From 73da5ff006800ba6c060a1d96fd09e4b4a5648b4 Mon Sep 17 00:00:00 2001
From: Brett Laptop <tri11paragon@tpgc.me>
Date: Mon, 18 Nov 2024 19:50:46 -0500
Subject: [PATCH] about to start convert

---
 ...ce (conflicted copy 2024-11-18 173055).xml | 222 ++++++++++++++++++
 CMakeLists.txt                                |   2 +-
 build_emscripten.sh                           |   0
 include/assign3/array.h                       |   4 +-
 include/assign3/functions.h                   |  17 ++
 include/assign3/manager.h                     |  19 +-
 include/assign3/som.h                         |  18 +-
 src/functions.cpp                             |  34 +++
 ...in (conflicted copy 2024-11-18 194147).cpp | 125 ++++++++++
 src/main.cpp                                  |  80 ++++++-
 src/manager.cpp                               |  88 +++----
 src/som.cpp                                   |  66 +++++-
 12 files changed, 581 insertions(+), 94 deletions(-)
 create mode 100644 .idea/workspace (conflicted copy 2024-11-18 173055).xml
 mode change 100755 => 100644 build_emscripten.sh
 create mode 100644 src/main (conflicted copy 2024-11-18 194147).cpp

diff --git a/.idea/workspace (conflicted copy 2024-11-18 173055).xml b/.idea/workspace (conflicted copy 2024-11-18 173055).xml
new file mode 100644
index 0000000..7688f0a
--- /dev/null
+++ b/.idea/workspace (conflicted copy 2024-11-18 173055).xml	
@@ -0,0 +1,222 @@
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+}</component>
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diff --git a/CMakeLists.txt b/CMakeLists.txt
index a7b9ac7..ba280ad 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.25)
-project(COSC-4P80-Assignment-3 VERSION 0.0.20)
+project(COSC-4P80-Assignment-3 VERSION 0.0.21)
 include(FetchContent)
 
 option(ENABLE_ADDRSAN "Enable the address sanitizer" OFF)
diff --git a/build_emscripten.sh b/build_emscripten.sh
old mode 100755
new mode 100644
diff --git a/include/assign3/array.h b/include/assign3/array.h
index 63cfaed..c2085fb 100644
--- a/include/assign3/array.h
+++ b/include/assign3/array.h
@@ -44,8 +44,8 @@ namespace assign3
                     case shape_t::GRID_OFFSET_WRAP:
                         for (blt::size_t j = 0; j < height; j++)
                             for (blt::size_t i = 0; i < width; i++)
-                                map.emplace_back(dimensions, (j % 2 == 0 ? static_cast<Scalar>(i) : static_cast<Scalar>(i) + 0.5f),
-                                                 static_cast<Scalar>(static_cast<double>(j) * (std::sqrt(3) / 2.0)));
+                                map.emplace_back(dimensions, (j % 2 == 0 ? static_cast<Scalar>(i) : static_cast<Scalar>(i) + 0.5f), j);
+                        // static_cast<Scalar>(static_cast<double>(j) * (std::sqrt(3) / 2.0))
                         break;
                 }
             }
diff --git a/include/assign3/functions.h b/include/assign3/functions.h
index 1c6bd52..468a1e6 100644
--- a/include/assign3/functions.h
+++ b/include/assign3/functions.h
@@ -77,6 +77,23 @@ namespace assign3
             blt::i32 width, height;
     };
     
+    struct axial_distance_function_t : public distance_function_t
+    {
+        [[nodiscard]] Scalar distance(blt::span<const Scalar> x, blt::span<const Scalar> y) const final;
+    };
+    
+    struct toroidal_axial_distance_function_t : public distance_function_t
+    {
+        public:
+            toroidal_axial_distance_function_t(blt::i32 width, blt::i32 height): width(width), height(height)
+            {}
+            
+            [[nodiscard]] Scalar distance(blt::span<const Scalar> x, blt::span<const Scalar> y) const final;
+        
+        private:
+            blt::i32 width, height;
+    };
+    
 }
 
