using System;
using System.Collections.Generic;
using UnityEngine;
#if UNITY_MATHEMATICS
using Unity.Mathematics;
using static Unity.Mathematics.math;
#endif

namespace NanoBrain {

    /// <summary>
    /// A neuron is a basic Nucleus
    /// </summary>
    /// A neuron combines the weighted input from other neurons and applies an activation function to it
    /// to compute the output value:
    /// \code
    ///    Vector3 combination = NanoBrain::Neuron::Combinator(bias, synapses);
    ///    Vector3 output = NanoBrain::Neuron::Activator(combination);
    /// \endcode
    /// The synapses are connections to other neurons.
    /// Each connection has a weight which is used to multiply the output of that other neuron
    /// before it is used by the combinator.
    [Serializable]
    public class Neuron : Nucleus {

        /// <summary>
        /// Create a new Neuron in a Cluster instance
        /// </summary>
        /// <param name="parent">The parent cluster in which the new Neuron should be created</param>
        /// <param name="name">The name of the new Neuron</param>
        public Neuron(Cluster parent, string name) {
            this.parent = parent;
            this.name = name;
            if (this.parent != null) {
                this.parent.nuclei ??= new();
                this.parent.nuclei.Add(this);
            }
        }

        #region Serialization

        /// <summary>
        /// The bias
        /// </summary>
        /// The bias which a value which is always added to the combined value of the neuron
        /// It does not have a synapse and therefore no weight of source nucleus
        //[HideInInspector]
        public Vector3 bias = Vector3.zero;

        #region Synapses

        [SerializeField]
        private List<Synapse> _synapses = new();
        /// <summary>
        /// The synapses of the nucleus
        /// </summary>
        public List<Synapse> synapses => _synapses;

        /// <summary>
        /// Add a new synapse to this nuclues
        /// </summary>
        /// <param name="sendingNucleus">The nucleus from which the signals may originate</param>
        /// <param name="weight">The weight applied to the input. Default value = 1</param>
        /// <returns>The created Synapse</returns>
        /// This will add a new input to this nucleus with the given weight.
        public Synapse AddSynapse(Neuron sendingNucleus, float weight = 1) {
            Synapse synapse = new(sendingNucleus, weight);
            this.synapses.Add(synapse);
            return synapse;
        }

        /// <summary>
        /// Find a synapse
        /// </summary>
        /// <param name="sender">The sender of the input to the Synapse</param>
        /// <returns>The found Synapse or null when the sender has no synapse to this nucleus.</returns>
        public Synapse GetSynapse(Nucleus sender) {
            foreach (Synapse synapse in this.synapses)
                if (synapse.neuron == sender)
                    return synapse;
            return null;
        }

        /// <summary>
        /// Remove a synapse from a Nucleus
        /// </summary>
        /// <param name="sendingNucleus">Remote the synapse connecting to this Nucleus</param>
        public void RemoveSynapse(Nucleus sendingNucleus) {
            this.synapses.RemoveAll(synapse => synapse.neuron == sendingNucleus);
        }

        #endregion Synapses

        /// <summary>
        /// Set the bias, recalculate the output and update all Nuclei receiving from this Nucleus
        /// </summary>
        /// <param name="inputValue"></param>
        public virtual void SetBias(Vector3 inputValue) {
            this.bias = inputValue;
            this.lastUpdate = Time.time;
            this.parent?.UpdateFromNucleus(this);
        }

        /// <summary>
        /// The type of combinators
        /// </summary>
        /// A combinator combines the weighted values of the synapses to a single value
        public enum CombinatorType {
            /// Add the weighted values together
            Sum,
            /// Multiply the weighted values
            Product,
        }
        /// <summary>
        /// The type of combinator used for this Neuron
        /// </summary>
        [HideInInspector]
        public CombinatorType combinator = CombinatorType.Sum;

        /// <summary>
        /// The type of 
        /// </summary>
        public enum ActivationType {
            Linear,
            Power,
            Sqrt,
            Reciprocal,
            Tanh,
            Binary,
            Normalized,
            Custom
        }
        /// <summary>
        /// The activation function
        /// </summary>
        [SerializeField]
        [HideInInspector]
        public ActivationType _activator;
        /// <summary>
        /// The activation funtion
        /// </summary>
        public ActivationType activator {
            get { return _activator; }
            set {
                _activator = value;
                //this.curve = GenerateCurve();
            }
        }

