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Fixes for new data structures #2

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merged 1 commit into from Apr 30, 2023
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Fixes for new data structures #2

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3 changes: 3 additions & 0 deletions README
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Expand Up @@ -60,3 +60,6 @@ signature of mcell_ran4_init function and fix hashseed2 argument.

20230228 Fix error due to inconsistent array dimensions. Required by
https://github.com/neuronsimulator/nrn/pull/2024 in NEURON 9+.

20230420 Updated MOD files for compatibility with the new data
structures in the upcoming version 9.0 of NEURON.
67 changes: 45 additions & 22 deletions intf6.mod
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Expand Up @@ -25,6 +25,16 @@ 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*);
Expand Down Expand Up @@ -533,8 +543,15 @@ ENDVERBATIM
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[ip->dvi[i]->_prop->_type])(ip->dvi[i], wts, idty);
_p=_pnt->_prop->param; _ppvar=_pnt->_prop->dparam; ip=IDP; // restore pointers each time
(*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)) {
Expand Down Expand Up @@ -1301,14 +1318,20 @@ PROCEDURE callback (fl) {
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[jp->dvi[i]->_prop->_type])(jp->dvi[i], wts, idtflg);
_p=upnt->_prop->param; _ppvar=upnt->_prop->dparam; // restore pointers
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] || (*(id0**)&(jp->dvi[i]->_prop->dparam[2]))->dead)) i++;
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)
Expand Down Expand Up @@ -1479,7 +1502,7 @@ FUNCTION getdvi () {
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=*((id0**) &((das[i]->_prop->dparam)[2])); // #define sop *_ppvar[2].pval
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]++;
Expand Down Expand Up @@ -1546,7 +1569,7 @@ VERBATIM
dvt=qp->dvt; das=qp->dvi;
for (j=0;j<dvt;j++) {
if (getactive && qp->sprob[j]==0) continue;
if (ip==*((id0**) &((das[j]->_prop->dparam)[2]))) {
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;
Expand Down Expand Up @@ -1588,7 +1611,7 @@ FUNCTION adjlist () {
}
iSyns=0;
for(j=0;j<qp->dvt;j++){
rp=*((id0**) &((qp->dvi[j]->_prop->dparam)[2])); // #define sop *_ppvar[2].pval
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;
Expand Down Expand Up @@ -1666,7 +1689,7 @@ FUNCTION svdvi () {
if(!qp->dvt)continue; //don't write empty pointers if no divergence
for(i=0;i<qp->dvt;i++){
pnnt=qp->dvi[i];
fwrite(&(*(id0**)&(pnnt->_prop->dparam[2]))->id,sizeof(unsigned int),1,fp); // id of output cell
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
Expand Down Expand Up @@ -1854,7 +1877,7 @@ int* getpeconv (id0* ip,int* psz) {
dvt=qp->dvt;
das=qp->dvi;
for (j=0;j<dvt;j++) {
if (ip==*((id0**) &((das[j]->_prop->dparam)[2]))) {
if (ip == id0ptr(das[j]->_prop)) {
if (k>=*psz) {
psz[0]*=2;
pfrom=(int*) realloc((void*)pfrom,psz[0]*sizeof(int));
Expand All @@ -1881,7 +1904,7 @@ int* getpiconv (id0* ip,int* psz) {
dvt=qp->dvt;
das=qp->dvi;
for (j=0;j<dvt;j++) {
if (ip==*((id0**) &((das[j]->_prop->dparam)[2]))) {
if (ip == id0ptr(das[j]->_prop)) {
if (k>=*psz) {
psz[0]*=2;
pfrom=(int*) realloc((void*)pfrom,psz[0]*sizeof(int));
Expand All @@ -1901,7 +1924,7 @@ int myfindidx (id0* ppre,int poid) {
int i; Point_process** das; id0* ppo;
das=ppre->dvi;
for(i=0;i<ppre->dvt;i++) {
ppo=*((id0**) &((das[i]->_prop->dparam)[2])); // #define sop *_ppvar[2].pval
ppo = id0ptr(das[i]->_prop); // #define sop *_ppvar[2].pval
if(ppo->id==poid) return i;
}
return -1;
Expand Down Expand Up @@ -1931,7 +1954,7 @@ static void applyEDOPE (id0* pcell,double myspkt) {
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=*((id0**) &((pcell->dvi[i]->_prop->dparam)[2])); // #define sop *_ppvar[2].pval
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) {
Expand Down Expand Up @@ -1970,7 +1993,7 @@ static void applyIDOPE (id0* pcell,double myspkt) {
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=*((id0**) &((pcell->dvi[i]->_prop->dparam)[2])); // #define sop *_ppvar[2].pval
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) {
Expand Down Expand Up @@ -2009,7 +2032,7 @@ static void applyEXSTDP (id0* pcell,double myspkt) {
}
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=*((id0**) &((pcell->dvi[i]->_prop->dparam)[2])); // #define sop *_ppvar[2].pval
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) {
Expand Down Expand Up @@ -2053,7 +2076,7 @@ static void applyIXSTDP (id0* pcell,double myspkt) {
}
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=*((id0**) &((pcell->dvi[i]->_prop->dparam)[2])); // #define sop *_ppvar[2].pval
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) {
Expand Down Expand Up @@ -2267,7 +2290,7 @@ static void setdvi2 (double *y,double *d,char* s,int dvt,int flag,double* w1,dou
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=(*(id0**)&(pnnt->_prop->dparam[2]))->dead)) {
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++;
Expand Down Expand Up @@ -2307,7 +2330,7 @@ static void setdvi3 (double *y, double *d, char* s, int dvt, double* w1, double*
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=(*(id0**)&(pnnt->_prop->dparam[2]))->dead)) {
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];
}
Expand Down Expand Up @@ -2342,7 +2365,7 @@ PROCEDURE prune () {
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=*((id0**) &((ip->dvi[j]->_prop->dparam)[2])); // #define sop *_ppvar[2].pval
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
}
}
Expand Down Expand Up @@ -2387,7 +2410,7 @@ PROCEDURE turnoff () {
lop(pg->ce,(unsigned int)x[i]);
dvt=qp->dvt; das=qp->dvi;
for (j=0;j<dvt;j++) {
ip=*((id0**) &((das[j]->_prop->dparam)[2])); // sop is *_ppvar[2].pval
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]) {
Expand Down Expand Up @@ -3070,7 +3093,7 @@ static id0* getlp (Object *ob, unsigned int i) {
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=*((id0**) &((pmt->_prop->dparam)[2])); // #define sop *_ppvar[2].pval
myp = id0ptr(pmt->_prop); // #define sop *_ppvar[2].pval
return myp;
}

Expand All @@ -3081,7 +3104,7 @@ static id0* lop (Object *ob, unsigned int i) {
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=*((id0**) &((pmt->_prop->dparam)[2])); // #define sop *_ppvar[2].pval
qp = id0ptr(pmt->_prop); // #define sop *_ppvar[2].pval
return qp;
}

Expand Down