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nifti_types.pas
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unit nifti_types;
{$IFDEF FPC}
{$mode objfpc}{$ENDIF}{$H+}
interface
uses
Classes, SysUtils;
type
TNIFTI2hdr = packed record //Next: analyze Format Header structure
HdrSz : longint; //MUST BE 540
magic: array [1..8] of ansichar; //valid sig
datatype, bitpix: word;
dim: array [0..7] of int64; //unused
intent_p1,intent_p2,intent_p3: double;
pixdim: array [0..7] of double; //unused
vox_offset: int64;
scl_slope,scl_inter,cal_max,cal_min,slice_duration,toffset: double;
slice_start, slice_end: int64;
descrip: array[1..80] of ansichar;
aux_file: array[1..24] of ansichar;
qform_code, sform_code: longint;
quatern_b,quatern_c,quatern_d,
qoffset_x,qoffset_y,qoffset_z: double;
srow_x: array[0..3]of double;
srow_y: array[0..3]of double;
srow_z: array[0..3]of double;
slice_code, xyzt_units, intent_code: longint;
intent_name: array[1..16] of ansichar;
dim_info: byte;
unused_str: array[1..15] of ansichar;
end; //TNIFTI2hdr Header Structure
TNIFTIhdr = packed record //Next: analyze Format Header structure
HdrSz : longint; //MUST BE 348
Data_Type: array [1..10] of ansichar; //unused
db_name: array [1..18] of ansichar; //unused
extents: longint; //unused
session_error: smallint; //unused
regular: ansichar; ////unused: in Analyze 7.5 this must be 114
dim_info: byte; //MRI slice order
dim: array[0..7] of smallint; //Data array dimensions
intent_p1, intent_p2, intent_p3: single;
intent_code: smallint;
datatype: smallint;
bitpix: smallint;
slice_start: smallint;
pixdim: array[0..7]of single;
vox_offset: single;
scl_slope: single;//scaling slope
scl_inter: single;//scaling intercept
slice_end: smallint;
slice_code: byte; //e.g. ascending
xyzt_units: byte; //e.g. mm and sec
cal_max,cal_min: single; //unused
slice_duration: single; //time for one slice
toffset: single; //time axis to shift
glmax, glmin: longint; //UNUSED
descrip: array[1..80] of ansichar;
aux_file: array[1..24] of ansichar;
qform_code, sform_code: smallint;
quatern_b,quatern_c,quatern_d,
qoffset_x,qoffset_y,qoffset_z: single;
srow_x: array[0..3]of single;
srow_y: array[0..3]of single;
srow_z: array[0..3]of single;
intent_name: array[1..16] of ansichar;
magic: longint;
end; //TNIFTIhdr Header Structure
TAnalyzeHdrSection = packed record //Next: analyze Format Header structure
Pad: array [1..253] of byte;
originator: array [1..5] of smallint; (* 105 + 10 *)
end;//TAnalyzeHdrSection Structure
const
K_bz2Bytes_headerAndImageCompressed = -4;
K_bz2Bytes_onlyImageCompressed = -3;
K_gzBytes_headerAndImageCompressed = -2;
K_gzBytes_onlyImageCompressed= -1;
K_gzBytes_headerAndImageUncompressed= 0;
//DataTypes
kDT_BINARY =1; // binary (1 bit/voxel)
kDT_UNSIGNED_CHAR =2; // unsigned char (8 bits/voxel)
kDT_UINT8 = kDT_UNSIGNED_CHAR;