        #endregion Serialization

#if UNITY_MATHEMATICS

        /// <summary>
        /// The output value of the neuron
        /// </summary>
        [HideInInspector]
        protected float3 _outputValue;
        /// <summary>
        /// The output value of the neuron
        /// </summary>
        public virtual float3 outputValue {
            get { return _outputValue; }
            set {
                _outputValue = value;
                if (this.isFiring)
                    WhenFiring?.Invoke();
            }
        }
        /// <summary>
        /// The magnitude of the neuron output
        /// </summary>
        public float outputMagnitude => length(_outputValue);
        /// <summary>
        /// The squared magnitude of the neuron output
        /// </summary>
        public float outputSqrMagnitude => lengthsq(_outputValue);

#else

        /// <summary>
        /// The output value of the neuron
        /// </summary>
        protected Vector3 _outputValue;
        /// <summary>
        /// The output value of the neuron
        /// </summary>
        public virtual Vector3 outputValue {
            get { return _outputValue; }
            set {
                _outputValue = value;
                if (this.isFiring)
                    WhenFiring?.Invoke();
            }
        }
        /// <summary>
        /// The magnitude of the neuron output
        /// </summary>
        public float outputMagnitude => _outputValue.magnitude;    
        /// <summary>
        /// The squared magnitude of the neuron output
        /// </summary>
        public float outputSqrMagnitude => _outputValue.sqrMagnitude;

#endif
        /// <summary>
        /// True if the neuron have a positive value with magnitude > 0.5
        /// </summary>
        public bool isFiring => this.outputMagnitude > 0.5f;
        /// <summary>
        /// An action which is called every time the neuron is updated and is firing
        /// </summary>
        public Action WhenFiring;

        /// <summary>
        /// When true, the value will not be reset after timeToSleep.
        /// </summary>
        public bool persistOutput = false;
        /// <summary>
        /// True when the neuron is not persisting and has not be updated for timeToSleep seconds
        /// </summary>
        public virtual bool isSleeping => !persistOutput && (Time.time - this.lastUpdate > timeToSleep);
        /// <summary>
        /// Check if the neuron is sleeping.
        /// </summary>
        /// This will reset the output value if it is sleeping
        public void SleepCheck() {
            if (this.isSleeping && this.outputSqrMagnitude > 0) {
#if UNITY_MATHEMATICS
                this._outputValue = new float3(0, 0, 0);
#else
                this._outputValue = new Vector3(0,0,0);
#endif
            }
        }

        /// <summary>
        /// The time at which the last update has been done
        /// </summary>
        [HideInInspector]
        public float lastUpdate = 0;
        /// <summary>
        /// Time in seconds after the last update the neuron can go to sleep
        /// </summary>
        public static readonly float timeToSleep = 0.5f;

        /// <summary>
        /// When true, Unity will pause exection when this neuron is updated
        /// </summary>
        /// Pausing is implemented using [Debug.Break()](https://docs.unity3d.com/ScriptReference/Debug.Break.html)
        public bool breakOnUpdate = false;

        /// \copydoc NanoBrain::Nucleus::ShallowCloneTo
        public override Nucleus ShallowCloneTo(Cluster parent) {
            Neuron clone = new(parent, this.name) {
                // prefabNucleus = this
            };
            CloneFields(clone);
            return clone;
        }

        /// <summary>
        /// Copy relevant fields of this neuron to the given neuron
        /// </summary>
        /// <param name="clone"></param>
        protected virtual void CloneFields(Neuron clone) {
            clone.bias = this.bias;
            clone.persistOutput = this.persistOutput;
            clone.combinator = this.combinator;
            clone.activator = this.activator;
            clone.breakOnUpdate = this.breakOnUpdate;
        }

