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nifti_foreign.pas
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nifti_foreign.pas
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unit nifti_foreign;
//{$DEFINE MRIcron}
interface
//{$mode objfpc} //test
{$mode Delphi}
{$H+}
{$DEFINE GZIP}
{$Include isgui.inc}//<- {$DEFINE GUI}
//{$DEFINE GL10} //define for MRIcroGL1.0, comment for MRIcroGL1.2 and later
{$H+}
{$IFDEF GL10}
{$Include isgui.inc}
{$ENDIF}
uses
{$IFDEF Surfice}define_types,{$ENDIF}
{$IFDEF MRIcron}define_types,{$ENDIF}
{$IFDEF GL10} define_types, {$IFNDEF FPC}gziod,{$ELSE}gzio2,{$ENDIF}{$ENDIF}
{$IFDEF GZIP}zstream, {$ENDIF}
{$IFDEF GUI}
dialogs,
{$ELSE}
dialogsx,
{$ENDIF}
//ClipBrd,
nifti_types, sysutils, classes, StrUtils, math;//2015! dialogsx
const
kIVers = ' i2nii v1.0.0707';
{$IFDEF GL10}
procedure NII_Clear (out lHdr: TNIFTIHdr);
procedure NII_SetIdentityMatrix (var lHdr: TNIFTIHdr); //create neutral rotation matrix
{$ELSE}
const
//seee README.attributes.html and parser_int.c
//FUNC_FIM_TYPE = 0; // 1 value
//FUNC_THR_TYPE = 1; //obsolete
kFUNC_NOT_STAT =0;
kFUNC_COR_TYPE =2;// Correlation Coeff # Samples, # Fit Param, # Orts
kFUNC_TT_TYPE = 3;// Student t Degrees-of-Freedom (DOF)
kFUNC_FT_TYPE = 4;// F ratio Numerator DOF, Denominator DOF
kFUNC_ZT_TYPE = 5;// Standard Normal -- none --
kFUNC_CT_TYPE = 6;// Chi-Squared DOF
kFUNC_BT_TYPE = 7;// Incomplete Beta Parameters "a" and "b"
kFUNC_BN_TYPE = 8;// Binomial # Trials, Probability per trial
kFUNC_GT_TYPE = 9;// Gamma Shape, Scale
kFUNC_PT_TYPE = 10;// Poisson Mean
kFUNC_NO_STAT_AUX = 13;
type
TFloatVec = record
ar: array of single;
dx: single;
x0: single;
function nar: integer; inline;
end;
type
TAFNI = record
jv: integer; //statistical code
nv: integer; //number of parameters that follow (may be 0)
param: array [0..2] of single;
scl_slopex: single;
minVal, maxVal, maxAbsVal: single;
nam: string[64];
FDRcurv: TFloatVec;
end;
TAFNIs = array of TAFNI;
type
mat44 = array [0..3, 0..3] of Single;
{$IFNDEF MRIcron}
ByteRA = array [1..1] of byte;
Bytep = ^ByteRA;
procedure UnGZip(const FileName: string; buffer: bytep; offset, sz: integer);
{$ENDIF}
{$ENDIF}
function readAFNIHeader(var fname: string; var nhdr: TNIFTIhdr; var gzBytes: int64; var swapEndian, isAllVolumesSame: boolean; var AFNIs: TAFNIs; var fLabels: TStringList): boolean; overload;
function readAFNIHeader(var fname: string; var nhdr: TNIFTIhdr; var gzBytes: int64; var swapEndian: boolean): boolean; overload;
function isINTERFILE(var fname: string): boolean;
function readForeignHeader(var lFilename: string; var lHdr: TNIFTIhdr; var gzBytes: int64; var swapEndian, isDimPermute2341: boolean; out xDim64: int64): boolean; overload;
function readForeignHeader(var lFilename: string; var lHdr: TNIFTIhdr; var gzBytes: int64; var swapEndian, isDimPermute2341: boolean): boolean; overload;
function IsReadable(fnm: string): boolean;
procedure convertForeignToNifti(var nhdr: TNIFTIhdr);
