SyneRBI · KrisThielemans · May 11, 2023 · Jun 1, 2023 · Jun 1, 2023 · Jun 1, 2023
diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml
@@ -44,7 +44,12 @@ jobs:
           DEVEL_BUILD: "ON"
           EXTRA_BUILD_FLAGS: "-DUSE_ITK=ON"
           CMAKE_BUILD_TYPE: "Release"
-        # need to upgrade Gadgetron before we can enable gcc 10
+        - os: ubuntu-latest
+          compiler: gcc
+          compiler_version: 9
+          DEVEL_BUILD: "ON"
+          EXTRA_BUILD_FLAGS: "-DUSE_ITK=ON -DDISABLE_Gadgetron:BOOL=ON"
+          CMAKE_BUILD_TYPE: "Release"
         #- os: ubuntu-latest
         #  compiler: gcc
         #  compiler_version: 10

diff --git a/CHANGES.md b/CHANGES.md
@@ -1,7 +1,6 @@
 # ChangeLog
 
 ## v3.5.0
-* GitHub Action: remove temporarily the Ubuntu 20.04 build, #1178
 * MR
   - Re-designed handling of "irregular" ISMRMRD acquisitions, making it user-controlled and more flexible. See https://github.com/SyneRBI/SIRF/pull/1174 for more information
   - Allow user to set radial, goldenangle, spiral and rpe trajectories
@@ -14,6 +13,13 @@
 * C++
   - added `examples_data_path` and utility functions such as `append_path` in `common/utilities.h`
 
+* Other, including CMake files
+  - resolve dependencies such that DISABLE_Gadgetron works now
+  - split some C interfaces into separate libraries, i.e. cinterface-sirf and cinterface-Reg
+
+* GitHub Action:
+   - add a build with DISABLE_Gadgetron
+
 ## v3.4.0
 
 * MR:

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,7 +1,10 @@
 
 #========================================================================
 # Author: Kris Thielemans
-# Copyright 2016 - 2020 University College London
+# Author: Evgueni Ovtchinnikov
+# Author: Edoardo Pasca
+# Author: Richard Brown
+# Copyright 2016 - 2023 University College London
 # Copyright 2016 - 2020 Science Technology Facilities Council
 #
 #  Licensed under the Apache License, Version 2.0 (the "License");
@@ -40,7 +43,7 @@ option(DISABLE_Gadgetron "Disable building the SIRF interface to Gadgetron" OFF)
 if (NOT DISABLE_Gadgetron)
   set(default_CXX_version 17)
 else()
-  message(WARNING "Gadgetron not found. Set gadgetron_DIR if you do have it.")
+  message(STATUS "Gadgetron disabled.")
   set (default_CXX_version 11)
 endif()
 UseCXX(${default_CXX_version})

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -1,8 +1,9 @@
 
 #========================================================================
 # Author: Richard Brown, Kris Thielemans
-# Copyright 2016 - 2020 University College London
-# Copyright 2016 - 2020 Science Technology Facilities Council
+# Author: Evgueni Ovtchinnikov
+# Copyright 2016 - 2023 University College London
+# Copyright 2016 - 2023 Science Technology Facilities Council
 #
 #  Licensed under the Apache License, Version 2.0 (the "License");
 #  you may not use this file except in compliance with the License.
@@ -33,49 +34,13 @@ else()
   set(CMAKE_MODULE_PATH "${CMAKE_MODULE_PATH};${ISMRMRD_DIR}")
   find_package(FFTW3 COMPONENTS single REQUIRED)
   ADD_SUBDIRECTORY(xGadgetron)
-  set(SIRF_BUILT_WITH_ISMRMRD TRUE PARENT_SCOPE)
+  set(SIRF_BUILT_WITH_ISMRMRD TRUE) # set for directories "below"
+  set(SIRF_BUILT_WITH_ISMRMRD TRUE PARENT_SCOPE) # set for directory "above"
   set(ISMRMRD_VERSION ${ISMRMRD_VERSION} PARENT_SCOPE)
+  # TODO use target_compile_definitions
+  add_definitions(-DSIRF_BUILT_WITH_ISMRMRD)
 endif()
 
