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Commit fd822951 authored by Ali Can Demiralp's avatar Ali Can Demiralp
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Merge branch 'develop'

parents c53e4e3a 7b021d82
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CMakeLists.txt
+ 36
− 20
View file @ fd822951
################################################## Project ################################################## ################################################## Project ##################################################
cmake_minimum_required(VERSION 3.10 FATAL_ERROR) cmake_minimum_required(VERSION 3.10 FATAL_ERROR)
project (nifti VERSION 1.0 LANGUAGES CXX) project (nifti VERSION 1.0 LANGUAGES C)
list (APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake) list (APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake)
set_property (GLOBAL PROPERTY USE_FOLDERS ON) set_property (GLOBAL PROPERTY USE_FOLDERS ON)
set (CMAKE_CXX_STANDARD 17) set (CMAKE_CXX_STANDARD 17)
set (CMAKE_CXX_VISIBILITY_PRESET hidden)
set (CMAKE_VISIBILITY_INLINES_HIDDEN 1)
include (set_max_warning_level) include (set_max_warning_level)
set_max_warning_level () set_max_warning_level ()
################################################## Options ################################################## ################################################## Options ##################################################
option(BUILD_SHARED_LIBS "Build shared (dynamic) libraries." ON)
option(BUILD_TESTS "Build tests." OFF) option(BUILD_TESTS "Build tests." OFF)
################################################## Sources ################################################## ################################################## Sources ##################################################
file(GLOB_RECURSE PROJECT_HEADERS include/*.h include/*.i include/*.hpp include/*.ipp) file(GLOB_RECURSE PROJECT_HEADERS include/*.h include/*.hpp)
file(GLOB_RECURSE PROJECT_SOURCES source/*.c source/*.cpp)
file(GLOB_RECURSE PROJECT_CMAKE_UTILS cmake/*.cmake) file(GLOB_RECURSE PROJECT_CMAKE_UTILS cmake/*.cmake)
file(GLOB_RECURSE PROJECT_MISC *.md *.txt) file(GLOB_RECURSE PROJECT_MISC *.md *.txt)
set (PROJECT_EXPORT_HPP include/${PROJECT_NAME}/export.hpp)
set (PROJECT_FILES set (PROJECT_FILES
${PROJECT_HEADERS} ${PROJECT_HEADERS}
${PROJECT_SOURCES}
${PROJECT_CMAKE_UTILS} ${PROJECT_CMAKE_UTILS}
${PROJECT_MISC}) ${PROJECT_MISC}
${PROJECT_EXPORT_HPP})
include (assign_source_group) include (assign_source_group)
assign_source_group(${PROJECT_FILES}) assign_source_group(${PROJECT_FILES})
...@@ -38,25 +45,31 @@ if (UNIX) ...@@ -38,25 +45,31 @@ if (UNIX)
list(APPEND PROJECT_COMPILE_DEFINITIONS -DHAVE_FDOPEN -DUSE_STAT) list(APPEND PROJECT_COMPILE_DEFINITIONS -DHAVE_FDOPEN -DUSE_STAT)
endif () endif ()
################################################## Targets ################################################## ################################################## Targets ##################################################
add_library(${PROJECT_NAME} INTERFACE) add_library(${PROJECT_NAME} ${PROJECT_FILES})
target_include_directories(${PROJECT_NAME} INTERFACE target_include_directories(${PROJECT_NAME} PUBLIC
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include> $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