function FSize (lFName: String): Int64;
function isTIFF(fnm: string): boolean;
procedure nifti_mat44_to_quatern( lR :mat44; out qb, qc, qd, qx, qy, qz, dx, dy, dz, qfac : single);
implementation
const
kNaNSingle : single = 1/0;
Type
vect4 = array [0..3] of Single;
mat33 = array [0..2, 0..2] of Single;
vect3 = array [0..2] of Single;
ivect3 = array [0..2] of integer;
procedure printf(str: string);
begin
{$IFDEF Windows}
if IsConsole then //'System' in uses
writeln(str);
{$ENDIF}
{$IFDEF UNIX} writeln(str);{$ENDIF}
end;
function IsReadable(fnm: string): boolean;
//https://wiki.freepascal.org/macOS_Programming_Tips#Determining_if_a_file_is_readable
{$IFDEF Darwin}
var
f: file;
b: byte;
{$ENDIF}
begin
result := false;
if not fileexists(fnm) then exit;
if FSize(fnm) < 2 then exit;
{$IFDEF Darwin}
AssignFile(f, fnm);
{$I+}
try
FileMode := fmOpenRead; //Set file access to read only
Reset(f, 1);
if ioresult <> 0 then
exit;
b := 0;
BlockRead(f, b, sizeof(b)); //Byte-order Identifier
CloseFile(f);
result := true;
except
result := false;
end;
{$ELSE}
result := true;
{$ENDIF}
end;
{$IFDEF GL10}
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);
dim[0] := 4;
for lInc := 1 to 7 do
dim[lInc] := 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;
{$ENDIF}
function UpCaseExt(lFileName: string): string;
var lI: integer;
l2ndExt,lExt : string;
begin
lExt := ExtractFileExt(lFileName);
if length(lExt) > 0 then
for lI := 1 to length(lExt) do
lExt[lI] := upcase(lExt[lI]);
result := lExt;
if lExt <> '.GZ' then exit;
lI := length(lFileName) - 6;
if li < 1 then exit;
l2ndExt := upcase(lFileName[lI])+upcase(lFileName[lI+1])+upcase(lFileName[li+2])+upcase(lFileName[li+3]);
if (l2ndExt = '.NII')then
result := l2ndExt+lExt
else if (l2ndExt = 'BRIK') and (lI > 1) and (lFileName[lI-1] = '.') then
result := '.BRIK'+lExt;
end;
{$IFNDEF GL10}
procedure UnGZip(const FileName: string; buffer: bytep; offset, sz: integer);
{$IFDEF GZIP}
var
decomp: TGZFileStream;
skip: array of byte;
begin
decomp := TGZFileStream.create(FileName, gzopenread);
if offset > 0 then begin
setlength(skip, offset);
decomp.Read(skip[0], offset);
end;
//buffer^[0] := 0; //BlockRead should be out not var: https://fpc-pascal.freepascal.narkive.com/M2rzyAkf/blockread-and-buffers
//decomp.Read(buffer[0], sz);
decomp.Read(buffer[1], sz);
decomp.free;
end;
{$ELSE}
begin
{$IFDEF UNIX} writeln('Recompile with GZ support!'); {$ENDIF}
end;
{$ENDIF}
{$ENDIF}
(* function isECAT(fnm: string): boolean;
type
THdrMain = packed record //Next: ECAT signature
magic: array[1..14] of char;
end;
var
f: file;
mhdr: THdrMain;
begin
result := false;
if not fileexists(fnm) then exit;
if DirectoryExists(fnm) then exit;
if FSize(fnm) < 32 then exit;
{$I-}
AssignFile(f, fnm);
FileMode := fmOpenRead; //Set file access to read only
Reset(f, 1);
{$I+}
if ioresult <> 0 then
exit;
BlockRead(f, mhdr, sizeof(mhdr));
closefile(f);