 #endif //COSC_4P80_ASSIGNMENT_3_FUNCTIONS_H
diff --git a/include/assign3/manager.h b/include/assign3/manager.h
index 176c9bc..5669ec9 100644
--- a/include/assign3/manager.h
+++ b/include/assign3/manager.h
@@ -82,10 +82,6 @@ namespace assign3
             
             void cleanup();
             
-            std::vector<float> get_neuron_activations(const data_file_t& file);
-            
-            static std::vector<float> normalize_data(const std::vector<float>& data);
-            
             void draw_som(neuron_render_info_t info, const std::function<blt::vec4(render_data_t)>& color_func);
             
             void draw_debug(const data_file_t& file);
@@ -97,19 +93,22 @@ namespace assign3
                 switch (static_cast<shape_t>(selected_som_mode))
                 {
                     case shape_t::GRID:
-                    case shape_t::GRID_OFFSET:
                         distance_function = std::make_unique<euclidean_distance_function_t>();
                         break;
-                    case shape_t::GRID_OFFSET_WRAP:
                     case shape_t::GRID_WRAP:
                         distance_function = std::make_unique<toroidal_euclidean_distance_function_t>(som_width, som_height);
                         break;
+                    case shape_t::GRID_OFFSET:
+                        distance_function = std::make_unique<axial_distance_function_t>();
+                        break;
+                    case shape_t::GRID_OFFSET_WRAP:
+                        distance_function = std::make_unique<toroidal_axial_distance_function_t>(som_width, som_height);
+                        break;
                 }
-                error_plotting.clear();
                 som = std::make_unique<som_t>(motor_data.files[currently_selected_network], som_width, som_height, max_epochs,
-                                              distance_function.get(), static_cast<shape_t>(selected_som_mode),
+                                              distance_function.get(), topology_function.get(), static_cast<shape_t>(selected_som_mode),
                                               static_cast<init_t>(selected_init_type), normalize_init);
-                error_plotting.push_back(som->topological_error(motor_data.files[currently_selected_network]));
+                som->compute_neuron_activations();
             }
         
         private:
@@ -118,8 +117,6 @@ namespace assign3
             std::unique_ptr<topology_function_t> topology_function;
             std::unique_ptr<distance_function_t> distance_function;
             
-            std::vector<Scalar> error_plotting;
-            
             blt::gfx::font_renderer_t fr2d{};
             blt::gfx::batch_renderer_2d br2d;
             
diff --git a/include/assign3/som.h b/include/assign3/som.h
index 909957b..9e1327c 100644
--- a/include/assign3/som.h
+++ b/include/assign3/som.h
@@ -30,17 +30,23 @@ namespace assign3
     {
         public:
             som_t(const data_file_t& file, blt::size_t width, blt::size_t height, blt::size_t max_epochs, distance_function_t* dist_func,
-                  shape_t shape, init_t init, bool normalize);
+                  topology_function_t* topology_function, shape_t shape, init_t init, bool normalize);
             
             blt::size_t get_closest_neuron(const std::vector<Scalar>& data);
             
             Scalar find_closest_neighbour_distance(blt::size_t v0);
             
-            void train_epoch(Scalar initial_learn_rate, topology_function_t* basis_func);
+            void train_epoch(Scalar initial_learn_rate);
             
             blt::vec2 get_topological_position(const std::vector<Scalar>& data);
             
-            Scalar topological_error(const data_file_t& data);
+            Scalar topological_error();
+            
+            void compute_neuron_activations(Scalar distance = 2, Scalar activation = 0.5);
+            
+            void write_activations(std::ostream& out);
+            
+            void write_topology_errors(std::ostream& out);
             
             [[nodiscard]] const array_t& get_array() const
             { return array; }
@@ -50,6 +56,9 @@ namespace assign3
             
