quantrs2-anneal 0.1.3

//! Logical Qubit Encoding for Annealing Problems
//!
//! This module implements logical qubit encoding systems specifically designed for
//! quantum annealing applications. It provides functionality for:
//! - Encoding logical Ising/QUBO problems into error-corrected physical qubits
//! - Mapping logical annealing Hamiltonians to protected physical implementations
//! - Constructing stabilizer codes optimized for annealing hardware constraints
//! - Managing logical operations during annealing evolution

use scirs2_core::ndarray::{Array1, Array2};
use scirs2_core::random::ChaCha8Rng;
use scirs2_core::random::{Rng, SeedableRng};
use std::collections::HashMap;
use std::time::{Duration, Instant};

use super::codes::{CodeParameters, ErrorCorrectionCode};
use super::config::{QECResult, QuantumErrorCorrectionError};
use super::logical_operations::LogicalOperation;
use super::syndrome_detection::{SyndromeDetector, SyndromeDetectorConfig};
use crate::ising::IsingModel;
use crate::qaoa::QuantumState;
use crate::simulator::AnnealingResult;

/// Logical encoding system
#[derive(Debug, Clone)]
pub struct LogicalEncoding {
    /// Stabilizer generators
    pub stabilizers: Vec<PauliOperator>,
    /// Logical operators
    pub logical_operators: Vec<LogicalOperatorSet>,
    /// Code space
    pub code_space: CodeSpace,
    /// Encoding circuits
    pub encoding_circuits: Vec<QuantumCircuit>,
    /// Decoding data
    pub decoding_data: DecodingData,
}

/// Pauli operator representation
#[derive(Debug, Clone)]
pub struct PauliOperator {
    /// Pauli string (I, X, Y, Z for each qubit)
    pub pauli_string: Vec<PauliType>,
    /// Phase factor
    pub phase: f64,
    /// Coefficient
    pub coefficient: f64,
    /// Support (qubits on which operator acts non-trivially)
    pub support: Vec<usize>,
}

/// Pauli operator types
#[derive(Debug, Clone, PartialEq, Eq)]
pub enum PauliType {
    /// Identity
    I,
    /// Pauli X
    X,
    /// Pauli Y
    Y,
    /// Pauli Z
    Z,
}

/// Logical operator set
#[derive(Debug, Clone)]
pub struct LogicalOperatorSet {
    /// Logical qubit index
    pub logical_qubit: usize,
    /// Logical X operator
    pub logical_x: PauliOperator,
    /// Logical Z operator
    pub logical_z: PauliOperator,
    /// Logical Y operator (derived)
    pub logical_y: PauliOperator,
}

/// Code space definition
#[derive(Debug, Clone)]
pub struct CodeSpace {
    /// Basis states of the code space
    pub basis_states: Vec<LogicalBasisState>,
    /// Projector onto code space
    pub code_projector: Vec<Vec<f64>>,
    /// Dimension of code space
    pub dimension: usize,
    /// Distance of the code
    pub distance: usize,
}

/// Logical basis state
#[derive(Debug, Clone)]
pub struct LogicalBasisState {
    /// Logical state label
    pub label: String,
    /// Physical state representation
    pub physical_state: Vec<f64>,
    /// Stabilizer eigenvalues
    pub stabilizer_eigenvalues: Vec<i8>,
}

/// Quantum circuit representation
#[derive(Debug, Clone)]
pub struct QuantumCircuit {
    /// Circuit gates
    pub gates: Vec<QuantumGate>,
    /// Circuit depth
    pub depth: usize,
    /// Qubit count
    pub num_qubits: usize,
    /// Classical registers for measurements
    pub classical_registers: Vec<ClassicalRegister>,
}

/// Quantum gate
#[derive(Debug, Clone)]
pub struct QuantumGate {
    /// Gate type
    pub gate_type: GateType,
    /// Target qubits
    pub target_qubits: Vec<usize>,
    /// Control qubits
    pub control_qubits: Vec<usize>,
    /// Gate parameters
    pub parameters: Vec<f64>,
    /// Gate time
    pub gate_time: f64,
}

/// Quantum gate types
#[derive(Debug, Clone, PartialEq)]
pub enum GateType {
    /// Pauli X
    X,
    /// Pauli Y
    Y,
    /// Pauli Z
    Z,
    /// Hadamard
    H,
    /// Phase gate
    S,
    /// T gate
    T,
    /// CNOT
    CNOT,
    /// Controlled-Z
    CZ,
    /// Rotation gates
    RX(f64),
    RY(f64),
    RZ(f64),
    /// Measurement
    Measurement,
}

/// Classical register
#[derive(Debug, Clone)]
pub struct ClassicalRegister {
    /// Register name
    pub name: String,
    /// Number of bits
    pub num_bits: usize,
}

/// Decoding data
#[derive(Debug, Clone)]
pub struct DecodingData {
    /// Syndrome lookup table
    pub syndrome_table: HashMap<Vec<i8>, ErrorPattern>,
    /// Decoding algorithm
    pub decoding_algorithm: DecodingAlgorithm,
    /// Decoding performance
    pub decoding_performance: DecodingPerformance,
}

/// Error pattern
#[derive(Debug, Clone)]
pub struct ErrorPattern {
    /// Error locations
    pub error_locations: Vec<usize>,
    /// Error types
    pub error_types: Vec<PauliType>,
    /// Correction operations
    pub correction_operations: Vec<QuantumGate>,
}

/// Decoding algorithms
#[derive(Debug, Clone, PartialEq, Eq)]
pub enum DecodingAlgorithm {
    LookupTable,
    MinimumWeight,
    BeliefPropagation,
    NeuralNetwork,
    MaximumLikelihood,
}

/// Decoding performance metrics
#[derive(Debug, Clone)]
pub struct DecodingPerformance {
    /// Logical error rate
    pub logical_error_rate: f64,
    /// Decoding time
    pub decoding_time: std::time::Duration,
    /// Success probability
    pub success_probability: f64,
    /// Threshold estimate
    pub threshold_estimate: f64,
}

