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MOD-C-2-CPP: Compatibility fixed for NEURON 9.0, 8.2 and 8.1 (#1)
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* Fixing infot.mod for NEURON 9.0.0

* Adding changes in infot.mod and misc.h from 136095

* Revert unneeded changes to misc.h

* Added changelog in readme

* Fixed intf_6.mod and related fixes in misc.h

* fixups for new 8.2 wheels

* more compatibility fixes

* fixup 8.1.0

* add include

* Cleanup for merge.

* Object member is called template in C in 8.2

* Include stdint.h for uint32_t.

* Remove duplicate declaration of functions

* mcell_ran4_init: pass a value

* mcell_ran4_init: update readme

* hashseed2: probable bugfix

* cntpx -> cntpxy probable typo (compiler warning fix)

Co-authored-by: Olli Lupton <[email protected]>
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@iomaganaris @olupton
iomaganaris and olupton authored May 27, 2022
1 parent 5f80336 commit bd54e22
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Showing 9 changed files with 215 additions and 198 deletions.
6 changes: 6 additions & 0 deletions README
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Original file line number Diff line number Diff line change
Expand Up @@ -47,5 +47,11 @@ babbling noise can be changed by resetting the value of 'inputseed'
in Line 13 in stim.hoc. After resetting these parameters and
saving the files, simulations can then be started as above.

CHANGELOG

20160921 Updates from the Lytton lab to allow the model to run on mac
OS X.

20220517 Updated MOD files to contain valid C++ and be compatible with
the upcoming versions 8.2 and 9.0 of NEURON. Updated to use post ~2011
signature of mcell_ran4_init function and fix hashseed2 argument.
41 changes: 22 additions & 19 deletions infot.mod
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,9 @@ VERBATIM
#include <stdlib.h>
#include <math.h>
static const double* ITsortdata = NULL; /* used in the quicksort algorithm */
static double tetrospks2(), pdfpr(), tetrospks3();
static double tetrospks2 (double* X1d,double* X2d,double* XO,int szX1,int szXO,int shuf);
static void pdfpr (double* pdf,int szp,int dim, char* name);
static double tetrospks3 (double* X1d,double* X2d,double* X3d,double* XO,int szX1,int szXO,int shuf);
static int dbxi[10];

typedef struct ITNode_ {
Expand All @@ -42,9 +44,9 @@ typedef struct ITNode_ {

ITNode* allocITNode(int idims) {
ITNode* p;
p = calloc(1,sizeof(ITNode));
p = (ITNode*)calloc(1,sizeof(ITNode));
if(!p) { printf("allocITNode: out of mem!\n"); hxe(); return 0x0; }
p->pvals = calloc(idims,sizeof(int));
p->pvals = (int*)calloc(idims,sizeof(int));
return p;
}

Expand Down Expand Up @@ -411,7 +413,7 @@ double tentropd (double* x,double* y,int iLen,int nbins,int xpast,int ypast,int
dsum=0.0;
*sig=-1e6;//init sig to neg
*nTE = 0.0;
sh=cntjxy=cntjx=cntpx=cntpx=0; teavg=testd=te=teout=0.0;
sh=cntjxy=cntjx=cntpx=cntpxy=0; teavg=testd=te=teout=0.0;

px = nbins>0 ? getnormd(x,iLen,nbins) : doublep2intp(x,iLen); //discretize x to nbins, or just copy to ints
py = nbins>0 ? getnormd(y,iLen,nbins) : doublep2intp(y,iLen); //discretize y to nbins, or just copy to ints
Expand Down Expand Up @@ -508,7 +510,7 @@ double tentropd (double* x,double* y,int iLen,int nbins,int xpast,int ypast,int
}
if(verbose>1) {printf("cntjxy=%d\n",cntjxy);
for(i=0;i<cntjxy;i++) {
printf("pjointxy%d: [");
printf("pjointxy: [");
for(j=0;j<jointd;j++) printf("%d ",pjointxy[i][j]);
printf("] , cnt=%d, p=%g\n",pjointxy[i][jointd],pjointxy[i][jointd]/(double)N);
}
Expand Down Expand Up @@ -717,13 +719,13 @@ static double ntedir (void* vv) {
// of X1spikecounts,X2spikecounts onto X3spikecounts
static double tentropspks (void* vv) {
double *X1,*X2,*XO,*X3; int szX1,szX2,szXO,shuf,szX3;
szX1 = vector_instance_px(vv,&X1);
szX1 = vector_instance_px((IvocVect*)vv,&X1);
if((szX2=vector_arg_px(1,&X2))!=szX1) {
printf("tentropspks ERRA: X1,X2 must have same size (%d,%d)\n",szX1,szX2); return -1.0; }
szXO=ifarg(2)?vector_arg_px(2,&XO):0;
shuf=ifarg(3)?((int)*getarg(3)):0;
szX3=ifarg(4)?vector_arg_px(4,&X3):0;
if(szX3) tetrospks3(X1,X2,X3,XO,szX1,szXO,shuf);
if(szX3) return tetrospks3(X1,X2,X3,XO,szX1,szXO,shuf);
else return tetrospks2(X1,X2,XO,szX1,szXO,shuf);
}