$<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}> $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}>
$<INSTALL_INTERFACE:include>) $<INSTALL_INTERFACE:include> PRIVATE source)
target_include_directories(${PROJECT_NAME} INTERFACE ${PROJECT_INCLUDE_DIRS}) target_include_directories(${PROJECT_NAME} PUBLIC ${PROJECT_INCLUDE_DIRS})
target_link_libraries (${PROJECT_NAME} INTERFACE ${PROJECT_LIBRARIES}) target_link_libraries (${PROJECT_NAME} PUBLIC ${PROJECT_LIBRARIES})
target_compile_definitions(${PROJECT_NAME} INTERFACE ${PROJECT_COMPILE_DEFINITIONS}) target_compile_definitions(${PROJECT_NAME} PUBLIC ${PROJECT_COMPILE_DEFINITIONS})
set_target_properties (${PROJECT_NAME} PROPERTIES LINKER_LANGUAGE CXX)
if(NOT BUILD_SHARED_LIBS)
string (TOUPPER ${PROJECT_NAME} PROJECT_NAME_UPPER)
set_target_properties(${PROJECT_NAME} PROPERTIES COMPILE_FLAGS -D${PROJECT_NAME_UPPER}_STATIC)
endif()
# Hack for header-only project to appear in the IDEs. ################################################## Postbuild ##################################################
add_library(${PROJECT_NAME}_ STATIC ${PROJECT_FILES}) include (GenerateExportHeader)
target_include_directories(${PROJECT_NAME}_ PUBLIC string (TOUPPER ${PROJECT_NAME} PROJECT_NAME_UPPER)
${CMAKE_CURRENT_SOURCE_DIR}/include generate_export_header(${PROJECT_NAME}
${CMAKE_CURRENT_BINARY_DIR}) EXPORT_FILE_NAME ${PROJECT_SOURCE_DIR}/include/${PROJECT_NAME}/export.hpp
target_include_directories(${PROJECT_NAME}_ PUBLIC ${PROJECT_INCLUDE_DIRS}) EXPORT_MACRO_NAME ${PROJECT_NAME_UPPER}_EXPORT
target_link_libraries (${PROJECT_NAME}_ PUBLIC ${PROJECT_LIBRARIES}) STATIC_DEFINE ${PROJECT_NAME_UPPER}_STATIC
target_compile_definitions(${PROJECT_NAME}_ PUBLIC ${PROJECT_COMPILE_DEFINITIONS}) )
set_target_properties (${PROJECT_NAME}_ PROPERTIES LINKER_LANGUAGE CXX)
################################################## Testing ################################################## ################################################## Testing ##################################################
if(BUILD_TESTS) if(BUILD_TESTS)
...@@ -79,7 +92,10 @@ if(BUILD_TESTS) ...@@ -79,7 +92,10 @@ if(BUILD_TESTS)
endif() endif()
################################################## Installation ################################################## ################################################## Installation ##################################################
install(TARGETS ${PROJECT_NAME} EXPORT ${PROJECT_NAME}-config) install(TARGETS ${PROJECT_NAME} EXPORT ${PROJECT_NAME}-config
ARCHIVE DESTINATION lib
LIBRARY DESTINATION lib
RUNTIME DESTINATION bin)
install(DIRECTORY include/ DESTINATION include) install(DIRECTORY include/ DESTINATION include)
install(EXPORT ${PROJECT_NAME}-config DESTINATION cmake) install(EXPORT ${PROJECT_NAME}-config DESTINATION cmake)
export (TARGETS ${PROJECT_NAME} FILE ${PROJECT_NAME}-config.cmake) export (TARGETS ${PROJECT_NAME} FILE ${PROJECT_NAME}-config.cmake)
include/nifti/nifti1_io.h
+ 0
− 2
View file @ fd822951
...@@ -553,5 +553,3 @@ typedef struct { ...@@ -553,5 +553,3 @@ typedef struct {
/*=================*/ /*=================*/
#endif /* _NIFTI_IO_HEADER_ */ #endif /* _NIFTI_IO_HEADER_ */
#include "nifti1_io.i"
\ No newline at end of file
include/nifti/nifti2.h deleted 100644 → 0
+ 0
− 117
View file @ c53e4e3a
/** \file nifti2.h
\brief Header structure for NIFTI-2 format.