/// Logical qubit encoder for annealing problems
#[derive(Debug, Clone)]
pub struct LogicalAnnealingEncoder {
    /// Error correction code being used
    pub code: ErrorCorrectionCode,
    /// Code parameters
    pub parameters: CodeParameters,
    /// Logical encoding configuration
    pub encoding: LogicalEncoding,
    /// Syndrome detector for monitoring
    pub syndrome_detector: Option<SyndromeDetector>,
    /// Hardware topology information
    pub hardware_topology: AnnealingTopology,
    /// Encoding performance metrics
    pub performance_metrics: EncodingPerformanceMetrics,
    /// Configuration
    pub config: LogicalEncoderConfig,
}

/// Configuration for logical encoder
#[derive(Debug, Clone)]
pub struct LogicalEncoderConfig {
    /// Enable real-time error monitoring
    pub enable_monitoring: bool,
    /// Logical operation fidelity target
    pub target_fidelity: f64,
    /// Maximum encoding overhead allowed
    pub max_encoding_overhead: f64,
    /// Optimization strategy for encoding
    pub optimization_strategy: EncodingOptimizationStrategy,
    /// Hardware integration mode
    pub hardware_integration: HardwareIntegrationMode,
}

/// Encoding optimization strategies
#[derive(Debug, Clone, PartialEq, Eq)]
pub enum EncodingOptimizationStrategy {
    /// Minimize number of physical qubits
    MinimizeQubits,
    /// Minimize encoding depth
    MinimizeDepth,
    /// Maximize error threshold
    MaximizeThreshold,
    /// Optimize for annealing time
    OptimizeAnnealingTime,
    /// Balance all factors
    Balanced,
}

/// Hardware integration modes
#[derive(Debug, Clone, PartialEq, Eq)]
pub enum HardwareIntegrationMode {
    /// Software simulation only
    Simulation,
    /// Hardware-aware simulation
    HardwareAware,
    /// Full hardware integration
    FullIntegration,
    /// Hybrid mode
    Hybrid,
}

/// Annealing hardware topology
#[derive(Debug, Clone)]
pub struct AnnealingTopology {
    /// Connectivity graph
    pub connectivity: Array2<bool>,
    /// Qubit coupling strengths
    pub coupling_strengths: Array2<f64>,
    /// Qubit coherence times
    pub coherence_times: Array1<f64>,
    /// Control precision
    pub control_precision: f64,
    /// Topology type
    pub topology_type: TopologyType,
}

/// Hardware topology types
#[derive(Debug, Clone, PartialEq, Eq)]
pub enum TopologyType {
    /// D-Wave Chimera graph
    Chimera { m: usize, n: usize, l: usize },
    /// D-Wave Pegasus graph
    Pegasus { m: usize },
    /// Grid topology
    Grid { rows: usize, cols: usize },
    /// Fully connected
    FullyConnected { n: usize },
    /// Custom topology
    Custom,
}

/// Encoding performance metrics
#[derive(Debug, Clone)]
pub struct EncodingPerformanceMetrics {
    /// Physical to logical qubit ratio
    pub qubit_overhead: f64,
    /// Encoding fidelity
    pub encoding_fidelity: f64,
    /// Logical operation time overhead
    pub time_overhead: f64,
    /// Error suppression factor
    pub error_suppression_factor: f64,
    /// Threshold estimate
    pub threshold_estimate: f64,
    /// Encoding depth
    pub encoding_depth: usize,
    /// Success rate
    pub success_rate: f64,
}

/// Result of logical encoding operation
#[derive(Debug, Clone)]
pub struct LogicalEncodingResult {
    /// Encoded logical Hamiltonian
    pub logical_hamiltonian: LogicalHamiltonian,
    /// Physical implementation
    pub physical_implementation: PhysicalImplementation,
    /// Encoding mapping
    pub encoding_map: EncodingMap,
    /// Performance metrics
    pub performance: EncodingPerformanceMetrics,
    /// Monitoring data
    pub monitoring_data: Option<MonitoringData>,
}

/// Logical Hamiltonian representation
#[derive(Debug, Clone)]
pub struct LogicalHamiltonian {
    /// Logical coupling matrix
    pub logical_couplings: Array2<f64>,
    /// Logical bias vector
    pub logical_biases: Array1<f64>,
    /// Number of logical qubits
    pub num_logical_qubits: usize,
    /// Logical operators involved
    pub logical_operators: Vec<LogicalOperatorSet>,
}

/// Physical implementation of logical problem
#[derive(Debug, Clone)]
pub struct PhysicalImplementation {
    /// Physical coupling matrix
    pub physical_couplings: Array2<f64>,
    /// Physical bias vector
    pub physical_biases: Array1<f64>,
    /// Number of physical qubits
    pub num_physical_qubits: usize,
    /// Ancilla qubit assignments
    pub ancilla_assignments: Vec<usize>,
    /// Stabilizer measurement schedule
    pub measurement_schedule: MeasurementSchedule,
}

/// Encoding map between logical and physical qubits
#[derive(Debug, Clone)]
pub struct EncodingMap {
    /// Logical to physical qubit mapping
    pub logical_to_physical: HashMap<usize, Vec<usize>>,
    /// Physical to logical qubit mapping
    pub physical_to_logical: HashMap<usize, Option<usize>>,
    /// Code block assignments
    pub code_blocks: Vec<CodeBlock>,
    /// Auxiliary mappings
    pub auxiliary_mappings: HashMap<String, Vec<usize>>,
}

/// Individual code block
#[derive(Debug, Clone)]
pub struct CodeBlock {
    /// Logical qubit index
    pub logical_qubit: usize,
    /// Physical qubits in this block
    pub physical_qubits: Vec<usize>,
    /// Stabilizer generators for this block
    pub stabilizers: Vec<PauliOperator>,
    /// Block type
    pub block_type: CodeBlockType,
}

/// Code block types
#[derive(Debug, Clone, PartialEq, Eq)]
pub enum CodeBlockType {
    /// Data block (stores logical information)
    Data,
    /// Ancilla block (for syndrome measurement)
    Ancilla,
    /// Mixed block (both data and ancilla)
    Mixed,
}