-
-
-##########################################################################
-#                             Registration                               #
-##########################################################################
-option(DISABLE_Registration "Disable building the SIRF registration package" OFF)
-if (DISABLE_Registration)
-  message(STATUS "Registration support disabled.")
-  set(SPM_BOOL_STR "0" PARENT_SCOPE)
-  set(SIRF_BUILT_WITH_REGISTRATION False PARENT_SCOPE)
-else()
-  FIND_PACKAGE(NIFTYREG 1.5.61 REQUIRED)
-  # NIFTYREG
-  FOREACH(NR_lib ${NIFTYREG_LIBRARIES})
-    find_library(${NR_lib}_full_path "${NR_lib}" "${NIFTYREG_LIBRARY_DIRS}")
-    if(NOT ${NR_lib}_full_path)
-      message(FATAL_ERROR "${NR_lib} not found")
-    endif()
-    SET(NR_libs_full_path "${NR_libs_full_path};${${NR_lib}_full_path}")
-  ENDFOREACH()
-  # If niftyreg was bulit with OpenMP
-  if (NIFTYREG_BUILT_WITH_OPENMP)
-    find_package(OpenMP REQUIRED)
-    if (OpenMP_CXX_FOUND)
-      SET(NR_libs_full_path "${NR_libs_full_path};OpenMP::OpenMP_CXX")
-    endif()
-  endif()
-  # If niftyreg was bulit with CUDA
-  if (NIFTYREG_BUILT_WITH_CUDA)
-    find_package(CUDA REQUIRED)
-    SET(NR_libs_full_path "${NR_libs_full_path};${CUDA_CUDA_LIBRARY};${CUDA_CUDART_LIBRARY}")
-  endif()
-  ADD_SUBDIRECTORY(Registration)
-  set(SPM_BOOL_STR ${SPM_BOOL_STR} PARENT_SCOPE)
-  set(SIRF_BUILT_WITH_REGISTRATION TRUE PARENT_SCOPE)
-endif()
-
-
-
 ##########################################################################
 #                                 STIR                                   #
 ##########################################################################
@@ -111,38 +76,76 @@ else()
     set(Parallelproj_BOOL_STR "0")
   endif()
   ADD_SUBDIRECTORY(xSTIR)
+  set(SIRF_BUILT_WITH_STIR TRUE)
   set(SIRF_BUILT_WITH_STIR TRUE PARENT_SCOPE)
   set(STIR_VERSION ${STIR_VERSION} PARENT_SCOPE)
+  # TODO use target_compile_definitions
+  add_definitions(-DSIRF_BUILT_WITH_STIR)
+
 endif()
 set(NiftyPET_BOOL_STR ${NiftyPET_BOOL_STR} PARENT_SCOPE)
 set(Parallelproj_BOOL_STR ${Parallelproj_BOOL_STR} PARENT_SCOPE)
 
