F/vtc fracture final

.gitignore

@@ -9,6 +9,8 @@ build*/
 CMakeUserPresets.json
 *~*.TMP
 
+.DS_Store
+
 .idea/*
 .vs/*
 .vscode/*

README.md

@@ -55,13 +55,21 @@ We have made available to the medical simulation community a large set of burn i
 
 ## Release Notes 
 
-### 8.0.0 (November 2024)
+### 8.2.0 (January 2025)
+- Marshall / UnMarshall code migrated from Load/UnLoad functions to private API
+- Additioanl Unit Test for all Seralization code
+- Equality operators
+- Refactored SEScalarTypes
+- Added Enums for all CDM Enums
+- Seperated SESubstance between Definition and State
+- ~~~~
+### 8.0.0 
 - Modified Scenario CDM to require <ACTIONS> Tag around individual actions
 - Allowed import of external ActionList and DataRequestList
 - Updated CMAKE to minimum 3.20
 - Improved various features
 
-### 7.6.0 (December 2023)
+### 7.6.0
 - Improved SWIG bindings
 - Improved Various Models
 
@@ -92,12 +100,10 @@ We support the [contributor covenant](https://github.com/BioGearsEngine/Engine/b
 
 Contributing 
 -------------
-Details will be filled in shortly. In the meantime, if you have a contribution or issue to post/push feel free to contact abaird@ara.com with the details. 
+Details will be filled in shortly. In the meantime, if you have a contribution or issue to post/push feel free to contact biogears@ara.com with the details. 
 
 You can access our public Slack through our [development website](https://www.biogears.dev/).
 
 Additional Documentation
 --------------------------
 For more detailed documentation including model discussions and implementation details can be found at www.BioGearsEngine.com
-
-

cmake/cmake-common_logic.cmake

@@ -32,14 +32,14 @@ set_property(GLOBAL PROPERTY AUTOGEN_SOURCE_GROUP  "Generated")
 ####
 function(verify_package package)
   cmake_parse_arguments(_l
-    REQUIRED 
+    "REQUIRED;QUIET"
     ""
     ""
      ${ARGN})
   find_package(${package} CONFIG ${_l_UNPARSED_ARGUMENTS} QUIET)
   if(NOT ${package}_FOUND)
     find_package(${package} ${_l_UNPARSED_ARGUMENTS} QUIET)
-    if(NOT ${package}_FOUND)
+    if(NOT ${package}_FOUND AND NOT _l_QUIET)
       message(WARNING "The following packages ${package} were not found."
         "For native compilations setting CMAKE_PREFIX_PATH can solve this problem"
         "For cross complilation try expanding your CMAKE_FIND_ROOT_PATH"

projects/CMakeLists.txt

@@ -143,7 +143,11 @@ STRING(APPEND VS_DEBUGGER_ENV_PATH "%PATH%")
 
 LIST(APPEND VS_DEBUGGER_ENVIRONMENT_LIST "${VS_DEBUGGER_ENV_PATH}")
 message(STATUS "VS_DEBUGGER_ENVIRONMENT_LIST=${VS_DEBUGGER_ENVIRONMENT_LIST}")
-# add_subdirectory(unit)
+
+
+add_subdirectory(unit)
+
+
 add_subdirectory(biogears-common)
 add_subdirectory(biogears)
 add_subdirectory(test_driver)

projects/biogears-common/include/biogears/framework/result.tci.h

@@ -306,7 +306,7 @@ T Result<T, E>::unwrap() {
   static_assert(!std::is_same<T, E>::value, "Result and Error can not be the same type.");
   assert(is_ok());
   return dump_ok();
-};
+}; 
 
 template<typename T, typename E>
 E Result<T, E>::unwrap_err() {

projects/biogears-common/src/math/angles.cpp

@@ -133,7 +133,7 @@ static_assert(Anglef(1.f) + Anglef(2.f) == 3.f, "");
 static_assert(0.f + 1.0_f_i + 2.0_f_j + 3.0_f_k == Quaternionf(0.f, 1.f, 2.f, 3.f), "");
 static_assert(Quaternionf(1.f, 2.f, 3.f, 4.f).real() + Quaternionf(1.f, 2.f, 3.f, 4.f).pure() == Quaternionf(1.f, 2.f, 3.f, 4.f), "");
 static_assert((Quaternionf(1.f, 1.f, 1.f, 1.f) * Quaternionf(1.f, 1.f, 1.f, 1.f).conj()).w() == 4.0f, "");
-#endif()
+#endif
 
