// Define waveform memory field structure
typedef struct {
    uint32_t dimensions;          // Number of dimensions in the field
    uint32_t* resolution;         // Resolution for each dimension
    float* damping_factors;       // Damping factor for each dimension
    complex_t*** field;           // Multi-dimensional complex field values
    field_parameters_t params;    // Field parameters (viscosity, elasticity, etc.)
    timestamp_t last_update;      // Last field update timestamp
} waveform_field_t;

// Initialize waveform memory field
waveform_field_t* init_waveform_field(uint32_t dimensions, uint32_t* resolution) {
    waveform_field_t* field = (waveform_field_t*)malloc(sizeof(waveform_field_t));
    
    // Set basic parameters
    field->dimensions = dimensions;
    field->resolution = (uint32_t*)malloc(dimensions * sizeof(uint32_t));
    memcpy(field->resolution, resolution, dimensions * sizeof(uint32_t));
    
    // Initialize damping factors (controls persistence)
    field->damping_factors = (float*)malloc(dimensions * sizeof(float));
    for (uint32_t i = 0; i < dimensions; i++) {
        // Default to gentle damping that allows long persistence
        field->damping_factors[i] = 0.9995f;
    }
    
    // Allocate field memory (simplified for clarity)
    field->field = allocate_complex_field(dimensions, resolution);
    
    // Initialize with zero values
    clear_field(field);
    
    // Set field parameters
    init_field_parameters(&field->params);
    
    // Set timestamp
    field->last_update = get_current_timestamp();
    
    return field;
}

// Update wave dynamics in the field
void update_wave_dynamics(waveform_field_t* field, double delta_time) {
    // Calculate effective time step (for stable simulation)
    float dt = calculate_effective_timestep(field, delta_time);
    
    // Store previous field state for update calculations
    complex_t*** prev_field = copy_field_state(field);
    
    // For each point in the field (simplified for clarity)
    for (uint32_t x = 0; x < field->resolution[0]; x++) {
        for (uint32_t y = 0; y < field->resolution[1]; y++) {
            // Calculate Laplacian (sum of neighboring values - center value)
            complex_t laplacian = calculate_laplacian(prev_field, x, y, field->dimensions);
            
            // Apply wave equation: acceleration = c² * laplacian
            complex_t acceleration = complex_multiply_scalar(
                laplacian, field->params.propagation_speed_squared);
            
            // Update field value using verlet integration
            field->field[x][y] = calculate_next_field_value(
                field->field[x][y], prev_field[x][y], acceleration, dt);
            
            // Apply damping (controls persistence)
            apply_damping(field, x, y, dt);
        }
    }
    
    // Apply boundary conditions
    apply_boundary_conditions(field);
    
    // Update timestamp
    field->last_update = get_current_timestamp();
    
    // Free temporary field copy
    free_field_state(prev_field, field->dimensions, field->resolution);
}

// Encode data into harmonic wave patterns
void encode_harmonic_data(waveform_field_t* field, 
                       void* data, size_t data_size,
                       encoding_schema_t* schema) {
    // Convert raw data to harmonic components
    harmonic_components_t* components = extract_harmonic_components(
        data, data_size, schema);
    
    // For each harmonic component
    for (uint32_t i = 0; i < components->count; i++) {
        harmonic_t* h = &components->harmonics[i];
        
        // Calculate wave parameters
        float amplitude = h->amplitude;
        float frequency = h->frequency;
        float phase = h->phase;
        vector_t* direction = h->direction;
        
        // Apply harmonic wave to field
        apply_harmonic_wave(field, amplitude, frequency, phase, direction);
    }
    
    // Apply non-linear transformations for higher-order encoding
    if (schema->use_nonlinear_encoding) {
        apply_nonlinear_transformations(field, schema->nonlinear_params);
    }
    
    // Normalize field if needed
    if (schema->normalize_after_encoding) {
        normalize_field(field);
    }
    
    // Free harmonic components
    free_harmonic_components(components);
}

// Create neural echo from activation pattern
echo_t* create_neural_echo(waveform_field_t* field, 
                         activation_pattern_t* pattern,
                         echo_params_t* params) {
    // Allocate echo structure
    echo_t* echo = (echo_t*)malloc(sizeof(echo_t));
    
    // Set basic parameters
    echo->creation_time = get_current_timestamp();
    echo->initial_strength = params->initial_strength;
    echo->current_strength = params->initial_strength;
    echo->decay_rate = params->decay_rate;
    echo->resonance_profile = copy_resonance_profile(params->resonance_profile);
    
