/* Author: Xu Zhang @UConn, Jan., 2019
Standard CCTC model under Harmaline tremor condition
Spike times of every cell, membrane voltage traces of all IONs
and one of the PCs (no.19 of 0-39) are recorded and saved inside the
"./recordings/HARMALINE/" folder.
*/

load_file("nrngui.hoc")

load_file("rngRead.hoc") // Load rng seeds
noiseSwitch=1 // Membrane and synaptic noises, 1/0 = turn on/off
dt = 0.0125 // Cannot be set larger, otherwise ION and DCN would have different dynamics
v_init = -57
tstop = 6000 // Simulation period

// Loading individual cells
load_file("cell_ION.hoc")
load_file("cell_PC.hoc")
load_file("cell_DCN.hoc")
load_file("cell_TC.hoc")
load_file("cell_MC.hoc")

// Loading synaptic connections
load_file("syn_ION_PC.hoc")
load_file("syn_PC_DCN.hoc")
load_file("syn_DCN_ION.hoc")
load_file("syn_DCN_TC.hoc")
load_file("syn_TC_MC.hoc")
load_file("syn_MC_GrL.hoc")
load_file("syn_GrL_PC.hoc")

// Change the ION properties into Harmaline condition
for i = 0,7 {
	IONcell[i].gbar_ioh = 0.02 // (mS/cm2)
	IONcell[i].gbar_ioCa = 0.3 // (mS/cm2) Harmaline
	ocION[i].amp = -2e-3
	ocION[i].del = 0
	ocION[i].dur = 1e10
}

// // (No need to) push ION into oscillations
// objref stimION[8]
// for i = 0,7 {
// IONcell[i] stimION[i] = new IClamp(0.5)
// stimION[i].amp = 5e-3
// stimION[i].del = 1000
// stimION[i].dur = 20
// }

access DCNcell

// Record PC (Must be included)
objref rec_v_PC[40]
for i = 0,39 {
	rec_v_PC[i] = new Vector()
	rec_v_PC[i].record(&PCcell[i].v(0.5))
}

// Record PC APs
objref apc_PC[40], apPC[40]
for i = 0,39 {
	PCcell[i] apc_PC[i] = new APCount(0.5)
	apc_PC[i].thresh = -45
	apPC[i] = new Vector()
	apc_PC[i].record(apPC[i])
}

// Record ION
objref apc_ION[8], apION[8]
for i = 0,7 {
	IONcell[i] apc_ION[i] = new APCount(0.5)
	apc_ION[i].thresh = -45
	apION[i] = new Vector()
	apc_ION[i].record(apION[i])
}

// Record ION membrane voltage
objref rec_v_ION[8]
for i = 0,7 {
	rec_v_ION[i] = new Vector()
	rec_v_ION[i].record(&IONcell[i].v(0.5))
}

// Record GrL
objref apGrC[4]
for i = 0,3 {
	apGrC[i] = new Vector()
	syn_grcsc_ampa[i].record(apGrC[i])
}
objref apGoC[4]
for i = 0,3 {
	apGoC[i] = new Vector()
	syn_gocgrc_gaba[i].record(apGoC[i])
}
objref apSTL[4]
for i = 0,3 {
	apSTL[i] = new Vector()
	syn_scgoc_gaba[i].record(apSTL[i])
}

// Record NO
objref apc_NO, apNO
NOcell apc_NO = new APCount(0.5)
apc_NO.thresh = -30
apNO = new Vector()
apc_NO.record(apNO)

// Record DCN
objref apc_DCN, apDCN
DCNcell apc_DCN = new APCount(0.5)
apc_DCN.thresh = -30
apDCN = new Vector()
apc_DCN.record(apDCN)

// Record DCN
objref rec_v_DCN
rec_v_DCN = new Vector()
rec_v_DCN.record(&DCNcell.v(0.5))

// Record NO
objref rec_v_NO
rec_v_NO = new Vector()
rec_v_NO.record(&NOcell.v(0.5))

// Record Vim
objref apc_Vim, apVim
TCcell apc_Vim = new APCount(0.5)
apc_Vim.thresh = -30
apVim = new Vector()
apc_Vim.record(apVim)

// Record Vim
objref rec_v_Vim
rec_v_Vim = new Vector()
rec_v_Vim.record(&TCcell.v(0.5))

// Record PYN
objref apc_PYN[20], apPYN[20]
for i = 0,19 {
	PYcell[i] apc_PYN[i] = new APCount(0.5)
	apc_PYN[i].thresh = -30
	apPYN[i] = new Vector()
	apc_PYN[i].record(apPYN[i])
}

