[1.3.34] 2025-06-15

- Added .clang-format file for consistent code formatting across IDEs and agents.
- Added AGENTS.md to give some basic instructions for AI agents.

*Context*
 - Reworked Context::cleanDeletedUUIDs() and Context::cleanDeletedObjectIDs() to erase invalid IDs using iterators, preventing unsigned underflow issues when vectors are empty.
 - Fixed a loop in Context::loadMTL() that could cause unsigned underflow.
 - Context::writeOBJ() can now maintain object groups based on the value of the primitive data "object_label".
 - Context::writeOBJ() was defining normals (if enabled), but they were not being assigned to faces. This has been fixed.
 - Improved stability of Tube::appendTubeSegment(), Context::addConeObject(), Context::addTubeObject(), and helios::rotatePointAboutLine() to prevent dividing by nearly zero when the vector length is very small.
 - Added helios::powi() function to calculate integer powers of a number, which is more efficient than using std::pow() for integer exponents and avoids having to do "a = b*b*b*b", for example.
 - Added methods Context::scaleObjectAboutOrigin() and Context::rotateObjectAboutOrigin() to scale and rotate an object about its origin, which can be set with Context::setObjectOrigin().

 *Radiation*
 - Added many new camera response spectra to the spectral library (spectral_data/camera_spectral_library.xml).
 - The spectral labels were not correct for the default DGK colorboard (CameraCalibration::addDefaultColorboard()).
 - Added the ability to create the Calibrite ColorChecker Classic in the scene. Accordingly added explicit functions CameraCalibration::addDGKColorboard() and CameraCalibration::addCalibriteColorboard() to add the two available color boards.
 - Added RadiationModel::applyImageProcessingPipeline() to apply a digital camera-like processing pipeline to an image.

 *Plant Architecture*
 - Added capability to scale petioles of the same internode independently.

Author: bnbailey-psl

.clang-format

@@ -0,0 +1,57 @@
+---
+Language: Cpp
+BasedOnStyle: LLVM
+AccessModifierOffset: -4
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignOperands: true
+AlignTrailingComments: false
+AlwaysBreakTemplateDeclarations: Yes
+BraceWrapping: 
+  AfterCaseLabel: false
+  AfterClass: false
+  AfterControlStatement: false
+  AfterEnum: false
+  AfterFunction: false
+  AfterNamespace: false
+  AfterStruct: false
+  AfterUnion: false
+  AfterExternBlock: false
+  BeforeCatch: false
+  BeforeElse: false
+  BeforeLambdaBody: false
+  BeforeWhile: false
+  SplitEmptyFunction: true
+  SplitEmptyRecord: true
+  SplitEmptyNamespace: true
+BreakBeforeBraces: Custom
+BreakConstructorInitializers: AfterColon
+BreakConstructorInitializersBeforeComma: false
+ColumnLimit: 250
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+ContinuationIndentWidth: 8
+IncludeCategories: 
+  - Regex: '^<.*'
+    Priority: 1
+  - Regex: '^".*'
+    Priority: 2
+  - Regex: '.*'
+    Priority: 3
+IncludeIsMainRegex: '([-_](test|unittest))?$'
+IndentCaseLabels: true
+IndentWidth: 4
+InsertNewlineAtEOF: true
+MacroBlockBegin: ''
+MacroBlockEnd: ''
+MaxEmptyLinesToKeep: 2
+NamespaceIndentation: All
+SpaceAfterCStyleCast: true
+SpaceAfterTemplateKeyword: false
+SpaceBeforeRangeBasedForLoopColon: false
+SpaceInEmptyParentheses: false
+SpacesInAngles: false
+SpacesInConditionalStatement: false
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+TabWidth: 4
+...

.github/workflows/linux_GPU_selftests.yaml

@@ -0,0 +1,54 @@
+name: Build and Run on Linux EC2 GPU Instance
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+env:
+  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
+  BUILD_TYPE: Release
+
+permissions:
+  id-token: write
+  contents: read
+
+jobs:
+
+  start-gpu:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: aws-actions/configure-aws-credentials@v2
+        with:
+          role-to-assume: ${{ secrets.OIDC_ROLE_ARN }}
+          aws-region: us-west-2
+      - run: |
+          aws ec2 start-instances --instance-ids ${{ secrets.EC2_INSTANCE_ID }}
+          aws ec2 wait instance-running --instance-ids ${{ secrets.EC2_INSTANCE_ID }}
+
+  run_samples_linux:
+    # The CMake configure and build commands are platform agnostic and should work equally well on Windows or Mac.
+    # You can convert this to a matrix build if you need cross-platform coverage.
+    # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
+    runs-on: [self-hosted]
+    needs: start-gpu
+    steps:
+      - uses: actions/checkout@v3
+      - name: Bash script
+        run: |
+          cd utilities
+          ./run_samples.sh --visbuildonly
+  
+
+  stop-gpu:
+    needs: run_samples_linux
+    runs-on: ubuntu-latest
+    steps:
+      - uses: aws-actions/configure-aws-credentials@v2
+        with:
+          role-to-assume: ${{ secrets.OIDC_ROLE_ARN }}
+          aws-region: us-west-2
+      - run: |
+          aws ec2 stop-instances --instance-ids ${{ secrets.EC2_INSTANCE_ID }}
+          aws ec2 wait instance-stopped --instance-ids ${{ secrets.EC2_INSTANCE_ID }}

