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Fix infot.mod #1

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merged 23 commits into from
May 27, 2022
Merged

Fix infot.mod #1

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5753ed3
Fix infot.mod
iomaganaris May 16, 2022
1df7e71
“initial”
May 16, 2022
c5d5eb4
fixing for neuron 9.0
May 16, 2022
11afe8c
fixing for neuron 9.0
May 16, 2022
b091506
more work
May 17, 2022
ad87672
9.0.0 works almost without warnings
May 17, 2022
b99bf52
8.1.0 & 9.0.0 work, except for 8.2.0 ctemplate issue
May 17, 2022
148d1a2
works with all versions
May 17, 2022
fd80ad3
works with all versions
May 17, 2022
92735a7
Added changelog in readme
iomaganaris May 17, 2022
db4d3b7
small fixes based on review
May 18, 2022
dcdddbc
fixup for new wheels, drop register keyword, drop values.h for macOS
olupton May 19, 2022
0eb8038
fixup for new 8.2 wheel
olupton May 19, 2022
2cce6fa
fix warnings
olupton May 23, 2022
75466d4
add comments about C compilation warnings
olupton May 23, 2022
7c83f84
reduce diff and preserve probably-buggy behaviour.
olupton May 23, 2022
a1d83b9
reduce diff and preserve probably-buggy behaviour.
olupton May 23, 2022
66dcd35
Object member is called template in C in 8.2
olupton May 23, 2022
b5e40d6
Addressed Pramod's comments
iomaganaris May 24, 2022
927bcdc
mcell_ran4_init: pass a value
olupton May 24, 2022
8978dcc
mcell_ran4_init: update readme
olupton May 24, 2022
eeca94f
hashseed2: probable bugfix
olupton May 24, 2022
65313b1
cntpx -> cntpxy probable typo (compiler warning fix)
olupton May 24, 2022
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14 changes: 10 additions & 4 deletions clampex.mod
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,9 @@ ASSIGNED {
}

VERBATIM
#ifndef NRN_VERSION_GTEQ_8_2_0
extern double chkarg();
#endif

typedef struct CEXData {
#if 1
Expand All @@ -31,7 +33,7 @@ typedef struct CEXData {
}CEXData;
#define CEXD CEXData* cexd = (CEXData*)((unsigned long)pointer);

static void reverse(b, n ) char* b; int n; {
static void reverse(char* b, int n) {
int i, j, v_;
for (i=0, j=n-1; i<j; ++i, --j) {
v_ = b[i];
Expand All @@ -40,7 +42,7 @@ static void reverse(b, n ) char* b; int n; {
}
}

static void header_endian(h) char* h; {
static void header_endian(char* h) {
char* b;
int i;
b = h;
Expand All @@ -59,7 +61,7 @@ static void header_endian(h) char* h; {
}
}

static double get_parm(i, h) int i; char* h; {
static double get_parm(int i, char* h) {
char* b;
float* f;
long* n;
Expand Down Expand Up @@ -143,8 +145,12 @@ FUNCTION parm() {

PROCEDURE datavec() {
VERBATIM
#ifndef NRN_VERSION_GTEQ_8_2_0
double* hoc_pgetarg();
#endif

int ntrace, trace, i, length;
double* pd, *hoc_pgetarg();
double* pd;
short* tr;
CEXD
length = (int)get_parm(3, cexd->header);
Expand Down
2 changes: 1 addition & 1 deletion field.mod
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
VERBATIM
#include "misc.h"
#define NSW 5 // store into this many ww field vecs
static void* ww[NSW];
static IvocVect* ww[NSW];
static double* wwo[NSW];
static int ixp1;
ENDVERBATIM
Expand Down
39 changes: 21 additions & 18 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 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 perhaps be fabs */
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same?

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I added this (there's a C compiler warning) and was happy to leave it in, but I can remove it if you like.

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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