if ((mhdr.magic[1] <> 'M') or (mhdr.magic[2] <> 'A') or (mhdr.magic[3] <> 'T') or (mhdr.magic[4] <> 'R') or (mhdr.magic[5] <> 'I') or (mhdr.magic[6] <> 'X')) then
exit;
result := true;
end; *)
function FSize (lFName: String): Int64;
var SearchRec: TSearchRec;
begin
result := 0;
if not fileexists(lFName) then exit;
FindFirst(lFName, faAnyFile, SearchRec);
result := SearchRec.size;
FindClose(SearchRec);
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 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;
procedure pswap4r ( 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; //proc Xswap4r
procedure pswap4i(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; //proc swap4
function swap64r(s : double):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);
try
swap64r:=outguy.float;
except
swap64r := 0;
exit;
end;{}
end;
FUNCTION specialsingle (var s:single): boolean;
//returns true if s is Infinity, NAN or Indeterminate
//4byte IEEE: msb[31] = signbit, bits[23-30] exponent, bits[0..22] mantissa
//exponent of all 1s = Infinity, NAN or Indeterminate
CONST kSpecialExponent = 255 shl 23;
VAR Overlay: LongInt ABSOLUTE s;
BEGIN
IF ((Overlay AND kSpecialExponent) = kSpecialExponent) THEN
RESULT := true
ELSE
RESULT := false;
END;
function isBioFormats(fnm: string): string;
//detect LIF and LIFF format or other Imagej/Fiji Bioformat
const
LIF_MAGIC_BYTE = $70;
LIF_MEMORY_BYTE = $2a;
var
f: file;
bs: array[0..255] of byte;
begin
result := '';
if not fileexists(fnm) then exit;
if DirectoryExists(fnm) then exit;
if FSize(fnm) < 256 then exit;
{$I-}
AssignFile(f, fnm);
FileMode := fmOpenRead; //Set file access to read only
Reset(f, 1);
{$I+}
if ioresult <> 0 then
exit;
bs[0] := 0; //BlockRead should be out not var: https://fpc-pascal.freepascal.narkive.com/M2rzyAkf/blockread-and-buffers
BlockRead(f, bs, sizeof(bs)); //Byte-order Identifier
if (bs[8] = LIF_MEMORY_BYTE) and ((bs[0] = LIF_MAGIC_BYTE) or (bs[3] = LIF_MAGIC_BYTE)) then
result := 'LIF'; //file can be read using LIFReader.java
if (bs[4] = ord('i')) and (bs[5] = ord('m')) and (bs[6] = ord('p')) and (bs[7] = ord('r')) then
result := 'LIFF'; //Openlab LIFF format OpenLabReader.java
if (bs[0] = $D0) and (bs[1] = $CF) and (bs[2] = $11) and (bs[3] = $E0) then //IPW_MAGIC_BYTES = 0xd0cf11e0
result := 'IPW'; //IPWReader.java
if (bs[0] = ord('i')) and (bs[1] = ord('i')) and (bs[2] = ord('i')) and (bs[3] = ord('i')) then
result := 'IPL';//IPLabReader.java
if (bs[0] = $89) and (bs[1] = $48) and (bs[2] = $44) and (bs[3] = $46) then //IPW_MAGIC_BYTES = 0xd0cf11e0
result := 'HDF';//Various readers: ImarisHDFReader, CellH5Reader, etc
if (bs[0] = $DA) and (bs[1] = $CE) and (bs[2] = $BE) and (bs[3] = $0A) then//DA CE BE 0A
result := 'ND2';//MAGIC_BYTES_1 ND2Reader
if (bs[0] = $6a) and (bs[1] = $50) and (bs[2] = $20) and (bs[3] = $20) then
result := 'ND2';//MAGIC_BYTES_2 ND2Reader
if (bs[208] = $4D) and (bs[209] = $41) and (bs[210] = $50) then
result := 'MAP';//MRCReader http://www.ccpem.ac.uk/mrc_format/mrc2014.php
