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nifti_foreign.pas
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nifti_foreign.pas
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unit nifti_foreign;
interface
{$H+}
{$Include isgui.inc}
uses
{$IFNDEF FPC}
gziod,
{$ELSE}
gzio2,
{$ENDIF}
{$IFDEF GUI}
dialogs,
{$ELSE}
dialogsx,
{$ENDIF}
nifti_types, define_types, sysutils, classes, StrUtils,nifti_dicom;//2015! dialogsx
function readForeignHeader (var lFilename: string; var lHdr: TNIFTIhdr; var gzBytes: int64; var swapEndian: boolean): boolean;
procedure NII_Clear (var lHdr: TNIFTIHdr);
procedure NII_SetIdentityMatrix (var lHdr: TNIFTIHdr); //create neutral rotation matrix
implementation
Type
mat44 = array [0..3, 0..3] of Single;
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;
{$IFDEF GUI}
procedure ShowMsg(s: string);
begin
Showmessage(s);
end;
{$ENDIF}
procedure fromMatrix (m: mat44; var 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; var 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;
var 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 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 (var 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] := 128;
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 ZERO_MAT44(var 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(var 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_mat33_mul( A,B: mat33): mat33;
var
i,j: integer;
begin
for i:=0 to 3 do
for j:=0 to 3 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(var 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 convertForeignToNifti(var nhdr: TNIFTIhdr);
var
i,nonSpatialMult: integer;
qto_xyz: mat44;
//dumqx, dumqy, dumqz,
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.datatype = 4) or (nhdr.datatype = 512) then nhdr.bitpix := 16;
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 := kNIFTI_XFORM_SCANNER_ANAT;
end;
procedure NSLog( str: string);
begin
showmsg(str);
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;
DecimalSeparator := '.';
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 nii_readpic (var fname: string; var nhdr: TNIFTIhdr; var gzBytes: int64; var swapEndian: boolean): boolean;
const
kBIORAD_HEADER_SIZE = 76;
kBIORAD_NOTE_HEADER_SIZE = 16;
kBIORAD_NOTE_SIZE = 80;
Type
Tbiorad_header = packed record //Next: PIC Format Header structure
nx, ny : word; // 0 2*2 image width and height in pixels
npic: SmallInt; // 4 2 number of images in file
ramp1_min: SmallInt; // 6 2*2 LUT1 ramp min. and max.
ramp1_max: SmallInt;
notes: LongInt; // 10 4 no notes=0; has notes=non zero
byte_format: SmallInt; // 14 2 bytes=TRUE(1); words=FALSE(0)
n : word; // 16 2 image number within file
name: array [1..32] of char; // 18 32 file name
merged: SmallInt; // 50 2 merged format
color1 : word; // 52 2 LUT1 color status
file_id : word; // 54 2 valid .PIC file=12345
ramp2_min: SmallInt; // 56 2*2 LUT2 ramp min. and max.
ramp2_max: SmallInt;
color2: word; // 60 2 LUT2 color status
edited: SmallInt; // 62 2 image has been edited=TRUE(1)
lens: SmallInt; // 64 2 Integer part of lens magnification
mag_factor: single; // 66 4 4 byte real mag. factor (old ver.)
dummy1, dummy2, dummy3: word; // 70 6 NOT USED (old ver.=real lens mag.)
end; // biorad_header;
Tbiorad_note_header = packed record
blank: SmallInt; // 0 2
note_flag: LongInt; // 2 4
blank2: LongInt; // 6 4
note_type: SmallInt; // 10 2
blank3: LongInt; // 12 4
note: array[1..kBIORAD_NOTE_SIZE] of char;
end;//biorad_note_header;
var
bhdr : Tbiorad_header;
nh: Tbiorad_note_header;
lHdrFile: file;
//s: string;
i, bytesHdrImg, nNotes: integer;
begin
result := false;
{$I-}
AssignFile(lHdrFile, fname);
FileMode := 0; //Set file access to read only
Reset(lHdrFile, 1);
{$I+}
if ioresult <> 0 then begin
NSLog('Error in reading BioRad PIC header.'+inttostr(IOResult));
FileMode := 2;
exit;
end;
BlockRead(lHdrFile, bhdr, sizeof(Tbiorad_header));
if (bhdr.file_id <> 12345) then begin //signature not found!