             [[nodiscard]] blt::size_t get_max_epochs() const
             { return max_epochs; }
+            
+            [[nodiscard]] const std::vector<Scalar>& get_topological_errors() const
+            { return topological_errors; }
         
         private:
             array_t array;
@@ -57,6 +66,9 @@ namespace assign3
             blt::size_t current_epoch = 0;
             blt::size_t max_epochs;
             distance_function_t* dist_func;
+            topology_function_t* topology_function;
+            
+            std::vector<Scalar> topological_errors;
     };
     
 }
diff --git a/src/functions.cpp b/src/functions.cpp
index 90a592c..486da5d 100644
--- a/src/functions.cpp
+++ b/src/functions.cpp
@@ -54,4 +54,38 @@ namespace assign3
         Scalar y_min = std::min(y_diff, static_cast<Scalar>(height) - y_diff);
         return std::sqrt(x_min * x_min + y_min * y_min);
     }
+    
+    Scalar axial_distance_function_t::distance(blt::span<const Scalar> x, blt::span<const Scalar> y) const
+    {
+        static thread_local std::vector<Scalar> distances;
+        distances.clear();
+        Scalar total = 0;
+        for (auto [q, r] : blt::in_pairs(x, y))
+        {
+            distances.push_back(std::abs(q - r));
+            total += distances.back();
+        }
+        
+        Scalar min = distances.front();
+        for (auto v : distances)
+            min = std::min(min, v);
+
+        return total - min;
+    }
+    
+    Scalar axial_distance(Scalar q1, Scalar r1, Scalar q2, Scalar r2) {
+        return (std::abs(q1 - q2) + std::abs(r1 - r2) + std::abs((q1 + r1) - (q2 + r2))) / 2;
+    }
+    
+    Scalar toroidal_axial_distance_function_t::distance(blt::span<const Scalar> x, blt::span<const Scalar> y) const
+    {
+        BLT_ASSERT(x.size() == 2 && y.size() == 2);
+        
+        Scalar x_diff = std::abs(x[0] - y[0]);
+        Scalar y_diff = std::abs(x[1] - y[1]);
+        Scalar x_min = std::min(x_diff, static_cast<Scalar>(width) - x_diff);
+        Scalar y_min = std::min(y_diff, static_cast<Scalar>(height) - y_diff);
+        Scalar total = x_min + y_min;
+        return total - std::min(x_min, y_min);
+    }
 }
\ No newline at end of file
diff --git a/src/main (conflicted copy 2024-11-18 194147).cpp b/src/main (conflicted copy 2024-11-18 194147).cpp
new file mode 100644
index 0000000..c30f011
--- /dev/null
+++ b/src/main (conflicted copy 2024-11-18 194147).cpp	
@@ -0,0 +1,125 @@
+#include <blt/std/logging.h>
+#include <blt/parse/argparse.h>
+#include <blt/gfx/window.h>
+#include "blt/gfx/renderer/resource_manager.h"
+#include "blt/gfx/renderer/camera.h"
+#include "implot.h"
+#include <assign3/file.h>
+#include <assign3/manager.h>
+
+using namespace assign3;
+
+blt::gfx::matrix_state_manager global_matrices;
+blt::gfx::resource_manager resources;
+blt::gfx::first_person_camera_2d camera;
+assign3::motor_data_t data{};
+assign3::renderer_t renderer{data, resources, global_matrices};
+
+void init(const blt::gfx::window_data&)
+{
+    using namespace blt::gfx;
+    BLT_INFO("Hello World!");
+    
