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nifti1_io.h
Go to the documentation of this file.00001 #ifndef _NIFTI_IO_HEADER_ 00002 #define _NIFTI_IO_HEADER_ 00003 00004 #include <stdio.h> 00005 #include <stdlib.h> 00006 #include <string.h> 00007 #include <math.h> 00008 #include <ctype.h> 00009 00010 #ifndef DONT_INCLUDE_ANALYZE_STRUCT 00011 #define DONT_INCLUDE_ANALYZE_STRUCT /*** not needed herein ***/ 00012 #endif 00013 #include "nifti1.h" /*** NIFTI-1 header specification ***/ 00014 00015 #include "znzlib/znzlib.h" 00016 00017 /*=================*/ 00018 #ifdef __cplusplus 00019 extern "C" { 00020 #endif 00021 /*=================*/ 00022 00023 /*****===================================================================*****/ 00024 /***** File nifti1_io.h == Declarations for nifti1_io.c *****/ 00025 /*****...................................................................*****/ 00026 /***** This code is released to the public domain. *****/ 00027 /*****...................................................................*****/ 00028 /***** Author: Robert W Cox, SSCC/DIRP/NIMH/NIH/DHHS/USA/EARTH *****/ 00029 /***** Date: August 2003 *****/ 00030 /*****...................................................................*****/ 00031 /***** Neither the National Institutes of Health (NIH), nor any of its *****/ 00032 /***** employees imply any warranty of usefulness of this software for *****/ 00033 /***** any purpose, and do not assume any liability for damages, *****/ 00034 /***** incidental or otherwise, caused by any use of this document. *****/ 00035 /*****===================================================================*****/ 00036 00037 /* 00038 Modified by: Mark Jenkinson (FMRIB Centre, University of Oxford, UK) 00039 Date: July/August 2004 00040 00041 Mainly adding low-level IO and changing things to allow gzipped files 00042 to be read and written 00043 Full backwards compatability should have been maintained 00044 */ 00045 00046 /********************** Some sample data structures **************************/ 00047 00048 typedef struct { /** 4x4 matrix struct **/ 00049 float m[4][4] ; 00050 } mat44 ; 00051 00052 typedef struct { /** 3x3 matrix struct **/ 00053 float m[3][3] ; 00054 } mat33 ; 00055 00056 /*...........................................................................*/ 00057 00058 typedef struct { /** Image storage struct **/ 00059 00060 int ndim ; /* last dimension greater than 1 (1..7) */ 00061 int nx,ny,nz , nt,nu,nv,nw ; /* dimensions of grid array */ 00062 int dim[8] ; /* dim[0]=ndim, dim[1]=nx, etc. */ 00063 int nvox ; /* number of voxels = nx*ny*nz*... */ 00064 int nbyper ; /* bytes per voxel */ 00065 int datatype ; /* type of data in voxels: DT_* code */ 00066 00067 float dx,dy,dz , dt,du,dv,dw ; /* grid spacings */ 00068 float pixdim[8] ; /* pixdim[1]=dx, etc. */ 00069 00070 float scl_slope , scl_inter ; /* scaling parameters */ 00071 00072 float cal_min , cal_max ; /* calibration parameters */ 00073 00074 int qform_code , sform_code ; /* codes for (x,y,z) space meaning */ 00075 00076 int freq_dim , /* indexes (1,2,3, or 0) for MRI */ 00077 phase_dim , slice_dim ; /* directions in dim[]/pixdim[] */ 00078 00079 int slice_code ; /* code for slice timing pattern */ 00080 int slice_start , slice_end ; /* indexes for start & stop of slices */ 