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reduced-passive.pDE_28Jan15-09-41-37.log-cbest.hoc
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reduced-passive.pDE_28Jan15-09-41-37.log-cbest.hoc
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// ------hoc_main--->>/home/ximi/Projects/ParSims/reduced-passive.hoc<<---------------
// Initialize
{
// load_file( "eTrace-p.hoc", "eTrace_loaded" )
chdir("/home/ximi/Projects/ParSims")
load_file( "eTrace-p.hoc", "eTrace_loaded" )
load_file( "stdrun.hoc" )
load_file( "eMorph-p.hoc" )
load_file( "do_log.hoc" )
}
nrn_load_dll("/home/ximi/Projects/ParSims/from_axon_new/ca1n1-mod/x86_64/.libs/libnrnmech.so" )
//================================================================================
func vdef(){
if( name_declared( $s1 ) == 5 ) return 1
return 0
}
//================================================================================
func Boltz(){
return 1/(1+exp(($1-$2)/$3))
}
func max(){ local i, im
im = $1
for i=1, numarg() if( $i>im ) im = $i
return im
}
func GaussLike(){ // x, A, W, D
return $2*exp(-($1-$4)^2/$3 )
}
// Perpendicular y distance
func ydistP(){
// if(ismembrane("morpho")){
// return abs(0.5*(y0_morpho+y1_morpho))
// }else { return abs( y3d(0)+y3d(n3d()-1) )/2}
return distance(0.5)
}
//================================================================================
objref eM
eM = new eMorph()
eM.idebug = 1
dfc_idebug = 0
proc mulfit_cell_init() {
soma { distance() } // set soma(0.5) as reference point
//adj_e_pas = G_e_pas - G_e_pas_slope * tgt_bldiff
//printf( "adj_e_pas %g G_e_pas %g G_e_pas_slope %g tgt_bldiff %g\n", adj_e_pas, G_e_pas, G_e_pas_slope, tgt_bldiff )
forall {
do_pas()
do_Naf() // does Naf and Nav16
do_h()
do_KDR()
do_KA()
}
// if( vdef( "RmCm_spine_gbar")) execute("eM.RmCm_spine_gbar = RmCm_spine_gbar") // defaults to 0 in template
Spnum = 30000
if( vdef( "Spine_number")) Spnum = Spine_number
eM.Spine_Comp_RmCm_f3d( "n400_af3d", Spnum ) // We perform Spine compensation after all else is set.
//eM.use_morpho_xyz=1
//eM.Spine_Comp_RmCm_n400_JAI(Spnum)
eM.idebug = 0 // show debug info only on first run
set_nseg( lambda_f_d )
//axon_hill {
// diam(0:1)=soma.diam(1):diam(0)
//}
}
//--------------------------------------------------------------------------------
proc set_nseg(){ local ns, lfd
nseg_tot = 0
lfd = $1
soma area( 0.5 )
forall {
if( lfd <= 0 ) ns = 1
if( lfd > 0 ) ns = int((L/($1 *lambda_f(100))+.9)/2)*2 + 1
if( ns > nseg ) nseg = ns
nseg_tot += nseg
}
printf( "lambda-d %g nseg_tot %d\n", lfd, nseg_tot )
}
//--------------------------------------------------------------------------------
proc do_pas(){
if( !ismembrane("epasn") ) insert epasn
//e_pas = adj_e_pas
g_epasn = 1 / ( G_Rm * 1000 )
Ra = G_Ra//*1000
cm = G_cm
ifsec "soma" {
if( vdef( "soma_l")) L=soma_l
if( vdef( "soma_diam")) diam=soma_diam
if( vdef( "soma_cm" )) cm = soma_cm
if( vdef( "soma_Rm" )) g_epasn = 1/ ( soma_Rm * 1000 )
if( vdef( "soma_Ra" )) Ra = soma_Ra//*1000
}
ifsec "axon" { // aX_ => generic for all axons but Hillock
if( vdef( "aX_cm" )) cm = aX_cm
if( vdef( "aX_Rm" )) g_epasn = 1/ ( aX_Rm * 1000 )
if( vdef( "aX_Ra" )) Ra = aX_Ra//*1000
}
ifsec "axon_mnode" { // aXm_ special for myelin can override generic
if( vdef("aXm_cm")) cm = aXm_cm
if( vdef("aXm_Rm")) g_epasn = 1/ ( aXm_Rm * 1000 )
if( vdef("aXm_Ra")) Ra = aXm_Ra//*1000
}
ifsec "axon_inode" { // aXr_ special for nodes of Ranvier can override generic
if( vdef("aXr_cm")) cm = aXr_cm
if( vdef("aXr_Rm")) g_epasn = 1/ ( aXr_Rm * 1000 )
if( vdef("aXr_Ra")) Ra = aXr_Ra//*1000
}
ifsec "axon_iseg[0]" {
//if(vdef("aX_iseg_l")) L=aX_iseg_l*0.5
L=30
diam=1
}
ifsec "axon_iseg[1]" {
//if(vdef("aX_iseg_l")) L=aX_iseg_l*0.5
L=40
diam=1
}
ifsec "axon_hill" {
if(vdef("axon_hill_l")){
L=axon_hill_l
}else{L=5}
diam(0:1)=2.8:1
}
}
//--------------------------------------------------------------------------------
proc do_Naf(){
