Broadening of activity with flow across neural structures (Lytton et al. 2008)

 Download zip file   Auto-launch 
Help downloading and running models
Accession:116830
"Synfire chains have long been suggested as a substrate for perception and information processing in the nervous system. However, embedding activation chains in a densely connected nervous matrix risks spread of signal that will obscure or obliterate the message. We used computer modeling and physiological measurements in rat hippocampus to assess this problem of activity broadening. We simulated a series of neural modules with feedforward propagation and random connectivity within each module and from one module to the next. ..."
Reference:
1 . Lytton WW, Orman R, Stewart M (2008) Broadening of activity with flow across neural structures. Perception 37:401-7 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Activity Patterns; Temporal Pattern Generation; Spatio-temporal Activity Patterns;
Implementer(s): Lytton, William [billl at neurosim.downstate.edu];
: $Id: vecst.mod,v 1.253 2005/10/07 21:30:32 billl Exp $
 
:* COMMENT
COMMENT
thresh   turns analog vec to BVBASE,1 vec separating at thresh (scalar or vec)
triplet  return location of a triplet in a vector
onoff    turns state vec on or off depending on values in other vecs
bpeval   used by backprop: vo=outp*(1-outp)*del
w        like where but sets chosen nums // modified from .wh in 1.23
dest.xing(src,tvec,thresh) determines where vector crosses in a positive direction 
dest.snap(src,tvec,dt) interpolate src with tvec to prior dt step, saves only highest value
xzero    count 0 crossings by putting in a 1 or -1
negwrap  wrap negative values around to pos (with flag just set to 0)
indset(ind,val) sets spots indexed by ind to val
ismono([arg]) checks if a vector is monotonically increaseing (-1 decreasing)
count(num) count the number of nums in vec
scr.fewind(ind,veclist) // uses ind as index into other vecs
ind.findx(vecAlist,vecBlist) // uses ind as index into vecA's to load in vecB's
ind.sindx(vecAlist,vecBlist) // replace ind elements in vecA's with vecB's values
ind.sindv(vecAlist,valvec) // replace ind elements in vecA's with vals
scr.nind(ind,vec1,vec2[,vec3,vec4]) // uses ind to elim elems in other vecs
ind.keyind(key,vec1,vec2[,vec3,vec4]) // pick out bzw. values from vectors
ind.slct(key,args,veclist) // pick out bzw. values from vectors
ind.slor(key,args,veclist) // do OR rather than AND function of slct
vdest.intrp(flag) // interpolate numbers replacing numbers given as flag
v.insct(v1,v2)   // return v1 intersect v2
vdest.cull(vsrc,key)   // remove values found in key
vdest.redundout(vsrc[,INDFLAG])  // remove repeat values, with flag return indices
ind.mredundout(veclistA[,INDFLAG,veclistB]) // remove repeats from parallel vectors
v.cvlv(v1,v2)   // convolve v1 with v2
v2d      copy into a double block
d2v      copy out of a double block NB: same as vec.from_double()
smgs     rewrite of sumgauss form ivovect.cpp
smsy     sum syn potentials off a tvec
iwr      write integers
ird      read integers
ident     give pointer addresses and sizes
lcat     concatentate all vectors from a list
fread2   like vec.fread but uses flag==6 for unsigned int
vfill    fill vdest with multiple instances of vsrc until reach size
Non-vector routines
isojt    compare 2 objects to see if they're of the same type
eqojt    compare 2 object pointers to see if they point to same thing
sumabs   return sum of absolute values
round_local    round off to nearest integer (_local prevents duplic. mswin name)
ENDCOMMENT

NEURON {
  SUFFIX nothing
  GLOBAL BVBASE, RES, VECST_INSTALLED  : bit vector base number (typically 0 or -1)
}

PARAMETER {
  BVBASE = -1.
  VECST_INSTALLED=0
  : misc
  ERR=-1.3479e121

  : 0 args
  ALL=-1.3479e120
  NEG=-1.3478e120
  POS=-1.3477e120
  CHK=-1.3476e120
  NOZ=-1.3475e120
  : 1 arg
  GTH=-1.3474e120
  GTE=-1.3473e120
  LTH=-1.3472e120
  LTE=-1.3471e120
  EQU=-1.3470e120
  EQV=-1.3469e120 : value equal to same row value in parallel vector
  EQW=-1.3468e120 : value found in other vector
  NEQ=-1.3467e120
  SEQ=-1.3466e120
  RXP=-1.3465e120
  : 2 args
  IBE=-1.3464e120
  EBI=-1.3463e120
  IBI=-1.3462e120
  EBE=-1.3461e120
}

ASSIGNED { RES }

VERBATIM
#include <stdlib.h>
#include <math.h>
#include <limits.h> /* contains MAXLONG */
#include <sys/time.h> 
extern double* hoc_pgetarg();
extern double hoc_call_func(Symbol*, int narg);
extern FILE* hoc_obj_file_arg(int narg);
extern Object** hoc_objgetarg();
extern void vector_resize();
extern int vector_instance_px();
extern void* vector_arg();
extern double* vector_vec();
extern double hoc_epsilon;
extern double chkarg();
extern void set_seed();
extern int ivoc_list_count(Object*);
extern Object* ivoc_list_item(Object*, int);
extern int hoc_is_double_arg(int narg);
int list_vector_px();
int list_vector_px2();
int list_vector_resize();
static double sc[6];

typedef struct BVEC {
 int size;
 int bufsize;
 short *x;
 Object* o;
} bvec;

#define BYTEHEADER int _II__;  char *_IN__; char _OUT__[16]; int BYTESWAP_FLAG=0;
#define BYTESWAP(_X__,_TYPE__) \
    if (BYTESWAP_FLAG == 1) { \
	_IN__ = (char *) &(_X__); \
	for (_II__=0;_II__<sizeof(_TYPE__);_II__++) { \
		_OUT__[_II__] = _IN__[sizeof(_TYPE__)-_II__-1]; } \
	(_X__) = *((_TYPE__ *) &_OUT__); \
    }

#define UNCODE(_X_,_J_,_Y_) {(_Y_)=floor((_X_)/sc[(_J_)])/sc[4]; \
                             (_Y_)=floor(sc[4]*((_Y_)-floor(_Y_))+0.5);}
ENDVERBATIM

:* v1.ident() gives addresses and sizes
VERBATIM
static double ident(void* vv) {
  int nx,bsz; double* x;
  nx = vector_instance_px(vv, &x);
  bsz=vector_buffer_size(vv);
  printf("Obj*%x Dbl*%x Size: %d Bufsize: %d\n",vv,x,nx,bsz);
}
ENDVERBATIM
 
:* v1.indset(ind,x[,y]) sets indexed values to x and other values to optional y
VERBATIM
static double indset(void* vv) {
	int i, nx, ny, nz, flag;
	double* x, *y, *z, val, val2 ;
	nx = vector_instance_px(vv, &x);
	ny = vector_arg_px(1, &y);
        if (hoc_is_object_arg(2)) { 
          flag=1;
          nz = vector_arg_px(2, &z); 
          if (ny!=nz) { hoc_execerror("v.indset: Vector sizes don't match.", 0); }
        } else { flag=0; val=*getarg(2); }
        if (ifarg(3)) { 
          val2 = *getarg(3); 
          for (i=0; i<nx; i++) { x[i]=val2; }
        }
	for (i=0; i<ny; i++) {
	  if (y[i] > nx) { hoc_execerror("v.indset: Index exceeds vector size", 0); }
          if (flag) x[(int)y[i]]=z[i]; else x[(int)y[i]]=val;
        }
	return i;
}
ENDVERBATIM
 
VERBATIM
/* Maintain parallel int vector to avoid slowness of repeated casts */
static int scrsz=0;
static unsigned int *scr;
static double dcr[100]; // scratch area for doubles
ENDVERBATIM

:* tmp.fewind(ind,veclist)
: picks out numbers from multiple vectors using index ind
VERBATIM
static double fewind (void* vv) {
  int i, j, nx, ni, nv[10], num;
  Object* ob;
  double *x, *ind, *vvo[10];
  nx = vector_instance_px(vv, &x);
  ni = vector_arg_px(1, &ind);
  ob = *hoc_objgetarg(2);
  num = ivoc_list_count(ob);
  if (num>10) hoc_execerror("ERR: fewind can only handle 10 vectors", 0);
  for (i=0;i<num;i++) { 
    nv[i] = list_vector_px(ob, i, &vvo[i]);
    if (nx!=nv[i]) { printf("fewind ERR %d %d %d\n",i,nx,nv[i]);
      hoc_execerror("Vectors must all be same size: ", 0); }
  }
  if (ni>scrsz) { 
    if (scrsz>0) { free(scr); scr=(unsigned int *)NULL; }
    scrsz=ni+10000;
    scr=(unsigned int *)ecalloc(scrsz, sizeof(int));
  }
  for (i=0;i<ni;i++) { scr[i]=(int)ind[i]; /* copy into integer array */
    if (scr[i]>=nx || scr[i]<0) { printf("fewind ERR1 %d %d\n",scr[i],nx);
    hoc_execerror("Index vector out-of-bounds", 0); }
  }
  for (j=0;j<num;j++) {
    for (i=0;i<ni;i++) x[i]=vvo[j][scr[i]];    
    for (i=0;i<ni;i++) vvo[j][i]=x[i];   
    list_vector_resize(ob, j, ni);
  }
  return ni;
}
ENDVERBATIM


