[1.3.49] 2025-09-11

## Context
- Fixes for zlib and pnglib building on old linux systems

## Radiation
- Fixed assigmnment of image IDs in JSON image segementation mask output files

Author: bnbailey-psl

core/include/Context.h

@@ -19,19 +19,19 @@
 //! Macro for marking functions as deprecated with optional custom message.
 // MSVC requires __declspec to come BEFORE the function declaration
 #if __cplusplus >= 201402L && defined(__has_cpp_attribute) && __has_cpp_attribute(deprecated)
-    #define DEPRECATED_MSG(msg, func) [[deprecated(msg)]] func
-    #define DEPRECATED_NOMSG(func) [[deprecated]] func
+#define DEPRECATED_MSG(msg, func) [[deprecated(msg)]] func
+#define DEPRECATED_NOMSG(func) [[deprecated]] func
 #elif defined(__GNUC__) || defined(__clang__)
-    #define DEPRECATED_MSG(msg, func) func __attribute__((deprecated(msg)))
-    #define DEPRECATED_NOMSG(func) func __attribute__((deprecated))
+#define DEPRECATED_MSG(msg, func) func __attribute__((deprecated(msg)))
+#define DEPRECATED_NOMSG(func) func __attribute__((deprecated))
 #elif defined(_MSC_VER)
-    // MSVC has issues with custom deprecation messages, use simple deprecation
-    #define DEPRECATED_MSG(msg, func) __declspec(deprecated) func
-    #define DEPRECATED_NOMSG(func) __declspec(deprecated) func
+// MSVC has issues with custom deprecation messages, use simple deprecation
+#define DEPRECATED_MSG(msg, func) __declspec(deprecated) func
+#define DEPRECATED_NOMSG(func) __declspec(deprecated) func
 #else
-    #pragma message("WARNING: You need to implement DEPRECATED for this compiler")
-    #define DEPRECATED_MSG(msg, func) func
-    #define DEPRECATED_NOMSG(func) func
+#pragma message("WARNING: You need to implement DEPRECATED for this compiler")
+#define DEPRECATED_MSG(msg, func) func
+#define DEPRECATED_NOMSG(func) func
 #endif
 
 // Helper macro to count arguments
@@ -72,13 +72,13 @@ constexpr float PI_F = 3.14159265358979323846f;
 #include <map>
 #include <memory>
 #include <random>
+#include <set>
 #include <sstream>
 #include <stdexcept>
 #include <thread>
 #include <type_traits>
 #include <unordered_map>
 #include <vector>
-#include <set>
 
 #ifdef USE_OPENMP
 #include <omp.h>
@@ -1065,7 +1065,8 @@ namespace helios {
      * \param[in] max_iterations [optional] Maximum number of iterations to allow before exiting solver.
      * \return Value of function zero (best estimate even if not converged).
      */
-    [[nodiscard]] float fzero(float (*function)(float value, std::vector<float> &variables, const void *parameters), std::vector<float> &variables, const void *parameters, float init_guess, bool &converged, float err_tol = 0.0001f, int max_iterations = 100);
+    [[nodiscard]] float fzero(float (*function)(float value, std::vector<float> &variables, const void *parameters), std::vector<float> &variables, const void *parameters, float init_guess, bool &converged, float err_tol = 0.0001f,
+                              int max_iterations = 100);
 
     //! Function to perform linear interpolation based on a vector of discrete (x,y) values
     /**
@@ -1177,16 +1178,16 @@ namespace helios {
      * \note This function searches for assets in multiple locations: build directory, system install locations, and custom paths
      * \ingroup functions
      */
-    [[nodiscard]] std::filesystem::path resolveAssetPath(const std::string& relativePath);
+    [[nodiscard]] std::filesystem::path resolveAssetPath(const std::string &relativePath);
 
-    //! Resolve plugin-specific asset path  
+    //! Resolve plugin-specific asset path
     /**
      * \param[in] pluginName Name of the plugin (e.g., "visualizer", "plantarchitecture", "radiation")
      * \param[in] assetPath Relative path within the plugin's asset directory
      * \return Absolute path to the plugin asset file
      * \ingroup functions
      */
-    [[nodiscard]] std::filesystem::path resolvePluginAsset(const std::string& pluginName, const std::string& assetPath);
+    [[nodiscard]] std::filesystem::path resolvePluginAsset(const std::string &pluginName, const std::string &assetPath);
 
