Module: NIFTI

Defined in:
lib/nifti.rb,
lib/nifti/stream.rb,
lib/nifti/n_read.rb,
lib/nifti/version.rb,
lib/nifti/n_write.rb,
lib/nifti/n_object.rb,
lib/nifti/constants.rb

Overview

NIFTI is the main namespace for all Ruby NIfTI classes, constants and methods.

Defined Under Namespace

Classes: NObject, NRead, NWrite, Stream

Constant Summary

VERSION =

Current Version of NIFTI

"0.0.1"
CPU_ENDIAN =

System (CPU) Endianness.

endian_type[Array(x).pack("L*")]
CUSTOM_SS =

Custom string used for (un)packing big endian signed short.

"k*"
CUSTOM_SL =

Custom string used for (un)packing big endian signed long.

"r*"
XFORM_CODES =

Q/S Form Transform codes defined in the nifti header Reference: nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html

{
  0 => 'NIFTI_XFORM_UNKNOWN',       # Arbitrary coordinates (Method 1). 
  1 => 'NIFTI_XFORM_SCANNER_ANAT',  # Scanner-based anatomical coordinates
  2 => 'NIFTI_XFORM_ALIGNED_ANAT',  # Coordinates aligned to another file's, or to anatomical "truth".
  3 => 'NIFTI_XFORM_TALAIRACH',     # Coordinates aligned to Talairach-Tournoux Atlas; (0,0,0)=AC, etc.
  4 => 'NIFTI_XFORM_MNI_152'        # MNI 152 normalized coordinates
}
NIFTI_DATATYPES =

Take a NIFTI TypeCode and return datatype and bitpix

From Jimmy Shen: Set bitpix according to datatype /*Acceptable values for datatype are*/

  0 None                     (Unknown bit per voxel) % DT_NONE, DT_UNKNOWN 
  1 Binary                         (ubit1, bitpix=1) % DT_BINARY 
  2 Unsigned char         (uchar or uint8, bitpix=8) % DT_UINT8, NIFTI_TYPE_UINT8 
  4 Signed short                  (int16, bitpix=16) % DT_INT16, NIFTI_TYPE_INT16 
  8 Signed integer                (int32, bitpix=32) % DT_INT32, NIFTI_TYPE_INT32 
 16 Floating point    (single or float32, bitpix=32) % DT_FLOAT32, NIFTI_TYPE_FLOAT32 
 32 Complex, 2 float32      (Use float32, bitpix=64) % DT_COMPLEX64, NIFTI_TYPE_COMPLEX64
 64 Double precision  (double or float64, bitpix=64) % DT_FLOAT64, NIFTI_TYPE_FLOAT64 
128 uint8 RGB                 (Use uint8, bitpix=24) % DT_RGB24, NIFTI_TYPE_RGB24 
256 Signed char            (schar or int8, bitpix=8) % DT_INT8, NIFTI_TYPE_INT8 
511 Single RGB              (Use float32, bitpix=96) % DT_RGB96, NIFTI_TYPE_RGB96
512 Unsigned short               (uint16, bitpix=16) % DT_UNINT16, NIFTI_TYPE_UNINT16 
768 Unsigned integer             (uint32, bitpix=32) % DT_UNINT32, NIFTI_TYPE_UNINT32

1024 Signed long long (int64, bitpix=64) % DT_INT64, NIFTI_TYPE_INT64 1280 Unsigned long long (uint64, bitpix=64) % DT_UINT64, NIFTI_TYPE_UINT64 1536 Long double, float128 (Unsupported, bitpix=128) % DT_FLOAT128, NIFTI_TYPE_FLOAT128 1792 Complex128, 2 float64 (Use float64, bitpix=128) % DT_COMPLEX128, NIFTI_TYPE_COMPLEX128 2048 Complex256, 2 float128 (Unsupported, bitpix=256) % DT_COMPLEX128, NIFTI_TYPE_COMPLEX128

{
    0 => "Unknown",
    # 1 => "", Can't find a single bit encoding in ruby's unpack method?
    2 => "OB",
    4 => "SS",
    8 => "SL",
   16 => "FL",
   32 => "FD",
   64 => "FD",
  128 => "RGBUnknown",
  256 => "BY",
  511 => "RGBUnknown",
  512 => "US",
  768 => "UL"
 # 1024 => "",
 # 1280 => "",
 # 1536 => "",
 # 1792 => "",
 # 2048 => ""
}
HEADER_SIGNATURE =

The NIFTI signature is hardcoded by bytes. This consists of arrays for each item in the signature, where item is the name of the item, item is the length in bytes of the item, and dim is the Format string to use in packing/unpacking the item.

[
  #                           /**********************/    /**********************/     /***************/
  # struct nifti_1_header {  /* NIFTI-1 usage      */    /*ANALYZE 7.5 field(s)*/     /* Byte offset */
  #                         /**********************/    /**********************/     /***************/
  #  int   sizeof_hdr;    /*!< MUST be 348           */  /* int sizeof_hdr;      */   /*   0 */
  ['sizeof_hdr', 4, 'SL'],

  #  char  data_type[10]; /*!< ++UNUSED++            */  /* char data_type[10];  */   /*   4 */
  ['data_type', 10, 'STR'],

  #  char  db_name[18];   /*!< ++UNUSED++            */  /* char db_name[18];    */   /*  14 */
  ['db_name', 18, 'STR'],

  #  int   extents;       /*!< ++UNUSED++            */  /* int extents;         */   /*  32 */
  ['extents', 4, "SL"],

  #  short session_error; /*!< ++UNUSED++            */  /* short session_error; */   /*  36 */
  ['session_error', 2, "SS"],