if( vdef( "Gbar_Naf" )){
if( !ismembrane("Naf_i0")) insert Naf_i0
nai0_na_ion = 10
nao0_na_ion = 145
nai=nai0_na_ion
nao=nao0_na_ion
ena=nernst(nai0_na_ion, nao0_na_ion,1)
gbar_Naf_i0 = Gbar_Naf // default value unless overriden below
ifsec "soma" if(vdef("s0_Gbar_Naf")) gbar_Naf_i0 = s0_Gbar_Naf
ifsec "axon_hill" if(vdef("aXh_Gbar_Naf")) gbar_Naf_i0 = aXh_Gbar_Naf
ifsec "axon_mnode" if(vdef("aXm_Gbar_Naf")) gbar_Naf_i0 = aXm_Gbar_Naf
if( issection("axon_mnode.*") || issection("axon_hill.*" ) ) return
ifsec "axon_iseg" {
//if(!ismembrane("Naf_i1")) {
insert Naf_i1
uninsert Naf_i0
//}
ifsec "axon_iseg[0]" if( vdef("aXi0_Gbar_Naf")) gbar_Naf_i1 = aXi0_Gbar_Naf
ifsec "axon_iseg[1]" if( vdef("aXi1_Gbar_Naf")) gbar_Naf_i1 = aXi1_Gbar_Naf
}
ifsec "axon_inode" if( vdef("aXr_Gbar_Naf")) gbar_Naf_i0 =aXr_Gbar_Naf
}
}
//--------------------------------------------------------------------------------
proc do_KDR(){ local i
if( vdef( "Gbar_KDR" )){
if( !ismembrane("KDR_i1") ) insert KDR_i1
ki0_k_ion=140
ko0_k_ion=2.5
ki=ki0_k_ion
ko=ko0_k_ion
ek=nernst(ki0_k_ion, ko0_k_ion, 1)
gbar_KDR_i1 = Gbar_KDR
if(vdef("Gbar_KDR_dslope") && !issection("axon.*")) gbar_KDR_i1 = Gbar_KDR *(1+Gbar_KDR_dslope*ydistP())
ifsec "soma" if(vdef("s0_Gbar_KDR")) gbar_KDR_i1 = s0_Gbar_KDR
ifsec "axon_hill" if(vdef("s0_Gbar_KDR")) gbar_KDR_i1 = s0_Gbar_KDR
ifsec "axon_hill" if(vdef("aXh_Gbar_KDR")) gbar_KDR_i1 = aXh_Gbar_KDR
ifsec "axon" if( vdef("aX_Gbar_KDR")) gbar_KDR_i1 = aX_Gbar_KDR
ifsec "axon_iseg" {
if( vdef( "aXi_Gbar_KDR" )) gbar_KDR_i1 = aXi_Gbar_KDR
ifsec "axon_iseg[0]" if( vdef( "aXi0_Gbar_KDR" )) gbar_KDR_i1 = aXi0_Gbar_KDR
ifsec "axon_iseg[1]" if( vdef( "aXi1_Gbar_KDR" )) gbar_KDR_i1 = aXi1_Gbar_KDR
}
ifsec "axon_node" if( vdef( "aXr_Gbar_KDR" )) gbar_KDR_i1 = aXr_Gbar_KDR
ifsec "axon_myelin" if( vdef( "aXm_Gbar_KDR" )) gbar_KDR_i1 = aXm_Gbar_KDR
}
}
//--------------------------------------------------------------------------------
proc do_KA(){ local i
if( vdef( "Gbar_KA" )){
if( !ismembrane("KA_i1") ) insert KA_i1
ki0_k_ion = 140
ko0_k_ion = 2.5
ki=ki0_k_ion
ko=ko0_k_ion
ek = nernst(ki0_k_ion, ko0_k_ion, 1)
gbar_KA_i1 = Gbar_KA
if(vdef("Gbar_KA_dslope") && !issection("axon.*")) gbar_KA_i1 = Gbar_KA *(1+Gbar_KA_dslope*ydistP() )
ifsec "axon_hill" if(vdef("aXh_Gbar_KA")) gbar_KA_i1 = aXh_Gbar_KA
ifsec "axon_myelin" if(vdef("aXm_Gbar_KA")) gbar_KA_i1 = aXm_Gbar_KA
if( issection("axon_myelin.*") || issection("axon_hill.*" ) ) return
ifsec "axon" if( vdef("aX_Gbar_KA")) gbar_KA_i1 = aX_Gbar_KA
ifsec "axon_iseg" {
if( vdef( "aXi_Gbar_KA" )) gbar_KA_i1 = aXi_Gbar_KA
ifsec "axon_iseg[0]" if( vdef( "aXi0_Gbar_KA" )) gbar_KA_i1 = aXi0_Gbar_KA
ifsec "axon_iseg[1]" if( vdef( "aXi1_Gbar_KA" )) gbar_KA_i1 = aXi1_Gbar_KA
}
ifsec "axon_inode" if( vdef( "aXr_Gbar_KA" )) gbar_KA_i1 = aXr_Gbar_KA
ifsec "axon_mnode" if( vdef( "aXm_Gbar_KA" )) gbar_KA_i1 = aXm_Gbar_KA
}
}
//--------------------------------------------------------------------------------
proc do_h(){ local i
if( vdef( "Gbar_h" )){
if( !ismembrane("h_i0") ) insert h_i0
eh_i0 = G_eh
gbar_h_i0 = Gbar_h
if(vdef("Gbar_h_dslope") && !issection("axon.*")) gbar_h_i0 = Gbar_h *(1+Gbar_h_dslope*ydistP() )
//ifsec "axon_hill" if(vdef("aXh_Gbar_h")) gbar_h_i0 = aXh_Gbar_h
//ifsec "axon_myelin" if(vdef("aXm_Gbar_h")) gbar_h_i0 = aXm_Gbar_h
//if( issection("axon_myelin.*") || issection("axon_hill.*" ) ) return
//ifsec "axon" if( vdef("aX_Gbar_h")) gbar_h_i0 = aX_Gbar_h
//ifsec "axon_iseg" {
// if( vdef( "aXi_Gbar_h" )) gbar_h_i0 = aXi_Gbar_h
// ifsec "axon_iseg[0]" if( vdef( "aXi0_Gbar_h" )) gbar_h_i0 = aXi0_Gbar_h
// ifsec "axon_iseg[1]" if( vdef( "aXi0_Gbar_h" )) gbar_h_i0 = aXi1_Gbar_h
//}
//ifsec "axon_node" if( vdef( "aXr_Gbar_h" )) gbar_h_i0 = aXr_Gbar_h
//ifsec "axon_myelin" if( vdef( "aXm_Gbar_h" )) gbar_h_i0 = aXm_Gbar_h
}
}
//----------------------------------------------------------------------
objref iss
init_first = 1