CloseFile(lHdrFile);
NSLog('Error in reading BioRad PIC header file ID not 12345.');
exit;
end;
nhdr.dim[0]:=3;//3D
nhdr.dim[1]:=bhdr.nx;
nhdr.dim[2]:=bhdr.ny;
nhdr.dim[3]:=bhdr.npic;
nhdr.dim[4]:=1;
nhdr.pixdim[1]:=1.0;
nhdr.pixdim[2]:=1.0;
nhdr.pixdim[3]:=1.0;
if (bhdr.byte_format = 1) then
nhdr.datatype := kDT_UINT8 // 2
else
nhdr.datatype := kDT_UINT16;
nhdr.vox_offset := kBIORAD_HEADER_SIZE;
bytesHdrImg := sizeof(Tbiorad_header)+bhdr.nx*bhdr.ny*bhdr.npic*bhdr.byte_format;
nNotes := (Filesize(lHdrFile) - bytesHdrImg) div (kBIORAD_NOTE_HEADER_SIZE+kBIORAD_NOTE_SIZE);
if (nNotes > 0) then begin
seek(lHdrFile, bytesHdrImg);
for i := 1 to nNotes do begin
BlockRead(lHdrFile, nh, sizeof(Tbiorad_note_header));
if(nh.note_type=1) then continue; // These are not interesting notes
if AnsiStartsStr('AXIS_2 ', nh.note) then
nhdr.pixdim[1] := parsePicString(nh.note);
if AnsiStartsStr('AXIS_3 ', nh.note) then
nhdr.pixdim[2] := parsePicString(nh.note);
if AnsiStartsStr('AXIS_4 ', nh.note) then
nhdr.pixdim[3] := parsePicString(nh.note);
end;
end;
CloseFile(lHdrFile);
nhdr.sform_code := 1;
nhdr.srow_x[0]:=nhdr.pixdim[1];nhdr.srow_x[1]:=0.0;nhdr.srow_x[2]:=0.0;nhdr.srow_x[3]:=0.0;
nhdr.srow_y[0]:=0.0;nhdr.srow_y[1]:=nhdr.pixdim[2];nhdr.srow_y[2]:=0.0;nhdr.srow_y[3]:=0.0;
nhdr.srow_z[0]:=0.0;nhdr.srow_z[1]:=0.0;nhdr.srow_z[2]:=-nhdr.pixdim[3];nhdr.srow_z[3]:=0.0;
convertForeignToNifti(nhdr);
result := true;
end;
function readMGHHeader (var fname: string; var nhdr: TNIFTIhdr; var gzBytes: int64; var swapEndian: boolean): boolean;
Type
Tmgh = packed record //Next: MGH Format Header structure
version, width,height,depth,nframes,mtype,dof : longint;
goodRASFlag: smallint;
spacingX,spacingY,spacingZ,xr,xa,xs,yr,ya,ys,zr,za,zs,cr,ca,cs: single;
end;
var
mgh: Tmgh;
lBuff: Bytep;
lExt: string;
lHdrFile: file;
PxyzOffset, Pcrs: vect4;
i,j: integer;
base: single;
m: mat44;
begin
result := false;
lExt := UpCaseExt(fname);
if (lExt = '.MGZ') then begin
lBuff := @mgh;
UnGZip(fname,lBuff,0,sizeof(Tmgh)); //1388
gzBytes := K_gzBytes_headerAndImageCompressed;
end else begin //if MGZ, else assume uncompressed MGH
gzBytes := 0;
{$I-}
AssignFile(lHdrFile, fname);
FileMode := 0; //Set file access to read only
Reset(lHdrFile, 1);
{$I+}
if ioresult <> 0 then begin
NSLog('Error in reading MGH header.'+inttostr(IOResult));
FileMode := 2;
exit;
end;
BlockRead(lHdrFile, mgh, sizeof(Tmgh));
CloseFile(lHdrFile);
end;
{$IFDEF ENDIAN_BIG} //data always stored big endian
swapEndian := false;
{$ELSE}
swapEndian := true;
swap4(mgh.version);
swap4(mgh.width);
swap4(mgh.height);
swap4(mgh.depth);
swap4(mgh.nframes);
swap4(mgh.mtype);
swap4(mgh.dof);
mgh.goodRASFlag := swap(mgh.goodRASFlag);
Xswap4r(mgh.spacingX);
Xswap4r(mgh.spacingY);
Xswap4r(mgh.spacingZ);
Xswap4r(mgh.xr);
Xswap4r(mgh.xa);
Xswap4r(mgh.xs);
Xswap4r(mgh.yr);
Xswap4r(mgh.ya);
Xswap4r(mgh.ys);
Xswap4r(mgh.zr);
Xswap4r(mgh.za);
Xswap4r(mgh.zs);
Xswap4r(mgh.cr);
Xswap4r(mgh.ca);
Xswap4r(mgh.cs);
{$ENDIF}
if ((mgh.version <> 1) or (mgh.mtype < 0) or (mgh.mtype > 4)) then begin
