Support VTK 9.x

.github/workflows/portability.yml

@@ -30,6 +30,8 @@ jobs:
             extra-build-args: ""
           - image: chaste/runner:jammy.portability-05
             extra-build-args: ""
+          - image: chaste/runner:jammy.portability-06
+            extra-build-args: ""
           - image: chaste/runner:jammy.portability-03
             extra-build-args: "-DChaste_USE_CVODE=OFF -DChaste_USE_VTK=OFF"
 

CMakeLists.txt

@@ -194,6 +194,20 @@ if (WIN32 OR CYGWIN)
 endif (WIN32 OR CYGWIN)
 
 
+###############################################
+####  Create interface library for dependencies
+###############################################
+
+# See https://github.com/Chaste/Chaste/issues/36 re supporting VTK 9.x.
+#
+# Approach is to create a interface library (with no source files) that all Chaste dependencies are linked to. This
+# library is then linked against all Chaste libraries and executables.
+#
+# This allows modern CMake imported targets to be used for our dependencies, rather than populating lists of libaries
+# and include directories as we currently to. For now, this will only affect VTK 9.x, but should be expanded to all
+# dependencies in the future.
+add_library(Chaste_COMMON_DEPS INTERFACE)
+
 ################################
 #  FIND THIRD PARTY LIBRARIES  #
 ################################
@@ -322,33 +336,40 @@ if (Chaste_AUTO_INSTALL_DEPS)
     endforeach ()
 endif ()
 
-
 ################################
 ####  Find VTK
 ################################
 if (Chaste_USE_VTK)
-    # First pass will identify the version number
-    find_package (VTK REQUIRED)
-    message (STATUS "VTK version: ${VTK_MAJOR_VERSION}.${VTK_MINOR_VERSION}")
-
-    # Depending on the VTK version, we need different components. 5.x require the following
-    if (VTK_MAJOR_VERSION EQUAL 5)
-        find_package(VTK COMPONENTS vtkIO vtkCommon vtkGraphics z REQUIRED)
-        # 6.0 and 6.1 require the following
-    elseif ((VTK_MAJOR_VERSION EQUAL 6) AND (VTK_MINOR_VERSION LESS 2))
-        find_package(
-                VTK COMPONENTS vtkCommonCore vtkCommonDataModel vtkFiltersCore vtkFiltersGeneral vtkFiltersGeneric
-                vtkFiltersGeometry vtkFiltersModeling vtkFiltersSources vtkIOCore vtkIOGeometry vtkIOLegacy vtkIOXML
-                REQUIRED
-        )
-        # 6.2 and up, up to and including 8.x, require the following
-    elseif (VTK_MAJOR_VERSION LESS 9)
+    # The complexity here is for two reasons:
+    #   1. VTK has renamed its components several times
+    #   2. From VTK 9, a simple call to find_package(VTK) will try to find QT, which is not a Chaste dependency
+    #
+    # We first find the VTK common library, which can have one of two names: this will populate the VTK version
+    # number. This is then used to find the specific list of required VTK components.
+
+    # List of possible base modules across different VTK versions
+    set(POSSIBLE_VTK_BASE_MODULES vtkCommonCore CommonCore)
+
+    foreach (BASE_MODULE ${POSSIBLE_VTK_BASE_MODULES})
+        find_package(VTK COMPONENTS ${BASE_MODULE} QUIET)
+        if (VTK_FOUND)
+            message (STATUS "VTK version: ${VTK_MAJOR_VERSION}.${VTK_MINOR_VERSION}")
+            break()
+        endif ()
+    endforeach ()
+
+    if (NOT ${VTK_FOUND})
+        message(FATAL_ERROR "Did not find VTK")
+    endif ()
+
+    # Depending on the VTK version, we need different components.
+    if (VTK_MAJOR_VERSION LESS 9)
         find_package(
                 VTK COMPONENTS vtkCommonCore vtkCommonDataModel vtkFiltersCore vtkFiltersGeneral vtkFiltersGeneric
                 vtkFiltersGeometry vtkFiltersModeling vtkFiltersSources vtkIOCore vtkIOGeometry vtkIOLegacy
                 vtkIOParallelXML vtkIOXML REQUIRED
         )
-        # VTK 9.0 and above require the following
+    # VTK 9.0 and above require the following
     else ()
         find_package(
                 VTK COMPONENTS CommonCore CommonDataModel FiltersCore FiltersGeneral FiltersGeneric FiltersGeometry
@@ -503,8 +524,12 @@ list (APPEND Chaste_LINK_LIBRARIES "${MPI_CXX_LIBRARIES}")
 