 
     //! Resolve file path using standard Helios resolution hierarchy
@@ -1196,28 +1197,28 @@ namespace helios {
      * 2. Checks relative to current working directory first
      * 3. Falls back to checking relative to HELIOS_BUILD environment variable path
      * 4. Throws helios_runtime_error if file not found in either location
-     * 
+     *
      * \param[in] filename File name with or without path (e.g., "texture.jpg" or "models/texture.jpg")
      * \return Absolute canonical path to the file
      * \ingroup functions
      */
-    [[nodiscard]] std::filesystem::path resolveFilePath(const std::string& filename);
+    [[nodiscard]] std::filesystem::path resolveFilePath(const std::string &filename);
 
     //! Resolve spectral data file path
     /**
      * \param[in] spectraFile Spectral data filename with or without path (e.g., "camera_spectral_library.xml")
      * \return Absolute path to the spectral data file
      * \ingroup functions
      */
-    [[nodiscard]] std::filesystem::path resolveSpectraPath(const std::string& spectraFile);
+    [[nodiscard]] std::filesystem::path resolveSpectraPath(const std::string &spectraFile);
 
     //! Validate that an asset file exists and is readable
     /**
      * \param[in] assetPath Path to the asset file to validate
      * \return True if the file exists and is readable, false otherwise
      * \ingroup functions
      */
-    [[nodiscard]] bool validateAssetPath(const std::filesystem::path& assetPath);
+    [[nodiscard]] bool validateAssetPath(const std::filesystem::path &assetPath);
 
     //! Find the project root directory (directory containing top-level CMakeLists.txt)
     /**
@@ -1226,7 +1227,7 @@ namespace helios {
      * \note Searches upward from startPath for a directory containing CMakeLists.txt
      * \ingroup functions
      */
-    [[nodiscard]] std::filesystem::path findProjectRoot(const std::filesystem::path& startPath = std::filesystem::current_path());
+    [[nodiscard]] std::filesystem::path findProjectRoot(const std::filesystem::path &startPath = std::filesystem::current_path());
 
     //! Resolve file path using project-based resolution strategy
     /**
@@ -1236,7 +1237,7 @@ namespace helios {
      * \throws std::runtime_error if file cannot be found
      * \ingroup functions
      */
-    [[nodiscard]] std::filesystem::path resolveProjectFile(const std::string& relativePath);
+    [[nodiscard]] std::filesystem::path resolveProjectFile(const std::string &relativePath);
 
     //! Read values contained in a text file into a one-dimensional vector of floats
     /**

core/include/doctest_utils.h

@@ -43,7 +43,8 @@ set(PNGLIB_VERSION ${PNGLIB_MAJOR}.${PNGLIB_MINOR}.${PNGLIB_RELEASE})
 # needed packages
 #find_package(ZLIB REQUIRED)
 
-set( ZLIB_INCLUDE_DIR "${PROJECT_BINARY_DIR}/lib/zlib;${CMAKE_CURRENT_SOURCE_DIR}/../zlib" )
+# CRITICAL: List build directory FIRST to ensure libpng uses generated zconf.h with z_size_t fixes
+set( ZLIB_INCLUDE_DIR "${CMAKE_BINARY_DIR}/lib/zlib;${CMAKE_CURRENT_SOURCE_DIR}/../zlib" )
 if( UNIX AND NOT APPLE)
     set( ZLIB_LIBRARY ${CMAKE_BINARY_DIR}/lib/libz.a )#BNB 12/6/2022
 endif( UNIX AND NOT APPLE)
@@ -55,6 +56,19 @@ if( WIN32 )
 endif( WIN32 )
 include_directories(${ZLIB_INCLUDE_DIR})
 
