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nifti1_io.h
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nifti1_io.h
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/** \file nifti1_io.h
\brief Data structures for using nifti1_io API.
- Written by Bob Cox, SSCC NIMH
- Revisions by Rick Reynolds, SSCC NIMH
*/
#ifndef _NIFTI_IO_HEADER_
#define _NIFTI_IO_HEADER_
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <ctype.h>
#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. *****/
/*****===================================================================*****/
/*
Modified by: Mark Jenkinson (FMRIB Centre, University of Oxford, UK)
Date: July/August 2004
Mainly adding low-level IO and changing things to allow gzipped files
to be read and written
Full backwards compatability should have been maintained
Modified by: Rick Reynolds (SSCC/DIRP/NIMH, National Institutes of Health)
Date: December 2004
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 ;
/*...........................................................................*/
/*! \enum analyze_75_orient_code
* \brief Old-style analyze75 orientation
* codes.
*/
typedef enum _analyze75_orient_code {
a75_transverse_unflipped = 0,
a75_coronal_unflipped = 1,
a75_sagittal_unflipped = 2,
a75_transverse_flipped = 3,
a75_coronal_flipped = 4,
a75_sagittal_flipped = 5,
a75_orient_unknown = 6
} analyze_75_orient_code;
/*! \struct nifti_image
\brief High level data structure for open nifti datasets in the
nifti1_io API. Note that this structure is not part of the
nifti1 format definition; it is used to implement one API
for reading/writing formats in the nifti1 format.
*/
typedef struct { /*!< Image storage struct **/
int ndim ; /*!< last dimension greater than 1 (1..7) */
int nx ; /*!< dimensions of grid array */
int ny ; /*!< dimensions of grid array */
int nz ; /*!< dimensions of grid array */
int nt ; /*!< dimensions of grid array */
int nu ; /*!< dimensions of grid array */
int nv ; /*!< dimensions of grid array */
int nw ; /*!< dimensions of grid array */
int dim[8] ; /*!< dim[0]=ndim, dim[1]=nx, etc. */
size_t nvox ; /*!< number of voxels = nx*ny*nz*...*nw */
int nbyper ; /*!< bytes per voxel, matches datatype */
int datatype ; /*!< type of data in voxels: DT_* code */
float dx ; /*!< grid spacings */
float dy ; /*!< grid spacings */
float dz ; /*!< grid spacings */
float dt ; /*!< grid spacings */
float du ; /*!< grid spacings */
float dv ; /*!< grid spacings */
float dw ; /*!< grid spacings */
float pixdim[8] ; /*!< pixdim[1]=dx, etc. */
float scl_slope ; /*!< scaling parameter - slope */
float scl_inter ; /*!< scaling parameter - intercept */
float cal_min ; /*!< calibration parameter, minimum */
float cal_max ; /*!< calibration parameter, maximum */
int qform_code ; /*!< codes for (x,y,z) space meaning */
int sform_code ; /*!< codes for (x,y,z) space meaning */
int freq_dim ; /*!< indexes (1,2,3, or 0) for MRI */
int phase_dim ; /*!< directions in dim[]/pixdim[] */
int slice_dim ; /*!< directions in dim[]/pixdim[] */
int slice_code ; /*!< code for slice timing pattern */
int slice_start ; /*!< index for start of slices */
int slice_end ; /*!< index for end of slices */
float slice_duration ; /*!< time between individual slices */
/*! quaternion transform parameters
[when writing a dataset, these are used for qform, NOT qto_xyz] */