:* ind.findx(vecAlist,vecBlist) 
: uses ind as index into vecA's to load in vecB's (for select); a nondestructive fewind()
VERBATIM
static double findx (void* vv) {
  int i, j, ni, nx, av[11], bv[11], num;
  Object *ob1, *ob2;
  double *ind, *avo[11], *bvo[11];
  ni = vector_instance_px(vv, &ind);
  ob1 = *hoc_objgetarg(1);
  ob2 = *hoc_objgetarg(2);
  num = ivoc_list_count(ob1);
  i = ivoc_list_count(ob2);
  if (i!=num) hoc_execerror("findx ****ERRA****: lists have different counts", 0);
  if (num>11) hoc_execerror("findx ****ERRB****: can only handle 11 vectors", 0);
  for (i=0;i<num;i++) { 
    av[i]=list_vector_px(ob1, i, &avo[i]); // source vectors
    if (av[0]!=av[i]) { printf("findx ****ERRC**** %d %d %d\n",i,av[0],av[i]);
      hoc_execerror("Src vectors must all be same size: ", 0); }
  }
  nx=av[0]; // size of source vecs
  for (i=0;i<num;i++) { 
    bv[i]=list_vector_px2(ob2, i, &bvo[i], &vv); /* dest vectors */
    if (vector_buffer_size(vv)<ni) { 
      printf("findx ****ERRD**** arg#%d need:%d sz:%d\n",num+i+1,ni,vector_buffer_size(vv));
      hoc_execerror("Destination vector with insufficient size: ", 0); 
    } else {
      vector_resize(vv, ni);
    }
  }
  if (ni>scrsz) { 
    if (scrsz>0) { free(scr); scr=(unsigned int *)NULL; }
    scrsz=ni+10000;
    scr=(unsigned int *)ecalloc(scrsz, sizeof(int));
  }
  for (i=0;i<ni;i++) { scr[i]=(int)ind[i]; // copy into integer array
    if (scr[i]>=nx || scr[i]<0) { printf("findx ****ERRE**** **** IND:%d SZ:%d\n",scr[i],nx);
      hoc_execerror("Index vector out-of-bounds", 0); }
  }
  for (j=0,i=0;j<num;j++) for (i=0;i<ni;i++) bvo[j][i]=avo[j][scr[i]];    
  return ni;
}
ENDVERBATIM

:* ind.sindx(vecAlist,vecBlist)
: uses ind as index into vecA's to replace with elements from vecB's
VERBATIM
static double sindx (void* vv) {
  int i, j, ni, nx, av[11], bv[11], num;
  Object *ob1, *ob2;
  double *ind, *avo[11], *bvo[11];
  ni = vector_instance_px(vv, &ind);
  ob1 = *hoc_objgetarg(1);
  ob2 = *hoc_objgetarg(2);
  num = ivoc_list_count(ob1);
  i = ivoc_list_count(ob2);
  if (num!=i) hoc_execerror("sindx ****ERRA****: two vec lists have different counts", 0);
  if (num>11) hoc_execerror("sindx ****ERRB****: can only handle 11 vectors", 0);
  for (i=0;i<num;i++) { 
    av[i]=list_vector_px(ob1, i, &avo[i]); // dest vectors
    if (av[0]!=av[i]) { printf("sindx ****ERRC**** %d %d %d\n",i,av[0],av[i]);
      hoc_execerror("Dest. vectors must all be same size: ", 0); }
  }
  nx=av[0]; // size of dest vecs
  for (i=0;i<num;i++) { 
    bv[i]=list_vector_px(ob2, i, &bvo[i]); /* source vectors */
  if (bv[i]!=ni) { 
    printf("sindx ****ERRD**** arg#%d does note match ind length %d vs %d\n",num+i+1,ni,bv[i]);
    hoc_execerror("Source vector with insufficient size: ", 0); }
  }
  if (ni>scrsz) { 
    if (scrsz>0) { free(scr); scr=(unsigned int *)NULL; }
    scrsz=ni+10000;
    scr=(unsigned int *)ecalloc(scrsz, sizeof(int));
  }
  for (i=0;i<ni;i++) { scr[i]=(int)ind[i]; // copy into integer array
    if (scr[i]>=nx || scr[i]<0) { 
      printf("sindx ****ERRE**** IND:%d SZ:%d\n",scr[i],nx);
      hoc_execerror("Index vector out-of-bounds", 0); }
  }
  for (j=0,i=0;j<num;j++) for (i=0;i<ni;i++) avo[j][scr[i]]=bvo[j][i];
  return ni;
}
ENDVERBATIM

:* ind.sindv(vecAlist,valvec)
: uses ind as index into vecA's to replace with values in valvec
VERBATIM
static double sindv(void* vv) {
  int i, j, ni, nx, av[11], bv, num;
  Object* ob;
  double *ind, *avo[11], *bvo;
  ni = vector_instance_px(vv, &ind);
  ob = *hoc_objgetarg(1);
  bv=vector_arg_px(2, &bvo); // source vector
  num = ivoc_list_count(ob);
  if (num>11) hoc_execerror("sindv ****ERRA****: can only handle 11 vectors", 0);
  for (i=0;i<num;i++) { 
    av[i]=list_vector_px(ob, i, &avo[i]); // dest vectors
    if (av[0]!=av[i]) { printf("sindv ****ERRC**** %d %d %d\n",i,av[0],av[i]);
      hoc_execerror("Dest. vectors must all be same size: ", 0); }
  }
  nx=av[0]; // size of source vecs
  if (bv!=num) { 
    printf("sindv ****ERRD**** Vector arg does note match list count %d vs %d\n",num,bv);
    hoc_execerror("Source vector is wrong size: ", 0); }
  if (ni>scrsz) { 
    if (scrsz>0) { free(scr); scr=(unsigned int *)NULL; }
    scrsz=ni+10000;
    scr=(unsigned int *)ecalloc(scrsz, sizeof(int));
  }
  for (i=0;i<ni;i++) { scr[i]=(int)ind[i]; // copy into integer array
    if (scr[i]>=nx || scr[i]<0) { 
      printf("sindv ****ERRE**** IND:%d SZ:%d\n",scr[i],nx);
      hoc_execerror("Index vector out-of-bounds", 0); }
  }
  for (j=0,i=0;j<num;j++) for (i=0;i<ni;i++) avo[j][scr[i]]=bvo[j];
  return ni;
}
ENDVERBATIM

:* ind.slct(key,args,veclist)
: picks out indices of numbers in key from multiple vectors
VERBATIM
static double slct (void* vv) {
  int i, j, k, m, n, p, ni, nk, na, nv[10], num, fl, lc, field[10];
  Object* lob;
  double *ind, *key, *arg, *vvo[10], val;

  ni = vector_instance_px(vv, &ind); // vv is ind
  nk = vector_arg_px(1, &key);
  na = vector_arg_px(2, &arg);
  lob = *hoc_objgetarg(3);
  num = ivoc_list_count(lob);
  if (num>10) hoc_execerror("ERR: vecst::slct can only handle 10 vectors", 0);