iss_unstable = 0 // set 0 to find out; once set avoid running again
proc init() { local v0, v1
if( init_first ){
init_first = 0
// calculate G_e_pas_slope to adjust e_pas for each trace's baseline
//G_e_pas_slope = 0
//G_e_pas += 1
mulfit_cell_init()
iss.init_steady_state // init_steady_state()
if( check_iss_unstable()) return
v1 = v
//G_e_pas -= 1
mulfit_cell_init()
iss.init_steady_state // init_steady_state()
if( check_iss_unstable()) return
v0 = v
//G_e_pas_slope = 1/(v1-v0)
//printf( "init: G_e_pas_slope %g\n", G_e_pas_slope )
}
mulfit_cell_init()
init_last_call() // hook to insert changes just before run() call
iss.init_steady_state() // init_steady_state()
if( check_iss_unstable()) return
}
// Hook to insert changes just before run() call (can be redefined later)
proc init_last_call(){
}
//----------------------------------------------------------------------
func check_iss_unstable(){
if( iss.dV > iss_unstable_th ){
iss_unstable = 1
printf( ">>>init: UNSTABLE Steady State iss.dV=%g iss_unstable_th=%g; setting tstop=20<<<\n", \
iss.dV, iss_unstable_th )
tstop = 20
return 1
}
return 0
}
//----------------------------------------------------------------------
objref stim
proc do_cell(){
forall delete_section()
chdir("/home/ximi/Projects/ParSims")
load_file( 1, $s1 ) // load cell
if( numarg()>1 ) load_file( 1, $s2 ) // load axon
soma {
stim = new IClamp(0.5)
}
// chdir("/Volumes/d1/Users/ximing/Projects/ParSims/pDE")
}
//================================================================================
// pDE interface related code
begintemplate pDE_fit_case
strdef id, Mtemplate, Mfunc, scaleF, hoc_var, hoc_before, hoc_after, tgt_file, tgt_before, tgt_after
public id, Mtemplate, Mfunc, scaleF, hoc_var, hoc_before, hoc_after, tgt_file, tgt_before, tgt_after
public scaleF, tgt_bldiff
proc init(){
id = $s1
Mtemplate = $s2
Mfunc = $s3
scaleF = $s4
hoc_var = $s5
hoc_before = $s6
hoc_after = $s7
tgt_file = $s8
tgt_before = $s9
tgt_after = $s10
tgt_bldiff = 0 // baseline differential from avg of tgt set
}
endtemplate pDE_fit_case
proc dfc_do_cmd(){ localobj so, sf
sf = new StringFunctions()
so = new str_obj()
sprint( so.s1, "%s;", $s1 )
while( strcmp( so.s1, "")){
sf.head( so.s1, ";", so.s2 )
if( strcmp( so.s2, "" )) {
if( dfc_idebug ) printf( "\ndfc_do_cmd: %s\n", so.s2 )
if( numarg() == 1 ) execute( so.s2 )
if( numarg() == 2 ) execute( so.s2, $o2 )
if( numarg() == 3 ) $o3.append( new str_obj( so.s2 ))
}
sf.tail( so.s1, ";", so.s1 )
}
}
//----------------------------------------------------------------------------------------------------
objref pDE_fc_list
objref dfc_tgt, dfc_tgtL
{ blmin=1 blMax=19 } // baseline limits (ms)
func dfc_load_dfc_tgt(){ local i localobj fc_i, sf, str, pDE_fc_i
pDE_fc_i=$o1
sf=new StringFunctions() str=new str_obj()
dfc_tgt = new eTrace()
dfc_tgt.idebug = dfc_idebug
dfc_do_cmd( pDE_fc_i.tgt_before )
if( sf.head( pDE_fc_i.tgt_file, ".txt$", str.s1 ) >= 0 ) dfc_tgt.load_file_home( pDE_fc_i.tgt_file )
if( sf.head( pDE_fc_i.tgt_file, ".htf$", str.s1 ) >= 0 ) dfc_tgt.load_htf_1p0c( pDE_fc_i.tgt_file, "HOME" )
dfc_do_cmd( pDE_fc_i.tgt_after )
return dfc_tgt.vec_v.mean( round(blmin/dfc_tgt.dt_sample), round(blMax/dfc_tgt.dt_sample)) // return mean from blmin to blMax
}
func round(){ return int( 0.5 + $1 ) }
proc dfc_load_traces(){ local i, j, tmp, bl_avg, bl_i localobj pDE_fc_i, blV
dfc_tgtL = new List()
blV = new Vector()
bl_avg = 0
for i=0, pDE_fc_list.count-1 {
bl_i = dfc_load_dfc_tgt( pDE_fc_list.o(i) )
dfc_tgtL.append( dfc_tgt )
blV.append( bl_i )
bl_avg += (bl_i - bl_avg)/(i+1) // clever way to compute running avg
}
printf( "dfc_load_traces: found bl_avg %g.\n", bl_avg )
if( vdef( "BL_avg" )) {
printf( "dfc_load_traces: Using preset BL_avg %g\n", BL_avg )
bl_avg = BL_avg // Use BL_avg if defined in pDE script
}
for i=0, pDE_fc_list.count-1 {
pDE_fc_list.o(i).tgt_bldiff = bl_avg - blV.x[i]
