Merge branch 'development'

janhohenheim · Nov 17, 2016 · ea47a92 · ea47a92
2 parents 97bb1ab + 298f093
commit ea47a92
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Showing 68 changed files with 2,041 additions and 785 deletions.
diff --git a/.appveyor.yml b/.appveyor.yml
@@ -1,2 +1,10 @@
+configuration:
+  - Release
+
 build_script:
-  - msbuild %solution_name%
+  - msbuild %solution_name%
+
+test_script:
+  - C:\projects\jnf-neat\x64\Release\xor_two_bits.exe
+  - C:\projects\jnf-neat\x64\Release\xor_three_bits.exe
+  - C:\projects\jnf-neat\x64\Release\EvenNumbers.exe
diff --git a/.gitignore b/.gitignore
@@ -410,3 +410,5 @@ cmake_install.cmake
 install_manifest.txt
 Testing/
 *.cmake
+cmake-build-debug/
+
diff --git a/.travis.yml b/.travis.yml
@@ -8,6 +8,7 @@ addons:
     sources:
       - ubuntu-toolchain-r-test
 script:
-  - cmake -DCMAKE_CXX_COMPILER=g++-6 CMakeLists.txt
-  - make 
-  - travis_wait make test
+  - cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=g++-6 .
+  - make
+  - ctest --verbose
+
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -8,13 +8,20 @@ endif()
 
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/out/lib)
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/out/tests)
+set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -Wall")
 
+set(CMAKE_C_FLAGS -fPIC)
 set(CMAKE_CXX_FLAGS -fPIC)
 
 add_subdirectory(Core)
 
 add_library(Hippocrates SHARED $<TARGET_OBJECTS:Core>)
+set(THREADS_PREFER_PTHREAD_FLAG ON)
+find_package(Threads REQUIRED)
+
 target_link_libraries(Hippocrates -lstdc++fs)
+target_link_libraries(Hippocrates Threads::Threads)
 