  for (i=0,j=0,k=0;i<num;i++,j++) { 
    nv[i] = list_vector_px(lob, i, &vvo[i]);
    if (ni!=nv[i] && (key[j]!=EQW || k!=1)) {
      printf("vecst::slct ERR %d %d %d %d %d\n",i,j,k,ni,nv[i]);
      hoc_execerror("index and searched vectors must all be same size: ", 0); 
    }
    if (key[j]==EQW || key[j]==EQV) if (k==0){j--;k++;} else k=0; // EQW,EQV take 2 vector args 
  }
  for (j=0;j<num;j++) { // look for fields
    field[j]=-1;
    if (key[j]<=EBE && key[j]>=ALL) { field[j]=0;
    } else for (m=1;m<=5;m++) {
      if (key[j]<=EBE*(m+1) && key[j]>=ALL*(m+1)) { // m is is field key 1-5
        key[j]/=(m+1);
        field[j]=m;
      }
    }
    if (field[j]==-1) {printf("vecst::slct ERRF %g\n",key[j]); hoc_execerror("",0); }
  }
  if (2*nk!=na) { printf("vecst::slct ERR3 %d %d\n",nk,na); 
    hoc_execerror("Arg vector must be double key length",0); }
  for (i=0,n=0;i<nk;i++) if (key[i]==EQV || key[i]==EQW) n++; // special cases take 2 vec args
  if (nk+n!=num) { 
    printf("vecst::slct ERR2 %d(keys)+%d(EQV/W)!=%d(vecs)\n",nk,n,num); 
    hoc_execerror("Key length must be number of vecs + num of EQV/W",0); }
  for (j=0,k=0,m=0;j<ni;j++) { // j steps through elements of vectors
    for (i=0,m=0,n=0,fl=1;i<num;i++,n++,m+=2) { // i steps thru key, m thru args
      if (field[n]==0) val=vvo[i][j]; else UNCODE(vvo[i][j],field[n],val);
      if (key[n]==ALL) continue; // OK - do nothing
      if (key[n]==NOZ)        { if (val==0.) {fl=0; break;} else continue; 
      } else if (key[n]==POS) { if (val<=0.) {fl=0; break;} else continue; 
      } else if (key[n]==NEG) { if (val>=0.) {fl=0; break;} else continue; 
      } else if (key[n]==GTH) { if (val<=arg[m]) {fl=0; break;} else continue; 
      } else if (key[n]==GTE) { if (val< arg[m]) {fl=0; break;} else continue; 
      } else if (key[n]==LTH) { if (val>=arg[m]) {fl=0; break;} else continue; 
      } else if (key[n]==LTE) { if (val> arg[m]) {fl=0; break;} else continue; 
      } else if (key[n]==EQU) { if (val!=arg[m]) {fl=0; break;} else continue; 
      } else if (key[n]==EQV) { if (val!=vvo[i+1][j]) { 
          fl=0; break;} else { i++; continue; }
      } else if (key[n]==EQW) {  // check value against values in following vec
        fl=0; // assume it's not going to match
        for (p=0;p<nv[i+1];p++) if (val==vvo[i+1][p]) {fl=1; break;}
        if (fl==0) break; else { i++; continue; }
      } else if (key[n]==NEQ) { if (val==arg[m]) {fl=0; break;} else continue; 
      } else if (key[n]==IBE) { if ((val< arg[m])||(val>=arg[m+1])) {
          fl=0; break; } else continue;  // IBE="[)" include-bracket-exclude
      } else if (key[n]==EBI) { if ((val<=arg[m])||(val> arg[m+1])) { 
          fl=0; break; } else continue;   // "(]" : exclude-bracket-include
      } else if (key[n]==IBI) { if ((val< arg[m])||(val> arg[m+1])) {
          fl=0; break; } else continue;   // "[]" : include-bracket-include
      } else if (key[n]==EBE) { if ((val<=arg[m])||(val>=arg[m+1])) {
          fl=0; break; } else continue;   // "()" : exclude-bracket-exclude
      } else {printf("vecst::slct ERR4 %g\n",key[n]); hoc_execerror("Unknown key",0);}
    }
    if (fl) ind[k++]=j; // all equal
  }
  vector_resize(vv, k);
  return k;
}
ENDVERBATIM

:* ind.slor(key,args,vec1,vec2[,vec3,vec4,...])
: picks out indices of numbers in key from multiple vectors
VERBATIM
static double slor(void* vv) {
  int i, j, k, m, n, p, ni, nk, na, nv[10], num, fl, field[10];
  Object* lob;
  double *ind, *key, *arg, *vvo[10], val;

  ni = vector_instance_px(vv, &ind); // vv is ind
  nk = vector_arg_px(1, &key);
  na = vector_arg_px(2, &arg);
  lob = *hoc_objgetarg(3);
  num = ivoc_list_count(lob);
  if (num>10) hoc_execerror("ERR: vecst::slor can only handle 10 vectors", 0);

  for (i=0,j=0,k=0;i<num;i++,j++) { 
    nv[i] = list_vector_px(lob, i, &vvo[i]);
    if (ni!=nv[i] && (key[j]!=EQW || k!=1)) {
      printf("vecst::slct ERR %d %d %d %d %d\n",i,j,k,ni,nv[i]);
      hoc_execerror("index and searched vectors must all be same size: ", 0); 
    }
    if (key[j]==EQW || key[j]==EQV) if (k==0){j--;k++;} else k=0; // k counts 2 vecs
  }
  for (j=0;j<num;j++) { // look for fields
    field[j]=-1;
    if (key[j]<=EBE && key[j]>=ALL) { field[j]=0;
    } else for (m=1;m<=5;m++) {
      if (key[j]<=EBE*(m+1) && key[j]>=ALL*(m+1)) { // m is is field key 1-5
        key[j]/=(m+1);
        field[j]=m;
      }
    }
    if (field[j]==-1) {printf("vecst::slct ERRF %g\n",key[j]); hoc_execerror("",0); }
  }
  if (2*nk!=na) { printf("vecst::slor ERR3 %d %d\n",nk,na); 
    hoc_execerror("Arg vector must be double key length",0); }
  for (i=0,n=0;i<nk;i++) if (key[i]==EQV || key[i]==EQW) n++; // special case takes 2 vec args
  if (nk+n!=num) { 
    printf("vecst::slor ERR2 %d(keys)+%d(EQV)!=%d(vecs)\n",nk,n,num); 
    hoc_execerror("Key length must be number of vecs + num of EQV",0); }
  for (j=0,k=0,m=0;j<ni;j++) { // j steps through elements of vectors
    for (i=0,m=0,n=0,fl=0;i<num;i++,n++,m+=2) { // i steps thru key, m thru args
      if (field[n]==0) val=vvo[i][j]; else UNCODE(vvo[i][j],field[n],val);
      if (key[n]==ALL) {fl=1; break;} // OK - do nothing
      if (key[n]==NOZ)        { if (val==0.) continue; else {fl=1; break;} 
      } else if (key[n]==POS) { if (val<=0.) continue; else {fl=1; break;} 
      } else if (key[n]==NEG) { if (val>=0.) continue; else {fl=1; break;} 
      } else if (key[n]==GTH) { if (val<=arg[m]) continue; else {fl=1; break;} 
      } else if (key[n]==GTE) { if (val< arg[m]) continue; else {fl=1; break;} 
      } else if (key[n]==LTH) { if (val>=arg[m]) continue; else {fl=1; break;} 
      } else if (key[n]==LTE) { if (val> arg[m]) continue; else {fl=1; break;} 
      } else if (key[n]==EQU) { if (val!=arg[m]) continue; else {fl=1; break;} 
      } else if (key[n]==EQV) { if (val!=vvo[i+1][j]) continue; else { 
          i++; fl=1; break; }
      } else if (key[n]==EQW) {  // check value against values in following vec
        fl=0; // assume it's not going to match
        for (p=0;p<nv[i+1];p++) if (val==vvo[i+1][p]) {fl=1; break;}
        if (fl==1) break; else { i++; continue; }
      } else if (key[n]==NEQ) { if (val==arg[m]) continue; else {fl=1; break;} 
      } else if (key[n]==IBE) { if ((val< arg[m])||(val>=arg[m+1])) {
          continue; } else {fl=1; break;}  // IBE="[)" include-bracket-exclude
      } else if (key[n]==EBI) { if ((val<=arg[m])||(val> arg[m+1])) { 
          continue; } else {fl=1; break;}   // "(]" : exclude-bracket-include
      } else if (key[n]==IBI) { if ((val< arg[m])||(val> arg[m+1])) {
          continue; } else {fl=1; break;}   // "[]" : include-bracket-include
      } else if (key[n]==EBE) { if ((val<=arg[m])||(val>=arg[m+1])) {
          continue; } else {fl=1; break;}   // "()" : exclude-bracket-exclude
      } else {printf("vecst::slor ERR4 %g\n",key[n]); hoc_execerror("Unknown key",0);}
    }
    if (fl) ind[k++]=j; // all equal
  }
  vector_resize(vv, k);
  return k;
}
ENDVERBATIM

:* v.iwr()
VERBATIM
static double iwr(void* vv) {
  int i, j, nx;
  double *x;
  FILE* f, *hoc_obj_file_arg();
  f = hoc_obj_file_arg(1);
  nx = vector_instance_px(vv, &x);
  if (nx>scrsz) { 
    if (scrsz>0) { free(scr); scr=(unsigned int *)NULL; }
    scrsz=nx+10000;
    scr=(unsigned int *)ecalloc(scrsz, sizeof(int));
  }
  for (i=0;i<nx;i++) scr[i]=(int)x[i]; /* copy into integer array */
  fwrite(&nx,sizeof(int),1,f);  // write out the size
  fwrite(scr,sizeof(int),nx,f);
  return nx;
}
ENDVERBATIM

:* v.ird()
VERBATIM
static double ird(void* vv) {
  int i, j, nx, n;
  double *x;
  FILE* f, *hoc_obj_file_arg();
  f = hoc_obj_file_arg(1);
  nx = vector_instance_px(vv, &x);
  fread(&n,sizeof(int),1,f);  // size
  if (n>scrsz) { 
    if (scrsz>0) { free(scr); scr=(unsigned int *)NULL; }
    scrsz=n+10000;
    scr=(unsigned int *)ecalloc(scrsz, sizeof(int));
  }
  if (n!=nx) { 
    nx=vector_buffer_size(vv);
    if (n<=nx) {
      vector_resize(vv, n); nx=n; 
    } else {
      printf("%d > %d :: ",n,nx);
      hoc_execerror("Vector max capacity too small for ird ", 0);
    }
  }
  fread(scr,sizeof(int),n,f);
  for (i=0;i<nx;i++) x[i]=(double)scr[i];
  return n;
}
ENDVERBATIM

