nifti1_io.c

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#define _NIFTI1_IO_C_

#include "nifti1_io.h"   /* typedefs, prototypes, macros, etc. */

/*****===================================================================*****/
/*****     Sample functions to deal with NIFTI-1 and ANALYZE files       *****/
/*****...................................................................*****/
/*****            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.     *****/
/*****===================================================================*****/

/** \file nifti1_io.c
    \brief main collection of nifti1 i/o routines
           - written by Bob Cox, SSCC NIMH
           - revised by Mark Jenkinson, FMRIB
           - revised by Rick Reynolds, SSCC, NIMH
           - revised by Kate Fissell, University of Pittsburgh

        The library history can be viewed via "nifti_tool -nifti_hist".
    <br>The library version can be viewed via "nifti_tool -nifti_ver".
 */

/*! global history and version strings, for printing */
static char * gni_history[] = 
{
  "----------------------------------------------------------------------\n"
  "history (of nifti library changes):\n"
  "\n",
  "0.0  August, 2003 [rwcox]\n"
  "     (Robert W Cox of the National Institutes of Health, SSCC/DIRP/NIMH)\n"
  "   - initial version\n"
  "\n",
  "0.1  July/August, 2004 [Mark Jenkinson]\n"
  "     (FMRIB Centre, University of Oxford, UK)\n"
  "   - Mainly adding low-level IO and changing things to allow gzipped\n"
  "     files to be read and written\n"
  "   - Full backwards compatability should have been maintained\n"
  "\n",
  "0.2  16 Nov 2004 [rickr]\n"
  "     (Rick Reynolds of the National Institutes of Health, SSCC/DIRP/NIMH)\n"
  "   - included Mark's changes in the AFNI distribution (including znzlib/)\n"
  "     (HAVE_ZLIB is commented out for the standard distribution)\n"
  "   - modified nifti_validfilename() and nifti_makebasename()\n"
  "   - added nifti_find_file_extension()\n"
  "\n",
  "0.3  3 Dec 2004 [rickr]\n"
  "   - note: header extensions are not yet checked for\n"
  "   - added formatted history as global string, for printing\n"
  "   - added nifti_disp_lib_hist(), to display the nifti library history\n"
  "   - added nifti_disp_lib_version(), to display the nifti library history\n",
  "   - re-wrote nifti_findhdrname()\n"
  "       o used nifti_find_file_extension()\n"
  "       o changed order of file tests (default is .nii, depends on input)\n"
  "       o free hdrname on failure\n"
  "   - made similar changes to nifti_findimgname()\n"
  "   - check for NULL return from nifti_findhdrname() calls\n",
  "   - removed most of ERREX() macros\n"
  "   - modified nifti_image_read()\n"
  "       o added debug info and error checking (on gni_debug > 0, only)\n"
  "       o fail if workingname is NULL\n"
  "       o check for failure to open header file\n"
  "       o free workingname on failure\n"
  "       o check for failure of nifti_image_load()\n"
  "       o check for failure of nifti_convert_nhdr2nim()\n",
  "   - changed nifti_image_load() to int, and check nifti_read_buffer return\n"
  "   - changed nifti_read_buffer() to fail on short read, and to count float\n"
  "     fixes (to print on debug)\n"
  "   - changed nifti_image_infodump to print to stderr\n"
  "   - updated function header comments, or moved comments above header\n"
  "   - removed const keyword\n"
  "   - added LNI_FERR() macro for error reporting on input files\n"
  "\n",
  "0.4  10 Dec 2004 [rickr]  - added header extensions\n"
  "   - in nifti1_io.h:\n"
  "       o added num_ext and ext_list to the definition of nifti_image\n"
  "       o made many functions static (more to follow)\n"
  "       o added LNI_MAX_NIA_EXT_LEN, for max nifti_type 3 extension length\n",
  "   - added __DATE__ to version output in nifti_disp_lib_version()\n"
  "   - added nifti_disp_matrix_orient() to print orientation information\n"
  "   - added '.nia' as a valid file extension in nifti_find_file_extension()\n"
  "   - added much more debug output\n"
  "   - in nifti_image_read(), in the case of an ASCII header, check for\n"
  "     extensions after the end of the header\n",