 enable_testing()
 add_subdirectory(Tests)
+
diff --git a/Core/CMakeLists.txt b/Core/CMakeLists.txt
@@ -1,2 +1,2 @@
-file(GLOB SOURCES Sources/Headers/*.h Sources/Implementations/*.cpp)
+file(GLOB_RECURSE SOURCES [RELATIVE Sources] *.cpp *.hpp *.c *.h)
 add_library(Core SHARED OBJECT ${SOURCES})
diff --git a/Core/Core.vcxproj b/Core/Core.vcxproj
@@ -78,13 +78,15 @@
       <AdditionalIncludeDirectories>
       </AdditionalIncludeDirectories>
       <AdditionalOptions>/DLL %(AdditionalOptions)</AdditionalOptions>
+      <PreprocessorDefinitions> _UNICODE;UNICODE;%(PreprocessorDefinitions)</PreprocessorDefinitions>
     </ClCompile>
   </ItemDefinitionGroup>
   <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
     <ClCompile>
       <WarningLevel>Level3</WarningLevel>
       <Optimization>Disabled</Optimization>
       <SDLCheck>true</SDLCheck>
+      <PreprocessorDefinitions> _UNICODE;UNICODE;%(PreprocessorDefinitions)</PreprocessorDefinitions>
     </ClCompile>
   </ItemDefinitionGroup>
   <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
@@ -94,6 +96,7 @@
       <FunctionLevelLinking>true</FunctionLevelLinking>
       <IntrinsicFunctions>true</IntrinsicFunctions>
       <SDLCheck>true</SDLCheck>
+      <PreprocessorDefinitions> _UNICODE;UNICODE;%(PreprocessorDefinitions)</PreprocessorDefinitions>
     </ClCompile>
     <Link>
       <EnableCOMDATFolding>true</EnableCOMDATFolding>
@@ -107,40 +110,48 @@
       <FunctionLevelLinking>true</FunctionLevelLinking>
       <IntrinsicFunctions>true</IntrinsicFunctions>
       <SDLCheck>true</SDLCheck>
+      <PreprocessorDefinitions> _UNICODE;UNICODE;%(PreprocessorDefinitions)</PreprocessorDefinitions>
     </ClCompile>
     <Link>
       <EnableCOMDATFolding>true</EnableCOMDATFolding>
       <OptimizeReferences>true</OptimizeReferences>
     </Link>
   </ItemDefinitionGroup>
   <ItemGroup>
-    <ClInclude Include="Sources\Headers\body.h" />
-    <ClInclude Include="Sources\Headers\gene.h" />
-    <ClInclude Include="Sources\Headers\genome.h" />
-    <ClInclude Include="Sources\Headers\logger.h" />
-    <ClInclude Include="Sources\Headers\neural_network.h" />
-    <ClInclude Include="Sources\Headers\neural_network_trainer.h" />
-    <ClInclude Include="Sources\Headers\neuron.h" />
-    <ClInclude Include="Sources\Headers\organism.h" />
-    <ClInclude Include="Sources\Headers\species.h" />
-    <ClInclude Include="Sources\Headers\species_manager.h" />
-    <ClInclude Include="Sources\Headers\supervised_training_body.h" />
-    <ClInclude Include="Sources\Headers\trained_neural_network.h" />
-    <ClInclude Include="Sources\Headers\training_data.h" />
-    <ClInclude Include="Sources\Headers\training_parameters.h" />
+    <ClInclude Include="Sources\Headers\body.hpp" />
+    <ClInclude Include="Sources\Headers\gene.hpp" />
+    <ClInclude Include="Sources\Headers\genome.hpp" />
+    <ClInclude Include="Sources\Headers\innovation_cacher.hpp" />
+    <ClInclude Include="Sources\Headers\jsmn.h" />
+    <ClInclude Include="Sources\Headers\logger.hpp" />
+    <ClInclude Include="Sources\Headers\neural_network.hpp" />
+    <ClInclude Include="Sources\Headers\neural_network_trainer.hpp" />
+    <ClInclude Include="Sources\Headers\neuron.hpp" />
+    <ClInclude Include="Sources\Headers\organism.hpp" />
+    <ClInclude Include="Sources\Headers\species.hpp" />
+    <ClInclude Include="Sources\Headers\species_manager.hpp" />
+    <ClInclude Include="Sources\Headers\supervised_training_body.hpp" />
+    <ClInclude Include="Sources\Headers\trained\classifier.hpp" />
+    <ClInclude Include="Sources\Headers\trained\trained_neural_network.hpp" />
+    <ClInclude Include="Sources\Headers\training_data.hpp" />
+    <ClInclude Include="Sources\Headers\training_parameters.hpp" />
+    <ClInclude Include="Sources\Headers\type.hpp" />
+    <ClInclude Include="Sources\Headers\utility.hpp" />
   </ItemGroup>
   <ItemGroup>
     <ClCompile Include="Sources\Implementations\gene.cpp" />
     <ClCompile Include="Sources\Implementations\genome.cpp" />
+    <ClCompile Include="Sources\Implementations\innovation_cacher.cpp" />
+    <ClCompile Include="Sources\Implementations\jsmn.c" />
     <ClCompile Include="Sources\Implementations\logger.cpp" />
     <ClCompile Include="Sources\Implementations\neural_network.cpp" />
     <ClCompile Include="Sources\Implementations\neural_network_trainer.cpp" />
     <ClCompile Include="Sources\Implementations\neuron.cpp" />
     <ClCompile Include="Sources\Implementations\organism.cpp" />
     <ClCompile Include="Sources\Implementations\species.cpp" />
     <ClCompile Include="Sources\Implementations\species_manager.cpp" />
-    <ClCompile Include="Sources\Implementations\trained_neural_network.cpp" />
     <ClCompile Include="Sources\Implementations\training_parameters.cpp" />
+    <ClCompile Include="Sources\Implementations\utility.cpp" />
   </ItemGroup>
   <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
   <ImportGroup Label="ExtensionTargets">