printf( "dfc_load_traces i %d bli %g bl_avg %g tgt_bldiff %g\n", i, blV.x[i], bl_avg, pDE_fc_list.o(i).tgt_bldiff )
}
}
//----------------------------------------------------------------------------------------------------
strdef cell_file_name, axon_file_name // so they can be defined in pDE VERBATIM
proc pDE_init_cell(){
// Not needed here. Out so that dfc_run_agai works pDE_asg() // so that do_cell can use name_declared() calls
// do_cell( "n420t-pc2-L10000-ignoreD-newsoma.hoc", "naceaxon-m-0-long.hoc" )
// do_cell( "n420t-pc2-L10000-ignoreD-newsoma.hoc", "Meeks-axon-0.hoc" )
// do_cell( "n420t-pc2-L10000-ignoreD-newsoma.hoc", "ca1b-rot-axon-750-aE-v2.hoc" )
// do_cell( "n420t-pc2-L10000-ignoreD-newsoma.hoc", "my-ca1-isegs-myelin.hoc" )
// do_cell( "n420t-pc2-L10000-DL.hoc", "my-ca1-isegs-myelin.hoc" )
if( strcmp(cell_file_name,"")==0 ) cell_file_name = "n420t-pc2-L10000-ignoreD-newsoma.hoc"
//if( strcmp(axon_file_name,"")==0 ) axon_file_name = "my-ca1-isegs-myelin.hoc"
do_cell( cell_file_name)
if( vdef( "soma_diam_f")) forsec "soma" { diam *= soma_diam_f printf( "soma diam %s %g\n", secname(), diam ) }
{ cvode.active(1) cvode.atol(1.e-10) }
iss = new initss( cvode, -80 ) // iss_v_init = -80
iss.idebug = 0.5
iss_unstable_th = 0.1
iss_unstable_penalty = 1e20
execute( "access soma" ) // avoid sintax error if soma is not created at compile time
}
//----------------------------------------------------------------------------------------------------
obfunc set_sim_stim(){ local i localobj eT, sT
{ eT = $o1 sT=$o2 }
{ eT.stim_amp=sT.amp eT.stim_del=sT.del eT.stim_dur=sT.dur }
return eT
}
//----------------------------------------------------------------------------------------------------
objref dfc_i, dfc_tgt_i, dfc_sim, dfc_sim_rec, dfc_simL, dfc_eD
objref dfc_recL, dfc_simL_i, dfc_sim_recL
dfc_first = 1
func pDE_do_fit_case(){ local i, icase, irec localobj str, sL
icase = $1
if( dfc_first ) {
dfc_first = 0
dfc_simL = new List()
pDE_asg() // so that init_cell and load_traces can use vdef() calls
dfc_load_traces()
pDE_init_cell()
}
dfc_i = pDE_fc_list.o( icase )
dfc_tgt_i = dfc_tgtL.o( icase )
str = new str_obj()
execute( str.sPrint( "dfc_eD = new %s()", dfc_i.Mtemplate ).s1 )
dfc_eD.idebug = dfc_idebug
tstop = dfc_tgt_i.vec_t.x[ dfc_tgt_i.vec_t.size-1 ] + dfc_tgt_i.dt_sample
dfc_recL = new List()
sL = str.split( dfc_i.hoc_var, ";" ) // split to get list of recording section locations
for i=0, sL.count-1 execute( str.sPrint( "%s dfc_recL.append( new SectionRef())", sL.o(i).s1 ).s1 )
dfc_do_cmd( dfc_i.hoc_before ) // hoc_before here; so stim parms can be set in hoc_before code
dfc_sim_recL = new List()
for irec=0, dfc_recL.count-1 {
dfc_sim_recL.append( new eTrace() )
set_sim_stim( dfc_sim_recL.o(irec), stim )
// dfc_sim_recL.o(irec).stim_amp = stim.amp
// dfc_sim_recL.o(irec).stim_dur = stim.dur
// dfc_sim_recL.o(irec).stim_del = stim.del
dfc_sim_recL.o(irec).idebug = dfc_idebug
dfc_sim_recL.o(irec).dt_sample = -1 // -1 => non-uniform for cvode
dfc_sim_recL.o(irec).name = sL.o(irec).s1 // place recording section in name
dfc_recL.o(irec).sec cvode.record( &v(0.5), dfc_sim_recL.o(irec).vec_v, dfc_sim_recL.o(irec).vec_t )
}
access dfc_recL.o(0).sec
if( ! iss_unstable ){ // run only if previous case was stable (ie not unstable); see init()
printf( "\n\t" )
system( "date" )
printf( "case %s\n", dfc_i.id )
tgt_bldiff = dfc_i.tgt_bldiff
pDE_asg()
run()
dfc_simL_i = new List()
for irec=0, dfc_recL.count-1 dfc_simL_i.append( dfc_sim_recL.o(irec).copy() )
dfc_simL.append( dfc_simL_i )
}
if( iss_unstable ){
dfc_err = iss.dV / iss_unstable_th * iss_unstable_penalty
}else{
dfc_do_cmd( dfc_i.hoc_after ) // hoc_after
dfc_err = 0
// dfc_err = dfc_eD.listM( dfc_i.Mfunc, dfc_sim, dfc_tgtLi )
dfc_eD.ilog = 1
printf( "id %s ", dfc_i.id )
// sprint( str.s1, "dfc_err = dfc_eD.%s( dfc_sim, dfc_tgt_i )", dfc_i.Mfunc )
// sprint( str.s1, "dfc_err = dfc_eD.%s( dfc_simL_i.o(0), dfc_tgt_i )", dfc_i.Mfunc )