    // Convert activation pattern to field perturbation
    field_perturbation_t* perturbation = activation_to_perturbation(pattern);
    
    // Apply perturbation to field
    apply_perturbation(field, perturbation);
    
    // Store perturbation signature for later retrieval
    echo->signature = extract_perturbation_signature(perturbation);
    
    // Free temporary structures
    free_perturbation(perturbation);
    
    return echo;
}

// Update echo strength based on time
void update_echo_strength(echo_t* echo, waveform_field_t* field) {
    // Get time elapsed since creation
    double elapsed_time = get_elapsed_time(echo->creation_time);
    
    // Calculate decay factor based on elapsed time and decay rate
    float decay_factor = calculate_decay_factor(elapsed_time, echo->decay_rate);
    
    // Apply decay to echo strength
    echo->current_strength = echo->initial_strength * decay_factor;
    
    // If strength falls below threshold, mark for cleanup
    if (echo->current_strength < ECHO_STRENGTH_THRESHOLD) {
        echo->marked_for_cleanup = true;
    }
    
    // Update field to reflect changes in echo strength
    update_field_for_echo(field, echo);
}

// Retrieve information through resonant stimulation
retrieval_result_t* retrieve_through_resonance(waveform_field_t* field, 
                                           query_pattern_t* query,
                                           retrieval_params_t* params) {
    // Create result container
    retrieval_result_t* result = create_retrieval_result();
    
    // Convert query to resonant probe
    resonant_probe_t* probe = create_resonant_probe(query);
    
    // Apply probe to field
    apply_resonant_probe(field, probe);
    
    // Measure resonance response at each point
    resonance_map_t* response = measure_resonance_response(field, probe);
    
    // Extract local maxima in resonance map
    peak_set_t* peaks = extract_resonance_peaks(response, params->threshold);
    
    // Sort peaks by strength
    sort_peaks(peaks);
    
    // For each peak above threshold
    for (uint32_t i = 0; i < peaks->count && i < params->max_results; i++) {
        // Extract information from resonance peak
        echo_t* echo = extract_echo_from_peak(field, &peaks->peaks[i]);
        
        // Convert echo to result entry
        result_entry_t* entry = convert_echo_to_result(echo, response);
        
        // Add to result set
        add_to_result_set(result, entry);
        
        // Free echo
        free_echo(echo);
    }
    
    // Clean up resources
    free_resonant_probe(probe);
    free_resonance_map(response);
    free_peak_set(peaks);
    
    return result;
}

// Reinforce echo pattern
void reinforce_echo(waveform_field_t* field, 
                  echo_t* echo,
                  reinforcement_params_t* params) {
    // Calculate reinforcement factor based on parameters
    float reinforcement_factor = calculate_reinforcement_factor(params);
    
    // Boost echo strength
    float new_strength = echo->current_strength * (1.0f + reinforcement_factor);
    
    // Cap at maximum strength
    echo->current_strength = min(new_strength, MAX_ECHO_STRENGTH);
    
    // Reset creation time if full renewal
    if (params->full_renewal) {
        echo->creation_time = get_current_timestamp();
    } else {
        // Adjust decay rate based on partial reinforcement
        echo->decay_rate = calculate_adjusted_decay_rate(
            echo->decay_rate, params->decay_adjustment_factor);
    }
    
    // Create reinforcement perturbation
    field_perturbation_t* perturbation = create_reinforcement_perturbation(
        echo, reinforcement_factor);
    
    // Apply to field
    apply_perturbation(field, perturbation);
    
    // Free resources
    free_perturbation(perturbation);
}

// Initialize NESH system
NESH* nesh_init(nesh_config_t* config) {
    NESH* nesh = (NESH*)malloc(sizeof(NESH));
    
    // Initialize based on configuration
    uint32_t dimensions = config ? config->dimensions : DEFAULT_DIMENSIONS;
    uint32_t* resolution = config ? config->resolution : DEFAULT_RESOLUTION;
    
    // Set up waveform field
    nesh->waveform_space = init_waveform_field(dimensions, resolution);
    
    // Initialize echo system
    nesh->echo_system = init_echo_system();
    
    // Initialize retrieval system
    nesh->retrieval_system = init_retrieval_system();
    
    // Initialize embedding system
    nesh->embedding_system = init_embedding_system(dimensions);
    
