reorganise to cope with DISABLE_*

The synergistic library/executables/tests have now been adapted for DISABLE_Gadgetron etc. The work-around in common/utilities.* has therefore been removed. a job with DISABLE_Gadgetron has been added to GHA Fixes SyneRBI#622
KrisThielemans · May 11, 2023 · 4f97a0b · 4f97a0b
1 parent 802227f
commit 4f97a0b
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Showing 19 changed files with 119 additions and 247 deletions.
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/CMakeLists.txt b/CMakeLists.txt
@@ -40,7 +40,7 @@ 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/data b/data
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -33,8 +33,11 @@ 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()
 
 
@@ -71,7 +74,10 @@ else()
   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()
 
 
@@ -111,38 +117,26 @@ 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                                #
 ##########################################################################
 # Synergistic code currently only works if STIR (with ITK), ISMRMRD and Registration are built
+# Currently cannot do this as ImageData.read depends on synergistic/ImageDataWrapper
 option(DISABLE_Synergistic "Disable building the synergistic code" OFF)
 if (DISABLE_Synergistic)
   message(STATUS "Synergistic code disabled.")
 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.")
-    endif()
-    if (DISABLE_Registration)
-      MESSAGE(STATUS "Registration missing.")
-    endif()
-  endif()
+  ADD_SUBDIRECTORY(Synergistic)
 endif()
 
 ADD_SUBDIRECTORY(common)
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);

diff --git a/src/Synergistic/cSyn/tests/CMakeLists.txt b/src/Synergistic/cSyn/tests/CMakeLists.txt
@@ -16,18 +16,23 @@
 #
 #=========================================================================
 
-SET(CMAKE_POSITION_INDEPENDENT_CODE True)
 
+if (SIRF_BUILT_WITH_REGISTRATION)
 ADD_EXECUTABLE(test_conv_img test_conv_img.cpp ${STIR_REGISTRIES})
 TARGET_LINK_LIBRARIES(test_conv_img LINK_PUBLIC cgadgetron csirf iutilities cstir Reg csyn)
 INSTALL(TARGETS test_conv_img DESTINATION ${CMAKE_INSTALL_PREFIX}/bin)
 
 set(MR_vendor_dicom_as_nifti "${CMAKE_SOURCE_DIR}/data/examples/MR/zenodo/dicom_as_nifti.nii")
 set(MR_SIRF_recon "${CMAKE_SOURCE_DIR}/data/examples/MR/zenodo/SIRF_recon.h5")
 
+if (SIRF_BUILT_WITH_STIR)
 ADD_TEST(NAME SYN_TEST_STIR_TO_NIFTI_CPLUSPLUS 
 	COMMAND test_conv_img ${MR_vendor_dicom_as_nifti} "STIR" "Reg"
 	WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+endif()
+if (SIRF_BUILT_WITH_ISMRMRD)
 ADD_TEST(NAME SYN_TEST_GADGETRON_TO_NIFTI_CPLUSPLUS 
 	COMMAND test_conv_img ${MR_SIRF_recon} "Gadgetron" "Reg"
 	WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+endif()
+endif()
diff --git a/src/Synergistic/cSyn/tests/test_conv_img.cpp b/src/Synergistic/cSyn/tests/test_conv_img.cpp
@@ -22,8 +22,6 @@ limitations under the License.
 #include <iostream>
 #include <string>
 
-#include "sirf/Gadgetron/gadgetron_data_containers.h"
-#include "sirf/STIR/stir_data_containers.h"
 #include "sirf/Reg/NiftiImageData3D.h"
 #include "sirf/Syn/utilities.h"
 
@@ -57,4 +55,4 @@ int main(int argc, char* argv[])
 	else
 		std::cout << "engine " << eng_out << " not supported yet\n";
 	return 1;
-}
+}
diff --git a/src/Synergistic/cSyn/utilities.cpp b/src/Synergistic/cSyn/utilities.cpp
@@ -1,7 +1,7 @@
 /*
 SyneRBI Synergistic Image Reconstruction Framework (SIRF)
 Copyright 2020 Rutherford Appleton Laboratory STFC
-Copyright 2020 University College London
+Copyright 2020, 2023 University College London
 
 This is software developed for the Collaborative Computational
 Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR)
@@ -26,34 +26,48 @@ limitations under the License.
 
