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unit crop;
interface
function CropNIfTI(lL,lR,lA,lP,lD,lV: integer):boolean;
implementation
uses nifti_hdr, nifti_img,define_types, GraphicsMathLibrary,dialogs, nifti_img_view;
procedure NIFTIhdr_SlicesToCoord (var lHdr: TNIFTIhdr; lXslice,lYslice,lZslice: integer; var lXmm,lYmm,lZmm: single);
//ignores origin offset
begin
lXmm := (lHdr.srow_x[0]*lXslice)+ (lHdr.srow_x[1]*lYslice)+(lHdr.srow_x[2]*lzslice);
lYmm := (lHdr.srow_y[0]*lXslice)+ (lHdr.srow_y[1]*lYslice)+(lHdr.srow_y[2]*lzslice);
lZmm := (lHdr.srow_z[0]*lXslice)+ (lHdr.srow_z[1]*lYslice)+(lHdr.srow_z[2]*lzslice);
end;
function CropNIfTI(lL,lR,lA,lP,lD,lV: integer):boolean;
//to do : data swapping (errors on detection and writing zero in reverse order)
var
lInHdr,lOutHdr: TNIFTIhdr;
lOutname,lExt: string;
lXmm,lYmm,lZmm: single;
lMat: TMatrix;
lOutPos,lSlice,lVol,lVolBytes,lImgSamples,lInc,
lX,lY,lZ,lBPP, lB,
lInZOffset,lInYOffset,lInSliceSz,lInXSz,lInPos,lImgOffset: integer;
lBuffer: bytep;
(*lSrcBuffer,lBuffer, lBuffUnaligned: bytep;
l32Buf,lImgBuffer: singlep;
l16Buf : SmallIntP;
l32BufI : LongIntP;*)
lWordX: Word;
lSPM2: boolean;
lOutF,lInF: File;
lACrop,lPCrop,lDorsalCrop,lVentralCrop,lLCrop,lRCrop: integer;
lByteSwap: boolean;
begin
result := false;
if (gMRIcroOverlay[kBGOverlayNum].ScrnBufferItems < 1) or (gBGImg.ScrnDim[3] < 2) or (gBGImg.ScrnMM[3] = 0) then begin
showmessage('Please load a 3D background image for neck removal.');
exit;
end;
if (gBGImg.Resliced) then begin
showmessage('You must switch reslicing OFF (Help/Preferences) for image cropping.');
exit;
end;
lInHdr := gMRIcroOverlay[kBGOverlayNum].NIFTIHdr;
//check orthogonal alignment....
if lInHdr.dim[4] > 1 then begin
Showmessage('Only able to Crop 3D images (reorienting 4D could disrupt slice timing and diffusion directions.');
exit;
end;
//Next create reordered or trimmed image in the correct format
case lInHdr.datatype of
kDT_UNSIGNED_CHAR,kDT_SIGNED_SHORT,kDT_UINT16, kDT_SIGNED_INT,kDT_FLOAT:;//Supported
else begin
Showmessage('Crop 3D unsupported datatype.');
exit;
end;
end;
//Msg('Cropping NIfTI/Analyze image '+lFileName);
lOutHdr := lInHdr;
lImgSamples := lInHdr.dim[1]*lInHdr.dim[2]*lInHdr.dim[3];
lBPP := (lInHdr.bitpix div 8); //bytes per pixel
(*lVolBytes := lImgSamples*lBPP;
//Msg('Automatically Cropping image');
lBuffer := (@lSrcBuffer^[lImgOffset+1]);
GetMem(lBuffUnaligned ,(sizeof(single)*lImgSamples) + 16);
{$IFDEF FPC}
lImgBuffer := align(lBuffUnaligned,16);
{$ELSE}
lImgBuffer := SingleP($fffffff0 and (integer(lBuffUnaligned)+15));
{$ENDIF}
case lInHdr.datatype of
kDT_UNSIGNED_CHAR : begin //8 bit
for lInc := 1 to lImgSamples do
lImgBuffer^[lInc] := lBuffer^[lInc];
end;
kDT_SIGNED_SHORT{,kDT_UINT16}: begin //16-bit int
l16Buf := SmallIntP(lBuffer );
if lByteSwap then begin
for lInc := 1 to lImgSamples do