        /// <summary>
        /// Delete the give neuron
        /// </summary>
        /// <param name="nucleus">The neuron to delete</param>
        public static void Delete(Nucleus nucleus) {
            if (nucleus == null)
                return;
            if (nucleus is Neuron neuron) {
                foreach (Synapse synapse in neuron.synapses) {
                    if (synapse.neuron is Neuron synapse_nucleus) {
                        if (synapse_nucleus.receivers.Count > 1) {
                            // there is another nucleus feeding into this input nucleus
                            synapse_nucleus.receivers.RemoveAll(r => r == nucleus);
                        }
                        else {
                            // No other links, delete it.
                            Neuron.Delete(synapse_nucleus);
                        }
                    }
                }
                foreach (Nucleus receiver in neuron.receivers) {
                    if (receiver is not Neuron receiverNeuron)
                        continue;
                    if (receiver != null && receiverNeuron.synapses != null)
                        receiverNeuron.synapses.RemoveAll(s => s.neuron == nucleus);
                }
            }
            else if (nucleus is Cluster cluster) {
                // remove all receivers for this cluster
                foreach (Nucleus clusterNucleus in cluster.nuclei) {
                    if (clusterNucleus is Neuron output) {
                        foreach (Nucleus receiver in output.receivers) {
                            if (receiver is not Neuron receiverNeuron)
                                continue;
                            receiverNeuron.synapses.RemoveAll(s => s.neuron == output);
                        }
                    }
                }
            }

            if (nucleus.parent.prefab != null) {
                nucleus.parent.nuclei.RemoveAll(n => n == nucleus);
                nucleus.parent.RefreshOutputs();
            }
        }

        /// \copydoc NanoBrain::Nucleus::UpdateStateIsolated
        public override void UpdateStateIsolated() {
            if (breakOnUpdate) {
                Debug.Break();
            }
            var combination = Combinator(this.bias, this.synapses);
            this.outputValue = Activator(combination);
            this.lastUpdate = Time.time;
        }

        #region Combinator

#if UNITY_MATHEMATICS

        /// <summary>
        /// The combinator which combines the bias with the values from all synapses
        /// </summary>
        /// <param name="bias">The bias of the neuron</param>
        /// <param name="synapses">The synapses of the neuron</param>
        /// <returns></returns>
        protected float3 Combinator(float3 bias, List<Synapse> synapses) {
            switch (combinator) {
                case CombinatorType.Sum:
                    return CombinatorSum(bias, synapses);
                case CombinatorType.Product:
                    return CombinatorProduct(bias, synapses);
                default:
                    return CombinatorSum(bias, synapses);
            }
        }

        /// <summary>
        /// Sum the bias and synpase outputs together
        /// </summary>
        /// <param name="bias">The bias of the neuron</param>
        /// <param name="synapses">The synapses of the neuron</param>
        /// <returns></returns>
        public static float3 CombinatorSum(float3 bias, List<Synapse> synapses) {
            float3 sum = bias;
            foreach (Synapse synapse in synapses) {
                synapse.neuron.SleepCheck();
                sum += synapse.weight * synapse.neuron.outputValue;
            }
            return sum;
        }

        /// <summary>
        /// Multiply the synapse outputs together
        /// </summary>
        /// <param name="bias">The bias of the neuron</param>
        /// <param name="synapses">The synapses of the neuron</param>
        /// <returns>The result of the multiplication</returns>
        public static float3 CombinatorProduct(float3 bias, List<Synapse> synapses) {
            float3 product = bias;
            foreach (Synapse synapse in synapses) {
                synapse.neuron.SleepCheck();
                product *= synapse.weight * synapse.neuron.outputValue;
            }
            return product;
        }

#else

        /// <summary>
        /// The combinator which combines the bias with the values from all synapses
        /// </summary>
        /// <param name="bias">The bias of the neuron</param>
        /// <param name="synapses">The synapses of the neuron</param>
        /// <returns></returns>
        protected Vector3 Combinator(Vector3 bias, List<Synapse> synapses) {
            switch (combinator) {
                case CombinatorType.Sum: return CombinatorSum(bias, synapses);
                case CombinatorType.Product: return CombinatorProduct(bias, synapses);
                default: return CombinatorSum(bias, synapses);
            }
        }

        /// <summary>
        /// Sum the bias and synpase outputs together
        /// </summary>
        /// <param name="bias">The bias of the neuron</param>
        /// <param name="synapses">The synapses of the neuron</param>
        /// <returns></returns>
        public static Vector3 CombinatorSum(Vector3 bias, List<Synapse> synapses) {
            float3 sum = bias;
            foreach (Synapse synapse in synapses) {
                synapse.neuron.SleepCheck();
                sum += synapse.weight * synapse.neuron.outputValue;
            }
            return sum;
        }