 
 ##########################################################################
-#                             Synergistic                                #
+#                             Registration                               #
 ##########################################################################
-# Synergistic code currently only works if STIR (with ITK), ISMRMRD and Registration are built
-option(DISABLE_Synergistic "Disable building the synergistic code" OFF)
-if (DISABLE_Synergistic)
-  message(STATUS "Synergistic code disabled.")
+# Note:
+# The Python/MATLAB interface for Reg depends on STIR sadly, so STIR stuff
+# needs to come first. We could add some checks here to see if Registration should be
+# disabled, but we'll just check it in the cReg/CMakeLists.txt and leave it to the user
+# to either enable STIR or disable Registration.
+option(DISABLE_Registration "Disable building the SIRF registration package" OFF)
+if (DISABLE_Registration)
+  message(STATUS "Registration support disabled.")
+  set(SPM_BOOL_STR "0" PARENT_SCOPE)
+  set(SIRF_BUILT_WITH_REGISTRATION False PARENT_SCOPE)
 else()
-  if ((NOT DISABLE_STIR) AND (NOT DISABLE_Gadgetron) AND (NOT DISABLE_Registration) AND "${STIR_BUILT_WITH_ITK}")
-    MESSAGE(STATUS "Registration, ISMRMRD and STIR (with ITK) have been built. Building synergistic code.")
-    ADD_SUBDIRECTORY(Synergistic)
-  else()
-    MESSAGE(STATUS "One or more of the following components are missing: Registration, ISMRMRD and STIR (with ITK). Synergistic code will not be built.")
-    if (DISABLE_STIR)
-      MESSAGE(STATUS "STIR missing.")
-    elseif(NOT STIR_BUILT_WITH_ITK)
-      MESSAGE(STATUS "STIR not built with ITK.")
-    endif()
-    if (DISABLE_Gadgetron)
-      MESSAGE(STATUS "ISMRMRD missing.")
+  FIND_PACKAGE(NIFTYREG 1.5.61 REQUIRED)
+  # NIFTYREG
+  FOREACH(NR_lib ${NIFTYREG_LIBRARIES})
+    find_library(${NR_lib}_full_path "${NR_lib}" "${NIFTYREG_LIBRARY_DIRS}")
+    if(NOT ${NR_lib}_full_path)
+      message(FATAL_ERROR "${NR_lib} not found")
     endif()
-    if (DISABLE_Registration)
-      MESSAGE(STATUS "Registration missing.")
+    SET(NR_libs_full_path "${NR_libs_full_path};${${NR_lib}_full_path}")
+  ENDFOREACH()
+  # If niftyreg was bulit with OpenMP
+  if (NIFTYREG_BUILT_WITH_OPENMP)
+    find_package(OpenMP REQUIRED)
+    if (OpenMP_CXX_FOUND)
+      SET(NR_libs_full_path "${NR_libs_full_path};OpenMP::OpenMP_CXX")
     endif()
   endif()
+  # If niftyreg was bulit with CUDA
+  if (NIFTYREG_BUILT_WITH_CUDA)
+    find_package(CUDA REQUIRED)
+    SET(NR_libs_full_path "${NR_libs_full_path};${CUDA_CUDA_LIBRARY};${CUDA_CUDART_LIBRARY}")
+  endif()
+  ADD_SUBDIRECTORY(Registration)
+  set(SPM_BOOL_STR ${SPM_BOOL_STR} PARENT_SCOPE)
+  set(SIRF_BUILT_WITH_REGISTRATION TRUE)
+  set(SIRF_BUILT_WITH_REGISTRATION TRUE PARENT_SCOPE)
+  # TODO use target_compile_definitions
+  add_definitions(-DSIRF_BUILT_WITH_REGISTRATION)
+endif()
+
+
+##########################################################################
+#                             Synergistic                                #
+##########################################################################
+if (NOT BUILD_PYTHON AND NOT BUILD_MATLAB)
+  # Currently only offer to disable synergistic library when not using Python/MATLAB,
+  # as their ImageData.read depends on synergistic/ImageDataWrapper (TODO)
+  option(DISABLE_Synergistic "Disable building the synergistic code" OFF)
+else()
+  # DISABLE_Synergistic will be not set, which in CMake means it is equivalent to FALSE
+endif()
+
+if (DISABLE_Synergistic)
+  message(STATUS "Synergistic code disabled.")
+else()
+  ADD_SUBDIRECTORY(Synergistic)
 endif()
 
 ADD_SUBDIRECTORY(common)
diff --git a/src/Registration/cReg/CMakeLists.txt b/src/Registration/cReg/CMakeLists.txt
@@ -1,6 +1,9 @@
 #========================================================================
+# Author: Evgueni Ovtchinnikov
+# Author: Kris Thielemans
 # Author: Richard Brown
-# Copyright 2018 - 2020 University College London
+# Copyright 2018-2021, 2023 University College London
+# Copyright 2018-2023 Science Technology Facilities Council
 #
 #  Licensed under the Apache License, Version 2.0 (the "License");
 #  you may not use this file except in compliance with the License.
@@ -34,11 +37,6 @@ SET(SOURCES
   "NiftiImageData3DDeformation.cpp"
   "NiftiImageData3DDisplacement.cpp")
 