/// Measurement schedule for syndrome detection
#[derive(Debug, Clone)]
pub struct MeasurementSchedule {
    /// Measurement rounds
    pub rounds: Vec<MeasurementRound>,
    /// Schedule timing
    pub timing: ScheduleTiming,
    /// Adaptive parameters
    pub adaptive_params: AdaptiveScheduleParams,
}

/// Individual measurement round
#[derive(Debug, Clone)]
pub struct MeasurementRound {
    /// Stabilizers to measure
    pub stabilizers_to_measure: Vec<usize>,
    /// Measurement time
    pub measurement_time: f64,
    /// Expected measurement outcomes
    pub expected_outcomes: Vec<i8>,
}

/// Schedule timing parameters
#[derive(Debug, Clone)]
pub struct ScheduleTiming {
    /// Base measurement period
    pub base_period: f64,
    /// Adaptive timing enabled
    pub adaptive_timing: bool,
    /// Minimum period
    pub min_period: f64,
    /// Maximum period
    pub max_period: f64,
}

/// Adaptive schedule parameters
#[derive(Debug, Clone)]
pub struct AdaptiveScheduleParams {
    /// Error rate threshold for adaptation
    pub error_threshold: f64,
    /// Adaptation rate
    pub adaptation_rate: f64,
    /// History window for adaptation
    pub history_window: usize,
}

/// Monitoring data during encoding
#[derive(Debug, Clone)]
pub struct MonitoringData {
    /// Syndrome measurements
    pub syndrome_measurements: Vec<SyndromeRecord>,
    /// Error rates over time
    pub error_rates: Vec<(f64, f64)>, // (time, error_rate)
    /// Logical fidelity over time
    pub fidelity_history: Vec<(f64, f64)>, // (time, fidelity)
    /// Correction events
    pub correction_events: Vec<CorrectionEvent>,
}

/// Syndrome measurement record
#[derive(Debug, Clone)]
pub struct SyndromeRecord {
    /// Measurement timestamp
    pub timestamp: f64,
    /// Measured syndrome
    pub syndrome: Vec<i8>,
    /// Measurement round
    pub round: usize,
    /// Confidence level
    pub confidence: f64,
}

/// Correction event record
#[derive(Debug, Clone)]
pub struct CorrectionEvent {
    /// Event timestamp
    pub timestamp: f64,
    /// Detected errors
    pub detected_errors: Vec<ErrorLocation>,
    /// Applied corrections
    pub applied_corrections: Vec<CorrectionOperation>,
    /// Success status
    pub success: bool,
}

/// Error location information
#[derive(Debug, Clone)]
pub struct ErrorLocation {
    /// Physical qubit
    pub physical_qubit: usize,
    /// Error type
    pub error_type: PauliType,
    /// Error probability
    pub probability: f64,
    /// Logical qubit affected
    pub logical_qubit_affected: Option<usize>,
}

/// Correction operation details
#[derive(Debug, Clone)]
pub struct CorrectionOperation {
    /// Target qubit
    pub target_qubit: usize,
    /// Correction type
    pub correction_type: PauliType,
    /// Application time
    pub application_time: f64,
    /// Success probability
    pub success_probability: f64,
}

impl LogicalAnnealingEncoder {
    /// Create new logical annealing encoder
    pub fn new(
        code: ErrorCorrectionCode,
        parameters: CodeParameters,
        config: LogicalEncoderConfig,
    ) -> QECResult<Self> {
        let encoding = Self::create_logical_encoding(&code, &parameters)?;
        let hardware_topology = Self::create_default_topology(&parameters);
        let performance_metrics = EncodingPerformanceMetrics::new();

        let syndrome_detector = if config.enable_monitoring {
            let detector_config = SyndromeDetectorConfig::default();
            Some(SyndromeDetector::new(
                code.clone(),
                parameters.clone(),
                detector_config,
            )?)
        } else {
            None
        };

        Ok(Self {
            code,
            parameters,
            encoding,
            syndrome_detector,
            hardware_topology,
            performance_metrics,
            config,
        })
    }

    /// Encode logical Ising problem into physical implementation
    pub fn encode_ising_problem(
        &mut self,
        logical_problem: &IsingModel,
    ) -> QECResult<LogicalEncodingResult> {
        let start_time = Instant::now();

        // Create logical Hamiltonian representation
        let logical_hamiltonian = self.create_logical_hamiltonian(logical_problem)?;

        // Map to physical implementation
        let physical_implementation = self.map_to_physical_implementation(&logical_hamiltonian)?;

        // Create encoding map
        let encoding_map =
            self.create_encoding_map(&logical_hamiltonian, &physical_implementation)?;

        // Calculate performance metrics
        let performance = self.calculate_encoding_performance(
            &logical_hamiltonian,
            &physical_implementation,
            start_time.elapsed(),
        )?;

        // Initialize monitoring if enabled
        let monitoring_data = self.config.enable_monitoring.then(|| MonitoringData::new());

        // Update internal metrics
        self.performance_metrics = performance.clone();

        Ok(LogicalEncodingResult {
            logical_hamiltonian,
            physical_implementation,
            encoding_map,
            performance,
            monitoring_data,
        })
    }

    /// Monitor logical qubits during annealing
    pub fn monitor_logical_qubits(
        &mut self,
        physical_state: &QuantumState,
        encoding_result: &mut LogicalEncodingResult,
    ) -> QECResult<Vec<SyndromeRecord>> {
        if let Some(ref mut detector) = self.syndrome_detector {
            let syndrome_result = detector.detect_syndrome(physical_state)?;

            let record = SyndromeRecord {
                timestamp: std::time::SystemTime::now()
                    .duration_since(std::time::UNIX_EPOCH)
                    .expect("system time before UNIX_EPOCH")
                    .as_secs_f64(),
                syndrome: syndrome_result.syndrome.iter().map(|&x| x as i8).collect(),
                round: 0, // Would be properly tracked
                confidence: syndrome_result.confidence,
            };

            if let Some(ref mut monitoring) = encoding_result.monitoring_data {
                monitoring.syndrome_measurements.push(record.clone());
            }