NSLog('Error: first value in a MGH header should be 1 and data type should be in the range 1..4.');
exit;
end;
if (mgh.mtype = 0) then
nhdr.datatype := kDT_UINT8
else if (mgh.mtype = 4) then
nhdr.datatype := kDT_INT16
else if (mgh.mtype = 1) then
nhdr.datatype := kDT_INT32
else if (mgh.mtype = 3) then
nhdr.datatype := kDT_FLOAT32;
nhdr.dim[1]:=mgh.width;
nhdr.dim[2]:=mgh.height;
nhdr.dim[3]:=mgh.depth;
nhdr.dim[4]:=mgh.nframes;
nhdr.pixdim[1]:=mgh.spacingX;
nhdr.pixdim[2]:=mgh.spacingY;
nhdr.pixdim[3]:=mgh.spacingZ;
nhdr.vox_offset := 284;
nhdr.sform_code := 1;
//convert MGH to NIfTI transform see Bruce Fischl mri.c MRIxfmCRS2XYZ https://github.com/neurodebian/freesurfer/blob/master/utils/mri.c
LOAD_MAT44(m,mgh.xr*nhdr.pixdim[1],mgh.yr*nhdr.pixdim[2],mgh.zr*nhdr.pixdim[3],0,
mgh.xa*nhdr.pixdim[1],mgh.ya*nhdr.pixdim[2],mgh.za*nhdr.pixdim[3],0,
mgh.xs*nhdr.pixdim[1],mgh.ys*nhdr.pixdim[2],mgh.zs*nhdr.pixdim[3],0);
base := 0.0; //0 or 1: are voxels indexed from 0 or 1?
Pcrs[0] := (nhdr.dim[1]/2.0)+base;
Pcrs[1] := (nhdr.dim[2]/2.0)+base;
Pcrs[2] := (nhdr.dim[3]/2.0)+base;
Pcrs[3] := 1;
for i:=0 to 3 do begin //multiply Pcrs * m
PxyzOffset[i] := 0;
for j := 0 to 3 do
PxyzOffset[i] := PxyzOffset[i]+ (m[i,j]*Pcrs[j]);
end;
nhdr.srow_x[0]:=m[0,0]; nhdr.srow_x[1]:=m[0,1]; nhdr.srow_x[2]:=m[0,2]; nhdr.srow_x[3]:=mgh.cr - PxyzOffset[0];
nhdr.srow_y[0]:=m[1,0]; nhdr.srow_y[1]:=m[1,1]; nhdr.srow_y[2]:=m[1,2]; nhdr.srow_y[3]:=mgh.ca - PxyzOffset[1];
nhdr.srow_z[0]:=m[2,0]; nhdr.srow_z[1]:=m[2,1]; nhdr.srow_z[2]:=m[2,2]; nhdr.srow_z[3]:=mgh.cs - PxyzOffset[2];
convertForeignToNifti(nhdr);
result := true;
end;
procedure splitStr(delimiter: char; str: string; mArray: TStrings);
begin
mArray.Clear;
mArray.Delimiter := delimiter;
mArray.DelimitedText := str;
end;
procedure splitStrStrict(delimiter: char; S: string; sl: TStrings);
begin
sl.Clear;
sl.Delimiter := delimiter;
sl.DelimitedText := '"' + StringReplace(S, sl.Delimiter, '"' + sl.Delimiter + '"', [rfReplaceAll]) + '"';
end;
function cleanStr (S:string): string; // "(12.31)" ->"12.31"
begin
result := StringReplace(S, '(', '', [rfReplaceAll]);
result := StringReplace(result, ')', '', [rfReplaceAll]);
end;
(*function FSize (lFName: String): Int64;
var SearchRec: TSearchRec;
begin
result := 0;
if not fileexistsex(lFName) then exit;
FindFirst(lFName, faAnyFile, SearchRec);
result := SearchRec.size;
FindClose(SearchRec);
end; *)
(*procedure report_mat(m: mat33);
begin
showmsg('mat = ['+floattostr(m[0,0])+' ' +floattostr(m[0,1]) +' ' +floattostr(m[0,2]) +'; '
+floattostr(m[1,0])+' ' +floattostr(m[1,1]) +' ' +floattostr(m[1,2]) +'; '
+floattostr(m[2,0])+' ' +floattostr(m[2,1]) +' ' +floattostr(m[2,2]) +'] ');
end;*)
type TFByte = File of Byte;
procedure ReadLnBin(var f: TFByte; var s: string);
const
kEOLN = $0A;
var
bt : Byte;
begin
s := '';
while (not EOF(f)) do begin
Read(f,bt);
if bt = kEOLN then exit;
s := s + Chr(bt);
end;
end;
function readVTKHeader (var fname: string; var nhdr: TNIFTIhdr; var gzBytes: int64; var swapEndian: boolean): boolean;