  "   - added nifti_read_extensions() function\n"
  "   - added nifti_read_next_extension() function\n"
  "   - added nifti_add_exten_to_list() function\n"
  "   - added nifti_check_extension() function\n"
  "   - added nifti_write_extensions() function\n"
  "   - added nifti_extension_size() function\n"
  "   - in nifti_set_iname_offest():\n"
  "       o adjust offset by the extension size and the extender size\n",
  "       o fixed the 'ceiling modulo 16' computation\n"
  "   - in nifti_image_write_hdr_img2(): \n"
  "       o added extension writing\n"
  "       o check for NULL return from nifti_findimgname()\n"
  "   - include number of extensions in nifti_image_to_ascii() output\n"
  "   - in nifti_image_from_ascii():\n"
  "       o return bytes_read as a parameter, computed from the final spos\n"
  "       o extract num_ext from ASCII header\n"
  "\n",
  "0.5  14 Dec 2004 [rickr]  - added sub-brick reading functions\n"
  "   - added nifti_brick_list type to nifti1_io.h, along with new prototypes\n"
  "   - added main nifti_image_read_bricks() function, with description\n"
  "   - added nifti_image_load_bricks() - library function (requires nim)\n"
  "   - added valid_nifti_brick_list() - library function\n"
  "   - added free_NBL() - library function\n",
  "   - added update_nifti_image_for_brick_list() for dimension update\n"
  "   - added nifti_load_NBL_bricks(), nifti_alloc_NBL_mem(),\n"
  "           nifti_copynsort() and force_positive() (static functions)\n"
  "   - in nifti_image_read(), check for failed load only if read_data is set\n"
  "   - broke most of nifti_image_load() into nifti_image_load_prep()\n"
  "\n",
  "0.6  15 Dec 2004 [rickr]  - added sub-brick writing functionality\n"
  "   - in nifti1_io.h, removed znzlib directory from include - all nifti\n"
  "       library files are now under the nifti directory\n"
  "   - nifti_read_extensions(): print no offset warning for nifti_type 3\n"
  "   - nifti_write_all_data():\n"
  "       o pass nifti_brick_list * NBL, for optional writing\n"
  "       o if NBL, write each sub-brick, sequentially\n",
  "   - nifti_set_iname_offset(): case 1 must have sizeof() cast to int\n"
  "   - pass NBL to nifti_image_write_hdr_img2(), and allow NBL or data\n"
  "   - added nifti_image_write_bricks() wrapper for ...write_hdr_img2()\n"
  "   - included compression abilities\n"
  "\n",
  "0.7  16 Dec 2004 [rickr] - minor changes to extension reading\n"
  "\n",
  "0.8  21 Dec 2004 [rickr] - restrict extension reading, and minor changes\n"
  "   - in nifti_image_read(), compute bytes for extensions (see remaining)\n"
  "   - in nifti_read_extensions(), pass 'remain' as space for extensions,\n"
  "        pass it to nifti_read_next_ext(), and update for each one read \n"
  "   - in nifti_check_extension(), require (size <= remain)\n",
  "   - in update_nifti_image_brick_list(), update nvox\n"
  "   - in nifti_image_load_bricks(), make explicit check for nbricks <= 0\n"
  "   - in int_force_positive(), check for (!list)\n"
  "   - in swap_nifti_header(), swap sizeof_hdr, and reorder to struct order\n"
  "   - change get_filesize functions to signed ( < 0 is no file or error )\n",
  "   - in nifti_validfilename(), lose redundant (len < 0) check\n"
  "   - make print_hex_vals() static\n"
  "   - in disp_nifti_1_header, restrict string field widths\n"
  "\n",
  "0.9  23 Dec 2004 [rickr] - minor changes\n"
  "   - broke ASCII header reading out of nifti_image_read(), into new\n"
  "        functions has_ascii_header() and read_ascii_image()\n",
  "   - check image_read failure and znzseek failure\n"
  "   - altered some debug output\n"
  "   - nifti_write_all_data() now returns an int\n"
  "\n",
  "0.10 29 Dec 2004 [rickr]\n"
  "   - renamed nifti_valid_extension() to nifti_check_extension()\n"
  "   - added functions nifti_makehdrname() and nifti_makeimgname()\n"
  "   - added function valid_nifti_extensions()\n"
  "   - in nifti_write_extensions(), check for validity before writing\n",
  "   - rewrote nifti_image_write_hdr_img2():\n"
  "       o set write_data and leave_open flags from write_opts\n"
  "       o add debug print statements\n"
  "       o use nifti_write_ascii_image() for the ascii case\n"