00081 float slice_duration ; /* time between individual slices */ 00082 00083 float quatern_b, quatern_c, /* quaternion transform parameters */ 00084 quatern_d, qoffset_x, /* [when writing a dataset, these ] */ 00085 qoffset_y, qoffset_z, /* [are used for qform, NOT qto_xyz] */ 00086 qfac ; 00087 00088 mat44 qto_xyz ; /* qform: transform (i,j,k) to (x,y,z) */ 00089 mat44 qto_ijk ; /* qform: transform (x,y,z) to (i,j,k) */ 00090 00091 mat44 sto_xyz ; /* sform: transform (i,j,k) to (x,y,z) */ 00092 mat44 sto_ijk ; /* sform: transform (x,y,z) to (i,j,k) */ 00093 00094 float toffset ; /* time coordinate offset */ 00095 00096 int xyz_units , time_units ; /* dx,dy,dz & dt units: NIFTI_UNITS_* code */ 00097 00098 int nifti_type ; /* 0==ANALYZE, 2==NIFTI-1 (2 files), 00099 1==NIFTI-1 (1 file) , 00100 3==NIFTI-ASCII (1 file) */ 00101 int intent_code ; /* statistic type (or something) */ 00102 float intent_p1, intent_p2, /* intent parameters */ 00103 intent_p3 ; 00104 char intent_name[16] ; 00105 00106 char descrip[80], aux_file[24]; 00107 00108 char *fname ; /* header filename (.hdr or .nii) */ 00109 char *iname ; /* image filename (.img or .nii) */ 00110 int iname_offset ; /* offset into iname where data starts */ 00111 int swapsize ; /* swapping unit in image data (might be 0) */ 00112 int byteorder ; /* byte order on disk (MSB_ or LSB_FIRST) */ 00113 void *data ; /* pointer to data: nbyper*nvox bytes */ 00114 00115 int num_ext ; /* number of extensions in ext_list */ 00116 nifti1_extension * ext_list ; /* array of extension structures (with data)*/ 00117 00118 } nifti_image ; 00119 00120 00121 00122 /* struct for return from nifti_image_read_bricks() */ 00123 typedef struct { 00124 int nbricks; /* the number of allocated pointers in 'bricks' */ 00125 int bsize; /* the length of each data block, in bytes */ 00126 void ** bricks; /* array of pointers to data blocks */ 00127 } nifti_brick_list; 00128 00129 00130 /*****************************************************************************/ 00131 /*--------------- Prototypes of functions defined in this file --------------*/ 00132 00133 char *nifti_datatype_string ( int dt ) ; 00134 char *nifti_units_string ( int uu ) ; 00135 char *nifti_intent_string ( int ii ) ; 00136 char *nifti_xform_string ( int xx ) ; 00137 char *nifti_slice_string ( int ss ) ; 00138 char *nifti_orientation_string( int ii ) ; 00139 00140 int nifti_is_inttype( int dt ) ; 00141 00142 mat44 mat44_inverse( mat44 R ) ; 00143 00144 mat33 mat33_inverse( mat33 R ) ; 00145 mat33 mat33_polar ( mat33 A ) ; 00146 float mat33_rownorm( mat33 A ) ; 00147 float mat33_colnorm( mat33 A ) ; 00148 float mat33_determ ( mat33 R ) ; 00149 mat33 mat33_mul ( mat33 A , mat33 B ) ; 00150 00151 void swap_2bytes ( int n , void *ar ) ; 00152 void swap_4bytes ( int n , void *ar ) ; 00153 void swap_8bytes ( int n , void *ar ) ; 00154 void swap_16bytes( int n , void *ar ) ; 00155 void swap_Nbytes ( int n , int siz , void *ar ) ; 00156 00157 void swap_nifti_header( struct nifti_1_header *h , int is_nifti ) ; 00158 unsigned int get_filesize( char *pathname ) ; 00159 00160 /* main routine for reading a dataset into a brick list */ 00161 nifti_image *nifti_image_read_bricks(char *hname , int nbricks, int * blist, 00162 nifti_brick_list * NBL ); 00163 int nifti_image_load_bricks(nifti_image *nim , int nbricks, int *blist, 00164 nifti_brick_list * NBL ); 00165 void free_NBL( nifti_brick_list * NBL ); 00166 00167 /* main routine for reading a dataset into a single image */ 00168 nifti_image *nifti_image_read ( char *hname , int read_data ) ; 00169 int nifti_image_load ( nifti_image *nim ) ; 00170 void nifti_image_unload ( nifti_image *nim ) ; 00171 void nifti_image_free ( nifti_image *nim ) ; 00172 void nifti_image_write ( nifti_image *nim ) ; 00173 void nifti_image_infodump( nifti_image *nim ) ; 00174 00175 void nifti_disp_lib_hist( void ) ; /* to display library history */ 00176 void nifti_disp_lib_version( void ) ; /* to display library version */ 00177 int nifti_disp_matrix_orient( char * mesg, mat44 mat ); 00178 00179 char * nifti_image_to_ascii ( nifti_image *nim ) ; 00180 nifti_image *nifti_image_from_ascii( char *str, int * bytes_read ) ; 00181 00182 size_t nifti_get_volsize(nifti_image *nim) ; 00183 00184 /* basic file operations */ 00185 int is_nifti_file( char *hname ) ; 00186 char * nifti_find_file_extension( char * name ) ; 00187 int nifti_validfilename(char* fname) ; 00188 00189 int disp_nifti_1_header( char * info, nifti_1_header * hp ) ; 00190 void nifti_set_debug_level( int level ) ; 00191 int print_hex_vals( char * data, int nbytes, FILE * fp ) ; 00192 00193 int valid_nifti_brick_list(nifti_image * nim , int nbricks, int * blist, 00194 int disp_error); 00195 00196 00197 void nifti_datatype_sizes( int datatype , int *nbyper, int *swapsize ) ; 00198 00199 void mat44_to_quatern( mat44 R , 00200 float *qb, float *qc, float *qd, 00201 float *qx, float *qy, float *qz, 00202 float *dx, float *dy, float *dz, float *qfac ) ; 00203 00204 mat44 quatern_to_mat44( float qb, float qc, float qd, 00205 float qx, float qy, float qz, 00206 float dx, float dy, float dz, float qfac ); 00207 00208 mat44 make_orthog_mat44( float r11, float r12, float r13 , 00209 float r21, float r22, float r23 , 00210 float r31, float r32, float r33 ) ; 00211 00212 int unescape_string( char *str ) ; /* string utility functions */ 00213 char *escapize_string( char *str ) ; 00214 00215 int short_order(void) ; /* CPU byte order */ 00216 00217 00218 /* Orientation codes that might be returned from mat44_to_orientation(). */ 00219 00220 #define NIFTI_L2R 1 /* Left to Right */ 00221 #define NIFTI_R2L 2 /* Right to Left */ 00222 #define NIFTI_P2A 3 /* Posterior to Anterior */ 00223 #define NIFTI_A2P 4 /* Anterior to Posterior */ 00224 #define NIFTI_I2S 5 /* Inferior to Superior */ 00225 #define NIFTI_S2I 6 /* Superior to Inferior */ 00226 00227 void mat44_to_orientation( mat44 R , int *icod, int *jcod, int *kcod ) ; 00228 00229 /*--------------------- Low level IO routines ------------------------------*/ 00230 00231 static char * nifti_findhdrname (char* fname); 00232 static char * nifti_findimgname (char* fname , int nifti_type); 00233 static int nifti_is_gzfile (char* fname); 00234 00235 char * nifti_makebasename(char* fname); 00236 00237 /* extension routines */ 00238 static int nifti_read_extensions( nifti_image *nim, znzFile fp ); 00239 static int nifti_read_next_extension( nifti1_extension * nex, 00240 nifti_image *nim, znzFile fp ); 00241 static int nifti_add_exten_to_list( nifti1_extension * new_ext, 00242 nifti1_extension ** list, int new_length ); 00243 static int