diff --git a/Core/Core.vcxproj.filters b/Core/Core.vcxproj.filters
@@ -9,48 +9,66 @@
       <UniqueIdentifier>{93995380-89BD-4b04-88EB-625FBE52EBFB}</UniqueIdentifier>
       <Extensions>h;hh;hpp;hxx;hm;inl;inc;xsd</Extensions>
     </Filter>
+    <Filter Include="Headers\trained">
+      <UniqueIdentifier>{1b3a181c-c7b8-45a2-a69a-d9d44c2916a2}</UniqueIdentifier>
+    </Filter>
   </ItemGroup>
   <ItemGroup>
-    <ClInclude Include="Sources\Headers\body.h">
+    <ClInclude Include="Sources\Headers\utility.hpp">
+      <Filter>Headers</Filter>
+    </ClInclude>
+    <ClInclude Include="Sources\Headers\body.hpp">
+      <Filter>Headers</Filter>
+    </ClInclude>
+    <ClInclude Include="Sources\Headers\gene.hpp">
       <Filter>Headers</Filter>
     </ClInclude>
-    <ClInclude Include="Sources\Headers\gene.h">
+    <ClInclude Include="Sources\Headers\genome.hpp">
       <Filter>Headers</Filter>
     </ClInclude>
-    <ClInclude Include="Sources\Headers\genome.h">
+    <ClInclude Include="Sources\Headers\logger.hpp">
       <Filter>Headers</Filter>
     </ClInclude>
-    <ClInclude Include="Sources\Headers\logger.h">
+    <ClInclude Include="Sources\Headers\neural_network.hpp">
       <Filter>Headers</Filter>
     </ClInclude>
-    <ClInclude Include="Sources\Headers\neural_network.h">
+    <ClInclude Include="Sources\Headers\neural_network_trainer.hpp">
       <Filter>Headers</Filter>
     </ClInclude>
-    <ClInclude Include="Sources\Headers\neural_network_trainer.h">
+    <ClInclude Include="Sources\Headers\neuron.hpp">
       <Filter>Headers</Filter>
     </ClInclude>
-    <ClInclude Include="Sources\Headers\neuron.h">
+    <ClInclude Include="Sources\Headers\organism.hpp">
       <Filter>Headers</Filter>
     </ClInclude>
-    <ClInclude Include="Sources\Headers\organism.h">
+    <ClInclude Include="Sources\Headers\species.hpp">
       <Filter>Headers</Filter>
     </ClInclude>
-    <ClInclude Include="Sources\Headers\species.h">
+    <ClInclude Include="Sources\Headers\species_manager.hpp">
       <Filter>Headers</Filter>
     </ClInclude>
-    <ClInclude Include="Sources\Headers\trained_neural_network.h">
+    <ClInclude Include="Sources\Headers\supervised_training_body.hpp">
       <Filter>Headers</Filter>
     </ClInclude>
-    <ClInclude Include="Sources\Headers\training_parameters.h">
+    <ClInclude Include="Sources\Headers\training_data.hpp">
       <Filter>Headers</Filter>
     </ClInclude>
-    <ClInclude Include="Sources\Headers\species_manager.h">
+    <ClInclude Include="Sources\Headers\training_parameters.hpp">
       <Filter>Headers</Filter>
     </ClInclude>
-    <ClInclude Include="Sources\Headers\supervised_training_body.h">
+    <ClInclude Include="Sources\Headers\jsmn.h">
       <Filter>Headers</Filter>
     </ClInclude>
-    <ClInclude Include="Sources\Headers\training_data.h">
+    <ClInclude Include="Sources\Headers\innovation_cacher.hpp">
+      <Filter>Headers</Filter>
+    </ClInclude>
+    <ClInclude Include="Sources\Headers\trained\classifier.hpp">
+      <Filter>Headers\trained</Filter>
+    </ClInclude>
+    <ClInclude Include="Sources\Headers\trained\trained_neural_network.hpp">
+      <Filter>Headers\trained</Filter>
+    </ClInclude>
+    <ClInclude Include="Sources\Headers\type.hpp">
       <Filter>Headers</Filter>
     </ClInclude>
   </ItemGroup>
@@ -79,14 +97,20 @@
     <ClCompile Include="Sources\Implementations\species.cpp">
       <Filter>Implementations</Filter>
     </ClCompile>
-    <ClCompile Include="Sources\Implementations\trained_neural_network.cpp">
-      <Filter>Implementations</Filter>
-    </ClCompile>
     <ClCompile Include="Sources\Implementations\training_parameters.cpp">
       <Filter>Implementations</Filter>
     </ClCompile>
     <ClCompile Include="Sources\Implementations\species_manager.cpp">
       <Filter>Implementations</Filter>
     </ClCompile>
+    <ClCompile Include="Sources\Implementations\jsmn.c">
+      <Filter>Implementations</Filter>
+    </ClCompile>
+    <ClCompile Include="Sources\Implementations\utility.cpp">
+      <Filter>Implementations</Filter>
+    </ClCompile>
+    <ClCompile Include="Sources\Implementations\innovation_cacher.cpp">
+      <Filter>Implementations</Filter>
+    </ClCompile>
   </ItemGroup>
 </Project>
diff --git a/Core/Sources/Headers/body.h → Core/Sources/Headers/body.hpp b/Core/Sources/Headers/body.h → Core/Sources/Headers/body.hpp
@@ -1,5 +1,6 @@
 #pragma once
 #include <vector>
+#include "type.hpp"
 
 namespace Hippocrates {
 
@@ -14,16 +15,16 @@ class IBody {
 	virtual auto operator=(IBody&&)&->IBody& = default;
 
 	virtual auto Reset() -> void = 0;
-	virtual auto Update(const std::vector<float>& networkOutputs) -> void = 0;
+	virtual auto Update(const Type::neuron_values_t& networkOutputs) -> void = 0;
 	virtual auto HasFinishedTask() const -> bool = 0;
-	virtual auto GetFitness() const -> double = 0;
+	virtual auto GetFitness() const -> Type::fitness_t = 0;
 