  "       o rewrote the logic of all cases to be easier to follow\n",
  "   - broke out code as nifti_write_ascii_image() function\n"
  "   - added debug to top-level write functions, and free the znzFile\n"
  "   - removed unused internal function nifti_image_open()\n"
  "\n",
  "0.11 30 Dec 2004 [rickr] - small mods\n"
  "   - moved static function prototypes from header to C file\n"
  "   - free extensions in nifti_image_free()\n"
  "\n",
  "1.0  07 Jan 2005 [rickr] - INITIAL RELEASE VERSION\n"
  "   - added function nifti_set_filenames()\n"
  "   - added function nifti_read_header()\n"
  "   - added static function nhdr_looks_good()\n"
  "   - added static function need_nhdr_swap()\n"
  "   - exported nifti_add_exten_to_list symbol\n",
  "   - fixed #bytes written in nifti_write_extensions()\n"
  "   - only modify offset if it is too small (nifti_set_iname_offset)\n"
  "   - added nifti_type 3 to nifti_makehdrname and nifti_makeimgname\n"
  "   - added function nifti_set_filenames()\n"
  "\n",
  "1.1  07 Jan 2005 [rickr]\n"
  "   - in nifti_read_header(), swap if needed\n"
  "\n",
  "1.2  07 Feb 2005 [kate fissell c/o rickr] \n"
  "   - nifti1.h: added doxygen comments for main struct and #define groups\n"
  "   - nifti1_io.h: added doxygen comments for file and nifti_image struct\n"
  "   - nifti1_io.h: added doxygen comments for file and some functions\n"
  "   - nifti1_io.c: changed nifti_copy_nim_info to use memcpy\n"
  "\n",
  "1.3  09 Feb 2005 [rickr]\n"
  "   - nifti1.h: added doxygen comments for extension structs\n"
  "   - nifti1_io.h: put most #defines in #ifdef _NIFTI1_IO_C_ block\n"
  "   - added a doxygen-style description to every exported function\n"
  "   - added doxygen-style comments within some functions\n"
  "   - re-exported many znzFile functions that I had made static\n"
  "   - re-added nifti_image_open (sorry, Mark)\n"
  "   - every exported function now has 'nifti' in the name (19 functions)\n",
  "   - made sure every alloc() has a failure test\n"
  "   - added nifti_copy_extensions function, for use in nifti_copy_nim_info\n"
  "   - nifti_is_gzfile: added initial strlen test\n"
  "   - nifti_set_filenames: added set_byte_order parameter option\n"
  "     (it seems appropriate to set the BO when new files are associated)\n"
  "   - disp_nifti_1_header: prints to stdout (a.o.t. stderr), with fflush\n"
  "\n",
  "1.4  23 Feb 2005 [rickr] - sourceforge merge\n"
  "   - merged into the nifti_io CVS directory structure at sourceforge.net\n"
  "   - merged in 4 changes by Mark, and re-added his const keywords\n"
  "   - cast some pointers to (void *) for -pedantic compile option\n"
  "   - added nifti_free_extensions()\n"
  "\n",
  "1.5  02 Mar 2005 [rickr] - started nifti global options\n"
  "   - gni_debug is now g_opts.debug\n"
  "   - added validity check parameter to nifti_read_header\n"
  "   - need_nhdr_swap no longer does test swaps on the stack\n"
  "\n",
  "1.6  05 April 2005 [rickr] - validation and collapsed_image_read\n"
  "   - added nifti_read_collapsed_image(), an interface for reading partial\n"
  "     datasets, specifying a subset of array indices\n"
  "   - for read_collapsed_image, added static functions: rci_read_data(),\n"
  "     rci_alloc_mem(), and make_pivot_list()\n",
  "   - added nifti_nim_is_valid() to check for consistency (more to do)\n"
  "   - added nifti_nim_has_valid_dims() to do many dimensions tests\n"
  "\n",
  "1.7  08 April 2005 [rickr]\n"
  "   - added nifti_update_dims_from_array() - to update dimensions\n"
  "   - modified nifti_makehdrname() and nifti_makeimgname():\n"
  "       if prefix has a valid extension, use it (else make one up)\n"
  "   - added nifti_get_intlist - for making an array of ints\n"
  "   - fixed init of NBL->bsize in nifti_alloc_NBL_mem()  {thanks, Bob}\n"
  "\n",
  "1.8  14 April 2005 [rickr]\n"
  "   - added nifti_set_type_from_names(), for nifti_set_filenames()\n"
  "     (only updates type if number of files does not match it)\n"
  "   - added is_valid_nifti_type(), just to be sure\n"
  "   - updated description of nifti_read_collapsed_image() for *data change\n"
  "     (if *data is already set, assume memory exists for results)\n"