+    global_matrices.create_internals();
+    resources.load_resources();
+    renderer.create();
+    
+    ImPlot::CreateContext();
+}
+
+void update(const blt::gfx::window_data& window_data)
+{
+    using namespace blt::gfx;
+    global_matrices.update_perspectives(window_data.width, window_data.height, 90, 0.1, 2000);
+    
+    camera.update();
+    camera.update_view(global_matrices);
+    global_matrices.update();
+    
+    renderer.render();
+}
+
+void destroy(const blt::gfx::window_data&)
+{
+    global_matrices.cleanup();
+    resources.cleanup();
+    renderer.cleanup();
+    ImPlot::DestroyContext();
+    blt::gfx::cleanup();
+    BLT_INFO("Goodbye World!");
+}
+
+void load_data_files(const std::string& str)
+{
+    data.files = assign3::data_file_t::load_data_files_from_path(str);
+    for (auto& v : data.files)
+        v = v.normalize();
+    data.update();
+}
+
+void action_start_graphics(const std::vector<std::string>& argv_vector)
+{
+    blt::arg_parse parser{};
+    
+    parser.addArgument(blt::arg_builder{"--file", "-f"}
+                               .setDefault("../data")
+                               .setHelp("Path to data files").build());
+    
+    auto args = parser.parse_args(argv_vector);
+    
+    load_data_files(args.get<std::string>("file"));
+    
+    blt::gfx::init(blt::gfx::window_data{"My Sexy Window", init, update, destroy}.setSyncInterval(1).setMaximized(true));
+}
+
+void action_test(const std::vector<std::string>& argv_vector)
+{
+    blt::arg_parse parser{};
+    
+    parser.addArgument(blt::arg_builder{"--file", "-f"}
+                               .setDefault("../data")
+                               .setHelp("Path to data files").build());
+    
+    auto args = parser.parse_args(argv_vector);
+    
+    load_data_files(args.get<std::string>("file"));
+    
+    
+}
+
+void action_convert(const std::vector<std::string>& argv_vector)
+{
+
+}
+
+int main(int argc, const char** argv)
+{
+    std::vector<std::string> argv_vector;
+    for (int i = 0; i < argc; i++)
+        argv_vector.emplace_back(argv[i]);
+    
+    blt::arg_parse parser{};
+    
+    parser.addArgument(blt::arg_builder{"action"}
+                               .setAction(blt::arg_action_t::SUBCOMMAND)
+                               .setHelp("Action to run. Can be: [graphics, test, convert]").build());
+    
+    auto args = parser.parse_args(argv_vector);
+    
+    if (!args.contains("action"))
+    {
+        BLT_ERROR("Please provide an action");
+        return 0;
+    }
+    
+    argv_vector.erase(argv_vector.begin() + 1);
+    
+    auto action = blt::string::toLowerCase(args.get<std::string>("action"));
+    if (action == "graphics")
+        action_start_graphics(argv_vector);
+    else if (action == "test")
+        action_test(argv_vector);
+    else if (action == "convert")
+        action_convert(argv_vector);
+    
+}
diff --git a/src/main.cpp b/src/main.cpp
index 7de4ab8..e54b2e8 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -49,18 +49,82 @@ void destroy(const blt::gfx::window_data&)
     BLT_INFO("Goodbye World!");
 }
 