+# MANYLINUX COMPATIBILITY FIX - Apply z_size_t fix for libpng
+if(CMAKE_SYSTEM_NAME STREQUAL "Linux")
+    if(DEFINED ENV{CIBUILDWHEEL} OR DEFINED ENV{AUDITWHEEL_PLAT} OR "$ENV{AUDITWHEEL_PLAT}" MATCHES "manylinux")
+        message(STATUS "libpng: Applying manylinux z_size_t compatibility fix")
+        # Force inclusion of stddef.h to ensure size_t is available before any zlib headers
+        set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -include stddef.h")
+        # CRITICAL: Force libpng to use build directory zlib headers with z_size_t fixes
+        # Use -I to prepend the build directory to the include search path
+        set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -I${CMAKE_BINARY_DIR}/lib/zlib")
+        message(STATUS "libpng: Applied stddef.h inclusion and forced build zlib headers for manylinux compatibility")
+    endif()
+endif()
+
 if(NOT WIN32)
   find_library(M_LIBRARY
     NAMES m

core/include/global.h

@@ -59,49 +59,33 @@ endif()
 check_include_file(unistd.h Z_HAVE_UNISTD_H)
 check_include_file(stdarg.h HAVE_STDARG_H)
 
-# Comprehensive zlib compatibility fixes for manylinux and older containers
-# Critical: Force STDC definition BEFORE configure_file() to ensure proper z_size_t typedef
+# Targeted zlib compatibility fix for manylinux containers
+# Check for multiple indicators of manylinux environment
 if(CMAKE_SYSTEM_NAME STREQUAL "Linux")
-    message(STATUS "Applying Linux-specific zlib compatibility fixes")
-
-    # CRITICAL: Set STDC in CMAKE_REQUIRED_DEFINITIONS for configure time
-    set(CMAKE_REQUIRED_DEFINITIONS ${CMAKE_REQUIRED_DEFINITIONS} -DSTDC=1)
-
-    # Force STDC definition for compile time as well
-    add_definitions(-DSTDC=1)
-
-    # Force __STDC__ definition as backup (some compilers check this instead)
-    add_definitions(-D__STDC__=1)
-
-    # Ensure stdarg.h definitions are available
-    if(HAVE_STDARG_H)
-        add_definitions(-DHAVE_STDARG_H)
-    endif()
-
-    # Additional compatibility definitions
-    add_definitions(-D_GNU_SOURCE)
-
-    # Check if we're in a manylinux container and apply additional fixes
-    if(DEFINED ENV{CIBUILDWHEEL})
-        message(STATUS "Detected manylinux container - applying enhanced zlib compatibility fixes")
-
-        # Force size_t availability by including stddef.h
-        add_definitions(-DHAVE_STDDEF_H=1)
-
-        # Ensure proper include paths for system headers
-        include_directories(/usr/include)
-
-        # Additional manylinux-specific compiler flags
-        set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=gnu99")
-
-        # CRITICAL: Direct workaround for z_size_t definition issues in manylinux2014
-        # The conditional logic in zconf.h isn't working correctly with older CentOS 7 headers
-        # So we bypass it entirely by directly defining z_size_t as size_t
-        add_definitions(-Dz_size_t=size_t)
-        message(STATUS "Applied direct z_size_t=size_t workaround for manylinux compatibility")
+    # Debug: Always show environment detection
+    message(STATUS "zlib: Linux detected, checking manylinux environment...")
+    message(STATUS "zlib: CIBUILDWHEEL env var: $ENV{CIBUILDWHEEL}")
+    message(STATUS "zlib: AUDITWHEEL_PLAT env var: $ENV{AUDITWHEEL_PLAT}")
+
+    # Check for manylinux indicators
+    if(DEFINED ENV{CIBUILDWHEEL} OR DEFINED ENV{AUDITWHEEL_PLAT} OR "$ENV{AUDITWHEEL_PLAT}" MATCHES "manylinux")
+        message(STATUS "Applying manylinux-specific zlib z_size_t compatibility fix")
+
+        # CRITICAL: Force inclusion of stddef.h before any zlib headers are processed
+        # This ensures size_t is available when zconf.h processes the z_size_t typedef
+        # The zconf.h logic should then correctly use: typedef size_t z_size_t;
+        # Apply globally so that libpng and other dependencies also get this fix
+        set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -include stddef.h")
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -include stddef.h")
+
+        # Also set parent scope so this applies to the entire build
+        set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS}" PARENT_SCOPE)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}" PARENT_SCOPE)
+
+        message(STATUS "Applied z_size_t fix: forced stddef.h inclusion for manylinux")
+    else()
+        message(STATUS "Not a manylinux environment, skipping z_size_t fix")
     endif()
-
-    message(STATUS "Linux zlib compatibility: STDC=1, __STDC__=1, HAVE_STDDEF_H=1")
 endif()
 