//VTK Simple Legacy Formats : STRUCTURED_POINTS : BINARY
// http://daac.hpc.mil/gettingStarted/VTK_DataFormats.html
// https://github.com/bonilhamusclab/MRIcroS/blob/master/%2BfileUtils/%2Bvtk/readVtk.m
// http://www.ifb.ethz.ch/education/statisticalphysics/file-formats.pdf
// ftp://ftp.tuwien.ac.at/visual/vtk/www/FileFormats.pdf
// "The VTK data files described here are written in big endian form"
label
666;
var
f: TFByte;//TextFile;
strlst: TStringList;
str: string;
i, num_vox: integer;
begin
gzBytes := 0;
{$IFDEF ENDIAN_BIG}
swapEndian := false;
{$ELSE}
swapEndian := true;
{$ENDIF}
result := false;
strlst:=TStringList.Create;
AssignFile(f, fname);
Reset(f,1);
ReadLnBin(f, str); //signature: '# vtk DataFile'
if pos('VTK', UpperCase(str)) <> 3 then begin
showmessage('Not a VTK file');
goto 666;
end;
ReadLnBin(f, str); //comment: 'Comment: created with MRIcroS'
ReadLnBin(f, str); //kind: 'BINARY' or 'ASCII'
if pos('BINARY', UpperCase(str)) <> 1 then begin // '# vtk DataFile'
showmessage('Only able to read binary VTK file:'+str);
goto 666;
end;
ReadLnBin(f, str); // kind, e.g. "DATASET POLYDATA" or "DATASET STRUCTURED_ POINTS"
if pos('STRUCTURED_POINTS', UpperCase(str)) = 0 then begin
showmessage('Only able to read VTK images saved as STRUCTURED_POINTS, not '+ str);
goto 666;
end;
while (str <> '') and (pos('POINT_DATA', UpperCase(str)) = 0) do begin
ReadLnBin(f, str);
strlst.DelimitedText := str;
if pos('DIMENSIONS', UpperCase(str)) <> 0 then begin //e.g. "DIMENSIONS 128 128 128"
nhdr.dim[1] := StrToIntDef(strlst[1],1);
nhdr.dim[2] := StrToIntDef(strlst[2],1);
nhdr.dim[3] := StrToIntDef(strlst[3],1);
end; //dimensions
if (pos('ASPECT_RATIO', UpperCase(str)) <> 0) or (pos('SPACING', UpperCase(str)) <> 0) then begin //e.g. "ASPECT_RATIO 1.886 1.886 1.913"
nhdr.pixdim[1] := StrToFloatDef(strlst[1],1);
nhdr.pixdim[2] := StrToFloatDef(strlst[2],1);
nhdr.pixdim[3] := StrToFloatDef(strlst[3],1);
//showmessage(format('%g %g %g',[nhdr.pixdim[1], nhdr.pixdim[2], nhdr.pixdim[3] ]));
end; //aspect ratio
if (pos('ORIGIN', UpperCase(str)) <> 0) then begin //e.g. "ASPECT_RATIO 1.886 1.886 1.913"
nhdr.srow_x[3] := -StrToFloatDef(strlst[1],1);
nhdr.srow_y[3] := -StrToFloatDef(strlst[2],1);
nhdr.srow_z[3] := -StrToFloatDef(strlst[3],1);
//showmessage(format('%g %g %g',[nhdr.pixdim[1], nhdr.pixdim[2], nhdr.pixdim[3] ]));
end; //aspect ratio
end; //not POINT_DATA
if pos('POINT_DATA', UpperCase(str)) = 0 then goto 666;
num_vox := StrToIntDef(strlst[1],0);
if num_vox <> (nhdr.dim[1] * nhdr.dim[2] * nhdr.dim[3]) then begin
showmessage(format('Expected POINT_DATA to equal %dx%dx%d',[nhdr.dim[1], nhdr.dim[2], nhdr.dim[3] ]));
goto 666;
end;
ReadLnBin(f, str);
if pos('SCALARS', UpperCase(str)) = 0 then goto 666; //"SCALARS scalars unsigned_char"
strlst.DelimitedText := str;
str := UpperCase(strlst[2]);
//dataType is one of the types bit, unsigned_char, char, unsigned_short, short, unsigned_int, int, unsigned_long, long, float, or double
if pos('UNSIGNED_CHAR', str) <> 0 then
nhdr.datatype := kDT_UINT8 //
else if pos('SHORT', str) <> 0 then
