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nifti 2022-08-02 (11eb262d)
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Code extracted from:

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

at commit 11eb262d939fc139ddc3fe5b508179c637ffbf19 (master).
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@hjmjohnson
NIFTI Upstream authored and hjmjohnson committed Aug 2, 2022
1 parent af2ec74 commit 4384cbd
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Showing 4 changed files with 131 additions and 102 deletions.
1 change: 1 addition & 0 deletions CMakeLists.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -158,6 +158,7 @@ elseif(NOT WIN32)
else()
set(NIFTI_SYSTEM_MATH_LIB "")
endif()
mark_as_advanced(NIFTI_SYSTEM_MATH_LIB)
#######################################################################
add_subdirectory(znzlib)
add_subdirectory(niftilib)
Expand Down
143 changes: 70 additions & 73 deletions niftilib/nifti1_io.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -546,7 +546,7 @@ nifti_image *nifti_image_read_bricks(const char * hname, int nbricks,

if( !hname || !NBL ){
fprintf(stderr,"** nifti_image_read_bricks: bad params (%p,%p)\n",
hname, (void *)NBL);
(const void *)hname, (void *)NBL);
return NULL;
}

Expand Down Expand Up @@ -1415,8 +1415,6 @@ char const *nifti_orientation_string( int ii )
\param nbyper pointer to return value: number of bytes per voxel
\param swapsize pointer to return value: size of swap blocks
\return appropriate values at nbyper and swapsize
The swapsize is set to 0 if this datatype doesn't ever need swapping.
\sa NIFTI1_DATATYPES in nifti1.h
Expand Down Expand Up @@ -2142,7 +2140,7 @@ void nifti_mat44_to_orientation( mat44 R , int *icod, int *jcod, int *kcod )
*
* Due to alignment of structures at some architectures (e.g. on ARM),
* stick to char variables.
* Fixes http://bugs.debian.org/446893 Yaroslav <debian@onerussian.com>
* Fixes <http://bugs.debian.org/446893> Yaroslav <debian @ onerussian.com>
*
*//*--------------------------------------------------------------------*/
void nifti_swap_2bytes( size_t n , void *ar ) /* 2 bytes at a time */
Expand Down Expand Up @@ -2581,7 +2579,7 @@ int nifti_validfilename(const char* fname)
\return a pointer to the extension substring within the original
function input parameter name, or NULL if not found.
\caution Note that if the input parameter is is immutabale
\warning Note that if the input parameter is is immutabale
(i.e. a const char *) then this function performs an
implicit casting away of the mutability constraint and
the return parameter will appear as a mutable
Expand Down Expand Up @@ -2831,8 +2829,8 @@ char * nifti_findhdrname(const char* fname)
/*! check current directory for existing image file
\param fname filename to check for
\nifti_type nifti_type for dataset - this determines whether to
first check for ".nii" or ".img" (since both may exist)
\param nifti_type nifti_type for dataset - this determines whether to
first check for ".nii" or ".img" (since both may exist)
\return filename of data/img file on success and NULL if no appropriate
file could be found
Expand Down Expand Up @@ -3077,7 +3075,7 @@ int nifti_set_filenames( nifti_image * nim, const char * prefix, int check,

if( !nim || !prefix ){
fprintf(stderr,"** nifti_set_filenames, bad params %p, %p\n",
(void *)nim,prefix);
(void *)nim,(const void *)prefix);
return -1;
}

Expand Down Expand Up @@ -3403,7 +3401,7 @@ int nifti_set_type_from_names( nifti_image * nim )

if( !nim->fname || !nim->iname ){
fprintf(stderr,"** NSTFN: missing filename(s) fname @ %p, iname @ %p\n",
nim->fname, nim->iname);
(const void *)nim->fname, (const void *)nim->iname);
return -1;
}

Expand Down Expand Up @@ -4489,7 +4487,7 @@ static int nifti_read_extensions( nifti_image *nim, znzFile fp, int remain )
\param nim - nifti_image to add extension to
\param data - raw extension data
\param length - length of raw extension data
\param len - length of raw extension data
\param ecode - extension code
\sa extension codes NIFTI_ECODE_* in nifti1_io.h
Expand Down Expand Up @@ -4571,7 +4569,7 @@ static int nifti_fill_extension( nifti1_extension *ext, const char * data,