//GatanReader.java
closefile(f);
end;
function isTIFF(fnm: string): boolean;
var
f: file;
w: word;
begin
result := false;
if not fileexists(fnm) then exit;
if DirectoryExists(fnm) then exit;
if FSize(fnm) < 32 then exit;
{$I-}
AssignFile(f, fnm);
FileMode := fmOpenRead; //Set file access to read only
Reset(f, 1);
{$I+}
if ioresult <> 0 then
exit;
w := 0;
BlockRead(f, w, sizeof(w)); //Byte-order Identifier
if (w = $4D4D) or (w = $4949) then
result := true;
closefile(f);
end;
{$IFDEF GUI}
procedure ShowMsg(s: string);
begin
Showmessage(s);
end;
{$ENDIF}
procedure fromMatrix (m: mat44; out r11,r12,r13,r21,r22,r23,r31,r32,r33: double);
begin
r11 := m[0,0];
r12 := m[0,1];
r13 := m[0,2];
r21 := m[1,0];
r22 := m[1,1];
r23 := m[1,2];
r31 := m[2,0];
r32 := m[2,1];
r33 := m[2,2];
end;
function Matrix2D (r11,r12,r13,r21,r22,r23,r31,r32,r33: double): mat33;
begin
result[0,0] := r11;
result[0,1] := r12;
result[0,2] := r13;
result[1,0] := r21;
result[1,1] := r22;
result[1,2] := r23;
result[2,0] := r31;
result[2,1] := r32;
result[2,2] := r33;
end;
function nifti_mat33_determ( R: mat33 ):double; //* determinant of 3x3 matrix */
begin
result := r[0,0]*r[1,1]*r[2,2]
-r[0,0]*r[2,1]*r[1,2]
-r[1,0]*r[0,1]*r[2,2]
+r[1,0]*r[2,1]*r[0,2]
+r[2,0]*r[0,1]*r[1,2]
-r[2,0]*r[1,1]*r[0,2] ;
end;
function nifti_mat33_rownorm( A: mat33 ): single; // max row norm of 3x3 matrix
var
r1,r2,r3: single ;
begin
r1 := abs(A[0,0])+abs(A[0,1])+abs(A[0,2]);
r2 := abs(A[1,0])+abs(A[1,1])+abs(A[1,2]);
r3 := abs(A[2,0])+abs(A[2,1])+abs(A[2,2]);
if( r1 < r2 ) then r1 := r2 ;
if( r1 < r3 ) then r1 := r3 ;
result := r1 ;
end;
procedure fromMatrix33 (m: mat33; out r11,r12,r13,r21,r22,r23,r31,r32,r33: double);
begin
r11 := m[0,0];
r12 := m[0,1];
r13 := m[0,2];
r21 := m[1,0];
r22 := m[1,1];
r23 := m[1,2];
r31 := m[2,0];
r32 := m[2,1];
r33 := m[2,2];
end;
function nifti_mat33_inverse( R: mat33 ): mat33; //* inverse of 3x3 matrix */
var
r11,r12,r13,r21,r22,r23,r31,r32,r33 , deti: double ;
begin
FromMatrix33(R,r11,r12,r13,r21,r22,r23,r31,r32,r33);
deti := r11*r22*r33-r11*r32*r23-r21*r12*r33
+r21*r32*r13+r31*r12*r23-r31*r22*r13 ;
if( deti <> 0.0 ) then deti := 1.0 / deti ;
result[0,0] := deti*( r22*r33-r32*r23) ;
result[0,1] := deti*(-r12*r33+r32*r13) ;
result[0,2] := deti*( r12*r23-r22*r13) ;
result[1,0] := deti*(-r21*r33+r31*r23) ;
result[1,1] := deti*( r11*r33-r31*r13) ;
result[1,2] := deti*(-r11*r23+r21*r13) ;
result[2,0] := deti*( r21*r32-r31*r22) ;
result[2,1] := deti*(-r11*r32+r31*r12) ;
result[2,2] := deti*( r11*r22-r21*r12) ;
end;
function nifti_mat33_colnorm( A: mat33 ): single; //* max column norm of 3x3 matrix */
var
r1,r2,r3: single ;
begin
r1 := abs(A[0,0])+abs(A[1,0])+abs(A[2,0]) ;
r2 := abs(A[0,1])+abs(A[1,1])+abs(A[2,1]) ;
r3 := abs(A[0,2])+abs(A[1,2])+abs(A[2,2]) ;
if( r1 < r2 ) then r1 := r2 ;
if( r1 < r3 ) then r1 := r3 ;
result := r1 ;
end;
function nifti_mat33_polar( A: mat33 ): mat33;
var
k:integer;