*/
#ifndef __NIFTI2_HEADER
#define __NIFTI2_HEADER
/*---------------------------------------------------------------------------*/
/* Changes to the header from NIFTI-1 to NIFTI-2 are intended to allow for
larger and more accurate fields. The changes are as follows:
- short dim[8] -> int64_t dim[8]
- float intent_p1,2,3 -> double intent_p1,2,3 (3 fields)
- float pixdim[8] -> double pixdim[8]
- float vox_offset -> int64_t vox_offset
- float scl_slope -> double scl_slope
- float scl_inter -> double scl_inter
- float cal_max -> double cal_max
- float cal_min -> double cal_min
- float slice_duration -> double slice_duration
- float toffset -> double toffset
- short slice_start -> int64_t slice_start
- short slice_end -> int64_t slice_end
- char slice_code -> int32_t slice_code
- char xyzt_units -> int32_t xyzt_units
- short intent_code -> int32_t intent_code
- short qform_code -> int32_t qform_code
- short sform_code -> int32_t sform_code
- float quatern_b,c,d -> double quatern_b,c,d (3 fields)
- float srow_x,y,z[4] -> double srow_x,y,z[4] (3 fields)
- char magic[4] -> char magic[8]
- char unused_str[15] -> padding added at the end of the header
- previously unused fields have been removed:
data_type, db_name, extents, session_error, regular, glmax, glmin
- the field order has been changed, notably with magic after sizeof_hdr
2 Jan, 2014 [rickr]
-----------------------------------------------------------------------------*/
#include <stdint.h>
/*=================*/
#ifdef __cplusplus
extern "C" {
#endif
/*=================*/
/*! \struct nifti_2_header
\brief Data structure defining the fields in the nifti2 header.
This binary header should be found at the beginning of a valid
NIFTI-2 header file.
*/
/* hopefully cross-platform solution to byte padding added by some compilers */
#pragma pack(push)
#pragma pack(1)
/*****************************/ /***********************/ /************/
struct nifti_2_header { /* NIFTI-2 usage */ /* NIFTI-1 usage */ /* offset */
/*****************************/ /***********************/ /************/
int32_t sizeof_hdr; /*!< MUST be 540 */ /* MUST be 348 */ /* 0 */
char magic[8]; /*!< MUST be valid signature */ /* char magic[4] */ /* 4 */
int16_t datatype; /*!< Defines data type! */ /* short datatype */ /* 12 */
int16_t bitpix; /*!< Number bits/voxel */ /* short bitpix */ /* 14 */
int64_t dim[8]; /*!< Data array dimensions */ /* short dim[8] */ /* 16 */
double intent_p1; /*!< 1st intent parameter */ /* float intent_p1 */ /* 80 */
double intent_p2; /*!< 2nd intent parameter */ /* float intent_p2 */ /* 88 */
double intent_p3; /*!< 3rd intent parameter */ /* float intent_p3 */ /* 96 */
double pixdim[8]; /*!< Grid spacings */ /* float pixdim[8] */ /* 104 */
int64_t vox_offset; /*!< Offset into .nii file */ /* float vox_offset */ /* 168 */
double scl_slope; /*!< Data scaling: slope */ /* float scl_slope */ /* 176 */
double scl_inter; /*!< Data scaling: offset */ /* float scl_inter */ /* 184 */
double cal_max; /*!< Max display intensity */ /* float cal_max */ /* 192 */
double cal_min; /*!< Min display intensity */ /* float cal_min */ /* 200 */
double slice_duration; /*!< Time for 1 slice */ /* float slice_duration*/ /* 208 */
double toffset; /*!< Time axis shift */ /* float toffset */ /* 216 */
int64_t slice_start; /*!< First slice index */ /* short slice_start */ /* 224 */
int64_t slice_end; /*!< Last slice index */ /* short slice_end */ /* 232 */
char descrip[80]; /*!< any text you like */ /* char descrip[80] */ /* 240 */
char aux_file[24]; /*!< auxiliary filename */ /* char aux_file[24] */ /* 320 */
int32_t qform_code; /*!< NIFTI_XFORM_* code */ /* short qform_code */ /* 344 */
int32_t sform_code; /*!< NIFTI_XFORM_* code */ /* short sform_code */ /* 348 */