// execute( str.s1 )
execute( str.sPrint( "dfc_err=%s", dfc_i.Mfunc).s1 )
}
execute( str.sPrint( "dfc_scaleF = %s", dfc_i.scaleF ).s1 )
printf( " dfc_scaleF %g pDE_do_fit_case %g\n", dfc_scaleF, dfc_err*dfc_scaleF )
return dfc_err * dfc_scaleF
}
//----------------------------------------------------------------------------------------------------
begintemplate recSpec
objref sr, eT
strdef name
public name, sr, vr, eT, dist, tzc
proc init(){
sr = new SectionRef()
name = secname()
vr = $1
dist = distance( vr )
eT = new eTrace()
}
public set_eT
obfunc set_eT(){
eT = $o1.copy()
eT.resample_dt(0.01)
eT.vec_dv.deriv( eT.vec_v, eT.dt_sample, 2 )
eT.vec_ddv = new Vector()
eT.vec_ddv.deriv( eT.vec_dv, eT.dt_sample, 2 )
tzc = eT.vec_t.x( eT.vec_v.indwhere(">=",0) )
return eT
}
public sort_dist
obfunc sort_dist(){ local i localobj iO, iOs, rL, rLs
rL = $o1
iO = new Vector()
for i=0, rL.count-1 iO.append( rL.o(i).dist )
iOs = iO.sortindex()
rLs = new List()
for i=0, rL.count-1 rLs.append( rL.o(iOs.x[i]) )
return rLs
}
endtemplate recSpec
//----------------------------------------------------------------------------------------------------
// Run again case icase and return eTrace results
obfunc dfc_run_againL(){ local i, icase localobj eT, eT1, dfc_i, dfc_tgt_i, rL, eTL
icase = $1
dfc_i = pDE_fc_list.o( icase )
dfc_tgt_i = dfc_tgtL.o( icase )
pDE_init_cell()
dfc_do_cmd( dfc_i.hoc_before )
tstop = dfc_tgt_i.vec_t.x[ dfc_tgt_i.vec_t.size-1 ] + dfc_tgt_i.dt_sample
tgt_bldiff = dfc_i.tgt_bldiff
rL = new List()
access soma
distance()
rL.append( new recSpec( x ))
forsec "axon" for (x) if(x>0&&x<1) rL.append( new recSpec( x ))
eTL = new List()
for i=0, rL.count-1 {
eTL.append( new eTrace() )
set_sim_stim( eTL.o(i), stim )
rL.o(i).sr.sec cvode.record( &v( rL.o(i).vr ), eTL.o(i).vec_v, eTL.o(i).vec_t )
}
run()
for i=0, rL.count-1 rL.o(i).set_eT( eTL.o(i) )
return rL
}
// Return (and plot if pG present) rL for each parm value variation runs vp+ivp*k1 to vp+ivp*k2 in ivp steps
// ( icase, "var", vp, ivp, k1, k2 [, pG [,opt]] )
obfunc dfc_var_runsL(){ local i, imin, tmin, icase, vp, ivp, nv, k, k1, k2, opt localobj eT, eT1, eTL, str, pG, rL, rLL
icase = $1
str = new str_obj( $s2 )
{ vp=$3 ivp=$4 k1=$5 k2=$6 }
rLL = new List()
for k=k1, k2 {
nv = vp + ivp * k
sprint( str.s2, "%s=%g", str.s1, nv )
execute( str.s2 )
rL = dfc_run_againL(icase)
rL.o(0).eT.name = str.s2
rLL.append( rL )
}
if( numarg()>6 ){
eT = plot_rLL_dt( rLL )
$o7 = eT.plotG
{ eT.plotG.view(0,0,10,10, 100+20+300*1.8, 100, 300*2.5, 200*3 ) eT.plotG.exec_menu( "View = plot" ) }
{ opt = 101 if( numarg()>8 ) opt = $9 }
pG = new Graph(0)
for k=0, rLL.count-1 pG = rLL.o(k).o(0).eT.iso_spike(dfc_seg_look_options(),1,-0.5,0).plot_ddv( pG, opt, k+1 )
{ pG.view(0,0,10,10, 100, 100, 300*1.8, 200*3 ) pG.exec_menu( "View = plot" ) }
$o8 = pG
}
return rLL
}
obfunc plot_rLL_dt(){ local k, i, imin, tmin localobj eT, eT1, rLL, rL
rLL = $o1
eT = new eTrace()
eT.plotG = new Graph(0)
for k=0, rLL.count-1 {
rL = rLL.o(k)
tmin = 1e70
for i=0, rL.count-1 {
eT.plotG.mark( rL.o(i).dist, rL.o(i).tzc, "s", 5, axon_color( rL.o(i).name), 1 )
if( rL.o(i).tzc<tmin ){ imin=i tmin=rL.o(i).tzc }
}
for i=0, rL.count-1 if( rL.o(i).tzc==tmin ) eT.plotG.mark( rL.o(i).dist, rL.o(i).tzc, "S", 6, axon_color( rL.o(i).name), 1 )
// if(k==0){ eT.plotG=new Graph() eT.plotG.align( 1, 1 ) eT.plotG.label( 1-1/22, 1-1/22 ) }
eT1 = rL_td_eT( rL )
sprint( eT1.name, "%s t=%4.2f vel=%4.2f", rL.o(0).eT.name, tmin, axon_speed(rL) )
eT.addplot_c( eT1, k%7+1 )
}
return eT
}
obfunc run_plot_all_axon_ddv(){ local i, icase, tspk, tL, tR localobj pG, rL, sf, eT
icase = $1
tL=-0.5 if( numarg()>1 )tL=$2
tR=0 if( numarg()>2 )tR=$3
sf = new StringFunctions()
rL = dfc_run_againL( icase ) // rL.o(0) is soma
pG = new Graph()
rL.o(0).eT.copy().iso_spike(dfc_seg_look_options(),1,-0.5,0, &tspk )
printf( "tspk %g\n", tspk )
for i=0, rL.count-1 {
