: $Id: intf6.mod,v 1.100 2012/04/05 22:38:25 samn Exp $
:* main COMMENT
COMMENT
intf6.mod was branched from intf.mod version 847 on 10jul13 -- look at intf.mod RCS
log/diffs to see anything prior. note that AM2,NM2,GA2 code was mostly taken from
intf.mod version 815.
artificial cell incorporating 4 input weights with different time constants and signs
typically a fast AMPA, slow NMDA, and fast GABAA
features:
1. Mg dependence for NMDA activation
2. depolarization blockade
3. AHP affects both Vm and refractory period (adaptation)
4. decrementing excitatory and/or inhibitory activity post spk (another adaptation)
since artificial cells only do calculations when they receive events, a set of vec
pointers are maintained to allow state var information storage when event arrives
(see initrec() and record())
ENDCOMMENT
:* main VERBATIM block
VERBATIM
#include "misc.h"
#include <unistd.h>
#ifdef NRN_MECHANISM_DATA_IS_SOA
#define get_dparam(prop) _nrn_mechanism_access_dparam(prop)
#define get_type(prop) _nrn_mechanism_get_type(prop)
#define id0ptr(prop) static_cast<id0*>(_nrn_mechanism_access_dparam(prop)[2].get<void*>())
#else
#define get_dparam(prop) prop->dparam
#define get_type(prop) prop->_type
#define id0ptr(prop) (*((id0**)&(prop->dparam[2])))
#endif
static int ctt(unsigned int, char**);
static void setdvi2(double*,double*,char*,int,int,double*,double*);
static void setdvi3(double*,double*,char*,int,double*,double*);
void gsort3 (double *, Point_process **, char*, int, double *, Point_process **,char*);
void gsort2 (double *, Point_process **, int, double *, Point_process **);
void gsort5 (double *, Point_process **, char*, double*, double*, int,
double *, Point_process **, char*,double*, double*);
// Definitions for synaptic scaling procs
void raise_activity_sensor(double time);
void decay_activity_sensor(double time);
void update_scale_factor(double time);
void dynamicdelete(double time);
double get_avg_activity();
#define PI 3.14159265358979323846264338327950288419716939937510
#define nil 0
#define CTYPp 100 // CTYPp>CTYPi from labels.hoc
#define SOP (((id0*) _p_sop)->vp)
#define IDP (*((id0**) &(_p_sop)))
#define NSW 100 // just store voltages
#define NSV 12//10 state variables (+1 for time,+1 for extra field at end and extra offset in loops in record)
#define FOFFSET 100 // flag offset for net_receive()
#define WRNUM 5 // a single INTF6 can store into this many ww field vecs
#define DELM(X,Y) (*(pg->delm+(X)*CTYPi+(Y)))
#define DELD(X,Y) (*(pg->deld+(X)*CTYPi+(Y)))
#define DVG(X,Y) ((int)*(pg->dvg+(X)*CTYPi+(Y)))
// #define DVG(X,Y,Z) ((int)*(pg->dvg+(X)*CTYPi+(Y)))
#define WMAT(X,Y,Z) (*(pg->wmat+(X)*CTYPi*STYPi+(Y)*STYPi+(Z)))
#define WD0(X,Y,Z) (*(pg->wd0 +(X)*CTYPi*STYPi+(Y)*STYPi+(Z)))
#define NUMC(X) (*(pg->numc+(X)))
#define HVAL(X) (*(hoc_objectdata[(hoc_get_symbol((X)))->u.oboff]._pval))
#define HPTR(X) (hoc_objectdata[(hoc_get_symbol((X)))->u.oboff]._pval)
// for recording (?)
typedef struct VPT {
unsigned int id;
unsigned int size;
unsigned int p;
IvocVect* vv[NSV];
double* vvo[NSV];
} vpt;
// each column can have one of these
typedef struct POSTGRP { // postsynaptic group
double *dvg; double *delm; double *deld; double *ix; double *ixe; double *wmat; double *wd0;
double *numc; // num cells by type
unsigned int col; // COLUMN ID
double* jrid; // for recording SPIKES
double* jrtv;
IvocVect* jridv;
IvocVect* jrtvv;
unsigned int jtpt,jtmax,jrmax;
unsigned long jri,jrj;
unsigned long spktot,eventtot;
double *isp, *vsp, *wsp, *sysp; // arrays for external inputs
int vspn;
double *lastspk; // array with last spike times for all cells
unsigned int cesz; // size of ce
Object *ce; // cell list
struct POSTGRP *next;
} postgrp;
// each cell gets one of these, note that postgrp pointer is an element
typedef struct ID0 {
vpt *vp;
postgrp *pg; // <-- pointer to get to postsynaptic cells, shared by cells in a column
float wscale[WRNUM];
Point_process **dvi; // each cell has a divergence list
Point_process **cvi; // each cell has a convergence list
double *del; // each syn has its own intrinsic delay
char *syns; // each syn has a type
unsigned char *sprob; // each syn has a firing probability 0-255->0-1
double* wgain; // gain for synapses - used for plasticity
double* pplasttau; // plasticity tau for synapse
double* pplastinc; // plasticity inc for synapse (max inc)
double* pplastmaxw; // max weight gain for plasticity
double* pdope; // dopamine eligibility
////////////////////////////////////////////////////////////////////////////////////////////////
// THE PARAMETERS IN THIS 'BLOCK' ARE ASSOCIATED WITH HOMEOSTATIC SYNAPTIC SCAING
double activity; // Slow-varying cell activity value
double max_err; // Maximum saturation value for the activity sensor
double max_scale; // Maximum scaling factor
double lastupdate; // Time of last activity sensor decay / spike update
double goal_activity; // Target firing rate
double activity_integral_err; // Integral record of cell's activity divergence from target activity
double scalefactor; // Derived activity-dependent scaling factor, by which to multiply AMPA weights
////////////////////////////////////////////////////////////////////////////////////////////////
int* peconv; // IDs of E cells converging on this cell
int econvsz; // # of E cells converging on this cell
int* piconv; // IDs of I cells convering on this cell
int iconvsz; // # of I cells converging on this cell
double* syw1; // synaptic weights (parallel to divergence list) -- used for AMPA,GABAA
double* syw2; // synaptic weights -- used for NMDA,GABAB -- these lists only used when wsetting==1
unsigned int dvt;
unsigned int id; // within-COLUMN ID
unsigned int col; // COLUMN
unsigned int rvb;
unsigned int rvi;
unsigned int spkcnt;
unsigned int blkcnt;
unsigned int gid; // global ID
int rve;
char wreci[WRNUM]; // since use -1 as a flag
char errflag;
// type -> vbr MUST REMAIN unbroked BLOCK -- see flag()
// when adding flags also augment iflags, iflnum
// only use first 3 letters with flag() -- see iflags
unsigned char type; // |
unsigned char inhib; // |
unsigned char record;// |
unsigned char wrec; // |
unsigned char jttr; // |
unsigned char input; // |
unsigned char vinflg;// |
unsigned char invl0; // |
unsigned char jcn; // |
unsigned char dead; // |
unsigned char vbr; // |
char dbx; // |
char flag; // |
char out; // |
// end BLOCK
} id0;
// globals -- range vars must be malloc'ed in the CONSTRUCTOR
static double activityoneovertau; // for homeostatic synaptic scaling: Store 1/tau for faster calculations
static vpt *vp; // vp, pg, ip are used as temporary pointers
static id0 *ip, *qp, *rp;
static int inumcols=0;
static int ippgbufsz=0;
static postgrp **ppg=0x0;
static postgrp *pg;
static Object *CTYP;
static Point_process *pmt, *tpnt;
static char *name;
static Symbol* cbsv;
// iflags string use to find flags -- note that only 1st 3 chars are used to identify
static char iflags[100]="typ inh rec wre jtt inp vin inv jcn dea vbr dbx fla out";
static char iflnum=14, iflneg=11, errflag; // turn on after generating an error message
static double *jsp, *invlp;
void freesywv (id0*);
static id0* lop (Object *, unsigned int );
static id0* getlp (Object *, unsigned int);
static id0 *lopr(); // accessed by all INTF6, get pointer from list
static void applyEXSTDP (id0* ppo,double pospkt); // apply standard STDP from E->X cells
static void applyIXSTDP (id0* ppo,double pospkt); // apply STDP from I->X cells
static void applyEDOPE (id0* ppo,double pospkt); // apply DOPAMINE eligibility
static void applyIDOPE (id0* ppo,double pospkt); // apply DOPAMINE eligibility
static double vii[NSV]; // temp storage
static unsigned int wwpt,wwsz,wwaz; // pointer, size for shared ww vectors
static unsigned int sead, spikes[CTYPp], blockcnt[CTYPp]; // 'sead' vs global 'seed'/ used elsewhere
static unsigned int AMo[CTYPp],NMo[CTYPp],GAo[CTYPp]; // count overages for types
static unsigned int AMo2[CTYPp],NMo2[CTYPp],GAo2[CTYPp]; // count overages for types (farther from soma)
static char* CNAME[CTYPp]; // 20 should be > CTYPi
static int cty[CTYPp], process, ctymap[CTYPp];
static int CTYN, CTYPi, STYPi, dscrsz; // from labels.hoc
static double qlimit, *dscr;
FILE *wf1, *wf2, *tf;
IvocVect* ww[NSW];
double* wwo[NSW];
static int AM=0, NM=1, GA=2, GB=3, AM2=4, NM2=5, GA2=6, SU=3, IN=4, DP=2; // from labels.hoc
static double wts[13],hsh[13]; // for jitcons to use as a junk pointer
static void spkoutf2();
ENDVERBATIM
:* NEURON, PARAMETER, ASSIGNED blocks
NEURON {
ARTIFICIAL_CELL INTF6
RANGE VAM, VNM, VGA, AHP :::: cell state variables
RANGE VAM2, VNM2, VGA2 :::: state vars for distal dend inputs
RANGE Vm :::: derived var
: parameters
RANGE tauAM, tauNM, tauGA :::: synaptic params
RANGE tauAM2, tauNM2, tauGA2 :::: synaptic params meant for distal dends
RANGE tauahp, ahpwt :::: intrinsic params
RANGE tauRR , RRWght :::: relative refrac. period tau, wght of Vblock-VTH for refrac
RANGE RMP,VTH,Vblock,VTHC,VTHR :::: Vblock for depol blockade
RANGE incRR : whether allow VTHC to increment past RRWght*(Vblock-VTH) over successive refrac periods
RANGE nbur,tbur,refrac,AHP2REF :::: burst size, interval; refrac period and extender
RANGE invl,oinvl,WINV,invlt :::: interval bursting params
RANGE Vbrefrac
RANGE STDAM, STDNM, STDGA :::: specific amounts of STD for each type of synapse
:::: NB: before using STDAM,STDNM,STDGA need to debug/check
:::: for possible unintended interations with wts,_args
:::: to make sure no interference with the weights in net_receive
::::
RANGE mg0 :::: sensitivity to Mg2+, used in rates
RANGE maxnmc :::: maximum NMDA 'conductance', used in rates
GLOBAL EAM, ENM, EGA,mg :::: "reverse potential" distance from rest
GLOBAL spkht, wwwid,wwht :::: display: spike height, width/ht for pop spikes
GLOBAL stopoq :::: flags: stop if q is empty, use STD
: other stuff
POINTER sop :::: Structure pointer for other range vars
RANGE spck,xloc,yloc,zloc
RANGE t0,tg,twg,refractory,trrs :::: t0,tg save times for analytic calc
RANGE cbur :::: burst statevar
RANGE WEX :::: weight of external input < 0 == inhib, > 0 ==excit
RANGE EXSY :::: synapse target of external input
RANGE lfpscale :::: scales contribution to lfp, only if cell is being recorded in wrecord
GLOBAL vdt,nxt,RES,ESIN,Psk :::: table look up values for exp,sin
GLOBAL prnum, nsw, rebeg :::: for debugging moves
GLOBAL subsvint, jrsvn, jrsvd, jrtime, jrtm :::: output params
GLOBAL DEAD_DIV, seedstep :::: dead cells on div list?
GLOBAL seaddvioff :::: seed offset for dvi/del
GLOBAL WVAR,DELMIN
GLOBAL savclock,slowset,FLAG
GLOBAL tmax,installed,verbose :::: simplest output
GLOBAL pathbeg,pathend,PATHMEASURE,pathidtarg,pathtytarg,seadsetting,pathlen
GLOBAL maxplastt : maximum difference in time between spikes to apply plasticity over
GLOBAL plaststartT : when plasticity is turned on
GLOBAL plastendT : when plasticity is turned off
GLOBAL resetplast : whether to reset all wgain entries to 1 at start of run
GLOBAL wsetting : setting for weights. 0=use WMAT,WD0. 1=use syw1,syw2.
GLOBAL ESTDP : whether to use STDP @ E->X synapses
GLOBAL ISTDP : whether to use STDP @ I->X synapses
GLOBAL SOFTSTDP : whether to use soft bounds for STDP
GLOBAL EPOTW,EDEPW,IPOTW,IDEPW : STDP potentiation vs depression factors for increments
GLOBAL nextGID : don't mess with this unless have a good reason!
GLOBAL EDOPE : whether using dopamine-style learning for E->X weights
GLOBAL IDOPE : whether using dopamine-style learning for I->X weights
GLOBAL DOPE : whether using dopamine-style learning
GLOBAL FORWELIGTR : forward (pre-to-post-synaptic propagation) eligibility traces
GLOBAL BACKELIGTR : backward (post-to-pre-synaptic propagation) eligibility traces
GLOBAL EXPELIGTR : use an exponential decay for the eligibility traces?
GLOBAL maxeligtrdur: maximum eligibilty trace duration (in ms)
GLOBAL reseteligtr : reset eligibility trace after synapse rewarded/punished
: VARIABLES RELATING TO HOMEOSTATIC SYNAPTIC SCALING (IMPLEMENTED BY MARK ROWAN)
GLOBAL scaling : Is compensatory scaling switched on for all cells? Default is off. Globally set.
GLOBAL dynamicdel : Is dynamic scaling factor-proportional deletion switched on? Default is off.
GLOBAL delspeed : Rate constant for spontaneous deletion (Alzheimer's experiments)
GLOBAL scaleinhib : Set to TRUE (1) for I-cell scaling in addition to E-cell scaling. Default is off (0).
GLOBAL activitytau : Activity time constant (ms^-1)
GLOBAL activitybeta : Scaling strength constant (s^-1 Hz^-1)
GLOBAL activitygamma : Scaling update constant (s^-2 Hz^-1)
}
: PARAMETER block - sets all variables to defaults at start
PARAMETER {
tauAM = 10 (ms)
tauNM = 300 (ms)
tauGA = 10 (ms)
tauAM2 = 20 (ms)
tauNM2 = 300 (ms)
tauGA2 = 20 (ms)
invl = 100 (ms)
WINV = 0
ahpwt = 0
tauahp= 10 (ms)
tauRR = 6 (ms)
refrac = 5 (ms)
AHP2REF = 0.0 : default is no refrac period increment/decrmenet
Vbrefrac = 20 (ms)
RRWght = 0.75
wwwid = 10
wwht = 10
VTH = -45 : fixed spike threshold
VTHC = -45
VTHR = -45
incRR = 0
Vblock = -20 : level of depolarization blockade
vdt = 0.1 : time step for saving state var
mg = 1 : for NMDA Mg dep.
sop=0
nbur=1
tbur=2
RMP=-65
EAM = 65
ENM = 90
EGA = -15
spkht = 50
prnum = -1
nsw=0
rebeg=0
subsvint=0
jrsvn=1e4 jrsvd=1e4 jrtime=-1 jrtm=-1
seedstep=44340
seaddvioff=9102098713763e-134
DEAD_DIV=1
WVAR=0.2
stopoq=0
PATHMEASURE=0
verbose=1
seadsetting=0
pathidtarg=-1
DELMIN=1e-5 : min delay to bother using queue -- otherwise considered simultaneous
STDAM=0
STDNM=0
STDGA=0
mg0 = 3.57
maxnmc = 1.0
lfpscale = 1.0
maxplastt = 10.0
plaststartT = -1 : default of -1 means always on (when seadsetting==3)
plastendT = -1 : default of -1 means always on (when seadsetting==3)
resetplast = 1 : default to reset wgain entries to 1 at start of run
wsetting = 0 : default -- use WMAT,WD0
ISTDP = 0 : no I->X STDP by default
ESTDP = 1 : E->X STDP by default, when t in bounds of plaststartT,plastendT and plasticity on (seadsetting==3)
SOFTSTDP = 1 : by default uses soft-bounds
EPOTW = 1 : Weight by which STDP produces potentiation if t(post)>t(pre) at an E->[anything] synapse
EDEPW = 1 : can bias towards depression by having EDEPW > 1 or EPOTW < 1
IPOTW = 1
IDEPW = 1
nextGID = 0
DOPE = 0 : no dopamine-based learning by default
EDOPE = 0 : no dopamine-based learning by default
IDOPE = 0 : no dopamine-based learning by default
FORWELIGTR = 1 : turn on forward eligibility traces by default
BACKELIGTR = 0 : turn off backward eligibility traces by default
EXPELIGTR = 1 : turn on exponential decay of eligibilty traces by default
maxeligtrdur = 100.0 : set maximum eligibility trace time to 100 ms by default
reseteligtr = 0 : don't reset by default
: default values for homeostatic synaptic scaling
scaling = 0 : Compensatory synaptic scaling defaults to 'off'
dynamicdel = 0 : Dynamic deletion defaults to 'off'
delspeed = 0.0 : Rate constant for dynamic deletion
scaleinhib = 0 : Whether or not we should scale I cells as well as E cells
activitytau = 100.0e3 : Activity sensor time constant (ms^-1) (van Rossum et al., 2000)
activitybeta = 4.0e-8 : was e-5 Scaling strength constant (s^-1 Hz^-1) (van Rossum et al., 2000)
activitygamma = 1.0e-10 : was e-7 Scaling update constant (s^-2 Hz^-1) (van Rossum et al., 2000)
}
ASSIGNED {
Vm VAM VNM VGA AHP VAM2 VNM2 VGA2
t0 tg twg refractory nxt xloc yloc zloc trrs
WEX EXSY RES ESIN Psk cbur invlt oinvl tmax spck savclock slowset FLAG
installed
pathbeg pathend pathtytarg pathlen
}
:* CONSTRUCTOR, DESTRUCTOR, INITIAL
:** CONSTRUCT: create a structure to save the identity of this unit and char integer flags
CONSTRUCTOR {
VERBATIM
{ int lid,lty,lin,lco,lgid,i; unsigned int sz;
if (ifarg(1)) { lid=(int) *getarg(1); } else { lid= UINT_MAX; } // ID
if (ifarg(2)) { lty=(int) *getarg(2); } else { lty= -1; } // type
if (ifarg(3)) { lin=(int) *getarg(3); } else { lin= -1; } // inhib
if (ifarg(4)) { lco=(int) *getarg(4); } else { lco= -1; } // column
_p_sop = (double*)ecalloc(1, sizeof(id0)); // important that calloc sets all flags etc to 0
ip = IDP;
ip->id=lid; ip->type=lty; ip->inhib=lin; ip->col=lco;
ip->pg=0x0; ip->dvi=0x0; ip->del=0x0; ip->sprob=0x0;
ip->syns=0x0; ip->wgain=0x0; ip->peconv=ip->piconv=0x0; ip->syw1=ip->syw2=0x0;
ip->pplasttau=0x0; ip->pplastinc=0x0; ip->pplastmaxw=0x0; ip->pdope=0x0;
ip->dead = ip->invl0 = ip->record = ip->jttr = ip->input = 0; // all flags off
ip->dvt = ip->vbr = ip->wrec = ip->jcn = ip->out = 0;
for (i=0;i<WRNUM;i++) {ip->wreci[i]=-1; ip->wscale[i]=-1.0;}
ip->rve=-1;
pathbeg=-1;
slowset=0;
////////////////////////////////////////////////////////////////////////////////////////////////
// THE PARAMETERS IN THIS 'BLOCK' ARE ASSOCIATED WITH HOMEOSTATIC SYNAPTIC SCAING
ip->activity = 0; // Sensor for this cell's recent activity (default 0MHz i.e. cycles per ms)
ip->max_err = 0; // Max error value
ip->max_scale = 100; // Max scaling factor
ip->lastupdate = 0; // Time of last activity sensor decay / spike update
ip->scalefactor = 1.0; // Default scaling factor for this cell's AMPA synapses
ip->goal_activity = -1; // Cell's target activity (MHz i.e. cycles per ms)
ip->activity_integral_err = 0.0; // Integral of cell's activity divergence from target activity
////////////////////////////////////////////////////////////////////////////////////////////////
ip->gid = nextGID; nextGID += 1.0;// global identifier
process=(int)getpid();
CNAME[SU]="SU"; CNAME[DP]="DP"; CNAME[IN]="IN";
if (installed==2.0 && ip->pg) { // jitcondiv was previously run
sz=ivoc_list_count(ip->pg->ce);
if(verbose) printf("\t**** WARNING new INTF6 created: may want to rerun jitcondiv ****\n");
} else installed=1.0; // set or reset it
cbsv=0x0;
}
ENDVERBATIM
}
PROCEDURE resetscaling () {
VERBATIM
ip = IDP;
// THE PARAMETERS IN THIS 'BLOCK' ARE ASSOCIATED WITH HOMEOSTATIC SYNAPTIC SCAING
ip->activity = 0; // Sensor for this cell's recent activity (default 0MHz i.e. cycles per ms)
ip->max_err = 0; // Max error value
ip->max_scale = 100; // Max scaling factor
ip->lastupdate = 0; // Time of last activity sensor decay / spike update
ip->scalefactor = 1.0; // Default scaling factor for this cell's AMPA synapses
ip->goal_activity = -1; // Cell's target activity (MHz i.e. cycles per ms)
ip->activity_integral_err = 0.0; // Integral of cell's activity divergence from target activity
ENDVERBATIM
}
DESTRUCTOR {
VERBATIM {
free(IDP);
}
ENDVERBATIM
}
:** INITIAL
INITIAL { LOCAL id
reset()
t0 = 0
tg = 0
twg = 0
trrs = 0
tmax=0
pathend=-1
pathlen=0
VERBATIM
{ int i,ix;
ip=IDP;
_lid=(double)ip->id;
ip->spkcnt=0;
ip->blkcnt=0;
ip->errflag=0;
ip->pg->lastspk[ip->id]=-1;
for (i=0;i<CTYN;i++){ix=cty[i]; blockcnt[ix]=spikes[ix]=AMo[ix]=NMo[ix]=GAo[ix]=AMo2[ix]=NMo2[ix]=GAo2[ix]=0;}
if(seadsetting==3 && resetplast && ip->wgain) for(i=0;i<ip->dvt;i++) ip->wgain[i]=1.0; // reset learning
if(seadsetting==3 && ip->pdope) for(i=0;i<ip->dvt;i++) ip->pdope[i] = -1e9; // turn off eligibility trace
}
ENDVERBATIM
jrsvn=jrsvd jrtime=jrtm
: init with vinset(0) if will turn on via a NetCon with w5=1
if (vinflag()) { randspk() net_send(nxt,2)}
if (recflag()) { recini() } : recini() resets for recording, cf recinit()
if (pathbeg==id) {
stoprun=0
net_send(0,2)
} : send at time 0
rebeg=0 : will reset this to restart storage for rec,wrec
:
: SN - NB - SHOULD PROBABLY RESET AT LEAST SOME OF THE
: PARAMS ASSOCIATED WITH HOMEOSTATIC SYNAPTIC SCALING HERE
:
: Store fixed value of 1/tau - users should not modify this!!