-# If we're also wrapping to python or matlab, include the c-files
-IF(BUILD_PYTHON OR BUILD_MATLAB)
-	SET(SOURCES ${SOURCES} "cReg.cpp" "cReg_p.cpp")
-ENDIF()
-
 # Add SPM source
 IF(SPM_FOUND)
   SET(SOURCES ${SOURCES} "SPMRegistration.cpp")
@@ -130,4 +128,13 @@ FOREACH(elem ${REG_executables})
     INSTALL(TARGETS ${elem} DESTINATION ${CMAKE_INSTALL_PREFIX}/bin)
 ENDFOREACH(elem ${REG_executables})
 
+IF(BUILD_PYTHON OR BUILD_MATLAB)
+  ADD_LIBRARY(cinterface-Reg cReg.cpp cReg_p.cpp)
+  # add dependencies. Note that cstir is required for deleteTextWriter sadly
+  if (NOT SIRF_BUILT_WITH_STIR)
+    message(FATAL_ERROR "Python/MATLAB interface for Registration currently depends on STIR.")
+  endif()
+  target_link_libraries(cinterface-Reg Reg cstir)
+endif()
+
 ADD_SUBDIRECTORY(tests)
diff --git a/src/Registration/cReg/cReg_p.cpp b/src/Registration/cReg/cReg_p.cpp
@@ -20,6 +20,7 @@ limitations under the License.
 */
 
 #include "sirf/iUtilities/DataHandle.h"
+#include "sirf/iUtilities/iutilities.h"
 #include "sirf/Reg/cReg_p.h"
 #include "sirf/Reg/NiftiImageData3D.h"
 #include "sirf/Reg/Registration.h"
@@ -33,13 +34,6 @@ limitations under the License.
 
 using namespace sirf;
 
-extern "C"
-char* charDataFromHandle(const void* ptr);
-extern "C"
-int intDataFromHandle(const void* ptr);
-extern "C"
-float floatDataFromHandle(const void* ptr);
-
 static void*
 parameterNotFound(const char* name, const char* file, int line) 
 {

diff --git a/src/Registration/cReg/include/sirf/Reg/NiftyResample.h b/src/Registration/cReg/include/sirf/Reg/NiftyResample.h
@@ -34,7 +34,6 @@ limitations under the License.
 #include <vector>
 #include <iostream>
 #include "sirf/Reg/Resample.h"
-#include "sirf/iUtilities/iutilities.h"
 
 namespace NiftyMoMo {
 class BSplineTransformation;

diff --git a/src/Registration/cReg/include/sirf/Reg/NiftyResampler.h b/src/Registration/cReg/include/sirf/Reg/NiftyResampler.h
@@ -34,7 +34,6 @@ limitations under the License.
 #include <vector>
 #include <iostream>
 #include "sirf/Reg/Resample.h"
-#include "sirf/iUtilities/iutilities.h"
 
 namespace NiftyMoMo {
 class BSplineTransformation;

diff --git a/src/Registration/cReg/include/sirf/Reg/Resample.h b/src/Registration/cReg/include/sirf/Reg/Resample.h
@@ -32,7 +32,6 @@ limitations under the License.
 #include <vector>
 #include <memory>
 #include "sirf/Reg/Transformation.h"
-#include "sirf/iUtilities/iutilities.h"
 
 namespace sirf {
 

diff --git a/src/Registration/mReg/CMakeLists.txt b/src/Registration/mReg/CMakeLists.txt
@@ -61,8 +61,8 @@ if(BUILD_MATLAB)
   target_include_directories(mreg PUBLIC ${Matlab_INCLUDE_DIRS})
   # fix output name and link flags
   SET_TARGET_PROPERTIES(mreg PROPERTIES
-        SUFFIX ".${MATLAB_MEX_EXT}" PREFIX "${MATLAB_PREFIX}") 
-  target_link_libraries(mreg Reg iutilities csirf cstir ${Matlab_LIBRARIES})
+        SUFFIX ".${MATLAB_MEX_EXT}" PREFIX "${MATLAB_PREFIX}")
+  target_link_libraries(mreg cinterface-Reg ${Matlab_LIBRARIES})
   INSTALL(TARGETS mreg DESTINATION "${MATLAB_DEST}")
   INSTALL(FILES ${mreg_h} DESTINATION "${MATLAB_DEST}")
   INSTALL(FILES ${SOURCES} DESTINATION "${MATLAB_DEST}/+sirf/+Reg")

diff --git a/src/Registration/mReg/printer.h b/src/Registration/mReg/printer.h
@@ -24,7 +24,7 @@ limitations under the License.
 