AGENTS.md

@@ -0,0 +1,11 @@
+## Code Style
+- Code style should follow the style given in .clang-format. 
+
+## Testing
+- Do not try to run utilities/run_samples.sh. It will time out.
+- If changes are made to docstrings or function signatures, build the documentation file `doc/Doxyfile` using doxygen. Some notes on this are given below:
+  - Run `doxygen doc/Doxyfile` to generate the documentation from the root directory not the `doc` directory.
+  - Check doxygen output for warnings. It is ok to ignore warnings of the form " warning: Member XXX is not documented." 
+  - The main concern when changing docstrings or function signatures is the potential for breaking \ref references, which produces a warning like:  warning: unable to resolve reference to XXX for \ref command".
+    When fixing these, don't just remove the funciton signature or use markdown `` ticks to suppress the warning. It is important to keep the signature in the reference for overloaded functions/methods. Figure out why the function signature is not matching and thus causing Doxygen to treat it as plain text.
+  - You tend to flag hash symbols in code blocks as erroneous and propose to add a double hash (e.g., '##include "Context.h"'). This is not needed and ends up rendering the double hash.

core/CMake_project.txt

@@ -4,6 +4,11 @@ set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)
 
+# If a build type is not specified, explicitly set it to Debug.
+if (NOT CMAKE_CONFIGURATION_TYPES AND NOT CMAKE_BUILD_TYPE)
+    set(CMAKE_BUILD_TYPE Debug CACHE STRING "" FORCE)
+endif()
+
 file(MAKE_DIRECTORY "${CMAKE_BINARY_DIR}/lib")
 configure_file( "${BASE_DIRECTORY}/core/lib/detect_GPU_compute.cmake" "${CMAKE_BINARY_DIR}/lib/detect_GPU_compute.cmake" COPYONLY )
 
@@ -34,6 +39,9 @@ set( CMAKE_LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib" CACHE STRING "" )
 add_executable( ${EXECUTABLE_NAME} ${SOURCE_FILES} )
 add_subdirectory( "${BASE_DIRECTORY}/core" "lib" )
 target_link_libraries( ${EXECUTABLE_NAME} helios)
+if (CMAKE_CXX_COMPILER_ID STREQUAL "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 9)
+    target_link_libraries(${EXECUTABLE_NAME} stdc++fs)
+endif()
 if(APPLE) #get rid of annoying duplicate library warning on Mac
     set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,-no_warn_duplicate_libraries")
 endif()
@@ -48,13 +56,14 @@ foreach(PLUGIN ${PLUGINS})
     target_link_libraries( ${EXECUTABLE_NAME} ${PLUGIN} )
     if( NOT APPLE )
         target_link_libraries( ${PLUGIN} helios )
+        if (CMAKE_CXX_COMPILER_ID STREQUAL "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 9)
+            target_link_libraries(${PLUGIN} stdc++fs)
+        endif()
     endif()
 endforeach(PLUGIN)
 include_directories( "${PLUGIN_INCLUDE_PATHS};${CMAKE_CURRENT_SOURCE_DIRECTORY}" )
 
-if( CMAKE_BUILD_TYPE STREQUAL Debug OR CMAKE_BUILD_TYPE STREQUAL "RelWithDebInfo" )
-    target_compile_definitions(helios PRIVATE HELIOS_DEBUG)
-endif()
+target_compile_definitions(helios PUBLIC $<$<CONFIG:Debug>:HELIOS_DEBUG>  $<$<CONFIG:RelWithDebInfo>:HELIOS_DEBUG> )
 
 if( ENABLE_OPENMP )
     find_package(OpenMP)

core/include/Context.h

@@ -579,8 +579,11 @@ class CompoundObject{
 
     //! Affine transformation matrix
     float transform[16];
+
+    //! Origin position of the object about which it can be scaled and rotated
+    helios::vec3 object_origin;
 
-    //! Flag to indicate whether all object primitives are in tact. If any primitives have been deleted, this flag will be set to false.
+    //! Flag to indicate whether all object primitives are intact. If any primitives have been deleted, this flag will be set to false.
     bool primitivesarecomplete = true;
 
     std::map<std::string,HeliosDataType > object_data_types;
@@ -3567,6 +3570,15 @@ class Context{
      */
     void setObjectAverageNormal(uint ObjID, const vec3& origin, const vec3& new_normal) const;
 