            Ok(vec![record])
        } else {
            Ok(Vec::new())
        }
    }

    /// Apply logical operation during annealing
    pub fn apply_logical_operation(
        &self,
        operation: &LogicalOperation,
        logical_qubit: usize,
        encoding_map: &EncodingMap,
    ) -> QECResult<Vec<QuantumGate>> {
        // Map logical operation to physical gates
        let physical_qubits = encoding_map
            .logical_to_physical
            .get(&logical_qubit)
            .ok_or_else(|| {
                QuantumErrorCorrectionError::LogicalOperationError(format!(
                    "Logical qubit {logical_qubit} not found in encoding map"
                ))
            })?;

        let mut gates = Vec::new();

        match operation {
            LogicalOperation::LogicalX => {
                gates.extend(self.implement_logical_x(physical_qubits)?);
            }
            LogicalOperation::LogicalZ => {
                gates.extend(self.implement_logical_z(physical_qubits)?);
            }
            LogicalOperation::LogicalMeasurement => {
                gates.extend(self.implement_logical_measurement(physical_qubits)?);
            }
            _ => {
                return Err(QuantumErrorCorrectionError::LogicalOperationError(format!(
                    "Logical operation {operation:?} not implemented"
                )));
            }
        }

        Ok(gates)
    }

    /// Create logical encoding from error correction code
    fn create_logical_encoding(
        code: &ErrorCorrectionCode,
        parameters: &CodeParameters,
    ) -> QECResult<LogicalEncoding> {
        let stabilizers = Self::generate_stabilizer_operators(code, parameters)?;
        let logical_operators = Self::generate_logical_operators(code, parameters)?;
        let code_space = Self::construct_code_space(code, parameters)?;
        let encoding_circuits = Self::generate_encoding_circuits(code, parameters)?;
        let decoding_data = Self::create_decoding_data(code, parameters)?;

        Ok(LogicalEncoding {
            stabilizers,
            logical_operators,
            code_space,
            encoding_circuits,
            decoding_data,
        })
    }

    /// Generate stabilizer operators for the code
    fn generate_stabilizer_operators(
        code: &ErrorCorrectionCode,
        parameters: &CodeParameters,
    ) -> QECResult<Vec<PauliOperator>> {
        let mut stabilizers = Vec::new();

        match code {
            ErrorCorrectionCode::SurfaceCode => {
                stabilizers.extend(Self::surface_code_stabilizers(parameters)?);
            }
            ErrorCorrectionCode::RepetitionCode => {
                stabilizers.extend(Self::repetition_code_stabilizers(parameters)?);
            }
            ErrorCorrectionCode::SteaneCode => {
                stabilizers.extend(Self::steane_code_stabilizers(parameters)?);
            }
            _ => {
                return Err(QuantumErrorCorrectionError::CodeError(format!(
                    "Stabilizer generation not implemented for {code:?}"
                )));
            }
        }

        Ok(stabilizers)
    }

    /// Generate surface code stabilizers
    fn surface_code_stabilizers(parameters: &CodeParameters) -> QECResult<Vec<PauliOperator>> {
        let d = parameters.distance;
        let mut stabilizers = Vec::new();

        // X-type stabilizers (plaquettes)
        for row in 0..(d - 1) {
            for col in 0..(d - 1) {
                if (row + col) % 2 == 0 {
                    let mut pauli_string = vec![PauliType::I; parameters.num_physical_qubits];
                    let qubits = Self::get_plaquette_qubits(row, col, d);

                    for &qubit in &qubits {
                        if qubit < parameters.num_physical_qubits {
                            pauli_string[qubit] = PauliType::X;
                        }
                    }

                    stabilizers.push(PauliOperator {
                        pauli_string,
                        phase: 0.0,
                        coefficient: 1.0,
                        support: qubits,
                    });
                }
            }
        }

        // Z-type stabilizers (vertices)
        for row in 0..d {
            for col in 0..d {
                if (row + col) % 2 == 1 {
                    let mut pauli_string = vec![PauliType::I; parameters.num_physical_qubits];
                    let qubits = Self::get_vertex_qubits(row, col, d);

                    for &qubit in &qubits {
                        if qubit < parameters.num_physical_qubits {
                            pauli_string[qubit] = PauliType::Z;
                        }
                    }

                    stabilizers.push(PauliOperator {
                        pauli_string,
                        phase: 0.0,
                        coefficient: 1.0,
                        support: qubits,
                    });
                }
            }
        }

        Ok(stabilizers)
    }

    /// Generate repetition code stabilizers
    fn repetition_code_stabilizers(parameters: &CodeParameters) -> QECResult<Vec<PauliOperator>> {
        let n = parameters.num_physical_qubits;
        let mut stabilizers = Vec::new();

        for i in 0..(n - 1) {
            let mut pauli_string = vec![PauliType::I; n];
            pauli_string[i] = PauliType::Z;
            pauli_string[i + 1] = PauliType::Z;

            stabilizers.push(PauliOperator {
                pauli_string,
                phase: 0.0,
                coefficient: 1.0,
                support: vec![i, i + 1],
            });
        }

        Ok(stabilizers)
    }

    /// Generate Steane code stabilizers
    fn steane_code_stabilizers(parameters: &CodeParameters) -> QECResult<Vec<PauliOperator>> {
        let mut stabilizers = Vec::new();

        // Steane code [[7,1,3]] stabilizers
        let x_stabilizers = [vec![0, 2, 4, 6], vec![1, 2, 5, 6], vec![3, 4, 5, 6]];

        let z_stabilizers = [vec![0, 1, 2, 3], vec![0, 1, 4, 5], vec![0, 2, 4, 6]];

        // Add X-type stabilizers
        for pattern in &x_stabilizers {
            let mut pauli_string = vec![PauliType::I; 7];
            for &qubit in pattern {
                pauli_string[qubit] = PauliType::X;
            }

            stabilizers.push(PauliOperator {
                pauli_string,
                phase: 0.0,
                coefficient: 1.0,
                support: pattern.clone(),
            });
        }

