Module: NIFTI
- Defined in:
- lib/nifti.rb,
lib/nifti/n_read.rb,
lib/nifti/stream.rb,
lib/nifti/n_image.rb,
lib/nifti/n_write.rb,
lib/nifti/version.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: NImage, NObject, NRead, NWrite, Stream
Constant Summary collapse
- VERSION =
Current Version of NIFTI
"0.0.2"- 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_UNINT321024 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 =
[ # /**********************/ /**********************/ /***************/ # 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 **/ # # ]