VERBATIM
activityoneovertau = 1.0 / activitytau; //@
ENDVERBATIM
: resetscaling()
}
PROCEDURE reset () {
Vm = RMP
VAM = 0
VNM = 0
VGA = 0
AHP=0
VAM2 = 0
VNM2 = 0
VGA2 = 0
invlt = -1
t0 = t
tg = t
twg = t
trrs = t
cbur = 0 : # bursts left to 0, just in case
spck = 0 : spike count to 0
refractory = 0 : 1 means cell is absolute refractory
VTHC=VTH :set current threshold to absolute threshold value
VTHR=VTH :set this one too to make sure it's initialized
}
VERBATIM
unsigned int GetDVIDSeedVal(unsigned int id) {
double x[2];
if (seadsetting==1) {
sead=((unsigned int)ip->id+seaddvioff)*1e6;
} else {
if (seadsetting==2) printf("Warning: GetDVIDSeedVal called with wt rand turned off\n");
x[0]=(double)id; x[1]=seaddvioff;
sead=hashseed2(2, x);
}
return sead;
}
ENDVERBATIM
: seed for divergence and delays -- not yet used
FUNCTION DVIDSeed(){
VERBATIM
return (double)GetDVIDSeedVal(IDP->id);
ENDVERBATIM
}
:* NET_RECEIVE
NET_RECEIVE (wAM,wNM,wGA,wGB,wAM2,wNM2,wGA2,wflg) { LOCAL tmp,jcn,id
INITIAL { wAM=wAM wNM=wNM wGA=wGA wGB=wGB wAM2=wAM2 wNM2=wNM2 wGA2=wGA2 wflg=0}
: intra-burst, generate next spike as needed
VERBATIM
id0 *ppre; int prty,poty,prin,prid,poid,ii,sy,nsyn,distal; double STDf,wgain,syw1,syw2; //@
ENDVERBATIM
tmax=t
VERBATIM
if (stopoq && !qsz()) stoprun=1;
ip=IDP; pg=ip->pg; ppre = 0x0; poid=ip->id;
if (ip->dead) return; // this cell has died
_ljcn=ip->jcn; _lid=ip->id;
tpnt = _pnt; // this pnt
if (PATHMEASURE) { // do all code for this
if (_lflag==2 || _lflag<0) { // on the callback -- distribute to divergence list
double idty; int i;
if (_lflag==2) ip->flag=-1;
idty=(double)(FOFFSET+ip->id)+1e-2*(double)ip->type+1e-3*(double)ip->inhib+1e-4;
for (i=0;i<ip->dvt && !stoprun;i++) if (ip->sprob[i]) {
(*pnt_receive[get_type(ip->dvi[i]->_prop)])(ip->dvi[i], wts, idty);
// restore pointers each time
#ifdef NRN_MECHANISM_DATA_IS_SOA
neuron::legacy::set_globals_from_prop(_pnt->_prop, _ml_real, _ml, _iml);
#else
_p=_pnt->_prop->param;
#endif
_ppvar = get_dparam(_pnt->_prop);
ip=IDP;
}
return; // else see if destination has been reached
} else if (_lflag!=2 && (pathtytarg==(double)ip->type || pathidtarg==(double)ip->id)) {
if (pathend==(double)ip->id) return; // means that coming back here again
ip->flag=(unsigned char)floor(t)+1; // type-target or id-target
pathend=(double)ip->id;
pathlen=tmax+1; // tmax gives pathlength
stoprun=1.;
return;
// deadends:visited || no output ||stopped
} else if (ip->flag || ip->dvt==0 || stoprun) {
return; // inhib cell is a deadend; don't revisit anyone
} else if (ip->inhib) {
if (!ip->flag) ip->flag=(unsigned char)floor(t)+1;
} else { // first callback will be from the stim
ip->flag=(unsigned char)floor(t)+1;
#if defined(t)
net_send((void**)0x0, wts,tpnt,t+1.,-1.); // the callback call
#else
net_send((void**)0x0, wts,tpnt,1.,-1.); // the callback call
#endif
return;
}
}
// MR: Synaptic scaling and deletion logic
if (dynamicdel) {
dynamicdelete(t); // Calculate probabilistically whether or not this cell should die
}
// SN - is the following line needed when not running synaptic scaling?
decay_activity_sensor(t); // Allow activity sensor to decay on every update
if (scaling) {
if (ip->goal_activity < 0) {
// If scaling has just been turned on, set goal activity to historical average firing rate
// This is only meaningful if sensor has had a chance to measure correct activity over
// a relatively long period of time, so don't call setscaling(1) until at least ~800s.
//ip->goal_activity = get_avg_activity();
ip->goal_activity = ip->activity; // Take current activity sensor value
//ip->max_err = ip->goal_activity * 0.5; // Error value saturates at +- 50% of goal activity rate
}
if (!ip->inhib || scaleinhib) {
// Only update if cell is not inhib OR we are scaling all I+E cells
update_scale_factor(t); // Run synaptic scaling procedure to find scalefactor
}
}
ip->lastupdate = t; // Store time of last update
if (_lflag==OK) { FLAG=OK; flag(); return; } // identify internal call with errflag
if (_lflag<0) { callback(_lflag); return; }
pg->eventtot+=1;
// if(flag==0) { printf("flag==0!\n"); }
ENDVERBATIM
VERBATIM
if (ip->dbx>2)
ENDVERBATIM
{
pid()
printf("DB0: flag=%g Vm=%g",flag,VAM+VNM+VGA+RMP+AHP+VAM2+VNM2+VGA2)
if (flag==0) { printf(" (%g %g %g %g %g %g %g)",wAM,wNM,wGA,wAM2,wNM2,wGA2,wflg) }
printf("\n")
}
: causes of spiking: between VTH and Vblock, random from vsp (flag 2), within burst
:** JITcon code - only meant for intra-COLUMN events
if (flag>=FOFFSET) { : jitcon -- set up weights on the fly
VERBATIM {
// find type of presyn
prid = (int)(_lflag-FOFFSET); // that correct? - if not, put prid in wts[2]
poty=(int)ip->type;
prty=(int)(1e2*(_lflag-floor(_lflag)));
prin=(int)(1e3*(_lflag-floor(_lflag)-prty*1e-2)); // stuffed into this flag
distal = ((int) (_lflag * 1e5 + 0.5)) % 2;
if(distal){ sy=prin?GA2:AM2; } else { sy=prin?GA:AM; }
// if(verbose>4) printf("receive: %s->%s, prin=%d, distal=%d, sy=%d, _lflag=%.10f\n",\
// CNAME[ctymap[prty]],CNAME[ctymap[poty]],prin,distal,sy,_lflag);
STDf=_args[0]; // save value -- for short-term changes
wgain=_args[1]; // save value -- for plasticity
syw1=_args[2]; // save value -- for non-MATRIX weight 1 -- only used when wsetting==1
syw2=_args[3]; // save value -- for non-MATRIX weight 2 -- only used when wsetting==1
if(ip->dbx<-1) printf("prid%d,poid%d,wgain=%g\n",prid,poid,wgain);
for (ii=0;ii<=6;ii++) _args[ii]=0.; // clear _args (stores weights for later) to be safe
if (seadsetting==3) { // plasticity mode is on
ppre = getlp(pg->ce,prid); // get pointer to presynaptic cell
if(ip->dbx<-1) printf("ppre%p,pre%d->po%d,wg=%g\n",ppre,prid,ip->id,wgain);
if(ppre->inhib) { // only care about appropriate presynaptic cells for plasticity
if(!ISTDP && !IDOPE) ppre=0x0;
} else {
if(!ESTDP && !EDOPE) ppre=0x0;
}
}
if(ppre) { // appropriate presynaptic cell AND plasticity mode is on
for (ii=sy,nsyn=0;ii<sy+2;ii++) {
if(ii==AM2 || ii==AM || ii==GA || ii==GA2) { // AMPA,GABAA plasticity factor
if(wsetting==1.0) { // non-MATRIX weights and AMPA,GABAA plasticit
_args[ii] = ii == sy ? syw1 * wgain : syw2 * wgain;
} else { // MATRIX weights and AMPA/GABAA plasticity
_args[ii]=wgain*WMAT(prty,poty,ii)*WD0(prty,poty,ii);
}
if(ip->dbx<-1) printf("pre%d->po%d,sy=%d,wg=%g,w=%g\n",prid,ip->id,ii,wgain,_args[ii]);
} else { // non-AMPA/non-GABAA -->> no plasticity applied
if(wsetting==1.0) { // non-MATRIX weights and non AMPA
_args[ii] = ii == sy ? syw1 : syw2;
} else { // MATRIX weights and non AMPA
_args[ii]=WMAT(prty,poty,ii)*WD0(prty,poty,ii);
}
}
nsyn+=(_args[ii]>0.);
}
} else { // no plasticity applied
if(wsetting==1.0) { // non-MATRIX weights
_args[sy+0] = syw1;
_args[sy+1] = syw2;
nsyn = (_args[sy+0]>0.) + (_args[sy+1]>0.);
} else { // MATRIX weights
for (ii=sy,nsyn=0;ii<sy+2;ii++) nsyn+=((_args[ii]=WMAT(prty,poty,ii)*WD0(prty,poty,ii))>0.);
}
}
if (nsyn==0) return; //return for 0-weight events, before changing state vars or Vm
// *** Do synaptic scaling
if (scaling) {
for (ii=sy,nsyn=0;ii<sy+2;ii++) {
if (!ip->inhib) {
// Scale E cell
if (ii==AM2 || ii==AM) { // || ii==NM || ii == NM2) {
// Scale AMPA receptors by scalefactor (Turrigiano, 2008)
_args[ii] *= ip->scalefactor;
}
if (ii==GA || ii==GA2) {
// Scale GABA receptors by 1/scalefactor to model BDNF (Chandler and Grossberg, 2012)
_args[ii] *= 1 / ip->scalefactor;
}
} else {
// Scale I cell
// Scaling has opposite effects on I cells (if scaling is enabled for I cells)
if (ii==AM2 || ii==AM) { // || ii==NM || ii == NM2) {
// Scale I-cell AMPA receptors by 1/scalefactor
_args[ii] *= 1 / ip->scalefactor;
}
if (ii==GA || ii==GA2) {
// Scale I-cell GABA receptors by scalefactor
_args[ii] *= ip->scalefactor;
}
}
}
}
// *** Done synaptic scaling
if (seadsetting==3) { // empty 'if' to skip next clause
} else if (seadsetting!=2) { // not fixed weights
if (seadsetting==1) {
sead=(unsigned int)(floor(_lflag)*ip->id*seedstep); // all integers
} else { // hash on presynaptic id+FOFFSET,poid,seedstep
hsh[0]=floor(_lflag); hsh[1]=(double)ip->id; hsh[2]=seedstep;
sead=hashseed2(3, hsh); // hsh[] is just scratch pad
}
mcell_ran4(&sead, &_args[sy], 2, 1.);
for (ii=sy;ii<sy+2;ii++) { // scale appropriately;
_args[ii]=2*WVAR*(_args[ii]+0.5/WVAR-0.5)*WMAT(prty,poty,ii)*WD0(prty,poty,ii);
}
}
}
ENDVERBATIM
VERBATIM
if (ip->dbx>2)
ENDVERBATIM
{
pid()
printf("DF: flag=%g Vm=%g",flag,VAM+VNM+VGA+RMP+AHP+VAM2+VNM2+VGA2)
printf(" (%g %g %g %g %g %g %g)",wAM,wNM,wGA,wAM2,wNM2,wGA2,wflg)
printf("\n")
}
:** mid-burst
} else if (flag==4) {
cbur=cbur-1 : count down the spikes
if (cbur>0) {
net_send(tbur,4)
} else { : end of burst
refractory = 1 : signal that this cell is in refractory period
net_send(refrac-AHP*AHP2REF, 3) : send event for end of refractory
}
tmp=t
VERBATIM
if (ip->jttr)
ENDVERBATIM
{ tmp= t+jttr()/10 }
if (jcn) {
jitcon(tmp)
VERBATIM
if(ip->out)
ENDVERBATIM
{ net_event(tmp) }
} else { net_event(tmp) }
VERBATIM
spikes[ip->type]++; //@
ENDVERBATIM
spck=spck+1
VERBATIM
if (ip->dbx>0)
ENDVERBATIM
{ pid() printf("DBA: mid-burst event at %g, %g\n",tmp,cbur) }
VERBATIM
if (ip->record)
ENDVERBATIM
{ recspk(tmp) }
VERBATIM
if (ip->wrec)
ENDVERBATIM
{ wrecord(t) }
VERBATIM
return; //@ done
ENDVERBATIM
: start reading random spike times (or burst times) from vsp vector pointer
: this is signaled externally from a netstim with wflg=1, will turn off on next stim
: (NB wflg used in completely different context for GABAB) ?? is this still true ??
: this is bad -- should use a special netcon that just handles signals
} else if (flag==0 && wflg==1) {
VERBATIM
ip->input=1; //@
ENDVERBATIM
wflg=2 : set flag to turn off next time an external event comes from here
randspk()
net_send(nxt,2)
VERBATIM
return; //@ done
ENDVERBATIM
} else if (flag==0 && wflg==2) { : flag to stop random spikes
VERBATIM
ip->input=0; //@ inputs that are read from a vector of times -- see randspk()
ENDVERBATIM
wflg=1 : flag to turn on next time
VERBATIM
return; //@ done
ENDVERBATIM
}
: update state variables
VERBATIM
if (ip->record)
ENDVERBATIM
{ record() }
VERBATIM
if (ip->wrec)
ENDVERBATIM
{ wrecord(1e9) }
:** update state variables: VAM, VNM, VGA
if (VAM>hoc_epsilon) { VAM = VAM*EXP(-(t - t0)/tauAM) } else { VAM=0 } :AMPA
if (VNM>hoc_epsilon) { VNM = VNM*EXP(-(t - t0)/tauNM) } else { VNM=0 } :NMDA
if (VGA< -hoc_epsilon){ VGA = VGA*EXP(-(t - t0)/tauGA) } else { VGA=0 } :GABAA
if (VAM2>hoc_epsilon) {VAM2 = VAM2*EXP(-(t - t0)/tauAM2) } else { VAM2=0 } :AMPA from distal dends
if (VNM2>hoc_epsilon) {VNM2 = VNM2*EXP(-(t - t0)/tauNM2) } else { VNM2=0 } :NMDA from distal dends
if (VGA2< -hoc_epsilon){VGA2 = VGA2*EXP(-(t - t0)/tauGA2) } else { VGA2=0 } :GABAA more distal from soma
if(refractory==0){:once refractory period over, VTHC falls back towards VTH
if(VTHC>VTH) { :eg, for decelerating cells after firing, thresh increases
VTHC = VTH + (VTHR-VTH)*EXP(-(t-trrs)/tauRR)
} else if(RRWght<0 && VTHC<VTH) { :eg, for accelerating cells after firing, thresh decreases
VTHC = VTH - (VTHR-VTH)*EXP(-(t-trrs)/tauRR)
}
}
if (AHP< -hoc_epsilon){ AHP = AHP*EXP(-(t-t0)/tauahp) } else { AHP=0 } : adaptation
t0 = t : finished using t0
Vm = VAM+VNM+VGA+AHP+VAM2+VNM2+VGA2 : membrane deviation from rest
if (Vm> -RMP) {Vm= -RMP}: 65 mV above rest
if (Vm< RMP) {Vm= RMP} : 65 mV below rest
:*** only add weights if an external excitation
if (flag==0 || flag>=FOFFSET) {
: AMPA Erev=0 (0-RMP==65 mV above rest)
if (wAM>0) {
if (STDAM==0) { VAM = VAM + wAM*(1-Vm/EAM)
} else { VAM = VAM + (1-STDAM*STDf)*wAM*(1-Vm/EAM) }
if (VAM>EAM) {
VERBATIM
AMo[ip->type]++; //@
ENDVERBATIM
} else if (VAM<0) { VAM=0 }
}
if (wAM2>0) { : AMPA from distal dends
if (STDAM==0) { VAM2 = VAM2 + wAM2*(1-Vm/EAM)
} else { VAM2 = VAM2 + (1-STDAM*STDf)*wAM2*(1-Vm/EAM) }
if (VAM2>EAM) {
VERBATIM
AMo2[ip->type]++; //@
ENDVERBATIM
} else if (VAM2<0) { VAM2=0 }
}
: NMDA; Mg effect based on total activation in rates()
if (wNM>0 && VNM<ENM) {
if (STDNM==0) { VNM = VNM + wNM*rates(RMP+Vm)*(1-Vm/ENM)
} else { VNM = VNM + (1-STDNM*STDf)*wNM*rates(RMP+Vm)*(1-Vm/ENM) }
if (VNM>ENM) {
VERBATIM
NMo[ip->type]++; //@
ENDVERBATIM
} else if (VNM<0) { VNM=0 }
}
if (wNM2>0 && VNM2<ENM) { : NMDA from distal dends
if (STDNM==0) { VNM2 = VNM2 + wNM2*rates(RMP+Vm)*(1-Vm/ENM)
} else { VNM2 = VNM2 + (1-STDNM*STDf)*wNM2*rates(RMP+Vm)*(1-Vm/ENM) }
if (VNM2>ENM) {
VERBATIM
NMo2[ip->type]++; //@
ENDVERBATIM
} else if (VNM2<0) { VNM2=0 }
}
: GABAA , GABAA2 : note that all wts are positive
if (wGA>0 && VGA>EGA) { : the neg here gives the inhibition
if (STDGA==0) { VGA = VGA - wGA*(1-Vm/EGA)
} else { VGA = VGA - (1-STDGA*STDf)*wGA*(1-Vm/EGA) }
if (VGA<EGA) {
VERBATIM
GAo[ip->type]++; //@
ENDVERBATIM
VERBATIM
if (ip->dbx>2)
ENDVERBATIM
{
pid() printf("DB0A: flag=%g Vm=%g",flag,VAM+VNM+VGA+RMP+AHP+VAM2+VNM2+VGA2)
if (flag==0) { printf(" (%g %g %g %g %g %g)",wGA,EGA,VGA,Vm,AHP,STDf) }
VERBATIM
printf("\nAA:%d:%d\n\n",GAo[ip->type],ip->type); //@
ENDVERBATIM
}
} else if (VGA>0) { VGA=0 } : if want reversal of VGA need to also edit above
}
if (wGA2>0 && VGA2>EGA) { : the neg here gives the inhibition, GABAA2, inputs further from soma
if (STDGA==0) { VGA2 = VGA2 - wGA2*(1-Vm/EGA)
} else { VGA2 = VGA2 - (1-STDGA*STDf)*wGA2*(1-Vm/EGA) }
if (VGA2<EGA) {
VERBATIM
GAo2[ip->type]++; //@
ENDVERBATIM
VERBATIM
if (ip->dbx>2)
ENDVERBATIM
{
pid() printf("DB0A: flag=%g Vm=%g",flag,VAM+VNM+VGA+RMP+AHP+VAM2+VNM2+VGA2)
if (flag==0) { printf(" (%g %g %g %g %g %g)",wGA2,EGA,VGA2,Vm,AHP,STDf) }
VERBATIM
printf("\nAA:%d:%d\n\n",GAo2[ip->type],ip->type); //@
ENDVERBATIM
}
} else if (VGA2>0) { VGA2=0 } : if want reversal of VGA2 need to also edit above
}
:*** modulated interval firing; cf invlfire.mod
VERBATIM
if (ip->invl0)
ENDVERBATIM
{
Vm = RMP+VAM+VNM+VGA+AHP+VAM2+VNM2+VGA2
if (Vm>0) {Vm= 0 }
if (Vm<-90) {Vm=-90}
if (invlt==-1) { : activate for first time
if (Vm>RMP) {
oinvl=invl
invlt=t
net_send(invl,1)
}
} else {
tmp=shift(Vm)
if (tmp!=0) {
net_move(tmp)
if (id()<prnum) {
pid() printf("**** MOVE t=%g to %g Vm=%g %g,%g\n",t,tmp,Vm,invlt,oinvl) }
}
}
}
} else if (flag==1) { : modulated interval firing; cf invlfire.mod
: Vm=RMP+VAM+VNM+VGA+AHP+VAM2+VNM2+VGA2
if (WINV<0) {
if (jcn) {
jitcon(t)
VERBATIM
if(ip->out)
ENDVERBATIM
{ net_event(t) }
} else { net_event(t) } : bypass activation calculation
VERBATIM
spikes[ip->type]++; //@
ENDVERBATIM
spck=spck+1
VERBATIM
if (ip->dbx>0)
ENDVERBATIM
{pid() printf("DBC: interval event\n")}
VERBATIM
if (ip->record)
ENDVERBATIM
{ recspk(t) }
VERBATIM
if (ip->wrec)
ENDVERBATIM
{ wrecord(t) }
} else {
tmp = WINV*(1-Vm/EAM)
VAM = VAM + tmp :: activate interval depolarization
}
oinvl=invl
invlt=t
net_send(invl,1)
} else if (flag==2) { :** flag==2 -- read off external vec (vsp) for next random spike time or single from shock()
VERBATIM
if (ip->dbx>1)
ENDVERBATIM
{pid() printf("DBBa: randspk called: %g,%g\n",WEX,nxt)}
if (WEX>1e8) { : super-threshold event
if (jcn) {
jitcon(t)
VERBATIM
if(ip->out)
ENDVERBATIM
{ net_event(t) }
} else { net_event(t) } : bypass activation calculation
VERBATIM
spikes[ip->type]++; //@
ENDVERBATIM
spck=spck+1
VERBATIM
if (ip->dbx>0)
ENDVERBATIM
{pid() printf("DBB: randspk event @ t=%g\n",t)}
VERBATIM
if (ip->record)
ENDVERBATIM
{ recspk(t) }
VERBATIM
if (ip->wrec)
ENDVERBATIM
{ wrecord(t) }
} else if (WEX>0) { : excitatory input
if(EXSY==AM) {
tmp = WEX*(1-Vm/EAM)
VAM = VAM + tmp
} else if(EXSY==AM2) {
tmp = WEX*(1-Vm/EAM)
VAM2 = VAM2 + tmp
} else if(EXSY==NM) {
tmp = rates(RMP+Vm)*WEX*(1-Vm/ENM)
VNM = VNM + tmp
} else if(EXSY==NM2) {
tmp = rates(RMP+Vm)*WEX*(1-Vm/ENM)
VNM2 = VNM2 + tmp
}
} else if (WEX<0 && WEX!=-1e9) { : inhibitory input
if(EXSY==GA) {
tmp = WEX*(1-Vm/EGA)
VGA = VGA + tmp
} else { :GA2
tmp = WEX*(1-Vm/EGA)
VGA2 = VGA2 + tmp
}
}
if (WEX!=-1e9) { : code for single shock
randspk() : will set WEX for next time
VERBATIM
if (ip->input)
ENDVERBATIM
{ net_send(nxt,2) }
}
} else if (flag==3) {
refractory = 0 :end of absolute refractory period
trrs = t : save time of start of relative refractory period
VERBATIM
return; //@ done
ENDVERBATIM
}
:** check for Vm>VTH -> fire
Vm = VAM+VNM+VGA+RMP+AHP+VAM2+VNM2+VGA2 : WARNING -- Vm defined differently than above
if (Vm>0) {Vm= 0 }
if (Vm<-90) {Vm=-90}
if (refractory==0 && Vm>VTHC) {
VERBATIM
if (!ip->vbr && Vm>Vblock) {//@ do nothing
ENDVERBATIM
VERBATIM
ip->blkcnt++; blockcnt[ip->type]++; return; }//@
ENDVERBATIM
AHP = AHP - ahpwt
tmp=t
: note that jtt indicates jitter while jit indicates 'just-in-time'
VERBATIM
if (ip->jttr)
ENDVERBATIM
{ tmp= t+jttr() }
VERBATIM
//printf("spk t = %g\n",_ltmp); //@
ENDVERBATIM
VERBATIM
//printf("a ip->pg->lastspk[%d]=%g\n",ip->id,ip->pg->lastspk[ip->id]); //@
ENDVERBATIM
VERBATIM
raise_activity_sensor(t); //@ Update activity sensor
ENDVERBATIM
VERBATIM
ip->pg->lastspk[ip->id]=_ltmp; //@
ENDVERBATIM
VERBATIM
//printf("b ip->pg->lastspk[%d]=%g\n",ip->id,ip->pg->lastspk[ip->id]); //@
ENDVERBATIM
if (jcn) {