:* v.fread2()
VERBATIM
static double fread2(void* vv) {
  int i, j, nx, n, type, maxsz;
  double *x;
  FILE* fp, *hoc_obj_file_arg();
  BYTEHEADER

  fp = hoc_obj_file_arg(1);
  nx = vector_instance_px(vv, &x);
  maxsz=vector_buffer_size(vv);
  n = (int)*getarg(2);
  type = (int)*getarg(3);
  if (n>maxsz) {
    printf("%d > %d :: ",n,maxsz);
    hoc_execerror("Vector max capacity too small for fread2 ", 0);
  } else {
    vector_resize(vv, n);
  }
  if (type==6 || type==16) {         // unsigned ints
    unsigned int *xs;
    if (n>scrsz) { 
      if (scrsz>0) { free(scr); scr=(unsigned int *)NULL; }
      scrsz=n+10000;
      scr=(unsigned int *)ecalloc(scrsz, sizeof(int));
    }
    xs=(unsigned int*)scr;
    fread(xs,sizeof(int),n,fp);
    if (type==16) BYTESWAP_FLAG=1;
    for (i=0;i<n;i++) {
      BYTESWAP(scr[i],int)
      x[i]=(double)scr[i];
    }
    return n;
  } if (type==3 || type==13) { // straight float reads
    float *xf = (float *)malloc(n * (unsigned)sizeof(float));
    fread(xf,sizeof(float),n,fp);
    if (type==13) BYTESWAP_FLAG=1;
    for (i=0;i<n;i++) {
      BYTESWAP(xf[i],float)
      x[i]=(double)xf[i];
    }
    free((char *)xf);    
  } else hoc_execerror("Type unsupported in fread2 ", 0);
}
ENDVERBATIM

:* ind.insct(v1,v2)
: return v1 intersect v2
VERBATIM
static double insct (void* vv) {
	int i, j, k, nx, nv1, nv2, maxsz;
	double *x, *v1, *v2;
	nx = vector_instance_px(vv, &x);
        maxsz=vector_buffer_size(vv);
        vector_resize(vv, maxsz);
	nv1 = vector_arg_px(1, &v1);
	nv2 = vector_arg_px(2, &v2);
        for (i=0,k=0;i<nv1;i++) for (j=0;j<nv2;j++) if (v1[i]==v2[j]) {
          if (k<maxsz) { x[k++]=v1[i]; } else {k++;}}  /* v1[i] found in both vectors */
        if (k>maxsz) { 
          printf("\tinsct WARNING: ran out of room: %d<%d\n",maxsz,k);
        } else { vector_resize(vv, k); }
	return (double)k;
}
ENDVERBATIM

:* vdest.vfill(vsrc)
: fill vdest with multiple instances of vsrc until reach size
VERBATIM
static double vfill (void* vv) {
	int i, nx, nv1;
	double *x, *v1;
	nx = vector_instance_px(vv, &x);
	nv1 = vector_arg_px(1, &v1);
        for (i=0;i<nx;i++) x[i]=v1[i%nv1];
}
ENDVERBATIM

:* vec.cull(src,key)
: remove numbers in vec that are found in the key
VERBATIM
static double cull (void* vv) {
	int i, j, k, nx, nv1, nv2, maxsz, flag;
	double *x, *v1, *v2;
	nx = vector_instance_px(vv, &x);
        maxsz=vector_buffer_size(vv);
        vector_resize(vv, maxsz);
	nv1 = vector_arg_px(1, &v1);
	nv2 = vector_arg_px(2, &v2);
        for (i=0,k=0;i<nv1;i++) {
          flag=1;
          for (j=0;j<nv2;j++) if (v1[i]==v2[j]) flag=0;
          if (flag) {if (k<maxsz) { x[k++]=v1[i]; } else { k++; }}
        }
        if (k>maxsz) { 
          printf("\tcull WARNING: ran out of room: %d<%d\n",maxsz,k);
        } else { vector_resize(vv, k); }
	return (double)k;
}
ENDVERBATIM

:* dest.redundout(src[,INDFLAG])
: flag redundant numbers; must sort src first
: with indflag set just returns indices of locations rather than values
VERBATIM
static double redundout(void* vv) {
	int i, j, nx, nv1, maxsz, indflag;
	double *x, *v1, val;
        if (ifarg(2)) indflag=1; else indflag=0; 
	nx = vector_instance_px(vv, &x);
        maxsz=vector_buffer_size(vv);
        vector_resize(vv, maxsz);
	nv1 = vector_arg_px(1, &v1);
        val=v1[0]; x[0]=(indflag?0:val);
        for (j=1,i=1;i<nv1&&j<maxsz;i++) if (v1[i]!=val) { val=v1[i]; x[j++]=(indflag?i:val); }
        if (j==maxsz) { 
          printf("\tredundout WARNING: ran out of room: %d<needed\n",maxsz);
        } else { vector_resize(vv, j); }
	return (double)j;
}
ENDVERBATIM

:* ind.mredundout(veclistA[,INDFLAG,veclistB])
: check redundancy across multiple parallel vectors veclistA
: with indflag 1, returns index of matchs in ind but does not alter vecs in veclistA
: will also remove from veclistB in parallel 
: leaves the last of a series of matches 
: with indflag set just returns indices of locations rather than values
: NB using indices will to .remove match items will give results that differ from 
: direct use (last vs first of a series -- will be seen in the other columns -- ie veclistB)
VERBATIM
static double mredundout (void* vv) {
  int i, j, k, m, p, q, maxsz, ns, nx, av[11], bv[11], num, numb, indflag, match;
  Object *ob, *ob2;
  double *x, *avo[11], *bvo[11], val[11];
  void *vva[11],*vvb[11];
  nx = vector_instance_px(vv, &x);
  ob = *hoc_objgetarg(1);
  if (ifarg(2)) indflag=(int)*getarg(2); else indflag=0; 
  if (ifarg(3)) { 
    ob2 = *hoc_objgetarg(3);
    numb = ivoc_list_count(ob2);
  } else numb=0;
  maxsz=vector_buffer_size(vv);
  if (indflag) vector_resize(vv, maxsz); // else vector is not used
  num = ivoc_list_count(ob);
  if (num>11) hoc_execerror("mredundout ****ERRA****: can only handle 11 vectors", 0);
  for (i=0;i<num;i++) { 
    av[i]=list_vector_px2(ob, i, &avo[i], &vva[i]);
    if (av[0]!=av[i]) { printf("mredundout ****ERRC**** %d %d %d\n",i,av[0],av[i]);
      hoc_execerror("Vectors must all be same size: ", 0); }
  }
  ns=av[0]; // size of source vecs
  for (i=0;i<numb;i++) { 
    bv[i]=list_vector_px2(ob2, i, &bvo[i], &vvb[i]);
    if (ns!=bv[i]) { printf("mredundout ****ERRC2**** %d %d %d\n",i,ns,bv[i]);
      hoc_execerror("Vectors must all be same size: ", 0); }
  }
  if (ns/4>scrsz) { 
    if (scrsz>0) { free(scr); scr=(unsigned int *)NULL; }
    scrsz=ns/4+10000;
    scr=(unsigned int *)ecalloc(scrsz, sizeof(int));
  }
  for (j=0;j<num;j++) val[j]=avo[j][0]; // initialize the val array
  for (i=1,k=0;i<ns;i++) { 
    for (j=0,match=1;j<num;j++) {
      if (val[j]!=avo[j][i]) { match=0; break; } // if no match say so
    }
    if (match) { // add this one to the list
      if (k>=scrsz){printf("mredundout****ERRD**** over scr size %d\n",k);hoc_execerror("", 0);}
      scr[k++]=i; // flag to get rid of this one
    } else for (j=0;j<num;j++) val[j]=avo[j][i]; // copy next set of vals
  }
  if (indflag) { // just fill ind with indices of the repeats
    if (k>maxsz){printf("mredundout****ERRE**** vec overflow %d>%d\n",k,maxsz);hoc_execerror("", 0);}
    for (i=0;i<k;i++) x[i]=(double)scr[i];
    vector_resize(vv, k);
  } else { // remove all the repeat rows
    for (i=0,p=scr[0]; i<k-1; i++) { // iter thru the inds to remove
      for (m=scr[i],p--; m<scr[i+1]; m++,p++) { // move everything down till next ind
        for (j=0;j<num; j++) avo[j][p]=avo[j][m]; // go through all the A list vecs
        for (j=0;j<numb;j++) bvo[j][p]=bvo[j][m]; // go through B list vecs
      }
    }
    for (m=scr[i],p--; m<ns; m++,p++) { // finish up by moving down from last ind to end
      for (j=0;j<num; j++) avo[j][p]=avo[j][m]; 
      for (j=0;j<numb;j++) bvo[j][p]=bvo[j][m]; 
    }
    for (j=0;j<num; j++) vector_resize(vva[j], ns-k); // resize all the vectors
    for (j=0;j<numb;j++) vector_resize(vvb[j], ns-k);
  }
  return k;
}
ENDVERBATIM

:* vdest.cvlv(vsrc,vfilt)
: convolution
VERBATIM
static double cvlv(void* vv) {
  int i, j, k, nx, nsrc, nfilt;
  double *x, *src, *filt, sum, lpad, rpad;
  nx = vector_instance_px(vv, &x);
  nsrc = vector_arg_px(1, &src);
  nfilt = vector_arg_px(2, &filt);
  if (nx!=nsrc) { hoc_execerror("Vectors not same size: ", 0); }
  if (nfilt>nsrc) { hoc_execerror("Filter bigger than source ", 0); }
  for (i=0;i<nx;i++) {
    x[i]=0.0;
    for (j=0,k=i-(int)(nfilt/2);j<nfilt;j++,k++) {
      if (k>0 && k<nsrc-1) x[i]+=filt[j]*src[k];
    }
  }
}
ENDVERBATIM

