[1.3.27] 2025-02-11

**Some experimental OpenMP parallelization has been added. This is not enabled by default yet, but can be turned on by setting the CMake option ENABLE_OPENMP to ON.** **Updates to core CMakeLists.txt to use more modern CMake features.** *Context* - Context::pruneTubeNodes() was added to allow for removal of part of a tube object. *Plant Architecture* - Added ground cherry weed model. - Minor fix in PlantArchitecture::getPlsantLeafInclinationAngleDistribution() to prevent rare out of range index. - Changed PlantArchitecture::getPlantLeafInclinationAngleDistribution() to area-weight the distribution, and removed the 'normalize' optional argument. - Added PlantArchitecture::prunBranch() method to remove all or part of a branch and its downstream branches. - Removed shoot parameter 'elongation_rate'. There is now an 'elongation_rate_max' shoot parameter that can be set by the user. The actual elongation rate can be reduced dynamically if the carbohydrate model is enabled. - Many updates to carbohydrate model. Credit to Ethan Frehner for these updates. *LiDAR* - Added exportTriangleAzimuthDistribution() to write the triangulated azimuthal angle distribution to a file. Credit to Alejandra Ponce de Leon for this addition. - The output distribution from exportTriangleInclinationDistribution() was not being normalized. *Radiation* - Added bindweed spectra to the default library. - There was an error in the writeObjectDataLabelMap() method that could cause undefined behavior if the UUID in the pixel label map did not exist in the Context. - There was an error in the writeObjectDataLabelMap() method where the primitive UUID was being used instead of the object ID. - There was an error in the model that could cause incorrect assignment of radiative properties if runBand() is called with fewer bands than a previous call to runBand(). - The previous version could cause unnecessary updating of radiative properties, resulting in a performance hit. This has been fixed. - Revised the radiation plug-in CMakeLists.txt to use a modern CMake approach for building CUDA source files. This update should also enable indexing of .cu source files in IDEs such as CLion. Co-authored-by: Alejandra Ponce de Leon <[email protected]> Co-authored-by: Ethan Frehner <[email protected]>
PlantSimulationLab · Feb 12, 2025 · 31feb26 · 31feb26
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commit 31feb26
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diff --git a/core/CMakeLists.txt b/core/CMakeLists.txt
@@ -2,30 +2,43 @@ cmake_minimum_required(VERSION 3.15)
 
 project(helios)
 
-include_directories(include)
-
 if(NOT DEFINED CMAKE_SUPPRESS_DEVELOPER_WARNINGS)
      set(CMAKE_SUPPRESS_DEVELOPER_WARNINGS 1 CACHE INTERNAL "No dev warnings")
 endif()
 
-add_library( helios STATIC ${CMAKE_CURRENT_SOURCE_DIR}/src/Context.cpp;${CMAKE_CURRENT_SOURCE_DIR}/src/Context_fileIO.cpp;${CMAKE_CURRENT_SOURCE_DIR}/src/Context_data.cpp;${CMAKE_CURRENT_SOURCE_DIR}/src/global.cpp;${CMAKE_CURRENT_SOURCE_DIR}/src/selfTest.cpp;${CMAKE_CURRENT_SOURCE_DIR}/src/pugixml.cpp )
-
+# Defining Helios Context source files to be built
+set(HELIOS_SOURCES
+        src/Context.cpp
+        src/Context_fileIO.cpp
+        src/Context_data.cpp
+        src/global.cpp
+        src/selfTest.cpp
+        src/pugixml.cpp
+)
+add_library(helios STATIC ${HELIOS_SOURCES})
+
+# Defining Helios Context include files
+target_include_directories(helios
+        PUBLIC
+        $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+        $<INSTALL_INTERFACE:include>
+)
+
+# External libraries
 include_directories( "${CMAKE_CURRENT_SOURCE_DIR}/lib/zlib")
-add_subdirectory( "${CMAKE_CURRENT_SOURCE_DIR}/lib/zlib" "${CMAKE_BINARY_DIR}/lib/zlib" )
-target_link_libraries( zlibstatic )
+add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/lib/zlib"     "${CMAKE_BINARY_DIR}/lib/zlib")
 
 include_directories( "${CMAKE_CURRENT_SOURCE_DIR}/lib/libpng")
-add_subdirectory( "${CMAKE_CURRENT_SOURCE_DIR}/lib/libpng" "${CMAKE_BINARY_DIR}/lib/libpng" )
+add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/lib/libpng"   "${CMAKE_BINARY_DIR}/lib/libpng")
 add_dependencies( png_static zlibstatic )
 