X , Y , Z: mat33 ;
dif,alp,bet,gam,gmi : single;
begin
dif := 1;
k := 0;
X := A ;
gam := nifti_mat33_determ(X) ;
while( gam = 0.0 )do begin //perturb matrix
gam := 0.00001 * ( 0.001 + nifti_mat33_rownorm(X) ) ;
X[0,0] := X[0,0]+gam ;
X[1,1] := X[1,1]+gam ;
X[2,2] := X[2,2] +gam ;
gam := nifti_mat33_determ(X) ;
end;
while true do begin
Y := nifti_mat33_inverse(X) ;
if( dif > 0.3 )then begin // far from convergence
alp := sqrt( nifti_mat33_rownorm(X) * nifti_mat33_colnorm(X) ) ;
bet := sqrt( nifti_mat33_rownorm(Y) * nifti_mat33_colnorm(Y) ) ;
gam := sqrt( bet / alp ) ;
gmi := 1.0 / gam ;
end else begin
gam := 1.0;
gmi := 1.0 ; //close to convergence
end;
Z[0,0] := 0.5 * ( gam*X[0,0] + gmi*Y[0,0] ) ;
Z[0,1] := 0.5 * ( gam*X[0,1] + gmi*Y[1,0] ) ;
Z[0,2] := 0.5 * ( gam*X[0,2] + gmi*Y[2,0] ) ;
Z[1,0] := 0.5 * ( gam*X[1,0] + gmi*Y[0,1] ) ;
Z[1,1] := 0.5 * ( gam*X[1,1] + gmi*Y[1,1] ) ;
Z[1,2] := 0.5 * ( gam*X[1,2] + gmi*Y[2,1] ) ;
Z[2,0] := 0.5 * ( gam*X[2,0] + gmi*Y[0,2] ) ;
Z[2,1] := 0.5 * ( gam*X[2,1] + gmi*Y[1,2] ) ;
Z[2,2] := 0.5 * ( gam*X[2,2] + gmi*Y[2,2] ) ;
dif := abs(Z[0,0]-X[0,0])+abs(Z[0,1]-X[0,1])+abs(Z[0,2]-X[0,2])
+abs(Z[1,0]-X[1,0])+abs(Z[1,1]-X[1,1])+abs(Z[1,2]-X[1,2])
+abs(Z[2,0]-X[2,0])+abs(Z[2,1]-X[2,1])+abs(Z[2,2]-X[2,2]);
k := k+1 ;
if( k > 100) or (dif < 3.e-6 ) then begin
result := Z;
break ; //convergence or exhaustion
end;
X := Z ;
end;
result := Z ;
end;
procedure nifti_mat44_to_quatern( lR :mat44; out qb, qc, qd, qx, qy, qz, dx, dy, dz, qfac : single);
var
r11,r12,r13 , r21,r22,r23 , r31,r32,r33, xd,yd,zd , a,b,c,d : double;
P,Q: mat33; //3x3
begin
// offset outputs are read write out of input matrix
qx := lR[0,3];
qy := lR[1,3];
qz := lR[2,3];
//load 3x3 matrix into local variables
fromMatrix(lR,r11,r12,r13,r21,r22,r23,r31,r32,r33);
//compute lengths of each column; these determine grid spacings
xd := sqrt( r11*r11 + r21*r21 + r31*r31 ) ;
yd := sqrt( r12*r12 + r22*r22 + r32*r32 ) ;
zd := sqrt( r13*r13 + r23*r23 + r33*r33 ) ;
//if a column length is zero, patch the trouble
if( xd = 0.0 )then begin r11 := 1.0 ; r21 := 0; r31 := 0.0 ; xd := 1.0 ; end;
if( yd = 0.0 )then begin r22 := 1.0 ; r12 := 0; r32 := 0.0 ; yd := 1.0 ; end;
if( zd = 0.0 )then begin r33 := 1.0 ; r13 := 0; r23 := 0.0 ; zd := 1.0 ; end;
//assign the output lengths
dx := xd;
dy := yd;
dz := zd;
//normalize the columns
r11 := r11/xd ; r21 := r21/xd ; r31 := r31/xd ;
r12 := r12/yd ; r22 := r22/yd ; r32 := r32/yd ;
r13 := r13/zd ; r23 := r23/zd ; r33 := r33/zd ;
{ At this point, the matrix has normal columns, but we have to allow
for the fact that the hideous user may not have given us a matrix
with orthogonal columns. So, now find the orthogonal matrix closest
to the current matrix.
One reason for using the polar decomposition to get this
orthogonal matrix, rather than just directly orthogonalizing
the columns, is so that inputting the inverse matrix to R
will result in the inverse orthogonal matrix at this point.