// Record FSI
objref apc_FSI[2], apFSI[2]
for i = 0,1 {
	FScell[i] apc_FSI[i] = new APCount(0.5)
	apc_FSI[i].thresh = -30
	apFSI[i] = new Vector()
	apc_FSI[i].record(apFSI[i])
}


//////////////////////////////////////////////////////////////////
// Simulation starts											//
//																//
// Set up synaptic transmission delays between PC-DCN and PC-NO	//
proc advance() {
	if (t>PC2DCN_delay) {
		for i = 0,39 {
			PC2DCN_syn[i].vpre = rec_v_PC[i].x[rec_v_PC[i].size()-PC2DCN_delay/dt] // PC2DCN_delay defined in syn_PC_DCN.hoc
			PC2NO_syn[i].vpre = rec_v_PC[i].x[rec_v_PC[i].size()-PC2NO_delay/dt]
		}
	}
	fadvance()
}
//																//
run()															//
//																//
//////////////////////////////////////////////////////////////////

// Save PC (Just one PC)
objref sav_v_PC
sav_v_PC = new File()
sav_v_PC.wopen("recordings/HARMALINE/PC_v_all.txt")
rec_v_PC[19].printf(sav_v_PC)
sav_v_PC.close()

// Save PC APs
objref rec_PC
rec_PC = new File()
rec_PC.wopen("recordings/HARMALINE/ap_PC.txt")
for i = 0,39 {
	for j = 0,apPC[i].size()-1 {
		if (apPC[i].size()>0) {
			rec_PC.printf("%d,%f\n",i,apPC[i].x(j)) // Column 1 indicates no. of the PC (0-39) that corresponds to the AP (Column 2)
		}
	}
}
rec_PC.close()

// Save ION APs
objref rec_ION
rec_ION = new File()
rec_ION.wopen("recordings/HARMALINE/ap_ION.txt")
for i = 0,7 {
	for j = 0,apION[i].size()-1 {
		if (apION[i].size()>0) {
			rec_ION.printf("%d,%f\n",i,apION[i].x(j)) // Column 1 indicates no. of the ION (0-7) that corresponds to the AP (Column 2)
		}
	}
}
rec_ION.close()

// Save ION
objref sav_v_ION[8]

sav_v_ION[0] = new File()
sav_v_ION[0].wopen("recordings/HARMALINE/ION_v_all_0.txt")
rec_v_ION[0].printf(sav_v_ION[0])
sav_v_ION[0].close()

sav_v_ION[1] = new File()
sav_v_ION[1].wopen("recordings/HARMALINE/ION_v_all_1.txt")
rec_v_ION[1].printf(sav_v_ION[1])
sav_v_ION[1].close()

sav_v_ION[2] = new File()
sav_v_ION[2].wopen("recordings/HARMALINE/ION_v_all_2.txt")
rec_v_ION[2].printf(sav_v_ION[2])
sav_v_ION[2].close()

sav_v_ION[3] = new File()
sav_v_ION[3].wopen("recordings/HARMALINE/ION_v_all_3.txt")
rec_v_ION[3].printf(sav_v_ION[3])
sav_v_ION[3].close()

sav_v_ION[4] = new File()
sav_v_ION[4].wopen("recordings/HARMALINE/ION_v_all_4.txt")
rec_v_ION[4].printf(sav_v_ION[4])
sav_v_ION[4].close()

sav_v_ION[5] = new File()
sav_v_ION[5].wopen("recordings/HARMALINE/ION_v_all_5.txt")
rec_v_ION[5].printf(sav_v_ION[5])
sav_v_ION[5].close()

sav_v_ION[6] = new File()
sav_v_ION[6].wopen("recordings/HARMALINE/ION_v_all_6.txt")
rec_v_ION[6].printf(sav_v_ION[6])
sav_v_ION[6].close()

sav_v_ION[7] = new File()
sav_v_ION[7].wopen("recordings/HARMALINE/ION_v_all_7.txt")
rec_v_ION[7].printf(sav_v_ION[7])
sav_v_ION[7].close()