        /// <summary>
        /// Multiply the synapse outputs together
        /// </summary>
        /// <param name="bias">The bias of the neuron</param>
        /// <param name="synapses">The synapses of the neuron</param>
        /// <returns>The result of the multiplication</returns>
        public static Vector3 CombinatorProduct(Vector3 bias, List<Synapse> synapses) {
            float3 product = bias;
            foreach (Synapse synapse in synapses) {
                synapse.neuron.SleepCheck();
                product *= synapse.weight * synapse.neuron.outputValue;
            }
            return product;
        }

#endif
        #endregion Combinator

        #region Activator

#if UNITY_MATHEMATICS

        /// <summary>
        /// Apply the activation function to the input
        /// </summary>
        /// <param name="inputValue"></param>
        /// <returns>The result of applying the activation function</returns>
        // This does not allocate memory and seems faster than a switch expression
        protected float3 Activator(float3 inputValue) {
            switch (activator) {
                case ActivationType.Linear:
                    return ActivatorLinear(inputValue);
                case ActivationType.Sqrt:
                    return ActivatorSqrt(inputValue);
                case ActivationType.Power:
                    return ActivatorPower(inputValue);
                case ActivationType.Reciprocal:
                    return ActivatorReciprocal(inputValue);
                case ActivationType.Tanh:
                    return ActivatorTanh(inputValue);
                case ActivationType.Binary:
                    return ActivatorBinary(inputValue);
                case ActivationType.Normalized:
                    return ActivatorNormalized(inputValue);
                default:
                    return ActivatorLinear(inputValue);
            }
        }

        /// <summary>
        /// Linear activation function
        /// </summary>
        /// <param name="input">Input value</param>
        /// <returns>The unchanged value</returns>
        protected float3 ActivatorLinear(float3 input) {
            return input;
        }

        /// <summary>
        /// Square root activation function
        /// </summary>
        /// <param name="input">Input value</param>
        /// <returns>The square root of the input</returns>
        protected float3 ActivatorSqrt(float3 input) {
            float3 result = normalize(input) * MathF.Sqrt(length(input));
            return result;
        }

        /// <summary>
        /// Power activation function
        /// </summary>
        /// <param name="input">Input value</param>
        /// <returns>The input to the power of 2</returns>
        protected float3 ActivatorPower(float3 input) {
            float3 result = normalize(input) * MathF.Pow(length(input), 2);
            return result;
        }

        /// <summary>
        /// Reciprocal activation function
        /// </summary>
        /// <param name="input">Input value</param>
        /// <returns>1/input value</returns>
        protected float3 ActivatorReciprocal(float3 input) {
            float magnitude = length(input);
            if (magnitude == 0)
                return new float3(0, 0, 0);

            float3 result = normalize(input) * (1 / magnitude);
            return result;
        }

        /// <summary>
        /// Tanh activation function
        /// </summary>
        /// <param name="input">Input value</param>
        /// <returns>Tanh(input value)</returns>
        protected float3 ActivatorTanh(float3 input) {
            float magnitude = length(input);
            float3 result = normalize(input) * MathF.Tanh(magnitude);
            return result;
        }
        /// <summary>
        /// Binary activation function
        /// </summary>
        /// <param name="input">Input value</param>
        /// <returns>An uniform vector with magnitude between 0 and 1</returns>
        protected float3 ActivatorBinary(float3 input) {
            float magnitude = length(input);
            float value = Mathf.Clamp01(magnitude);
            return float3(value, value, value);
        }

        /// <summary>
        /// Normalize activation function
        /// </summary>
        /// <param name="input">Input value</param>
        /// <returns>The normalized vector</returns>
        protected float3 ActivatorNormalized(float3 input) {
            if (lengthsq(input) == 0)
                return input;
            float3 result = normalize(input);
            return result;
        }