If we just orthogonalized the columns, this wouldn't necessarily hold.}
Q := Matrix2D (r11,r12,r13, // 2D "graphics" matrix
r21,r22,r23,
r31,r32,r33);
P := nifti_mat33_polar(Q) ; //P is orthog matrix closest to Q
FromMatrix33(P,r11,r12,r13,r21,r22,r23,r31,r32,r33);
{ [ r11 r12 r13 ]
at this point, the matrix [ r21 r22 r23 ] is orthogonal
[ r31 r32 r33 ]
compute the determinant to determine if it is proper}
zd := r11*r22*r33-r11*r32*r23-r21*r12*r33
+r21*r32*r13+r31*r12*r23-r31*r22*r13 ; //should be -1 or 1
if( zd > 0 )then begin // proper
qfac := 1.0 ;
end else begin //improper ==> flip 3rd column
qfac := -1.0 ;
r13 := -r13 ; r23 := -r23 ; r33 := -r33 ;
end;
// now, compute quaternion parameters
a := r11 + r22 + r33 + 1.0;
if( a > 0.5 ) then begin //simplest case
a := 0.5 * sqrt(a) ;
b := 0.25 * (r32-r23) / a ;
c := 0.25 * (r13-r31) / a ;
d := 0.25 * (r21-r12) / a ;
end else begin //trickier case
xd := 1.0 + r11 - (r22+r33) ;// 4*b*b
yd := 1.0 + r22 - (r11+r33) ;// 4*c*c
zd := 1.0 + r33 - (r11+r22) ;// 4*d*d
if( xd > 1.0 ) then begin
b := 0.5 * sqrt(xd) ;
c := 0.25* (r12+r21) / b ;
d := 0.25* (r13+r31) / b ;
a := 0.25* (r32-r23) / b ;
end else if( yd > 1.0 ) then begin
c := 0.5 * sqrt(yd) ;
b := 0.25* (r12+r21) / c ;
d := 0.25* (r23+r32) / c ;
a := 0.25* (r13-r31) / c ;
end else begin
d := 0.5 * sqrt(zd) ;
b := 0.25* (r13+r31) / d ;
c := 0.25* (r23+r32) / d ;
a := 0.25* (r21-r12) / d ;
end;
if( a < 0.0 )then begin b:=-b ; c:=-c ; d:=-d; {a:=-a; this is not used} end;
end;
qb := b ;
qc := c ;
qd := d ;
end;
procedure ZERO_MAT33(out m: mat33); //note sets m[3,3] to one
var
i,j: integer;
begin
for i := 0 to 2 do
for j := 0 to 2 do
m[i,j] := 0.0;
m[2,2] := 1;
end;
procedure ZERO_MAT44(out m: mat44); //note sets m[3,3] to one
var
i,j: integer;
begin
for i := 0 to 3 do
for j := 0 to 3 do
m[i,j] := 0.0;
m[3,3] := 1;
end;
procedure LOAD_MAT33(out m: mat33; m00,m01,m02, m10,m11,m12, m20,m21,m22: single);
begin
m[0,0] := m00;
m[0,1] := m01;
m[0,2] := m02;
m[1,0] := m10;
m[1,1] := m11;
m[1,2] := m12;
m[2,0] := m20;
m[2,1] := m21;
m[2,2] := m22;
end;
function nifti_mat33vec_mul(m: mat33; v: vect3): vect3;
var
i: integer;
begin
for i := 0 to 2 do
result[i] := (v[0]*m[i,0])+(v[1]*m[i,1])+(v[2]*m[i,2]);
end;
function nifti_mat33_mul( A,B: mat33): mat33;
var
i,j: integer;
begin
for i:=0 to 2 do
for j:=0 to 2 do
result[i,j] := A[i,0] * B[0,j]
+ A[i,1] * B[1,j]
+ A[i,2] * B[2,j] ;
end;
procedure LOAD_MAT44(out m: mat44; m00,m01,m02,m03, m10,m11,m12,m13, m20,m21,m22,m23: single);
begin
m[0,0] := m00;
m[0,1] := m01;
m[0,2] := m02;
m[0,3] := m03;
m[1,0] := m10;
m[1,1] := m11;
m[1,2] := m12;
m[1,3] := m13;
m[2,0] := m20;
m[2,1] := m21;
m[2,2] := m22;
m[2,3] := m23;
m[3,0] := 0.0;
m[3,1] := 0.0;
m[3,2] := 0.0;
m[3,3] := 1.0;
end;
function validMatrix(var m: mat44): boolean;
var
i: integer;
begin
result := false;
for i := 0 to 2 do begin
if (m[0,i] = 0.0) and (m[1,i] = 0.0) and (m[2,i] = 0.0) then exit;