float quatern_b , quatern_c , quatern_d ,
qoffset_x , qoffset_y , qoffset_z ,
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 ; /*!< dx,dy,dz units: NIFTI_UNITS_* code */
int time_units ; /*!< dt units: NIFTI_UNITS_* code */
int nifti_type ; /*!< 0==ANALYZE, 1==NIFTI-1 (1 file),
2==NIFTI-1 (2 files),
3==NIFTI-ASCII (1 file) */
int intent_code ; /*!< statistic type (or something) */
float intent_p1 ; /*!< intent parameters */
float intent_p2 ; /*!< intent parameters */
float intent_p3 ; /*!< intent parameters */
char intent_name[16] ; /*!< optional description of intent data */
char descrip[80] ; /*!< optional text to describe dataset */
char aux_file[24] ; /*!< auxiliary filename */
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 ; /*!< swap 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 structs (with data) */
analyze_75_orient_code analyze75_orient; /*!< for old analyze files, orient */
} nifti_image ;
/* struct for return from nifti_image_read_bricks() */
typedef struct {
int nbricks; /* the number of allocated pointers in 'bricks' */
size_t bsize; /* the length of each data block, in bytes */
void ** bricks; /* array of pointers to data blocks */
} nifti_brick_list;
/*****************************************************************************/
/*------------------ NIfTI version of ANALYZE 7.5 structure -----------------*/
/* (based on fsliolib/dbh.h, but updated for version 7.5) */
typedef struct {
/* header info fields - describes the header overlap with NIfTI */
/* ------------------ */
int sizeof_hdr; /* 0 + 4 same */
char data_type[10]; /* 4 + 10 same */
char db_name[18]; /* 14 + 18 same */
int extents; /* 32 + 4 same */
short int session_error; /* 36 + 2 same */
char regular; /* 38 + 1 same */
char hkey_un0; /* 39 + 1 40 bytes */
/* image dimension fields - describes image sizes */
short int dim[8]; /* 0 + 16 same */
short int unused8; /* 16 + 2 intent_p1... */
short int unused9; /* 18 + 2 ... */
short int unused10; /* 20 + 2 intent_p2... */
short int unused11; /* 22 + 2 ... */
short int unused12; /* 24 + 2 intent_p3... */
short int unused13; /* 26 + 2 ... */
short int unused14; /* 28 + 2 intent_code */
short int datatype; /* 30 + 2 same */
short int bitpix; /* 32 + 2 same */
short int dim_un0; /* 34 + 2 slice_start */
float pixdim[8]; /* 36 + 32 same */
float vox_offset; /* 68 + 4 same */
float funused1; /* 72 + 4 scl_slope */
float funused2; /* 76 + 4 scl_inter */
float funused3; /* 80 + 4 slice_end, */
/* slice_code, */
/* xyzt_units */
float cal_max; /* 84 + 4 same */
float cal_min; /* 88 + 4 same */
float compressed; /* 92 + 4 slice_duration */
float verified; /* 96 + 4 toffset */
int glmax,glmin; /* 100 + 8 108 bytes */
/* data history fields - optional */
char descrip[80]; /* 0 + 80 same */
char aux_file[24]; /* 80 + 24 same */
char orient; /* 104 + 1 NO GOOD OVERLAP */
char originator[10]; /* 105 + 10 FROM HERE DOWN... */
char generated[10]; /* 115 + 10 */
char scannum[10]; /* 125 + 10 */
char patient_id[10]; /* 135 + 10 */
char exp_date[10]; /* 145 + 10 */
char exp_time[10]; /* 155 + 10 */
char hist_un0[3]; /* 165 + 3 */
int views; /* 168 + 4 */
int vols_added; /* 172 + 4 */
int start_field; /* 176 + 4 */
int field_skip; /* 180 + 4 */
int omax, omin; /* 184 + 8 */
int smax, smin; /* 192 + 8 200 bytes */
} nifti_analyze75; /* total: 348 bytes */