-target_link_libraries( helios png_static )
-
 include_directories("${CMAKE_BINARY_DIR}/lib/libjpeg-9a;${CMAKE_CURRENT_SOURCE_DIR}/lib/libjpeg-9a")
-add_subdirectory("lib/libjpeg-9a" "${CMAKE_BINARY_DIR}/lib/libjpeg-9a" )
-target_link_libraries( helios jpeg )
+add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/lib/libjpeg-9a" "${CMAKE_BINARY_DIR}/lib/libjpeg-9a")
+
+target_link_libraries( helios PRIVATE png_static  jpeg ) #note that zlib is already linked by libpng
 
 file( COPY "${CMAKE_CURRENT_SOURCE_DIR}/lib/images" DESTINATION "${CMAKE_BINARY_DIR}/lib/" )
 file( COPY "${CMAKE_CURRENT_SOURCE_DIR}/lib/models" DESTINATION "${CMAKE_BINARY_DIR}/lib/" )
 file( COPY "${CMAKE_CURRENT_SOURCE_DIR}/lib/testdata" DESTINATION "${CMAKE_BINARY_DIR}/lib/" )
 
-set( PLUGIN_INCLUDE_PATHS ${CMAKE_CURRENT_SOURCE_DIR}/include; PARENT_SCOPE )
+set( PLUGIN_INCLUDE_PATHS "${CMAKE_CURRENT_SOURCE_DIR}/include;" PARENT_SCOPE )
diff --git a/core/CMake_project.txt b/core/CMake_project.txt
@@ -1,7 +1,10 @@
+option(ENABLE_OPENMP "Enable building with OpenMP" OFF)
+
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
 if ( WIN32 )
-    SET(CMAKE_C_COMPILER_ID "MSVC")
-    SET(CMAKE_CXX_COMPILER_ID "MSVC")
-    SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /std:c++latest")
     string(REGEX REPLACE "/MD*" "/MT" CMAKE_C_FLAGS "${CMAKE_C_FLAGS}")
     string(REGEX REPLACE "/MD*" "/MT" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
     string(REGEX REPLACE "/W[0-4]" "/W1" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
@@ -13,15 +16,7 @@ if ( WIN32 )
         set( CMAKE_RUNTIME_OUTPUT_DIRECTORY_${OUTPUTCONFIG} "${CMAKE_BINARY_DIR}" )
         set( CMAKE_LIBRARY_OUTPUT_DIRECTORY_${OUTPUTCONFIG} "${CMAKE_BINARY_DIR}/lib" )
         set( CMAKE_ARCHIVE_OUTPUT_DIRECTORY_${OUTPUTCONFIG} "${CMAKE_BINARY_DIR}/lib" )
-    endforeach( OUTPUTCONFIG CMAKE_CONFIGURATION_TYPES )
-else()
-    SET(CMAKE_C_COMPILER_ID "GNU")
-    SET(CMAKE_CXX_COMPILER_ID "GNU")
-    SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++17")
-    if( CMAKE_BUILD_TYPE STREQUAL Debug )
-        SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g" )
-        SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g")
-    endif()
+    endforeach(OUTPUTCONFIG)
 endif()
 if( CMAKE_BUILD_TYPE STREQUAL Debug )
     SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DHELIOS_DEBUG" )
@@ -49,9 +44,31 @@ foreach(PLUGIN ${PLUGINS})
     endif()
     add_subdirectory( "${BASE_DIRECTORY}/plugins/${PLUGIN}" "${PROJECT_BINARY_DIR}/plugins/${PLUGIN}" )
     target_link_libraries( ${EXECUTABLE_NAME} ${PLUGIN} )
-    target_link_libraries( ${PLUGIN} helios )
+    if( NOT APPLE )
+        target_link_libraries( ${PLUGIN} helios )
+    endif()
 endforeach(PLUGIN)
 include_directories( "${PLUGIN_INCLUDE_PATHS};${CMAKE_CURRENT_SOURCE_DIRECTORY}" )
 
+if( ENABLE_OPENMP )
+    find_package(OpenMP)
+    if (OpenMP_CXX_FOUND)
+        message( "-- Enabling experimental OpenMP support" )
+        target_link_libraries(${EXECUTABLE_NAME} OpenMP::OpenMP_CXX)
+        target_compile_definitions(${EXECUTABLE_NAME} PRIVATE USE_OPENMP)
+        if ( WIN32 )
+            set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /openmp")
+        else()
+            set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp")
+        endif()
+    else()
+        if(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
+            message(WARNING "You are using Apple Clang compiler, which does not support OpenMP. The program will compile without OpenMP support.")
+        else()
+            message(WARNING "OpenMP not found! The program will compile without OpenMP support.")
+        endif()
+    endif()
+endif()
+
 enable_testing()
-add_test(Test0,"${EXECUTABLE_NAME}" "0")
+add_test(NAME Test0 COMMAND ${EXECUTABLE_NAME} 0)
diff --git a/core/include/Context.h b/core/include/Context.h
@@ -735,6 +735,12 @@ class Tube : public CompoundObject {
      */
     void setTubeNodes( const std::vector<helios::vec3> &node_xyz );
 