 //------------------------------------------------------------------------------
 auto azimuth_uncert_from_quat(const Quaternionf& q

projects/biogears-common/unit/test_common_OwningMutex.cpp

@@ -17,6 +17,7 @@
 //! Unit Test for Biogears-common Config
 //!
 #include <thread>
+#include <chrono>
 
 #include <gtest/gtest.h>
 

projects/biogears/CMakeLists.txt

@@ -53,13 +53,17 @@ file(GLOB_RECURSE biogears_xsd_list "${PROJECT_SOURCE_DIR}/share/xsd/biogears/*.
 file(GLOB_RECURSE cdm_xsd_list "${PROJECT_SOURCE_DIR}/share/xsd/cdm/*.xsd")
 
 set (BIOGEARS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
-set (BIOGEARS_BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/generated/$<CONFIG>)
-set (BIOGEARS_BINARY_BARE_DIR ${CMAKE_CURRENT_BINARY_DIR}/generated/)
-
+if (NOT APPLE)
+  set (GENERATED_PREFIX generated/$<CONFIG>)
+else()
+  set (GENERATED_PREFIX generated/)
+endif()
+set (BIOGEARS_BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/${GENERATED_PREFIX})
+set (BIOGEARS_BINARY_BARE_DIR ${CMAKE_CURRENT_BINARY_DIR}/${GENERATED_PREFIX})
 
 REGISTER_XSD_DIR( "${PROJECT_SOURCE_DIR}/share/xsd/"
                     CONFIG "${PROJECT_SOURCE_DIR}/share/xsd/BioGearsDataModel.cfg"
-                    PROJECT "generated/$<CONFIG>/biogears" COMPONENT "schema" RESOURCE_FOLDER "resources/schema"
+                    PROJECT "${GENERATED_PREFIX}/biogears" COMPONENT "schema" RESOURCE_FOLDER "resources/schema"
                     NO_TARGETS SOURCES_VAR XSD_SRCS HEADERS_VAR XSD_HDRS VERBOSITY 1)
 
 

projects/biogears/libBiogears/CMakeLists.txt

@@ -5,7 +5,7 @@ message(STATUS "  Configuring libbiogears")
 
 file(READ ${CMAKE_CURRENT_SOURCE_DIR}/include/biogears/config.h.in contents)
 string(CONFIGURE "${contents}" contents @ONLY)
-FILE(GENERATE OUTPUT  ${CMAKE_CURRENT_BINARY_DIR}/../generated/$<CONFIG>/biogears/config.h 
+FILE(GENERATE OUTPUT  ${CMAKE_CURRENT_BINARY_DIR}/../${GENERATED_PREFIX}/biogears/config.h 
               CONTENT   "${contents}"
      NEWLINE_STYLE LF)
 
@@ -62,7 +62,7 @@ if(Biogears_BUILD_STATIC)
    if(biogears_USE_OVERRIDE_CONTROL)
       target_compile_definitions( libbiogears PRIVATE BIOGEARS_USE_OVERRIDE_CONTROL)
    endif()
-  if(UNITTEST_biogears-core)
+  if(Biogears_BUILD_TEST)
      target_compile_definitions( libbiogears PUBLIC ENABLE_UNIT_TEST_API)
   endif()
   if(WIN32)
@@ -139,7 +139,7 @@ else()
     CXX_STANDARD 20
     )
   set_target_properties(libbiogears PROPERTIES SOVERSION "${Biogears_LIB_VERSION}")
-  if(UNITTEST_biogears-core)
+  if(Biogears_BUILD_TEST)
      target_compile_definitions( libbiogears PUBLIC ENABLE_UNIT_TEST_API)
   endif()
   ###############################################################################