if( sf.substr(rL.o(i).name, "node")>=0 || sf.substr(rL.o(i).name, "myelin")>=0 ) continue
pG.color( axon_color(rL.o(i).name ))
eT = rL.o(i).eT.copy().cut_at2( tspk+tR, tspk+tL )
eT.vec_t.add( tL )
// pG = rL.o(i).eT.copy().cut_at2(tspk+0.1,tspk-0.5).plot_ddv( pG, 001, axon_color(rL.o(i).name) )
eT.vec_ddv.line( pG , eT.vec_t )
}
pG.exec_menu( "View = plot" )
return pG
}
// calculate speed between nodes with min and max tzc
func axon_speed(){ local i, im, iM, vel localobj rL, sf
rL = $o1
sf = new StringFunctions()
im=iM=-1
for i=0, rL.count-1 if( sf.substr( rL.o(i).name, "node")>=0 ){
if( im<0 ) im=iM=i // set to first "node" match
if( rL.o(i).tzc < rL.o(im).tzc ) im=i
if( rL.o(i).tzc > rL.o(iM).tzc ) iM=i
}
vel = ( rL.o(iM).dist - rL.o(im).dist ) / ( rL.o(iM).tzc - rL.o(im).tzc ) * 1e-3 // um/ms * 1e-3 = m/s
printf( "axon_speed: i,tzc min %g %g Max %g %g vel %g\n", im, rL.o(im).tzc, iM, rL.o(iM).tzc, vel )
return vel
}
func axon_color(){ local i, col localobj str, sf
str = new str_obj( $s1 )
sf = new StringFunctions()
col = 1
if( sf.head( str.s1, "hill", str.s2 )> 0 ) col = 2
if( sf.head( str.s1, "iseg", str.s2 )> 0 ) col = 3
if( sf.head( str.s1, "prox", str.s2 )> 0 ) col = 4
if( sf.head( str.s1, "myelin", str.s2 )> 0 ) col = 5
if( sf.head( str.s1, "node", str.s2 )> 0 ) col = 6
return col
}
//----------------------------------------------------------------------------------------------------
// Run again case icase and return eTrace results
obfunc dfc_run_again(){ local icase localobj eT, eT1, dfc_i, dfc_tgt_i
icase = $1
dfc_i = pDE_fc_list.o( icase )
dfc_tgt_i = dfc_tgtL.o( icase )
pDE_init_cell()
dfc_do_cmd( dfc_i.hoc_before )
tstop = dfc_tgt_i.vec_t.x[ dfc_tgt_i.vec_t.size-1 ] + dfc_tgt_i.dt_sample
tgt_bldiff = dfc_i.tgt_bldiff
eT = new eTrace()
set_sim_stim( eT, stim )
soma cvode.record( &v(0.5), eT.vec_v, eT.vec_t )
run()
eT1 = eT.copy()
eT1.resample_dt(0.01)
eT1.vec_dv.deriv( eT1.vec_v, eT1.dt_sample, 2 )
eT1.vec_ddv = new Vector()
eT1.vec_ddv.deriv( eT1.vec_dv, eT1.dt_sample, 2 )
return eT1
}
//----------------------------------------------------------------------------------------------------
// Return (and plot if pG present) list of parm value variation runs vp+ivp*k1 to vp+ivp*k2 in ivp steps
obfunc dfc_var_runs(){ local icase, vp, ivp, nv, k, k1, k2, opt localobj eT, eTL, str, pG
icase = $1
str = new str_obj( $s2 )
{ vp=$3 ivp=$4 k1=$5 k2=$6 }
eTL = new List()
for k=k1, k2 {
nv = vp + ivp * k
sprint( str.s2, "%s = %g", str.s1, nv )
execute( str.s2 )
eT = dfc_run_again(icase)
eT.name = str.s2
eTL.append( eT )
}
if( numarg()>6 ){
{ opt = 101 if( numarg()>7 ) opt = $8 }
for k=0, eTL.count-1 pG=(eTL.o(k).iso_spike(dfc_seg_look_options(),1,1).plot_ddv( pG, opt, k+1 ))
// Note parens. below does not work
//for k=0, eTL.count-1 pG=eT.plot_ddv( pG, eTL.o(k).iso_spike(dfc_eD_options(),1,1), opt, k+1 )
$o7 = pG
}
return eTL
}
//----------------------------------------------------------------------------------------------------
proc dfc_plot_1(){ local i, n
$o1.plot_color = $3
$o1.plot_brush = $4
$o1.addplot( $o2 )
}
proc dfc_plot_place(){ local n
n = $2
$o1.plotG.unmap()
$o1.plotG.view(0,0,10,10, (n%5)*(300+20), 100+int(n/5)*(200+65), 300, 200 )
$o1.recenter()
}
func is_obj_name(){ local i localobj sf, str
str = new str_obj($s2) sf = new StringFunctions()
sprint( str.s2, "%s", $o1 )
if( sf.tail( str.s2, str.s1, str.s3 ) == sf.len(str.s1) ) return 1
return 0
}
objref igL
strdef pDE_log_name
obfunc plot_gen(){
igL = new pDE_log()
igL.read_n_plot( pDE_log_name, pDE_gen_N )
return igL
}
objref pG_axon, pG_sec
obfunc plot_axon(){ local i, in localobj str
pG_axon = new Graph()
pG_sec = new List()
str = new str_obj()
pG_sec.append( new str_obj( "axon_hill" ))
in = 19
if( vdef( "aX_iseg_n" )) in = aX_iseg_n
for i=0,in-1 pG_sec.append( str.copy().sPrint( "axon_iseg[%d]", i ) )
pG_sec.append( new str_obj( "axon_prox" ))
if( aX_node_n > 0 ){