jitcon(tmp)
VERBATIM
if(ip->out)
ENDVERBATIM
{ net_event(tmp) }
} else { net_event(tmp) }
VERBATIM
spikes[ip->type]++; //@
ENDVERBATIM
spck=spck+1
VERBATIM
if (ip->dbx>0)
ENDVERBATIM
{pid() printf("DBD: %g>VTH(%g) event at %g (STDf=%g)\n",Vm,VTHC,tmp,STDf)}
VERBATIM
if (ip->record)
ENDVERBATIM
{ recspk(tmp) }
VERBATIM
if (ip->wrec)
ENDVERBATIM
{ wrecord(tmp) }
if(incRR) { : additive
VTHC=VTHC+RRWght*(Vblock-VTH):increase threshold for relative refrac. period. NB: RRWght can be < 0
if(VTHC > Vblock) {VTHC=Vblock} else if(VTHC < RMP) {VTHC=RMP}
} else { : non-additive
VTHC=VTH+RRWght*(Vblock-VTH):increase threshold for relative refrac. period. NB: RRWght can be < 0
}
VTHR=VTHC :starting thresh value for relative refrac period, keep track of it
refractory = 1 : abs. refrac on = don't allow any more spikes/bursts to begin (even for IB cells)
if(seadsetting==3) { : apply learning rule
if(plaststartT<0 || plastendT<0 || (t>=plaststartT && t<=plastendT)) { : make sure plasticity on now
VERBATIM
if(ip->dbx<-1) printf("%d@%g applying plasticity\n",ip->id,ip->pg->lastspk[ip->id]); //@
ENDVERBATIM
VERBATIM
if(ESTDP) applyEXSTDP(ip,ip->pg->lastspk[ip->id]); //@
ENDVERBATIM
VERBATIM
if(ISTDP) applyIXSTDP(ip,ip->pg->lastspk[ip->id]); //@
ENDVERBATIM
VERBATIM
if(EDOPE) applyEDOPE(ip,ip->pg->lastspk[ip->id]); //@
ENDVERBATIM
VERBATIM
if(IDOPE) applyIDOPE(ip,ip->pg->lastspk[ip->id]); //@
ENDVERBATIM
}
}
if (nbur>1) {
cbur=nbur-1 net_send(tbur,4) : this is main source of burst events - A.P. firing with bursting
VERBATIM
return; //@ done
ENDVERBATIM
}
VERBATIM
if (ip->vbr && Vm>Vblock)
ENDVERBATIM
{
net_send(Vbrefrac,3)
VERBATIM
if (ip->dbx>0)
ENDVERBATIM
{pid() printf("DBE: %g %g\n",Vbrefrac,Vm)}
VERBATIM
return; //@ done
ENDVERBATIM
}
net_send(refrac-AHP*AHP2REF, 3) :event for end of abs. refrac., sent separately for IB cells @ end of burst
}
}
:* ancillary functions
:** jitcon() creates divergence and delays from rand seed
: jcn flags:
: 0 NetCons jcn==0
: 3 Jitcon without jitevent jcn==3 -- eliminated after v669
: 2 Jitcon with callback jcn==2 -- NOT DEBUGGED
: 1 Jitcon with callback with pointers jcn==1
PROCEDURE jitcon (tm) {
VERBATIM {
double mindel, randel, idty, *x; int prty, poty, i, j, k, dv;
Point_process *pnt; IvocVect* voi;
// qsz = nrn_event_queue_stats(stt);
// if (qsz>=qlimit) { printf("qlimit %g exceeded at t=%g\n",qlimit,t); qlimit*=2; }
ip=IDP; pg=ip->pg;
if(verbose>1) printf("col %d , ip %p, pg %p\n",ip->col,ip,pg);
if (!pg) {printf("No network defined -- must run jitcondiv()\n"); hxe();}
ip->spkcnt++; // jitcon() called from NET_RECEIVE which sets ip
if (pg->jrj<pg->jrmax) { // record spike time and cell ID
pg->jrid[pg->jrj]=(double)ip->id; pg->jrtv[pg->jrj]=_ltm;
pg->jrj++;
} else if (wf2 && pg->jrmax) spkoutf2(); // saving spike times
pg->jri++; // keep track of number of spikes
if (jrtm>0) {
if (t>jrtime) {
jrtime+=jrtm;
spkstats2(1.);
}
} else if (jrsvd>0 && pg->jri>jrsvn) {
jrsvn+=jrsvd; printf("t=%.02f %ld ",t,ip->pg->jri);
spkstats2(1.);
}
prty=(int)ip->type;
if (ip->jcn==1) if (ip->dvt>0) { // first callback
#if defined(t)
if (ip->jcn==1) if (ip->dvt>0) net_send((void**)0x0, wts,tpnt,t+ip->del[0],-1.);
#else
if (ip->jcn==1) if (ip->dvt>0) net_send((void**)0x0, wts,tpnt,ip->del[0],-1.);
#endif
}
}
ENDVERBATIM
}
: call spkstat from hoc to set global tf if desired for spkstats to file
PROCEDURE spkstats () {
VERBATIM {
if (ifarg(1)) tf=hoc_obj_file_arg(1); else tf=0x0;
}
ENDVERBATIM
}
: spkoutf() use wf2 for output of indices and times
PROCEDURE spkoutf () {
VERBATIM {
if (ifarg(2)) {
wf1=hoc_obj_file_arg(1); // index file
wf2=hoc_obj_file_arg(2);
} else if (wf1 != 0x0) {
spkoutf2();
wf1=(FILE*)0x0; wf2=(FILE*)0x0;
}
}
ENDVERBATIM
}
VERBATIM
static void spkoutf2 () {
fprintf(wf1,"//b9 -2 t%0.2f %ld %ld\n",t/1e3,pg->jrj,ftell(wf2));
fwrite(pg->jrtv,sizeof(double),pg->jrj,wf2); // write times
fwrite(pg->jrid,sizeof(double),pg->jrj,wf2); // write id
fflush(wf1); fflush(wf2);
pg->jrj=0;
}
ENDVERBATIM
PROCEDURE callhoc () {
VERBATIM
if (ifarg(1)) {
cbsv=hoc_lookup(gargstr(1));
} else {
cbsv=0x0;
}
ENDVERBATIM
}
: flag 1 means print it to a file, 2 means to both places
PROCEDURE spkstats2 (flag) {
VERBATIM {
int i, ix, flag; double clk;
ip=IDP; pg=ip->pg;
flag=(int)(_lflag+1e-6);
clk=clock()-savclock; savclock=clock();
if (cbsv) hoc_call_func(cbsv,0);
if (tf) fprintf(tf,"t=%.02f;%ld(%g) ",t,pg->jri,clk/1e6); else {
printf("t=%.02f;%ld(%g) ",t,pg->jri,clk/1e6); }
for (i=0;i<CTYN;i++) {
ix=cty[i];
pg->spktot+=spikes[ix];
if (tf) {
fprintf(tf,"%s:%d/%d:%d;%d;%d;%d;%d;%d ",CNAME[i],spikes[ix],\
blockcnt[ix],AMo[ix],NMo[ix],GAo[ix],AMo2[ix],NMo2[ix],GAo2[ix]);
} else {
printf("%s:%d/%d:%d;%d;%d;%d;%d;%d ",CNAME[i],spikes[ix],blockcnt[ix],\
AMo[ix],NMo[ix],GAo[ix],AMo2[ix],NMo2[ix],GAo2[ix]);
}
spck=0;
blockcnt[ix]=spikes[ix]=0;
AMo[ix]=NMo[ix]=GAo[ix]=AMo2[ix]=NMo2[ix]=GAo2[ix]=0;
}
if (tf && flag==2) { fprintf(tf,"\nt=%g tot_spks: %ld; tot_events: %ld\n",t,pg->spktot,pg->eventtot);
} else if (flag==2) { printf("\ntotal spikes: %ld; total events: %ld\n",pg->spktot,pg->eventtot);
} else if (tf) fprintf(tf,"\n"); else printf("\n");
}
ENDVERBATIM
}
PROCEDURE oobpr () {
VERBATIM {
int i,ix;
for (i=0;i<CTYN;i++){
ix=cty[i];
printf("%d:%d/%d:%d;%d;%d;%d;%d;%d ",ix,spikes[ix],blockcnt[ix],\
AMo[ix],NMo[ix],GAo[ix],AMo2[ix],NMo2[ix],GAo2[ix]);
}
printf("\n");
}
ENDVERBATIM
}
PROCEDURE callback (fl) {
VERBATIM {
int i; double idty, idtflg, del0, ddel; id0 *jp; Point_process *upnt; // these must be local
i=(unsigned int)((-_lfl)-1); // -1,-2,-3 -> 0,1,2
jp=IDP; upnt=tpnt; del0=jp->del[i]; ddel=0.;
idty=(double)(FOFFSET+jp->id)+1e-2*(double)jp->type+1e-3*(double)jp->inhib+1e-4;
while (ddel<=DELMIN) { // check if this del is worth waiting, else just send now
if (Vblock<VTHC) {
wts[0]=0; // send [0,1] for STD
} else if(STDAM || STDNM || STDGA) { // STDf=(1-STD) , ONLY SET wts[0] WHEN SHORT-TERM FACIL. ON
//NB: WTS IS TOO OVERUSED, CONFUSING!!!!!!!!!!!
//if anyone uses STD they should make sure doesn't
//cause problems in wts, _args !!!
wts[0]=(VTHC-VTH)/(Vblock-VTH); // just send [0,1] for STD
}
wts[1]=0.0; // default is no plasticity gain
if(seadsetting==3) { // check if should send plasticity gain
if(jp->inhib) {
if(ISTDP || IDOPE) wts[1]=jp->wgain[i];
} else {
if(ESTDP || EDOPE) wts[1]=jp->wgain[i];
}
}
if(wsetting==1.0 && jp->syw1 && jp->syw2) {wts[2]=jp->syw1[i]; wts[3]=jp->syw2[i]; } // non-MATRIX weights?
idtflg = idty + (1e-5 * jp->syns[i]);
// if(1) printf("s = %g : flg = %.10f\n",(1e-5*jp->syns[i]),idtflg);
if (jp->sprob[i]) (*pnt_receive[get_type(jp->dvi[i]->_prop)])(jp->dvi[i], wts, idtflg);
// restore pointers
#ifdef NRN_MECHANISM_DATA_IS_SOA
neuron::legacy::set_globals_from_prop(upnt->_prop, _ml_real, _ml, _iml);
#else
_p=upnt->_prop->param;
#endif
_ppvar = get_dparam(upnt->_prop);
i++;
if (i>=jp->dvt) return 0; // ran out
ddel=jp->del[i]-del0; // delays are relative to event; use difference in delays
}
// skip over pruned outputs and dead cells:
while (i<jp->dvt && (!jp->sprob[i] || id0ptr(jp->dvi[i]->_prop)->dead)) i++;
if (i<jp->dvt) {
ddel= jp->del[i] - del0;;
#if defined(t)
net_send((void**)0x0, wts,upnt,t+ddel,(double) -(i+1)); // next callback
#else
net_send((void**)0x0, wts,upnt,ddel,(double) -(i+1)); // next callback
#endif
}
}
ENDVERBATIM
}
: DEAD_DIV not checked in mkdvi()
: mkdvi() create the connectivity vectors for a random network
PROCEDURE mkdvi () {
VERBATIM {
int i,j,k,prty,poty,dv,dvt,dvii; double *x, *db, *dbs;
Object *lb; Point_process *pnnt, **da, **das;
ip=IDP; pg=ip->pg;//this should only be called after jitcondiv()
if (ip->dead) return 0;
prty=ip->type;
sead=GetDVIDSeedVal(ip->id);//seed for divergence and delays
for (i=0,k=0,dvt=0;i<CTYN;i++) { // dvt gives total divergence
poty=cty[i];
dvt+=DVG(prty,poty);
}
da =(Point_process **)malloc(dvt*sizeof(Point_process *));
das=(Point_process **)malloc(dvt*sizeof(Point_process *)); // das,dbs for after sort
db =(double *)malloc(dvt*sizeof(double)); // delays
dbs=(double *)malloc(dvt*sizeof(double)); // delays
for (i=0,k=0,dvii=0;i<CTYN;i++) { // cell types in cty[]
poty=cty[i];
dv=DVG(prty,poty);
if (dv>0) {
sead+=dv;
if (dv>dscrsz) {
printf("B:Divergence exceeds dscrsz: %d>%d for %d->%d\n",dv,dscrsz,prty,poty); hxe(); }
mcell_ran4(&sead, dscr , dv, pg->ixe[poty]-pg->ix[poty]+1);
for (j=0;j<dv;j++) {
if (!(lb=ivoc_list_item(pg->ce,(unsigned int)floor(dscr[j]+pg->ix[poty])))) {
printf("INTF6:callback %g exceeds %d for list ce\n",floor(dscr[j]+pg->ix[poty]),pg->cesz);
hxe(); }
pnnt=(Point_process *)lb->u.this_pointer;
da[j+dvii]=pnnt;
}
mcell_ran4(&sead, dscr , dv, 2*DELD(prty,poty));
for (j=0;j<dv;j++) {
db[j+dvii]=dscr[j]+DELM(prty,poty)-DELD(prty,poty); // +/- DELD
if (db[j+dvii]<0) db[j+dvii]=-db[j+dvii];
}
dvii+=dv;
}
}
gsort2(db,da,dvt,dbs,das);
ip->del=dbs; ip->dvi=das; ip->dvt=dvt; ip->syns=(char*)calloc(dvt,sizeof(char));
ip->sprob=(unsigned char *)malloc(dvt*sizeof(char *)); // release probability
for (i=0;i<dvt;i++) ip->sprob[i]=1; // start out with all firing
free(da); free(db); // keep das,dbs which are assigned to ip->dvi bzw ip->del
}
ENDVERBATIM
}
:* paths
PROCEDURE patha2b () {
VERBATIM
int i; double idty, *x; static Point_process *_pnt; static id0 *ip0;
ip=IDP; pg=ip->pg;
pathbeg=*getarg(1); pathidtarg=*getarg(2);
pathtytarg=-1; PATHMEASURE=1; pathlen=stopoq=0;
for (i=0;i<pg->cesz;i++) { lop(pg->ce,i);
if ((i==pathbeg || i==pathidtarg) && qp->inhib) {
pid(); printf("Checking to or from inhib cell\n" ); hxe(); }
qp->flag=qp->vinflg=0;
}
hoc_call_func(hoc_lookup("finitialize"), 0);
cvode_fadvance(1000.0); // this call will not return
ENDVERBATIM
}
:* paths
: pathgrps(vpre,vpos,vout) finds path lengths from pres to posts
FUNCTION pathgrps () {
VERBATIM
int i,j,k,na,nb,flag; double idty,*a,*b,*x,sum; static Point_process *_pnt; static id0 *ip0;
Symbol* s; char **pfl;
ip=IDP; pg=ip->pg;
x=0x0;
s=hoc_lookup("finitialize");
if (ifarg(2)) {
na=vector_arg_px(1,&a);
nb=vector_arg_px(2,&b);
if (ifarg(3)) x=vector_newsize(vector_arg(3),na*nb);
} else {
na=nb=pg->cesz; // may want to put output into an unsigned char eventually
if (ifarg(1)) x=vector_newsize(vector_arg(1),na*nb);
}
// if (scrsz<cesz) scrset(cesz);
pfl = (char **)malloc(pg->cesz * (unsigned)sizeof(char *));
for (i=0;i<pg->cesz;i++) { lop(pg->ce,i); scr[i]=qp->inhib; pfl[i]=&qp->flag; }
pathtytarg=-1; PATHMEASURE=1; pathlen=stopoq=0;
for (k=0,sum=0;k<na;k++) {
pathbeg=a[k];
if (scr[(int)pathbeg]) {
if (x) for (j=0;j<nb;j++) x[k*nb+j]=0.;
continue;
}
for (j=0;j<nb;j++) {
pathidtarg=b[j];
if (scr[(int)pathidtarg]) { if (x) x[k*nb+j]=0.;
continue;
}
// for (i=0;i<cesz;i++) {lop(ce,i); qp->flag=0;}
for (i=0;i<pg->cesz;i++) *pfl[i]=0;
hoc_call_func(s, 0);
cvode_fadvance(1000.0); // this call will not return
sum+=pathlen;
if (x) x[k*nb+j]=pathlen;
}
}
PATHMEASURE=0;
free(pfl);
_lpathgrps=sum/na/nb;
ENDVERBATIM
}
:* intf.getdvi() get divergence (& optionally associated vectors)
: intf.getdvi(index_vec,delay_vec[,prob_vec,wt1vec,wt2vec,distalsyns,wgain]) -- need both wt1vec and wt2vec
: index = postsynaptic IDs, delay = delay, prob = probability of firing, wt1/wt2 are base weights,
: distalsyns=distal/prox synapse,wgain is multiplier from plasticity/learning
: other forms of this function call:
: intf.getdvi(getactive.flag,vecs) with flag==1 return types instead of ids
: intf.getdvi(getactive.flag,vecs) with flag==2 then sum up number of each type
: intf.getdvi(getactive.flag,vecs) with flag==3 return column instead of ids
: with getactive flag ignores pruned connections ie 1.2 is getactive==1 and flag==2
FUNCTION getdvi () {
VERBATIM
{
int i,j,k,iarg,av1,a2,a3,a4,a6,a7,dvt,getactive=0,idx=0,*pact,prty,poty,sy,ii;
double *dbs, *x,*x1,*x2,*x3,*x4,*x5,*x6,*x7,idty,y[2],flag;
IvocVect* voi, *voi2,*voi3; Point_process **das;
ip=IDP; pg=ip->pg;
getactive=a2=a3=a4=0;
if (ip->dead) return 0.0;
dvt=ip->dvt;
dbs=ip->del; das=ip->dvi;
_lgetdvi=(double)dvt;
if (!ifarg(1)) return _lgetdvi; // just return the divergence value
iarg=1;
if (hoc_is_double_arg(iarg)) {
av1=2;
flag=*getarg(iarg++);
getactive=(int)flag;
flag-=(double)getactive; // flag is in the decimal place 1.2 has flag of 2
if (flag!=0) flag=floor(flag*10+hoc_epsilon); // avoid roundoff error
} else av1=1; // 1st vector arg
//just get active postsynapses (not dead and non pruned)
voi=vector_arg(iarg++);
if (flag==2) { x1=vector_newsize(voi,CTYPi); for (i=0;i<CTYPi;i++) x1[i]=0;
} else x1=vector_newsize(voi,dvt);
if (ifarg(iarg)) { voi=vector_arg(iarg++); x2=vector_newsize(voi,dvt); a2=1; }
if (ifarg(iarg)) { voi=vector_arg(iarg++); x3=vector_newsize(voi,dvt); a3=1;}
if (ifarg(iarg)) { // need 2 weight vecs for AM/NM or GA/GB
voi=vector_arg(iarg++); x4=vector_newsize(voi,dvt); a4=1;
voi=vector_arg(iarg++); x5=vector_newsize(voi,dvt);
}//for prox vs dist syn vec
if (ifarg(iarg)) { voi=vector_arg(iarg++); x6=vector_newsize(voi,dvt); a6=1;} else a6=0;
if (ifarg(iarg)) { voi=vector_arg(iarg++); x7=vector_newsize(voi,dvt); a7=1;} else a7=0;//plasticity wgain
idty=(double)(FOFFSET+ip->id)+1e-2*(double)ip->type+1e-3*(double)ip->inhib+1e-4;
prty=ip->type; sy=ip->inhib?GA:AM;
for (i=0,j=0;i<dvt;i++) {
qp = id0ptr(das[i]->_prop); // #define sop *_ppvar[2].pval
if (getactive && (qp->dead || ip->sprob[i]==0)) continue;
if (flag==1) { x1[j]=(double)qp->type;
} else if (flag==2) { x1[qp->type]++;
} else if (flag==3) { x1[j]=(double)qp->col;
} else x1[j]=(double)qp->id;
if (a2) x2[j]=dbs[i];
if (a3) x3[j]=(double)ip->sprob[i];
if (a4) {
if(ip->inhib){sy=ip->syns[i]?GA2:GA;} else {sy=ip->syns[i]?AM2:AM;}
poty = qp->type;
if(wsetting==1) { // non-wmat weights
y[0]=ip->syw1[i]; y[1]=ip->syw2[i];
} else {
if (seadsetting==2 || seadsetting==3) { // no randomization [or plasticity (also no randomization)]
for(ii=0;ii<2;ii++) y[ii]=WMAT(prty,poty,sy+ii)*WD0(prty,poty,sy+ii);
} else {
if (seadsetting==1) { // old sead setting
sead=(unsigned int)(FOFFSET+ip->id)*qp->id*seedstep;
} else { // hashed sead setting
hsh[0]=(double)(FOFFSET+ip->id); hsh[1]=(double)(qp->id); hsh[2]=seedstep;
sead=hashseed2(3, hsh);
}
mcell_ran4(&sead, y, 2, 1.);
for(ii=0;ii<2;ii++) {
y[ii]=2*WVAR*(y[ii]+0.5/WVAR-0.5)*WMAT(prty,poty,sy+ii)*WD0(prty,poty,sy+ii); }
}
}
x4[j]=y[0]; x5[j]=y[1];
}
if (a6) x6[j] = ip->syns[i]; // distal / prox syns
if (a7 && ip->wgain)x7[j]=ip->wgain[i];//weight gain from plasticity (stored separately from starting weight)
j++;
}
if (flag!=2 && j!=dvt) for (i=av1;i<iarg;i++) vector_resize(vector_arg(i),j);
_lgetdvi=(double)j;
}
ENDVERBATIM
}
: intf.getconv(getactive.flag,vecs) with flag==1 return types instead of ids
: flags getactive.flag flag==2 then sum up number of each type
FUNCTION getconv () {
VERBATIM
{
int iarg,i,j,k,dvt,sz,prfl,getactive; double *x,flag;
IvocVect* voi; Point_process **das; id0 *pp;
ip=IDP; pg=ip->pg; // this should only be called after jitcondiv()
sz=ip->dvt; // // assume conv similar to div
getactive=0;
if (ifarg(iarg=1) && hoc_is_double_arg(iarg)) {
flag=*getarg(iarg++);
getactive=(int)flag;
flag-=(double)getactive; // flag is in the decimal place 1.2 has flag of 2
if (flag!=0) flag=floor(flag*10+hoc_epsilon);
}
if (!ifarg(iarg)) prfl=0; else { prfl=1;
voi=vector_arg(iarg);
if (flag==2.) { x=vector_newsize(voi,CTYPi); for (i=0;i<CTYPi;i++) x[i]=0;
} else x=vector_newsize(voi,sz);
}
for (i=0,k=0; i<pg->cesz; i++) {
lop(pg->ce,i);
if (getactive && qp->dead) continue;
dvt=qp->dvt; das=qp->dvi;
for (j=0;j<dvt;j++) {
if (getactive && qp->sprob[j]==0) continue;
if (ip == id0ptr(das[j]->_prop)) {
if (prfl) {
if (flag!=2.0 && k>=sz) x=vector_newsize(voi,sz*=2);
if (flag==1.0) { x[k]=(double)qp->type;
} else if (flag==2.0) { x[qp->type]++;
} else x[k]=(double)qp->id;
}
k++;
break;
}
}
}
if (prfl && flag!=2) vector_resize(voi,k);
_lgetconv=(double)k;
}
ENDVERBATIM
}
: INTF6[0].adjlist(List,[startid,endid,exonly])
: returns adjacency list in first arg
: startid == optional 2nd arg specifies id from which to start
: endid == optional 3rd arg specifies id to end with
: exonly == optional 4th arg specifies to only store excitatory synapse information
FUNCTION adjlist () {
VERBATIM
Object* pList = *hoc_objgetarg(1);
ip=IDP; pg=ip->pg;
int iListSz=ivoc_list_count(pList),iCell,iStartID=ifarg(2)?*getarg(2):0,\
iEndID=ifarg(3)?*getarg(3):pg->cesz-1;
int skipinhib = ifarg(4)?*getarg(4):0, i,j,nv,*pused=(int*)calloc(pg->cesz,sizeof(int)),iSyns=0;
double **vvo = (double**)malloc(sizeof(double*)*iListSz),\
*psyns=(double*)calloc(pg->cesz,sizeof(double));
id0* rp;
for(iCell=iStartID;iCell<=iEndID;iCell++){
if(verbose && iCell%1000==0) printf("%d ",iCell);
lop(pg->ce,iCell);
if(!qp->dvt || (skipinhib && qp->inhib)){
list_vector_resize(pList,iCell,0);
continue;
}
iSyns=0;
for(j=0;j<qp->dvt;j++){
rp = id0ptr(qp->dvi[j]->_prop); // #define sop *_ppvar[2].pval
if(skipinhib && rp->inhib) continue; // if skip inhib cells...