:* vdest.intrp(flag)
: interpolate numbers replacing numbers given as flag
VERBATIM
static double intrp(void* vv) {
  int i, la, lb, nx;
  double *x, fl, a, b;
  nx = vector_instance_px(vv, &x);
  fl = *getarg(1);
  i=0; a=x[0]; la=0;
  if (a==fl) a=0;
  while (i<nx-1) {
    for (i=la+1;x[i]==fl && i<nx-1; i++) ; /* find the next one */
    b=x[i]; lb=i;
    for (i=la+1; i<lb; i++) x[i]= a + (b-a)/(lb-la)*(i-la);
    a=b; la=lb;
  }
  return (double)fl;
}
ENDVERBATIM

:* vec.sumabs()
: return sum of abs values
VERBATIM
static double sumabs(void* vv) {
  int i, nx;
  double *x, sum;
  nx = vector_instance_px(vv, &x);
  for (sum=0,i=0;i<nx; i++) sum+=fabs(x[i]);
  return sum;
}
ENDVERBATIM

:* tmp.nind(ind,vec1,vec2[,vec3,vec4,...])
: picks out numbers not in ind from multiple vectors
: ind must be sorted
VERBATIM
static double nind(void* vv) {
	int i, j, k, m, nx, ni, nv[10], num, c, last;
	double *x, *ind, *vvo[10];
	nx = vector_instance_px(vv, &x);
        for (i=0;ifarg(i);i++);
	if (i>9) hoc_execerror("ERR: nind can only handle 9 vectors", 0);
	num = i-2; /* number of vectors to be picked apart */
        for (i=0;i<num;i++) { 
          nv[i] = vector_arg_px(i+2, &vvo[i]);
          if (nx!=nv[i]) { printf("nind ERR %d %d %d\n",i,nx,nv[i]);
            hoc_execerror("Vectors must all be same size: ", 0); }
        }
        ni = vector_arg_px(1, &ind);
        c = nx-ni; /* the elems indexed are to be eliminated */
        if (ni>scrsz) { 
          if (scrsz>0) { free(scr); scr=(unsigned int *)NULL; }
          scrsz=ni+10000;
          scr=(unsigned int *)ecalloc(scrsz, sizeof(int));
        }
        for (i=0,last=-1;i<ni;i++) { 
          scr[i]=(int)ind[i]; /* copy into integer array */
          if (scr[i]<0 || scr[i]>=nx) hoc_execerror("nind(): Index out of bounds", 0);
          if (scr[i]<=last) hoc_execerror("nind(): indices should mono increase", 0);
          last=scr[i];
        }
        for (j=0;j<num;j++) { /* each output vec */
          for (i=0,last=-1,m=0;i<ni;i++) { /* the indices of ind */
            for (k=last+1;k<scr[i];k++) { x[m++]=vvo[j][k]; }
            last=scr[i];
          }
          for (k=last+1;k<nx;k++,m++) { x[m]=vvo[j][k]; }
          for (i=0;i<c;i++) vvo[j][i]=x[i];   
          vv=vector_arg(j+2); vector_resize(vv, c);
        }
	return c;
}
ENDVERBATIM

:* ind.keyind(key,vec1,vec2[,vec3,vec4,...])
: picks out indices of numbers in key from multiple vectors
VERBATIM
static double keyind(void* vv) {
  int i, j, k, ni, nk, nv[10], num;
  double *ind, *key, *vvo[10];
  ni = vector_instance_px(vv, &ind); // vv is ind
  for (i=0;ifarg(i);i++); i--; // drop back by one to get numarg()
  if (i>10) hoc_execerror("ERR: keyind can only handle 9 vectors", 0);
  num = i-1; /* number of vectors to be picked apart */
  for (i=0;i<num;i++) { 
    nv[i] = vector_arg_px(i+2, &vvo[i]);
    if (ni!=nv[i]) { printf("keyind ERR %d %d %d\n",i,ni,nv[i]);
    hoc_execerror("Non-key vectors must be same size: ", 0); }
  }
  nk = vector_arg_px(1, &key);
  if (nk!=num) { printf("keyind ERR2 %d %d\n",nk,num); 
    hoc_execerror("Key length must be number of vecs",0); }
  k=0;
  for (j=0;j<ni;j++) { // j steps through elements of vectors
    for (i=0;i<nk;i++) { // i steps through the key
      if (key[i]==ALL) continue; // OK - do nothing
      if (key[i]==NOZ)        { if (vvo[i][j]==0.) break; else continue; 
      } else if (key[i]==POS) { if (vvo[i][j]<=0.) break; else continue; 
      } else if (key[i]==NEG) { if (vvo[i][j]>=0.) break; else continue; 
      } else if (key[i]!=vvo[i][j]) break; // default
    }
    if (i==nk) ind[k++]=j; // all equal
  }
  vector_resize(vv, k);
  return k;
}
ENDVERBATIM
 
:* v1.thresh() threshold above and below thresh
VERBATIM
static double thresh(void* vv) {
  int i, nx, ny, cnt;
  double *x, *y, th;
  nx = vector_instance_px(vv, &x);
  cnt=0;
  if (hoc_is_object_arg(1)) { 
    ny = vector_arg_px(1, &y); th=0;
    if (nx!=ny) { hoc_execerror("Vector sizes don't match in thresh.", 0); }
    for (i=0; i<nx; i++) { if (x[i]>=y[i]) { x[i]= 1.; cnt++;} else { x[i]= BVBASE; } }
  } else { th = *getarg(1);
    for (i=0; i<nx; i++) { if (x[i] >= th) { x[i]= 1.; cnt++;} else { x[i]= BVBASE; } }
  }
  return cnt;
}
ENDVERBATIM
 
:* v1.triplet() return location of a triplet
VERBATIM
static double triplet(void* vv) {
  int i, nx;
  double *x, *y, a, b;
  nx = vector_instance_px(vv, &x);
  a = *getarg(1); b = *getarg(2);
  for (i=0; i<nx; i+=3) if (x[i]==a&&x[i+1]==b) break;
  if (i<nx) return (double)i; else return -1.;
}
ENDVERBATIM

:* state.onoff(volts,OBon,thresh,dur,refr)
:  looks at volts vector to decide if have reached threshold thresh
:  OBon takes account of burst dur and refractory period
VERBATIM
static double onoff(void* vv) {
  int i, j, n, nv, non, nt, nd, nr, num;
  double *st, *vol, *obon, *thr, *dur, *refr;
  n = vector_instance_px(vv, &st);
  nv   = vector_arg_px(1, &vol);
  non  = vector_arg_px(2, &obon);
  nt   = vector_arg_px(3, &thr);
  nd   = vector_arg_px(4, &dur);
  nr   = vector_arg_px(5, &refr);
  if (n!=nv||n!=non||n!=nt||n!=nd||n!=nr) {
    hoc_execerror("v.onoff: vectors not all same size", 0); }
  for (i=0,num=0;i<n;i++) {
    obon[i]--;
    if (obon[i]>0.) { st[i]=1.; continue; } /* cell must fire */
    if (vol[i]>=thr[i] && obon[i]<= -refr[i]) { /* past refractory period */
        st[i]=1.; obon[i]=dur[i]; num++;
    } else { st[i]= BVBASE; }
  }
  return num;
}
ENDVERBATIM
 
:* vo.bpeval(outp,del)
:  service routine for back-prop: vo=outp*(1-outp)*del
VERBATIM
static double bpeval(void* vv) {
  int i, n, no, nd, flag=0;
  double add,div;
  double *vo, *outp, *del;
  n = vector_instance_px(vv, &vo);
  no   = vector_arg_px(1, &outp);
  nd   = vector_arg_px(2, &del);
  if (ifarg(3) && ifarg(4)) { add= *getarg(3); div= *getarg(4); flag=1;}
  if (n!=no||n!=nd) hoc_execerror("v.bpeval: vectors not all same size", 0);
  if (flag) {
    for (i=0;i<n;i++) vo[i]=((outp[i]+add)/div)*(1.-1.*((outp[i]+add)/div))*del[i];
  } else {
    for (i=0;i<n;i++) vo[i]=outp[i]*(1.-1.*outp[i])*del[i];
  }
}
ENDVERBATIM
 
:* v1.sedit() string edit
VERBATIM
static double sedit(void* vv) {
  int i, n, ni, f=0;
  double *x, *ind, th, val;
  Symbol* s; char *op;
  op = gargstr(1);
  n = vector_instance_px(vv, &x);
  sprintf(op,"hello world");
  return (double)n;
}
ENDVERBATIM