if (m[i,0] = 0.0) and (m[i,1] = 0.0) and (m[i,2] = 0.0) then exit;
end;
result := true;
end;
procedure vCoord(var lV: vect3; lMat: mat33);
//transform X Y Z by matrix
var
lXi,lYi,lZi: single;
begin
lXi := lV[0]; lYi := lV[1]; lZi := lV[2];
lV[0] := (lXi*lMat[0,0]+lYi*lMat[0,1]+lZi*lMat[0,2]);
lV[1] := (lXi*lMat[1,0]+lYi*lMat[1,1]+lZi*lMat[1,2]);
lV[2] := (lXi*lMat[2,0]+lYi*lMat[2,1]+lZi*lMat[2,2]);
end;
procedure SetCenter(var nhdr: TNIFTIhdr);
var
v: vect3;
m: mat33;
i: integer;
begin
for i := 0 to 2 do begin
m[0,i] := nhdr.srow_x[i];
m[1,i] := nhdr.srow_y[i];
m[2,i] := nhdr.srow_z[i];
v[i] := nhdr.dim[i+1]*0.5;
end;
vCoord(v,m);
//Voxel2mm
//nhdr.srow_x[3]:=-0.5 * (d[0]*m[0,0]+ d[1]*m[0,1]+d[2]*m[0,2]);
nhdr.srow_x[3] := -v[0];
nhdr.srow_y[3] := -v[1];
nhdr.srow_z[3] := -v[2];
end;
procedure SetSForm(var nhdr: TNIFTIhdr);
begin
nhdr.srow_x[0]:=nhdr.pixdim[1]; nhdr.srow_x[1]:=0; nhdr.srow_x[2]:=0; nhdr.srow_x[3]:=-(nhdr.dim[1]-2.0)/2.0*nhdr.pixdim[1];
nhdr.srow_y[0]:=0; nhdr.srow_y[1]:=nhdr.pixdim[2]; nhdr.srow_y[2]:=0; nhdr.srow_y[3]:=-(nhdr.dim[2]-2.0)/2.0*nhdr.pixdim[2];
nhdr.srow_z[0]:=0; nhdr.srow_z[1]:=0; nhdr.srow_z[2]:=nhdr.pixdim[3]; nhdr.srow_z[3]:=-(nhdr.dim[3]-2.0)/2.0*nhdr.pixdim[3];
end;
procedure convertForeignToNifti(var nhdr: TNIFTIhdr);
var
i,nonSpatialMult: integer;
qto_xyz: mat44;
dumdx, dumdy, dumdz: single;
begin
nhdr.HdrSz := 348; //used to signify header does not need to be byte-swapped
nhdr.magic:=kNIFTI_MAGIC_EMBEDDED_HDR;
if (nhdr.dim[3] = 0) then nhdr.dim[3] := 1; //for 2D images the 3rd dim is not specified and set to zero
nhdr.dim[0] := 3; //for 2D images the 3rd dim is not specified and set to zero
nonSpatialMult := 1;
for i := 4 to 7 do
if nhdr.dim[i] > 0 then
nonSpatialMult := nonSpatialMult * nhdr.dim[i];
if (nonSpatialMult > 1) then begin
nhdr.dim[0] := 4;
nhdr.dim[4] := nonSpatialMult;
for i := 5 to 7 do
nhdr.dim[i] := 0;
end;
nhdr.bitpix := 8;
if (nhdr.scl_slope = 0.0) then
nhdr.scl_slope := 1.0;
if (nhdr.datatype = 4) or (nhdr.datatype = 512) then nhdr.bitpix := 16;
if (nhdr.datatype = kDT_RGB) or (nhdr.datatype = kDT_RGBplanar3D) then nhdr.bitpix := 24;
if (nhdr.datatype = 8) or (nhdr.datatype = 16) or (nhdr.datatype = 768) then nhdr.bitpix := 32;
if (nhdr.datatype = 32) or (nhdr.datatype = 64) or (nhdr.datatype = 1024) or (nhdr.datatype = 1280) then nhdr.bitpix := 64;
LOAD_MAT44(qto_xyz, nhdr.srow_x[0], nhdr.srow_x[1], nhdr.srow_x[2], nhdr.srow_x[3],
nhdr.srow_y[0], nhdr.srow_y[1], nhdr.srow_y[2], nhdr.srow_y[3],
nhdr.srow_z[0], nhdr.srow_z[1], nhdr.srow_z[2], nhdr.srow_z[3]);
if not validMatrix(qto_xyz) then begin
nhdr.sform_code := 0;
nhdr.qform_code := 0;
for i := 0 to 3 do begin
nhdr.srow_x[i] := 0;
nhdr.srow_y[i] := 0;
nhdr.srow_z[i] := 0;
end;
nhdr.srow_x[0] := 1;
nhdr.srow_y[1] := 1;
nhdr.srow_z[2] := 1;
exit;
end;
nhdr.sform_code := 1;
nifti_mat44_to_quatern( qto_xyz , nhdr.quatern_b, nhdr.quatern_c, nhdr.quatern_d,nhdr.qoffset_x,nhdr.qoffset_y,nhdr.qoffset_z, dumdx, dumdy, dumdz,nhdr.pixdim[0]) ;