 if(MSVC)

core/lib/libpng/CMakeLists.txt

@@ -8,19 +8,6 @@
 #ifndef ZCONF_H
 #define ZCONF_H
 
-/* Manylinux and older container compatibility fixes */
-#ifdef __linux__
-  /* Ensure STDC compliance detection works in manylinux containers */
-  #if defined(__GNUC__) && !defined(STDC) && !defined(__STDC__)
-    #define STDC 1
-    #define __STDC__ 1
-  #endif
-  /* Ensure we have access to size_t */
-  #ifndef _STDDEF_H
-    #include <stddef.h>
-  #endif
-#endif
-
 #cmakedefine Z_PREFIX
 #cmakedefine Z_HAVE_UNISTD_H
 

core/lib/zlib/CMakeLists.txt

@@ -250,7 +250,8 @@
 #  define z_longlong long long
 #  if defined(NO_SIZE_T)
      typedef unsigned NO_SIZE_T z_size_t;
-#  elif defined(STDC)
+#  elif defined(STDC) || defined(__STDC__) || defined(__GNUC__) || defined(__linux__)
+     /* Enhanced STDC detection for manylinux containers and modern compilers */
 #    include <stddef.h>
      typedef size_t z_size_t;
 #  else

core/lib/zlib/zconf.h.cmakein

@@ -78,7 +78,7 @@ bool Context::doesTextureFileExist(const char *texture_file) const {
     try {
         auto resolved_path = resolveFilePath(texture_file);
         return std::filesystem::exists(resolved_path);
-    } catch (const std::runtime_error&) {
+    } catch (const std::runtime_error &) {
         return false;
     }
 }
@@ -460,7 +460,7 @@ std::vector<uint> Context::getAllUUIDs() const {
     if (all_uuids_cache_valid) {
         return cached_all_uuids;
     }
-    
+
     // Rebuild cache
     cached_all_uuids.clear();
     cached_all_uuids.reserve(primitives.size());
@@ -798,7 +798,7 @@ void Context::getDomainBoundingBox(const std::vector<uint> &UUIDs, vec2 &xbounds
 
 // Parallelize the outer loop over primitives. Use "for" inside the parallel region.
 #pragma omp for nowait
-        for (int i = 0; i < (int)UUIDs.size(); i++) {
+        for (int i = 0; i < (int) UUIDs.size(); i++) {
             // For each primitive:
             const std::vector<vec3> &verts = getPrimitivePointer_private(UUIDs[i])->getVertices();
             // Update local bounding box for each vertex in this primitive.
@@ -2122,7 +2122,7 @@ std::vector<uint> Context::addTube(uint radial_subdivisions, const std::vector<v
         if (fabs(vec.z) > 0.95f) {
             nvec = vec3(1.0f, 0.0f, 0.0f); // Use horizontal direction for vertical axes
         }
-        
+
         convec = cross(nvec, vec);
         convec.normalize();
         nvec = cross(vec, convec);
@@ -2228,7 +2228,7 @@ std::vector<uint> Context::addTube(uint radial_subdivisions, const std::vector<v
         if (fabs(vec.z) > 0.95f) {
             nvec = vec3(1.0f, 0.0f, 0.0f); // Use horizontal direction for vertical axes
         }
-        
+
         convec = cross(nvec, vec);
         convec.normalize();
         nvec = cross(vec, convec);
@@ -2295,7 +2295,7 @@ std::vector<uint> Context::addTube(uint radial_subdivisions, const std::vector<v
 
     // Remove invalid UUIDs (zeros) from the vector
     UUIDs.erase(std::remove(UUIDs.begin(), UUIDs.end(), 0), UUIDs.end());
-    
+
     return UUIDs;
 }
 