 #include "stir/TextWriter.h"
 
-class mexTextPrinter : public aTextWriter {
+class mexTextPrinter : public stir::aTextWriter {
 public:
 	virtual void write(const char* text) const {
         //mexPrintf("mexPrintf is called...\n");

diff --git a/src/Registration/pReg/CMakeLists.txt b/src/Registration/pReg/CMakeLists.txt
@@ -38,7 +38,7 @@ set(SWIG_MODULE_pyreg_EXTRA_DEPS "${cREG_INCLUDE_DIR}/sirf/Reg/cReg.h")
 
 SWIG_ADD_LIBRARY(pyreg LANGUAGE python TYPE MODULE SOURCES pyreg.i)
 TARGET_INCLUDE_DIRECTORIES(${SWIG_MODULE_pyreg_REAL_NAME} PUBLIC ${Python_INCLUDE_DIRS})
-SWIG_LINK_LIBRARIES(pyreg PUBLIC Reg ${Python_LIBRARIES})
+SWIG_LINK_LIBRARIES(pyreg PUBLIC cinterface-Reg ${Python_LIBRARIES})
 
 INSTALL(TARGETS ${SWIG_MODULE_pyreg_REAL_NAME} DESTINATION "${PYTHON_DEST}/sirf")
 INSTALL(FILES 

diff --git a/src/Synergistic/CMakeLists.txt b/src/Synergistic/CMakeLists.txt
@@ -20,15 +20,19 @@ SET(CMAKE_POSITION_INDEPENDENT_CODE True)
 
 # Executables
 SET(SYN_executables
+    sirf_convert_image_type
+    )
+if (SIRF_BUILT_WITH_REGISTRATION)
+list(APPEND SYN_executables
     sirf_registration
     sirf_do_images_match
     sirf_resample
-    sirf_convert_image_type
-    )
+)
+endif()
 
 FOREACH(elem ${SYN_executables})
     ADD_EXECUTABLE(${elem} ${elem}.cpp ${STIR_REGISTRIES})
-    TARGET_LINK_LIBRARIES(${elem} LINK_PUBLIC csirf iutilities cstir cgadgetron Reg)
+    TARGET_LINK_LIBRARIES(${elem} LINK_PUBLIC csirf csyn)
     INSTALL(TARGETS ${elem} DESTINATION ${CMAKE_INSTALL_PREFIX}/bin)
 ENDFOREACH(elem ${SYN_executables})
 

diff --git a/src/Synergistic/cSyn/CMakeLists.txt b/src/Synergistic/cSyn/CMakeLists.txt
@@ -28,7 +28,15 @@ target_include_directories(csyn PUBLIC
 target_include_directories(csyn PUBLIC
   "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>$<INSTALL_INTERFACE:include>"
   )
-target_link_libraries(csyn PUBLIC cgadgetron cstir Reg)
+if(SIRF_BUILT_WITH_ISMRMRD)
+  target_link_libraries(csyn PUBLIC cgadgetron)
+endif()
+if(SIRF_BUILT_WITH_STIR)
+  target_link_libraries(csyn PUBLIC cstir)
+endif()
+if(SIRF_BUILT_WITH_REGISTRATION)
+  target_link_libraries(csyn PUBLIC Reg)
+endif()
 target_compile_definitions(csyn PRIVATE WIN32_LEAN_AND_MEAN)
 
 install(DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/include/"

diff --git a/src/Synergistic/cSyn/include/sirf/Syn/utilities.h b/src/Synergistic/cSyn/include/sirf/Syn/utilities.h
@@ -29,8 +29,11 @@ limitations under the License.
 */
 
 #pragma once
-
+#include <string>
+#include <memory>
 namespace sirf {
+        class ImageData;
+
 	class ImageDataWrap {
 	public:
 		ImageDataWrap(const std::string &filename, const std::string &engine, bool verbose);