  #  char  regular;       /*!< ++UNUSED++            */  /* char regular;        */   /*  38 */
  ['regular', 1, "STR"],

  #  char  dim_info;      /*!< MRI slice ordering.   */  /* char hkey_un0;       */   /*  39 */
  ['dim_info', 1, "BY"],


  #                                       /*--- was image_dimension substruct ---*/
  #  short dim[8];        /*!< Data array dimensions.*/  /* short dim[8];        */   /*  40 */
  ['dim', 16, "US"],

  #  float intent_p1;     /*!< 1st intent parameter. */  /* short unused8;       */   /*  56 */
  ['intent_p1', 4, "FL"],

  #  float intent_p2;     /*!< 2nd intent parameter. */  /* short unused10;      */   /*  60 */
  ['intent_p2', 4, "FL"],
  #                                                      /* short unused11;      */
  #  float intent_p3;     /*!< 3rd intent parameter. */  /* short unused12;      */   /*  64 */
  ['intent_p3', 4, "FL"],

  #  short intent_code;   /*!< NIFTIINTENT code.     */  /* short unused14;      */   /*  68 */
  ['intent_code', 2, "US"],

  #  short datatype;      /*!< Defines data type!    */  /* short datatype;      */   /*  70 */
  ['datatype', 2, "US"],

  #  short bitpix;        /*!< Number bits/voxel.    */  /* short bitpix;        */   /*  72 */
  ['bitpix', 2, "US"],

  #  short slice_start;   /*!< First slice index.    */  /* short dim_un0;       */   /*  74 */
  ['slice_start', 2, "US"],

  #  float pixdim[8];     /*!< Grid spacings.        */  /* float pixdim[8];     */   /*  76 */
  ['pixdim', 32, "FL"],

  #  float vox_offset;    /*!< Offset into .nii file */  /* float vox_offset;    */   /* 108 */
  ['vox_offset', 4, "FL"],

  #  float scl_slope;     /*!< Data scaling: slope.  */  /* float funused1;      */   /* 112 */
  ['scl_slope', 4, "FL"],

  #  float scl_inter;     /*!< Data scaling: offset. */  /* float funused2;      */   /* 116 */
  ['scl_inter', 4, "FL"],

  #  short slice_end;     /*!< Last slice index.     */  /* float funused3;      */   /* 120 */
  ['slice_end', 2, "US"],

  #  char  slice_code;    /*!< Slice timing order.   */                               /* 122 */
  ['slice_code', 1, "BY"],

  #  char  xyzt_units;    /*!< Units of pixdim[1..4] */                               /* 123 */
  ['xyzt_units', 1, "BY"],

  #  float cal_max;       /*!< Max display intensity */  /* float cal_max;       */   /* 124 */
  ['cal_max', 4, "FL"],

  #  float cal_min;       /*!< Min display intensity */  /* float cal_min;       */   /* 128 */
  ['cal_min', 4, "FL"],

  #  float slice_duration;/*!< Time for 1 slice.     */  /* float compressed;    */   /* 132 */
  ['slice_duration', 4, "FL"],

  #  float toffset;       /*!< Time axis shift.      */  /* float verified;      */   /* 136 */
  ['toffset', 4, "FL"],

  #  int   glmax;         /*!< ++UNUSED++            */  /* int glmax;           */   /* 140 */
  ['glmax', 4, "UL"],

  #  int   glmin;         /*!< ++UNUSED++            */  /* int glmin;           */   /* 144 */
  ['glmin', 4, "UL"],

  #                                          /*--- was data_history substruct ---*/
  #  char  descrip[80];   /*!< any text you like.    */  /* char descrip[80];    */   /* 148 */
  ['descrip', 80, "STR"],

  #  char  aux_file[24];  /*!< auxiliary filename.   */  /* char aux_file[24];   */   /* 228 */
  ['aux_file', 24, "STR"],

  # 
  #  short qform_code;    /*!< NIFTIXFORM code.      */  /*-- all ANALYZE 7.5 ---*/   /* 252 */
  ['qform_code', 2, "US"],                           #   /*   fields below here  */
                                                    #    /*   are replaced       */
  #  short sform_code;    /*!< NIFTIXFORM code.      */                               /* 254 */
  ['sform_code', 2, "US"],
  #                                                      
  #  float quatern_b;     /*!< Quaternion b param.    */                              /* 256 */
  ['quatern_b', 4, "FL"],

  #  float quatern_c;     /*!< Quaternion c param.    */                              /* 260 */
  ['quatern_c', 4, "FL"],

  #  float quatern_d;     /*!< Quaternion d param.    */                              /* 264 */
  ['quatern_d', 4, "FL"],


  #  float qoffset_x;     /*!< Quaternion x shift.    */                              /* 268 */
  ['qoffset_x', 4, "FL"],

  #  float qoffset_y;     /*!< Quaternion y shift.    */                              /* 272 */
  ['qoffset_y', 4, "FL"],

  #  float qoffset_z;     /*!< Quaternion z shift.    */                              /* 276 */
  ['qoffset_z', 4, "FL"],

  #  float srow_x[4];     /*!< 1st row affine transform.   */                         /* 280 */
  ['srow_x', 16, "FL"],

  #  float srow_y[4];     /*!< 2nd row affine transform.   */                         /* 296 */
  ['srow_y', 16, "FL"],

  #  float srow_z[4];     /*!< 3rd row affine transform.   */                         /* 312 */
  ['srow_z', 16, "FL"],

  # 
  # 
  #  char intent_name[16];/*!< name or meaning of data.  */                         /* 328 */
  ['intent_name', 16, "STR"],

  # 
  # 
  #  char magic[4];       /*!< MUST be "ni1\0" or "n+1\0". */                         /* 344 */
  ['magic', 4, "STR"]

  # } ;                   /** 348 bytes total **/
  # 
  # 


]