 \author Richard Brown
 \author Evgueni Ovtchinnikov
+\author Kris Thielemans
 \author SyneRBI
 */
 
+#ifdef SIRF_BUILT_WITH_ISMRMRD
 #include "sirf/Gadgetron/gadgetron_data_containers.h"
+#endif
+#ifdef SIRF_BUILT_WITH_STIR
 #include "sirf/STIR/stir_data_containers.h"
+#endif
+#ifdef SIRF_BUILT_WITH_REGISTRATION
 #include "sirf/Reg/NiftiImageData3D.h"
+#endif
 #include "sirf/Syn/utilities.h"
 
 using namespace sirf;
 
 ImageDataWrap::ImageDataWrap(const std::string &filename, const std::string &engine, bool verbose)
 {
+  img_sptr_ = 0;
+#ifdef SIRF_BUILT_WITH_REGISTRATION
     if (strcmp(engine.c_str(), "Reg") == 0) {
         std::shared_ptr<NiftiImageData<float> > nifti_sptr = 
 		std::make_shared<NiftiImageData3D<float> >(filename);
         if (verbose) nifti_sptr->print_header();
         img_sptr_ = nifti_sptr;
     }
-    else if (strcmp(engine.c_str(), "STIR") == 0) {
+#endif
+#ifdef SIRF_BUILT_WITH_STIR
+    if (strcmp(engine.c_str(), "STIR") == 0) {
         img_sptr_ = std::make_shared<STIRImageData>(filename);
     }
-    else if (strcmp(engine.c_str(), "Gadgetron") == 0) {
+#endif
+#ifdef SIRF_BUILT_WITH_ISMRMRD
+    if (strcmp(engine.c_str(), "Gadgetron") == 0) {
         std::shared_ptr<GadgetronImagesVector> gadgetron_sptr(new GadgetronImagesVector);
 		gadgetron_sptr->read(filename);
         if (verbose) gadgetron_sptr->print_header(0);
         img_sptr_ = gadgetron_sptr;
     }
-    else
+#endif
+    if (!img_sptr_)
         throw std::runtime_error("unknown engine - " + engine + ".\n");
 
     // If verbose print geom info

diff --git a/src/Synergistic/sirf_convert_image_type.cpp b/src/Synergistic/sirf_convert_image_type.cpp
@@ -27,65 +27,56 @@ limitations under the License.
 \author SyneRBI
 */
 
+#include "sirf/Syn/utilities.h"
+#ifdef SIRF_BUILT_WITH_REGISTRATION
 #include "sirf/Reg/NiftiImageData3D.h"
+#endif
+#ifdef SIRF_BUILT_WITH_ISMRMRD
 #include "sirf/Gadgetron/gadgetron_data_containers.h"
+#endif
+#ifdef SIRF_BUILT_WITH_STIR
 #include "sirf/STIR/stir_data_containers.h"
+#endif
 
 using namespace sirf;
 