 # make sure VTK libraries added after HDF5 so VTK's link with HDF5 isn't used
 if (Chaste_USE_VTK)
-    list (APPEND Chaste_INCLUDES "${VTK_INCLUDE_DIRS}")
-    list (APPEND Chaste_LINK_LIBRARIES "${VTK_LIBRARIES}")
+    if (VTK_MAJOR_VERSION LESS 9)
+        list(APPEND Chaste_INCLUDES "${VTK_INCLUDE_DIRS}")
+        list(APPEND Chaste_LINK_LIBRARIES "${VTK_LIBRARIES}")
+    else ()
+        target_link_libraries(Chaste_COMMON_DEPS INTERFACE ${VTK_LIBRARIES})
+    endif ()
 endif ()
 
 

cell_based/test/population/TestVertexBasedCellPopulation.hpp

@@ -1607,7 +1607,7 @@ class TestVertexBasedCellPopulation : public AbstractCellBasedTestSuite
         TS_ASSERT(vtk_file.Exists());
 
         // Check that we have 144 (6*4*6) edges and 68 cells
-        ifstream vtk_file_stream;
+        std::ifstream vtk_file_stream;
         vtk_file_stream.open (vtk_file.GetAbsolutePath());
         std::stringstream vtk_file_string_buffer;
         vtk_file_string_buffer << vtk_file_stream.rdbuf();
@@ -1678,7 +1678,7 @@ class TestVertexBasedCellPopulation : public AbstractCellBasedTestSuite
         TS_ASSERT(vtk_file.Exists());
 
         // Check that we have 144 (6*4*6) edges and 68 cells
-        ifstream vtk_file_stream;
+        std::ifstream vtk_file_stream;
         vtk_file_stream.open (vtk_file.GetAbsolutePath());
         std::stringstream vtk_file_string_buffer;
         vtk_file_string_buffer << vtk_file_stream.rdbuf();

cmake/Modules/ChasteMacros.cmake

@@ -147,6 +147,7 @@ macro(Chaste_ADD_TEST _testTargetName _filename)
             set_source_files_properties("${_test_real_output_filename}" PROPERTIES GENERATED true)
 
             add_executable(${exeTargetName} "${_test_real_output_filename}" ${_filename} ${ARGN})
+            target_link_libraries(${exeTargetName} PRIVATE Chaste_COMMON_DEPS)
         endif()
 
         set(test_exe $<TARGET_FILE:${exeTargetName}>)
@@ -318,6 +319,7 @@ macro(Chaste_DO_COMMON component)
     # Make component library, if component contains any source files
     if (NOT Chaste_${component}_SOURCES STREQUAL "")
         add_library(chaste_${component} ${Chaste_${component}_SOURCES} ${ARGN})
+        target_link_libraries(chaste_${component} PRIVATE Chaste_COMMON_DEPS)
         if (BUILD_SHARED_LIBS)
             target_link_libraries(chaste_${component} LINK_PUBLIC ${Chaste_LIBRARIES})
             set(static_extension "a")
@@ -429,6 +431,7 @@ macro(Chaste_DO_APPS_COMMON component)
             set(component_library )
         endif()
         add_executable(${appName} ${app})
+        target_link_libraries(${appName} PRIVATE Chaste_COMMON_DEPS)
         #set_target_properties(${appName} PROPERTIES RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/src)
 
         if (NOT ${component} STREQUAL "")
@@ -528,6 +531,7 @@ macro(Chaste_DO_TEST_COMMON component)
     file(GLOB_RECURSE test_sources RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.cpp)
     if(test_sources)
         add_library(test${component} STATIC ${test_sources})
+        target_link_libraries(test${component} PRIVATE Chaste_COMMON_DEPS)
         set(COMPONENT_LIBRARIES ${COMPONENT_LIBRARIES} test${component})
     endif()
 

global/CMakeLists.txt

@@ -57,6 +57,7 @@ int main( )
 ")
 
 add_executable(timekeeper "${generate_dir}/timekeeper.cpp")
+target_link_libraries(timekeeper PRIVATE Chaste_COMMON_DEPS)
 
 ###################################################################
 #  Setup command to generate Version and BuildInfo at build-time  #

mesh/src/reader/VtkMeshReader.cpp

@@ -103,11 +103,16 @@ void VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::CommonConstructor()
         mVtkCellType = VTK_LINE;
     }
 