// Save GrC
objref f_GrC[8]

f_GrC[0] = new File()
f_GrC[0].wopen("recordings/HARMALINE/apGrC_0.txt")
apGrC[0].printf(f_GrC[0])
f_GrC[0].close()

f_GrC[1] = new File()
f_GrC[1].wopen("recordings/HARMALINE/apGrC_1.txt")
apGrC[1].printf(f_GrC[1])
f_GrC[1].close()

f_GrC[2] = new File()
f_GrC[2].wopen("recordings/HARMALINE/apGrC_2.txt")
apGrC[2].printf(f_GrC[2])
f_GrC[2].close()

f_GrC[3] = new File()
f_GrC[3].wopen("recordings/HARMALINE/apGrC_3.txt")
apGrC[3].printf(f_GrC[3])
f_GrC[3].close()

// Save GoC
objref f_GoC[8]

f_GoC[0] = new File()
f_GoC[0].wopen("recordings/HARMALINE/apGoC_0.txt")
apGoC[0].printf(f_GoC[0])
f_GoC[0].close()

f_GoC[1] = new File()
f_GoC[1].wopen("recordings/HARMALINE/apGoC_1.txt")
apGoC[1].printf(f_GoC[1])
f_GoC[1].close()

f_GoC[2] = new File()
f_GoC[2].wopen("recordings/HARMALINE/apGoC_2.txt")
apGoC[2].printf(f_GoC[2])
f_GoC[2].close()

f_GoC[3] = new File()
f_GoC[3].wopen("recordings/HARMALINE/apGoC_3.txt")
apGoC[3].printf(f_GoC[3])
f_GoC[3].close()

// Save STL
objref f_STL[8]

f_STL[0] = new File()
f_STL[0].wopen("recordings/HARMALINE/apSTL_0.txt")
apSTL[0].printf(f_STL[0])
f_STL[0].close()

f_STL[1] = new File()
f_STL[1].wopen("recordings/HARMALINE/apSTL_1.txt")
apSTL[1].printf(f_STL[1])
f_STL[1].close()

f_STL[2] = new File()
f_STL[2].wopen("recordings/HARMALINE/apSTL_2.txt")
apSTL[2].printf(f_STL[2])
f_STL[2].close()

f_STL[3] = new File()
f_STL[3].wopen("recordings/HARMALINE/apSTL_3.txt")
apSTL[3].printf(f_STL[3])
f_STL[3].close()

// Save NO
objref NO_all
NO_all = new Vector()
objref rec_NO
rec_NO = new File()
NO_all.append(apNO)
rec_NO.wopen("recordings/HARMALINE/ap_NO.txt")
NO_all.printf(rec_NO)
rec_NO.close()

// Save DCN
objref DCN_all
DCN_all = new Vector()
objref rec_DCN
rec_DCN = new File()
DCN_all.append(apDCN)
rec_DCN.wopen("recordings/HARMALINE/ap_DCN.txt")
DCN_all.printf(rec_DCN)
rec_DCN.close()

// Save DCN
objref sav_v_DCN
sav_v_DCN = new File()
sav_v_DCN.wopen("recordings/HARMALINE/DCN_v_all.txt")
rec_v_DCN.printf(sav_v_DCN)
sav_v_DCN.close()

// Save NO
objref sav_v_NO
sav_v_NO = new File()
sav_v_NO.wopen("recordings/HARMALINE/NO_v_all.txt")
rec_v_NO.printf(sav_v_NO)
sav_v_NO.close()

// Save Vim
objref Vim_all
Vim_all = new Vector()
objref rec_Vim
rec_Vim = new File()
Vim_all.append(apVim)
rec_Vim.wopen("recordings/HARMALINE/ap_Vim.txt")
Vim_all.printf(rec_Vim)
rec_Vim.close()

// Save Vim
objref sav_v_Vim
sav_v_Vim = new File()
sav_v_Vim.wopen("recordings/HARMALINE/Vim_v_all.txt")
rec_v_Vim.printf(sav_v_Vim)
sav_v_Vim.close()

// Save PYN
objref PYN_all
PYN_all = new Vector()
objref rec_PYN
rec_PYN = new File()
for i = 0,19 {
	PYN_all.append(apPYN[i])
}
rec_PYN.wopen("recordings/HARMALINE/ap_PYN.txt")
PYN_all.printf(rec_PYN)
rec_PYN.close()

// Save FSI
objref FSI_all
FSI_all = new Vector()
objref rec_FSI
rec_FSI = new File()
for i = 0,1 {
	FSI_all.append(apFSI[i])
}
rec_FSI.wopen("recordings/HARMALINE/ap_FSI.txt")
FSI_all.printf(rec_FSI)
rec_FSI.close()

// quit()