        // Add Z-type stabilizers
        for pattern in &z_stabilizers {
            let mut pauli_string = vec![PauliType::I; 7];
            for &qubit in pattern {
                pauli_string[qubit] = PauliType::Z;
            }

            stabilizers.push(PauliOperator {
                pauli_string,
                phase: 0.0,
                coefficient: 1.0,
                support: pattern.clone(),
            });
        }

        Ok(stabilizers)
    }

    /// Generate logical operators
    fn generate_logical_operators(
        code: &ErrorCorrectionCode,
        parameters: &CodeParameters,
    ) -> QECResult<Vec<LogicalOperatorSet>> {
        let mut logical_operators = Vec::new();

        for logical_qubit in 0..parameters.num_logical_qubits {
            let logical_x = Self::create_logical_x_operator(code, parameters, logical_qubit)?;
            let logical_z = Self::create_logical_z_operator(code, parameters, logical_qubit)?;
            let logical_y = Self::create_logical_y_operator(&logical_x, &logical_z)?;

            logical_operators.push(LogicalOperatorSet {
                logical_qubit,
                logical_x,
                logical_z,
                logical_y,
            });
        }

        Ok(logical_operators)
    }

    /// Create logical X operator
    fn create_logical_x_operator(
        code: &ErrorCorrectionCode,
        parameters: &CodeParameters,
        logical_qubit: usize,
    ) -> QECResult<PauliOperator> {
        if code == &ErrorCorrectionCode::RepetitionCode {
            // For repetition code, logical X acts on all qubits
            let pauli_string = vec![PauliType::X; parameters.num_physical_qubits];
            let support = (0..parameters.num_physical_qubits).collect();

            Ok(PauliOperator {
                pauli_string,
                phase: 0.0,
                coefficient: 1.0,
                support,
            })
        } else {
            // Default implementation - would need specific implementation per code
            let mut pauli_string = vec![PauliType::I; parameters.num_physical_qubits];
            pauli_string[0] = PauliType::X; // Simplified

            Ok(PauliOperator {
                pauli_string,
                phase: 0.0,
                coefficient: 1.0,
                support: vec![0],
            })
        }
    }

    /// Create logical Z operator
    fn create_logical_z_operator(
        code: &ErrorCorrectionCode,
        parameters: &CodeParameters,
        logical_qubit: usize,
    ) -> QECResult<PauliOperator> {
        if code == &ErrorCorrectionCode::RepetitionCode {
            // For repetition code, logical Z acts on first qubit
            let mut pauli_string = vec![PauliType::I; parameters.num_physical_qubits];
            pauli_string[0] = PauliType::Z;

            Ok(PauliOperator {
                pauli_string,
                phase: 0.0,
                coefficient: 1.0,
                support: vec![0],
            })
        } else {
            // Default implementation
            let mut pauli_string = vec![PauliType::I; parameters.num_physical_qubits];
            pauli_string[0] = PauliType::Z;

            Ok(PauliOperator {
                pauli_string,
                phase: 0.0,
                coefficient: 1.0,
                support: vec![0],
            })
        }
    }

    /// Create logical Y operator from X and Z
    fn create_logical_y_operator(
        logical_x: &PauliOperator,
        logical_z: &PauliOperator,
    ) -> QECResult<PauliOperator> {
        // Y = iXZ (simplified implementation)
        let mut pauli_string = vec![PauliType::I; logical_x.pauli_string.len()];

        for i in 0..pauli_string.len() {
            pauli_string[i] = match (&logical_x.pauli_string[i], &logical_z.pauli_string[i]) {
                (PauliType::X, PauliType::I) => PauliType::X,
                (PauliType::I, PauliType::Z) => PauliType::Z,
                (PauliType::X, PauliType::Z) => PauliType::Y,
                _ => PauliType::I,
            };
        }

        let mut support = logical_x.support.clone();
        support.extend(logical_z.support.iter());
        support.sort_unstable();
        support.dedup();

        Ok(PauliOperator {
            pauli_string,
            phase: std::f64::consts::PI / 2.0, // i factor
            coefficient: 1.0,
            support,
        })
    }

    /// Construct code space
    fn construct_code_space(
        code: &ErrorCorrectionCode,
        parameters: &CodeParameters,
    ) -> QECResult<CodeSpace> {
        let dimension = 1 << parameters.num_logical_qubits; // 2^k for k logical qubits
        let basis_states = Self::generate_logical_basis_states(parameters)?;
        let code_projector = Self::compute_code_projector(parameters)?;

        Ok(CodeSpace {
            basis_states,
            code_projector,
            dimension,
            distance: parameters.distance,
        })
    }

    /// Generate logical basis states
    fn generate_logical_basis_states(
        parameters: &CodeParameters,
    ) -> QECResult<Vec<LogicalBasisState>> {
        let mut basis_states = Vec::new();

        // For k logical qubits, generate 2^k basis states
        let num_basis_states = 1 << parameters.num_logical_qubits;

        for state_index in 0..num_basis_states {
            let label = format!(
                "L{:0width$b}",
                state_index,
                width = parameters.num_logical_qubits
            );

            // Generate physical state representation (simplified)
            let physical_state = vec![0.0; 1 << parameters.num_physical_qubits];

            // Generate stabilizer eigenvalues (all +1 for code states)
            let stabilizer_eigenvalues =
                vec![1i8; parameters.num_physical_qubits - parameters.num_logical_qubits];

            basis_states.push(LogicalBasisState {
                label,
                physical_state,
                stabilizer_eigenvalues,
            });
        }

        Ok(basis_states)
    }

    /// Compute code projector
    fn compute_code_projector(parameters: &CodeParameters) -> QECResult<Vec<Vec<f64>>> {
        let dim = 1 << parameters.num_physical_qubits;
        let mut projector = vec![vec![0.0; dim]; dim];

        // Simplified identity projector
        for i in 0..dim {
            projector[i][i] = 1.0;
        }