pG_sec.append( new str_obj( "axon_node[0]" ))
pG_sec.append( new str_obj( "axon_myelin[0]" ))
}
pG_sec.append( new str_obj( "soma" )) // put last so that soma is accessed at the end below
for i=0, pG_sec.count-1 {
execute( pG_sec.o(0).sPrint( "access %s", pG_sec.o(i).s1 ).s1 )
pG_axon.mark( distance(0.5), gbar_Naf_i1, "+", 12, 2, 1 )
pG_axon.mark( distance(0.5), gbar_KDR_i1, "o", 12, 3, 1 )
}
pG_axon.exec_menu( "View = plot" )
return pG_axon
}
objref dfc_ddVpG
obfunc dfc_pG_ddV(){ local i, iopt localobj pG
pG = $o1
iopt = $2
if( iopt==0 ) for i=0,dfc_tgtL.count-1 { dfc_pG_one_ddV(pG,i,001,0,1) dfc_pG_one_ddV(pG,i,001,1,2) }
if( iopt==1 ) for i=0,dfc_tgtL.count-1 { dfc_pG_one_ddV(pG,i,001,0,i+1,1) dfc_pG_one_ddV(pG,i,001,1,i+1,2) }
if( iopt==2 ) for i=0,dfc_tgtL.count-1 { dfc_pG_one_ddV(pG,i,010,0,1) dfc_pG_one_ddV(pG,i,010,1,2) }
if( iopt==3 ) for i=0,dfc_tgtL.count-1 { dfc_pG_one_ddV(pG,i,010,0,i+1,1) dfc_pG_one_ddV(pG,i,010,1,i+1,2) }
return pG
}
obfunc dfc_pG_one_ddV(){ local icase, iopt, isel, icol, ibrush localobj eT, pG, eTc
if(numarg()>0 ) pG=$o1
if( object_id( pG )==0 ) { pG = new Graph() }
icase=$2 iopt=$3 isel=$4 icol=$5
dfc_i = pDE_fc_list.o( icase )
ibrush=1 if( numarg()>5 ) ibrush=$6
pG.brush( ibrush )
if( isel==0 ) eTc = dfc_tgtL.o(icase)
if( isel==1 ) eTc = dfc_simL.o(icase).o(0)
if( eTc.stim_amp<0.2 || eTc.stim_amp==0.75 ) return pG
eT = eTc.iso_spike( dfc_seg_look_options(), 1, -0.65, 0.45 )
if( object_id(eT)>0) eT.plot_ddv( pG, iopt, icol )
return pG
}
// per fit-case: dfc_simL has one list entry (with eTraces); dfc_tgtL has one eTrace
proc dfc_plot_all(){ local i, j localobj eTi
for i=0, dfc_simL.count-1 {
eTi = dfc_tgtL.o(i)
for j=0, dfc_simL.o(i).count-1 dfc_plot_1( eTi, dfc_simL.o(i).o(j), 2+j, 1 )
dfc_plot_1( eTi, eTi, 1, 1 )
// for j=0, dfc_tgtL.o(i).count-1 dfc_plot_1( eTi, dfc_tgtL.o(i).o(j), 1, 1 )
dfc_plot_place( eTi, i )
eTi.plotG.menu_action("plot_gen","plot_gen()" )
eTi.plotG.menu_action("plot_axon","plot_axon()" )
eTi.plotG.menu_action("plot_ddVs_all","dfc_ddVpG=new Graph() dfc_pG_ddV(dfc_ddVpG,0)" )
eTi.plotG.menu_action("plot_ddVs_color","dfc_ddVpG=new Graph() dfc_pG_ddV(dfc_ddVpG,1)" )
eTi.plotG.menu_action("plot_dVs","dfc_ddVpG=new Graph() dfc_pG_ddV(dfc_ddVpG,2)" )
eTi.plotG.menu_action("plot_dVs_color","dfc_ddVpG=new Graph() dfc_pG_ddV(dfc_ddVpG,3)" )
}
}
proc dfc_plot_all_old(){ local i
for i=0, dfc_simL.count-1 dfc_plot_one( dfc_simL.o(i), dfc_tgtL.o(i), i )
}
//================================================================================
obfunc rL_td_eT(){ local i localobj rL, eT, sIc, sI
rL = $o1
eT = new eTrace()
sIc = new Vector()
for i=0, rL.count-1 sIc.append( rL.o(i).dist )
sI = sIc.sortindex()
for i=0, rL.count-1 {
eT.vec_t.append( rL.o(sI.x[i]).dist)
eT.vec_v.append( rL.o(sI.x[i]).tzc )
}
return eT
}
//--------------------------------------------------------------------------------
// Usage above
// objref rLL, pGd, pG
// { pDE_asg() rLL = dfc_var_runsL( 0, "aXh_Gbar_Naf", aXh_Gbar_Naf, aXh_Gbar_Naf*0.1, -2, 2, pGd, pG ) }
// abort()
// end of pDE interface related code
//================================================================================
// ------end hoc_main------
//----- pDE VERBATIM -----
cell_file_name="n400td-pc2-sp-axn.hoc"
obfunc dfc_set_stims_etc(){
print "check pDE dfc_set_stims++++++++++++++++++++"
/*
if(vdef("aX_hill_nseg"))\
execute( "if(axon_hill.nseg<aX_hill_nseg) axon_hill.nseg=aX_hill_nseg" )
if(vdef("aX_iseg_nseg")) \
execute( "for i=0,aX_iseg_n-1 {if(axon_iseg[i].nseg<aX_iseg_nseg) axon_iseg[i].nseg= aX_iseg_nseg }" )
if(vdef("aX_prox_nseg")) \
execute( "for i=0,aX_prox_n-1 {if(axon_prox[i].nseg<aX_prox_nseg) axon_prox[i].nseg= aX_prox_nseg }" )
if( vdef("aX_mnode_nseg" )) \
execute( "forsec \"mnode\" if(nseg<aX_mnode_nseg) nseg= aX_mnode_nseg" )
*/
// execute( "axon_prox.nseg = aX_prox_nseg" )
// execute( "for i=0,aX_iseg_n-1 {axon_iseg[i].nseg= aX_iseg_nseg }" )