    // Set up default parameters
    nesh->default_echo_params = init_default_echo_params();
    nesh->default_retrieval_params = init_default_retrieval_params();
    
    return nesh;
}

// Store neural activation pattern as echo
echo_t* nesh_store_activation(NESH* nesh, 
                           activation_pattern_t* pattern,
                           echo_params_t* params) {
    // Use default parameters if none provided
    echo_params_t* echo_params = params ? params : nesh->default_echo_params;
    
    // Create neural echo
    echo_t* echo = create_neural_echo(nesh->waveform_space, pattern, echo_params);
    
    // Register echo with management system
    register_echo(nesh->echo_system, echo);
    
    // Store echo metadata in index
    index_echo(nesh->retrieval_system, echo);
    
    // Return echo reference
    return echo;
}

// Retrieve information by resonance
retrieval_result_t* nesh_retrieve(NESH* nesh, 
                               query_pattern_t* query,
                               retrieval_params_t* params) {
    // Use default parameters if none provided
    retrieval_params_t* retrieval_params = params ? params : nesh->default_retrieval_params;
    
    // Perform resonant retrieval
    retrieval_result_t* result = retrieve_through_resonance(
        nesh->waveform_space, query, retrieval_params);
    
    // Check if echoes need reinforcement
    if (retrieval_params->reinforce_on_retrieval) {
        // Reinforce each retrieved echo
        for (uint32_t i = 0; i < result->count; i++) {
            echo_t* echo = find_echo_by_id(nesh->echo_system, result->entries[i]->echo_id);
            if (echo) {
                reinforcement_params_t reinforce_params = {
                    .reinforcement_strength = retrieval_params->reinforcement_strength,
                    .full_renewal = false,
                    .decay_adjustment_factor = 0.9f
                };
                reinforce_echo(nesh->waveform_space, echo, &reinforce_params);
            }
        }
    }
    
    return result;
}

// Update NESH system
void nesh_update(NESH* nesh, double delta_time) {
    // Update wave dynamics
    update_wave_dynamics(nesh->waveform_space, delta_time);
    
    // Update echo strengths
    update_all_echoes(nesh->echo_system, nesh->waveform_space);
    
    // Clean up expired echoes
    cleanup_expired_echoes(nesh->echo_system, nesh->waveform_space);
    
    // Perform system maintenance
    perform_system_maintenance(nesh);
}

// Visualize waveform field as 2D projection
visualization_data_t* visualize_waveform_field(waveform_field_t* field, 
                                           visualization_params_t* params) {
    // Create visualization container
    visualization_data_t* vis = create_visualization_data(params);
    
    // Determine projection axes
    uint32_t axis1 = params->axes[0];
    uint32_t axis2 = params->axes[1];
    
    // For each pixel in visualization
    for (uint32_t y = 0; y < params->height; y++) {
        for (uint32_t x = 0; x < params->width; x++) {
            // Convert visualization coordinates to field coordinates
            float field_x = map_range(x, 0, params->width, 0, field->resolution[axis1]);
            float field_y = map_range(y, 0, params->height, 0, field->resolution[axis2]);
            
            // Sample field at position
            complex_t value = sample_field_at(field, axis1, field_x, axis2, field_y);
            
            // Calculate color based on field value
            color_t color = field_value_to_color(value, params->color_mapping);
            
            // Set pixel in visualization
            set_visualization_pixel(vis, x, y, color);
        }
    }
    
    // Apply post-processing
    if (params->apply_post_processing) {
        apply_visualization_post_processing(vis, params->post_processing_params);
    }
    
    return vis;
}

// Optimize NESH performance
void optimize_nesh_performance(NESH* nesh, optimization_level_t level) {
    // Adjust field resolution based on available resources
    if (level == OPTIMIZATION_PERFORMANCE) {
        // Lower resolution for better performance
        resize_waveform_field(nesh->waveform_space, PERFORMANCE_RESOLUTION);
    } else if (level == OPTIMIZATION_BALANCED) {
        // Balanced resolution
        resize_waveform_field(nesh->waveform_space, BALANCED_RESOLUTION);
    } else if (level == OPTIMIZATION_QUALITY) {
        // Higher resolution for better quality
        resize_waveform_field(nesh->waveform_space, QUALITY_RESOLUTION);
    }
    
    // Adjust echo cleanup parameters
    nesh->echo_system->cleanup_threshold = get_cleanup_threshold(level);
    nesh->echo_system->cleanup_interval = get_cleanup_interval(level);
    
    // Configure update frequency
    nesh->update_interval = get_update_interval(level);
    
    // Set dimension-specific damping
    set_dimension_specific_damping(nesh->waveform_space, level);
    