double quatern_b; /*!< Quaternion b param */ /* float quatern_b */ /* 352 */
double quatern_c; /*!< Quaternion c param */ /* float quatern_c */ /* 360 */
double quatern_d; /*!< Quaternion d param */ /* float quatern_d */ /* 368 */
double qoffset_x; /*!< Quaternion x shift */ /* float qoffset_x */ /* 376 */
double qoffset_y; /*!< Quaternion y shift */ /* float qoffset_y */ /* 384 */
double qoffset_z; /*!< Quaternion z shift */ /* float qoffset_z */ /* 392 */
double srow_x[4]; /*!< 1st row affine transform*/ /* float srow_x[4] */ /* 400 */
double srow_y[4]; /*!< 2nd row affine transform*/ /* float srow_y[4] */ /* 432 */
double srow_z[4]; /*!< 3rd row affine transform*/ /* float srow_z[4] */ /* 464 */
int32_t slice_code; /*!< Slice timing order */ /* char slice_code */ /* 496 */
int32_t xyzt_units; /*!< Units of pixdim[1..4] */ /* char xyzt_units */ /* 500 */
int32_t intent_code; /*!< NIFTI_INTENT_* code */ /* short intent_code */ /* 504 */
char intent_name[16];/*!< name or meaning of data */ /* char intent_name[16]*/ /* 508 */
char dim_info; /*!< MRI slice ordering */ /* char dim_info */ /* 524 */
char unused_str[15]; /*!< unused, filled with \0 */ /* 525 */
}; /****** total bytes: 540 */
typedef struct nifti_2_header nifti_2_header;
/* restore packing behavior */
#pragma pack(pop)
/* base swap test on the suggested version check, rather than dim[0]
swap4(348)==1543569408, swap4(540)==469893120 */
#define NIFTI2_NEEDS_SWAP(h) \
((h).sizeof_hdr == 1543569408 || (h).sizeof_hdr == 469893120)
/*=================*/
#ifdef __cplusplus
}
#endif
/*=================*/
#endif /* __NIFTI2_HEADER */
include/nifti/nifti2_io.h deleted 100644 → 0
+ 0
− 736
View file @ c53e4e3a
/** \file nifti2_io.h
\brief Data structures for using nifti2_io API.
- Written by Bob Cox, SSCC NIMH
- Revisions by Rick Reynolds, SSCC NIMH
*/
#ifndef _NIFTI2_IO_HEADER_
#define _NIFTI2_IO_HEADER_
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <limits.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 "nifti2.h" /*** NIFTI-2 header specification ***/
#include "znzlib.h"
/*=================*/
#ifdef __cplusplus
extern "C" {
#endif
/*=================*/
/*****===================================================================*****/
/***** File nifti2_io.h == Declarations for nifti2_io.c *****/
/*****...................................................................*****/
/***** This code is a modification of nifti1_io.h. *****/
/*****...................................................................*****/
/***** 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, particularly involving
extensions and nifti_brick_list.
......................................................................
Modified by: Rick Reynolds (SSCC/DIRP/NIMH, National Institutes of Health)
Date: August 2013
Converted to be based on nifti_2_header.
** NOT BACKWARD COMPATABLE **
These routines will read/write both NIFTI-1 and NIFTI-2 image files,
but modification to the _calling_ routies is necessary, since:
a. the main nifti_image type has changed (to nifti2_image)
b. some image field types have been altered (to have larger size)
c. some routines have been changed to apply to multiple NIFTI types
*/
/********************** 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 { /** 4x4 matrix struct (double) **/
double m[4][4] ;
} nifti_dmat44 ;
typedef struct { /** 3x3 matrix struct (double) **/
double m[3][3] ;
} nifti_dmat33 ;
/*...........................................................................*/
/*! \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
nifti2_io API. Note that this structure is not part of the
nifti2 format definition; it is used to implement one API
for reading/writing datasets in the nifti1 or nifti2 formats.