stim.amp=$1
stim.dur=$2
stim.del=$3
print "check stim.del +++++++++++++++++++++++++++"
dfc_options_all( dfc_eD )
return stim
}
obfunc dfc_set_tgt(){
print "dfc_set_tgt()+++++++++++++++++++++++++++"
dfc_tgt.stim_amp=$1
dfc_tgt.stim_dur=$2
dfc_tgt.stim_del=$3
if( numarg()>3 ) dfc_tgt.cut_at2($4,$5)
return dfc_tgt
}
proc dfc_sim_BBF(){
dfc_simL_i.o(0).dc_shift(stim.del+BBFdelay,stim.del+stim.dur+BBFdelay,-BBF*stim.amp)
}
//================================================================================
// New stuff for pkbeg posfix
obfunc dfc_seg_look_options(){ local i localobj dI
dI = new eMatch() if( numarg()>0)dI =$o1
dI.seg_option = 1101
dI.seg_dt = 0.09
dI.seg_slp_dt = 0.09
dI.seg_slp_th = 10
dI.seg_v_th = 0
dI.seg_tiny_last = 0
if( strcmp(dfc_i.id,"072006b-2ms+1500pA-pkbeg") == 0 ){ dI.seg_dt=dI.seg_slp_dt= 0.02 }
return dI
}
obfunc dfc_options_all(){ local i localobj eD
if( numarg()==0 ) eD = dfc_seg_look_options()
if( numarg()> 0 ) eD = dfc_seg_look_options($o1)
eD.match_option = 5.2
eD.alpha = eD.beta = eD.gamma = eD.delta = eD.eta = eD.mF1 = eD.mF2 = eD.pkP = eD.pkPs = 0
eD.ilog = 1
return eD
}
// rough match to train;
// necessary to avoid traces that don't return to baseline
// also check spikes also appear in axon
func dfc_trim(){ local i, t0_tail, f1, f2, r1, r2, res localobj eD
f1=$1 f2=$2
eD = dfc_options_all(dfc_eD)
eD.eta = 1
eD.mF2 = 200
eD.pkP = 1500*5
eD.pkPs = 1
eD.pkPsA = 1
t0_tail = stim.del + stim.dur // end of stimulus
eD.tmin = t0_tail // compare tails after end stimulus: axon vs tgt
r2 = eD.m0( dfc_simL_i.o(1), dfc_tgt_i )
eD.tmin = 0
printf( "\n\t >>dfc_trim: DfpwPkdVa_aXe: " )
r1 = eD.DfpwPkdVa_aXe(dfc_simL_i,dfc_tgt_i,-1,-1) // 800=8.90, 400=15.2, 200=30.82, 1500=6.7
res = r1*f1 + r2*f2
printf( "\n\t dfc_trim t0_tail %g r1,2 %g %g f1,f2 %g %g ri*fi %g %g\n\t res %g<<\n",\
t0_tail, r1,r2, f1,f2, r1*f1, r2*f2, res )
return res
}
//================================================================================
// match first spike (up to tmax)
// gamma and delta to match dV and ddV; largely independent of trace length/stim.amp
// eta scaled by trace length
//================================================================================
func dfc_pkbeg(){ local i, tmax, dV_f, eta_f, r1 localobj eD
tmax = $1
dV_f = 45*2
eta_f = 300 + 100/(tmax-stim.del-1.1) // A + B/(time from stim.del to base of spike) A=for spike; B for before spike
eD = dfc_eD // eD = dfc_options_all(dfc_eD)
// eD.mF2 = 200*10
eD.mF2 = 6000 * stim.amp // peak time error proportional to stimulation amplitude
eD.pkP = 1500*5
eD.pkPs = 1
eD.phi = 600/116/10 // range_dV/range_V old=0.4 * 10
eD.phi_1 = 0.5+0.15
eD.phi_2 = 0.45-0.02
eD.chi = 1000/116/100 // range_ddV/range_V old=0.02 * 8
eD.chi_1 = 0.5+0.15
eD.chi_2 = 0.15
if( numarg()>1) eD.chi_2=$2 // adhoc inserted to override
eD.phi*=dV_f eD.chi*=dV_f
eD.eta = eta_f
// eD.mF2=0 eD.pkP=1000*eta_f // for initial pop for Naf & KDR parms
eD.tmax = tmax
printf( "\n\t >>dfc_pkbeg: DfpwPkdVa: " )
r1 = eD.DfpwPkdVa(dfc_simL_i.o(0),dfc_tgt_i) // 800=8.90, 400=15.2, 200=30.82, 1500=6.7
printf( "\n\t dfc_pkbeg: r1 %g \n\t<<\n", r1 )
return r1
}
//----- ENDVERBATIM-----
strdef pDE_log_name
proc pDE_asg(){
// hoc pDE gen variables
pDE_log_name = "/home/ximi/Projects/ParSims/reduced-passive.pDE_28Jan15-09-41-37.log"
pDE_gen_N = 0
pDE_Pop_ibest = 0
// hoc set variables
dfc_PassWgt = 1
RmCm_spine_gbar = 0
Spine_number = 30000
BL_avg = -74.3052
BBF = 1.6
BBFdelay = 0
lambda_f_d = 0.1
G_eh = -30
celsius = 35
aX_iseg_n = 2
s0_Gbar_Naf = 500
aXh_Gbar_Naf = 500
aXi0_Gbar_Naf = 2500
aXi1_Gbar_Naf = 3500
aXr_Gbar_Naf = 3000
aXm_Gbar_Naf = 50
gates_n_Naf_i0 = 1
vhalf_n_Naf_i0 = -30
slope_n_Naf_i0 = -4.8
tauA_n_Naf_i0 = 0.01
tauG_n_Naf_i0 = 0.8
vhalf_h_Naf_i0 = -64
slope_h_Naf_i0 = 9.06
tauA_h_Naf_i0 = 8
tauG_h_Naf_i0 = 0.5
gates_n_Naf_i1 = 1
vhalf_n_Naf_i1 = -35
slope_n_Naf_i1 = -5
tauA_n_Naf_i1 = 0.01
tauG_n_Naf_i1 = 0.5