Fixing infot.mod for NEURON 9.0.0

README

@@ -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.

infot.mod

@@ -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_ {
@@ -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;
 }
 
@@ -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
@@ -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);
         }
@@ -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);
 }
 
@@ -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);
@@ -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(); }
     }
@@ -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]; 
@@ -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);
@@ -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);
@@ -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;
@@ -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];