if(!rp->dead && qp->sprob[j]>0. && !pused[rp->id]){
pused[rp->id]=1;
psyns[iSyns++]=rp->id;
}
}
list_vector_resize(pList, iCell, iSyns);
list_vector_px(pList, iCell, &vvo[iCell]);
memcpy(vvo[iCell],psyns,sizeof(double)*iSyns);
for(j=0;j<iSyns;j++)pused[(int)psyns[j]]=0;
}
free(vvo); free(pused); free(psyns);
if (verbose) printf("\n");
return 1.0;
ENDVERBATIM
}
FUNCTION rddvi () {
VERBATIM
Point_process *pnnt;
FILE* fp;
int i, iCell;
unsigned int iOutID;
Object* lb;
fp=hoc_obj_file_arg(1);
ip=IDP; pg=ip->pg;
printf("reading: ");
for(iCell=0;iCell<pg->cesz;iCell++){
if(iCell%1000==0)printf("%d ",iCell);
lop(pg->ce,iCell);
int ret;
ret = fread(&qp->id,sizeof(unsigned int),1,fp); // read id
ret = fread(&qp->type,sizeof(unsigned char),1,fp); // read type id
ret = fread(&qp->col,sizeof(unsigned int),1,fp); // read column id
ret = fread(&qp->dead,sizeof(unsigned char),1,fp); // read alive/dead status
ret = fread(&qp->dvt,sizeof(unsigned int),1,fp); // read divergence size
//free up old pointers
if(qp->del){ free(qp->del); free(qp->dvi); free(qp->sprob);
qp->dvt=0; qp->dvi=(Point_process**)0x0; qp->del=(double*)0x0; qp->sprob=(unsigned char *)0x0; }
//if divergence == 0 , continue
if(!qp->dvt) continue;
qp->dvi = (Point_process**)malloc(sizeof(Point_process*)*qp->dvt);
for(i=0;i<qp->dvt;i++){
ret = fread(&iOutID,sizeof(unsigned int),1,fp); // id of output cell
if (!(lb=ivoc_list_item(pg->ce,iOutID))) {
printf("INTF6:callback %d exceeds %d for list ce\n",iOutID,pg->cesz); hxe(); }
qp->dvi[i]=(Point_process *)lb->u.this_pointer;
}
qp->del = (double*)malloc(sizeof(double)*qp->dvt);
ret = fread(qp->del,sizeof(double),qp->dvt,fp); // read divergence delays
qp->sprob = (unsigned char*)malloc(sizeof(unsigned char)*qp->dvt);
ret = fread(qp->sprob,sizeof(unsigned char),qp->dvt,fp); // read divergence firing probabilities
}
printf("\n");
return 1.0;
ENDVERBATIM
}
FUNCTION svdvi () {
VERBATIM
Point_process *pnnt;
FILE* fp;
int i , iCell;
fp=hoc_obj_file_arg(1);
ip=IDP; pg=ip->pg;
printf("writing: ");
for(iCell=0;iCell<pg->cesz;iCell++){
if(iCell%1000==0)printf("%d ",iCell);
lop(pg->ce,iCell);
fwrite(&qp->id,sizeof(unsigned int),1,fp); // write id
fwrite(&qp->type,sizeof(unsigned char),1,fp); // write type id
fwrite(&qp->col,sizeof(unsigned int),1,fp); // write column id
fwrite(&qp->dead,sizeof(unsigned char),1,fp); // write alive/dead status
fwrite(&qp->dvt,sizeof(unsigned int),1,fp); // write divergence size
if(!qp->dvt)continue; //don't write empty pointers if no divergence
for(i=0;i<qp->dvt;i++){
pnnt=qp->dvi[i];
fwrite(&(id0ptr(pnnt->_prop)->id), sizeof(unsigned int), 1, fp); // id of output cell
}
fwrite(qp->del,sizeof(double),qp->dvt,fp); // write divergence delays
fwrite(qp->sprob,sizeof(unsigned char),qp->dvt,fp); // write divergence firing probabilities
}
printf("\n");
return 1.0;
ENDVERBATIM
}
: INTF6[0].setdvir(wiringlist,delaylist[,flag]) // flag default is 0 to pass to setdvi2()
: INTF6[0].setdvir(wiringlist,delaylist,startid,endid)
: INTF6[0].setdvir(wiringlist,delaylist,startid,endid,flag)
: INTF6[0].setdvir(wiringlist,delaylist,idvec,flag)
: should either use just with flag == 0 to setup all dvi outputs of cells
: or with flag == 1 to incrementally setup outputs from cells and on the last
: set of outputs from a range of cells call with flag == 2 to setup sprob and sort dvi list
: alternatively, can call setdvir with flag == 1, and at end just call INTF6.finishdvir to finalize
FUNCTION setdvir () {
VERBATIM
ListVec* pListWires,*pListDels;
int i,dn,flag,dvt,idvfl,iCell,iStartID,iEndID,nidv,end;
double *y, *d, *idvec; unsigned char pdead;
ip=IDP; pg=ip->pg;
pListWires = AllocListVec(*hoc_objgetarg(1));
idvfl=flag=0; iStartID=0; iEndID=pg->cesz-1;
if(!pListWires){printf("setalldvi ERRA: problem initializing wires list arg!\n"); hxe();}
pListDels = AllocListVec(*hoc_objgetarg(2));
if(!pListDels){ printf("setalldvi ERRA: problem initializing delays list arg!\n");
FreeListVec(&pListWires); hxe(); }
if (ifarg(3) && !ifarg(4)) {
flag=(int)*getarg(3);
} else if (hoc_is_double_arg(3)) {
iStartID=(int)*getarg(3);
iEndID = (int)*getarg(4);
if(ifarg(5)) flag=(int)*getarg(5);
} else {
nidv=vector_arg_px(3, &idvec);
idvfl=1;
if (ifarg(4)) flag=(int)*getarg(4);
}
end=idvfl?nidv:(iEndID-iStartID+1);
for (i=0;i<end;i++) {
if(i%1000==0) printf("%d",i/1000);
iCell=idvfl?idvec[i]:(iStartID+i);
lop(pg->ce,iCell);
if (qp->dead) continue;
y=pListWires->pv[i]; dvt=pListWires->plen[i];
if(!dvt) continue; //skip empty div lists
d=pListDels->pv[i]; dn=pListDels->plen[i];
if (dn!=dvt) {printf("setdvir() ERR vec sizes for wire,delay list entries not equal %d: %d %d\n",i,dvt,dn); hxe();}
setdvi2(y,d,0x0,dvt,flag,0x0,0x0);
}
FreeListVec(&pListWires);
FreeListVec(&pListDels);
return 1.0;
ENDVERBATIM
}
PROCEDURE clrdvi () {
VERBATIM
int i;
ip=IDP; pg=ip->pg;
for (i=0;i<pg->cesz;i++) {
lop(pg->ce,i);
if (qp->dvt!=0x0) {
free(qp->dvi); free(qp->del); free(qp->sprob);
qp->dvt=0; qp->dvi=(Point_process**)0x0; qp->del=(double*)0x0; qp->sprob=(unsigned char *)0x0;
if(wsetting==1) freesywv(qp);
}
}
ENDVERBATIM
}
: int.setdviv(prevec,postvec,delvec,distal,wt1,wt2)
PROCEDURE setdviv () {
VERBATIM
int i,j,k,l,nprv,dvt,*scr; double *prv,*pov,*dlv,x,*ds,*w1,*w2; char* s;
ip=IDP; pg=ip->pg;
nprv=vector_arg_px(1, &prv);
i=vector_arg_px(2, &pov);
j=vector_arg_px(3, &dlv);
if(ifarg(4)) { s=(char*)calloc((l=vector_arg_px(4,&ds)),sizeof(char)); for(k=0;k<l;k++) s[k]=ds[k]; k=0;
} else s=0x0;
if (nprv!=i || i!=j || j!=l) {printf("intf:setdviv ERRA: %d %d %d %d\n",nprv,i,j,l); hxe();}
if (wsetting==1) {
i=vector_arg_px(5, &w1);
j=vector_arg_px(6, &w2);
if (nprv!=i || i!=j) {printf("intf:setdviv ERRB: %d %d %d\n",nprv,i,j); hxe();}
}
// start by counting the prids so will know the size that we need for realloc()
scr=(int *)ecalloc(pg->cesz, sizeof(int));
for (i=0;i<pg->cesz;i++) scr[i]=0;
for (i=0,j=-1;i<nprv;i++) {
if ((int)prv[i]<j) { printf("intf:setdviv ERRC vecs should be sorted by prid vec\n");hxe(); }
j=(int)prv[i];
scr[j]++;
}
if (ip->dbx>1) for (i=0;i<pg->cesz;i++) printf("%d ",scr[i]);
for (i=-1,k=0;k<nprv;k+=dvt) { if(i%1000==0) printf(".");
if ((int)prv[k]==i) {printf("intf:setdviv ERRD number repeated %g %d %d\n",prv[k],i,k);hxe();}
i=(int)prv[k]; // index for presyn cell
lop(pg->ce,i); // set the container to that cell
dvt=scr[i]; // the number of postsyns for that
if (ip->dbx>0) printf("DBA:%d,%d,%d ",i,dvt,k);
if (qp->dead) continue;
if (dvt>0) {
if (wsetting==1) {
setdvi3(pov+k,dlv+k,s+k,dvt,w1+k,w2+k); // no flag -- will just replace the divergence list
} else {
setdvi2(pov+k,dlv+k,s?s+k:0x0,dvt,1,0x0,0x0);
}
}
}
if(s) free(s);
ENDVERBATIM
}
VERBATIM
void setupsywv (id0* p, int sz) {
p->syw1 = p->syw1!=0x0 ? (double*) realloc((double*) p->syw1, sz*sizeof(double)) :
(double*) calloc(sz,sizeof(double));
p->syw2 = p->syw2!=0x0 ? (double*) realloc((double*) p->syw2, sz*sizeof(double)) :
(double*) calloc(sz,sizeof(double));
}
//void myfree(void** p) {
// int* ip;
// if(p[0]) free(p[0]);
// ip = (int*) p[0];
// ip = 0x0;
//}
void freesywv (id0* p) {
if(p->syw1) free(p->syw1); p->syw1=0x0;
if(p->syw2) free(p->syw2); p->syw2=0x0;
}
ENDVERBATIM
: intf.setsywv(weight vector 1, weight vector 2)
FUNCTION setsywv () {
VERBATIM
int sz,n1,n2; double *psyw1,*psyw2; id0* ip;
ip=IDP; pg=ip->pg; sz=ip->dvt;
if((n1=vector_arg_px(1, &psyw1))!=sz || (n2=vector_arg_px(2, &psyw2))!=sz) {
printf("setsywv ERRA: make sure weight vector sizes (%d,%d) same size as div(%d)\n",n1,n2,sz);
return 0.0;
}
setupsywv(ip,sz); // setup pointers
memcpy(ip->syw1,psyw1,sizeof(double)*sz); // copy
memcpy(ip->syw2,psyw2,sizeof(double)*sz);
return sz;
ENDVERBATIM
}
: intf.getsywv(weight vector 1, weight vector 2)
FUNCTION getsywv () {
VERBATIM
int sz,n1,n2; double *psyw1,*psyw2; id0* ip;
ip=IDP; pg=ip->pg; sz=ip->dvt;
if(!ip->syw1 || !ip->syw2) {
printf("getsywv ERRA: syw1,syw2 were never initialized with setsywv!\n");
return 0.0;
}
if((n1=vector_arg_px(1, &psyw1))!=sz || (n2=vector_arg_px(2, &psyw2))!=sz) {
printf("getsywv ERRB: make sure weight vector sizes (%d,%d) same size as div(%d)\n",n1,n2,sz);
return 0.0;
}
memcpy(psyw1,ip->syw1,sizeof(double)*sz); // copy
memcpy(psyw2,ip->syw2,sizeof(double)*sz);
return sz;
ENDVERBATIM
}
VERBATIM
// get presynaptic excitatory cells in a double*, psz[0] has size
int* getpeconv (id0* ip,int* psz) {
Point_process **das; int* pfrom;
int i,j,k,dvt;
*psz=ip->dvt>0?ip->dvt:16; pg=ip->pg;
pfrom=(int*) calloc(psz[0],sizeof(int));
for (i=0,k=0; i<pg->cesz; i++) {
lop(pg->ce,i);
if(qp->inhib) continue; // skip presynaptic inhib cells
dvt=qp->dvt;
das=qp->dvi;
for (j=0;j<dvt;j++) {
if (ip == id0ptr(das[j]->_prop)) {
if (k>=*psz) {
psz[0]*=2;
pfrom=(int*) realloc((void*)pfrom,psz[0]*sizeof(int));
}
pfrom[k]=qp->id;
k++;
break;
}
}
}
*psz=k;
return pfrom;
}
// get presynaptic inhibitory cells in a double*, psz[0] has size
int* getpiconv (id0* ip,int* psz) {
Point_process **das; int* pfrom;
int i,j,k,dvt;
*psz=ip->dvt>0?ip->dvt:16; pg=ip->pg;
pfrom=(int*) calloc(psz[0],sizeof(int));
for (i=0,k=0; i<pg->cesz; i++) {
lop(pg->ce,i);
if(!qp->inhib) continue; // skip presynaptic excitatory cells
dvt=qp->dvt;
das=qp->dvi;
for (j=0;j<dvt;j++) {
if (ip == id0ptr(das[j]->_prop)) {
if (k>=*psz) {
psz[0]*=2;
pfrom=(int*) realloc((void*)pfrom,psz[0]*sizeof(int));
}
pfrom[k]=qp->id;
k++;
break;
}
}
}
*psz=k;
return pfrom;
}
int myfindidx (id0* ppre,int poid) {
int i; Point_process** das; id0* ppo;
das=ppre->dvi;
for(i=0;i<ppre->dvt;i++) {
ppo = id0ptr(das[i]->_prop); // #define sop *_ppvar[2].pval
if(ppo->id==poid) return i;
}
return -1;
}
// apply dopamine eligibility trace from E->X cells
// pcell is a cell that just spiked, myspkt is time of spike
static void applyEDOPE (id0* pcell,double myspkt) {
int poid,prid,sz,i,idx; postgrp* pg; double d,inc,tmp,pinc,tau,maxw; id0* ppre, *ppo;
if(seadsetting!=3.) return; // seadsetting==3 for EDOPE, must be set before network setup
poid=pcell->id; pg=pcell->pg;
if(pcell->dbx<-1) printf("applyEDOPE: pcell=%p\n",pcell);
if (FORWELIGTR) { // if forward eligibility traces are turned on (post after pre)
for(i=0;i<pcell->econvsz;i++) {//check presynaptic E cells, if they fired within maxplastt turn on eligibility trace
prid = pcell->peconv[i]; // presynaptic id
if(pg->lastspk[prid]<0) continue; // cell didn't spike
if( (d = myspkt - pg->lastspk[prid] ) > maxplastt) continue; // time difference
if(verbose>2) printf("spk%d:%g, spk%d:%g, d=%g\n",prid,pg->lastspk[prid],poid,pg->lastspk[poid],d);
ppre = getlp(pg->ce,prid); // get pointer to presynaptic cell
idx = myfindidx(ppre,poid); // find the index of poid in ppre's div
if(idx<0){printf("**** applyEDOPE ERR: bad idx = %d!!!!!!!!!\n",idx); return;}
if( ! ( inc = ppre->pplastinc[idx] ) ) continue;
ppre->pdope[idx] = t; // store time elig. trace turned on
if(verbose>2) printf("EDOPEA:ppre->inhib=%d,pcell->inhib=%d,d=%g,tau=%g,d/tau=%g, %d->%d\n",ppre->inhib,pcell->inhib,d,tau,d/tau,prid,poid);
}
}
if (BACKELIGTR) { // if backward eligibility traces are turned on (pre after post)
if(pcell->inhib) return; // only EDOPE from E cells
for(i=0;i<pcell->dvt;i++) { // check postsynaptic targets, if they fired within maxplastt, turn on eligibility trace
ppo = id0ptr(pcell->dvi[i]->_prop); // #define sop *_ppvar[2].pval
poid = ppo->id;
if(pg->lastspk[poid]<0) continue;
if( (d = myspkt - pg->lastspk[poid] ) <= maxplastt) {
if( ! ( inc = pcell->pplastinc[i] ) ) continue;
pcell->pdope[i] = -t; // store time elig. trace turned on, -t means it was post-before-pre
if(verbose>2) printf("EDOPEB:ppo->inhib=%d,d=%g,tau=%g,d/tau=%g, %d->%d\n",ppo->inhib,d,tau,d/tau,prid,poid);
}
}
}
}
// apply dopamine eligibility trace from I->X cells
// pcell is a cell that just spiked, myspkt is time of spike
// GLC, 1/12/12 -- It's not really clear to me how eligibility traces should be
// implemented in the case of I->X connections. Until we've done more literature
// search on this, I think we should avoid using DA learning on I->X connections.
