#ifndef _NIFTI_IO_HEADER_ #define _NIFTI_IO_HEADER_ #include #include #include #include #include #ifndef DONT_INCLUDE_ANALYZE_STRUCT #define DONT_INCLUDE_ANALYZE_STRUCT /*** not needed herein ***/ #endif #include "nifti1.h" /*** NIFTI-1 header specification ***/ #include "znzlib.h" /*=================*/ #ifdef __cplusplus extern "C" { #endif /*=================*/ /*****===================================================================*****/ /***** File nifti1_io.h == Declarations for nifti1_io.c *****/ /*****...................................................................*****/ /***** This code is released to the public domain. *****/ /*****...................................................................*****/ /***** Author: Robert W Cox, SSCC/DIRP/NIMH/NIH/DHHS/USA/EARTH *****/ /***** Date: August 2003 *****/ /*****...................................................................*****/ /***** Neither the National Institutes of Health (NIH), nor any of its *****/ /***** employees imply any warranty of usefulness of this software for *****/ /***** any purpose, and do not assume any liability for damages, *****/ /***** incidental or otherwise, caused by any use of this document. *****/ /*****===================================================================*****/ /* Date: July/August 2004 Modified by: Mark Jenkinson (FMRIB Centre, University of Oxford, UK) Mainly adding low-level IO and changing things to allow gzipped files to be read and written Full backwards compatability should have been maintained Date: December 2004 Modified by: Rick Reynolds (SSCC/DIRP/NIMH, National Institutes of Health) Modified and added many routines for I/O. */ /********************** Some sample data structures **************************/ typedef struct { /** 4x4 matrix struct **/ float m[4][4] ; } mat44 ; typedef struct { /** 3x3 matrix struct **/ float m[3][3] ; } mat33 ; /*...........................................................................*/ typedef struct { /** Image storage struct **/ int ndim ; /* last dimension greater than 1 (1..7) */ int nx,ny,nz , nt,nu,nv,nw ; /* dimensions of grid array */ int dim[8] ; /* dim[0]=ndim, dim[1]=nx, etc. */ int nvox ; /* number of voxels = nx*ny*nz*... */ int nbyper ; /* bytes per voxel */ int datatype ; /* type of data in voxels: DT_* code */ float dx,dy,dz , dt,du,dv,dw ; /* grid spacings */ float pixdim[8] ; /* pixdim[1]=dx, etc. */ float scl_slope , scl_inter ; /* scaling parameters */ float cal_min , cal_max ; /* calibration parameters */ int qform_code , sform_code ; /* codes for (x,y,z) space meaning */ int freq_dim , /* indexes (1,2,3, or 0) for MRI */ phase_dim , slice_dim ; /* directions in dim[]/pixdim[] */ int slice_code ; /* code for slice timing pattern */ int slice_start , slice_end ; /* indexes for start & stop of slices */ float slice_duration ; /* time between individual slices */ float quatern_b, quatern_c, /* quaternion transform parameters */ quatern_d, qoffset_x, /* [when writing a dataset, these ] */ qoffset_y, qoffset_z, /* [are used for qform, NOT qto_xyz] */ qfac ; mat44 qto_xyz ; /* qform: transform (i,j,k) to (x,y,z) */ mat44 qto_ijk ; /* qform: transform (x,y,z) to (i,j,k) */ mat44 sto_xyz ; /* sform: transform (i,j,k) to (x,y,z) */ mat44 sto_ijk ; /* sform: transform (x,y,z) to (i,j,k) */ float toffset ; /* time coordinate offset */ int xyz_units , time_units ; /* dx,dy,dz & dt units: NIFTI_UNITS_* code */ int nifti_type ; /* 0==ANALYZE, 2==NIFTI-1 (2 files), 1==NIFTI-1 (1 file) , 3==NIFTI-ASCII (1 file) */ int intent_code ; /* statistic type (or something) */ float intent_p1, intent_p2, /* intent parameters */ intent_p3 ; char intent_name[16] ; char descrip[80], aux_file[24]; char *fname ; /* header filename (.hdr or .nii) */ char *iname ; /* image filename (.img or .nii) */ int iname_offset ; /* offset into iname where data starts */ int swapsize ; /* swapping unit in image data (might be 0) */ int byteorder ; /* byte order on disk (MSB_ or LSB_FIRST) */ void *data ; /* pointer to data: nbyper*nvox bytes */ int num_ext ; /* number of extensions in ext_list */ nifti1_extension * ext_list ; /* array of extension structures (with data)*/ } nifti_image ; /* struct for return from nifti_image_read_bricks() */ typedef struct { int nbricks; /* the number of allocated pointers in 'bricks' */ int bsize; /* the length of each data block, in bytes */ void ** bricks; /* array of pointers to data blocks */ } nifti_brick_list; /*****************************************************************************/ /*--------------- Prototypes of functions defined in this file --------------*/ char *nifti_datatype_string ( int dt ) ; char *nifti_units_string ( int uu ) ; char *nifti_intent_string ( int ii ) ; char *nifti_xform_string ( int xx ) ; char *nifti_slice_string ( int ss ) ; char *nifti_orientation_string( int ii ) ; int nifti_is_inttype( int dt ) ; mat44 mat44_inverse( mat44 R ) ; mat33 mat33_inverse( mat33 R ) ; mat33 mat33_polar ( mat33 A ) ; float mat33_rownorm( mat33 A ) ; float mat33_colnorm( mat33 A ) ; float mat33_determ ( mat33 R ) ; mat33 mat33_mul ( mat33 A , mat33 B ) ; void swap_2bytes ( int n , void *ar ) ; void swap_4bytes ( int n , void *ar ) ; void swap_8bytes ( int n , void *ar ) ; void swap_16bytes( int n , void *ar ) ; void swap_Nbytes ( int n , int siz , void *ar ) ; void swap_nifti_header( struct nifti_1_header *h , int is_nifti ) ; int get_filesize( char *pathname ) ; nifti_image *nifti_image_read_bricks(char *hname , int nbricks, int * blist, nifti_brick_list * NBL ); int nifti_image_load_bricks(nifti_image *nim , int nbricks, int *blist, nifti_brick_list * NBL ); void free_NBL( nifti_brick_list * NBL ); /* main read/write routines */ nifti_image *nifti_image_read ( char *hname , int read_data ) ; int nifti_image_load ( nifti_image *nim ) ; void nifti_image_unload ( nifti_image *nim ) ; void nifti_image_free ( nifti_image *nim ) ; void nifti_image_write ( nifti_image *nim ) ; void nifti_image_write_bricks(nifti_image *nim, nifti_brick_list * NBL); void nifti_image_infodump( nifti_image *nim ) ; void nifti_disp_lib_hist( void ) ; /* to display library history */ void nifti_disp_lib_version( void ) ; /* to display library version */ int nifti_disp_matrix_orient( char * mesg, mat44 mat ); char * nifti_image_to_ascii ( nifti_image *nim ) ; nifti_image *nifti_image_from_ascii( char *str, int * bytes_read ) ; size_t nifti_get_volsize(nifti_image *nim) ; /* basic file operations */ int nifti_set_filenames(nifti_image * nim, char * prefix, int check); char * nifti_makehdrname (char * prefix, int nifti_type, int check, int comp); char * nifti_makeimgname (char * prefix, int nifti_type, int check, int comp); int is_nifti_file (char *hname); char * nifti_find_file_extension(char * name); int nifti_validfilename(char* fname); int disp_nifti_1_header( char * info, nifti_1_header * hp ) ; void nifti_set_debug_level( int level ) ; int valid_nifti_brick_list(nifti_image * nim , int nbricks, int * blist, int disp_error); void nifti_datatype_sizes( int datatype , int *nbyper, int *swapsize ) ; void mat44_to_quatern( mat44 R , float *qb, float *qc, float *qd, float *qx, float *qy, float *qz, float *dx, float *dy, float *dz, float *qfac ) ; mat44 quatern_to_mat44( float qb, float qc, float qd, float qx, float qy, float qz, float dx, float dy, float dz, float qfac ); mat44 make_orthog_mat44( float r11, float r12, float r13 , float r21, float r22, float r23 , float r31, float r32, float r33 ) ; int short_order(void) ; /* CPU byte order */ /* Orientation codes that might be returned from mat44_to_orientation(). */ #define NIFTI_L2R 1 /* Left to Right */ #define NIFTI_R2L 2 /* Right to Left */ #define NIFTI_P2A 3 /* Posterior to Anterior */ #define NIFTI_A2P 4 /* Anterior to Posterior */ #define NIFTI_I2S 5 /* Inferior to Superior */ #define NIFTI_S2I 6 /* Superior to Inferior */ void mat44_to_orientation( mat44 R , int *icod, int *jcod, int *kcod ) ; /*--------------------- Low level IO routines ------------------------------*/ char * nifti_findhdrname (char* fname); char * nifti_findimgname (char* fname , int nifti_type); int nifti_is_gzfile (char* fname); char * nifti_makebasename(char* fname); /* other routines */ nifti_1_header * nifti_read_header(char * hname, int * swap); nifti_image * nifti_copy_nim_info(nifti_image* src); nifti_image * nifti_simple_init_nim(); struct nifti_1_header nifti_convert_nim2nhdr(nifti_image* nim); nifti_image * nifti_convert_nhdr2nim(struct nifti_1_header nhdr, char* fname); void nifti_set_iname_offset(nifti_image *nim); int nifti_add_exten_to_list( nifti1_extension * new_ext, nifti1_extension ** list, int new_length ); char * nifti_strdup(char *str); /*-------------------- Some C convenience macros ----------------------------*/ /* nifti extension codes */ #define NIFTI_ECODE_UNKNOWN 0 #define NIFTI_ECODE_DICOM 2 #define NIFTI_ECODE_AFNI 4 #undef LNI_FERR /* local nifti file error, to be compact and repetative */ #define LNI_FERR(func,msg,file) \ fprintf(stderr,"** ERROR (%s): %s '%s'\n",func,msg,file) #undef swap_2 #undef swap_4 #define swap_2(s) swap_2bytes(1,&(s)) /* s is a 2-byte short; swap in place */ #define swap_4(v) swap_4bytes(1,&(v)) /* v is a 4-byte value; swap in place */ /***** isfinite() is a C99 macro, which is present in many C implementations already *****/ #undef IS_GOOD_FLOAT #undef FIXED_FLOAT #ifdef isfinite /* use isfinite() to check floats/doubles for goodness */ # define IS_GOOD_FLOAT(x) isfinite(x) /* check if x is a "good" float */ # define FIXED_FLOAT(x) (isfinite(x) ? (x) : 0) /* fixed if bad */ #else # define IS_GOOD_FLOAT(x) 1 /* don't check it */ # define FIXED_FLOAT(x) (x) /* don't fix it */ #endif #undef ASSIF /* assign v to *p, if possible */ #define ASSIF(p,v) if( (p)!=NULL ) *(p) = (v) #undef MSB_FIRST #undef LSB_FIRST #undef REVERSE_ORDER #define LSB_FIRST 1 #define MSB_FIRST 2 #define REVERSE_ORDER(x) (3-(x)) /* convert MSB_FIRST <--> LSB_FIRST */ #define LNI_MAX_NIA_EXT_LEN 100000 /* consider a longer extension invalid */ /*=================*/ #ifdef __cplusplus } #endif /*=================*/ #endif /* _NIFTI_IO_HEADER_ */