if( !ext || !data || len < 0 ){
fprintf(stderr,"** fill_ext: bad params (%p,%p,%d)\n",
(void *)ext, data, len);
(void *)ext, (const void *)data, len);
return -1;
} else if( ! nifti_is_valid_ecode(ecode) ){
fprintf(stderr,"** warning: writing unknown ecode %d\n", ecode);
Expand Down Expand Up @@ -4819,7 +4817,7 @@ static znzFile nifti_image_load_prep( nifti_image *nim )
if ( g_opts.debug > 0 ){
if( !nim ) fprintf(stderr,"** ERROR: N_image_load: no nifti image\n");
else fprintf(stderr,"** ERROR: N_image_load: bad params (%p,%d,%u)\n",
nim->iname, nim->nbyper, (unsigned)nim->nvox);
(const void *)nim->iname, nim->nbyper, (unsigned)nim->nvox);
}
return NULL;
}
Expand Down Expand Up @@ -5903,8 +5901,6 @@ znzFile nifti_write_ascii_image(nifti_image *nim, const nifti_brick_list * NBL,
fields from the qto_xyz matrix, you can use the utility function
nifti_mat44_to_quatern()
\return 0 on success, -1 on error
\sa nifti_image_write_bricks, nifti_image_free, nifti_set_filenames,
nifti_image_write_hdr_img
*//*------------------------------------------------------------------------*/
Expand Down Expand Up @@ -6193,15 +6189,16 @@ char *nifti_image_to_ascii( const nifti_image *nim )

if( nim == NULL ) return NULL ; /* stupid caller */

buf = (char *)calloc(1,65534); /* longer than needed, to be safe */
const size_t bufLen = 65534; /* longer than needed, to be safe */
buf = (char *)calloc(1,bufLen);
if( !buf ){
fprintf(stderr,"** NITA: failed to alloc %d bytes\n",65534);
fprintf(stderr,"** NITA: failed to alloc %zu bytes\n",bufLen);
return NULL;
}

sprintf( buf , "<nifti_image\n" ) ; /* XML-ish opener */
snprintf( buf , bufLen , "<nifti_image\n" ) ; /* XML-ish opener */

sprintf( buf+strlen(buf) , " nifti_type = '%s'\n" ,
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " nifti_type = '%s'\n" ,
(nim->nifti_type == NIFTI_FTYPE_NIFTI1_1) ? "NIFTI-1+"
:(nim->nifti_type == NIFTI_FTYPE_NIFTI1_2) ? "NIFTI-1"
:(nim->nifti_type == NIFTI_FTYPE_ASCII ) ? "NIFTI-1A"
Expand All @@ -6215,126 +6212,126 @@ char *nifti_image_to_ascii( const nifti_image *nim )
- The result is that the NIFTI ASCII-format header is XML-compliant. */

ebuf = escapize_string(nim->fname) ;
sprintf( buf+strlen(buf) , " header_filename = %s\n",ebuf); free(ebuf);
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " header_filename = %s\n",ebuf); free(ebuf);

ebuf = escapize_string(nim->iname) ;
sprintf( buf+strlen(buf) , " image_filename = %s\n", ebuf); free(ebuf);
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " image_filename = %s\n", ebuf); free(ebuf);

sprintf( buf+strlen(buf) , " image_offset = '%d'\n" , nim->iname_offset );
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " image_offset = '%d'\n" , nim->iname_offset );