+    //! Remove a portion of the tube downstream of a specified node
+    /**
+     * \param[in] node_index Index of the tube segment node beyond which will be removed
+     */
+    void pruneTubeNodes( uint node_index );
+
 protected:
 
     std::vector<helios::vec3> nodes;
@@ -4793,6 +4799,13 @@ class Context{
      */
     void scaleTubeLength( uint ObjID, float scale_factor );
 
+    //! Remove a portion of the tube downstream of a specified node
+    /**
+     * \param[in] ObjID object ID of the Tube object
+     * \param[in] node_index Index of the tube segment node beyond which will be removed
+     */
+    void pruneTubeNodes( uint ObjID, uint node_index );
+
     //! Set tube vertex coordinates at each segment node
     /**
      * \param[in] ObjID object ID of the Tube object

diff --git a/core/include/global.h b/core/include/global.h
@@ -53,6 +53,10 @@ constexpr float PI_F = 3.14159265358979323846f;
 #include <iomanip>
 #include <filesystem>
 
+#ifdef USE_OPENMP
+#include <omp.h>
+#endif
+
 typedef unsigned int uint;
 
 #include "helios_vector_types.h"

diff --git a/core/src/Context.cpp b/core/src/Context.cpp
@@ -3913,6 +3913,33 @@ void Tube::setTubeNodes( const std::vector<helios::vec3> &node_xyz ){
 
 }
 
+void Tube::pruneTubeNodes( uint node_index ){
+
+    if( node_index >= nodes.size() ){
+        helios_runtime_error("ERROR (Tube::pruneTubeNodes): Node index of " + std::to_string(node_index) + " is out of bounds.");
+    }
+
+    if( node_index == 0 ){
+        context->deleteObject(this->OID);
+        return;
+    }
+
+    nodes.erase( nodes.begin() + node_index, nodes.end() );
+    triangle_vertices.erase( triangle_vertices.begin() + node_index, triangle_vertices.end() );
+    radius.erase( radius.begin() + node_index, radius.end() );
+    colors.erase( colors.begin() + node_index, colors.end() );
+
+    int ii=0;
+    for (int i = node_index; i < nodes.size() - 1; i++) {
+        for(int j=0; j < subdiv; j++ ) {
+            context->deletePrimitive(UUIDs.at(ii));
+            context->deletePrimitive(UUIDs.at(ii+1));
+            ii += 2;
+        }
+    }
+
+}
+
 void Tube::updateTriangleVertices(){
 
     vec3 v0, v1, v2;
@@ -8212,6 +8239,13 @@ void Context::scaleTubeLength( uint ObjID, float scale_factor ){
     dynamic_cast<Tube*>(objects.at(ObjID))->scaleTubeLength(scale_factor);
 }
 
+void Context::pruneTubeNodes( uint ObjID, uint node_index ){
+    if( objects.find(ObjID) == objects.end() ) {
+        helios_runtime_error("ERROR (Context::pruneTubeNodes): ObjectID of " + std::to_string(ObjID) + " does not exist in the Context.");
+    }
+    dynamic_cast<Tube*>(objects.at(ObjID))->pruneTubeNodes(node_index);
+}
+
 void Context::setTubeNodes( uint ObjID, const std::vector<helios::vec3> &node_xyz ){
     if( objects.find(ObjID) == objects.end() ) {
         helios_runtime_error("ERROR (Context::setTubeNodes): ObjectID of " + std::to_string(ObjID) + " does not exist in the Context.");

diff --git a/core/src/Context_fileIO.cpp b/core/src/Context_fileIO.cpp
@@ -4142,10 +4142,10 @@ void Context::writeOBJ( const std::string &filename, const std::vector<uint> &UU
   // - it would make more sense to write patches  as quads rather than two triangles
 
   if( UUIDs.empty() ){
-    std::cout << "WARNING (Context::writeOBJ): No primitives found to write - OBJ file will not be written." << std::endl;
+    std::cout << "WARNING (Context::writeOBJ): No primitives found to write - OBJ file " << filename << " will not be written." << std::endl;
     return;
   }else if( filename.empty() ){
-    std::cout << "WARNING (Context::writeOBJ): Filename was empty - OBJ file will not be written." << std::endl;
+    std::cout << "WARNING (Context::writeOBJ): Filename was empty - OBJ file " << filename << " will not be written." << std::endl;
     return;
   }
 

diff --git a/core/src/global.cpp b/core/src/global.cpp
@@ -3051,7 +3051,7 @@ float helios::interp1( const std::vector<helios::vec2> &points, float x ) {
 