    // Configure parallel processing
    if (level == OPTIMIZATION_PERFORMANCE) {
        enable_parallel_processing(nesh, true);
        set_parallel_processing_threads(nesh, MAX_AVAILABLE_THREADS);
    } else if (level == OPTIMIZATION_BALANCED) {
        enable_parallel_processing(nesh, true);
        set_parallel_processing_threads(nesh, BALANCED_THREAD_COUNT);
    } else {
        enable_parallel_processing(nesh, false);
    }
}

// Integrate NESH with NuMap
void integrate_with_numap(NESH* nesh, NuMap* numap) {
    // Connect NESH's waveform memory to NuMap's hexagonal grid
    map_hex_grid_to_waveform(numap->grid, nesh->waveform_space);
    
    // Set up memory transfer protocols
    setup_memory_transfer(numap, nesh);
    
    // Create shared embedding space
    create_shared_embedding_space(numap->embedding_system, nesh->embedding_system);
    
    // Configure resonance patterns
    configure_resonance_patterns(numap, nesh);
    
    // Initialize hierarchical memory architecture
    init_hierarchical_memory(numap, nesh);
}

// Integrate NESH with Aurora
void integrate_with_aurora(NESH* nesh, Aurora* aurora) {
    // Connect NESH as temporal memory system for Aurora
    connect_nesh_to_aurora(nesh, aurora);
    
    // Configure activation pattern transfer
    setup_activation_transfer(aurora, nesh);
    
    // Set up temporal continuity mechanisms
    setup_temporal_continuity(aurora, nesh);
    
    // Configure resonance-based memory recall
    setup_resonance_recall(aurora, nesh);
    
    // Initialize consciousness state preservation
    init_consciousness_preservation(aurora, nesh);
}

// Integrate NESH with ECHO 13D
void integrate_with_echo13d(NESH* nesh, ECHO13D* echo13d) {
    // Connect NESH's waveform space to audio processing
    connect_waveform_to_audio(nesh->waveform_space, echo13d->audio_processor);
    
    // Set up voice pattern storage
    setup_voice_pattern_storage(echo13d, nesh);
    
    // Configure voice recognition mechanisms
    setup_voice_recognition(echo13d, nesh);
    
    // Initialize harmonic voice synthesis
    init_harmonic_voice_synthesis(echo13d, nesh);
}

#include "nesh.h"

int main() {
    // Initialize NESH with default configuration
    NESH* nesh = nesh_init(NULL);
    
    printf("Initialized NESH Memory Network\n");
    
    // Create a simple activation pattern
    activation_pattern_t* pattern = create_simple_activation_pattern();
    
    printf("Created activation pattern with %d neurons\n", pattern->neuron_count);
    
    // Store activation as echo
    echo_t* echo = nesh_store_activation(nesh, pattern, NULL);
    
    printf("Stored echo with ID %d and initial strength %.2f\n", 
           echo->id, echo->initial_strength);
    
    // Update system (simulating time passing)
    for (int i = 0; i < 10; i++) {
        nesh_update(nesh, 0.1); // 100ms per update
    }
    
    // Create query pattern (similar to original)
    query_pattern_t* query = create_similar_query_pattern(pattern, 0.8f);
    
    // Retrieve through resonance
    retrieval_result_t* result = nesh_retrieve(nesh, query, NULL);
    
    printf("Retrieved %d results\n", result->count);
    
    if (result->count > 0) {
        printf("Top result echo ID: %d\n", result->entries[0]->echo_id);
        printf("Match strength: %.2f\n", result->entries[0]->match_strength);
    }
    
    // Clean up resources
    free_activation_pattern(pattern);
    free_query_pattern(query);
    free_retrieval_result(result);
    nesh_free(nesh);
    
    return 0;
}

// Demonstrate wave pattern manipulation
void demonstrate_wave_patterns() {
    // Initialize NESH with specific configuration
    nesh_config_t config = {
        .dimensions = 3,
        .resolution = (uint32_t[]){64, 64, 64}
    };
    NESH* nesh = nesh_init(&config);
    
    printf("Initialized NESH with 3D waveform field (64x64x64)\n");
    
    // Create harmonic wave components
    harmonic_components_t* components = create_harmonic_components(3);
    add_harmonic(components, 1.0f, 5.0f, 0.0f, (vector_t){1.0f, 0.0f, 0.0f});
    add_harmonic(components, 0.5f, 7.0f, PI/4, (vector_t){0.0f, 1.0f, 0.0f});
    add_harmonic(components, 0.3f, 11.0f, PI/2, (vector_t){0.0f, 0.0f, 1.0f});
    
    printf("Created harmonic components\n");
    