static void applyIDOPE (id0* pcell,double myspkt) {
int poid,prid,sz,i,idx; postgrp* pg; double d,inc,tmp,pinc,tau,maxw; id0* ppre, *ppo;
if(seadsetting!=3.) return; // seadsetting==3 for IDOPE, must be set before network setup
poid=pcell->id; pg=pcell->pg;
if(pcell->dbx<-1) printf("applyplast: pcell=%p\n",pcell);
if (FORWELIGTR) { // if forward eligibility traces are turned on (post after pre)
for(i=0;i<pcell->iconvsz;i++) {//check presynaptic I cells, if they fired earlier, depress synapse
prid = pcell->piconv[i]; // presynaptic id
if(pg->lastspk[prid]<0) continue; // cell didn't spike
if( (d = myspkt - pg->lastspk[prid] ) > maxplastt) continue; // time difference
if(verbose>2) printf("spk%d:%g, spk%d:%g, d=%g\n",prid,pg->lastspk[prid],poid,pg->lastspk[poid],d);
ppre = getlp(pg->ce,prid); // get pointer to presynaptic cell
idx = myfindidx(ppre,poid); // find the index of poid in ppre's div
if(idx<0){printf("**** applyISSTDP ERR: bad idx = %d!!!!!!!!!\n",idx); return;}
if( ! ( inc = ppre->pplastinc[idx] ) ) continue;
ppre->pdope[idx] = t; // store time elig. trace turned on
if(verbose>2) printf("IDOPEA:ppre->inhib=%d,pcell->inhib=%d,d=%g,tau=%g,d/tau=%g, %d->%d\n",ppre->inhib,pcell->inhib,d,tau,d/tau,prid,poid);
}
}
if(BACKELIGTR) { // if backward eligibility traces are turned on (pre after post)
if(!pcell->inhib) return; // IDOPE only from I cells
for(i=0;i<pcell->dvt;i++) { // check postsynaptic targets, if within maxplastt,
ppo = id0ptr(pcell->dvi[i]->_prop); // #define sop *_ppvar[2].pval
poid = ppo->id;
if(pg->lastspk[poid]<0) continue;
if( (d = myspkt - pg->lastspk[poid] ) <= maxplastt) {
if( ! ( inc = pcell->pplastinc[i] ) ) continue;
pcell->pdope[i] = -t; // store time elig. trace turned on, -t means it was post-before-pre
if(verbose>2) printf("IDOPEB:ppo->inhib=%d,d=%g,tau=%g,d/tau=%g, %d->%d\n",ppo->inhib,d,tau,d/tau,prid,poid);
}
}
}
}
// apply plasticity from E->X cells
// pcell is a cell that just spiked, myspkt is time of spike
static void applyEXSTDP (id0* pcell,double myspkt) {
int poid,prid,sz,i,idx; postgrp* pg; double d,inc,tmp,pinc,tau,maxw; id0* ppre, *ppo;
if(seadsetting!=3.) return; // seadsetting==3 for STDP, must be set before network setup
poid=pcell->id; pg=pcell->pg;
if(pcell->dbx<-1) printf("applyEXSTDP: pcell=%p\n",pcell);
for(i=0;i<pcell->econvsz;i++) {//check presynaptic E cells, if they fired earlier, potentiate synapse
prid = pcell->peconv[i]; // presynaptic id
if(pg->lastspk[prid]<0) continue; // cell didn't spike
if( (d = myspkt - pg->lastspk[prid] ) > maxplastt) continue; // time difference
if(verbose>2) printf("spk%d:%g, spk%d:%g, d=%g\n",prid,pg->lastspk[prid],poid,pg->lastspk[poid],d);
ppre = getlp(pg->ce,prid); // get pointer to presynaptic cell
idx = myfindidx(ppre,poid); // find the index of poid in ppre's div
if(idx<0){printf("**** applyEXSTDP ERR: bad idx = %d!!!!!!!!!\n",idx); return;}
if( ! ( inc = ppre->pplastinc[idx] ) ) continue;
tau = ppre->pplasttau[idx];
maxw = ppre->pplastmaxw[idx];
tmp = ppre->wgain[idx]; // temp - holds original wgain level
if(SOFTSTDP) inc *= (1.0 - tmp / maxw); // soft bound for potentiation
ppre->wgain[idx] += EPOTW * inc * exp( -d / tau ); // increment the wgain of the synapse
if(ppre->wgain[idx]<0.) ppre->wgain[idx]=0.; // check bounds of wgain
else if(!SOFTSTDP && ppre->wgain[idx]>maxw) ppre->wgain[idx]=maxw;
if(verbose>2) printf("PLAST:ppre->inhib=%d,pcell->inhib=%d,d=%g,tau=%g,d/tau=%g, %d->%d: inc=%g, wgA=%g, wgB=%g\n",ppre->inhib,pcell->inhib,d,tau,d/tau,prid,poid,inc,tmp,ppre->wgain[idx]);
}
if(pcell->inhib) return; // only STDP from E cells
for(i=0;i<pcell->dvt;i++) { // check postsynaptic targets, if they fired earlier, depress the synapse
ppo = id0ptr(pcell->dvi[i]->_prop); // #define sop *_ppvar[2].pval
poid = ppo->id;
if(pg->lastspk[poid]<0) continue;
if( (d = myspkt - pg->lastspk[poid] ) < maxplastt) {
if( ! ( inc = pcell->pplastinc[i] ) ) continue;
tau = pcell->pplasttau[i];
maxw = pcell->pplastmaxw[i];
tmp = pcell->wgain[i]; // temp - holds original wgain level
if(SOFTSTDP) inc *= (tmp / maxw); // soft bound for depression
pcell->wgain[i] -= EDEPW * inc * exp( -d / tau ); // increment the wgain of the synapse
if(pcell->wgain[i]<0.) pcell->wgain[i]=0.; // check bounds of wgain
else if(!SOFTSTDP && pcell->wgain[i]>maxw) pcell->wgain[i]=maxw;
if(verbose>2) printf("DEP:ppo->inhib=%d,d=%g,tau=%g,d/tau=%g, %d->%d: inc=%g, wgA=%g, wgB=%g\n",ppo->inhib,d,tau,d/tau,prid,poid,inc,tmp,pcell->wgain[i]);
}
}
}
// apply plasticity from I->X cells
// pcell is a cell that just spiked, myspkt is time of spike
static void applyIXSTDP (id0* pcell,double myspkt) {
int poid,prid,sz,i,idx; postgrp* pg; double d,inc,tmp,pinc,tau,maxw; id0* ppre, *ppo;
if(seadsetting!=3.) return; // seadsetting==3 for STDP, must be set before network setup
poid=pcell->id; pg=pcell->pg;
if(pcell->dbx<-1) printf("applyplast: pcell=%p\n",pcell);
for(i=0;i<pcell->iconvsz;i++) {//check presynaptic I cells, if they fired earlier, depress synapse
prid = pcell->piconv[i]; // presynaptic id
if(pg->lastspk[prid]<0) continue; // cell didn't spike
if( (d = myspkt - pg->lastspk[prid] ) > maxplastt) continue; // time difference
if(verbose>2) printf("spk%d:%g, spk%d:%g, d=%g\n",prid,pg->lastspk[prid],poid,pg->lastspk[poid],d);
ppre = getlp(pg->ce,prid); // get pointer to presynaptic cell
idx = myfindidx(ppre,poid); // find the index of poid in ppre's div
if(idx<0){printf("**** applyISSTDP ERR: bad idx = %d!!!!!!!!!\n",idx); return;}
if( ! ( inc = ppre->pplastinc[idx] ) ) continue;
tau = ppre->pplasttau[idx];
maxw = ppre->pplastmaxw[idx];
tmp = ppre->wgain[idx]; // temp - holds original wgain level
if(SOFTSTDP) inc *= (tmp / maxw); // soft bound for depression
ppre->wgain[idx] -= IDEPW * inc * exp( -d / tau ); // increment the wgain of the synapse
if(ppre->wgain[idx]<0.) ppre->wgain[idx]=0.; // check bounds of wgain
else if(!SOFTSTDP && ppre->wgain[idx]>maxw) ppre->wgain[idx]=maxw;
if(verbose>2) printf("DEP:ppre->inhib=%d,pcell->inhib=%d,d=%g,tau=%g,d/tau=%g, %d->%d: inc=%g, wgA=%g, wgB=%g\n",ppre->inhib,pcell->inhib,d,tau,d/tau,prid,poid,inc,tmp,ppre->wgain[idx]);
}
if(!pcell->inhib) return; // this STDP only from I cells
for(i=0;i<pcell->dvt;i++) { // check postsynaptic targets, if they fired earlier, potentiate the synapse
ppo = id0ptr(pcell->dvi[i]->_prop); // #define sop *_ppvar[2].pval
poid = ppo->id;
if(pg->lastspk[poid]<0) continue;
if( (d = myspkt - pg->lastspk[poid] ) < maxplastt) {
if( ! ( inc = pcell->pplastinc[i] ) ) continue;
tau = pcell->pplasttau[i];
maxw = pcell->pplastmaxw[i];
tmp = pcell->wgain[i]; // temp - holds original wgain level
if(SOFTSTDP) inc *= (1.0 - tmp / maxw); // soft bound for potentiation
pcell->wgain[i] += IPOTW * inc * exp( -d / tau ); // increment the wgain of the synapse
if(pcell->wgain[i]<0.) pcell->wgain[i]=0.; // check bounds of wgain
else if(!SOFTSTDP && pcell->wgain[i]>maxw) pcell->wgain[i]=maxw;
if(verbose>2) printf("PLAST:ppo->inhib=%d,d=%g,tau=%g,d/tau=%g, %d->%d: inc=%g, wgA=%g, wgB=%g\n",ppo->inhib,d,tau,d/tau,prid,poid,inc,tmp,pcell->wgain[i]);
}
}
}
ENDVERBATIM
: intf.geteconv(vec) - get presynaptic E cell IDs
FUNCTION geteconv () {
VERBATIM
int i; double *x; IvocVect *voi;
ip=IDP; pg=ip->pg;
if(!ip->peconv) ip->peconv=getpeconv(ip,&ip->econvsz);
voi=vector_arg(1);
x=vector_newsize(voi,ip->econvsz);
for(i=0;i<ip->econvsz;i++) x[i]=(double)ip->peconv[i];
return ip->econvsz;
ENDVERBATIM
}
: intf.geticonv(vec) - get presynaptic I cell IDs
FUNCTION geticonv () {
VERBATIM
int i; double *x; IvocVect *voi;
ip=IDP; pg=ip->pg;
if(!ip->piconv) ip->piconv=getpiconv(ip,&ip->iconvsz);
voi=vector_arg(1);
x=vector_newsize(voi,ip->iconvsz);
for(i=0;i<ip->iconvsz;i++) x[i]=(double)ip->piconv[i];
return ip->iconvsz;
ENDVERBATIM
}
: finishdvi2 () -- finalize dvi , sort dvi , allocate and set sprob
VERBATIM
static void finishdvi2 (struct ID0* p) {
Point_process **da,**das;
double *db,*dbs,*w1,*w1s,*w2,*w2s;
char *syns,*synss;
int i, dvt;
db=p->del;
da=p->dvi;
dvt=p->dvt;
syns=p->syns;
dbs=(double*)malloc(dvt*sizeof(double)); // sorted delays
das=(Point_process**)malloc(dvt*sizeof(Point_process*)); // parallel sorted dvi
synss=(char*)malloc(dvt*sizeof(char)); // sorted syns
if(wsetting==1 && p->syw1 && p->syw2) {
w1=p->syw1;
w2=p->syw2;
w1s=(double*)malloc(dvt*sizeof(double)); //mem for sorted weights
w2s=(double*)malloc(dvt*sizeof(double));
gsort5(db,da,syns,w1,w2,dvt,dbs,das,synss,w1s,w2s); //sort it all
p->syw1=w1s; p->syw2=w2s; //sorted weights
free(w1); free(w2); // free old ones
} else gsort3(db,da,syns,dvt,dbs,das,synss);
p->del=dbs; p->dvi=das; p->syns=synss;// sorted versions
free(db); free(da); free(syns); // free old mem
p->sprob=(unsigned char*)realloc((void*)p->sprob,(size_t)dvt*sizeof(char));// release probability
for (i=0;i<dvt;i++) p->sprob[i]=1; // start out with all firing
p->wgain=(double*)realloc((void*)p->wgain,(size_t)dvt*sizeof(double));//synaptic weight gain
for (i=0;i<dvt;i++) p->wgain[i]=1.0; // start out at wmat level
p->peconv = getpeconv(p,&p->econvsz); // get econv
p->piconv = getpiconv(p,&p->iconvsz); // get iconv
if(seadsetting==3) {
p->pplasttau = (double*)realloc((void*)p->pplasttau,(size_t)dvt*sizeof(double));
p->pplastinc = (double*)realloc((void*)p->pplastinc,(size_t)dvt*sizeof(double));
p->pplastmaxw = (double*)realloc((void*)p->pplastmaxw,(size_t)dvt*sizeof(double));
if(DOPE) p->pdope = (double*)realloc((void*)p->pdope,(size_t)dvt*sizeof(double));
}
}
ENDVERBATIM
: finalize dvi for all cells
PROCEDURE finishdvir () {
VERBATIM
int iCell;
ip=IDP; pg=ip->pg;
for(iCell=0;iCell<pg->cesz;iCell++){
lop(pg->ce,iCell);
finishdvi2(qp);
}
ENDVERBATIM
}
: finishdvi() -- finalize dvi , sort dvi, allocate and set sprob, for this single cell
PROCEDURE finishdvi () {
VERBATIM
finishdvi2(IDP);
ENDVERBATIM
}
: intf.setplast(vwgain,vplasttau,vplastinc,vplastmaxw)
: seadsetting must be 3, vectors must have same size as dvi
FUNCTION setplast () {
VERBATIM
double *wgain,*pplasttau,*pplastinc,*pplastmaxw;
if(seadsetting!=3) {printf("setplast ERR0: seadsetting must be 3, plast mode off!\n"); return 0;}
ip=IDP; pg=ip->pg;
if(vector_arg_px(1,&wgain) != ip->dvt ||
vector_arg_px(2,&pplasttau) != ip->dvt ||
vector_arg_px(3,&pplastinc) != ip->dvt ||
vector_arg_px(4,&pplastmaxw) != ip->dvt) {printf("setplast ERR1: input vectors must have size %d!\n",ip->dvt); return 0;}
memcpy(ip->wgain,wgain,sizeof(double)*ip->dvt);
memcpy(ip->pplasttau,pplasttau,sizeof(double)*ip->dvt);
memcpy(ip->pplastinc,pplastinc,sizeof(double)*ip->dvt);
memcpy(ip->pplastmaxw,pplastmaxw,sizeof(double)*ip->dvt);
return 0.0;
ENDVERBATIM
}
: intf.getplast(vwgain,vplasttau,vplastinc,vplastmaxw)
: seadsetting must be 3, vectors must have same size as dvi
FUNCTION getplast () {
VERBATIM
double *wgain,*pplasttau,*pplastinc,*pplastmaxw;
if(seadsetting!=3) {printf("getplast ERR0: seadsetting must be 3, plast mode off!\n"); return 0;}
ip=IDP; pg=ip->pg;
ip=IDP; pg=ip->pg;
if(vector_arg_px(1,&wgain) != ip->dvt ||
vector_arg_px(2,&pplasttau) != ip->dvt ||
vector_arg_px(3,&pplastinc) != ip->dvt ||
vector_arg_px(4,&pplastmaxw) != ip->dvt) {printf("getplast ERR1: output vectors must have size %d!\n",ip->dvt); return 0;}
memcpy(wgain,ip->wgain,sizeof(double)*ip->dvt);
memcpy(pplasttau,ip->pplasttau,sizeof(double)*ip->dvt);
memcpy(pplastinc,ip->pplastinc,sizeof(double)*ip->dvt);
memcpy(pplastmaxw,ip->pplastmaxw,sizeof(double)*ip->dvt);
return 1.0;
ENDVERBATIM
}
: setdvi(cell#s,dels[,dist,flag,w1,w2]) flag 1: grow internal vecs; flag 2: grow and do final sort
: w1,w2 are weight vectors -- i.e. for AM2,NM2. should only be used when wsetting==1
PROCEDURE setdvi () {
VERBATIM {
int i,j,k,dvt,flag; double *d, *y, *ds, *w1, *w2; char* s;
if (! ifarg(1)) {printf("setdvi(v1,v2[,v3,flag]): v1:cell#s; v2:delays; v3:distal synapses\n"); return 0; }
ip=IDP; pg=ip->pg; // this should only be called after jitcondiv()
if (ip->dead) return 0;
dvt=vector_arg_px(1, &y);
i=vector_arg_px(2, &d);
s=ifarg(3)?(char*)calloc((j=vector_arg_px(3,&ds)),sizeof(char)):0x0;
if(s) for(k=0;k<j;k++) s[k]=(char)ds[k];
if (ifarg(4)) flag=(int)*getarg(4); else flag=0;
if (i!=dvt || i==0 || (j>0 && j!=i)) {printf("setdvi() ERR vec sizes: %d %d %d\n",dvt,i,j); hxe();}
w1=w2=0x0;
if(ifarg(5) && wsetting!=1){printf("setdvi ERR: only use weight vecs when wsetting==1!\n"); hxe();}
if(ifarg(5) && dvt!=vector_arg_px(5,&w1)){printf("setdvi ERR: wrong size for w1 vector!\n"); hxe();}
if(ifarg(6) && dvt!=vector_arg_px(6,&w2)){printf("setdvi ERR: wrong size for w2 vector!\n"); hxe();}
setdvi2(y,d,s,dvt,flag,w1,w2);
}
return 0;
ENDVERBATIM
}
VERBATIM
// setdvi2(divid_vec,del_vec,syns_vec,div_cnt,flag,w1,w2)
// flag 1 means just augment, 0or2: sort by del, 0: clear lists and replace
static void setdvi2 (double *y,double *d,char* s,int dvt,int flag,double* w1,double* w2) {
int i,j,ddvi; double *db, *dbs, *w1s, *w2s; unsigned char pdead; unsigned int b,e; char* syns;
Object *lb; Point_process *pnnt, **da, **das;
ddvi=(int)DEAD_DIV;
ip=IDP; pg=ip->pg;
if(wsetting==1 && (!w1 || !w2)) {
printf("setdvi2 ERR: wsetting==1, must provide w1,w2 arrays!\n");
hxe();
}
if (flag==0) { b=0; e=dvt; // begin to end
if (ip->dvi) {
free(ip->dvi); free(ip->del); free(ip->sprob); free(ip->syns);
ip->dvt=0; ip->dvi=(Point_process**)0x0; ip->del=(double*)0x0; ip->sprob=(unsigned char *)0x0; ip->syns=(char*)0x0;
if(ip->wgain){free(ip->wgain); ip->wgain=0x0;}
if(ip->peconv){free(ip->peconv); ip->peconv=0x0;}
if(ip->piconv){free(ip->piconv); ip->piconv=0x0;}
if(ip->pplasttau){free(ip->pplasttau);ip->pplasttau=0x0;}
if(ip->pplastinc){free(ip->pplastinc);ip->pplastinc=0x0;}
if(ip->pplastmaxw){free(ip->pplastmaxw);ip->pplastmaxw=0x0;}
if(ip->pdope){free(ip->pdope);ip->pdope=0x0;}
if(wsetting==1) freesywv(ip);
} // make sure all null pointers for realloc
} else {
if (ip->dvt==0) {
ip->dvi=(Point_process**)0x0; ip->del=(double*)0x0; ip->sprob=(unsigned char *)0x0; ip->syns=(char*)0x0;
ip->wgain=0x0; ip->peconv=0x0; ip->piconv=0x0;
ip->pplasttau=0x0; ip->pplastinc=0x0; ip->pplastmaxw=0x0; ip->pdope=0x0;
if(wsetting==1) freesywv(ip);
}
b=ip->dvt;
e=ip->dvt+dvt; // dvt is amount to grow
}
da=(Point_process **)realloc((void*)ip->dvi,(size_t)(e*sizeof(Point_process *)));
db=(double*)realloc((void*)ip->del,(size_t)(e*sizeof(double)));
syns=(char*)realloc((void*)ip->syns,(size_t)(e*sizeof(char)));
if(wsetting==1) {
w1s=(double*)realloc((void*)ip->syw1,(size_t)(e*sizeof(double)));
w2s=(double*)realloc((void*)ip->syw2,(size_t)(e*sizeof(double)));
}
for (i=b,j=0;j<dvt;j++) { // i thru da[] j thru y, k to append
// div can grow at lower rate if dead cells are encountered
if (!(lb=ivoc_list_item(pg->ce,(unsigned int)y[j]))) {
printf("INTF6:callback %g exceeds %d for list ce\n",y[j],pg->cesz); hxe(); }
pnnt=(Point_process *)lb->u.this_pointer;
if (ddvi==1 || !(pdead = id0ptr(pnnt->_prop)->dead)) {
da[i]=pnnt; db[i]=d[j]; syns[i]=s?s[j]:0;
if(wsetting==1){w1s[i]=w1[j]; w2s[i]=w2[j];}
i++;
}
}
if ((dvt=i)<e) { // will need to shrink these arrays
da=(Point_process **)realloc((void*)da,(size_t)(dvt*sizeof(Point_process *)));
db=(double*)realloc((void*)db,(size_t)(dvt*sizeof(double)));
syns=(char*)realloc((void*)syns,(size_t)(dvt*sizeof(char)));
if(wsetting==1) {
w1s=(double*)realloc((void*)w1s,(size_t)(dvt*sizeof(double)));
w2s=(double*)realloc((void*)w2s,(size_t)(dvt*sizeof(double)));
}
}
ip->dvt=dvt; ip->del=db; ip->dvi=da; ip->syns=syns;
if(wsetting==1){ip->syw1=w1s; ip->syw2=w2s;}
if (flag!=1) finishdvi2(ip); // do sort
}
ENDVERBATIM
VERBATIM
// setdvi3(divid_vec,del_vec,syns_vec,div_cnt,w1,w2)