     //If the caller's X value is less than the smallest X value in the table,
     //we can't interpolate.
-    if (iter == points.cbegin() and x <= points.cbegin()->x) {
+    if (iter == points.cbegin() && x <= points.cbegin()->x) {
         return points.cbegin()->y;
     }
 

diff --git a/doc/CHANGELOG b/doc/CHANGELOG
@@ -2023,4 +2023,32 @@ The radiation model has been re-designed, with the following primary additions:
 - Added mouse-based camera controls in the interactive visualizer. Credit to Sean Banks for this update.
 
 *Plant Architecture*
-- Added methods for querying bulk properties of a plant (total leaf count, stem height, plant height, leaf angle distribution) and write plant mesh vertices to file.
+- Added methods for querying bulk properties of a plant (total leaf count, stem height, plant height, leaf angle distribution) and write plant mesh vertices to file.
+
+[1.3.27] 2025-02-11
+
+**Some experimental OpenMP parallelization has been added. This is not enabled by default yet, but can be turned on by setting the CMake option ENABLE_OPENMP to ON.**
+**Updates to core CMakeLists.txt to use more modern CMake features.**
+
+*Context*
+- Context::pruneTubeNodes() was added to allow for removal of part of a tube object.
+
+*Plant Architecture*
+- Added ground cherry weed model.
+- Minor fix in PlantArchitecture::getPlsantLeafInclinationAngleDistribution() to prevent rare out of range index.
+- Changed PlantArchitecture::getPlantLeafInclinationAngleDistribution() to area-weight the distribution, and removed the 'normalize' optional argument.
+- Added PlantArchitecture::prunBranch() method to remove all or part of a branch and its downstream branches.
+- Removed shoot parameter 'elongation_rate'. There is now an 'elongation_rate_max' shoot parameter that can be set by the user. The actual elongation rate can be reduced dynamically if the carbohydrate model is enabled.
+- Many updates to carbohydrate model. Credit to Ethan Frehner for these updates.
+
+*LiDAR*
+- Added exportTriangleAzimuthDistribution() to write the triangulated azimuthal angle distribution to a file. Credit to Alejandra Ponce de Leon for this addition.
+- The output distribution from exportTriangleInclinationDistribution() was not being normalized.
+
+*Radiation*
+- Added bindweed spectra to the default library.
+- There was an error in the writeObjectDataLabelMap() method that could cause undefined behavior if the UUID in the pixel label map did not exist in the Context.
+- There was an error in the writeObjectDataLabelMap() method where the primitive UUID was being used instead of the object ID.
+- There was an error in the model that could cause incorrect assignment of radiative properties if runBand() is called with fewer bands than a previous call to runBand().
+- The previous version could cause unnecessary updating of radiative properties, resulting in a performance hit. This has been fixed.
+- Revised the radiation plug-in CMakeLists.txt to use a modern CMake approach for building CUDA source files. This update should also enable indexing of .cu source files in IDEs such as CLion.
diff --git a/doc/Doxyfile b/doc/Doxyfile
@@ -1298,7 +1298,7 @@ HTML_EXTRA_STYLESHEET  =
 # files will be copied as-is; there are no commands or markers available.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_EXTRA_FILES       =
+HTML_EXTRA_FILES = /Users/bnbailey/Dropbox/Helios/doc/assets/doxygen-awesome-darkmode-toggle.js
 
 # The HTML_COLORSTYLE tag can be used to specify if the generated HTML output
 # should be rendered with a dark or light theme.
@@ -1611,7 +1611,7 @@ DISABLE_INDEX          = NO
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-GENERATE_TREEVIEW      = NO
+GENERATE_TREEVIEW      = YES
 
 # When both GENERATE_TREEVIEW and DISABLE_INDEX are set to YES, then the
 # FULL_SIDEBAR option determines if the side bar is limited to only the treeview
@@ -1623,7 +1623,7 @@ GENERATE_TREEVIEW      = NO
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-FULL_SIDEBAR           = NO
+FULL_SIDEBAR           = YES
 
 # The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
 # doxygen will group on one line in the generated HTML documentation.
@@ -1702,7 +1702,7 @@ USE_MATHJAX            = NO
 # The default value is: MathJax_2.
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
-MATHJAX_VERSION        = MathJax_2
+MATHJAX_VERSION        = MathJax_3
 
 # When MathJax is enabled you can set the default output format to be used for
 # the MathJax output. For more details about the output format see MathJax