    // Apply components to field
    apply_harmonic_components(nesh->waveform_space, components);
    
    printf("Applied harmonic components to field\n");
    
    // Create interference pattern by adding second set of harmonics
    harmonic_components_t* components2 = create_harmonic_components(2);
    add_harmonic(components2, 0.7f, 6.0f, PI/3, (vector_t){0.7f, 0.7f, 0.0f});
    add_harmonic(components2, 0.4f, 9.0f, PI/6, (vector_t){0.5f, 0.0f, 0.5f});
    
    // Apply second set of components
    apply_harmonic_components(nesh->waveform_space, components2);
    
    printf("Applied second set of harmonics to create interference pattern\n");
    
    // Create visualization parameters
    visualization_params_t vis_params = {
        .width = 800,
        .height = 600,
        .axes = {0, 1}, // X-Y projection
        .color_mapping = COLOR_MAPPING_PHASE,
        .apply_post_processing = true
    };
    
    // Create visualization
    visualization_data_t* vis = visualize_waveform_field(
        nesh->waveform_space, &vis_params);
    
    printf("Created field visualization (%dx%d)\n", vis->width, vis->height);
    
    // Save visualization to file
    save_visualization_to_file(vis, "wave_pattern.png");
    
    printf("Saved visualization to wave_pattern.png\n");
    
    // Clean up resources
    free_harmonic_components(components);
    free_harmonic_components(components2);
    free_visualization_data(vis);
    nesh_free(nesh);
}

// Demonstrate temporal memory characteristics
void demonstrate_temporal_memory() {
    // Initialize NESH
    NESH* nesh = nesh_init(NULL);
    
    printf("Initialized NESH for temporal memory demonstration\n");
    
    // Create a sequence of activation patterns
    const int sequence_length = 5;
    activation_pattern_t* patterns[sequence_length];
    echo_t* echoes[sequence_length];
    
    // Create and store sequence of patterns
    for (int i = 0; i < sequence_length; i++) {
        // Create pattern with some sequential property
        patterns[i] = create_sequential_pattern(i);
        
        // Configure echo parameters with different strengths and decay rates
        echo_params_t params = {
            .initial_strength = 1.0f - (i * 0.1f), // Decreasing strength
            .decay_rate = 0.1f + (i * 0.05f)       // Increasing decay rate
        };
        
        // Store as echo
        echoes[i] = nesh_store_activation(nesh, patterns[i], ¶ms);
        
        printf("Stored pattern %d with strength %.2f and decay rate %.2f\n",
               i, params.initial_strength, params.decay_rate);
    }
    
    // Simulate time passing (10 seconds, 100ms steps)
    for (int t = 0; t < 100; t++) {
        nesh_update(nesh, 0.1);
        
        // Every 20 steps, check echo strengths
        if (t % 20 == 0) {
            printf("\nAfter %.1f seconds:\n", t * 0.1);
            for (int i = 0; i < sequence_length; i++) {
                printf("  Echo %d strength: %.3f\n", i, echoes[i]->current_strength);
            }
        }
        
        // At t=50, reinforce one of the echoes
        if (t == 50) {
            printf("\nReinforcing echo 2 at t=5.0s\n");
            reinforcement_params_t reinforce_params = {
                .reinforcement_strength = 0.5f,
                .full_renewal = true,
                .decay_adjustment_factor = 0.8f
            };
            reinforce_echo(nesh->waveform_space, echoes[2], &reinforce_params);
        }
    }
    
    // Try to retrieve using a query similar to pattern 2
    query_pattern_t* query = create_similar_query_pattern(patterns[2], 0.9f);
    
    // Set up retrieval parameters
    retrieval_params_t retrieve_params = {
        .threshold = 0.5f,
        .max_results = 3,
        .reinforce_on_retrieval = true,
        .reinforcement_strength = 0.3f
    };
    
    // Perform retrieval
    retrieval_result_t* result = nesh_retrieve(nesh, query, &retrieve_params);
    
    printf("\nRetrieval results for query similar to pattern 2:\n");
    for (uint32_t i = 0; i < result->count; i++) {
        printf("  Result %d: Echo ID %d, Match strength %.3f\n",
               i, result->entries[i]->echo_id, result->entries[i]->match_strength);
    }
    
    // Clean up resources
    for (int i = 0; i < sequence_length; i++) {
        free_activation_pattern(patterns[i]);
    }
    free_query_pattern(query);
    free_retrieval_result(result);
    nesh_free(nesh);
}