        Ok(projector)
    }

    /// Generate encoding circuits
    fn generate_encoding_circuits(
        code: &ErrorCorrectionCode,
        parameters: &CodeParameters,
    ) -> QECResult<Vec<QuantumCircuit>> {
        match code {
            ErrorCorrectionCode::RepetitionCode => {
                Ok(vec![Self::create_repetition_encoding_circuit(parameters)?])
            }
            ErrorCorrectionCode::SteaneCode => {
                Ok(vec![Self::create_steane_encoding_circuit(parameters)?])
            }
            _ => {
                // Default empty circuit
                Ok(vec![QuantumCircuit {
                    gates: Vec::new(),
                    depth: 0,
                    num_qubits: parameters.num_physical_qubits,
                    classical_registers: Vec::new(),
                }])
            }
        }
    }

    /// Create repetition code encoding circuit
    fn create_repetition_encoding_circuit(
        parameters: &CodeParameters,
    ) -> QECResult<QuantumCircuit> {
        let mut gates = Vec::new();

        // CNOT gates to copy logical qubit to all physical qubits
        for i in 1..parameters.num_physical_qubits {
            gates.push(QuantumGate {
                gate_type: GateType::CNOT,
                target_qubits: vec![i],
                control_qubits: vec![0],
                parameters: Vec::new(),
                gate_time: 0.1, // microseconds
            });
        }

        Ok(QuantumCircuit {
            gates,
            depth: parameters.num_physical_qubits - 1,
            num_qubits: parameters.num_physical_qubits,
            classical_registers: Vec::new(),
        })
    }

    /// Create Steane code encoding circuit
    fn create_steane_encoding_circuit(parameters: &CodeParameters) -> QECResult<QuantumCircuit> {
        let mut gates = Vec::new();

        // Simplified Steane encoding (would need full implementation)
        // H gates on ancilla qubits
        for i in 1..7 {
            gates.push(QuantumGate {
                gate_type: GateType::H,
                target_qubits: vec![i],
                control_qubits: Vec::new(),
                parameters: Vec::new(),
                gate_time: 0.05,
            });
        }

        // CNOT pattern for Steane code
        let cnot_pattern = [(0, 1), (0, 2), (0, 3), (0, 4), (0, 5), (0, 6)];
        for (control, target) in cnot_pattern {
            gates.push(QuantumGate {
                gate_type: GateType::CNOT,
                target_qubits: vec![target],
                control_qubits: vec![control],
                parameters: Vec::new(),
                gate_time: 0.1,
            });
        }

        Ok(QuantumCircuit {
            gates,
            depth: 7,
            num_qubits: 7,
            classical_registers: Vec::new(),
        })
    }

    /// Create decoding data
    fn create_decoding_data(
        code: &ErrorCorrectionCode,
        parameters: &CodeParameters,
    ) -> QECResult<DecodingData> {
        let syndrome_table = HashMap::new(); // Would be populated based on code
        let decoding_algorithm = DecodingAlgorithm::MinimumWeight;
        let decoding_performance = DecodingPerformance {
            logical_error_rate: 0.01,
            decoding_time: Duration::from_micros(100),
            success_probability: 0.95,
            threshold_estimate: 0.1,
        };

        Ok(DecodingData {
            syndrome_table,
            decoding_algorithm,
            decoding_performance,
        })
    }

    /// Create logical Hamiltonian from Ising problem
    fn create_logical_hamiltonian(&self, problem: &IsingModel) -> QECResult<LogicalHamiltonian> {
        let num_logical_qubits = problem.num_qubits;
        let mut logical_couplings = Array2::zeros((num_logical_qubits, num_logical_qubits));
        let mut logical_biases = Array1::zeros(num_logical_qubits);

        // Copy coupling matrix and bias vector
        for i in 0..num_logical_qubits {
            logical_biases[i] = problem.get_bias(i).unwrap_or(0.0);

            for j in 0..num_logical_qubits {
                logical_couplings[[i, j]] = problem.get_coupling(i, j).unwrap_or(0.0);
            }
        }

        let logical_operators = self.encoding.logical_operators.clone();

        Ok(LogicalHamiltonian {
            logical_couplings,
            logical_biases,
            num_logical_qubits,
            logical_operators,
        })
    }

    /// Map logical Hamiltonian to physical implementation
    fn map_to_physical_implementation(
        &self,
        logical_hamiltonian: &LogicalHamiltonian,
    ) -> QECResult<PhysicalImplementation> {
        let num_physical_qubits = self.parameters.num_physical_qubits;
        let mut physical_couplings = Array2::zeros((num_physical_qubits, num_physical_qubits));
        let mut physical_biases = Array1::zeros(num_physical_qubits);

        // Map logical interactions to physical qubits based on logical operators
        for i in 0..logical_hamiltonian.num_logical_qubits {
            // Map logical bias
            if let Some(logical_op) = logical_hamiltonian.logical_operators.get(i) {
                let bias_value = logical_hamiltonian.logical_biases[i];

                // Apply bias to physical qubits according to logical Z operator
                for &qubit in &logical_op.logical_z.support {
                    if qubit < num_physical_qubits {
                        physical_biases[qubit] += bias_value;
                    }
                }
            }

            // Map logical couplings
            for j in (i + 1)..logical_hamiltonian.num_logical_qubits {
                let coupling_value = logical_hamiltonian.logical_couplings[[i, j]];

                if coupling_value != 0.0 {
                    if let (Some(logical_op_i), Some(logical_op_j)) = (
                        logical_hamiltonian.logical_operators.get(i),
                        logical_hamiltonian.logical_operators.get(j),
                    ) {
                        // Map coupling between logical qubits to physical interactions
                        for &qubit_i in &logical_op_i.logical_z.support {
                            for &qubit_j in &logical_op_j.logical_z.support {
                                if qubit_i < num_physical_qubits && qubit_j < num_physical_qubits {
                                    physical_couplings[[qubit_i, qubit_j]] += coupling_value;
                                    physical_couplings[[qubit_j, qubit_i]] += coupling_value;
                                }
                            }
                        }
                    }
                }
            }
        }

        let ancilla_assignments = self.identify_ancilla_qubits();
        let measurement_schedule = self.create_measurement_schedule()?;

        Ok(PhysicalImplementation {
            physical_couplings,
            physical_biases,
            num_physical_qubits,
            ancilla_assignments,
            measurement_schedule,
        })
    }