-	virtual auto ProvideNetworkWithInputs() const -> std::vector<float> = 0;
+	virtual auto ProvideNetworkWithInputs() const -> Type::neuron_values_t= 0;
 
 	virtual auto GetInputCount() const -> std::size_t = 0;
 	virtual auto GetOutputCount() const -> std::size_t = 0;
 
-	virtual auto GetMaximumFitness() const -> double = 0;
+	virtual auto GetMaximumFitness() const ->Type::fitness_t = 0;
 };
 
 }
diff --git a/Core/Sources/Headers/gene.h → Core/Sources/Headers/gene.hpp b/Core/Sources/Headers/gene.h → Core/Sources/Headers/gene.hpp
@@ -1,30 +1,32 @@
 #pragma once
 #include <cstddef>
 #include <string>
+#include "../Headers/utility.hpp"
+#include "../Headers/type.hpp"
+
 namespace Hippocrates {
 
 struct Gene {
-public:
 	Gene();
 	Gene(const Gene& other) = default;
 	Gene(Gene&& other) = default;
+	Gene(std::string json);
 	~Gene() = default;
 
 	auto operator=(const Gene& other) -> Gene& = default;
 	auto operator=(Gene&& other) -> Gene& = default;
+	auto operator==(const Gene& other) const -> bool;
 
 	auto SetRandomWeight() -> void;
 	auto GetJSON() const->std::string;
 
 	std::size_t from = 0;
 	std::size_t to = 0;
-	float weight = 0.0f;
-	std::size_t historicalMarking = numberOfExistingGenes++;
+	Type::connection_weight_t weight = 0.0f;
+	static constexpr auto invalidHistoricalMarking = std::numeric_limits<std::size_t>::max();
+	std::size_t historicalMarking = invalidHistoricalMarking;
 	bool isEnabled = true;
 	bool isRecursive = false;
-
-private:
-	static std::size_t numberOfExistingGenes;
 };
 
 }
diff --git a/Core/Sources/Headers/genome.h → Core/Sources/Headers/genome.hpp b/Core/Sources/Headers/genome.h → Core/Sources/Headers/genome.hpp
@@ -1,7 +1,7 @@
 #pragma once
 
-#include "gene.h"
-#include "training_parameters.h"
+#include "gene.hpp"
+#include "training_parameters.hpp"
 #include <vector>
 
 namespace Hippocrates {
@@ -13,11 +13,15 @@ class Genome {
 	std::size_t inputCount = 0U;
 	std::size_t outputCount = 0U;
 	std::size_t neuronCount = 0U;
+	auto ParseGenesJson(std::string json) -> std::vector<Gene>;
 
 public:
 	explicit Genome(std::size_t inputCount, std::size_t outputCount, TrainingParameters parameters);
+	explicit Genome(std::string json);
+	explicit Genome() = default;
 	Genome(const Genome& other) = default;
 	Genome(Genome&& other) = default;
+
 	~Genome() = default;
 
 	auto operator=(const Genome& other) -> Genome& = default;
@@ -41,7 +45,7 @@ class Genome {
 	auto InsertGeneAt(Gene gene, size_t index) -> void;
 
 	auto GetTrainingParameters() const -> const TrainingParameters& { return parameters; }
-	auto GetGeneticalDistanceFrom(const Genome& other) const -> double;
+	auto GetGeneticalDistanceFrom(const Genome& other) const -> Type::connection_weight_t;
 	auto DoesContainGene(const Gene& gene) const -> bool;
 	auto GetJSON() const->std::string;
 

diff --git a/Core/Sources/Headers/innovation_cacher.hpp b/Core/Sources/Headers/innovation_cacher.hpp
@@ -0,0 +1,24 @@
+#pragma once
+#include <vector>
+#include <type_traits>
+#include "genome.hpp"
+
+namespace Hippocrates {
+
+class InnovationCacher {
+public:
+	auto AssignAndCacheHistoricalMarkings(Genome& genome) -> void;
+	auto AssignAndCacheHistoricalMarking(Gene& gene) -> void;
+	auto Clear() -> void;
+
+private:
+	std::vector<Gene> cache;
+	using cache_iterator = decltype(cache)::iterator;
+	std::size_t nextHighestHistoricalMarking = 0;
+
+private:
+	auto GetAndIncrementNextHighestHistoricalMarking() -> std::size_t;
+	auto FindGeneInCache(const Gene& gene) -> cache_iterator;
+};
+
+}