sprintf(buf + strlen(buf), " ndim = '%d'\n", nim->ndim);
sprintf(buf + strlen(buf), " nx = '%d'\n", nim->nx);
snprintf(buf+strlen(buf), bufLen-strlen(buf), " ndim = '%d'\n", nim->ndim);
snprintf(buf+strlen(buf), bufLen-strlen(buf), " nx = '%d'\n", nim->nx);
if (nim->ndim > 1)
sprintf(buf + strlen(buf), " ny = '%d'\n", nim->ny);
snprintf(buf+strlen(buf), bufLen-strlen(buf), " ny = '%d'\n", nim->ny);
if (nim->ndim > 2)
sprintf(buf + strlen(buf), " nz = '%d'\n", nim->nz);
snprintf(buf+strlen(buf), bufLen-strlen(buf), " nz = '%d'\n", nim->nz);
if (nim->ndim > 3)
sprintf(buf + strlen(buf), " nt = '%d'\n", nim->nt);
snprintf(buf+strlen(buf), bufLen-strlen(buf), " nt = '%d'\n", nim->nt);
if (nim->ndim > 4)
sprintf(buf + strlen(buf), " nu = '%d'\n", nim->nu);
snprintf(buf+strlen(buf), bufLen-strlen(buf), " nu = '%d'\n", nim->nu);
if (nim->ndim > 5)
sprintf(buf + strlen(buf), " nv = '%d'\n", nim->nv);
snprintf(buf+strlen(buf), bufLen-strlen(buf), " nv = '%d'\n", nim->nv);
if (nim->ndim > 6)
sprintf(buf + strlen(buf), " nw = '%d'\n", nim->nw);
sprintf(buf + strlen(buf), " dx = '%g'\n", nim->dx);
snprintf(buf+strlen(buf), bufLen-strlen(buf), " nw = '%d'\n", nim->nw);
snprintf(buf+strlen(buf), bufLen-strlen(buf), " dx = '%g'\n", nim->dx);
if (nim->ndim > 1)
sprintf(buf + strlen(buf), " dy = '%g'\n", nim->dy);
snprintf(buf+strlen(buf), bufLen-strlen(buf), " dy = '%g'\n", nim->dy);
if (nim->ndim > 2)
sprintf(buf + strlen(buf), " dz = '%g'\n", nim->dz);
snprintf(buf+strlen(buf), bufLen-strlen(buf), " dz = '%g'\n", nim->dz);
if (nim->ndim > 3)
sprintf(buf + strlen(buf), " dt = '%g'\n", nim->dt);
snprintf(buf+strlen(buf), bufLen-strlen(buf), " dt = '%g'\n", nim->dt);
if (nim->ndim > 4)
sprintf(buf + strlen(buf), " du = '%g'\n", nim->du);
snprintf(buf+strlen(buf), bufLen-strlen(buf), " du = '%g'\n", nim->du);
if (nim->ndim > 5)
sprintf(buf + strlen(buf), " dv = '%g'\n", nim->dv);
snprintf(buf+strlen(buf), bufLen-strlen(buf), " dv = '%g'\n", nim->dv);
if (nim->ndim > 6)
sprintf(buf + strlen(buf), " dw = '%g'\n", nim->dw);
snprintf(buf+strlen(buf), bufLen-strlen(buf), " dw = '%g'\n", nim->dw);

sprintf( buf+strlen(buf) , " datatype = '%d'\n" , nim->datatype ) ;
sprintf( buf+strlen(buf) , " datatype_name = '%s'\n" ,
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " datatype = '%d'\n" , nim->datatype ) ;
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " datatype_name = '%s'\n" ,
nifti_datatype_string(nim->datatype) ) ;

sprintf( buf+strlen(buf) , " nvox = '%u'\n" , (unsigned)nim->nvox ) ;
sprintf( buf+strlen(buf) , " nbyper = '%d'\n" , nim->nbyper ) ;
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " nvox = '%u'\n" , (unsigned)nim->nvox ) ;
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " nbyper = '%d'\n" , nim->nbyper ) ;

sprintf( buf+strlen(buf) , " byteorder = '%s'\n" ,
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " byteorder = '%s'\n" ,
(nim->byteorder==MSB_FIRST) ? "MSB_FIRST" : "LSB_FIRST" ) ;

if( nim->cal_min < nim->cal_max ){
sprintf( buf+strlen(buf) , " cal_min = '%g'\n", nim->cal_min ) ;
sprintf( buf+strlen(buf) , " cal_max = '%g'\n", nim->cal_max ) ;
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " cal_min = '%g'\n", nim->cal_min ) ;
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " cal_max = '%g'\n", nim->cal_max ) ;
}

if( nim->scl_slope != 0.0 ){
sprintf( buf+strlen(buf) , " scl_slope = '%g'\n" , nim->scl_slope ) ;
sprintf( buf+strlen(buf) , " scl_inter = '%g'\n" , nim->scl_inter ) ;
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " scl_slope = '%g'\n" , nim->scl_slope ) ;
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " scl_inter = '%g'\n" , nim->scl_inter ) ;
}

if( nim->intent_code > 0 ){
sprintf( buf+strlen(buf) , " intent_code = '%d'\n", nim->intent_code ) ;
sprintf( buf+strlen(buf) , " intent_code_name = '%s'\n" ,
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " intent_code = '%d'\n", nim->intent_code ) ;
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " intent_code_name = '%s'\n" ,
nifti_intent_string(nim->intent_code) ) ;
sprintf( buf+strlen(buf) , " intent_p1 = '%g'\n" , nim->intent_p1 ) ;
sprintf( buf+strlen(buf) , " intent_p2 = '%g'\n" , nim->intent_p2 ) ;
sprintf( buf+strlen(buf) , " intent_p3 = '%g'\n" , nim->intent_p3 ) ;
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " intent_p1 = '%g'\n" , nim->intent_p1 ) ;
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " intent_p2 = '%g'\n" , nim->intent_p2 ) ;
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " intent_p3 = '%g'\n" , nim->intent_p3 ) ;