nhdr.qform_code := 0;//kNIFTI_XFORM_SCANNER_ANAT;
end;
procedure NSLog( str: string);
begin
{$IFDEF GUI}
showmsg(str);
{$ENDIF}
{$IFDEF UNIX}writeln(str);{$ENDIF}
end;
function parsePicString(s: string): single;
//given "AXIS_4 001 0.000000e+00 4.000000e-01 microns" return 0.4
var
sList : TStringList;
begin
result := 0.0;
{$IFDEF FPC}
DefaultFormatSettings.DecimalSeparator := '.' ;
{$ELSE}
DecimalSeparator := '.';
{$ENDIF}
sList := TStringList.Create;
sList.Delimiter := ' '; // Each list item will be blank separated
sList.DelimitedText := s;
if sList.Count > 4 then begin
//ShowMessage(sList[3]);
try
result := StrToFloat(sList[3]); // Middle blanks are not supported
except
//ShowMessage(Exception.Message);
end;
end;
sList.Free;
end;
function readVmr (var fname: string; isV16: boolean; var nhdr: TNIFTIhdr; var swapEndian: boolean): boolean;
//http://support.brainvoyager.com/automation-aamp-development/23-file-formats/385-developer-guide-26-the-format-of-vmr-files.html
Type
Tvmr_header = packed record //Next: VMR Format Header structure
ver, nx, ny, nz: word; // 0,4,8,12
end; // Tbv_header;
(*Tvmr_tail = packed record //
Xoff,Yoff,Zoff,FramingCube: int16; //v3
PosFlag,CoordSystem: int32;
X1, Y1, Z1,Xn,Yn,Zn, RXv,RYv,RZv, CXv,CYv,CZv: single;
nRmat, nCmat: int32;
Rfov, Cfov, Zthick, Zgap: single;
nTrans: int32;
LRconv: uint8;
vXres, vYres, vZres: single;
isResVerified, isTal: uint8;
min, mean, max: int32;
end; *)
var
vhdr : Tvmr_header;
//vtail : Tvmr_tail;
lHdrFile: file;
xSz, nvox, FSz, Hsz : integer;
begin
result := false;
{$I-}
AssignFile(lHdrFile, fname);
FileMode := fmOpenRead; //Set file access to read only
Reset(lHdrFile, 1);
{$I+}
if ioresult <> 0 then begin
NSLog('Error in reading vmr header.'+inttostr(IOResult));
FileMode := 2;
exit;
end;
FSz := Filesize(lHdrFile);
vhdr.nx := 0; //BlockRead should be out not var: https://fpc-pascal.freepascal.narkive.com/M2rzyAkf/blockread-and-buffers
BlockRead(lHdrFile, vhdr, sizeof(Tvmr_header));
nVox := vhdr.nx * vhdr.ny * vhdr.nz;
if isV16 then
xSz := (2 * nVox) + sizeof(Tvmr_header)
else
xSz := nVox + sizeof(Tvmr_header);//+ sizeof(Tvmr_tail);
Hsz := sizeof(Tvmr_header);
if (xSz > FSz) then begin //version 1? (6 byte header)
nVox := vhdr.ver * vhdr.nx * vhdr.ny;
if isV16 then
xSz := (2 * nVox) + 6
else
xSz := nVox + 6;
if (xSz = FSz) then begin //version 1
vhdr.nz := vhdr.ny;
vhdr.ny := vhdr.nx;
vhdr.nx := vhdr.ver;
vhdr.ver := 1;
Hsz := 6;
end;
end;
if (xSz > FSz) then begin //docs do not specify endian - wrong endian?
NSLog(format('Odd v16 or vmr format image %dx%dx%d ver %d sz %d', [vhdr.nx, vhdr.ny, vhdr.nz, vhdr.ver, FSz] ));
CloseFile(lHdrFile);
exit;
end;
//seek(lHdrFile, nVox + sizeof(Tvmr_header));
//BlockRead(lHdrFile, vtail, sizeof(Tvmr_tail));
CloseFile(lHdrFile);
swapEndian := false;
nhdr.dim[0]:=3;//3D
nhdr.dim[1]:=vhdr.nx;
nhdr.dim[2]:=vhdr.ny;
nhdr.dim[3]:=vhdr.nz;
nhdr.dim[4]:=1;