kDT_SIGNED_SHORT =4; // signed short (16 bits/voxel)
kDT_INT16 = kDT_SIGNED_SHORT;
kDT_SIGNED_INT =8; // signed int (32 bits/voxel)
kDT_INT32 = kDT_SIGNED_INT;
kDT_FLOAT =16; // float (32 bits/voxel)
kDT_FLOAT32 = kDT_FLOAT;
kDT_COMPLEX =32; // complex (64 bits/voxel)
kDT_DOUBLE =64; // double (64 bits/voxel)
kDT_FLOAT64 = kDT_DOUBLE;
kDT_RGB =128; // RGB triple (24 bits/voxel)
kDT_RGBplanar3D =129; //RRR..RGGG..GBBBB...B (24 bits/voxel) entire 3D volume continguous
kDT_RGBplanar2D =129; //RRR..RGGG..GBBBB...B (24 bits/voxel) each 2D slice saved sequentially
kDT_INT8 =256; // signed char (8 bits)
kDT_UINT16 =512; // unsigned short (16 bits)
kDT_UINT32 =768; // unsigned int (32 bits)
kDT_INT64 =1024; // long long (64 bits)
kDT_UINT64 =1280; // unsigned long long (64 bits)
kDT_FLOAT128 =1536; // long double (128 bits)
kDT_COMPLEX128 =1792; // double pair (128 bits)
kDT_COMPLEX256 =2048; // long double pair (256 bits)
kDT_RGBA32 =2304; // 4 byte RGBA (32 bits/voxel)
// slice_code values
kNIFTI_SLICE_SEQ_UNKNOWN = 0;
kNIFTI_SLICE_SEQ_INC = 1;
kNIFTI_SLICE_SEQ_DEC = 2;
kNIFTI_SLICE_ALT_INC = 3;
kNIFTI_SLICE_ALT_DEC = 4;
//xyzt_units values: note 3bit space and 3bit time packed into single byte
kNIFTI_UNITS_UNKNOWN = 0;
kNIFTI_UNITS_METER = 1;
kNIFTI_UNITS_MM = 2;
kNIFTI_UNITS_MICRON = 3;
kNIFTI_UNITS_SEC = 8;
kNIFTI_UNITS_MSEC = 16;
kNIFTI_UNITS_USEC = 24;
kNIFTI_UNITS_HZ = 32;
kNIFTI_UNITS_PPM = 40;
//qform_code, sform_code values
kNIFTI_XFORM_UNKNOWN = 0;
kNIFTI_XFORM_SCANNER_ANAT = 1;//Scanner-based anatomical coordinates
kNIFTI_XFORM_ALIGNED_ANAT = 2; //Coordinates aligned to another file e.g. EPI coregistered to T1
kNIFTI_XFORM_TALAIRACH = 3; //Talairach-Tournoux Atlas; (0,0,0)=AC, etc.
kNIFTI_XFORM_MNI_152 = 4; //MNI 152 normalized coordinates
kNIFTI_XFORM_OTHER_TEMPLATE = 5;
{$IFDEF ENDIAN_BIG}
//Magic values
kswapNIFTI_MAGIC_SEPARATE_HDR = $0031696E;
kswapNIFTI_MAGIC_EMBEDDED_HDR = $00312B6E;
kNIFTI_MAGIC_DCM = $0044434D;//DCM
//byte-swapped magic values
kNIFTI_MAGIC_SEPARATE_HDR = $6E693100;
kNIFTI_MAGIC_EMBEDDED_HDR = $6E2B3100;
kNIFTI_MAGIC_SEPARATE_HDR = $6E693200;
kNIFTI_MAGIC_EMBEDDED_HDR = $6E2B3200;
{$ELSE}
//Magic values
kNIFTI_MAGIC_SEPARATE_HDR = $0031696E;
kNIFTI_MAGIC_EMBEDDED_HDR = $00312B6E;
kNIFTI2_MAGIC_SEPARATE_HDR = $0032696E;
kNIFTI2_MAGIC_EMBEDDED_HDR = $00322B6E;
kNIFTI_MAGIC_DCM = $0044434D;//DCM
//byte-swapped magic values
kswapNIFTI_MAGIC_SEPARATE_HDR = $6E693100;
kswapNIFTI_MAGIC_EMBEDDED_HDR = $6E2B3100;
{$ENDIF}
//Statistics Intention
kNIFTI_INTENT_NONE =0;
kNIFTI_INTENT_CORREL =2;
kNIFTI_INTENT_TTEST =3;
kNIFTI_INTENT_FTEST =4;
kNIFTI_INTENT_ZSCORE =5;
kNIFTI_INTENT_CHISQ =6;
kNIFTI_INTENT_BETA =7;
kNIFTI_INTENT_BINOM =8;
kNIFTI_INTENT_GAMMA =9;
kNIFTI_INTENT_POISSON =10;
kNIFTI_INTENT_NORMAL =11;
kNIFTI_INTENT_FTEST_NONC =12;
kNIFTI_INTENT_CHISQ_NONC =13;