nhdr.datatype := kDT_INT16 //
else if pos('UNSIGNED_SHORT', str) <> 0 then
nhdr.datatype := kDT_UINT16 //
else if pos('INT', str) <> 0 then
nhdr.datatype := kDT_INT32 //
else if pos('FLOAT', str) <> 0 then
nhdr.datatype := kDT_FLOAT
else if pos('DOUBLE', str) <> 0 then
nhdr.datatype := kDT_DOUBLE
else begin
showmessage('Unknown VTK scalars type '+str);
goto 666;
end;
convertForeignToNifti(nhdr);
//showmessage(inttostr(nhdr.datatype));
ReadLnBin(f, str);
if pos('LOOKUP_TABLE', UpperCase(str)) = 0 then goto 666; //"LOOKUP_TABLE default"
nhdr.vox_offset := filepos(f);
//fill matrix
for i := 0 to 2 do begin
nhdr.srow_x[i] := 0;
nhdr.srow_y[i] := 0;
nhdr.srow_z[i] := 0;
end;
nhdr.srow_x[0] := nhdr.pixdim[1];
nhdr.srow_y[1] := nhdr.pixdim[2];
nhdr.srow_z[2] := nhdr.pixdim[3];
//showmessage('xx' +inttostr( filepos(f) ));
result := true;
666:
closefile(f);
strlst.Free;
end;
function readMHAHeader (var fname: string; var nhdr: TNIFTIhdr; var gzBytes: int64; var swapEndian: boolean): boolean;
//Read VTK "MetaIO" format image
//http://www.itk.org/Wiki/ITK/MetaIO/Documentation#Reading_a_Brick-of-Bytes_.28an_N-Dimensional_volume_in_a_single_file.29
//https://www.assembla.com/spaces/plus/wiki/Sequence_metafile_format
//http://itk-insight-users.2283740.n2.nabble.com/MHA-MHD-File-Format-td7585031.html
var
FP: TextFile;
str, tagName, elementNames: string;
ch: char;
isLocal,compressedData: boolean;
matOrient, mat, d, t: mat33;
//compressedDataSize,
nPosition, nOffset, matElements, matElementsOrient, headerSize, nItems, nBytes, i, channels, fileposBytes: longint;
offset,position, elementSize: array [0..3] of single;
transformMatrix: array [0..11] of single;
mArray: TStringList;
begin
result := false;
if not FileExistsEX(fname) then exit;
{$IFDEF FPC}
DefaultFormatSettings.DecimalSeparator := '.' ;
// DecimalSeparator := '.';
{$ELSE}
DecimalSeparator := '.';
{$ENDIF}
for i := 0 to 3 do begin
position[i] := 0;
offset[i] := 0;
elementSize[i] := 1;
end;
nPosition := 0;
nOffset := 0;
gzBytes := 0;
fileposBytes := 0;
//compressedDataSize := 0;
swapEndian := false;
isLocal := true; //image and header embedded in same file, if false detached image
headerSize := 0;
matElements := 0;
matElementsOrient := 0;
compressedData := false;
mArray := TStringList.Create;
Filemode := fmOpenRead;
AssignFile(fp,fname);
reset(fp);
while not EOF(fp) do begin
str := '';
while not EOF(fp) do begin
read(fp,ch);
inc(fileposBytes);
if (ch = chr($0D)) or (ch = chr($0A)) then break;
str := str+ch;
end;
if (length(str) < 1) or (str[1]='#') then continue;
splitstrStrict('=',str,mArray);
if (mArray.count < 2) then continue;
tagName := cleanStr(mArray[0]);
elementNames := mArray[1];
splitstr(',',elementNames,mArray);
nItems :=mArray.count;
if (nItems < 1) then continue;
for i := 0 to (nItems-1) do
mArray[i] := cleanStr(mArray[i]); //remove '(' and ')',
if AnsiContainsText(tagName, 'ObjectType') and (not AnsiContainsText(mArray.Strings[0], 'Image')) then begin
NSLog('Expecting file with tag "ObjectType = Image" instead of "ObjectType = '+mArray.Strings[0]+'"');