// based on setdvi2() but uses qp statt IDP and does reallocs
static void setdvi3 (double *y, double *d, char* s, int dvt, double* w1, double* w2) {
int i,j,ddvi; double *db, *dbs, *w1s, *w2s; unsigned char pdead; unsigned int b,e; char* syns;
Object *lb; Point_process *pnnt, **da, **das;
ddvi=(int)DEAD_DIV;
ip=qp; pg=ip->pg;
e=dvt; // begin to end
da=(Point_process **)realloc((void*)ip->dvi,(size_t)(e*sizeof(Point_process *)));
db=(double*)realloc((void*)ip->del,(size_t)(e*sizeof(double)));
syns=(char*)realloc((void*)ip->syns,(size_t)(e*sizeof(char)));
w1s=(double*)realloc((void*)ip->syw1,(size_t)(e*sizeof(double)));
w2s=(double*)realloc((void*)ip->syw2,(size_t)(e*sizeof(double)));
for (i=0,j=0;j<dvt;i++,j++) { // i thru da[] j thru y, k to append
// div can grow at lower rate if dead cells are encountered
if (!(lb=ivoc_list_item(pg->ce,(unsigned int)y[j]))) {
printf("INTF6:callback %g exceeds %d for list ce\n",y[j],pg->cesz); hxe(); }
pnnt=(Point_process *)lb->u.this_pointer;
if (ddvi==1 || !(pdead = id0ptr(pnnt->_prop)->dead)) {
da[i]=pnnt; db[i]=d[j]; syns[i]=s?s[j]:0;
w1s[i]=w1[j]; w2s[i]=w2[j];
}
}
ip->dvt=dvt; ip->del=db; ip->dvi=da; ip->syns=syns;
ip->syw1=w1s; ip->syw2=w2s;
finishdvi2(ip); // do sort
}
ENDVERBATIM
: prune(p[,potype,rand_seed]) // prune synapses with prob p [0,1], ie 0.1 prunes 10% of the divergence
: prune(vec) // fill in the pruning vec with binary values from vec
PROCEDURE prune () {
VERBATIM
{
id0* ppost; double *x, p; int nx,j,potype;
ip=IDP; pg=ip->pg;
if (hoc_is_double_arg(1)) { // prune a certain percent of targets
p=*getarg(1);
if (p<0 || p>1) {printf("INTF6:pruneERR0:need # [0,1] to prune [ALL,NONE]: %g\n",p); hxe();}
if (p==1.) printf("INTF6pruneWARNING: pruning 100%% of cell %d\n",ip->id);
if (verbose && ip->dvt>dscrsz) {
printf("INTF6pruneB:Div exceeds dscrsz: %d>%d\n",ip->dvt,dscrsz); hxe(); }
if (p==0.) {
for (j=0;j<ip->dvt;j++) ip->sprob[j]=1; // unprune completely
return 0; // now that unpruning is done, can return
}
potype=ifarg(2)?(int)*getarg(2):-1;
sead=(ifarg(3))?(unsigned int)*getarg(3):GetDVIDSeedVal(ip->id);//seed for divergence and delays
mcell_ran4(&sead, dscr , ip->dvt, 1.0); // random var (0,1)
if(potype==-1){ // prune all types of synapses
for (j=0;j<ip->dvt;j++) if (dscr[j]<p) ip->sprob[j]=0; // prune with prob p
} else { // only prune synapses with postsynaptic type == potype
for (j=0;j<ip->dvt;j++){
ppost = id0ptr(ip->dvi[j]->_prop); // #define sop *_ppvar[2].pval
if (ppost->type==potype && dscr[j]<p) ip->sprob[j]=0; // prune with prob p
}
}
} else { // confusing arg1==0->sprob[j]=1 for all j; but arg1=[0] (a vector)->sprob[0]=0
if (verbose) printf("INTF6 WARNING prune(vec) deprecated: use intf.sprob(vec) instead\n");
nx=vector_arg_px(1,&x);
if (nx!=ip->dvt) {printf("INTF6:pruneERRA:Wrong size vector:%d!=%d\n",nx,ip->dvt); hxe();}
for (j=0;j<ip->dvt;j++) ip->sprob[j]=(unsigned char)x[j];
}
}
return 0;
ENDVERBATIM
}
PROCEDURE sprob () {
VERBATIM
{
double *x; int nx,j;
ip=IDP; pg=ip->pg;
nx=vector_arg_px(1,&x);
if (nx!=ip->dvt) {printf("INTF6:pruneERRA:Wrong size vector:%d!=%d\n",nx,ip->dvt); hxe();}
if (ifarg(2)) { // "GET"
if (!hoc_is_str_arg(2)) { printf("INTF6 sprob()ERRA: only legit 2nd arg is 'GET'\n"); hxe();
} else for (j=0;j<ip->dvt;j++) x[j]=(double)ip->sprob[j];
} else {
for (j=0;j<ip->dvt;j++) ip->sprob[j]=(unsigned char)x[j];
}
}
ENDVERBATIM
}
: turnoff(v1,v2) turn off any connection from a cell in v1 to a cell with number in v2
: a global call that can be called from any INTF6
PROCEDURE turnoff () {
VERBATIM {
int nx,ny,i,j,k,dvt; double poid,*x,*y; Point_process **das; unsigned char off;
ip=IDP; pg=ip->pg;
nx=vector_arg_px(1,&x);
ny=vector_arg_px(2,&y);
if (ifarg(3)) off=(unsigned char)*getarg(3); else off=0;
for (i=0;i<nx;i++) {
lop(pg->ce,(unsigned int)x[i]);
dvt=qp->dvt; das=qp->dvi;
for (j=0;j<dvt;j++) {
ip = id0ptr(das[j]->_prop); // sop is *_ppvar[2].pval
poid=(double)ip->id; // postsyn id
for (k=0;k<ny;k++) {
if (poid==y[k]) {
qp->sprob[j]=off; break;
}
}
}
}
}
ENDVERBATIM
}
VERBATIM
// gsort2() sorts 2 parallel vectors -- delays and Point_process pointers
void gsort2 (double *db, Point_process **da,int dvt,double *dbs, Point_process **das) {
int i;
scr=scrset(dvt);
for (i=0;i<dvt;i++) scr[i]=i;
nrn_mlh_gsort(db, (int*)scr, dvt, cmpdfn);
for (i=0;i<dvt;i++) {
dbs[i]=db[scr[i]];
das[i]=da[scr[i]];
}
}
// gsort3() sorts 3 parallel vectors -- delays and Point_process pointers
void gsort3 (double *db, Point_process **da,char* syns,int dvt,double *dbs, Point_process **das,char* synss) {
int i;
scr=scrset(dvt);
for (i=0;i<dvt;i++) scr[i]=i;
nrn_mlh_gsort(db, (int*)scr, dvt, cmpdfn);//sorts indices in scr
for (i=0;i<dvt;i++) {
dbs[i]=db[scr[i]];
das[i]=da[scr[i]];
synss[i]=syns[scr[i]];
}
}
// gsort5() sorts 5 parallel vectors -- delays,Point_process pointers,weights,syn types
void gsort5 (double *db, Point_process **da, char* syns, double* w1,double* w2, int dvt,
double *dbs, Point_process **das,char* synss,double* w1s,double* w2s) {
int i;
scr=scrset(dvt);
for (i=0;i<dvt;i++) scr[i]=i;
nrn_mlh_gsort(db, (int*)scr, dvt, cmpdfn);//sorts indices in scr
for (i=0;i<dvt;i++) {
dbs[i]=db[scr[i]];
das[i]=da[scr[i]];
synss[i]=syns[scr[i]];
w1s[i]=w1[scr[i]];
w2s[i]=w2[scr[i]];
}
}
static void freedvi2 (struct ID0* jp) {
if (jp->dvi) {
free(jp->dvi); free(jp->del); free(jp->sprob); free(jp->syns);
if(jp->wgain){free(jp->wgain); jp->wgain=0x0;}
if(jp->peconv){free(jp->peconv); jp->peconv=0x0;}
if(jp->piconv){free(jp->piconv); jp->piconv=0x0;}
if(ip->pplasttau){free(ip->pplasttau);ip->pplasttau=0x0;}
if(ip->pplastinc){free(ip->pplastinc);ip->pplastinc=0x0;}
if(ip->pplastmaxw){free(ip->pplastmaxw);ip->pplastmaxw=0x0;}
if(ip->pdope){free(ip->pdope);ip->pdope=0x0;}
jp->dvt=0; jp->dvi=(Point_process**)0x0; jp->del=(double*)0x0; jp->sprob=(unsigned char *)0x0; jp->syns=(char *)0x0;
}
}
ENDVERBATIM
PROCEDURE freedvi () {
VERBATIM
{
id0 *jp;
jp=IDP;
freedvi2(jp);
}
ENDVERBATIM
}
FUNCTION qstats () {
VERBATIM {
double stt[3]; int lct,flag; FILE* tfo;
if (ifarg(1)) {tfo=hoc_obj_file_arg(1); flag=1;} else flag=0;
lct=cty[IDP->type];
_lqstats = nrn_event_queue_stats(stt);
printf("SPIKES: %d (%ld:%ld)\n",IDP->spkcnt,spikes[lct],blockcnt[lct]);
printf("QUEUE: Inserted %g; removed %g\n",stt[0],stt[2]);
if (flag) {
fprintf(tfo,"SPIKES: %d (%ld:%ld);",IDP->spkcnt,spikes[lct],blockcnt[lct]);
fprintf(tfo,"QUEUE: Inserted %g; removed %g remaining: %g\n",stt[0],stt[2],_lqstats);
}
}
ENDVERBATIM
}
FUNCTION qsz () {
VERBATIM {
double stt[3];
_lqsz = nrn_event_queue_stats(stt);
}
ENDVERBATIM
}
PROCEDURE qclr () {
VERBATIM {
clear_event_queue();
}
ENDVERBATIM
}
: mywmat(from,to,synapse) - return WMAT value from mod side
FUNCTION mywmat () {
VERBATIM {
int i,j,k;
i=(int)*getarg(1);
if(i<0 || i>=CTYPi){printf("mywmat ERR: arg 1=%d out of bounds (0,%d]\n",i,CTYPi); return -1;}
j = (int)*getarg(2);
if(j<0 || j>=CTYPi){printf("mywmat ERR: arg 2=%d out of bounds (0,%d]\n",j,CTYPi); return -1;}
k = (int)*getarg(3);
if(k<0 || k>=STYPi){printf("mywmat ERR: arg3=%d out of bounds (0,%d]\n",k,STYPi); return -1;}
return WMAT(i,j,k);
}
ENDVERBATIM
}
: mywmatpr - print out WMAT from mod side
PROCEDURE mywmatpr () {
VERBATIM {
double wm;
int i,j,k;
char *ct1,*ct2;
ip=IDP; pg=ip->pg;
for(i=0;i<CTYPi;i++) if(ctt(i,&ct1)!=0) {
for(j=0;j<CTYPi;j++) if(ctt(j,&ct2)!=0) {
for(k=0;k<STYPi;k++) {
if((wm=WMAT(i,j,k))>0) {
printf("wmat[%s][%s][%d]=%g\n",ct1,ct2,k,wm);
}
}
}
}
}
ENDVERBATIM
}
: intf.cinit() is alternative to jitcondiv() that just sets up cell specific params
PROCEDURE cinit () {
VERBATIM {
Symbol *sym; int i,j; unsigned int sz,colid; char *name;
pg=(postgrp *)calloc(1,sizeof(postgrp));
colid = (int)*getarg(2);
if(ppg==0x0) { // initial allocation
ippgbufsz = 5;
ppg = (postgrp**) calloc(ippgbufsz,sizeof(postgrp*));
inumcols = 1;
} else inumcols++;
if(inumcols >= ippgbufsz) { // need more memory? then realloc
ippgbufsz *= 2;
ppg = (postgrp**) realloc((void*)ppg,(size_t)ippgbufsz*sizeof(postgrp*));
}
ppg[inumcols-1] = pg;
pg->col = colid;
pg->ce = *hoc_objgetarg(1);
sym = hoc_lookup("CTYP");
CTYP = (*(hoc_objectdata[sym->u.oboff].pobj));
if (installed==2.0) { // jitcondiv was previously run
sz=ivoc_list_count(pg->ce);
if (sz==pg->cesz && colid==0) printf("\t**** INTF6 WARNING cesz unchanged: INTF6(s) created off-list ****\n");
} else installed=2.0;
pg->cesz = ivoc_list_count(pg->ce); if(verbose) printf("cesz=%d\n",pg->cesz);
pg->lastspk = (double*)calloc(pg->cesz,sizeof(double)); // last spike time of each cell
// not column specific
CTYPi=HVAL("CTYPi"); STYPi=HVAL("STYPi"); dscrsz=HVAL("scrsz"); dscr=HPTR("scr");
// column specific
pg->ix = hoc_pgetarg(3);
pg->ixe = hoc_pgetarg(4);
pg->numc = hoc_pgetarg(5); // numc
if(verbose){printf("CTYPi=%d\n",CTYPi);
for(i=0;i<CTYPi;i++) printf("ix[%d]=%g, ixe[%d]=%g\n",i,pg->ix[i],i,pg->ixe[i]);}
if (!pg->ce) {printf("INTF6 cinit() ERRA: ce not found\n"); hxe();}
if (ivoc_list_count(CTYP)!=CTYPi){
printf("INTF6 cinit() ERRB: %d %d\n",ivoc_list_count(CTYP),CTYPi); hxe(); }
for (i=0;i<pg->cesz;i++) { lop(pg->ce,i); qp->pg=pg; } // set all of the pg pointers for now
printf("Checking for possible seg error in double arrays: CTYPi==%d: ",CTYPi);
printf("%d %g\n",dscrsz,dscr[dscrsz-1]); // scratch area for doubles
for (i=0,j=0;i<CTYPi;i++) if (ctt(i,&name)!=0) {
cty[j]=i; CNAME[j]=name; ctymap[i]=j;
j++;
if (j>=CTYPp) {printf("jitcondiv() INTERRA\n"); hxe();}
}
CTYN=j; // number of cell types being used
for (i=0;i<CTYN;i++) printf("%s(%d)=%g ",CNAME[i],cty[i],NUMC(cty[i]));
printf("\n%d cell types being used in col %d\n",CTYN,colid);
}
ENDVERBATIM
}
: intf.jitcondiv() assigns pointers for hoc symbol storage
PROCEDURE jitcondiv () {
VERBATIM {
Symbol *sym; int i,j; unsigned int sz,colid; char *name;
pg=(postgrp *)calloc(1,sizeof(postgrp));
colid = (int)*getarg(2);
if(ppg==0x0) { // initial allocation
ippgbufsz = 5;
ppg = (postgrp**) calloc(ippgbufsz,sizeof(postgrp*));
inumcols = 1;
} else inumcols++;
if(inumcols >= ippgbufsz) { // need more memory? then realloc
ippgbufsz *= 2;
ppg = (postgrp**) realloc((void*)ppg,(size_t)ippgbufsz*sizeof(postgrp*));
}
ppg[inumcols-1] = pg;
pg->col = colid;
pg->ce = *hoc_objgetarg(1);
sym = hoc_lookup("CTYP");
CTYP = (*(hoc_objectdata[sym->u.oboff].pobj));
if (installed==2.0) { // jitcondiv was previously run
sz=ivoc_list_count(pg->ce);
if (sz==pg->cesz && colid==0) printf("\t**** INTF6 WARNING cesz unchanged: INTF6(s) created off-list ****\n");
} else installed=2.0;
pg->cesz = ivoc_list_count(pg->ce); if(verbose) printf("cesz=%d\n",pg->cesz);
pg->lastspk = (double*)calloc(pg->cesz,sizeof(double)); // last spike time of each cell
// not column specific
CTYPi=HVAL("CTYPi"); STYPi=HVAL("STYPi"); dscrsz=HVAL("scrsz"); dscr=HPTR("scr");
// column specific
pg->ix = hoc_pgetarg(3);
pg->ixe = hoc_pgetarg(4);
if(verbose){printf("CTYPi=%d\n",CTYPi);
for(i=0;i<CTYPi;i++) printf("ix[%d]=%g, ixe[%d]=%g\n",i,pg->ix[i],i,pg->ixe[i]);}
pg->dvg = hoc_pgetarg(5); // div
pg->numc = hoc_pgetarg(6); // numc
pg->wmat = hoc_pgetarg(7); // wmat
pg->wd0 = hoc_pgetarg(8); // wd0
pg->delm = hoc_pgetarg(9); // delm
pg->deld = hoc_pgetarg(10); // deld
if (!pg->ce) {printf("INTF6 jitcondiv ERRA: ce not found\n"); hxe();}
if (ivoc_list_count(CTYP)!=CTYPi){
printf("INTF6 jitcondiv ERRB: %d %d\n",ivoc_list_count(CTYP),CTYPi); hxe(); }
for (i=0;i<pg->cesz;i++) { lop(pg->ce,i); qp->pg=pg; } // set all of the pg pointers for now
// make sure no seg error:
printf("Checking for possible seg error in double arrays: CTYPi==%d: ",CTYPi);
// can access arbitrary member dvg[a][b] using (&dvg[a*CTYPi])[b] or dvg+a*CTYPi+b
printf("%d %d %d ",DVG(CTYPi-1,CTYPi-1),(int)pg->ix[CTYPi-1],(int)pg->ixe[CTYPi-1]);
printf("%g %g ",WMAT(CTYPi-1,CTYPi-1,STYPi-1),WD0(CTYPi-1,CTYPi-1,STYPi-1));
printf("%g %g ",DELM(CTYPi-1,CTYPi-1),DELD(CTYPi-1,CTYPi-1));
printf("%d %g\n",dscrsz,dscr[dscrsz-1]); // scratch area for doubles
for (i=0,j=0;i<CTYPi;i++) if (ctt(i,&name)!=0) {
cty[j]=i; CNAME[j]=name; ctymap[i]=j;
j++;
if (j>=CTYPp) {printf("jitcondiv() INTERRA\n"); hxe();}
}
CTYN=j; // number of cell types being used
for (i=0;i<CTYN;i++) printf("%s(%d)=%g ",CNAME[i],cty[i],NUMC(cty[i]));
printf("\n%d cell types being used in col %d\n",CTYN,colid);
}
ENDVERBATIM
}
: intf.jitrec(vec,tvec)
PROCEDURE jitrec () {
VERBATIM {
int i;
ip=IDP; pg=ip->pg;
if(verbose>1) printf("jitrec from col %d, ip=%p, pg=%p\n",ip->col,ip,pg);
if (! ifarg(2)) { // clear with jitrec() or jitrec(0)
pg->jrmax=0; pg->jridv=0x0; pg->jrtvv=0x0;
return 0;
}
i = vector_arg_px(1, &pg->jrid); // could just set up the pointers once
pg->jrmax=vector_arg_px(2, &pg->jrtv);
pg->jridv=vector_arg(1); pg->jrtvv=vector_arg(2);
pg->jrmax=vector_buffer_size(pg->jridv);
if (pg->jrmax!=vector_buffer_size(pg->jrtvv)) {
printf("jitrec() ERRA: not same size: %d %d\n",i,pg->jrmax); pg->jrmax=0; hxe(); }
pg->jri=pg->jrj=0; // needs to be set at beginning of run
}
return 0;
ENDVERBATIM
}
: PROCEDURE jitrecreset () {
: VERBATIM
: ip=IDP; pg=ip->pg;
: if(verbose>1) printf("jitrecreset from col %d, ip=%p, pg=%p\n",ip->col,ip,pg);
: pg->jrj=0; // needs to be set at beginning of run
: ENDVERBATIM
: }
: intf.scsv()
FUNCTION scsv () {
VERBATIM {
int ty=4; int i,j; unsigned int cnt=0;
ip=IDP; pg=ip->pg;
name = gargstr(1);
if ( !(wf1 = fopen(name,"w"))) { printf("Can't open %s\n",name); hxe(); }
fwrite(&pg->cesz,sizeof(int),1,wf1);
fwrite(&ty,sizeof(int),1,wf1);
for (i=0,j=0;i<pg->cesz;i++,j++) {
lop(pg->ce,i);
if (qp->spkcnt) {
dscr[j]=(double)(qp->spkcnt);
cnt++;
} else dscr[j]=0.0;
if (j>=dscrsz) {
fwrite(dscr,(size_t)sizeof(double),(size_t)dscrsz,wf1);
fflush(wf1);
j=0;
}
}
if (j>0) fwrite(dscr,(size_t)sizeof(double),(size_t)j,wf1);
fclose(wf1);
_lscsv=(double)cnt;
}
ENDVERBATIM
}
: intf.spkcnt(vec[,vec,flag])
: intf.spkcnt(min,max[,vec,flag]) flag=1 means reset all counts to 0
FUNCTION spkcnt () {
VERBATIM {
int nx, ny, i,j, ix, c, min, max, flag; unsigned int sum; double *y,*x;
ip=IDP; pg=ip->pg;
nx=ny=min=max=flag=0; i=1;
if (ifarg(i)) {
if (hoc_is_object_arg(i)) {
ny = vector_arg_px(i, &y); i++;
} else if (ifarg(i+1)) {
min=(int)*getarg(i); max=(int)*getarg(i+1); i+=2;
}
}
while (ifarg(i)) { // can pick up flag and vector in either order
if (hoc_is_object_arg(i)) { // output to a vector
nx = vector_arg_px(i, &x);
} else flag=(int)*getarg(i);
i++;
}
if (ny) max=ny; else if (max==0) max=pg->cesz; else max+=1; // enter max index wish to graph
if (nx && nx!=max-min) {
printf("INTF6 spkcnt() ERR: Vectors not same size %d %d\n",nx,max-min);hxe();}
for (i=min, sum=0;i<max;i++) {
if (ny) lop(pg->ce,(int)y[i]); else lop(pg->ce,i);
if (flag==2) sum+=(c=qp->blkcnt); else sum+=(c=qp->spkcnt);
if (nx) x[i]=(double)c;
if (flag==1) qp->spkcnt=qp->blkcnt=0;
}
_lspkcnt=(double)sum;
}
ENDVERBATIM
}
:** probejcd()
PROCEDURE probejcd () {
VERBATIM { int i,a[4];
ip=IDP; pg=ip->pg;
for (i=1;i<=3;i++) a[i]=(int)*getarg(i);
printf("CTYPi: %d, STYPi: %d, ",CTYPi,STYPi);
// printf("div: %d, ix: %d, ixe: %d, ",DVG(a[1],a[2]),(int)ix[a[1]],(int)ixe[a[1]]);
printf("wmat: %g, wd0: %g\n",WMAT(a[1],a[2],a[3]),WD0(a[1],a[2],a[3]));
}
ENDVERBATIM
}
:** randspk() sets next to next val in vector, this vector is handled globally
PROCEDURE randspk () {
VERBATIM
ip=IDP; pg=ip->pg;
if (ip->rvi > ip->rve) { // pointers go from rvi to rve inclusive
ip->input=0; // turn off
//nxt=-1.; // MR: Commented this out because it kills off the net_send / NET_RECEIVE feedback
// loop once the input spike vecs have finished. If we then push more spikes to the net
// at a later time, they'll never get picked up if nxt=-1 as the loop is dead.