-    //Determine if we have multiple cell types - such as cable elements in addition to tets/triangles
+#if (VTK_MAJOR_VERSION >= 9 && VTK_MINOR_VERSION >= 2)
+    const auto num_distinct_cell_types = static_cast<unsigned>(mpVtkUnstructuredGrid->GetDistinctCellTypesArray()->GetNumberOfTuples());
+#else  // VTK older than 9.2
     vtkCellTypes* cell_types = vtkCellTypes::New();
     mpVtkUnstructuredGrid->GetCellTypes(cell_types);
+    const auto num_distinct_cell_types = static_cast<unsigned>(cell_types->GetNumberOfTypes());
+    cell_types->Delete();
+#endif
 
-    if (cell_types->GetNumberOfTypes() > 1)
+    if (num_distinct_cell_types > 1u)
     {
         mNumCableElementAttributes = 1;
         for (unsigned cell_id = 0; cell_id < num_cells; ++cell_id)
@@ -133,9 +138,6 @@ void VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::CommonConstructor()
         mNumElements = num_cells;
     }
 
-    cell_types->Delete();
-
-
     // Extract the surface faces
     if (ELEMENT_DIM == 2u)
     {

mesh/test/reader/TestVtkMeshReader.hpp

@@ -73,7 +73,18 @@ typedef VtkMeshReader<3,3> MESH_READER3;
 
 class TestVtkMeshReader : public CxxTest::TestSuite
 {
-//Requires  "sudo aptitude install libvtk5-dev" or similar
+private:
+    bool IsRotation(const std::vector<unsigned>& sequence, const std::vector<unsigned>& target)
+    {
+        // Double the input sequence
+        std::vector<unsigned> doubled_sequence = sequence;
+        doubled_sequence.insert(doubled_sequence.end(), sequence.begin(), sequence.end());
+
+        // Search for the target sequence in the doubled sequence
+        return std::search(doubled_sequence.begin(), doubled_sequence.end(), target.begin(), target.end()) != doubled_sequence.end();
+    }
+
+    //Requires  "sudo aptitude install libvtk5-dev" or similar
 public:
 
     /**
@@ -202,27 +213,24 @@ class TestVtkMeshReader : public CxxTest::TestSuite
         TS_ASSERT_EQUALS(mesh_reader.GetNumFaces(), 20u);
         TS_ASSERT_EQUALS(mesh_reader.GetNumEdges(), 20u);
 
+        // We don't care which order the nodes are in the face data, as long as they are correct up to a rotation.
+        // For instance, here, first_face_data.NodeIndices could either be {11, 3, 0}, {0, 11, 3} or {3, 0, 11}.
+        // VTK 9.2 started producing a different ordering, which necessitated updating this test.
+        // See https://github.com/Chaste/Chaste/issues/36
+
         ElementData first_face_data = mesh_reader.GetNextFaceData();
-        TS_ASSERT_EQUALS(first_face_data.NodeIndices[0], 11u);
-        TS_ASSERT_EQUALS(first_face_data.NodeIndices[1], 3u);
-        TS_ASSERT_EQUALS(first_face_data.NodeIndices[2], 0u);
+        TS_ASSERT(IsRotation(first_face_data.NodeIndices, {11u, 3u, 0u}))
 
         ElementData next_face_data = mesh_reader.GetNextFaceData();
-        TS_ASSERT_EQUALS(next_face_data.NodeIndices[0], 3u);
-        TS_ASSERT_EQUALS(next_face_data.NodeIndices[1], 8u);
-        TS_ASSERT_EQUALS(next_face_data.NodeIndices[2], 0u);
+        TS_ASSERT(IsRotation(next_face_data.NodeIndices, {3u, 8u, 0u}))
 
         mesh_reader.Reset();
 
         first_face_data = mesh_reader.GetNextEdgeData();
-        TS_ASSERT_EQUALS(first_face_data.NodeIndices[0], 11u);
-        TS_ASSERT_EQUALS(first_face_data.NodeIndices[1], 3u);
-        TS_ASSERT_EQUALS(first_face_data.NodeIndices[2], 0u);
+        TS_ASSERT(IsRotation(first_face_data.NodeIndices, {11u, 3u, 0u}))
 
         next_face_data = mesh_reader.GetNextEdgeData();
-        TS_ASSERT_EQUALS(next_face_data.NodeIndices[0], 3u);
-        TS_ASSERT_EQUALS(next_face_data.NodeIndices[1], 8u);
-        TS_ASSERT_EQUALS(next_face_data.NodeIndices[2], 0u);
+        TS_ASSERT(IsRotation(next_face_data.NodeIndices, {3u, 8u, 0u}))
 
         for (unsigned face=2; face<mesh_reader.GetNumFaces(); face++)
         {