:* v1.w() a .where that sets elements in source vector
VERBATIM
static double w (void* vv) {
  int i, n, ni, f=0;
  double *x, *ind, th, val;
  Symbol* s; char *op;
  if (! ifarg(1)) { 
    printf("v1.w('op',thresh[,val,v2])\n"); 
    printf("  a .where that sets elements in v1 to val (default 0), if v2 => only look at these elements\n");
    printf("  'op'=='function name' is a .apply targeted by v2 called as func(x[i],thresh,val)\n");
    return -1.;
  }
  op = gargstr(1);
  n = vector_instance_px(vv, &x);
  th = *getarg(2);
  if (ifarg(3)) { val = *getarg(3); } else { val = 0.0; }
  if (ifarg(4)) {ni = vector_arg_px(4, &ind); f=1;} // just look at the spots indexed
  if (!strcmp(op,"==")) { 
    if (f==1) {for (i=0; i<ni;i++) {if (x[(int)ind[i]]==th) { x[(int)ind[i]] = val;}}
    } else {for (i=0; i<n; i++) {if (x[i]==th) { x[i] = val;}}}
  } else if (!strcmp(op,"!=")) {
    if (f==1) {for (i=0; i<ni;i++) {if (x[(int)ind[i]]!=th) { x[(int)ind[i]] = val;}}
    } else {for (i=0; i<n; i++) {if (x[i]!=th) { x[i] = val;}}}
  } else if (!strcmp(op,">")) {
    if (f==1) {for (i=0; i<ni;i++) {if (x[(int)ind[i]]>th) { x[(int)ind[i]] = val;}}
    } else {for (i=0; i<n; i++) {if (x[i]>th) { x[i] = val;}}}
  } else if (!strcmp(op,"<")) {
    if (f==1) {for (i=0; i<ni;i++) {if (x[(int)ind[i]]<th) { x[(int)ind[i]] = val;}}
    } else {for (i=0; i<n; i++) {if (x[i]<th) { x[i] = val;}}}
  } else if (!strcmp(op,">=")) {
    if (f==1) {for (i=0; i<ni;i++) {if (x[(int)ind[i]]>=th) { x[(int)ind[i]] = val;}}
    } else {for (i=0; i<n; i++) {if (x[i]>=th) { x[i] = val;}}}
  } else if (!strcmp(op,"<=")) {
    if (f==1) {for (i=0; i<ni;i++) {if (x[(int)ind[i]]<=th) { x[(int)ind[i]] = val;}}
    } else {for (i=0; i<n; i++) {if (x[i]<=th) { x[i] = val;}}}
  } else if ((s=hoc_lookup(op))) { // same as .apply but only does indexed ones
    if (f==1) {for (i=0; i<ni;i++) {
        hoc_pushx(x[(int)ind[i]]); hoc_pushx(th); hoc_pushx(val);
      x[(int)ind[i]]=hoc_call_func(s, 3);}
    } else {for (i=0; i<n;i++) {hoc_pushx(x[i]); hoc_pushx(th); hoc_pushx(val);
        x[i]=hoc_call_func(s, 3);}}
  }
  return (double)i;
}
ENDVERBATIM
  
:* dest.xing(src,tvec,thresh) 
:  dest.xing(src,thresh)  -- returns indices, change into time by .mul(tstep)
:  dest.xing(src)  -- default thresh=0; returns indices
: a .where that looks for threshold crossings and then doesn't pick another till
: comes back down again; places values from tvec in dest; interpolates
VERBATIM
static double xing(void* vv) {
  int i, j, nsrc, ndest, ntvec, f, maxsz, tvf;
  double *src, *dest, *tvec, th;
  tvf=0;
  ndest = vector_instance_px(vv, &dest);
  nsrc = vector_arg_px(1, &src);
  if (ifarg(3)) {
    ntvec = vector_arg_px(2, &tvec);
    th = *getarg(3);
    tvf=1; // flag that tvec being used
  } else if (ifarg(2)) {
    th = *getarg(2);
  } else th=0.0; // default threshold
  maxsz=vector_buffer_size(vv);
  vector_resize(vv, maxsz);
  if (tvf && nsrc!=ntvec) hoc_execerror("v.xing: vectors not all same size", 0);
  for (i=0,f=0,j=0; i<nsrc; i++) {
    if (src[i]>th) { /* ? passing thresh */
      if (f==0) { 
        if (j>=maxsz) {
          printf("(%d) :: ",maxsz);
          hoc_execerror("Dest vec too small in xing ", 0);
        }
        if (i>0) { /* don't record if first value is above thresh */
          if (tvf) {
            dest[j++] = tvec[i-1] + (tvec[i]-tvec[i-1])*(th-src[i-1])/(src[i]-src[i-1]);
          } else {
            dest[j++] = (i-1) + (th-src[i-1])/(src[i]-src[i-1]);
          }
        }
        f=1; 
      }
    } else {       /* below thresh */
      if (f==1) { f=0; } /* just passed going down */
    }
  }
  vector_resize(vv, j);
  return (double)i;
}
ENDVERBATIM

:* v1.xzero() looks for zero crossings 
VERBATIM
static double xzero(void* vv) {
  int i, n, nv, up;
  double *x, *vc, th, cnt=0.;
  n = vector_instance_px(vv, &x);
  nv = vector_arg_px(1, &vc);
  if (ifarg(2)) { th = *getarg(2); } else { th=0.0;}
  if (vc[0]<th) up=0; else up=1;  /* F or T */
  if (nv!=n) hoc_execerror("Vector size doesn't match.", 0);
  for (i=0; i<nv; i++) {
    x[i]=0.;
    if (up) { /* look for passing down */
      if (vc[i]<th) { x[i]=-1; up=0; cnt++; }
    } else if (vc[i]>th) { up=x[i]=1; cnt++; }
  }
  return cnt;
}
ENDVERBATIM

:* v1.negwrap([FLAG]) wrap neg values to pos, FLAG==0 set them to 0
VERBATIM
static double negwrap(void* vv) {
  int i, n, flag;
  double *x, cnt;
  n = vector_instance_px(vv, &x);
  if (ifarg(1)) flag = (int)*getarg(1); else flag=1; // default: do wrap
  for (i=0,cnt=0; i<n; i++) if (x[i]<0) { 
    x[i]=(flag?-x[i]:0.); 
    cnt++; 
  }
  return cnt;
}
ENDVERBATIM
  
:* v1.sw(FROM,TO) switchs all FROMs to TO
VERBATIM
static double sw(void* vv) {
  int i, n;
  double *x, fr, to;
  n = vector_instance_px(vv, &x);
  fr = *getarg(1);
  to = *getarg(2);
  for (i=0; i<n; i++) {
    if (x[i]==fr) { x[i] = to;}
  }
  return n;
}
ENDVERBATIM
 
:* v.b2v(bytevec) copies from vector to bytevec
VERBATIM
static double b2v(void* vv) {
  int i, n, num;
  double *x; bvec* to; Object *ob;
  n = vector_instance_px(vv, &x);
  ob = *(hoc_objgetarg(1));
  to = (bvec*)ob->u.this_pointer; // doesn't check that this is actually a bvec
  if (to->size!=n) { hoc_execerror("Vector and bytevec sizes don't match.", 0); }
  for (i=0; i<n; i++) x[i] = (double)to->x[i];
  return n;
}
ENDVERBATIM

:* v.v2d(&x) copies from vector to double area -- a seg error waiting to happen
VERBATIM
static double v2d(void* vv) {
  int i, n, num;
  double *x, *to;
  n = vector_instance_px(vv, &x);
  to = hoc_pgetarg(1);
  if (ifarg(2)) { num = *getarg(2); } else { num=-1;}
  if (num>-1 && num!=n) { hoc_execerror("Vector size doesn't match.", 0); }
  for (i=0; i<n; i++) {to[i] = x[i];}
  return n;
}
ENDVERBATIM
 
:* v.d2v(&x) copies from double area to vector -- a seg error waiting to happen
VERBATIM
static double d2v(void* vv) {
  int i, n, num;
  double *x, *fr;
  n = vector_instance_px(vv, &x);
  fr = hoc_pgetarg(1);
  if (ifarg(2)) { num = *getarg(2); } else { num=-1;}
  if (num>-1 && num!=n) { hoc_execerror("Vector size doesn't match.", 0); }
  for (i=0; i<n; i++) {x[i] = fr[i];}
  return n;
}
ENDVERBATIM
 
:* v.lcat(LIST)
VERBATIM
static double lcat(void* vv) {
  int i, j, k, n, lc, cap, maxsz;
  Object *ob1, *ob2;
  double *x, *fr; 
  void *vw;
  n = vector_instance_px(vv, &x);
  vector_resize(vv,maxsz=vector_buffer_size(vv)); // open it up fully
  ob1 = *hoc_objgetarg(1);
  lc = ivoc_list_count(ob1);
  for (i=0,j=0;i<lc && j<maxsz;i++) {
    cap = list_vector_px2(ob1, i, &fr, &vw);
    for (k=0;k<cap && j<maxsz;k++,j++) x[j]=fr[k];
  }
  if (i<lc || k<cap) printf("vecst lcat WARN: not all vecs copied\n");
  vector_resize(vv,j);
  return (double)j;
}
ENDVERBATIM