Field types changed for NIFTI-2 (note: ALL floats to doubles):
nx, ny, ..., nw, dim, nvox,
dx, dy, ..., dw, pixdim,
scl_slope, scl_inter, cal_min, cal_max,
slice_start, slice_end, slice_duration,
quatern_b,c,d, qoffset_x,y,z, qfac,
qto_xyz,ijk, sto_xyz,ijk,
toffset, intent_p1,2,3, iname_offset
*/
typedef struct { /*!< Image storage struct **/
int64_t ndim ; /*!< last dimension greater than 1 (1..7) */
int64_t nx ; /*!< dimensions of grid array */
int64_t ny ; /*!< dimensions of grid array */
int64_t nz ; /*!< dimensions of grid array */
int64_t nt ; /*!< dimensions of grid array */
int64_t nu ; /*!< dimensions of grid array */
int64_t nv ; /*!< dimensions of grid array */
int64_t nw ; /*!< dimensions of grid array */
int64_t dim[8] ; /*!< dim[0]=ndim, dim[1]=nx, etc. */
int64_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 */
double dx ; /*!< grid spacings */
double dy ; /*!< grid spacings */
double dz ; /*!< grid spacings */
double dt ; /*!< grid spacings */
double du ; /*!< grid spacings */
double dv ; /*!< grid spacings */
double dw ; /*!< grid spacings */
double pixdim[8] ; /*!< pixdim[1]=dx, etc. */
double scl_slope ; /*!< scaling parameter - slope */
double scl_inter ; /*!< scaling parameter - intercept */
double cal_min ; /*!< calibration parameter, minimum */
double 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 */
int64_t slice_start ; /*!< index for start of slices */
int64_t slice_end ; /*!< index for end of slices */
double slice_duration ; /*!< time between individual slices */
/*! quaternion transform parameters
[when writing a dataset, these are used for qform, NOT qto_xyz] */
double quatern_b , quatern_c , quatern_d ,
qoffset_x , qoffset_y , qoffset_z ,
qfac ;
nifti_dmat44 qto_xyz ; /*!< qform: transform (i,j,k) to (x,y,z) */
nifti_dmat44 qto_ijk ; /*!< qform: transform (x,y,z) to (i,j,k) */
nifti_dmat44 sto_xyz ; /*!< sform: transform (i,j,k) to (x,y,z) */
nifti_dmat44 sto_ijk ; /*!< sform: transform (x,y,z) to (i,j,k) */
double 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 ; /*!< see NIFTI_FTYPE_* codes, below:
0==ANALYZE,
1==NIFTI-1 (1 file),
2==NIFTI-1 (2 files),
3==NIFTI-ASCII (1 file)
4==NIFTI-2 (1 file),
5==NIFTI-2 (2 files) */
int intent_code ; /*!< statistic type (or something) */
double intent_p1 ; /*!< intent parameters */
double intent_p2 ; /*!< intent parameters */
double 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) */
int64_t 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 ;
/* allow clarity */
typedef nifti_image nifti2_image;
typedef 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. */
int64_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 */
} nifti1_image ;
/* struct for return from nifti_image_read_bricks() */
typedef struct {
int64_t nbricks; /* the number of allocated pointers in 'bricks' */
int64_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 ) ;
nifti_dmat44 nifti_dmat44_inverse( nifti_dmat44 R ) ;
int nifti_mat44_to_dmat44(mat44 * fm, nifti_dmat44 * dm);
int nifti_dmat44_to_mat44(nifti_dmat44 * dm, mat44 * fm);
nifti_dmat33 nifti_dmat33_inverse( nifti_dmat33 R ) ;
nifti_dmat33 nifti_dmat33_polar ( nifti_dmat33 A ) ;
double nifti_dmat33_rownorm( nifti_dmat33 A ) ;
double nifti_dmat33_colnorm( nifti_dmat33 A ) ;
double nifti_dmat33_determ ( nifti_dmat33 R ) ;
nifti_dmat33 nifti_dmat33_mul ( nifti_dmat33 A , nifti_dmat33 B ) ;
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 ( int64_t n , void *ar ) ;