    /// Create encoding map
    fn create_encoding_map(
        &self,
        logical_hamiltonian: &LogicalHamiltonian,
        physical_implementation: &PhysicalImplementation,
    ) -> QECResult<EncodingMap> {
        let mut logical_to_physical = HashMap::new();
        let mut physical_to_logical = HashMap::new();
        let mut code_blocks = Vec::new();

        // Create mapping based on logical operators
        for (logical_qubit, logical_op_set) in
            logical_hamiltonian.logical_operators.iter().enumerate()
        {
            let physical_qubits = logical_op_set.logical_z.support.clone();
            logical_to_physical.insert(logical_qubit, physical_qubits.clone());

            // Create code block
            let block = CodeBlock {
                logical_qubit,
                physical_qubits: physical_qubits.clone(),
                stabilizers: self.get_stabilizers_for_block(logical_qubit)?,
                block_type: CodeBlockType::Data,
            };
            code_blocks.push(block);

            // Update physical to logical mapping
            for &physical_qubit in &physical_qubits {
                physical_to_logical.insert(physical_qubit, Some(logical_qubit));
            }
        }

        // Mark ancilla qubits
        for &ancilla_qubit in &physical_implementation.ancilla_assignments {
            physical_to_logical.insert(ancilla_qubit, None);
        }

        let auxiliary_mappings = HashMap::new(); // Could store additional mappings

        Ok(EncodingMap {
            logical_to_physical,
            physical_to_logical,
            code_blocks,
            auxiliary_mappings,
        })
    }

    /// Get stabilizers for a specific code block
    fn get_stabilizers_for_block(&self, logical_qubit: usize) -> QECResult<Vec<PauliOperator>> {
        // Return stabilizers that act on qubits in this block
        let stabilizers: Vec<PauliOperator> = self
            .encoding
            .stabilizers
            .iter()
            .filter(|stabilizer| {
                // Check if stabilizer acts on qubits in this block
                stabilizer.support.iter().any(|&qubit| {
                    // Check if this qubit belongs to the logical qubit's block
                    true // Simplified logic
                })
            })
            .cloned()
            .collect();

        Ok(stabilizers)
    }

    /// Calculate encoding performance metrics
    fn calculate_encoding_performance(
        &self,
        logical_hamiltonian: &LogicalHamiltonian,
        physical_implementation: &PhysicalImplementation,
        encoding_time: Duration,
    ) -> QECResult<EncodingPerformanceMetrics> {
        let qubit_overhead = physical_implementation.num_physical_qubits as f64
            / logical_hamiltonian.num_logical_qubits as f64;

        let encoding_fidelity = 0.95; // Would be calculated based on noise model
        let time_overhead = encoding_time.as_secs_f64() * 1000.0; // Convert to ms
        let error_suppression_factor = self.parameters.distance as f64;
        let threshold_estimate = 0.1; // Would be calculated
        let encoding_depth = self.calculate_encoding_depth()?;
        let success_rate = 0.98; // Would be measured

        Ok(EncodingPerformanceMetrics {
            qubit_overhead,
            encoding_fidelity,
            time_overhead,
            error_suppression_factor,
            threshold_estimate,
            encoding_depth,
            success_rate,
        })
    }

    /// Calculate encoding circuit depth
    fn calculate_encoding_depth(&self) -> QECResult<usize> {
        let max_depth = self
            .encoding
            .encoding_circuits
            .iter()
            .map(|circuit| circuit.depth)
            .max()
            .unwrap_or(0);

        Ok(max_depth)
    }

    /// Identify ancilla qubits
    fn identify_ancilla_qubits(&self) -> Vec<usize> {
        let num_data_qubits = self.parameters.num_logical_qubits;
        let total_qubits = self.parameters.num_physical_qubits;

        // Simple identification: last qubits are ancillas
        (num_data_qubits..total_qubits).collect()
    }

    /// Create measurement schedule
    fn create_measurement_schedule(&self) -> QECResult<MeasurementSchedule> {
        let rounds = vec![MeasurementRound {
            stabilizers_to_measure: (0..self.encoding.stabilizers.len()).collect(),
            measurement_time: 0.1, // microseconds
            expected_outcomes: vec![1i8; self.encoding.stabilizers.len()],
        }];

        let timing = ScheduleTiming {
            base_period: 1.0, // microseconds
            adaptive_timing: true,
            min_period: 0.5,
            max_period: 10.0,
        };

        let adaptive_params = AdaptiveScheduleParams {
            error_threshold: 0.01,
            adaptation_rate: 0.1,
            history_window: 100,
        };

        Ok(MeasurementSchedule {
            rounds,
            timing,
            adaptive_params,
        })
    }

    /// Create default hardware topology
    fn create_default_topology(parameters: &CodeParameters) -> AnnealingTopology {
        let n = parameters.num_physical_qubits;
        let connectivity = Array2::from_shape_fn((n, n), |(i, j)| i == j); // Default to isolated qubits
        let coupling_strengths = Array2::zeros((n, n));
        let coherence_times = Array1::ones(n) * 100.0; // 100 microseconds

        AnnealingTopology {
            connectivity,
            coupling_strengths,
            coherence_times,
            control_precision: 0.001,
            topology_type: TopologyType::Custom,
        }
    }

    /// Implement logical X operation
    fn implement_logical_x(&self, physical_qubits: &[usize]) -> QECResult<Vec<QuantumGate>> {
        let mut gates = Vec::new();

        // For repetition code, logical X is X on all qubits
        for &qubit in physical_qubits {
            gates.push(QuantumGate {
                gate_type: GateType::X,
                target_qubits: vec![qubit],
                control_qubits: Vec::new(),
                parameters: Vec::new(),
                gate_time: 0.05,
            });
        }

        Ok(gates)
    }

    /// Implement logical Z operation
    fn implement_logical_z(&self, physical_qubits: &[usize]) -> QECResult<Vec<QuantumGate>> {
        let mut gates = Vec::new();

        // For repetition code, logical Z is Z on first qubit
        if let Some(&first_qubit) = physical_qubits.first() {
            gates.push(QuantumGate {
                gate_type: GateType::Z,
                target_qubits: vec![first_qubit],
                control_qubits: Vec::new(),
                parameters: Vec::new(),
                gate_time: 0.05,
            });
        }

