// Parameters for the full human network model

// ----------------------------SIMULATION-------------------------------
    Time_Step = 0.1
    Simul_Time = 2000
    sample_time = 0.1

// ----------------------------RD VALUES-------------------------------
    // RD Values
    PR_loss = 1 // fraction of photoreceptors lost
    RD_Late_Active = 1 // 1 = pr-loss, 0 = late stage RD
    BC_Syn_loss = 0

// ----------------------------LOCALISATION-----------------------------
    // Limits of the model (radius of the macular)
    radius_lim = 4          // mm

    // Size of retinal patch generated
    // Note: patch size should be larger than provided RGC patch due to edge effects
    // MAX PATCH SIZE OF 3X3
    Patch_size_x = 0.1     // mm
    Patch_size_y = 0.1    // mm

    // Eccentricity of the origin of the model
    // DO NOT USE (0,0) AS CENTRE, use -0.2 mm for x for accurate AII density
    Eccentricity_x = -1.2    // mm, RGC pop is at -1.2
    Eccentricity_y = 0      // mm

    // Fovea position
    Fovea_x = 0             // mm
    Fovea_y = 0             // mm

    // Thickness (values from Ferguson 2013)
    NFL_thickness = 0.031
    IPL_GCL_Thickness = 0.068 
    INL_Thickness = 0.03
    OPL_Thickness = 0.032
    ONL_PIS_Thickness = 0.077
    POS_Thickness = 0.037
    Retinal_total_thickness = 0.275  // mm, assumed constant in area of stimulation

    // Maximum number of each cell
    MaxNumPRs = 100000
    MaxNumHzs = 1000
    MaxNumBips = 10000
    MaxNumAIIs = 1000

    // Randomisation seed
    Seed = 4

// -------------------------------CONNECTIVITY------------------------------

    // Counters and Max Values
    MaxNumPRGapConnections = 50000
    NumPRGapConnections = 0
    MaxNumAIIGapConnections = 10000
    NumAIIGapConnections = 0
    MaxNumAmaGapConnections = 10000
    NumAmaGapConnections = 0
    maxNumDendConnec = 100

    // Max numbers, MODIFY FROM MAXIMUM VALUES IN MATRICES
    MaxNumRod2RBC = 8
    MaxNumCone2ONBC = 8
    MaxNumCone2OFFBC = 8
    MaxNumCone2HZ = 7
    MaxNumRBC2AII = 9
    MaxNumONBC2AII = 10
    MaxNumAII2OFFBC = 10
    MaxNumAII2OFFRGC = 10
    MaxNumBC2RGC = 5

    RGC_dend_buffer = 0.5
    RGC_dend_ratio = 3

    // Conductance values
    HomoPRGap = 0.5                     // Zhang 2005
    HeteroPRGap = 0.1                   // Zhang 2005
    HomoAIIGap = 1.16                   // using average value of - Veruki 2002 ranges between 0.31 to 1.46 nS, slope of I-V curve used
    Ama2BipGap = (0.1/MaxNumONBC2AII)*RD_Late_Active   // Veruki 2002 ranges between 0.1 to 3.35 nS

    HorizontalEXSynapticConductance = 0.05/(MaxNumCone2HZ*75) // Reduction factor due to geometry (i_syn is kept constant but g_syn is variable)
    HorizontalINSynapticConductance = -0.05/(MaxNumCone2HZ*75)

    ONBipSynapticConductance = 0.00256 //MaxNumCone2ONBC 	// Correction factor for conversion between population vs pathway
    OFFBipSynapticConductance = -0.00256 * (1-PR_loss) //MaxNumCone2OFFBC
    if(PR_loss > 0) {
        RodBipSynapticConductance = 0
    } else {
        RodBipSynapticConductance = 0.00256/MaxNumRod2RBC
    }

    AmaSynapticConductance = (0.00256/MaxNumAII2OFFBC)*RD_Late_Active
    Ama2GanSynapticConductance = (0.000256/MaxNumAII2OFFRGC)*(1-BC_Syn_loss)
    RodBip2AmaSynapticConductance = (0.00256/MaxNumRBC2AII)*RD_Late_Active
    GanSynapticConductance = (0.00256/MaxNumBC2RGC)*(1-BC_Syn_loss)

    // Thresholds
    HorizontalEXSynapticThreshold = -45
    HorizontalINSynapticThreshold = -47
    RodBipSynapticThreshold = -45
    ConeBipSynapticThreshold = -45
    AmaSynapticThreshold = -59
    Ama2ConeOFFBipThreshold = -59
    RodBip2AmaSynapticThreshold = -37
    ConeONGanSynapticThreshold = -40
    ConeOFFGanSynapticThreshold = -42

    // Parallel Context and Synaptic Counters
    synapse_counter = 0
    SVCounter = 0
    TVCounter = 0

    /* For a 0.09 x 0.09 mm size model at 1.2 mm eccentricity (4.17 degrees):
    PR_total_upper_cells = 260
    PR_total_lower_cells = 598
    HZ_total_upper_cells = 48
    HZ_total_lower_cells = 101
    BIP_total_upper_cells = 121
    BIP_total_lower_cells = 268
    AII_total_upper_cells = 12
    AII_total_lower_cells = 21 
    */

// -----------------------------Inputs-----------------------------

    // Stimulus parameters for light activation, Gap junctions are stable at 900 ms
    RodStimAmp = 0 //40
    RodStimDel = 900
    RodStimTime = 200

    ConeStimAmp = 0 //40 * (1 - PR_loss)
    ConeStimDel = 900
    ConeStimTime = 200