#else

        /// <summary>
        /// Apply the activation function to the input
        /// </summary>
        /// <param name="inputValue"></param>
        /// <returns>The result of applying the activation function</returns>
        // This does not allocate memory and seems faster than a switch expression
        protected Vector3 Activator(Vector3 inputValue) {
            switch (activator) {
                case ActivationType.Linear: return ActivatorLinear(inputValue);
                case ActivationType.Sqrt: return ActivatorSqrt(inputValue);
                case ActivationType.Power: return ActivatorPower(inputValue);
                case ActivationType.Reciprocal: return ActivatorReciprocal(inputValue);
                // case ActivationType.Tanh: return ActivatorTanh(inputValue);
                // case ActivationType.Binary: return ActivatorBinary(inputValue);
                // case ActivationType.Normalized: return ActivatorNormalized(inputValue);
                default: return ActivatorLinear(inputValue);
            }
        }

        /// <summary>
        /// Linear activation function
        /// </summary>
        /// <param name="input">Input value</param>
        /// <returns>The unchanged value</returns>
        protected Vector3 ActivatorLinear(Vector3 input) {
            return input;
        }

        /// <summary>
        /// Square root activation function
        /// </summary>
        /// <param name="input">Input value</param>
        /// <returns>The square root of the input</returns>
        protected Vector3 ActivatorSqrt(Vector3 input) {
            Vector3 result = input.normalized * System.MathF.Sqrt(input.magnitude);
            return result;
        }

        /// <summary>
        /// Power activation function
        /// </summary>
        /// <param name="input">Input value</param>
        /// <returns>The input to the power of 2</returns>
        protected Vector3 ActivatorPower(Vector3 input) {
            Vector3 result = input.normalized * System.MathF.Pow(input.magnitude, 2);
            return result;
        }

        /// <summary>
        /// Reciprocal activation function
        /// </summary>
        /// <param name="input">Input value</param>
        /// <returns>1/input value</returns>
        protected Vector3 ActivatorReciprocal(Vector3 input) {
            float magnitude = input.magnitude;
            if (magnitude == 0)
                return new Vector3(0, 0, 0);

            Vector3 result = input.normalized * (1 / magnitude);
            return result;
        }

#endif

        #endregion Activator

        #region Receivers

        /// <summary>
        /// The nuclei which have a synapse to this neuron
        /// </summary>
        [SerializeReference]
        [HideInInspector]
        private List<Nucleus> _receivers = new();
        /// <summary>
        /// The nuclei which have a synapse to this neuron
        /// </summary>
        public virtual List<Nucleus> receivers {
            get { return _receivers; }
            set { _receivers = value; }
        }

        /// <summary>
        /// Add a new receiver to this neuron
        /// </summary>
        /// <param name="receiverToAdd">The receiver to add</param>
        /// <param name="weight">The weight to use for the synapse to his neuron</param>
        public virtual void AddReceiver(Nucleus receiverToAdd, float weight = 1) {
            if (receiverToAdd is not Neuron receiverNeuron)
                return;
            this._receivers.Add(receiverNeuron);
            receiverNeuron.AddSynapse(this, weight);
            //Debug.Log($"Add synapse {this.clusterPrefab.name}.{this.name} -> {receiverToAdd.name} --- [{this.receivers.Count}]");

        }

        /// <summary>
        /// Remove a receiver to this neuron
        /// </summary>
        /// <param name="receiverToRemove">The receiver to remove</param>
        public virtual void RemoveReceiver(Nucleus receiverToRemove) {
            if (receiverToRemove is not Neuron receiverNeuron)
                return;
            this._receivers.RemoveAll(receiver => receiver == receiverNeuron);
            receiverNeuron.synapses.RemoveAll(synapse => synapse.neuron == this);

            // Nucleus prefabReceiver = receiverToRemove.prefabNucleus;
            // if (this.prefabNucleus is Neuron prefabNeuron && prefabReceiver != null) {
            //     prefabNeuron.receivers.RemoveAll(receiver => receiver == prefabReceiver);
            //     prefabReceiver.synapses.RemoveAll(synapse => synapse.neuron == prefabNeuron);
            // }
        }


        #endregion Receivers

        /// <summary>
        /// Process an external stimulus
        /// </summary>
        /// <param name="inputValue">The value of the stimulus</param>
        public virtual void ProcessStimulus(Vector3 inputValue) {
            this.lastUpdate = Time.time;
            this.bias = inputValue;
            this.parent?.UpdateFromNucleus(this);
        }
    }

}