if( nim->intent_name[0] != '\0' ){
ebuf = escapize_string(nim->intent_name) ;
sprintf( buf+strlen(buf) , " intent_name = %s\n",ebuf) ;
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " intent_name = %s\n",ebuf) ;
free(ebuf) ;
}
}

if( nim->toffset != 0.0 )
sprintf( buf+strlen(buf) , " toffset = '%g'\n",nim->toffset ) ;
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " toffset = '%g'\n",nim->toffset ) ;

if( nim->xyz_units > 0 )
sprintf( buf+strlen(buf) ,
snprintf( buf+strlen(buf) , bufLen-strlen(buf) ,
" xyz_units = '%d'\n"
" xyz_units_name = '%s'\n" ,
nim->xyz_units , nifti_units_string(nim->xyz_units) ) ;

if( nim->time_units > 0 )
sprintf( buf+strlen(buf) ,
snprintf( buf+strlen(buf) , bufLen-strlen(buf) ,
" time_units = '%d'\n"
" time_units_name = '%s'\n" ,
nim->time_units , nifti_units_string(nim->time_units) ) ;

if( nim->freq_dim > 0 )
sprintf( buf+strlen(buf) , " freq_dim = '%d'\n",nim->freq_dim ) ;
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " freq_dim = '%d'\n",nim->freq_dim ) ;
if( nim->phase_dim > 0 )
sprintf( buf+strlen(buf) , " phase_dim = '%d'\n",nim->phase_dim ) ;
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " phase_dim = '%d'\n",nim->phase_dim ) ;
if( nim->slice_dim > 0 )
sprintf( buf+strlen(buf) , " slice_dim = '%d'\n",nim->slice_dim ) ;
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " slice_dim = '%d'\n",nim->slice_dim ) ;
if( nim->slice_code > 0 )
sprintf( buf+strlen(buf) ,
snprintf( buf+strlen(buf) , bufLen-strlen(buf) ,
" slice_code = '%d'\n"
" slice_code_name = '%s'\n" ,
nim->slice_code , nifti_slice_string(nim->slice_code) ) ;
if( nim->slice_start >= 0 && nim->slice_end > nim->slice_start )
sprintf( buf+strlen(buf) ,
snprintf( buf+strlen(buf) , bufLen-strlen(buf) ,
" slice_start = '%d'\n"
" slice_end = '%d'\n" , nim->slice_start , nim->slice_end ) ;
if( nim->slice_duration != 0.0 )
sprintf( buf+strlen(buf) , " slice_duration = '%g'\n",
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " slice_duration = '%g'\n",
nim->slice_duration ) ;

if( nim->descrip[0] != '\0' ){
ebuf = escapize_string(nim->descrip) ;
sprintf( buf+strlen(buf) , " descrip = %s\n",ebuf) ;
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " descrip = %s\n",ebuf) ;
free(ebuf) ;
}

if( nim->aux_file[0] != '\0' ){
ebuf = escapize_string(nim->aux_file) ;
sprintf( buf+strlen(buf) , " aux_file = %s\n",ebuf) ;
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " aux_file = %s\n",ebuf) ;
free(ebuf) ;
}

if( nim->qform_code > 0 ){
int i,j,k ;

sprintf( buf+strlen(buf) ,
snprintf( buf+strlen(buf) , bufLen-strlen(buf) ,
" qform_code = '%d'\n"
" qform_code_name = '%s'\n"
" qto_xyz_matrix = '%g %g %g %g %g %g %g %g %g %g %g %g %g %g %g %g'\n" ,
Expand All @@ -6348,7 +6345,7 @@ char *nifti_image_to_ascii( const nifti_image *nim )
nim->qto_xyz.m[3][0] , nim->qto_xyz.m[3][1] ,
nim->qto_xyz.m[3][2] , nim->qto_xyz.m[3][3] ) ;

sprintf( buf+strlen(buf) ,
snprintf( buf+strlen(buf) , bufLen-strlen(buf) ,
" qto_ijk_matrix = '%g %g %g %g %g %g %g %g %g %g %g %g %g %g %g %g'\n" ,
nim->qto_ijk.m[0][0] , nim->qto_ijk.m[0][1] ,
nim->qto_ijk.m[0][2] , nim->qto_ijk.m[0][3] ,
Expand All @@ -6359,7 +6356,7 @@ char *nifti_image_to_ascii( const nifti_image *nim )
nim->qto_ijk.m[3][0] , nim->qto_ijk.m[3][1] ,
nim->qto_ijk.m[3][2] , nim->qto_ijk.m[3][3] ) ;