  "   - modified rci_alloc_mem() to allocate only if *data is NULL\n"
  "\n",
  "1.9  19 April 2005 [rickr]\n"
  "   - added extension codes NIFTI_ECODE_COMMENT and NIFTI_ECODE_XCEDE\n"
  "   - added nifti_type codes NIFTI_MAX_ECODE and NIFTI_MAX_FTYPE\n"
  "   - added nifti_add_extension() {exported}\n"
  "   - added nifti_fill_extension() as a static function\n"
  "   - added nifti_is_valid_ecode() {exported}\n",
  "   - nifti_type values are now NIFTI_FTYPE_* file codes\n"
  "   - in nifti_read_extensions(), decrement 'remain' by extender size, 4\n"
  "   - in nifti_set_iname_offset(), case 1, update if offset differs\n"
  "   - only output '-d writing nifti file' if debug > 1\n"
  "\n",
  "1.10 10 May 2005 [rickr]\n"
  "   - files are read using ZLIB only if they end in '.gz'\n"
  "\n",
  "1.11 12 August 2005 [kate fissell]\n"
  "   - Kate's 0.2 release packaging, for sourceforge\n"
  "\n",
  "1.12 17 August 2005 [rickr] - comment (doxygen) updates\n"
  "   - updated comments for most functions (2 updates from Cinly Ooi)\n"
  "   - added nifti_type_and_names_match()\n"
  "\n",
  "1.12a 24 August 2005 [rickr] - remove all tabs from Clibs/*/*.[ch]\n",
  "1.12b 25 August 2005 [rickr] - changes by Hans Johnson\n",
  "1.13  25 August 2005 [rickr]\n",
  "   - finished changes by Hans for Insight\n"
  "   - added const in all appropraite parameter locations (30-40)\n"
  "     (any pointer referencing data that will not change)\n"
  "   - shortened all string constants below 509 character limit\n"
  "1.14  28 October 2005 [HJohnson]\n",
  "   - use nifti_set_filenames() in nifti_convert_nhdr2nim()\n"
  "1.15  02 November 2005 [rickr]\n",
  "   - added skip_blank_ext to nifti_global_options\n"
  "   - added nifti_set_skip_blank_ext(), to set option\n"
  "   - if skip_blank_ext and no extensions, do not read/write extender\n"
  "1.16 18 November 2005 [rickr]\n",
  "   - removed any test or access of dim[i], i>dim[0]\n"
  "   - do not set pixdim for collapsed dims to 1.0, leave them as they are\n"
  "   - added magic and dim[i] tests in nifti_hdr_looks_good()\n"
  "   - added 2 size_t casts\n"
  "1.17 22 November 2005 [rickr]\n",
  "   - in hdr->nim, for i > dim[0], pass 0 or 1, else set to 1\n"
  "1.18 02 March 2006 [rickr]\n",
  "   - in nifti_alloc_NBL_mem(), fixed nt=0 case from 1.17 change\n"
  "1.19 23 May 2006 [HJohnson,rickr]\n",
  "   - nifti_write_ascii_image(): free(hstr)\n"
  "   - nifti_copy_extensions(): clear num_ext and ext_list\n"
  "1.20 27 Jun 2006 [rickr]\n",
  "   - nifti_findhdrname(): fixed assign of efirst to match stated logic\n"
  "     (problem found by Atle Bjørnerud)\n"
  "1.21 05 Sep 2006 [rickr] update for nifticlib-0.4 release\n",
  "   - was reminded to actually add nifti_set_skip_blank_ext()\n"
  "   - init g_opts.skip_blank_ext to 0\n"
  "1.22 01 Jun 2007 nifticlib-0.5 release\n",
  "1.23 05 Jun 2007 nifti_add_exten_to_list: revert on failure, free old list\n"
  "1.24 07 Jun 2007 nifti_copy_extensions: use esize-8 for data size\n"
  "1.25 12 Jun 2007 [rickr] EMPTY_IMAGE creation\n",
  "   - added nifti_make_new_header() - to create from dims/dtype\n"
  "   - added nifti_make_new_nim() - to create from dims/dtype/fill\n"
  "   - added nifti_is_valid_datatype(), and more debug info\n",
  "1.26 27 Jul 2007 [rickr] handle single volumes > 2^31 bytes (but < 2^32)\n",
  "1.27 28 Jul 2007 [rickr] nim->nvox, NBL-bsize are now type size_t\n"
  "1.28 30 Jul 2007 [rickr] size_t updates\n",
  "1.29 08 Aug 2007 [rickr] for list, valid_nifti_brick_list requires 3 dims\n"
  "1.30 08 Nov 2007 [Yaroslav/rickr]\n"
  "   - fix ARM struct alignment problem in byte-swapping routines\n",
  "1.31 29 Nov 2007 [rickr] for nifticlib-1.0.0\n"
  "   - added nifti_datatype_to/from_string routines\n"
  "   - added DT_RGBA32/NIFTI_TYPE_RGBA32 datatype macros (2304)\n"
  "   - added NIFTI_ECODE_FREESURFER (14)\n",
  "1.32 08 Dec 2007 [rickr]\n"
  "   - nifti_hdr_looks_good() allows ANALYZE headers (req. by V. Luccio)\n"
  "   - added nifti_datatype_is_valid()\n",
  "1.33 05 Feb 2008 [hansj,rickr] - block nia.gz use\n"
  "----------------------------------------------------------------------\n"
};
static char gni_version[] = "nifti library version 1.33 (5 Feb, 2008)";