Config::Gadget gadget) {
-        GDEBUG_STREAM("Legacy Matlab Gadget detected: " << gadget.name);
-        throw std::runtime_error("Currently not implemented.");
-    }
-
     class Legacy : public Parser<LegacySource> {
     public:
 
@@ -433,7 +422,6 @@ namespace {
         const std::list<std::pair<std::function<bool(const Config::Gadget &)>,
                                   std::function<Config::Node(Config::Gadget)>>> node_transformations{
             std::make_pair(is_legacy_python_gadget, transform_legacy_python_gadget),
-            std::make_pair(is_legacy_matlab_gadget, transform_legacy_matlab_gadget),
             std::make_pair([](auto _) { return true; }, [=](auto c) { return Config::Node(c); })
         };
 
@@ -572,8 +560,13 @@ namespace {
             };
         }
 
+        static std::string address_or_localhost(const std::string &s) {
+            return s.empty() ? "localhost" : s;
+        }
+
         static Config::Connect parse_connect(const pugi::xml_node &connect_node) {
             return Config::Connect {
+                address_or_localhost(connect_node.attribute("address").value()),
                 connect_node.attribute("port").value()
             };
         }
@@ -627,7 +620,6 @@ namespace Gadgetron::Server::Connection {
         pugi::xml_document doc{};
         auto config_node = doc.append_child("configuration");
         config_node.append_child("version").text().set(2);
-
         XMLSerializer::add_readers(config.readers, config_node);
         XMLSerializer::add_writers(config.writers, config_node);
         XMLSerializer::add_node(config.stream, config_node);

diff --git a/apps/gadgetron/connection/Config.h b/apps/gadgetron/connection/Config.h
@@ -56,7 +56,7 @@ namespace Gadgetron::Server::Connection {
         };
 
         struct Connect {
-            std::string port;
+            std::string address, port;
         };
 
         using Action = Core::variant<Execute, Connect>;