/*****************************************************************************/
/*--------------- Prototypes of functions defined in this file --------------*/
char const * nifti_datatype_string ( int dt ) ;
char const *nifti_units_string ( int uu ) ;
char const *nifti_intent_string ( int ii ) ;
char const *nifti_xform_string ( int xx ) ;
char const *nifti_slice_string ( int ss ) ;
char const *nifti_orientation_string( int ii ) ;
int nifti_is_inttype( int dt ) ;
mat44 nifti_mat44_inverse( mat44 R ) ;
mat33 nifti_mat33_inverse( mat33 R ) ;
mat33 nifti_mat33_polar ( mat33 A ) ;
float nifti_mat33_rownorm( mat33 A ) ;
float nifti_mat33_colnorm( mat33 A ) ;
float nifti_mat33_determ ( mat33 R ) ;
mat33 nifti_mat33_mul ( mat33 A , mat33 B ) ;
void nifti_swap_2bytes ( size_t n , void *ar ) ;
void nifti_swap_4bytes ( size_t n , void *ar ) ;
void nifti_swap_8bytes ( size_t n , void *ar ) ;
void nifti_swap_16bytes( size_t n , void *ar ) ;
void nifti_swap_Nbytes ( size_t n , int siz , void *ar ) ;
int nifti_datatype_is_valid (int dtype, int for_nifti);
int nifti_datatype_from_string(const char * name);
const char * nifti_datatype_to_string (int dtype);
int nifti_get_filesize( const char *pathname ) ;
void swap_nifti_header ( struct nifti_1_header *h , int is_nifti ) ;
void old_swap_nifti_header( struct nifti_1_header *h , int is_nifti );
int nifti_swap_as_analyze( nifti_analyze75 *h );
/* main read/write routines */
nifti_image *nifti_image_read_bricks(const char *hname , int nbricks,
const int *blist, nifti_brick_list * NBL);
int nifti_image_load_bricks(nifti_image *nim , int nbricks,
const int *blist, nifti_brick_list * NBL);
void nifti_free_NBL( nifti_brick_list * NBL );
nifti_image *nifti_image_read ( const 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 ) ;
int nifti_read_collapsed_image( nifti_image * nim, const int dims [8],
void ** data );
int nifti_read_subregion_image( nifti_image * nim,
const int *start_index, const int *region_size,
void ** data );
void nifti_image_write ( nifti_image * nim ) ;
void nifti_image_write_bricks(nifti_image * nim,
const nifti_brick_list * NBL);
void nifti_image_infodump( const 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( const char * mesg, mat44 mat );
int nifti_disp_type_list( int which );
char * nifti_image_to_ascii ( const nifti_image * nim ) ;
nifti_image *nifti_image_from_ascii( const char * str, int * bytes_read ) ;
size_t nifti_get_volsize(const nifti_image *nim) ;
/* basic file operations */
int nifti_set_filenames(nifti_image * nim, const char * prefix, int check,
int set_byte_order);
char * nifti_makehdrname (const char * prefix, int nifti_type, int check,
int comp);
char * nifti_makeimgname (const char * prefix, int nifti_type, int check,
int comp);
int is_nifti_file (const char *hname);
char * nifti_find_file_extension(const char * name);
int nifti_is_complete_filename(const char* fname);
int nifti_validfilename(const char* fname);
int disp_nifti_1_header(const char * info, const nifti_1_header * hp ) ;
void nifti_set_debug_level( int level ) ;
void nifti_set_skip_blank_ext( int skip ) ;
void nifti_set_allow_upper_fext( int allow ) ;
int valid_nifti_brick_list(nifti_image * nim , int nbricks,
const int * blist, int disp_error);
/* znzFile operations */
znzFile nifti_image_open(const char * hname, const char * opts, nifti_image ** nim);