projects/biogears/libBiogears/include/biogears/BiogearsEnums.h

@@ -0,0 +1,30 @@
+/**************************************************************************************
+Copyright 2019 Applied Research Associates, Inc.
+Licensed under the Apache License, Version 2.0 (the "License"); you may not use
+this file except in compliance with the License. You may obtain a copy of the License
+at:
+http://www.apache.org/licenses/LICENSE-2.0
+Unless required by applicable law or agreed to in writing, software distributed under
+the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
+CONDITIONS OF ANY KIND, either express or implied. See the License for the
+specific language governing permissions and limitations under the License.
+**************************************************************************************/
+
+#pragma once
+
+#include <ostream>
+
+#include "cdm/enums/SEActionEnums.h"
+#include "cdm/enums/SEAnesthesiaEnums.h"
+#include "cdm/enums/SECircuitEnums.h"
+#include "cdm/enums/SECompartmentEnums.h"
+#include "cdm/enums/SEEnvironmentEnums.h"
+#include "cdm/enums/SEPatientActionsEnums.h"
+#include "cdm/enums/SEPatientAssessmentEnums.h"
+#include "cdm/enums/SEPatientEnums.h"
+#include "cdm/enums/SEPhysiologyEnums.h"
+#include "cdm/enums/SEPropertyEnums.h"
+#include "cdm/enums/SESubstanceEnums.h"
+
+#include "engine/Controller/BioGearsEnums.h"
+

projects/biogears/libBiogears/include/biogears/cdm/CommonDataModel.h

@@ -26,17 +26,7 @@ namespace tatrc {
   }
 }
 }
-//using namespace mil::tatrc::phsyiology::datamodel;
-#define CDM_BIND_DECL(type)   \
-  namespace mil {             \
-    namespace tatrc {         \
-      namespace physiology {  \
-        namespace datamodel { \
-          class type;         \
-        }                     \
-      }                       \
-    }                         \
-  }
+
 namespace CDM = mil::tatrc::physiology::datamodel;
 
 #include <stdexcept>
@@ -47,8 +37,8 @@ namespace CDM = mil::tatrc::physiology::datamodel;
 #include <biogears/exports.h>
 namespace biogears {
 
-#pragma warning(disable: 4251)
 #pragma warning(push,0)
+#pragma warning(disable: 4251)
 #pragma warning(disable: 4275)
 struct BIOGEARS_API CommonDataModelException : public std::runtime_error {
   CommonDataModelException();
@@ -60,4 +50,5 @@ struct BIOGEARS_API CommonDataModelException : public std::runtime_error {
 }
 // Basics
 #include <biogears/cdm/Macros.h>
+#include <biogears/cdm/enums/SEPropertyEnums.h>
 #include <biogears/cdm/utils/Logger.h>

projects/biogears/libBiogears/include/biogears/cdm/Macros.h

@@ -11,9 +11,11 @@ specific language governing permissions and limitations under the License.
 **************************************************************************************/
 
 #pragma once
+#include <algorithm>
+#include <concepts>
 #include <map>
+#include <type_traits>
 #include <vector>
-#include <algorithm>
 
 namespace biogears {
 #define BLIM(input, min, max) (input = (input > max) ? max : ((input < min) ? min : input))
@@ -58,12 +60,40 @@ inline size_t _Hash_value(_InIt _Begin, _InIt _End)
   if (from.Has##name())   \
     Get##name().Merge(*from.m_##name);
 
-#define CDM_COPY(from, to)       \
-  {                              \
-    auto* bind = from->Unload(); \
-    to->Load(*bind);             \
-    delete bind;                 \
-  }
+template <class ContainerType>
+concept Container = requires(ContainerType a) {
+  requires std::regular<ContainerType>;
+  requires std::swappable<ContainerType>;
+  requires std::destructible<typename ContainerType::value_type>;
+  requires std::same_as<typename ContainerType::reference, typename ContainerType::value_type&>;
+  requires std::same_as<typename ContainerType::const_reference, const typename ContainerType::value_type&>;
+  requires std::forward_iterator<typename ContainerType::iterator>;
+  requires std::forward_iterator<typename ContainerType::const_iterator>;
+  requires std::signed_integral<typename ContainerType::difference_type>;
+  requires std::same_as<typename ContainerType::difference_type, typename std::iterator_traits<typename ContainerType::iterator>::difference_type>;
+  requires std::same_as<typename ContainerType::difference_type, typename std::iterator_traits<typename ContainerType::const_iterator>::difference_type>;
+  {
+    a.begin()
+  } -> std::same_as<typename ContainerType::iterator>;
+  {
+    a.end()
+  } -> std::same_as<typename ContainerType::iterator>;
+  {
+    a.cbegin()
+  } -> std::same_as<typename ContainerType::const_iterator>;
+  {
+    a.cend()
+  } -> std::same_as<typename ContainerType::const_iterator>;
+  {
+    a.size()
+  } -> std::same_as<typename ContainerType::size_type>;
+  {
+    a.max_size()
+  } -> std::same_as<typename ContainerType::size_type>;
+  {
+    a.empty()
+  } -> std::same_as<bool>;
+};
 
