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nifti 2023-05-22 (c135c3d4)
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Code extracted from:

    https://github.com/NIFTI-Imaging/nifti_clib.git

at commit c135c3d474c2db97c071e184d91460ce8b0027da (master).
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@seanm
NIFTI Upstream authored and seanm committed May 29, 2023
1 parent 5e40191 commit 8a04aa2
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Showing 3 changed files with 64 additions and 59 deletions.
35 changes: 19 additions & 16 deletions niftilib/nifti1_io.c
View file
Expand Up @@ -4396,6 +4396,7 @@ static int nifti_read_extensions( nifti_image *nim, znzFile fp, int remain )
nifti1_extender extdr; /* defines extension existence */
nifti1_extension extn; /* single extension to process */
nifti1_extension * Elist; /* list of processed extensions */
znz_off_t posn;
int count;

if( !nim || znz_isnull(fp) ) {
Expand All @@ -4405,16 +4406,17 @@ static int nifti_read_extensions( nifti_image *nim, znzFile fp, int remain )
return -1;
}

znz_off_t posn = znztell(fp);
posn = znztell(fp);

if( (posn != sizeof(nifti_1_header)) &&
(nim->nifti_type != NIFTI_FTYPE_ASCII) )
fprintf(stderr,"** WARNING: posn not header size (%lld, %lu)\n",
posn, sizeof(nifti_1_header));
(long long)posn, sizeof(nifti_1_header));

if( g_opts.debug > 2 )
fprintf(stderr,"-d nre: posn = %lld, offset = %d, type = %d, remain = %d\n",
posn, nim->iname_offset, nim->nifti_type, remain);
fprintf(stderr,"-d nre: posn = %lld, offset = %d, type = %d,"
" remain = %d\n",
(long long)posn, nim->iname_offset, nim->nifti_type, remain);

if( remain < 16 ){
if( g_opts.debug > 2 ){
Expand Down Expand Up @@ -6928,7 +6930,7 @@ int nifti_read_collapsed_image( nifti_image * nim, const int dims [8],
** stride array.
*/
static void
compute_strides(int *strides,const int *size,int nbyper)
compute_strides(int64_t *strides,const int *size,int nbyper)
{
int i;
strides[0] = nbyper;
Expand Down Expand Up @@ -6977,7 +6979,7 @@ int nifti_read_subregion_image( nifti_image * nim,
long int bytes = 0; /* total # bytes read */
size_t total_alloc_size; /* size of buffer allocation */
char *readptr; /* where in *data to read next */
int strides[7]; /* strides between dimensions */
int64_t strides[7]; /* strides between dimensions */
int collapsed_dims[8]; /* for read_collapsed_image */
int *image_size; /* pointer to dimensions in header */
long int initial_offset;
Expand Down Expand Up @@ -7343,10 +7345,11 @@ static int make_pivot_list(nifti_image * nim, const int dims[], int pivots[],
*//*-------------------------------------------------------------------*/
int * nifti_get_intlist( int nvals , const char * str )
{
int *subv = NULL ;
int *subv_realloc = NULL;
int ii , ipos , nout , slen ;
int ibot,itop,istep ;
int *subv = NULL ;
int *subv_realloc = NULL;
int ii , ipos , nout , slen ;
int ibot,itop,istep ;
long nused, temp ;
char *cpt ;

/* Meaningless input? */
Expand Down Expand Up @@ -7383,7 +7386,7 @@ int * nifti_get_intlist( int nvals , const char * str )
ibot = nvals-1 ; ipos++ ;
} else { /* decode an integer */
errno = 0;
long temp = strtol( str+ipos , &cpt , 10 ) ;
temp = strtol( str+ipos , &cpt , 10 ) ;
if( (temp == 0 && errno != 0) || temp <= INT_MIN || temp >= INT_MAX){
fprintf(stderr,"** ERROR: list index does not fit in int\n") ;
free(subv) ; return NULL ;
Expand All @@ -7399,7 +7402,7 @@ int * nifti_get_intlist( int nvals , const char * str )
ibot,nvals-1) ;
free(subv) ; return NULL ;
}
long nused = (cpt-(str+ipos)) ;
nused = (cpt-(str+ipos)) ;
if( ibot == 0 && nused == 0 ){
fprintf(stderr,"** ERROR: list syntax error '%s'\n",str+ipos) ;
free(subv) ; return NULL ;
Expand Down Expand Up @@ -7446,7 +7449,7 @@ int * nifti_get_intlist( int nvals , const char * str )
itop = nvals-1 ; ipos++ ;
} else { /* decode an integer */
errno = 0;
long temp = strtol( str+ipos , &cpt , 10 ) ;
temp = strtol( str+ipos , &cpt , 10 ) ;
if( (temp == 0 && errno != 0) || temp <= INT_MIN || temp >= INT_MAX){
fprintf(stderr,"** ERROR: list index does not fit in int\n") ;
free(subv) ; return NULL ;
Expand All @@ -7462,7 +7465,7 @@ int * nifti_get_intlist( int nvals , const char * str )
itop,nvals-1) ;
free(subv) ; return NULL ;
}
long nused = (cpt-(str+ipos)) ;
nused = (cpt-(str+ipos)) ;
if( itop == 0 && nused == 0 ){
fprintf(stderr,"** ERROR: index list syntax error '%s'\n",str+ipos) ;
free(subv) ; return NULL ;
Expand All @@ -7481,7 +7484,7 @@ int * nifti_get_intlist( int nvals , const char * str )
if( str[ipos] == '(' ){ /* decode an integer */
ipos++ ;
errno = 0;
long temp = strtol( str+ipos , &cpt , 10 ) ;
temp = strtol( str+ipos , &cpt , 10 ) ;
if( (temp == 0 && errno != 0) || temp <= INT_MIN || temp >= INT_MAX){
fprintf(stderr,"** ERROR: list index does not fit in int\n") ;
free(subv) ; return NULL ;
Expand All @@ -7491,7 +7494,7 @@ int * nifti_get_intlist( int nvals , const char * str )
fprintf(stderr,"** ERROR: index loop step is 0!\n") ;
free(subv) ; return NULL ;
}
long nused = (cpt-(str+ipos)) ;
nused = (cpt-(str+ipos)) ;
ipos += nused ;
if( str[ipos] == ')' ) ipos++ ;
if( (ibot-itop)*istep > 0 ){
Expand Down
7 changes: 4 additions & 3 deletions niftilib/nifti1_test.c
View file
Expand Up @@ -17,8 +17,9 @@ static int local_fileexists(const char* fname)
int main( int argc , char *argv[] )
{
nifti_image *nim ;
int iarg=1 , outmode=1 , argn=1, usegzip=0;
char *tmpstr;
int iarg=1 , outmode=1 , argn=1, usegzip=0;
char *tmpstr;
size_t ll;

if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
printf("Usage: nifti1_test [-n2|-n1|-na|-a2] infile [prefix]\n"
Expand Down Expand Up @@ -78,7 +79,7 @@ int main( int argc , char *argv[] )
if( nim->fname != NULL ) free(nim->fname) ;
if( nim->iname != NULL ) free(nim->iname) ;

size_t ll = strlen(argv[iarg]) ;
ll = strlen(argv[iarg]) ;
tmpstr = nifti_makebasename(argv[iarg]);
nim->fname = (char *)calloc(1,ll+8) ; strcpy(nim->fname,tmpstr) ;
nim->iname = (char *)calloc(1,ll+8) ; strcpy(nim->iname,tmpstr) ;
Expand Down

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