@@ -2578,8 +2578,8 @@ std::vector<uint> Context::addDisk(const int2 &Ndivs, const vec3 &center, const
 
             if (r == 0) {
                 uint triangle_uuid = addTriangle(make_vec3(0, 0, 0), make_vec3(rx_plus * cosf(theta), ry_plus * sinf(theta), 0), make_vec3(rx_plus * cosf(theta_plus), ry_plus * sinf(theta_plus), 0), texturefile, make_vec2(0.5, 0.5),
-                                         make_vec2(0.5f * (1.f + cosf(theta) * rx_plus / size.x), 0.5f * (1.f + sinf(theta) * ry_plus / size.y)),
-                                         make_vec2(0.5f * (1.f + cosf(theta_plus) * rx_plus / size.x), 0.5f * (1.f + sinf(theta_plus) * ry_plus / size.y)));
+                                                 make_vec2(0.5f * (1.f + cosf(theta) * rx_plus / size.x), 0.5f * (1.f + sinf(theta) * ry_plus / size.y)),
+                                                 make_vec2(0.5f * (1.f + cosf(theta_plus) * rx_plus / size.x), 0.5f * (1.f + sinf(theta_plus) * ry_plus / size.y)));
                 if (getPrimitiveArea(triangle_uuid) > 0) {
                     UUID.push_back(triangle_uuid);
                 } else {
@@ -2588,17 +2588,18 @@ std::vector<uint> Context::addDisk(const int2 &Ndivs, const vec3 &center, const
                 }
             } else {
                 uint triangle_uuid1 = addTriangle(make_vec3(rx * cosf(theta_plus), ry * sinf(theta_plus), 0), make_vec3(rx * cosf(theta), ry * sinf(theta), 0), make_vec3(rx_plus * cosf(theta), ry_plus * sinf(theta), 0), texturefile,
-                                         make_vec2(0.5f * (1.f + cosf(theta_plus) * rx / size.x), 0.5f * (1.f + sinf(theta_plus) * ry / size.y)), make_vec2(0.5f * (1.f + cosf(theta) * rx / size.x), 0.5f * (1.f + sinf(theta) * ry / size.y)),
-                                         make_vec2(0.5f * (1.f + cosf(theta) * rx_plus / size.x), 0.5f * (1.f + sinf(theta) * ry_plus / size.y)));
+                                                  make_vec2(0.5f * (1.f + cosf(theta_plus) * rx / size.x), 0.5f * (1.f + sinf(theta_plus) * ry / size.y)), make_vec2(0.5f * (1.f + cosf(theta) * rx / size.x), 0.5f * (1.f + sinf(theta) * ry / size.y)),
+                                                  make_vec2(0.5f * (1.f + cosf(theta) * rx_plus / size.x), 0.5f * (1.f + sinf(theta) * ry_plus / size.y)));
                 if (getPrimitiveArea(triangle_uuid1) > 0) {
                     UUID.push_back(triangle_uuid1);
                 } else {
                     deletePrimitive(triangle_uuid1);
                 }
-                
-                uint triangle_uuid2 = addTriangle(make_vec3(rx * cosf(theta_plus), ry * sinf(theta_plus), 0), make_vec3(rx_plus * cosf(theta), ry_plus * sinf(theta), 0), make_vec3(rx_plus * cosf(theta_plus), ry_plus * sinf(theta_plus), 0), texturefile,
-                                         make_vec2(0.5f * (1.f + cosf(theta_plus) * rx / size.x), 0.5f * (1.f + sinf(theta_plus) * ry / size.y)), make_vec2(0.5f * (1.f + cosf(theta) * rx_plus / size.x), 0.5f * (1.f + sinf(theta) * ry_plus / size.y)),
-                                         make_vec2(0.5f * (1.f + cosf(theta_plus) * rx_plus / size.x), 0.5f * (1.f + sinf(theta_plus) * ry_plus / size.y)));
+
+                uint triangle_uuid2 =
+                        addTriangle(make_vec3(rx * cosf(theta_plus), ry * sinf(theta_plus), 0), make_vec3(rx_plus * cosf(theta), ry_plus * sinf(theta), 0), make_vec3(rx_plus * cosf(theta_plus), ry_plus * sinf(theta_plus), 0), texturefile,
+                                    make_vec2(0.5f * (1.f + cosf(theta_plus) * rx / size.x), 0.5f * (1.f + sinf(theta_plus) * ry / size.y)), make_vec2(0.5f * (1.f + cosf(theta) * rx_plus / size.x), 0.5f * (1.f + sinf(theta) * ry_plus / size.y)),
+                                    make_vec2(0.5f * (1.f + cosf(theta_plus) * rx_plus / size.x), 0.5f * (1.f + sinf(theta_plus) * ry_plus / size.y)));
                 if (getPrimitiveArea(triangle_uuid2) > 0) {
                     UUID.push_back(triangle_uuid2);
                 } else {