znzFile nifti_image_write_hdr_img(nifti_image *nim, int write_data,
const char* opts);
znzFile nifti_image_write_hdr_img2( nifti_image *nim , int write_opts ,
const char* opts, znzFile imgfile, const nifti_brick_list * NBL);
size_t nifti_read_buffer(znzFile fp, void* dataptr, size_t ntot,
nifti_image *nim);
int nifti_write_all_data(znzFile fp, nifti_image * nim,
const nifti_brick_list * NBL);
size_t nifti_write_buffer(znzFile fp, const void * buffer, size_t numbytes);
nifti_image *nifti_read_ascii_image(znzFile fp, char *fname, int flen,
int read_data);
znzFile nifti_write_ascii_image(nifti_image *nim, const nifti_brick_list * NBL,
const char * opts, int write_data, int leave_open);
void nifti_datatype_sizes( int datatype , int *nbyper, int *swapsize ) ;
void nifti_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 nifti_quatern_to_mat44( float qb, float qc, float qd,
float qx, float qy, float qz,
float dx, float dy, float dz, float qfac );
mat44 nifti_make_orthog_mat44( float r11, float r12, float r13 ,
float r21, float r22, float r23 ,
float r31, float r32, float r33 ) ;
int nifti_short_order(void) ; /* CPU byte order */
/* Orientation codes that might be returned from nifti_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 nifti_mat44_to_orientation( mat44 R , int *icod, int *jcod, int *kcod ) ;
/*--------------------- Low level IO routines ------------------------------*/
char * nifti_findhdrname (const char* fname);
char * nifti_findimgname (const char* fname , int nifti_type);
int nifti_is_gzfile (const char* fname);
char * nifti_makebasename(const char* fname);
/* other routines */
struct nifti_1_header nifti_convert_nim2nhdr(const nifti_image* nim);
nifti_1_header * nifti_make_new_header(const int arg_dims[], int arg_dtype);
nifti_1_header * nifti_read_header(const char *hname, int *swapped, int check);
nifti_image * nifti_copy_nim_info(const nifti_image * src);
nifti_image * nifti_make_new_nim(const int dims[], int datatype,
int data_fill);
nifti_image * nifti_simple_init_nim(void);
nifti_image * nifti_convert_nhdr2nim(struct nifti_1_header nhdr,
const char * fname);
int nifti_hdr_looks_good (const nifti_1_header * hdr);
int nifti_is_valid_datatype (int dtype);
int nifti_is_valid_ecode (int ecode);
int nifti_nim_is_valid (nifti_image * nim, int complain);
int nifti_nim_has_valid_dims (nifti_image * nim, int complain);
int is_valid_nifti_type (int nifti_type);
int nifti_test_datatype_sizes (int verb);
int nifti_type_and_names_match (nifti_image * nim, int show_warn);
int nifti_update_dims_from_array(nifti_image * nim);
void nifti_set_iname_offset (nifti_image *nim);
int nifti_set_type_from_names (nifti_image * nim);
int nifti_add_extension(nifti_image * nim, const char * data, int len,
int ecode );
int nifti_compiled_with_zlib (void);
int nifti_copy_extensions (nifti_image *nim_dest,const nifti_image *nim_src);
int nifti_free_extensions (nifti_image *nim);
int * nifti_get_intlist (int nvals , const char *str);
char * nifti_strdup (const char *str);
int valid_nifti_extensions(const nifti_image *nim);
/*-------------------- Some C convenience macros ----------------------------*/
/* NIfTI-1.1 extension codes:
see http://nifti.nimh.nih.gov/nifti-1/documentation/faq#Q21 */
#define NIFTI_ECODE_IGNORE 0 /* changed from UNKNOWN, 29 June 2005 */
#define NIFTI_ECODE_DICOM 2 /* intended for raw DICOM attributes */