sprintf( buf+strlen(buf) ,
snprintf( buf+strlen(buf) , bufLen-strlen(buf) ,
" quatern_b = '%g'\n"
" quatern_c = '%g'\n"
" quatern_d = '%g'\n"
Expand All @@ -6372,7 +6369,7 @@ char *nifti_image_to_ascii( const nifti_image *nim )

nifti_mat44_to_orientation( nim->qto_xyz , &i,&j,&k ) ;
if( i > 0 && j > 0 && k > 0 )
sprintf( buf+strlen(buf) ,
snprintf( buf+strlen(buf) , bufLen-strlen(buf) ,
" qform_i_orientation = '%s'\n"
" qform_j_orientation = '%s'\n"
" qform_k_orientation = '%s'\n" ,
Expand All @@ -6384,7 +6381,7 @@ char *nifti_image_to_ascii( const nifti_image *nim )
if( nim->sform_code > 0 ){
int i,j,k ;

sprintf( buf+strlen(buf) ,
snprintf( buf+strlen(buf) , bufLen-strlen(buf) ,
" sform_code = '%d'\n"
" sform_code_name = '%s'\n"
" sto_xyz_matrix = '%g %g %g %g %g %g %g %g %g %g %g %g %g %g %g %g'\n" ,
Expand All @@ -6398,7 +6395,7 @@ char *nifti_image_to_ascii( const nifti_image *nim )
nim->sto_xyz.m[3][0] , nim->sto_xyz.m[3][1] ,
nim->sto_xyz.m[3][2] , nim->sto_xyz.m[3][3] ) ;

sprintf( buf+strlen(buf) ,
snprintf( buf+strlen(buf) , bufLen-strlen(buf) ,
" sto_ijk matrix = '%g %g %g %g %g %g %g %g %g %g %g %g %g %g %g %g'\n" ,
nim->sto_ijk.m[0][0] , nim->sto_ijk.m[0][1] ,
nim->sto_ijk.m[0][2] , nim->sto_ijk.m[0][3] ,
Expand All @@ -6411,7 +6408,7 @@ char *nifti_image_to_ascii( const nifti_image *nim )

nifti_mat44_to_orientation( nim->sto_xyz , &i,&j,&k ) ;
if( i > 0 && j > 0 && k > 0 )
sprintf( buf+strlen(buf) ,
snprintf( buf+strlen(buf) , bufLen-strlen(buf) ,
" sform_i_orientation = '%s'\n"
" sform_j_orientation = '%s'\n"
" sform_k_orientation = '%s'\n" ,
Expand All @@ -6420,9 +6417,9 @@ char *nifti_image_to_ascii( const nifti_image *nim )
nifti_orientation_string(k) ) ;
}

sprintf( buf+strlen(buf) , " num_ext = '%d'\n", nim->num_ext ) ;
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , " num_ext = '%d'\n", nim->num_ext ) ;

sprintf( buf+strlen(buf) , "/>\n" ) ; /* XML-ish closer */
snprintf( buf+strlen(buf) , bufLen-strlen(buf) , "/>\n" ) ; /* XML-ish closer */

nbuf = (int)strlen(buf) ;
buf = (char *)realloc((void *)buf, nbuf+1); /* cut back to proper length */
Expand Down Expand Up @@ -6457,7 +6454,7 @@ int nifti_short_order(void) /* determine this CPU's byte order */
/* macro to check lhs string against "n1"; if it matches,
interpret rhs string as a number, and put it into nim->"n2" */

#define QQNUM(n1,n2,tt) if( strcmp(lhs,#n1)==0 ) nim->n2=(tt)strtod(rhs,NULL)
#define QQNUM(n1,n2,tt) if( strcmp(lhs,#n1)==0 ) nim->n2=(tt)(strtod(rhs,NULL))

/* same, but where "n1" == "n2" */

Expand Down Expand Up @@ -6959,7 +6956,7 @@ compute_strides(int *strides,const int *size,int nbyper)
speed and possibly repeated calls to this function.
\return
- the total number of bytes read, or < 0 on failure
- the read and byte-swapped data, in 'data' </pre>
- the read and byte-swapped data, in 'data'
\sa nifti_image_read, nifti_image_free, nifti_image_read_bricks
nifti_image_load, nifti_read_collapsed_image
Expand Down
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