-int main(int argc, const char** argv)
+void load_data_files(const std::string& str)
 {
-    blt::arg_parse parser{};
-    
-    parser.addArgument(blt::arg_builder{"--file", "-f"}.setDefault("../data").setHelp("Path to data files").build());
-    
-    auto args = parser.parse_args(argc, argv);
-    
-    data.files = assign3::data_file_t::load_data_files_from_path(args.get<std::string>("file"));
+    data.files = assign3::data_file_t::load_data_files_from_path(str);
     for (auto& v : data.files)
         v = v.normalize();
     data.update();
+}
+
+void action_start_graphics(const std::vector<std::string>& argv_vector)
+{
+    blt::arg_parse parser{};
+    parser.setHelpExtras("graphics");
+    
+    parser.addArgument(blt::arg_builder{"--file", "-f"}
+                               .setDefault("../data")
+                               .setHelp("Path to data files").build());
+    
+    auto args = parser.parse_args(argv_vector);
+    
+    load_data_files(args.get<std::string>("file"));
     
     blt::gfx::init(blt::gfx::window_data{"My Sexy Window", init, update, destroy}.setSyncInterval(1).setMaximized(true));
 }
+
+void action_test(const std::vector<std::string>& argv_vector)
+{
+    blt::arg_parse parser{};
+    parser.setHelpExtras("test");
+    
+    parser.addArgument(blt::arg_builder{"--file", "-f"}
+                               .setDefault("../data")
+                               .setHelp("Path to data files").build());
+    
+    auto args = parser.parse_args(argv_vector);
+    
+    load_data_files(args.get<std::string>("file"));
+    
+    
+}
+
+void action_convert(const std::vector<std::string>& argv_vector)
+{
+    blt::arg_parse parser{};
+    parser.setHelpExtras("convert");
+    
+    auto args = parser.parse_args(argv_vector);
+}
+
+int main(int argc, const char** argv)
+{
+    std::vector<std::string> argv_vector;
+    for (int i = 0; i < argc; i++)
+        argv_vector.emplace_back(argv[i]);
+    
+    blt::arg_parse parser{};
+    
+    parser.addArgument(blt::arg_builder{"action"}
+                               .setAction(blt::arg_action_t::SUBCOMMAND)
+                               .setHelp("Action to run. Can be: [graphics, test, convert]").build());
+    
+    auto args = parser.parse_args(argv_vector);
+    
+    if (!args.contains("action"))
+    {
+        BLT_ERROR("Please provide an action");
+        return 0;
+    }
+    
+//    argv_vector.erase(argv_vector.begin() + 1);
+    
+    auto action = blt::string::toLowerCase(args.get<std::string>("action"));
+    if (action == "graphics")
+        action_start_graphics(argv_vector);
+    else if (action == "test")
+        action_test(argv_vector);
+    else if (action == "convert")
+        action_convert(argv_vector);
+    
+}
diff --git a/src/manager.cpp b/src/manager.cpp
index 3848d01..fe56908 100644
--- a/src/manager.cpp
+++ b/src/manager.cpp
@@ -123,8 +123,8 @@ namespace assign3
     {
         using namespace blt::gfx;
         
-        ImGui::ShowDemoWindow();
-        ImPlot::ShowDemoWindow();
+//        ImGui::ShowDemoWindow();
+//        ImPlot::ShowDemoWindow();
         
         if (ImGui::Begin("Controls"))
         {
@@ -137,7 +137,10 @@ namespace assign3
                     regenerate_network();
                 
                 if (ImGui::Button("Run Epoch"))
-                    som->train_epoch(initial_learn_rate, topology_function.get());
+                {
+                    som->train_epoch(initial_learn_rate);
+                    som->compute_neuron_activations();
+                }
                 ImGui::Checkbox("Run to completion", &running);
                 ImGui::Text("Epoch %ld / %ld", som->get_current_epoch(), som->get_max_epochs());
             }
@@ -152,8 +155,9 @@ namespace assign3
                 if (ImGui::ListBox("##InitType", &selected_init_type, get_selection_string, init_names.data(), static_cast<int>(init_names.size())))
                     regenerate_network();
                 ImGui::TextWrapped("Help: %s", init_helps[selected_init_type].c_str());
-                ImGui::Separator();
-                ImGui::Checkbox("Normalize Init Data", &normalize_init);
+                if (ImGui::Checkbox("Normalize Init Data", &normalize_init))
+                    regenerate_network();
+                ImGui::SeparatorText("Som Specifics");
                 if (ImGui::InputInt("SOM Width", &som_width) || ImGui::InputInt("SOM Height", &som_height) ||
                     ImGui::InputInt("Max Epochs", &max_epochs))
                     regenerate_network();
@@ -187,7 +191,11 @@ namespace assign3
                             static std::vector<std::string> names;
                             names.clear();
                             for (blt::size_t i = 0; i < som->get_array().get_map().size(); i++)
-                                names.push_back("Neuron " + std::to_string(i));
+                            {
+                                auto pos = som->get_array().from_index(i);
+                                names.push_back("Neuron " + std::to_string(i) +
+                                                " (" + std::to_string(pos.x()) + ", " + std::to_string(pos.y()) + ")");
+                            }
                             ImGui::Text("Select Neuron");
                             ImGui::ListBox("##SelectNeuron", &selected_neuron, get_selection_string, names.data(), static_cast<int>(names.size()));
                         }
@@ -199,14 +207,17 @@ namespace assign3
         ImGui::End();
         