} else if (t==0) { // initialization
nxt=pg->vsp[ip->rvi];
EXSY=pg->sysp[ip->rvi]; // synapse target for external input
WEX=pg->wsp[ip->rvi++]; // weight of external input
} else { // absolute times in vector -> interval
while ((nxt=pg->vsp[ip->rvi++]-t)<=1e-6) {
if (ip->rvi-1 > ip->rve) { printf("randspk() ERRA: "); chk(2.); hxe(); }
}
EXSY=pg->sysp[ip->rvi-1]; // rvi was incremented
WEX=pg->wsp[ip->rvi-1]; // rvi was incremented
}
ENDVERBATIM
: net_send(nxt,2) : can only be called from INITIAL or NET_RECEIVE blocks
}
:** vers gives version
PROCEDURE vers () {
printf("$Id: intf6.mod,v 1.100 2012/04/05 22:38:25 samn Exp $\n")
}
:** val(t,tstart) fills global vii[] to pass values back to record() (called from record())
VERBATIM
void val(double xx, double ta) {
vii[1]=VAM*EXP(-(xx - ta)/tauAM);
vii[2]=VNM*EXP(-(xx - ta)/tauNM);
vii[3]=VGA*EXP(-(xx - ta)/tauGA);
vii[5]=AHP*EXP(-(xx - ta)/tauahp);
vii[8]=VAM2*EXP(-(xx -ta)/tauAM2);
vii[9]=VNM2*EXP(-(xx - ta)/tauNM2);
vii[10]=VGA2*EXP(-(xx - ta)/tauGA2);
vii[6]=vii[1]+vii[2]+vii[3]+vii[4]+vii[5]+vii[8]+vii[9]+vii[10];
vii[7]=VTH + (VTHR-VTH)*EXP(-(xx-trrs)/tauRR) - RMP; // sub RMP, since gets added later
}
ENDVERBATIM
:** valps(t,tstart) like val but builds voltages for pop spike
VERBATIM
void valps (double xx, double ta) {
vii[1]=VAM*EXP(-(xx - ta)/tauAM);
vii[2]=VNM*EXP(-(xx - ta)/tauNM);
vii[3]=VGA*EXP(-(xx - ta)/tauGA);
vii[8]=VAM2*EXP(-(xx - ta)/tauAM2);
vii[9]=VNM2*EXP(-(xx - ta)/tauNM2);
vii[10]=VGA2*EXP(-(xx - ta)/tauGA2);
vii[6]=vii[1]+vii[2]-vii[3]+vii[8]+vii[9]-vii[10];
}
ENDVERBATIM
:** record() stores values since last tg into appropriate vecs
PROCEDURE record () {
VERBATIM {
int i,j,k,nz; double ti;
vp = SOP;
if(!vp) {printf("**** record ERRA: vp=NULL!\n"); return 0;}
if (tg>=t) return 0;
if (ip->record==1) {
while ((int)vp->p >= (int)vp->size-(int)((t-tg)/vdt)-10) {
vp->size*=2;
for (k=0;k<NSV;k++) if (vp->vv[k]!=0x0) vp->vvo[k]=vector_newsize(vp->vv[k], vp->size);
// printf("**** WARNING expanding recording room to %d (type%d id%d at %g)****\n",vp->size,IDP->type,IDP->id,t);
}
} else if ((int)vp->p > (int)vp->size-(int)((t-tg)/vdt)) { // shift if record==2
nz=(int)((t-tg)/vdt);
for (k=0;k<NSV;k++) if (vp->vv[k]!=0x0) {
if (nz>vp->size) {pid(); printf("Record WARNING: vec too short: %d %d\n",nz,vp->size);
vp->p=0;
} else {
for (i=nz,j=0; i<vp->size; i++,j++) vp->vvo[k][j]=vp->vvo[k][i];
vp->p=vp->size-nz;
}
}
}
for (ti=tg;ti<=t && vp->p < vp->size;ti+=vdt,vp->p++) {
val(ti,tg);
if (vp->vvo[0]!=0x0) vp->vvo[0][vp->p]=ti;
for (k=1;k<NSV-1;k++) if (vp->vvo[k]!=0x0) { // not nil pointer
vp->vvo[k][vp->p]=vii[k]+RMP;
}
for (;k<NSV;k++) if (vp->vvo[k]!=0x0) { // not nil pointer
vp->vvo[k][vp->p]=vii[k];
}
}
tg=t;
}
ENDVERBATIM
}
:** recspk() records a spike by writing a 10 into the main VM vector
PROCEDURE recspk (x) {
VERBATIM {
vp = SOP;
record();
if (vp->p > vp->size || vp->vvo[6]==0) return 0;
if (vp->p > 0) {
if (vp->vvo[0]!=0x0) vp->vvo[0][vp->p-1]=_lx;
vp->vvo[6][vp->p-1]=spkht; // the spike
} else {
if (vp->vvo[0]!=0x0) vp->vvo[0][0]=_lx;
vp->vvo[6][0]=spkht; // the spike
}
tg=_lx;
}
ENDVERBATIM
}
:** recclr() clear the vectors pointers
PROCEDURE recclr () {
VERBATIM
{int k;
if (IDP->record) {
if (SOP!=nil) {
vp = SOP;
vp->size=0; vp->p=0;
for (k=0;k<NSV;k++) { vp->vv[k]=nil; vp->vvo[k]=nil; }
} else printf("INTF6 recclr ERR: nil pointer\n");
}
IDP->record=0;
}
ENDVERBATIM
}
:** recfree() free the vpt pointer memory
PROCEDURE recfree () {
VERBATIM
if (SOP!=nil) {
free(SOP);
SOP=nil;
} else printf("INTF6 recfree ERR: nil pointer\n");
IDP->record=0;
ENDVERBATIM
}
:** initvspks() sets up vector from which to read random spike times
: this is a global procedure to set up pieces of a global vector
: all cells share one vector but read from different locations
: (CHANGED from intervals and global proc in v224)
: intf.initvspks(indices, times , weights, synapse types)
PROCEDURE initvspks () {
VERBATIM
{int max, i,err;
double last,lstt;
ip=IDP; pg=ip->pg;
if (! ifarg(1)) {printf("Return initvspks(indices,times,weights,syntypes)\n"); return 0.;}
if(verbose>1) printf("initvspks: col=%d, ip=%p, pg=%p, pg->isp=%p\n",ip->col,ip,pg,pg->isp);
if (pg->isp!=NULL) clrvspks();
ip=IDP; pg=ip->pg; err=0;
i = vector_arg_px(1, &pg->isp); // could just set up the pointers once
max=vector_arg_px(2, &pg->vsp);
if (max!=i) {err=1; printf("initvspks ERR: vecs of different size\n");}
if (max==0) {err=1; printf("initvspks ERR: vec not initialized\n");}
max=vector_arg_px(3, &pg->wsp);
if (max!=i) {err=1; printf("initvspks ERR: 3rd vec is of different size\n");}
max=vector_arg_px(4, &pg->sysp);
if (max!=i) {err=1; printf("initvspks ERR: 4th vec is of different size\n");}
pg->vspn=max;
if (!pg->ce) {printf("Need global ce for initvspks() since intf.mod501\n"); hxe();}
for (i=0,last=-1; i<max; ) { // move forward to first
if (pg->isp[i]!=last) { // new one
lop(pg->ce,(unsigned int)pg->isp[i]);
qp->rvb=qp->rvi=i;
qp->vinflg=qp->input=1;
last=pg->isp[i];
lstt=pg->vsp[i];
i++;
}
for (; i<max && pg->isp[i] == last; i++) { // move forward to last
if (pg->vsp[i]<=lstt) { pg->vsp[i]=lstt+0.00001; // CK: was err=1; this avoid monotonic error
printf("initvspks ERR: nonmonotonic for cell#%d: %g %g\n",qp->id,lstt,pg->vsp[i]); }
lstt=pg->vsp[i];
}
qp->rve=i-1;
if (subsvint>0) {
pg->vsp[qp->rve] = pg->vsp[qp->rvb]+subsvint;
pg->wsp[qp->rve] = pg->wsp[qp->rvb];
}
if (err) { qp->rve=0; hxe(); }
}
}
ENDVERBATIM
}
:** shock() reads random spike times from same db as initvspks() but just sends a single shock
: to each listed cell
: this is a global procedure that calls multiple cells
PROCEDURE shock () {
VERBATIM
{int max, i,err;
double last, lstt, *isp, *vsp, *wsp;
printf("WARNING: This routine appears to be defunct -- please check code in intf6.mod\n");
if (! ifarg(1)) {printf("Return shock(ivspks,vspks,wvspks)\n"); return 0.;}
ip=IDP; pg=ip->pg; err=0;
i = vector_arg_px(1, &isp); // could just set up the pointers once
max=vector_arg_px(2, &vsp);
if (max!=i) {err=1; printf("shock ERR: vecs of different size\n");}
if (max==0) {err=1; printf("shock ERR: vec not initialized\n");}
max=vector_arg_px(3, &wsp);
if (max!=i) {err=1; printf("shock ERR: 3rd vec is of different size\n");}
pg->vspn=max;
if (!pg->ce) {printf("Need global ce for shock()\n"); hxe();}
for (i=0,last=-1; i<max; ) { // move forward to first
if (isp[i]!=last) { // skip any redund indices
lop(pg->ce,(unsigned int)isp[i]);
WEX=-1e9; // code for shock
EXSY=AM; // set to AMPA, though doesn't matter for single shock
#if defined(t)
net_send((void**)0x0, wts,pmt,t+vsp[i],2.0); // 2 is randspk flag
#else
net_send((void**)0x0, wts,pmt,vsp[i],2.0); // 2 is randspk flag
#endif
i++;
}
}
}
ENDVERBATIM
}
PROCEDURE clrvspks () {
VERBATIM {
unsigned int i;
ip=IDP; pg=ip->pg;
if(verbose>1) printf("clrvspks: col=%d, ip=%p, pg=%p, pg->isp=%p\n",ip->col,ip,pg,pg->isp);
for (i=0; i<pg->cesz; i++) {
lop(pg->ce,i);
qp->vinflg=0;
}
}
ENDVERBATIM
}
: trvsp gets called globally to go through the vector
: first pass (arg 1) it replaces terminal values with 1e9
: second pass (arg 2) it replaces terminal values with first+subsvint
PROCEDURE trvsp ()
{
VERBATIM
int i, flag;
double ind, local_t0;
ip=IDP; pg=ip->pg;
flag=(int) *getarg(1);
if (subsvint==0.) {printf("trvsp"); return(0.);}
ind = pg->isp[0];
local_t0 = pg->vsp[0];
if (flag==1) {
for (i=0; i<pg->vspn; i++) {
if (pg->isp[i]!=ind) {
pg->vsp[i-1]=1.e9;
ind=pg->isp[i];
}
}
pg->vsp[pg->vspn-1]=1.e9;
} else if (flag==2) {
for (i=0; i<pg->vspn; i++) {
if (pg->isp[i]!=ind) {
pg->vsp[i-1] = local_t0 + subsvint;
ind = pg->isp[i];
local_t0 = pg->vsp[i];
}
}
pg->vsp[pg->vspn-1] = local_t0 + subsvint;
} else {printf("trvsp flag %d not recognized\n",flag); hxe();}
ENDVERBATIM
}
:** initjttr() sets up vector from which to read jitter
: -- key jtt to avoid confusion with jitcon=='just in time connection'
: this is a global not a range procedure -- just call once
PROCEDURE initjttr () {
VERBATIM
{int max, i, err=0;
ip=IDP; pg=ip->pg;
pg->jtpt=0;
if (! ifarg(1)) {printf("Return initjttr(vec)\n"); return(0.);}
max=vector_arg_px(1, &jsp);
if (max==0) {err=1; printf("initjttr ERR: vec not initialized\n");}
for (i=0; i<max; i++) if (jsp[i]<=0) {err=1;
printf("initjttr ERR: vec should be >0: %g\n",jsp[i]);}
if (err) { jsp=nil; pg->jtmax=0.; return(0.); }// hoc_execerror("",0);
if (max != pg->jtmax) {
printf("WARNING: resetting jtmax_INTF6 to %d\n",max); pg->jtmax=max; }
}
ENDVERBATIM
}
:* internal routines
VERBATIM
//** getlp(LIST,ITEM#) sets qp: take object from ob list @ index i and return pointer
// modeled on vector_arg_px(): picks up obj from list and resolves pointers
static id0* getlp (Object *ob, unsigned int i) {
Object *lb; id0* myp;
lb = ivoc_list_item(ob, i);
if (! lb) { printf("INTF6:getlp %d exceeds %d for list ce\n",i,pg->cesz); hxe();}
pmt=ob2pntproc(lb);
myp = id0ptr(pmt->_prop); // #define sop *_ppvar[2].pval
return myp;
}
//** lop(LIST,ITEM#) sets qp: take object from ob list @ index i and assign pointer to GLOBAL qp pointer
// modeled on vector_arg_px(): picks up obj from list and resolves pointers
static id0* lop (Object *ob, unsigned int i) {
Object *lb;
lb = ivoc_list_item(ob, i);
if (! lb) { printf("INTF6:lop %d exceeds %d for list ce\n",i,pg->cesz); hxe();}
pmt=ob2pntproc(lb);
qp = id0ptr(pmt->_prop); // #define sop *_ppvar[2].pval
return qp;
}
//*** lopr(LIST,ITEM#) sets qp and RANGE vars - same as lop() but also does RANGE
static id0* lopr (Object *ob, unsigned int i) {
id0* myp;
myp = lop(ob,i);
_hoc_setdata(pmt); // pmt is another global
return myp;
}
// use stoppo() as a convenient conditional breakpoint in gdb (gdb watching is too slow)
void stoppo () {
}
//** ctt(ITEM#) find cells that exist by name
static int ctt (unsigned int i, char** name) {
Object *lb;
if (NUMC(i)==0) return 0; // none of this cell type
lb = ivoc_list_item(CTYP, i);
if (! lb) { printf("INTF6:ctt %d exceeds %d for list CTYP\n",i,CTYPi); hxe();}
{*name=*(lb->u.dataspace->ppstr);}
return (int)NUMC(i);
}
ENDVERBATIM
PROCEDURE test () {
VERBATIM
char *str; int x;
x=ctt(7,&str);
printf("%s (%d)\n",str,x);
ENDVERBATIM
}
: lof can find object information
PROCEDURE lof () {
VERBATIM {
Object *ob; int num,i,ii,j,k,si,nx; double *vvo[7], *par; IvocVect *vv[7];
ob = *(hoc_objgetarg(1));
si=(int)*getarg(2);
num = ivoc_list_count(ob);
if (num!=7) { printf("INTF6 lof ERR %d>7\n",num); hxe(); }
for (i=0;i<num;i++) {
j = list_vector_px3(ob, i, &vvo[i], &vv[i]);
if (i==0) nx=j;
if (j!=nx) { printf("INTF6 lof ERR %d %d\n",j,nx); hxe(); }
}
// for (i=ix[si],ii=0;i<=ixe[si] && ii<nx;i++,ii++) {
// vvo[0][ii]=(double)i;
// par=lop(ce,i);
// for (j=20,k=1;j<25;j++,k++) { // NB these could move: Vm,VAM,VNM,VGA
// vvo[k][ii]=par[j];
// }
// }
}
ENDVERBATIM
}
:* initinvl() sets up vector from which to read intervals
: this is a global not a range procedure -- just call once
PROCEDURE initinvl () {
printf("initinvl() NOT BEING USED\n")
}
: invlflag() used internally; can't set from here; use initinvl() and range invlset()
FUNCTION invlflag () {
VERBATIM
ip=IDP; pg=ip->pg;
if (ip->invl0==1 && invlp==nil) { // err
printf("INTF6 invlflag ERR: pointer not initialized\n"); hoc_execerror("",0);
}
_linvlflag= (double)ip->invl0;
ENDVERBATIM
}
:** shift() returns the appropriate shift
FUNCTION shift (vl) {
VERBATIM
double expand, tmp, min, max;
//if (invlp==nil) {printf("INTF6 invlflag ERRa: pointer not initialized\n"); hoc_execerror("",0);}
if ((t<(invlt-invl)+invl/2) && invlt != -1) { // don't shift if less than halfway through
_lshift=0.; // flag for no shift
} else {
expand = -(_lvl-(-65))/20; // expand positive if hyperpolarized
if (expand>1.) expand=1.; if (expand<-1.) expand=-1.;
if (expand>0.) { // expand interval
max=1.5*invl;
tmp=oinvl+0.8*expand*(max-oinvl); // the amount we can add to the invl
} else {
min=0.5*invl;
tmp=oinvl+0.8*expand*(oinvl-min); // the amount we can reduce current invl
}
if (invlt+tmp<t+2) { // getting too near spike time
_lshift=0.;
} else {
oinvl=tmp; // new interval
_lshift=invlt+oinvl;
}
}
ENDVERBATIM
}
:* recini() called from INITIAL block to set vp->p to zero and open up vectors
PROCEDURE recini () {
VERBATIM
{ int k;
if (SOP==nil) {
printf("INTF6 record ERR: pointer not initialized\n"); hoc_execerror("",0);
} else {
vp = SOP;
vp->p=0;
// open up the vector maximally before writing into it; will correct size in fini
for (k=0;k<NSV;k++) if (vp->vvo[k]!=0) vector_resize(vp->vv[k], vp->size);
}}
ENDVERBATIM
}
:** fini() to finish up recording -- should be called from FinishMisc()
PROCEDURE fini () {
VERBATIM
{int k;
// initialization for next round, this will not be set if job terminates prematurely
IDP->rvi=IDP->rvb; // -- see vinset()
if (IDP->wrec) { wrecord(1e9); }
if (IDP->record) {
record(); // finish up
for (k=0;k<NSV;k++) if (vp->vvo[k]!=0) { // not nil pointer
vector_resize(vp->vv[k], vp->p);
}
}}
ENDVERBATIM
}
:** chk([flag]) with flag=1 prints out info on the record structure
: flag=2 prints out info on the global vectors
PROCEDURE chk (f) {
VERBATIM
{int i,lfg;
lfg=(int)_lf;
ip=IDP; pg=ip->pg;
printf("ID:%d; typ: %d; rec:%d wrec:%d inp:%d jtt:%d invl:%d\n",ip->id,ip->type,ip->record,ip->wrec,ip->input,ip->jttr,ip->invl0);
if (lfg==1) {
if (SOP!=nil) {
vp = SOP;
printf("p %d size %d tg %g\n",vp->p,vp->size,tg);
for (i=0;i<NSV;i++) if (vp->vv[i]) printf("%d %p %p;",i,vp->vv[i],vp->vvo[i]);
} else printf("Recording pointers not initialized");
}
if (lfg==2) {
printf("Global vectors for input and jitter (jttr): \n");
if (pg->vsp!=nil) printf("VSP: %p (%d/%d-%d)\n",pg->vsp,ip->rvi,ip->rvb,ip->rve); else printf("no VSP\n");
if (jsp!=nil) printf("JSP: %p (%d/%d)\n",jsp,pg->jtpt,pg->jtmax); else printf("no JSP\n");
}
if (lfg==3) {
if (pg->vsp!=nil) { printf("VSP: (%d/%d-%d)\n",ip->rvi,ip->rvb,ip->rve);
for (i=ip->rvb;i<=ip->rve;i++) printf("%d:%g ",i,pg->vsp[i]);
printf("\n");
} else printf("no VSP\n");
}
if (lfg==4) { // was used to give invlp[],invlmax
}
if (lfg==5) {
printf("wwpt %d wwsz %d\n WW vecs: ",wwpt,wwsz);
printf("wwwid %g wwht %d nsw %g\n WW vecs: ",wwwid,(int)wwht,nsw);
for (i=0;i<NSW;i++) printf("%d %p %p;",i,ww[i],wwo[i]);
}}
ENDVERBATIM
}
:** id() and pid() identify the cell -- printf and function return
FUNCTION pid () {
VERBATIM
printf("INTF6%d(%d/%d@%g) ",IDP->id,IDP->type,IDP->col,t);
_lpid = (double)IDP->id;
ENDVERBATIM
}
: intra-column identifier for cell
FUNCTION id () {
VERBATIM
if (ifarg(1)) IDP->id = (unsigned int) *getarg(1);
_lid = (double)IDP->id;
ENDVERBATIM
}
FUNCTION type () {
VERBATIM
if (ifarg(1)) IDP->type = (unsigned char) *getarg(1);
_ltype = (double)IDP->type;
ENDVERBATIM
}
: column identifier for cell
FUNCTION col () {
VERBATIM
ip = IDP;
if (ifarg(1)) ip->col = (unsigned int) *getarg(1);
_lcol = (double)ip->col;
ENDVERBATIM
}
: global identifier for cell
FUNCTION gid () {
VERBATIM
ip = IDP;
if (ifarg(1)) ip->gid = (unsigned int) *getarg(1);
_lgid = (double)ip->gid;
ENDVERBATIM
}
FUNCTION dbx () {
VERBATIM
ip = IDP;
if (ifarg(1)) ip->dbx = (unsigned char) *getarg(1);
_ldbx = (double)ip->dbx;
ENDVERBATIM
}
:** initrec(name,vec) sets up recording of name (see varnum for list) into a vector
PROCEDURE initrec () {
VERBATIM
{int i;
name = gargstr(1);
if (SOP==nil) {
IDP->record=1;
SOP = (vpt*)ecalloc(1, sizeof(vpt));
SOP->size=0;
}
if (IDP->record==0) {
recini();
IDP->record=1;
}
vp = SOP;
i=(int)varnum();
if (i==-1) {printf("INTF6 record ERR %s not recognized\n",name); hoc_execerror("",0); }
vp->vv[i]=vector_arg(2);
vector_arg_px(2, &(vp->vvo[i]));
if (vp->size==0) { vp->size=(unsigned int)vector_buffer_size(vp->vv[i]);
} else if (vp->size != (unsigned int)vector_buffer_size(vp->vv[i])) {
printf("INTF6 initrec ERR vectors not all same size: %d vs %d",vp->size,vector_buffer_size(vp->vv[i]));
hoc_execerror("", 0);
}}
ENDVERBATIM
}
:** varnum(statevar_name) returns index number associated with particular variable name
: called by initrec() using global name
FUNCTION varnum () { LOCAL i
i=-1
VERBATIM
if (strcmp(name,"time")==0) { _li=0.;
} else if (strcmp(name,"VAM")==0) { _li=1.;
} else if (strcmp(name,"VNM")==0) { _li=2.;
} else if (strcmp(name,"VGA")==0) { _li=3.;
} else if (strcmp(name,"AHP")==0) { _li=5.;
} else if (strcmp(name,"V")==0) { _li=6.;
} else if (strcmp(name,"VM")==0) { _li=6.; // 2 names for V
} else if (strcmp(name,"VTHC")==0) { _li=7.;
} else if (strcmp(name,"VAM2")==0) { _li=8.;
} else if (strcmp(name,"VNM2")==0) { _li=9.;
} else if (strcmp(name,"VGA2")==0) { _li=10.;
}
ENDVERBATIM
varnum=i
}
:** vecname(INDEX) prints name when given an index
PROCEDURE vecname () {
VERBATIM
int i;
i = (int)*getarg(1);
if (i==0) printf("time\n");
else if (i==1) printf("VAM\n");
else if (i==2) printf("VNM\n");
else if (i==3) printf("VGA\n");
else if (i==5) printf("AHP\n");
else if (i==6) printf("V\n");
else if (i==7) printf("VTHC\n");
else if (i==8) printf("VAM2\n");
else if (i==9) printf("VNM2\n");
else if (i==10) printf("VGA2\n");
ENDVERBATIM
}
:** initwrec(name,vec) sets up recording of sim field potential
PROCEDURE initwrec () {
VERBATIM
{int i, k, num, cap; Object* ob;
ob = *hoc_objgetarg(1); // list of vectors
num = ivoc_list_count(ob);
if (num>NSW) { printf("INTF6 initwrec() WARN: can only store %d ww vecs\n",NSW); hxe();}
nsw=(double)num;
for (k=0;k<num;k++) {
cap = list_vector_px2(ob, k, &wwo[k], &ww[k]);
if (k==0) wwsz=cap; else if (wwsz!=cap) {
printf("INTF6 initwrec ERR w-vecs size err: %d,%d,%d",k,wwsz,cap); hxe(); }
}
}
ENDVERBATIM
}
: popspk() is paste on gaussian for a pop spk: with vdt=0.1 -20 to 20 is 4 ms
: needs to be above location where is actively accessed
PROCEDURE popspk (x) {
TABLE Psk DEPEND wwwid,wwht FROM -40 TO 40 WITH 81
Psk = -wwht*exp(-2.*x*x/wwwid/wwwid)
}
PROCEDURE pskshowtable () {
VERBATIM
int j;
printf("_tmin_popspk:%g -_tmin_popspk:%g\n",_tmin_popspk,-_tmin_popspk);
for (j=0;j<=-2*(int)_tmin_popspk+1;j++) printf("%g ",_t_Psk[j]);
printf("\n");
ENDVERBATIM
}
:** wrecord() records voltages onto single global vector
PROCEDURE wrecord (te) {
VERBATIM
{int i,j,k,max,wrp; double ti,scale;
for (i=0;i<WRNUM && (wrp=(int)IDP->wreci[i])>-1;i++) {
// wrp: index for multiple field recordings
scale=(double)IDP->wscale[i];
if (_lte<1.e9) { // a spike recording
if (scale>0) {
max=(int)_tmin_popspk; // max of table max=-min
k=-(int)floor((_lte-rebeg)/vdt+0.5);
for (j= -max;j<=max && k+j>0 && k+j<wwsz;j++) {
wwo[wrp][k+j] += scale*_t_Psk[j+max]; // direct copy from the Psk table
}
}
} else if (twg>=t) { return 0;
} else {
for (ti=twg,k=(int)floor((twg-rebeg)/vdt+0.5);ti<=t && k<wwsz;ti+=vdt,k++) {
valps(ti,twg); // valps() for pop spike calculation
wwo[wrp][k]+=vii[6]*lfpscale;
if (IDP->dbx==-1) printf("%g:%g ",vii[6],wwo[wrp][k]);
}
}
}
if (_lte==1.e9) twg=ti;
}
return 0;
ENDVERBATIM
}
: backward compatibility -- note that index was 1-offset; convert to 0 offset here
: wrec() -- return value in wrec0
: wrec(VAL) -- set wrec0
: wrec(VAL,SCALE) -- set wrecIND and scaling for wrecIND
FUNCTION wrec () {
VERBATIM
{ int k,ix;
ip=IDP;
if (ifarg(1)) {