 template <class T>
 inline void Copy(const std::vector<T*>& from, std::vector<T*>& to)
@@ -109,12 +139,25 @@ inline void DELETE_VECTOR(std::vector<T>& vec)
   }
   vec.clear();
 }
-//This will delete all of the second items in a map and then clear the map to destroy all dangling pointers
+
+template <typename ContainerType>
+  requires Container<ContainerType> && std::is_pointer_v<typename ContainerType::value_type>
+inline void DELETE_CONTAINER_OF_POINTERS(ContainerType& container)
+{
+  for (auto& element : container) {
+    delete element;
+    element = nullptr;
+  }
+  container.clear();
+}
+// Th
+// This will delete all of the second items in a map and then clear the map to destroy all dangling pointers
 template <class T, class K>
-inline void DELETE_MAP_SECOND(std::map<T, K>& map)
+inline void DELETE_MAP_OF_POINTERS(std::map<T, K>& map)
 {
-  for (typename std::map<T, K>::iterator it = map.begin(); it != map.end(); ++it) {
-    delete it->second;
+  for (auto& [key,value] : map) {
+    delete value;
+    value = nullptr;
   }
   map.clear();
 }

projects/biogears/libBiogears/include/biogears/cdm/Serializer.h

@@ -30,7 +30,6 @@ specific language governing permissions and limitations under the License.
 #include <biogears/cdm/CommonDataModel.h>
 #include <biogears/exports.h>
 
-CDM_BIND_DECL(ObjectData)
 
 namespace biogears {
 class  Serializer {

projects/biogears/libBiogears/include/biogears/cdm/circuit/SECircuit.h

@@ -15,16 +15,15 @@ specific language governing permissions and limitations under the License.
 #include <biogears/cdm/circuit/SECircuitNode.h>
 #include <biogears/cdm/circuit/SECircuitPath.h>
 
-#define CIRCUIT_TEMPLATE typename CircuitBindType, typename NodeType, typename CircuitNodeBindType, typename PathType, typename CircuitPathBindType
-#define CIRCUIT_TYPES CircuitBindType, NodeType, CircuitNodeBindType, PathType, CircuitPathBindType
+#define CIRCUIT_TEMPLATE  typename NodeType,  typename PathType
+#define CIRCUIT_TYPES  NodeType,  PathType
 
-CDM_BIND_DECL(CircuitData)
 
 namespace biogears {
 namespace io {
   class Circuit;
 }
-
+#pragma warning(disable : 4661)
 template <CIRCUIT_TEMPLATE>
 class SECircuit : public Loggable {
   friend io::Circuit;
@@ -34,13 +33,7 @@ class SECircuit : public Loggable {
   SECircuit(const std::string& name, Logger* logger);
   virtual ~SECircuit();
 
-  virtual void Clear(); //clear memory
-
-  virtual bool Load(const CircuitBindType& in, const std::map<std::string, NodeType*>& nodes, const std::map<std::string, PathType*>& paths);
-  virtual CircuitBindType* Unload() const;
-
-protected:
-  virtual void Unload(CircuitBindType& data) const;
+  virtual void Invalidate(); // clear memory
 
 public:
   virtual std::string GetName() const;
@@ -105,5 +98,5 @@ class SECircuit : public Loggable {
   std::vector<PathType*> m_PolarizedElementPaths;
   std::map<const NodeType*, size_t> m_CalculatorIndex; // A unique id (starting at 0) for all nodes except the reference node
 };
+#pragma warning(default : 4661)
 }
-#include <biogears/cdm/circuit/SECircuit.inl>