         auto current_data_file = motor_data.files[currently_selected_network];
-        auto closest_type = get_neuron_activations(current_data_file);
         
         if (ImGui::Begin("Plots & Data"))
         {
             ImPlot::SetNextAxesLimits(0, som_width, 0, som_height, ImPlotCond_Always);
             if (ImPlot::BeginPlot("Activations", ImVec2(-1, 0), ImPlotFlags_NoInputs))
             {
-                auto rev = rotate90Clockwise(closest_type, som_width, som_height);
+                static std::vector<float> activations;
+                activations.clear();
+                for (const auto& n : som->get_array().get_map())
+                    activations.push_back(n.get_activation());
+                auto rev = rotate90Clockwise(activations, som_width, som_height);
 //                auto rev = closest_type;
 //                std::reverse(rev.begin(), rev.end());
                 ImPlot::PlotHeatmap("##data_map", rev.data(), som_height, som_width, 0, 0, "%.1f", ImPlotPoint(0, 0),
@@ -216,7 +227,7 @@ namespace assign3
             ImPlot::SetNextAxesLimits(0, max_epochs, 0, 1, ImPlotCond_Once);
             if (ImPlot::BeginPlot("Error"))
             {
-                ImPlot::PlotLine("##error", error_plotting.data(), static_cast<int>(error_plotting.size()));
+                ImPlot::PlotLine("##error", som->get_topological_errors().data(), static_cast<int>(som->get_topological_errors().size()));
                 ImPlot::EndPlot();
             }
         }
@@ -226,18 +237,17 @@ namespace assign3
         {
             if (som->get_current_epoch() < som->get_max_epochs())
             {
-                som->train_epoch(initial_learn_rate, topology_function.get());
-                error_plotting.push_back(som->topological_error(current_data_file));
+                som->train_epoch(initial_learn_rate);
+                som->compute_neuron_activations();
             }
         }
         
         
         if (!debug_mode)
         {
-            closest_type = normalize_data(closest_type);
             draw_som(neuron_render_info_t{}.set_base_pos({370, 145}).set_neuron_scale(120).set_neuron_padding({5, 5}),
-                     [&closest_type](render_data_t context) {
-                         auto type = closest_type[context.index];
+                     [](render_data_t context) {
+                         auto type = context.neuron.get_activation();
                          return type >= 0 ? blt::make_color(0, type, 0) : blt::make_color(-type, 0, 0);
                      });
         } else
@@ -247,33 +257,6 @@ namespace assign3
         fr2d.render();
     }
     
-    std::vector<float> renderer_t::get_neuron_activations(const data_file_t& file)
-    {
-        static std::vector<float> closest_type;
-        closest_type.clear();
-        closest_type.resize(som->get_array().get_map().size());
-        
-        
-        for (auto [i, v] : blt::enumerate(som->get_array().get_map()))
-        {
-            auto half = som->find_closest_neighbour_distance(i) / at_distance_measurement;
-//            auto sigma = std::sqrt(-(half * half) / (2 * std::log(requested_activation)));
-//            auto r = 1 / (2 * sigma * sigma);
-//
-            auto scale = topology_function->scale(half, requested_activation);
-            for (const auto& data : file.data_points)
-            {
-                auto ds = topology_function->call(v.dist(data.bins), scale);
-                if (data.is_bad)
-                    closest_type[i] -= ds;
-                else
-                    closest_type[i] += ds;
-            }
-        }
-        
-        return closest_type;
-    }
-    
     void renderer_t::draw_debug(const data_file_t& file)
     {
         switch (static_cast<debug_t>(debug_state))
@@ -307,9 +290,8 @@ namespace assign3
                 }
                 