end {else if AnsiContainsText(tagName, 'NDims') then begin
nDims := strtoint(mArray[0]);
if (nDims > 4) then begin
NSLog('Warning: only reading first 4 dimensions');
nDims := 4;
end;
end} else if AnsiContainsText(tagName, 'BinaryDataByteOrderMSB') then begin
{$IFDEF ENDIAN_BIG} //data always stored big endian
if not AnsiContainsText(mArray[0], 'True') then swapEndian := true;
{$ELSE}
if AnsiContainsText(mArray[0], 'True') then swapEndian := true;
{$ENDIF}
end {else if AnsiContainsText(tagName, 'BinaryData') then begin
if AnsiContainsText(mArray[0], 'True') then binaryData := true;
end else if AnsiContainsText(tagName, 'CompressedDataSize') then begin
compressedDataSize := strtoint(mArray[0]);
end} else if AnsiContainsText(tagName, 'CompressedData') then begin
if AnsiContainsText(mArray[0], 'True') then
compressedData := true;
end else if AnsiContainsText(tagName, 'Orientation') and (not AnsiContainsText(tagName, 'Anatomical') ) then begin
if (nItems > 12) then nItems := 12;
matElementsOrient := nItems;
for i := 0 to (nItems-1) do
transformMatrix[i] := strtofloat(mArray[i]);
if (matElementsOrient >= 12) then
LOAD_MAT33(matOrient, transformMatrix[0],transformMatrix[1],transformMatrix[2],
transformMatrix[4],transformMatrix[5],transformMatrix[6],
transformMatrix[8],transformMatrix[9],transformMatrix[10])
else if (matElementsOrient >= 9) then
LOAD_MAT33(matOrient, transformMatrix[0],transformMatrix[1],transformMatrix[2],
transformMatrix[3],transformMatrix[4],transformMatrix[5],
transformMatrix[6],transformMatrix[7],transformMatrix[8]);
end else if AnsiContainsText(tagName, 'TransformMatrix') then begin
if (nItems > 12) then nItems := 12;
matElements := nItems;
for i := 0 to (nItems-1) do
transformMatrix[i] := strtofloat(mArray[i]);
if (matElements >= 12) then
LOAD_MAT33(mat, transformMatrix[0],transformMatrix[1],transformMatrix[2],
transformMatrix[4],transformMatrix[5],transformMatrix[6],
transformMatrix[8],transformMatrix[9],transformMatrix[10])
else if (matElements >= 9) then
LOAD_MAT33(mat, transformMatrix[0],transformMatrix[1],transformMatrix[2],
transformMatrix[3],transformMatrix[4],transformMatrix[5],
transformMatrix[6],transformMatrix[7],transformMatrix[8]);
end else if AnsiContainsText(tagName, 'Position') then begin
if (nItems > 3) then nItems := 3;
nPosition := nItems;
for i := 0 to (nItems-1) do
position[i] := strtofloat(mArray[i]);
end else if AnsiContainsText(tagName, 'Offset') then begin
if (nItems > 3) then nItems := 3;
nOffset := nItems;
for i := 0 to (nItems-1) do
offset[i] := strtofloat(mArray[i]);
end else if AnsiContainsText(tagName, 'AnatomicalOrientation') then begin
//e.g. RAI
end else if AnsiContainsText(tagName, 'ElementSpacing') then begin
if (nItems > 4) then nItems := 4;
for i := 0 to (nItems-1) do
nhdr.pixdim[i+1] := strtofloat(mArray[i]);
end else if AnsiContainsText(tagName, 'DimSize') then begin
if (nItems > 4) then nItems := 4;
for i := 0 to (nItems-1) do
nhdr.dim[i+1] := strtoint(mArray[i]);
end else if AnsiContainsText(tagName, 'HeaderSize') then begin