:* v.mkcode(LIST,BITS) -- put together integer vectors from list by bit concatenating
VERBATIM
static double mkcode(void* vv) {
  int i, j, k, n, num, bits;
  Object *ob;
  double *x, *vvo[5];
  n = vector_instance_px(vv, &x);
  ob = *hoc_objgetarg(1);
  if (ifarg(2)) bits = *getarg(2); else bits=3;
  num = ivoc_list_count(ob);
  if (num!=5) hoc_execerror("mkcode ****ERRA****: can only handle 5 vectors", 0);
  for (i=0;i<num;i++) {  j=list_vector_px(ob, i, &vvo[i]);
    if (n!=j) { printf("mkcode ****ERRC**** %d %d %d\n",i,n,j);
      hoc_execerror("Vectors must all be same size: ", 0); }}
  for (i=0;i<n;i++) { // go through the vec length
    for (j=0,x[i]=0;j<5;j++) {
      if (vvo[j][i]<0. || vvo[j][i]>=sc[4] || floor(vvo[j][i]+0.5)!=vvo[j][i]) {
        printf("vec.mkcode OOB %g>%g in vec[%d].x[%d]\n",vvo[j][i],sc[4],j,i); hoc_execerror("", 0); }
        x[i]+=vvo[j][i]*sc[j+1];
    }
  }
  return (double)i;
}
ENDVERBATIM

:* v.uncode(val) -- take apart val and place in vector
: v.uncode(VECLIST) -- take apart vector items and place in vectors in list (cf uncodf)
: v.uncode(vec,field) -- take apart vector items and place requested field in vector
: v.uncode(field,val) -- replace field in v with val (cf recodf)
: v.uncode(field,vec) -- replace field in v with values from vec
VERBATIM
static double uncode (void* vv) {
  int i, j, n, ny, num, field;
  Object *ob;
  double *x, *y, *vvo[5], val, old;
  n = vector_instance_px(vv, &x);
  field=0;
  if (!ifarg(1)) { // numarg()==0
    printf("\tv.uncode(val) -- take apart val and place in vector\n\tv.uncode(VECLIST) -- take apart vector items and place in vectors in list (cf uncodf)\n\tv.uncode(vec,field) -- take apart vector items and place requested field in vector\n\tv.uncode(field,val) -- replace field in v with val (cf recodf)\n\tv.uncode(field,vec) -- replace field in v with values from vec\n"); return 0.;
  } else if (!ifarg(2)) { // numarg()==1
    if (hoc_is_double_arg(1)) {
      val = *getarg(1);
      if (vector_buffer_size(vv)<5) {
        hoc_execerror("uncode ****ERRA****: vector too small to resize(5)", 0);}
      vector_resize(vv,5);
      for (i=1;i<=5;i++) UNCODE(val,i,x[i-1])
      return x[0];
    } else {
      ob = *hoc_objgetarg(1);
      num = ivoc_list_count(ob);
      if (num!=5) hoc_execerror("uncode ****ERRA****: can only handle 5 vectors", 0);
      for (i=0;i<num;i++) {  j=list_vector_px(ob, i, &vvo[i]);
        if (n!=j) { printf("uncode ****ERRC**** %d %d %d\n",i,n,j);
          hoc_execerror("Vectors must all be same size: ", 0); }
      }
      for (i=0;i<n;i++) for (j=1;j<=5;j++) UNCODE(x[i],j,vvo[j-1][i]);
      return (double)i;
    }
  } else { // numarg()==2
    if (hoc_is_double_arg(1)) { // replace values
      field = (int)chkarg(1,1.,5.);
      ny=-1;
      if (hoc_is_double_arg(2)) {
        val=chkarg(2,0.,sc[4]-1); 
        if (floor(val+0.5)!=val) hoc_execerror("uncode(vec) ****ERRG****: non-int val", 0);
      } else {
        ny=vector_arg_px(2, &y);
        if (ny!=n) hoc_execerror("uncode(vec) ****ERRH****: diff sized vecs", 0);
      }
      for (i=0;i<n;i++) {
        UNCODE(x[i],field,old)
        if (ny>0)  {
          if (y[i]<0.||y[i]>=sc[4]||floor(y[i]+0.5)!=y[i]) {
            printf("vec.uncode ERRJ OOB %g (%g max) at %d\n",y[i],sc[4],i);hoc_execerror("", 0);}
          x[i] += sc[field]*(y[i]-old);
        } else {
          x[i] += sc[field]*(val -old);
        }
      }
      return (double)i;
    } else {  // fill single vector with values
      ny = vector_arg_px(1, &y);
      field = (int)chkarg(2,1.,5.);
      if (ny!=n) hoc_execerror("uncode(vec) ****ERRI****: diff sized vecs", 0);
      for (i=0;i<n;i++) UNCODE(x[i],field,y[i])
      return (double)i;
    }
  }
}
ENDVERBATIM
 
VERBATIM
//* list_vector_px(LIST,ITEM#,DOUBLE PTR ADDRESS) 
// modeled on vector_arg_px() picks up a vec from a list
int list_vector_px(Object *ob, int i, double** px) {
  Object* obv;
  int sz;
  obv = ivoc_list_item(ob, i);
  sz = vector_capacity(obv->u.this_pointer);
  *px = vector_vec(obv->u.this_pointer);
  return sz;
}

//* list_vector_px(LIST,ITEM#,DOUBLE PTR ADDRESS,VEC POINTER ADDRESS) 
//  returns the vector pointer as well as the double pointer
int list_vector_px2 (Object *ob, int i, double** px, void** vv) {
  Object* obv;
  int sz;
  obv = ivoc_list_item(ob, i);
  sz = vector_capacity(obv->u.this_pointer);
  *px = vector_vec(obv->u.this_pointer);
  *vv = (void*) obv->u.this_pointer;
  return sz;
}

//* list_vector_resize(LIST,ITEM#,NEW SIZE)
int list_vector_resize (Object *ob, int i, int sz) {
  Object* obv;
  int maxsz;
  obv = ivoc_list_item(ob, i);
  maxsz = vector_buffer_size(obv->u.this_pointer);
  if (sz>maxsz) {
    printf("max:%d request:%d ",maxsz,sz);
    hoc_execerror("Can't grow vector in list_vector_resize ", 0);
    return -1;
  }
  vector_resize(obv->u.this_pointer,sz);
  return sz;
}
ENDVERBATIM

:* v1.ismono([arg]) asks whether is monotonically increasing, with arg==-1 - decreasing
:  with arg==0 - all same
VERBATIM
static double ismono1(double *x, double n, int flag) {
  int i; double last;
  last=x[0]; 
  if (flag==1) {
    for (i=1; i<n && x[i]>=last; i++) last=x[i];
  } else if (flag==-1) {
    for (i=1; i<n && x[i]<=last; i++) last=x[i];
  } else if (flag==0) {
    for (i=1; i<n && x[i]==last; i++) ;
  }
  if (i==n) return 1.; else return 0.;
}

static double ismono(void* vv) {
  int i, n, flag;
  double *x,last;
  n = vector_instance_px(vv, &x);
  if (ifarg(1)) { flag = (int)*getarg(1); } else { flag = 1; }
  return ismono1(x,n,flag);
}
ENDVERBATIM
 
:* v1.count(num) returns number of instances of num
VERBATIM
static double count(void* vv) {
  int i, n, cnt=0;
  double *x,num;
  n = vector_instance_px(vv, &x);
  num = *getarg(1);
  for (i=0; i<n; i++) if (x[i]==num) cnt++;
  return cnt;
}
ENDVERBATIM

:* v1.round() rounds off to nearest integer
VERBATIM
static double round_local(void* vv) {
  int i, n;
  double *x;
  n = vector_instance_px(vv, &x);
  for (i=0; i<n; i++) x[i]=floor(x[i]+0.5);
  return (double)i;
}
ENDVERBATIM

PROCEDURE Expo (x) {
  TABLE RES FROM -20 TO 0 WITH 5000
  RES = exp(x)
}

FUNCTION AAA (x) {
  Expo(x)
  AAA = RES
}

:* dest.smgs(src,low,high,step,var)
:  rewrite of v.sumgauss() in nrn5.3::ivoc/ivocvect.cpp:1078
VERBATIM
static double smgs (void* vv) {	
  int i, j, nx, xv, nsum, points, maxsz;
  double *x, *sum;
  double  low , high , step , var , svar , scale , arg;

  nsum = vector_instance_px(vv, &sum);
  nx = vector_arg_px(1,&x);
  low = *getarg(2);
  high = *getarg(3);
  step = *getarg(4);
  var = *getarg(5);

  points = (int)((high-low)/step+hoc_epsilon);
  if (nsum!=points) { 
    maxsz=vector_buffer_size(vv);
    if (points<=maxsz) {
      nsum=points;  vector_resize(vv, nsum); 
    } else {
      printf("%d > %d :: ",points,maxsz);
      hoc_execerror("Vector max capacity too small in smgs ", 0);
    }
  }

  svar = -2.*var*var/step/step;
  scale = 1./sqrt(2.*M_PI)/var;

  for (j=0; j<points;j++) sum[j] = 0.;
  for (i=0;i<nx;i++) {
    xv = (int)((x[i]-low)/step + 0.5);
    for (j=xv; j<points && (arg=(j-xv)*(j-xv)/svar)>-20;j++) {
      Expo(arg);
      sum[j] += RES;
    }
    for (j=xv-1; j>=0 && (arg=(j-xv)*(j-xv)/svar)>-20;j--) {
      Expo(arg);
      sum[j] += RES;
    }
  }
  for (j=0; j<points;j++) sum[j] *= scale;
  return svar;
}
ENDVERBATIM