#define NIFTI_ECODE_AFNI 4 /* Robert W Cox: rwcox@nih.gov
https://afni.nimh.nih.gov/afni */
#define NIFTI_ECODE_COMMENT 6 /* plain ASCII text only */
#define NIFTI_ECODE_XCEDE 8 /* David B Keator: dbkeator@uci.edu
http://www.nbirn.net/Resources
/Users/Applications/
/xcede/index.htm */
#define NIFTI_ECODE_JIMDIMINFO 10 /* Mark A Horsfield:
mah5@leicester.ac.uk
http://someplace/something */
#define NIFTI_ECODE_WORKFLOW_FWDS 12 /* Kate Fissell: fissell@pitt.edu
http://kraepelin.wpic.pitt.edu
/~fissell/NIFTI_ECODE_WORKFLOW_FWDS
/NIFTI_ECODE_WORKFLOW_FWDS.html */
#define NIFTI_ECODE_FREESURFER 14 /* http://surfer.nmr.mgh.harvard.edu */
#define NIFTI_ECODE_PYPICKLE 16 /* embedded Python objects
http://niftilib.sourceforge.net
/pynifti */
/* LONI MiND codes: http://www.loni.ucla.edu/twiki/bin/view/Main/MiND */
#define NIFTI_ECODE_MIND_IDENT 18 /* Vishal Patel: vishal.patel@ucla.edu*/
#define NIFTI_ECODE_B_VALUE 20
#define NIFTI_ECODE_SPHERICAL_DIRECTION 22
#define NIFTI_ECODE_DT_COMPONENT 24
#define NIFTI_ECODE_SHC_DEGREEORDER 26 /* end LONI MiND codes */
#define NIFTI_ECODE_VOXBO 28 /* Dan Kimberg: www.voxbo.org */
#define NIFTI_ECODE_CARET 30 /* John Harwell: john@brainvis.wustl.edu
http://brainvis.wustl.edu/wiki
/index.php/Caret:Documentation
:CaretNiftiExtension */
#define NIFTI_ECODE_CIFTI 32 /* CIFTI-2_Main_FINAL_1March2014.pdf */
#define NIFTI_ECODE_VARIABLE_FRAME_TIMING 34
/* 36 is currently unassigned, waiting on NIFTI_ECODE_AGILENT_PROCPAR */
#define NIFTI_ECODE_EVAL 38 /* Munster University Hospital */
/* http://www.mathworks.com/matlabcentral/fileexchange/42997-dicom-to-nifti-converter */
#define NIFTI_ECODE_MATLAB 40 /* MATLAB extension */
/* Quantiphyse extension
https://quantiphyse.readthedocs.io/en/latest/advanced/nifti_extension.html*/
#define NIFTI_ECODE_QUANTIPHYSE 42 /* Quantiphyse extension */
/* Magnetic Resonance Spectroscopy (MRS)
link to come... */
#define NIFTI_ECODE_MRS 44 /* MRS extension */
#define NIFTI_MAX_ECODE 44 /******* maximum extension code *******/
/* nifti_type file codes */
#define NIFTI_FTYPE_ANALYZE 0
#define NIFTI_FTYPE_NIFTI1_1 1
#define NIFTI_FTYPE_NIFTI1_2 2
#define NIFTI_FTYPE_ASCII 3
#define NIFTI_MAX_FTYPE 3 /* this should match the maximum code */
/*------------------------------------------------------------------------*/
/*-- the rest of these apply only to nifti1_io.c, check for _NIFTI1_IO_C_ */
/* Feb 9, 2005 [rickr] */
#ifdef _NIFTI1_IO_C_
typedef struct {
int debug; /*!< debug level for status reports */
int skip_blank_ext; /*!< skip extender if no extensions */
int allow_upper_fext; /*!< allow uppercase file extensions */
} nifti_global_options;
typedef struct {
int type; /* should match the NIFTI_TYPE_ #define */
int nbyper; /* bytes per value, matches nifti_image */
int swapsize; /* bytes per swap piece, matches nifti_image */
char const * const name; /* text string to match #define */
} nifti_type_ele;
#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) nifti_swap_2bytes(1,&(s)) /* s: 2-byte short; swap in place */
#define swap_4(v) nifti_swap_4bytes(1,&(v)) /* v: 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 */
#endif /* _NIFTI1_IO_C_ section */
/*------------------------------------------------------------------------*/
/*=================*/
#ifdef __cplusplus
}
#endif
/*=================*/
#endif /* _NIFTI_IO_HEADER_ */