+    //! Set the origin position of the object about which it can be rotated and scaled
+    /**
+     * Note that this does not change the position of the object in the scene, but rather sets the origin point about which the object can later be rotated and scaled.
+     *
+     * \param[in] ObjID Identifier of the object.
+     * \param[in] origin (x,y,z) Coordinates of the new origin point.
+     */
+    void setObjectOrigin( uint ObjID, const vec3& origin ) const;
+
     //! Method to check whether an Object has texture data
     /**
      * \param[in] ObjID Identifier of the object.
@@ -4868,6 +4880,22 @@ class Context{
      */
     void rotateObject(const std::vector<uint>& ObjIDs, float rotation_radians, const vec3& rotation_origin, const vec3& rotation_axis_vector ) const;
 
+    //! Rotate a single compound object about an arbitrary line passing through the objects origin point
+    /**
+     * \param[in] ObjID Object ID to rotate
+     * \param[in] rotation_radians Rotation angle in radians
+     * \param[in] rotation_axis_vector Vector describing axis about which to rotate
+     */
+    void rotateObjectAboutOrigin(uint ObjID, float rotation_radians, const vec3& rotation_axis_vector ) const;
+
+    //! Rotate multiple compound objects about an arbitrary line passing through the objects origin point
+    /**
+     * \param[in] ObjIDs Vector of object IDs to translate
+     * \param[in] rotation_radians Rotation angle in radians
+     * \param[in] rotation_axis_vector Vector describing axis about which to rotate
+     */
+    void rotateObjectAboutOrigin(const std::vector<uint>& ObjIDs, float rotation_radians, const vec3& rotation_axis_vector ) const;
+
     //! Method to scale a compound object in the x-, y- and z-directions
     /**
      * \param[in] ObjID Object ID to scale
@@ -4896,22 +4924,38 @@ class Context{
      */
     void scaleObjectAboutCenter( const std::vector<uint>& ObjIDs, const helios::vec3 &scalefact ) const;
 
-    //! Method to scale a compound object in the x-, y- and z-directions
+    //! Method to scale a compound object in the x-, y- and z-directions about an arbitrary point
     /**
      * \param[in] ObjID Object ID to scale
      * \param[in] scalefact Scaling factor to apply in the x-, y- and z-directions
      * \param[in] point Cartesian coordinate of the point about which to scale
      */
     void scaleObjectAboutPoint( uint ObjID, const helios::vec3 &scalefact, const helios::vec3 &point ) const;
 
-    //! Method to scale a compound object in the x-, y- and z-directions
+    //! Method to scale a compound object in the x-, y- and z-directions about an arbitrary point
     /**
      * \param[in] ObjIDs Vector of object IDs to scale
      * \param[in] scalefact Scaling factor to apply in the x-, y- and z-directions
      * \param[in] point Cartesian coordinate of the point about which to scale
      */
     void scaleObjectAboutPoint( const std::vector<uint>& ObjIDs, const helios::vec3 &scalefact, const helios::vec3 &point ) const;
 
+    //! Method to scale a compound object in the x-, y- and z-directions about its origin point
+    /**
+     * \param[in] ObjID Object ID to scale
+     * \param[in] scalefact Scaling factor to apply in the x-, y- and z-directions
+     * \note By default the object origin is its center. This can be changed by setting the object origin using the setObjectOrigin method
+     */
+    void scaleObjectAboutOrigin( uint ObjID, const helios::vec3 &scalefact ) const;
+
+    //! Method to scale a compound object in the x-, y- and z-directions about its origin point
+    /**
+     * \param[in] ObjIDs Vector of object IDs to scale
+     * \param[in] scalefact Scaling factor to apply in the x-, y- and z-directions
+     * \note By default the object origin is its center. This can be changed by setting the object origin using the setObjectOrigin method
+     */
+    void scaleObjectAboutOrigin( const std::vector<uint>& ObjIDs, const helios::vec3 &scalefact ) const;
+
     //! Get primitive UUIDs associated with compound object (single object ID input)
     /**
      * \param[in] ObjID object ID to retrieve primitive UUIDs for

core/include/global.h

@@ -650,6 +650,14 @@ namespace helios {
      */
     [[nodiscard]] float asin_safe(float x);
 
+    //! Exponentiation function for integer powers
+    /**
+     * \param[in] base Base to be raised to a power
+     * \param[in] exp Exponent to which the base is raised (must be a non-negative integer)
+     */
+    template<typename T>
+    T powi(T base, std::size_t exp);
+
     //!Determine if two line segments intersect. The lines segments are defined by vertices (p1,q1) and (p2,q2)
     /**
      * \ingroup functions