:* dest.smsy(tvec,CVLV_VEC,tstop[,dt,del])
:  sum CVLV_VEC starting at each point given in tvec with optional delay
:  used for summing up syn potentials

:* int.vrdh(FILE,veclist,code)
: vector read header will read the headers from vecs saved with vread()
: needs to be generalized so reads code as well, also should do BYTESWAP
VERBATIM 
static double vrdh (void* vv) {	
  int code, i, num, n[2], maxsz;
  double *x;
  FILE* f;

  num = vector_instance_px(vv, &x);
  maxsz=vector_buffer_size(vv);
  f =     hoc_obj_file_arg(1);
  num = (int)*getarg(2); // number of vectors to look for

  if (maxsz<2*num){printf("vrdh ERR0 need %d room in vec\n",2*num);hoc_execerror("", 0);}
  vector_resize(vv, 2*num);

  for (i=0;i<num;i++) { 
    fread(&n,sizeof(int),2,f); // n[1] is type
    if (n[1]!=3){printf("vrdh ERRA code 3 only implemented %d:%d\n",i,n[1]);hoc_execerror("",0);}
    x[2*i]=(double)n[0]; // size
    x[2*i+1]=(double)n[1];
    fseek(f,(long)n[1],SEEK_CUR);
  }
  return num;
}
ENDVERBATIM

:* PROCEDURE install_vecst()
PROCEDURE install_vecst () {
  if (VECST_INSTALLED==1) {
    printf("$Id: vecst.mod,v 1.253 2005/10/07 21:30:32 billl Exp $\n")
  } else {
  VECST_INSTALLED=1
VERBATIM
  int i,j;
  install_vector_method("indset", indset);
  install_vector_method("thresh", thresh);
  install_vector_method("triplet", triplet);
  install_vector_method("onoff", onoff);
  install_vector_method("bpeval", bpeval);
  install_vector_method("w", w);
  install_vector_method("sedit", sedit);
  install_vector_method("xing", xing);
  install_vector_method("cvlv", cvlv);
  install_vector_method("intrp", intrp);
  install_vector_method("xzero", xzero);
  install_vector_method("negwrap", negwrap);
  install_vector_method("sw", sw);
  install_vector_method("ismono", ismono);
  install_vector_method("count", count);
  install_vector_method("round", round_local);
  install_vector_method("fewind", fewind);
  install_vector_method("findx", findx);
  install_vector_method("sindx", sindx);
  install_vector_method("sindv", sindv);
  install_vector_method("nind", nind);
  install_vector_method("keyind", keyind);
  install_vector_method("slct", slct);
  install_vector_method("slor", slor);
  install_vector_method("insct", insct);
  install_vector_method("cull", cull);
  install_vector_method("redundout", redundout);
  install_vector_method("mredundout", mredundout);
  install_vector_method("d2v", d2v);
  install_vector_method("v2d", v2d);
  install_vector_method("b2v", b2v);
  install_vector_method("iwr", iwr);
  install_vector_method("ird", ird);
  install_vector_method("smgs", smgs);
  install_vector_method("ident", ident);
  install_vector_method("lcat", lcat);
  install_vector_method("fread2", fread2);
  install_vector_method("vfill", vfill);
  install_vector_method("vrdh", vrdh);
  install_vector_method("mkcode", mkcode);
  install_vector_method("uncode", uncode);
  install_vector_method("sumabs", sumabs);
  for (i=0,j=5;i<=5;i++,j--) sc[i]=pow(2,10*j);
ENDVERBATIM
  }
}

: isojt(OB1,EXAMPLE_OBJ) return whether OB1 is an instance of EXAMPLE_OBJ
FUNCTION isojt () {
  VERBATIM
  Object *ob1, *ob2;
  ob1 = *hoc_objgetarg(1); ob2 = *hoc_objgetarg(2);
  if (!ob1) if (!ob2) return 1; else return 0;
  if (!ob2 || ob1->template != ob2->template) {
    return 0;
  }
  return 1;
  ENDVERBATIM
}

: ojtnum(OBJ) returns object number
: returns internal number of object, eg if vec[3] is Vector[432] returns 432
FUNCTION ojtnum () {
  VERBATIM
  Object *ob1;
  ob1 = *hoc_objgetarg(1);
  if (!ob1) return -1;
  return (double)ob1->index;
  ENDVERBATIM
}

: eqojt(OB1,OB2) return whether OB1 and OB2 point to same object
FUNCTION eqojt () {
  VERBATIM
  Object *ob1, *ob2;
  ob1 = *hoc_objgetarg(1); ob2 = *hoc_objgetarg(2);
  if (ob1 && ob2 && ob1==ob2) {
    return 1;
  }
  return 0;
  ENDVERBATIM
}

:* rdmany(FILE,veclist,code)
FUNCTION rdmany () {
  VERBATIM {
  int code, i, j, nx, nv, num, n[2];
  Object* ob;
  double *vvo[100], sf[2];
  FILE* f;

  f =     hoc_obj_file_arg(1);
  ob =   *hoc_objgetarg(2);
  code = *getarg(3);

  num = ivoc_list_count(ob);
  if (num>100) hoc_execerror("ERR: rdmany can only handle 100 vectors", 0);
  for (i=0;i<num;i++) { 
    nv = list_vector_px(ob, i, &vvo[i]);
    if (i==0) nx=nv;
    if (nx!=nv) { printf("rdmany ERR %d %d %d\n",i,nx,nv);
      hoc_execerror("Vectors must all be same size: ", 0); }
  }
  if (nx>scrsz) { 
    if (scrsz>0) { free(scr); scr=(unsigned int *)NULL; }
    scrsz=nx+10;
    scr=(unsigned int *)ecalloc(scrsz, sizeof(int));
  }
  if (code==2) {
    unsigned short *xs;
    xs=(unsigned short *)scr;
    for (i=0;i<num;i++) {
      fread(&n,sizeof(int),2,f);
      fread(&sf,sizeof(double),2,f);
      if (n[0]!=nx){printf("rdmany ERRA vec(%d) %d vs %d\n",i,nx,n[0]);hoc_execerror("", 0);}
      if (n[1]!=code){printf("rdmany ERRB code mismatch %d %d\n",n[1],code);hoc_execerror("", 0);}
      fread(xs,sizeof(short),n[0],f);
      for (j=0;j<n[0];j++) vvo[i][j]=(double)(xs[j]/sf[0] + sf[1]);
    }
  } else printf("rdmany() code %d not implemented\n",code);
  return num;
  }
  ENDVERBATIM
}

:* byteswap(FILE)
FUNCTION byteswap () {
  VERBATIM
  int n[2];
  double ret;
  FILE* f;
  BYTEHEADER

  f =     hoc_obj_file_arg(1);
  fread(&n,sizeof(int),2,f);
  if (n[1] < 1 || n[1] > 5) {
    BYTESWAP_FLAG = 1;
    ret = 1.; 
  } else ret = 0.;
  BYTESWAP(n[1],int)
  if (n[1] < 1 || n[1] > 5) { 
    printf("byteswap: Something wrong with location sampled: %d\n",n[1]);
    ret = -1.;
  }
  fseek(f,-2*sizeof(int),SEEK_CUR); // go back to where we started
  return ret;
  ENDVERBATIM
}


: mkcodf(val1,val2,val3,val4,val5) stuff 5 vals<=999 into a single double
FUNCTION mkcodf () {
  VERBATIM
  int i;
  double x,a;
  for (x=0.,i=1;i<=5;i++) { 
    a=chkarg(i,0.,sc[4]-1);
    if (floor(a+0.5)!=a) {
      printf("mkcodf restricted to integers %g\n",a);hoc_execerror("", 0);}
    x+=a*sc[i];
  }
  return x;
  ENDVERBATIM
}

: uncodf(code,i) returns field i (1-5) from code
FUNCTION uncodf () {
  VERBATIM
  int i;
  double x,ret, *ptr;
  x=*getarg(1);
  if (hoc_is_double_arg(2)) {
    i=(int)chkarg(2,1.,5.); 
    UNCODE(x,i,ret);
    return ret;
  } else {
    for (i=2;i<=6;i++) if (ifarg(i)) {
      ptr = hoc_pgetarg(i);
      UNCODE(x,i-1,*ptr);
    } else break;
    return *ptr;
  }
  ENDVERBATIM
}

: recodf(i,code,new) replaces field i (1-5) from code with new
FUNCTION recodf () {
  VERBATIM
  int i;
  double x, y, old;
  i=(int)chkarg(1,1.,5.); x=*getarg(2); y=chkarg(3,0.,sc[4]-1);
  UNCODE(x,i,old);
  return x + sc[i]*(y-old);
  ENDVERBATIM
}

: flor(val)
FUNCTION flor () {
  VERBATIM
  return floor(*getarg(1));
  ENDVERBATIM
}

Loading data, please wait...