kNIFTI_INTENT_LOGISTIC =14;
kNIFTI_INTENT_LAPLACE =15;
kNIFTI_INTENT_UNIFORM =16;
kNIFTI_INTENT_TTEST_NONC =17;
kNIFTI_INTENT_WEIBULL =18;
kNIFTI_INTENT_CHI =19;
kNIFTI_INTENT_INVGAUSS =20;
kNIFTI_INTENT_EXTVAL =21;
kNIFTI_INTENT_PVAL =22;
NIFTI_INTENT_LOGPVAL =23;
NIFTI_INTENT_LOG10PVAL =24;
kNIFTI_LAST_STATCODE = 24;//kNIFTI_INTENT_PVAL;
kNIFTI_INTENT_ESTIMATE =1001;
kNIFTI_FIRST_NONSTATCODE = kNIFTI_INTENT_ESTIMATE;
kNIFTI_INTENT_LABEL =1002;
kNIFTI_INTENT_NEURONAME =1003;
kNIFTI_INTENT_GENMATRIX =1004;
kNIFTI_INTENT_SYMMATRIX =1005;
kNIFTI_INTENT_DISPVECT =1006;
kNIFTI_INTENT_VECTOR =1007;
kNIFTI_INTENT_POINTSET =1008;
kNIFTI_INTENT_TRIANGLE =1009;
kNIFTI_INTENT_QUATERNION =1010;
procedure NIFTIhdr_SwapBytes (var lAHdr: TNIFTIhdr); //Swap Byte order for the Analyze type
function Swap2(s : SmallInt): smallint;
procedure swap4(var s : LongInt);
procedure swap8(var s : int64);
procedure Xswap8r(var s : double);
procedure NII_Clear (out lHdr: TNIFTIHdr);
procedure NII_SetIdentityMatrix (var lHdr: TNIFTIHdr); //create neutral rotation matrix
implementation
procedure NII_SetIdentityMatrix (var lHdr: TNIFTIHdr); //create neutral rotation matrix
var lInc: integer;
begin
with lHdr do begin
for lInc := 0 to 3 do
srow_x[lInc] := 0;
for lInc := 0 to 3 do
srow_y[lInc] := 0;
for lInc := 0 to 3 do
srow_z[lInc] := 0;
for lInc := 1 to 16 do
intent_name[lInc] := chr(0);
//next: create identity matrix: if code is switched on there will not be a problem
srow_x[0] := 1;
srow_y[1] := 1;
srow_z[2] := 1;
end;
end; //proc NIFTIhdr_IdentityMatrix
procedure NII_Clear (out lHdr: TNIFTIHdr);
var
lInc: integer;
begin
with lHdr do begin
HdrSz := sizeof(TNIFTIhdr);
for lInc := 1 to 10 do
Data_Type[lInc] := chr(0);
for lInc := 1 to 18 do
db_name[lInc] := chr(0);
extents:=0;
session_error:= 0;
regular:='r'{chr(0)};
dim_info:=(0);
intent_p1 := 0;
intent_p2 := 0;
intent_p3 := 0;
intent_code:=0;
datatype:=0 ;
bitpix:=0;
slice_start:=0;
for lInc := 1 to 7 do
pixdim[linc]:= 1.0;
vox_offset:= 0.0;
scl_slope := 1.0;
scl_inter:= 0.0;
slice_end:= 0;
slice_code := 0;
xyzt_units := 10;
cal_max:= 0.0;
cal_min:= 0.0;
slice_duration:=0;
toffset:= 0;
glmax:= 0;
glmin:= 0;
for lInc := 1 to 80 do
descrip[lInc] := chr(0);{80 spaces}
for lInc := 1 to 24 do
aux_file[lInc] := chr(0);{80 spaces}
{below are standard settings which are not 0}
bitpix := 16;//vc16; {8bits per pixel, e.g. unsigned char 136}
DataType := 4;//vc4;{2=unsigned char, 4=16bit int 136}
Dim[0] := 3;
Dim[1] := 256;
Dim[2] := 256;
Dim[3] := 1;
Dim[4] := 1; {n vols}
Dim[5] := 1;
Dim[6] := 1;
Dim[7] := 1;
glMin := 0;
glMax := 255;
qform_code := kNIFTI_XFORM_UNKNOWN;
sform_code:= kNIFTI_XFORM_UNKNOWN;
quatern_b := 0;
quatern_c := 0;
quatern_d := 0;
qoffset_x := 0;
qoffset_y := 0;
qoffset_z := 0;
NII_SetIdentityMatrix(lHdr);
magic := kNIFTI_MAGIC_SEPARATE_HDR;
end; //with the NIfTI header...