                 const auto& data_point = file.data_points[selected_data_point];
-                auto closest_type = normalize_data(get_neuron_activations(file));
                 draw_som(neuron_render_info_t{}.set_base_pos({370, 145}).set_neuron_scale(120).set_neuron_padding({0, 0}),
-                         [this, &neuron_positions, &data_point, &closest_type](render_data_t context) {
+                         [this, &neuron_positions, &data_point](render_data_t context) {
                              auto half = som->find_closest_neighbour_distance(context.index) / at_distance_measurement;
                              auto scale = topology_function->scale(half, requested_activation);
                              auto ds = topology_function->call(context.neuron.dist(data_point.bins), scale);
@@ -321,7 +303,7 @@ namespace assign3
                              auto text_height = text.getAssociatedText().getTextHeight();
                              text.setPosition(context.neuron_padded - blt::vec2{text_width / 2.0f, text_height / 2.0f}).setZIndex(1);
                              
-                             auto type = closest_type[context.index];
+                             auto type = context.neuron.get_activation();
                              return type >= 0 ? blt::make_color(0, type, 0) : blt::make_color(-type, 0, 0);
                          });
                 
@@ -334,7 +316,6 @@ namespace assign3
                 break;
             case debug_t::DISTANCE:
             {
-                auto closest_type = normalize_data(get_neuron_activations(file));
                 auto& selected_neuron_ref = som->get_array().get_map()[selected_neuron];
                 static std::vector<Scalar> distances_2d;
                 static std::vector<Scalar> distances_nd;
@@ -348,7 +329,7 @@ namespace assign3
                 }
                 
                 draw_som(neuron_render_info_t{}.set_base_pos({370, 145}).set_neuron_scale(120).set_neuron_padding({0, 0}),
-                         [this, &closest_type](render_data_t context) {
+                         [this](render_data_t context) {
                              auto& text = fr2d.render_text(
                                      "2D: " + std::to_string(distances_2d[context.index]) + "\nND: " +
                                      std::to_string(distances_nd[context.index]), 18).setColor(0.2, 0.2, 0.8);
@@ -357,24 +338,11 @@ namespace assign3
                              
                              if (static_cast<blt::size_t>(selected_neuron) == context.index)
                                  return blt::make_color(0, 0, 1);
-                             auto type = closest_type[context.index];
+                             auto type = context.neuron.get_activation();
                              return type >= 0 ? blt::make_color(0, type, 0) : blt::make_color(-type, 0, 0);
                          });
             }
                 break;
         }
     }
-    
-    std::vector<float> renderer_t::normalize_data(const std::vector<float>& data)
-    {
-        std::vector<float> return_data;
-        auto min_act = *std::min_element(data.begin(), data.end());
-        auto max_act = *std::max_element(data.begin(), data.end());
-        for (auto& v : data)
-        {
-            auto n = 2 * (v - min_act) / (max_act - min_act) - 1;
-            return_data.push_back(n);
-        }
-        return return_data;
-    }
 }
\ No newline at end of file
diff --git a/src/som.cpp b/src/som.cpp
index b8b0ec4..c37db04 100644
--- a/src/som.cpp
+++ b/src/som.cpp
@@ -27,14 +27,16 @@ namespace assign3
 {
     
     som_t::som_t(const data_file_t& file, blt::size_t width, blt::size_t height, blt::size_t max_epochs, distance_function_t* dist_func,
-                 shape_t shape, init_t init, bool normalize):
-            array(file.data_points.begin()->bins.size(), width, height, shape), file(file), max_epochs(max_epochs), dist_func(dist_func)
+                 topology_function_t* topology_function, shape_t shape, init_t init, bool normalize):
+            array(file.data_points.begin()->bins.size(), width, height, shape), file(file), max_epochs(max_epochs), dist_func(dist_func),
+            topology_function(topology_function)
     {
         for (auto& v : array.get_map())
             v.randomize(std::random_device{}(), init, normalize, file);
+        topological_errors.push_back(topological_error());
     }
     