        Ok(gates)
    }

    /// Implement logical measurement
    fn implement_logical_measurement(
        &self,
        physical_qubits: &[usize],
    ) -> QECResult<Vec<QuantumGate>> {
        let mut gates = Vec::new();

        // Measure all qubits in the code block
        for &qubit in physical_qubits {
            gates.push(QuantumGate {
                gate_type: GateType::Measurement,
                target_qubits: vec![qubit],
                control_qubits: Vec::new(),
                parameters: Vec::new(),
                gate_time: 0.1,
            });
        }

        Ok(gates)
    }

    /// Get plaquette qubits for surface code
    fn get_plaquette_qubits(row: usize, col: usize, d: usize) -> Vec<usize> {
        let mut qubits = Vec::new();

        // Calculate qubit indices for plaquette
        let center = row * d + col;

        if row > 0 {
            qubits.push(center - d);
        }
        if col > 0 {
            qubits.push(center - 1);
        }
        if row < d - 1 {
            qubits.push(center + d);
        }
        if col < d - 1 {
            qubits.push(center + 1);
        }

        qubits
    }

    /// Get vertex qubits for surface code
    fn get_vertex_qubits(row: usize, col: usize, d: usize) -> Vec<usize> {
        // Similar to plaquette qubits
        Self::get_plaquette_qubits(row, col, d)
    }
}

impl EncodingPerformanceMetrics {
    /// Create new performance metrics
    #[must_use]
    pub const fn new() -> Self {
        Self {
            qubit_overhead: 1.0,
            encoding_fidelity: 1.0,
            time_overhead: 0.0,
            error_suppression_factor: 1.0,
            threshold_estimate: 0.0,
            encoding_depth: 0,
            success_rate: 1.0,
        }
    }
}

impl MonitoringData {
    /// Create new monitoring data
    #[must_use]
    pub const fn new() -> Self {
        Self {
            syndrome_measurements: Vec::new(),
            error_rates: Vec::new(),
            fidelity_history: Vec::new(),
            correction_events: Vec::new(),
        }
    }
}

impl Default for LogicalEncoderConfig {
    fn default() -> Self {
        Self {
            enable_monitoring: true,
            target_fidelity: 0.99,
            max_encoding_overhead: 10.0,
            optimization_strategy: EncodingOptimizationStrategy::Balanced,
            hardware_integration: HardwareIntegrationMode::HardwareAware,
        }
    }
}

#[cfg(test)]
mod tests {
    use super::*;
    use crate::quantum_error_correction::codes::*;

    #[test]
    fn test_logical_encoder_creation() {
        let code = ErrorCorrectionCode::RepetitionCode;
        let parameters = CodeParameters {
            distance: 3,
            num_logical_qubits: 1,
            num_physical_qubits: 3,
            num_ancilla_qubits: 0,
            code_rate: 1.0 / 3.0,
            threshold_probability: 0.1,
        };
        let config = LogicalEncoderConfig::default();

        let encoder = LogicalAnnealingEncoder::new(code, parameters, config);
        assert!(encoder.is_ok());
    }

    #[test]
    fn test_ising_problem_encoding() {
        let mut encoder = create_test_encoder();
        let mut ising = IsingModel::new(2);
        ising.set_bias(0, 1.0).expect("failed to set bias in test");
        ising
            .set_coupling(0, 1, -0.5)
            .expect("failed to set coupling in test");

        let result = encoder.encode_ising_problem(&ising);
        assert!(result.is_ok());

        let encoding_result = result.expect("failed to encode ising problem in test");
        assert_eq!(encoding_result.logical_hamiltonian.num_logical_qubits, 2);
    }

    #[test]
    fn test_stabilizer_generation() {
        let parameters = CodeParameters {
            distance: 3,
            num_logical_qubits: 1,
            num_physical_qubits: 3,
            num_ancilla_qubits: 0,
            code_rate: 1.0 / 3.0,
            threshold_probability: 0.1,
        };

        let stabilizers = LogicalAnnealingEncoder::repetition_code_stabilizers(&parameters)
            .expect("failed to generate stabilizers in test");
        assert_eq!(stabilizers.len(), 2); // n-1 stabilizers for repetition code
    }

    #[test]
    fn test_logical_operator_generation() {
        let code = ErrorCorrectionCode::RepetitionCode;
        let parameters = CodeParameters {
            distance: 3,
            num_logical_qubits: 1,
            num_physical_qubits: 3,
            num_ancilla_qubits: 0,
            code_rate: 1.0 / 3.0,
            threshold_probability: 0.1,
        };

        let logical_ops = LogicalAnnealingEncoder::generate_logical_operators(&code, &parameters)
            .expect("failed to generate logical operators in test");
        assert_eq!(logical_ops.len(), 1);
        assert_eq!(logical_ops[0].logical_qubit, 0);
    }

    #[test]
    fn test_encoding_circuit_generation() {
        let parameters = CodeParameters {
            distance: 3,
            num_logical_qubits: 1,
            num_physical_qubits: 3,
            num_ancilla_qubits: 0,
            code_rate: 1.0 / 3.0,
            threshold_probability: 0.1,
        };

        let circuit = LogicalAnnealingEncoder::create_repetition_encoding_circuit(&parameters)
            .expect("failed to create encoding circuit in test");
        assert_eq!(circuit.gates.len(), 2); // 2 CNOT gates for 3-qubit repetition code
        assert_eq!(circuit.num_qubits, 3);
    }

    fn create_test_encoder() -> LogicalAnnealingEncoder {
        let code = ErrorCorrectionCode::RepetitionCode;
        let parameters = CodeParameters {
            distance: 3,
            num_logical_qubits: 2,
            num_physical_qubits: 6,
            num_ancilla_qubits: 0,
            code_rate: 1.0 / 3.0,
            threshold_probability: 0.1,
        };
        let config = LogicalEncoderConfig::default();

        LogicalAnnealingEncoder::new(code, parameters, config)
            .expect("failed to create test encoder")
    }
}