// CN model used in Saak V Ovsepian, Volker Steuber, Marie Le 
// Berre, Liam O'Hara, Valerie B O'Leary, and J. Oliver Dolly 
// (2013). A Defined Heteromeric KV1 Channel Stabilizes the 
// Intrinsic Pacemaking and Regulates the Efferent Code of Deep 
// Cerebellar Nuclear Neurons to Thalamic Targets. Journal of 
// Physiology (epub ahead of print). 
//
// written by Johannes Luthman, modified by Volker Steuber
//
// procedures for recording and saving data for the simulations 
// that replicate Figure 9 in Ovsepian et al. (2013)

// Declare objects and strings used for recording and saving data.
objref recT, recV, recTraceT, recTraceV
objref vZerosAndOnes, vSpikeTimes
objref recGgaba
objref traceMatrix, fileTrace, fileSpikeTimes
strdef strFileNameBase


proc InstantiateRecObjects() {

    recT = new Vector(nRecVectElements)
    recV = new Vector(nRecVectElements)

    // Create vectors to record traces.
    if (tTraceStop[0] > 0) {
        recTraceT = new Vector(sizeVectorOfTrace)
        recTraceV = new Vector(sizeVectorOfTrace)
        recGgaba = new Vector(sizeVectorOfTrace)
    }
}

proc SetupOutputFiles() {

    if (strcmp(strFilePrefix, "") == 0) {
        strFilePrefix = "OutputDCN"
    }
    sprint(strFileNameBase, "%s_soma_%gs", strFilePrefix, int(0.5 + (runTime/1000)))

    fileSpikeTimes = new File()
    sprint(strTemp, "%s_ap.dat", strFileNameBase) //"ap" = action potential
    printf("starting simulation with output name %s\n", strTemp)
    fileSpikeTimes.wopen(strTemp)
}

proc writeToTimeAndVoltVectors() {
    recT.x[iRecTimeVolt] = t
    recV.x[iRecTimeVolt] = soma.v(0.5)
}

proc writeToTraceVectors() { local subC, subSumGABAg, subSumGABAi, subSumExci
    
    recTraceT.x[iRecTrace] = t
    recTraceV.x[iRecTrace] = soma.v(0.5)

    // Record gaba conductance mean of all synapses.
    subSumGABAg=0
    for (subC=0; subC < INHTOTALSYNAPSES; subC=subC+1) {
        subSumGABAg = subSumGABAg + gaba[subC].g
    }
    recGgaba.x[iRecTrace] = subSumGABAg / INHTOTALSYNAPSES
}

proc writeSpikeTimesToFile() { local subC, subnIndeces, subnSpikes

    vZerosAndOnes = new Vector()
    vZerosAndOnes.spikebin(recV,-20) //feeding recV to spikebin gives vZerosAndOnes the same size as recV.
            // Some spikes reach just around 0 when excitatory synaptic input rates are high;
            // since not each dt is recorded, it's necessary to set the threshold to lower
            // than 0 to catch those spikes.

    // Run through the spike vector, containing 0s and 1s. For each 1, save
    // the corresponding time from recT to the new vector vSpikeTimes.
    subnIndeces = vZerosAndOnes.size()
    subnSpikes = 0
    vSpikeTimes = new Vector(subnIndeces)
    for(subC = 0; subC < subnIndeces; subC+=1) {
        if (vZerosAndOnes.x[subC] > 0.000001) {
            vSpikeTimes.x[subnSpikes] = recT.x[subC]
            subnSpikes+=1
        }
    }
    //Remove trailing zeroes from spike vector.
    if (subnSpikes > 0.0000001) {
        vSpikeTimes.resize(subnSpikes-1)
        vSpikeTimes.printf(fileSpikeTimes, "%g\n")
        fileSpikeTimes.flush()
    }
    if (t>=runTime) {
        fileSpikeTimes.close()
    }
} // end of writeSpikeTimesToFile()

proc writeTracesToFile() { local subC

    // Before saving, determine number of non-zero entries of the vectors.
    // (some extra lines may have been added)
    subC = sizeVectorOfTrace-1
    while (recTraceT.x[subC] < 0.0000001) {
        subC = subC-1
    }

    // First save time. (time is saved separately to save space,
    // due to its different requirement for the number of decimals)
    sprint(strTemp, "%s_time.dat", strFileNameBase)
    fileTrace = new File()
    fileTrace.wopen(strTemp)
    recTraceT.resize(subC + 1)
    recTraceT.printf(fileTrace, "%g\n")
    fileTrace.close()

    // Work on the traces. First instantiate a matrix to use for saving the data.
    traceMatrix = new Matrix(subC + 1, 2)
    recTraceV.resize(subC + 1)
    traceMatrix.setcol(0, recTraceV)
    recGgaba.resize(subC + 1)
    traceMatrix.setcol(1, recGgaba)

    // Create a file to contain the traces.
    sprint(strTemp, "%s_trace.dat", strFileNameBase)
    fileTrace = new File()
    fileTrace.wopen(strTemp)
    traceMatrix.fprint(0, fileTrace, "%.2e\t")
    fileTrace.close()
}