-    void som_t::train_epoch(Scalar initial_learn_rate, topology_function_t* basis_func)
+    void som_t::train_epoch(Scalar initial_learn_rate)
     {
         blt::random::random_t rand{std::random_device{}()};
         std::shuffle(file.data_points.begin(), file.data_points.end(), rand);
@@ -52,18 +54,18 @@ namespace assign3
             auto distance_min = find_closest_neighbour_distance(v0_idx);
             // this will find the required scaling factor to make a point in the middle between v0 and its closest neighbour activate 50%
             // from the perspective of the gaussian function
-            auto scale = basis_func->scale(distance_min * 0.5f, 0.5);
+            auto scale = topology_function->scale(distance_min * 0.5f, 0.5);
             
             for (auto [i, n] : blt::enumerate(array.get_map()))
             {
                 if (i == v0_idx)
                     continue;
-                auto dist = basis_func->call(neuron_t::distance(dist_func, v0, n), time_ratio * scale);
+                auto dist = topology_function->call(neuron_t::distance(dist_func, v0, n), time_ratio * scale);
                 n.update(current_data.bins, dist, eta);
             }
         }
-        
         current_epoch++;
+        topological_errors.push_back(topological_error());
     }
     
     blt::size_t som_t::get_closest_neuron(const std::vector<Scalar>& data)
@@ -139,12 +141,12 @@ namespace assign3
         return (dp1 * p_1) + (dp2 * p_2) + (dp3 * p_3);
     }
     
-    Scalar som_t::topological_error(const data_file_t& data)
+    Scalar som_t::topological_error()
     {
         Scalar total = 0;
         std::vector<std::pair<blt::size_t, Scalar>> distances;
         
-        for (const auto& x : data.data_points)
+        for (const auto& x : file.data_points)
         {
             distances.clear();
             for (const auto& [i, n] : blt::enumerate(array.get_map()))
@@ -171,7 +173,53 @@ namespace assign3
                 total += 1;
         }
         
-        return total / static_cast<Scalar>(data.data_points.size());
+        return total / static_cast<Scalar>(file.data_points.size());
+    }
+    
+    void som_t::compute_neuron_activations(Scalar distance, Scalar activation)
+    {
+        for (auto& n : array.get_map())
+            n.set_activation(0);
+        
+        Scalar min = std::numeric_limits<Scalar>::max();
+        Scalar max = std::numeric_limits<Scalar>::min();
+        
+        for (auto [i, v] : blt::enumerate(array.get_map()))
+        {
+            auto half = find_closest_neighbour_distance(i) / distance;
+//            auto sigma = std::sqrt(-(half * half) / (2 * std::log(requested_activation)));
+//            auto r = 1 / (2 * sigma * sigma);
+//
+            auto scale = topology_function->scale(half, activation);
+            for (const auto& data : file.data_points)
+            {
+                auto ds = topology_function->call(v.dist(data.bins), scale);
+                if (data.is_bad)
+                    v.activate(-ds);
+                else
+                    v.activate(ds);
+            }
+            
+            min = std::min(min, v.get_activation());
+            max = std::max(max, v.get_activation());
+        }
+        
+        for (auto& n : array.get_map())
+            n.set_activation(2 * (n.get_activation() - min) / (max - min) - 1);
+    }
+    
+    void som_t::write_activations(std::ostream& out)
+    {
+        out << "x,y,activation\n";
+        for (const auto& v : array.get_map())
+            out << v.get_x() << ',' << v.get_y() << ',' << v.get_activation() << '\n';
+    }
+    
+    void som_t::write_topology_errors(std::ostream& out)
+    {
+        out << "epoch,error\n";
+        for (auto [i, v] : blt::enumerate(topological_errors))
+            out << i << ',' << v << '\n';
     }