Expand Down Expand Up @@ -761,8 +763,8 @@ NTEL2DOFREE:
//*** Vind0.nte(Vind1,LIST,OUTVEC or OUTLIST) // do normalization with H(X2F|X2P)
static double nte (void* vv) {
int i, j, k, ii, jj, oi, nx, ny, omax, sz, ci, bg, flag, nshuf, szX, *x1i, *x2i, x1z, x2z;
ListVec *pLi; Object *obi,*ob; double *x, *y, *out, o1, o2, cnt, *vvo[3]; void *vvl;
nx = vector_instance_px(vv, &x); // index i vector
ListVec *pLi; Object *obi,*ob; double *x, *y, *out, o1, o2, cnt, *vvo[3]; IvocVect *vvl;
nx = vector_instance_px((IvocVect*)vv, &x); // index i vector
ny = vector_arg_px(1, &y); // index j vectors
pLi = AllocListVec(obi=*hoc_objgetarg(2)); // input vectors
ob = *hoc_objgetarg(3);
Expand All @@ -774,7 +776,7 @@ static double nte (void* vv) {
i = ivoc_list_count(ob);
if (i<3) {printf("nte() ERRA out list should be at least 3 (%d)\n",i); hxe();}
for (k=0;k<3;k++) {
j=list_vector_px3(ob, k, &vvo[k], &vvl);
j=list_vector_px3(ob, k, &vvo[k], (void**)&vvl);
if (k==0) omax=j; else if (omax!=j||j<10) {
printf("nte() ERRC: too small %d %d\n",j,omax); hxe(); }
}
Expand Down Expand Up @@ -859,18 +861,18 @@ double entropxfgxpd (double* pXP, double* pXFXP,int minv,int maxv,int szp) {
if (usetable && tmp[3]>=MINLOG2 && tmp[3]<=MAXLOG2) {
tmp[0] -=tmp[2]*_n_LOG2(tmp[3]);
} else { tmp[0] -=tmp[2]* log2d(tmp[3]); if (usetable&&verbose>0.4) {
printf("WARNA:%g outside of [%g,%g] TABLE\n",tmp[4],MINLOG2,MAXLOG2); }}}}
printf("WARNA:%g outside of [%g,%g] TABLE\n",tmp[3],MINLOG2,MAXLOG2); }}}}
return tmp[0];
}

//** entropxfgxp - get conditional entropy of X future given its past: H(XF|XP)
// Vector has elements of X
static double entropxfgxp (void* vv) {
double *x,*pXP,*pXFXP,dret;
int sz,minv,maxv,cnt,i,j,szp,*X;
sz = vector_instance_px(vv,&x);
int sz,minv,maxv,cnt,i,j,szp;
sz = vector_instance_px((IvocVect*)vv,&x);
cnt=0;
X=scrset(sz);
unsigned int* X=scrset(sz);
minv=1e9; maxv=-1e9;
for (i=0;i<sz;i++) {
X[i]=(int)x[i];
Expand Down Expand Up @@ -1099,6 +1101,7 @@ static double tetrospks2 (double* X1d,double* X2d,double* XO,int szX1,int szXO,i
cnt1/=sz; cnt2/=sz; // ignore if not enough of the windows are filled
if (cnt1<binmin) return -11.; else if (cnt2<binmin) return -12.;
if (binmax) if (cnt1>binmax) return -11.; else if (cnt2>binmax) return -12.;
/* this should probably be fabs in C */
if (abs(cnt1-cnt2)>cutoff) return -13.;
}
if(verbose>2)printf("tentropspks:minv1=%d,maxv1=%d,minv2=%d,maxv2=%d\n",minv1,maxv1,minv2,maxv2);
Expand Down Expand Up @@ -1165,7 +1168,7 @@ static double tetrospks2 (double* X1d,double* X2d,double* XO,int szX1,int szXO,i
}

// for debugging -- print out a pdf
static double pdfpr (double* pdf,int szp,int dim, char* name) {
static void pdfpr (double* pdf,int szp,int dim, char* name) {
double x,ds; int i,j,k,l,m,cnt,*nonzero;
ds=0.;
printf("Contents of PDF %s\n",name);
Expand Down Expand Up @@ -1306,9 +1309,9 @@ static double* ITgetrank (int n, double mdata[])
{ int i;
double* rank;
int* index;
rank = calloc(n,sizeof(double));
rank = (double*)calloc(n,sizeof(double));
if (!rank) return NULL;
index = calloc(n,sizeof(int));
index = (int*)calloc(n,sizeof(int));
if (!index)
{ free(rank);
return NULL;
Expand Down Expand Up @@ -1394,13 +1397,13 @@ static double mutinfb (void* v) {

double entropspksd (double* x,int sz) {
double *px,ret,dinf,size;
int i,*X,maxv,minv,cnt,err;
int i,maxv,minv,cnt,err;
if(sz<1) {printf("entropspks ERR0: min size must be > 0!\n"); return -1.0;}
size=(double)sz;
ret=-1.0; err=0;
px=NULL;
minv=1000000000; maxv=-1000000000;
X=scrset(sz*2); // move into integer arrays
unsigned int* X=scrset(sz*2); // move into integer arrays
cnt=0;
for (i=0;i<sz;i++) {
X[i]=(int)x[i];
Expand Down
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