nifti_write_extensions(znzFile fp, nifti_image *nim); 00244 static int nifti_valid_extension( nifti_image *nim, int size, int code ); 00245 static void update_nifti_image_for_brick_list(nifti_image * nim , int nbricks); 00246 00247 /* NBL routines */ 00248 static int nifti_load_NBL_bricks(nifti_image * nim , int * slist, int * sindex, 00249 nifti_brick_list * NBL, znzFile fp ); 00250 static int nifti_alloc_NBL_mem( nifti_image * nim, int nbricks, 00251 nifti_brick_list * nbl); 00252 static int nifti_copynsort(int nbricks, int *blist, int **slist, int **sindex); 00253 00254 00255 /* misc */ 00256 static int int_force_positive( int * list, int nel ); 00257 00258 00259 /* internal I/O routines */ 00260 static znzFile nifti_image_write_hdr_img(nifti_image *nim , int write_data , 00261 char* opts); 00262 static znzFile nifti_image_write_hdr_img2( nifti_image *nim , int write_data , 00263 char* opts, znzFile *imgfile ); 00264 static znzFile nifti_image_open(char *hname , char *opts , nifti_image **nim); 00265 static znzFile nifti_image_load_prep( nifti_image *nim ); 00266 static size_t nifti_read_buffer(znzFile fp, void* datatptr, size_t ntot, 00267 nifti_image *nim); 00268 00269 static void nifti_write_all_data(znzFile fp, nifti_image *nim); 00270 static size_t nifti_write_buffer(znzFile fp, void *buffer, size_t numbytes); 00271 00272 00273 /* other routines */ 00274 nifti_image * nifti_copy_nim_info(nifti_image* src); 00275 nifti_image * nifti_simple_init_nim(); 00276 struct nifti_1_header nifti_convert_nim2nhdr(nifti_image* nim); 00277 nifti_image * nifti_convert_nhdr2nim(struct nifti_1_header nhdr, 00278 char* fname); 00279 void nifti_set_iname_offset(nifti_image *nim); 00280 00281 /*-------------------- Some C convenience macros ----------------------------*/ 00282 00283 #undef LNI_FERR /* local nifti file error, to be compact and repetative */ 00284 #define LNI_FERR(func,msg,file) \ 00285 fprintf(stderr,"** ERROR (%s): %s '%s'\n",func,msg,file) 00286 00287 #undef swap_2 00288 #undef swap_4 00289 #define swap_2(s) swap_2bytes(1,&(s)) /* s is a 2-byte short; swap in place */ 00290 #define swap_4(v) swap_4bytes(1,&(v)) /* v is a 4-byte value; swap in place */ 00291 00292 /***** isfinite() is a C99 macro, which is 00293 present in many C implementations already *****/ 00294 00295 #undef IS_GOOD_FLOAT 00296 #undef FIXED_FLOAT 00297 00298 #ifdef isfinite /* use isfinite() to check floats/doubles for goodness */ 00299 # define IS_GOOD_FLOAT(x) isfinite(x) /* check if x is a "good" float */ 00300 # define FIXED_FLOAT(x) (isfinite(x) ? (x) : 0) /* fixed if bad */ 00301 #else 00302 # define IS_GOOD_FLOAT(x) 1 /* don't check it */ 00303 # define FIXED_FLOAT(x) (x) /* don't fix it */ 00304 #endif 00305 00306 #undef ASSIF /* assign v to *p, if possible */ 00307 #define ASSIF(p,v) if( (p)!=NULL ) *(p) = (v) 00308 00309 #undef MSB_FIRST 00310 #undef LSB_FIRST 00311 #undef REVERSE_ORDER 00312 #define LSB_FIRST 1 00313 #define MSB_FIRST 2 00314 #define REVERSE_ORDER(x) (3-(x)) /* convert MSB_FIRST <--> LSB_FIRST */ 00315 00316 #define LNI_MAX_NIA_EXT_LEN 100000 /* consider a longer extension invalid */ 00317 /*=================*/ 00318 #ifdef __cplusplus 00319 } 00320 #endif 00321 /*=================*/ 00322 00323 #endif /* _NIFTI_IO_HEADER_ */
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