end;
procedure swap4(var s : LongInt);
type
swaptype = packed record
case byte of
0:(Word1,Word2 : word); //word is 16 bit
1:(Long:LongInt);
end;
swaptypep = ^swaptype;
var
inguy:swaptypep;
outguy:swaptype;
begin
inguy := @s; //assign address of s to inguy
outguy.Word1 := swap(inguy^.Word2);
outguy.Word2 := swap(inguy^.Word1);
s:=outguy.Long;
end;
function Swap2(s : SmallInt): smallint;
type
swaptype = packed record
case byte of
0:(Word1 : word); //word is 16 bit
1:(Small1: SmallInt);
end;
swaptypep = ^swaptype;
var
inguy:swaptypep;
outguy:swaptype;
begin
inguy := @s; //assign address of s to inguy
outguy.Word1 := swap(inguy^.Word1);
result :=outguy.Small1;
end;
procedure swap8(var s : int64);
type
swaptype = packed record
case byte of
0:(Word1,Word2,Word3,Word4 : word); //word is 16 bit
//1:(float:double);
end;
swaptypep = ^swaptype;
var
inguy:swaptypep;
outguy:swaptype;
begin
inguy := @s; //assign address of s to inguy
outguy.Word1 := swap(inguy^.Word4);
outguy.Word2 := swap(inguy^.Word3);
outguy.Word3 := swap(inguy^.Word2);
outguy.Word4 := swap(inguy^.Word1);
inguy^.Word1 := outguy.Word1;
inguy^.Word2 := outguy.Word2;
inguy^.Word3 := outguy.Word3;
inguy^.Word4 := outguy.Word4;
end;
procedure Xswap8r(var s : double);
type
swaptype = packed record
case byte of
0:(Word1,Word2,Word3,Word4 : word); //word is 16 bit
//1:(float:double);
end;
swaptypep = ^swaptype;
var
inguy:swaptypep;
outguy:swaptype;
begin
inguy := @s; //assign address of s to inguy
outguy.Word1 := swap(inguy^.Word4);
outguy.Word2 := swap(inguy^.Word3);
outguy.Word3 := swap(inguy^.Word2);
outguy.Word4 := swap(inguy^.Word1);
inguy^.Word1 := outguy.Word1;
inguy^.Word2 := outguy.Word2;
inguy^.Word3 := outguy.Word3;
inguy^.Word4 := outguy.Word4;
end;
procedure Xswap4r( var s:single);
type
swaptype = packed record
case byte of
0:(Word1,Word2 : word); //word is 16 bit
end;
swaptypep = ^swaptype;
var
inguy:swaptypep;
outguy:swaptype;
begin
inguy := @s; //assign address of s to inguy
outguy.Word1 := swap(inguy^.Word2);
outguy.Word2 := swap(inguy^.Word1);
inguy^.Word1 := outguy.Word1;
inguy^.Word2 := outguy.Word2;
end;
procedure NIFTIhdr_SwapBytes (var lAHdr: TNIFTIhdr); //Swap Byte order for the Analyze type
var
lInc: integer;
begin
with lAHdr do begin
swap4(hdrsz);
swap4(extents);
session_error := swap2(session_error);
for lInc := 0 to 7 do
dim[lInc] := swap2(dim[lInc]);//666
Xswap4r(intent_p1);
Xswap4r(intent_p2);
Xswap4r(intent_p3);
intent_code:= swap2(intent_code);
datatype:= swap2(datatype);
bitpix := swap2(bitpix);
slice_start:= swap2(slice_start);
for lInc := 0 to 7 do
Xswap4r(pixdim[linc]);
Xswap4r(vox_offset);
{roi scale = 1}
Xswap4r(scl_slope);
Xswap4r(scl_inter);
slice_end := swap2(slice_end);
Xswap4r(cal_max);
Xswap4r(cal_min);
Xswap4r(slice_duration);
Xswap4r(toffset);
swap4(glmax);
swap4(glmin);
qform_code := swap2(qform_code);
sform_code:= swap2(sform_code);
Xswap4r(quatern_b);
Xswap4r(quatern_c);
Xswap4r(quatern_d);
Xswap4r(qoffset_x);
Xswap4r(qoffset_y);
Xswap4r(qoffset_z);
for lInc := 0 to 3 do //alpha
Xswap4r(srow_x[lInc]);
for lInc := 0 to 3 do //alpha
Xswap4r(srow_y[lInc]);
for lInc := 0 to 3 do //alpha
Xswap4r(srow_z[lInc]);
end; //with NIFTIhdr
end; //proc NIFTIhdr_SwapBytes
end.