void nifti_swap_4bytes ( int64_t n , void *ar ) ;
void nifti_swap_8bytes ( int64_t n , void *ar ) ;
void nifti_swap_16bytes( int64_t n , void *ar ) ;
void nifti_swap_Nbytes ( int64_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_header_version (const char * buf, int nbytes);
int64_t nifti_get_filesize( const char *pathname ) ;
void swap_nifti_header ( void * h , int ni_ver ) ;
void old_swap_nifti_header( struct nifti_1_header *h , int is_nifti );
void nifti_swap_as_analyze( nifti_analyze75 *h );
void nifti_swap_as_nifti1( nifti_1_header *h );
void nifti_swap_as_nifti2( nifti_2_header *h );
/* main read/write routines */
nifti_image *nifti_image_read_bricks(const char *hname , int64_t nbricks,
const int64_t *blist, nifti_brick_list * NBL);
int nifti_image_load_bricks(nifti_image *nim , int64_t nbricks,
const int64_t *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);
int64_t nifti_read_collapsed_image( nifti_image * nim,
const int64_t dims[8], void ** data);
int64_t nifti_read_subregion_image(nifti_image *nim, int64_t *start_index,
int64_t *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( int ver ) ; /* to display library history */
void nifti_disp_lib_version( void ) ; /* to display library version */
int nifti_disp_matrix_orient( const char * mesg, nifti_dmat44 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 ) ;
int64_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 ) ;
int disp_nifti_2_header( const char * info, const nifti_2_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 nifti_get_alter_cifti( void );
void nifti_set_alter_cifti( int alter_cifti );
int nifti_alter_cifti_dims(nifti_image * nim);
int valid_nifti_brick_list(nifti_image * nim , int64_t nbricks,
const int64_t * blist, int disp_error);
/* znzFile operations */
znzFile nifti_image_open(const char * hname, 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);
int64_t nifti_read_buffer(znzFile fp, void* datatptr, int64_t ntot,
nifti_image *nim);
int nifti_write_all_data(znzFile fp, nifti_image * nim,
const nifti_brick_list * NBL);
int64_t nifti_write_buffer(znzFile fp, const void * buffer, int64_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_dmat44_to_quatern(nifti_dmat44 R ,
double *qb, double *qc, double *qd,
double *qx, double *qy, double *qz,
double *dx, double *dy, double *dz, double *qfac);
nifti_dmat44 nifti_quatern_to_dmat44( double qb, double qc, double qd,
double qx, double qy, double qz,
double dx, double dy, double dz, double qfac );
nifti_dmat44 nifti_make_orthog_dmat44( double r11, double r12, double r13 ,
double r21, double r22, double r23 ,
double r31, double r32, double r33 ) ;
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 ) ;
void nifti_dmat44_to_orientation( nifti_dmat44 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 */
int nifti_convert_nim2n1hdr(const nifti_image* nim, nifti_1_header * hdr);
int nifti_convert_nim2n2hdr(const nifti_image* nim, nifti_2_header * hdr);
nifti_1_header * nifti_make_new_n1_header(const int64_t arg_dims[], int dtype);
nifti_2_header * nifti_make_new_n2_header(const int64_t arg_dims[], int dtype);
void * nifti_read_header(const char *hname, int *nver, int check);
nifti_1_header * nifti_read_n1_hdr(const char *hname, int *swapped, int check);
nifti_2_header * nifti_read_n2_hdr(const char *hname, int *swapped, int check);
nifti_image * nifti_copy_nim_info(const nifti_image * src);
nifti_image * nifti_make_new_nim(const int64_t dims[], int datatype,
int data_fill);