 static const std::shared_ptr<ImageData> image_as_sptr(const std::string &filename, const std::string &engine, const bool verbose)
 {
-    std::shared_ptr<ImageData> img_sptr;
-
-    if (strcmp(engine.c_str(), "Reg") == 0) {
-        std::shared_ptr<NiftiImageData<float> > nifti_sptr = std::make_shared<NiftiImageData3D<float> >(filename);
-        if (verbose) nifti_sptr->print_header();
-        img_sptr = nifti_sptr;
-    }
-    else if (strcmp(engine.c_str(), "STIR") == 0) {
-        img_sptr = std::make_shared<STIRImageData>(filename);
-    }
-
-    else if (strcmp(engine.c_str(), "Gadgetron") == 0) {
-        std::shared_ptr<GadgetronImagesVector> gadgetron_sptr(new GadgetronImagesVector);
-		gadgetron_sptr->read(filename);
-        if (verbose) gadgetron_sptr->print_header(0);
-        img_sptr = gadgetron_sptr;
-    }
-    else
-        throw std::runtime_error("unknown engine - " + engine + ".\n");
-
-    // If verbose print geom info
-    if (verbose) img_sptr->get_geom_info_sptr()->print_info();
-
-    // return
-    return img_sptr;
+  ImageDataWrap i(filename, engine, verbose);
+  return i.data_sptr();
 }
 
 static void convert_and_write_image(const std::string &filename, const std::string &engine, const std::shared_ptr<ImageData> &in_img_sptr, const std::string &param_file, const bool verbose)
 {
+#ifdef SIRF_BUILT_WITH_REGISTRATION
     if (strcmp(engine.c_str(), "Reg") == 0) {
         NiftiImageData<float> im(*in_img_sptr);
         im.write(filename);
         if (verbose) {
             im.print_header();
             im.get_geom_info_sptr()->print_info();
         }
+        return;
     }
-    else if (strcmp(engine.c_str(), "STIR") == 0) {
+#endif
+#ifdef SIRF_BUILT_WITH_STIR
+    if (strcmp(engine.c_str(), "STIR") == 0) {
         STIRImageData im(*in_img_sptr);
         if (param_file.empty())
             im.write(filename);
         else
             im.write(filename,param_file);
         if (verbose)
             im.get_geom_info_sptr()->print_info();
+        return;
     }
-    else if (strcmp(engine.c_str(), "Gadgetron") == 0) {
+#endif
+#ifdef SIRF_BUILT_WITH_ISMRMRD
+    if (strcmp(engine.c_str(), "Gadgetron") == 0) {
         throw std::runtime_error("Converter to GadgetronImagesVector not yet implemented.\n");
     }
-    else
-        throw std::runtime_error("unknown engine - " + engine + ".\n");
+#endif
+    throw std::runtime_error("unknown engine - " + engine + ".\n");
 }
 
 /// print usage

diff --git a/src/Synergistic/sirf_do_images_match.cpp b/src/Synergistic/sirf_do_images_match.cpp
@@ -28,25 +28,18 @@ limitations under the License.
 */
 
 #include "sirf/Reg/NiftiImageData3D.h"
-#include "sirf/Gadgetron/gadgetron_data_containers.h"
-#include "sirf/STIR/stir_data_containers.h"
-
+#include "sirf/Syn/utilities.h"
+#include <memory>
 
 using namespace sirf;
 
 static std::shared_ptr<const NiftiImageData3D<float> > image_as_sptr(const std::string &filename, const std::string &engine)
 {
-    if (strcmp(engine.c_str(), "Nifti") == 0)
-        return std::make_shared<const NiftiImageData3D<float> >(filename);
-    else if (strcmp(engine.c_str(), "STIR") == 0)
-        return std::make_shared<const NiftiImageData3D<float> >(STIRImageData(filename));
-    else if (strcmp(engine.c_str(), "Gadgetron") == 0) {
-        std::shared_ptr<GadgetronImageData> sptr_img(new GadgetronImagesVector);
-		sptr_img->read(filename);
-        return std::make_shared<const NiftiImageData3D<float> >(*sptr_img);
-    }
-    else
-        throw std::runtime_error("unknown engine - " + engine + ".\n");
+  ImageDataWrap i(filename, engine, false);
+  if (auto cast_sptr = std::dynamic_pointer_cast<NiftiImageData3D<float>>(i.data_sptr()))
+    return cast_sptr;
+  else
+    return std::make_shared<const NiftiImageData3D<float> >(i.data());
 }
 
 /// print usage