ix=(int)*getarg(1);
if (ix>=1) {
if (ix-1>=nsw) {
printf("Attempt to save into ww[%d] but only have %d\n",ix-1,(int)nsw); hxe();}
ip->wrec=1;
ip->wreci[0]=(char)ix-1;
ip->wscale[0]=1.; // default
if (ifarg(2)) ip->wscale[0]= (float)*getarg(2);
} else if (ix<=0) {
ip->wrec=0;
for (k=0;k<WRNUM;k++) { ip->wreci[k]=-1; ip->wscale[k]=-1.0; }
} else {printf("INTF6 wrec ERR flag(0/1) %d\n",ip->wrec); hxe();
}
}
_lwrec=(double)ip->wrec;
}
ENDVERBATIM
}
: wrc() -- return value in wrec0
: wrc(VAL) -- set wrec0
: wrc(IND,SCALE) -- set wrec0 and scaling for wrec0
FUNCTION wrc () {
VERBATIM
{ int i,ix;
ip=IDP;
if (ifarg(1)) { // 1 or 2 args
ix=(int)*getarg(1);
if (ix<0) {
ip->wrec=0;
for (i=0;i<WRNUM;i++) { ip->wreci[i]=-1; ip->wscale[i]=-1.0; }
} else {
for (i=0;i<WRNUM && ip->wreci[i]!=-1 && ip->wreci[i]!=ix;i++) {};
if (i==WRNUM) {
pid(); printf("INFT wrc() ERR: out of wreci pointers (max %d)\n",WRNUM); hxe();}
if (ix>=nsw) {printf("Attempt to save into ww[%d] but only have %d\n",ix,(int)nsw); hxe();}
ip->wrec=1;
ip->wreci[i]=ix;
if (ifarg(2)) ip->wscale[i]=(float)*getarg(2); else ip->wscale[i]=1.0;
}
} else {
for (i=0;i<WRNUM;i++) printf("%d:%g ",ip->wreci[i],ip->wscale[i]);
printf("\n");
}
_lwrc=(double)ip->wrec;
}
ENDVERBATIM
}
FUNCTION wwszset () {
VERBATIM
if (ifarg(1)) wwsz = (unsigned int) *getarg(1);
_lwwszset=(double)wwsz;
ENDVERBATIM
}
:** wwfree()
FUNCTION wwfree () {
VERBATIM
int k;
IDP->wrec=0;
wwsz=0; wwpt=0; nsw=0.;
for (k=0;k<NSW;k++) { ww[k]=nil; wwo[k]=nil; }
ENDVERBATIM
}
:** jttr() reads out of a noise vector (call from NET_RECEIVE block)
FUNCTION jttr () {
VERBATIM
ip=IDP; pg=ip->pg;
if (pg->jtmax>0 && pg->jtpt>=pg->jtmax) {
pg->jtpt=0;
printf("Warning, cycling through jttr vector at t=%g\n",t);
}
if (pg->jtmax>0) _ljttr = jsp[pg->jtpt++]; else _ljttr=0;
ENDVERBATIM
}
:** global_init() initialize globals shared by all INTF6s
PROCEDURE global_init () {
popspk(0) : recreate table if any change in wid or ht
VERBATIM
{ int i,j,k,c; double stt[3];
if (nsw>0. && wwo[0]!=0) { // do just once
printf("Initializing ww to record for %g (%g)\n",vdt*wwsz,vdt);
wwpt=0;
for (k=0;k<(int)nsw;k++) {
vector_resize(ww[k], wwsz);
for (j=0;j<wwsz;j++) wwo[k][j]=0.;
}
}
errflag=0;
for (i=0;i<CTYN;i++) blockcnt[cty[i]]=spikes[cty[i]]=0;
for(c=0;c<inumcols;c++) {
pg=ppg[c]; if(!pg) continue;
if (pg->jridv) { pg->jri=pg->jrj=0; vector_resize(pg->jridv, pg->jrmax); vector_resize(pg->jrtvv, pg->jrmax); }
pg->spktot=0;
pg->jtpt=0;
pg->eventtot=0;
}
}
ENDVERBATIM
}
PROCEDURE global_fini () {
VERBATIM
int c,k;
for (k=0;k<(int)nsw;k++) vector_resize(ww[k], (int)floor(t/vdt+0.5));
for(c=0;c<inumcols;c++) {
pg=ppg[c]; if(!pg) continue;
if (pg->jridv && pg->jrj<pg->jrmax) {
vector_resize(pg->jridv, pg->jrj);
vector_resize(pg->jrtvv, pg->jrj);
}
}
ENDVERBATIM
}
:* setting and getting flags: fflag, record,input,jttr
FUNCTION fflag () { fflag=1 }
FUNCTION thrh () { thrh=VTH-RMP }
: reflag() used internally; can't set from here; use recinit()
FUNCTION recflag () {
VERBATIM
_lrecflag= (double)IDP->record;
ENDVERBATIM
}
: vinflag() used internally; can't set from here; use global initvspks() and range vinset()
FUNCTION vinflag () {
VERBATIM
ip=IDP; pg=ip->pg;
if (ip->vinflg==0 && pg->vsp==nil) { // do nothing
} else if (ip->vinflg==1 && ip->rve==-1) {
printf("INTF6 vinflag ERR: pointer not initialized\n"); hoc_execerror("",0);
} else if (ip->rve >= 0) {
if (pg->vsp==nil) {
printf("INTF6 vinflag ERR1: pointer not initialized\n"); hoc_execerror("",0);
}
ip->rvi=ip->rvb;
ip->input=1;
}
_lvinflag= (double)ip->vinflg;
ENDVERBATIM
}
:** flag(name,[val,setall]) set or get a flag
: flag(name,vec) fill vec with flag value from all the cells
: seek names from iflags[] and look at location &ip->type -- beginning of flags
FUNCTION flag () {
VERBATIM
char *sf; static int ix,fi,setfl,nx; static unsigned char val; static double *x, delt;
ip=IDP; pg=ip->pg;
if (FLAG==OK) { // callback -- DO NOT SET FROM HOC
FLAG=0.;
if (stoprun) {slowset=0; return 0.0;}
if (IDP->dbx==-1)printf("slowset fi:%d ix:%d ss:%g delt:%g t:%g\n",fi,ix,slowset,delt,t);
if (t>slowset || ix>=pg->cesz) { // done
printf("Slow-setting of flag %d finished at %g: (%d,%g,%g)\n",fi,t,ix,delt,slowset);
slowset=0.; return 0.0;
}
if (ix<pg->cesz) {
lop(pg->ce,ix);
(&qp->type)[fi]=((fi>=iflneg)?(char)x[ix]:(unsigned char)x[ix]);
ix++;
#if defined(t)
net_send((void**)0x0, wts,tpnt,t+delt,OK); // OK is flag() flag
#else
net_send((void**)0x0, wts,tpnt,delt,OK);
#endif
}
return 0.0;
}
if (slowset>0 && ifarg(3)) {
printf("INTF6 flag() slowset ERR; attempted set during slowset: fi:%d ix:%d ss:%g delt:%g t:%g",\
fi,ix,slowset,delt,t);
return 0.0;
}
ip = IDP; setfl=ifarg(3);
if (ifarg(4)) { slowset=*getarg(4); delt=slowset/pg->cesz; slowset+=t; }
sf = gargstr(1);
for (fi=0;fi<iflnum && strncmp(sf, &iflags[fi*4], 3)!=0;fi++) ; // find flag by name
if (fi==iflnum) {printf("INTF6 ERR: %s not found as a flag (%s)\n",sf,iflags); hxe();}
if (ifarg(2)) {
if (hoc_is_double_arg(2)) { // either set to all or just to this one
val=(unsigned char)*getarg(2);
if (slowset) { // set one and come back
printf("NOT IMPLEMENTED\n"); // ****NOT IMPLEMENTED****
} else if (setfl) { // set them all
for (ix=0;ix<pg->cesz;ix++) { lop(pg->ce,ix); (&qp->type)[fi]=val; }
} else { // just set this one
(&ip->type)[fi]=((fi>=iflneg)?(char)val:val);
}
} else {
nx=vector_arg_px(2,&x);
if (nx!=pg->cesz) {
if (setfl) { printf("INTF6 flag ERR: vec sz mismatch: %d %d\n",nx,pg->cesz); hxe();
} else x=vector_newsize(vector_arg(2),pg->cesz);
}
if (setfl && slowset) { // set one and come back
ix=0;
lop(pg->ce,ix);
(&qp->type)[fi]=((fi>=iflneg)?(char)x[ix]:(unsigned char)x[ix]);
ix++;
#if defined(t)
net_send((void**)0x0, wts,tpnt,t+delt,OK); // OK is flag() flag
#else
net_send((void**)0x0, wts,tpnt,delt,OK);
#endif
} else for (ix=0;ix<pg->cesz;ix++) {
lop(pg->ce,ix);
if (setfl) { (&qp->type)[fi]=((fi>=iflneg)?(char)x[ix]:(unsigned char)x[ix]);
} else {
x[ix]=(double)((fi>=iflneg)?(char)(&qp->type)[fi]:(unsigned char)(&qp->type)[fi]);
}
}
}
}
_lflag=(double)((fi>=iflneg)?(char)(&ip->type)[fi]:(unsigned char)(&ip->type)[fi]);
ENDVERBATIM
}
FUNCTION allspck () {
VERBATIM
int i; double *x, sum; IvocVect *voi;
ip = IDP; pg=ip->pg;
voi=vector_arg(1); x=vector_newsize(voi,pg->cesz);
for (i=0,sum=0;i<pg->cesz;i++) { lopr(pg->ce,i);
x[i]=spck;
sum+=spck;
}
_lallspck=sum;
ENDVERBATIM
}
:** resetall()
PROCEDURE resetall () {
VERBATIM
int ii,i; unsigned char val;
ip=IDP; pg=ip->pg;
if(verbose>1) printf("resetall: ip=%p, col=%d, pg=%p\n",ip,pg->col,pg);
for (i=0;i<pg->cesz;i++) { lopr(pg->ce,i);
Vm=RMP; VAM=0; VNM=0; VGA=0; AHP=0; invlt=-1; VAM2=0; VNM2=0; VGA2=0;
t0=t; trrs=t; twg = t; cbur=0; spck=0; refractory=0; VTHC=VTHR=VTH;
}
ENDVERBATIM
}
:** floc(x,y[,z],vid,vdist,radius,type) // find cells within distance 'r' from a location
: type can be a number to pick up or a vector to find all
FUNCTION floc () {
VERBATIM
double x,y,z,r,min,rad, *ix, *dd, *tdy; int ii,i,n,cnt,ty,tvf; IvocVect *voi, *vod, *voty;
cnt=0; n=1000; r=0; z=ty=1e9; tvf=0;
ip = IDP; pg=ip->pg;
x = *getarg(1);
y = *getarg(2);
i=3;
if (ifarg(i)) if (hoc_is_double_arg(i)) { z=*getarg(3); i++; }
if (ifarg(i)) {
voi=vector_arg(i++); ix=vector_newsize(voi,n); // id vector
vod=vector_arg(i++); dd=vector_newsize(vod,n); // distance vector
r= *getarg(i++);
}
if (ifarg(i)) if (hoc_is_double_arg(i)) ty= *getarg(7); else { // type or -1 for EXCIT or -2 for INHIB
tvf=1; voty=vector_arg(i++); tdy=vector_newsize(voty,n); // type vector
}
r*=r; // squared for comparisons
for (i=0,min=1e9,ii=-1;i<pg->cesz;i++) { qp=lopr(pg->ce,i);
if (ty!=1e9 && ((ty>=0 && ty!=qp->type) || (ty==-1 && qp->inhib==1) || (ty==-2 && qp->inhib==0))) continue;
rad=(x-xloc)*(x-xloc)+(y-yloc)*(y-yloc)+(z==1e9?0.:((z-zloc)*(z-zloc))); // dist^2
if (r>0 && rad<r) {
// printf("AAAA: %d %g,%g,%g dist:%g (%g,%g,%g) mg0:%g\n",qp->id,xloc,yloc,zloc,sqrt(rad),x,y,z,mg0);
if (cnt>=n) { // resize the vectors
ix=vector_newsize(voi,n*=2);
dd=vector_newsize(vod,n);
if (tvf) tdy=vector_newsize(voty,n);
}
ix[cnt]=(double)i;
dd[cnt]=sqrt(rad);
if (tvf) tdy[cnt]=(double)qp->type;
cnt++;
} else if (rad<min) { min=rad; ii=i; }
}
if (r>0) {
ix=vector_newsize(voi,cnt); dd=vector_newsize(vod,cnt);
if (tvf) tdy=vector_newsize(voty,cnt);
_lfloc=(double)cnt; } else {
_lfloc=(double)ii; } // return the index of the closest cell found
ENDVERBATIM
}
:** invlset([val]) set or get the invl flag
FUNCTION invlset () {
VERBATIM
ip=IDP;
if (ifarg(1)) ip->invl0 = (unsigned char) *getarg(1);
_linvlset=(double)ip->invl0;
ENDVERBATIM
}
:** vinset([val]) set or get the input flag (for using shared input from a vector)
FUNCTION vinset () {
VERBATIM
ip=IDP;
if (ifarg(1)) ip->vinflg = (unsigned char) *getarg(1);
if (ip->vinflg==1) {
ip->input=1;
ip->rvi = ip->rvb;
}
_lvinset=(double)ip->vinflg;
ENDVERBATIM
}
:* TABLES
PROCEDURE EXPo (x) {
TABLE RES FROM -20 TO 0 WITH 5000
RES = exp(x)
}
FUNCTION EXP (x) {
EXPo(x)
EXP = RES
}
PROCEDURE ESINo (x) {
TABLE ESIN FROM 0 TO 2*PI WITH 3000 : one cycle
ESIN = sin(x)
}
FUNCTION rates (vv) {
: from Stevens & Jahr 1990a,b
rates = maxnmc / (1 + exp(0.062 (/mV) * -vv) * ( (mg / mg0) ) )
}
: apply dopamine reward/punishment using pdope pointers, which store eligiblity signals as times
: of occurrence -- intf.dopelearn(1=='DA-burst' -1=='DA-dip') -- applies dopamine learning to all cells
: in same ce as calling INTF6.
: rules:
: DA-burst with pre-before-post causes LTP.
: DA-burst with post-before-pre causes LTD.
: DA-dip with pre-before-post causes LTD.
: DA-dip with post-before-pre causes LTP.
FUNCTION dopelearn () {
VERBATIM
Point_process *pnnt;
int i , iCell, pot;
double tmp,maxw,inc,d,tau,pdopet;
if(seadsetting!=3.) return 0.0; // seadsetting==3 for DOPE, must be set before network setup
pot = (int) *getarg(1); //
ip=IDP; pg=ip->pg;
for(iCell=0;iCell<pg->cesz;iCell++){
lop(pg->ce,iCell);
if(!qp->dvt)continue; //don't write empty pointers if no divergence
for(i=0;i<qp->dvt;i++){
pdopet = fabs(qp->pdope[i]); // fabs for backwards elig trace (post before pre has neg sign)
d = t - pdopet; // time since eligibility trace turned on
if(qp->pdope[i] > -1e9 && d <= maxeligtrdur ) { // -1e9 means it wasn't activated. maxeligtrdur is max time
tmp = qp->wgain[i]; // current weight gain of synapse
maxw = qp->pplastmaxw[i]; // max possible weight for the synapse
tau = qp->pplasttau[i]; // time constant
if( ! ( inc = qp->pplastinc[i] ) ) continue; // if plasticity is off at this synapse
if(pot>0) { // DA-burst
if(qp->pdope[i] >= 0) { // DA-burst with pre-before-post -> LTP
if(SOFTSTDP) inc *= (1.0 - tmp / maxw); // soft bound for potentiation
if (EXPELIGTR) // if we want to use exponential decay
qp->wgain[i] += EPOTW * inc * exp( -d / tau ); // increment the wgain of the synapse
else
qp->wgain[i] += EPOTW * inc;
} else { // DA-burst with post-before-pre -> LTD
if(SOFTSTDP) inc *= (tmp / maxw); // soft bound for depression
if (EXPELIGTR) // if we want to use exponential decay
qp->wgain[i] -= EDEPW * inc * exp( -d / tau ); // increment the wgain of the synapse
else
qp->wgain[i] -= EDEPW * inc;
}
} else { // DA-dip
if(qp->pdope[i] >= 0) { // DA-dip with pre-before-post -> LTD
if(SOFTSTDP) inc *= (tmp / maxw); // soft bound for depression
if (EXPELIGTR) // if we want to use exponential decay
qp->wgain[i] -= EDEPW * inc * exp( -d / tau ); // increment the wgain of the synapse
else
qp->wgain[i] -= EDEPW * inc;
} else { // DA-dip with post-before-pre -> LTP
if(SOFTSTDP) inc *= (1.0 - tmp / maxw); // soft bound for potentiation
if (EXPELIGTR) // if we want to use exponential decay
qp->wgain[i] += EPOTW * inc * exp( -d / tau ); // increment the wgain of the synapse
else
qp->wgain[i] += EPOTW * inc;
}
}
// check bounds of wgain
if(qp->wgain[i]<0.) qp->wgain[i]=0.; else if(!SOFTSTDP && qp->wgain[i]>maxw) qp->wgain[i]=maxw;
if(reseteligtr) qp->pdope[i] = -1e9; // reset here once synapse rewarded/punished
}
}
}
return 1.0;
ENDVERBATIM
}
: intf.setdeletion - see comments below - used by homeostatic synaptic scaling
PROCEDURE setdeletion () {
VERBATIM
// Allow neurons to spontaneously die in proportion to their scaling factor (modified by
// a rate constant which can be supplied as an argument).
// This allows investigation into the progression of Alzheimer's disease as a via synaptic
// scaling (Small, 2008).
//
// ARGUMENT: dynamic deletion rate constant (<=0 turns off dynamic deletion, >0 turns it on and
// sets the rate constant).
double x = *getarg(1);
if (x <= 0) {
dynamicdel = 0; // Turn off dynamic deletion
} else {
dynamicdel = 1; // Turn on dynamic deletion
delspeed = x; // Set deletion rate constant
printf("Set dynamic deletion rate constant = %e\n", delspeed);
}
ENDVERBATIM
}
VERBATIM
void dynamicdelete (double time) {
// Allow this cell to die, with probability proportional to excitation and rate constant
// Integrate over time since last call.
// mcell_ran4 appears to take following args:
// seed, pointer to RNG output store, num. random values to generate, range of random var (?)
mcell_ran4(&sead, dscr, 1, 1.0); // Generate random value
double p = dscr[0]; // Get the random value generated by the mcell_ran4 call
double difference = ip->activity / ip->goal_activity; // Find magnitude of difference between activity and goal activity
// Check if p < (difference-2)^2 * delspeed, normalised by time since last check, t - t'.
//
// This means that when difference = 2, chance of deletion is zero
// (i.e. all cells are allowed to at least double their baseline firing rates without
// risking excitotoxicity).
// When difference = 3, chance of deletion per second is delspeed.
// When difference = 4, chance of deletion per second is exponentially higher, etc.
double x = difference - 2.0;
if (x < 0) {
x = 0; // Prevent scalefactors which are <1 from having a positive x^2
}
double threshold = x * x * delspeed * ((time - ip->lastupdate) / 1000.0);
if (p < threshold) {
printf("p = %e, threshold = %e from x^2 * delspeed * timegap:\nx = %e, x^2 = %e, delspeed = %e, x^2*delspeed = %e, timegap (s) = %e\n", p, threshold, x, x*x, delspeed, x*x*delspeed, (time-ip->lastupdate)/1000.0);
ip->dead = 1; // Kill cell
printf("Cell %d has just died (scalefactor = %f)\n\n", ip->id, ip->scalefactor);
}
}
ENDVERBATIM
VERBATIM
double get_avg_activity () {
//Start by implementing retrospectively (i.e. assume network has been trained according to
//pre-defined activity levels, but manually set targets retrospectively to these values by observation)
// - with more time, implement Turrigiano (2008)'s "Factor+ vs Factor-" which balances firing rates
// We could simply set goal_activity to be the current average activity value using
//return ip->activity;
// at an arbitrary time (e.g. when we turn on scaling). But as 'current' activity fluctuates, we don't
// want to be stuck maintaining an unrealistic average firing rate, in the case that the 'current'
// activity value was unusually high at the time of setting the goal.
// It would be better to record an average of the neuron's activity so far, and use that as the goal.
return ip->spkcnt / t;
}
ENDVERBATIM
VERBATIM
void raise_activity_sensor (double time) {
// Update the cell's activity sensor value, assuming this function has been called at the same
// time as a spike at time t
// REQUIRES: time of current spike in ms
// ENSURES: returns activity value in MHz (due to ms timing)
// Raise the activity by (-a + 1) / tau
ip->activity = ip->activity + (-ip->activity + 1.0) / activitytau;
// Update lastupdate time for next decay operation
// -- probably shouldn't set this here, as it's also set in the NET_RECEIVE block on every
// incoming event, and multiple updates of ip->lastupdate in different places will just lead
// to confusion
//ip->lastupdate = time;
// DEBUG: (pick a random cell ID)
//if (ip->id == 9 || ip->id == 10) {
// printf("spike from cell %d (inhib = %d) at time %f --> activity sensor = %f, target activity = %f, average activity = %f, scale = %f\n", ip->id, ip->inhib, time, ip->activity, ip->goal_activity, get_avg_activity(), ip->scalefactor);
//}
}
ENDVERBATIM
VERBATIM
void decay_activity_sensor (double time) {
// Decay the cell's activity sensor value according to the time since last decay update
// In van Rossum et al. (2000), this is called every discrete timestep t
// But this procedure is only called on NET_RECEIVE events, so we need to decay
// taking into account the time since the last decay operation.
// a_t = a_t0 * e(-(1/tau * t-t0))
ip->activity = ip->activity * exp(-activityoneovertau * (time - ip->lastupdate));
}
ENDVERBATIM
VERBATIM
void update_scale_factor (double time) {
// Implements weight scaling according to van Rossum et al. (2000)
// Get difference between goal and current activity
double err = ip->goal_activity - ip->activity;
// Bound error to max_err value in the case that the activity sensor saturates during epileptic activity
// This should prevent the integral from becoming excessively large over a relatively short time,
// and therefore affecting the scaling for a very long time into the future.
//if (err > ip->max_err) {
//err = ip->max_err;
//}
//if (err < -ip->max_err) {
//err = -ip->max_err;
//}
// Set scalefactor
ip->scalefactor += (activitybeta * ip->scalefactor * err + activitygamma * ip->scalefactor * ip->activity_integral_err);
// Bound scalefactor to max_scale to prevent Inf values
if (ip->scalefactor > ip->max_scale) {
ip->scalefactor = ip->max_scale;
}
// Calculate integral error term between sensor and target activity for next time (t')
double timecorrection = time - ip->lastupdate;
// e.g. If last update was 1ms ago, then the time correction = 1
// If last update was 0.1ms ago correction = 0.1, so the accumulated error will be much smaller
// If it's been a long time since the last update, the error will be correspondingly much larger
ip->activity_integral_err += (err * timecorrection);
// DEBUG: (pick a random cell ID)
//if (ip->id == 9 || ip->id == 10) {
// printf("cell %d err = %f, time-corrected err = %f, integral_err = %f\n", ip->id, err, (err * timecorrection), ip->activity_integral_err);
//}
}
ENDVERBATIM
: intf.scalefactor - optional arg sets value
: used by homeostatic synaptic scaling
FUNCTION scalefactor () {
VERBATIM
if (ifarg(1)) IDP->scalefactor = *getarg(1);
return IDP->scalefactor; // Return this cell's scale factor
ENDVERBATIM
}
: intf.activity - optional arg sets value
: used by homeostatic synaptic scaling
FUNCTION activity () {
VERBATIM
if (ifarg(1)) IDP->activity = *getarg(1);
return IDP->activity; // Return this cell's activity sensor value
ENDVERBATIM
}
: intf.goalactivity - optional arg sets value
: used by homeostatic synaptic scaling - target firing rate
FUNCTION goalactivity () {
VERBATIM
if (ifarg(1)) IDP->goal_activity = *getarg(1);
return IDP->goal_activity; // Return this cell's target activity value
ENDVERBATIM
}
: intf.isdead - is the cell dead?
FUNCTION isdead() {
VERBATIM
return IDP->dead; // Return this cell's 'dead' flag
ENDVERBATIM
}