nifti_image * nifti_simple_init_nim(void);
nifti_image * nifti_convert_n1hdr2nim(nifti_1_header nhdr,const char *fname);
nifti_image * nifti_convert_n2hdr2nim(nifti_2_header nhdr,const char *fname);
int nifti_looks_like_cifti(nifti_image * nim);
int nifti_hdr1_looks_good (const nifti_1_header * hdr);
int nifti_hdr2_looks_good (const nifti_2_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);
int64_t * nifti_get_int64list(int64_t nvals , const char *str);
int * nifti_get_intlist (int nvals , const char *str);
char * nifti_strdup (const char *str);
int valid_nifti_extensions(const nifti_image *nim);
int nifti_valid_header_size(int ni_ver, int whine);
/*-------------------- 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 */
#define NIFTI_MAX_ECODE 40 /******* maximum extension code *******/
/* nifti_type file codes */
#define NIFTI_FTYPE_ANALYZE 0 /* old ANALYZE */
#define NIFTI_FTYPE_NIFTI1_1 1 /* NIFTI-1 */
#define NIFTI_FTYPE_NIFTI1_2 2
#define NIFTI_FTYPE_ASCII 3
#define NIFTI_FTYPE_NIFTI2_1 4 /* NIFTI-2 */
#define NIFTI_FTYPE_NIFTI2_2 5
#define NIFTI_MAX_FTYPE 5 /* this should match the maximum code */
/*------------------------------------------------------------------------*/
/*-- the rest of these apply only to nifti2_io.c, check for _NIFTI2_IO_C_ */
#ifdef _NIFTI2_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 */
int alter_cifti; /*!< convert CIFTI dimensions */
} 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 */
#undef NIFTI_IS_16_BIT_INT
#define NIFTI_IS_16_BIT_INT(x) ((x) <= 32767 && (x) >= -32768)
#endif /* _NIFTI2_IO_C_ section */
/*------------------------------------------------------------------------*/
/*=================*/
#ifdef __cplusplus
}
#endif
/*=================*/
#endif /* _NIFTI2_IO_HEADER_ */
#include "nifti2_io.i"
\ No newline at end of file
include/nifti/nifti2_io.i deleted 100644 → 0
+ 0
− 9479
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Source diff could not be displayed: it is too large. Options to address this: view the blob.
include/nifti/znzlib.h
+ 0
− 2
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...@@ -120,5 +120,3 @@ int znzprintf(znzFile stream, const char *format, ...); ...@@ -120,5 +120,3 @@ int znzprintf(znzFile stream, const char *format, ...);
/*=================*/ /*=================*/
#endif #endif
#include "znzlib.i"
\ No newline at end of file
include/nifti/nifti1_io.i → source/nifti1_io.c
+ 2
− 0
View file @ fd822951
#define _NIFTI1_IO_C_ #define _NIFTI1_IO_C_
#include "nifti/nifti1_io.h" /* typedefs, prototypes, macros, etc. */
/*****===================================================================*****/ /*****===================================================================*****/
/***** Sample functions to deal with NIFTI-1 and ANALYZE files *****/ /***** Sample functions to deal with NIFTI-1 and ANALYZE files *****/
/*****...................................................................*****/ /*****...................................................................*****/
......
include/nifti/znzlib.i → source/znzlib.c
+ 2
− 0
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...@@ -21,6 +21,8 @@ NB: seeks for writable files with compression are quite restricted ...@@ -21,6 +21,8 @@ NB: seeks for writable files with compression are quite restricted
*/ */
#include "nifti/znzlib.h"
/* /*
znzlib.c (zipped or non-zipped library) znzlib.c (zipped or non-zipped library)
......
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