lImgBuffer^[lInc] := Swap(l16Buf^[lInc]);
end else begin
for lInc := 1 to lImgSamples do
lImgBuffer^[lInc] := l16Buf^[lInc];
end;
end;//16bit
kDT_SIGNED_INT: begin
l32Buf := SingleP(lBuffer );
if lByteSwap then //unswap and convert integer to float
for lInc := 1 to lImgSamples do
lImgBuffer^[lInc] := (Swap4r4i(l32Buf^[lInc]))
else //convert integer to float
for lInc := 1 to lImgSamples do
lImgBuffer^[lInc] := Conv4r4i(l32Buf^[lInc]);
end; //32-bit int
kDT_FLOAT: begin
l32Buf := SingleP(lBuffer);
for lInc := 1 to lImgSamples do
lImgBuffer[lInc] := l32Buf[lInc];
if lByteSwap then
for lInc := 1 to lImgSamples do
pswap4r(lImgBuffer^[lInc]); //faster as procedure than function see www.optimalcode.com
for lInc := 1 to lImgSamples do
if specialsingle(lImgBuffer^[lInc]) then lImgBuffer^[lInc] := 0.0;
//invert= for lInc := 1 to lImgSamples do l32Buf[lInc] := -l32Buf[lInc];
end; //32-bit float
else begin
Showmessage('Serious error: format not supported by Crop3D.');
exit;
end;
end; //case *)
lDorsalCrop := lD;
lVentralCrop := lV;
lLCrop := lL;
lRCrop := lR;
lACrop := lA;
lPCrop := lP;
//FreeMem(lBuffUnaligned);
if (lDorsalCrop = 0) and (lVentralCrop = 0)
and (lLCrop = 0) and (lRCrop = 0)
and (lACrop = 0) and (lPCrop = 0) then begin
Showmessage('Crop 3D quitting: no need to delete slices.');
//Freemem(lSrcBuffer);
end;
if (lDorsalCrop < 0) or (lVentralCrop < 0)
or (lLCrop < 0) or (lRCrop < 0)
or (lACrop < 0) or (lPCrop < 0) then begin
Showmessage('Crop 3D quitting: negative values should be impossible.');
//Freemem(lSrcBuffer);
end;
//next compute size of cropped volume
lOutHdr.Dim[1] := lInHdr.Dim[1]-lLCrop-lRCrop;
lOutHdr.Dim[2] := lInHdr.Dim[2]-lACrop-lPCrop;
lOutHdr.Dim[3] := lInHdr.Dim[3]-lDorsalCrop-lVentralCrop;
lVolBytes := lOutHdr.dim[1]*lOutHdr.dim[2]*lOutHdr.dim[3]*lBPP;
//next: readjust origin to take into account removed slices
//REQUIRES images to be aligned to nearest orthogonal to canonical space [1 0 0; 0 1 0; 0 0 1]
NIFTIhdr_SlicesToCoord (lInHdr,lLCrop,lPCrop,lVentralCrop, lXmm,lYmm,lZmm);
lOutHdr.srow_x[3] := lInHdr.srow_x[3] + lXmm;
lOutHdr.srow_y[3] := lInHdr.srow_y[3] + lYmm;
lOutHdr.srow_z[3] := lInHdr.srow_z[3] + lZmm;
lMat := Matrix3D (
lOutHdr.srow_x[0], lOutHdr.srow_x[1], lOutHdr.srow_x[2], lOutHdr.srow_x[3],
lOutHdr.srow_y[0], lOutHdr.srow_y[1], lOutHdr.srow_y[2], lOutHdr.srow_y[3],
lOutHdr.srow_z[0], lOutHdr.srow_z[1], lOutHdr.srow_z[2], lOutHdr.srow_z[3],
0, 0, 0, 1);
nifti_mat44_to_quatern( lMat,
lOutHdr.quatern_b,lOutHdr.quatern_c,lOutHdr.quatern_d,
lOutHdr.qoffset_x,lOutHdr.qoffset_y,lOutHdr.qoffset_z,
lXmm, lYmm, lZmm, lOutHdr.pixdim[0]{QFac});
//note we write and read to the same buffer - we will always SHRINK output
//no need to byteswap data - we will save in the save format as stored
lOutPos := 0;
lInSliceSz := lInHdr.dim[1]*lInHdr.dim[2]*lBPP;
lInXSz := lInHdr.dim[1]*lBPP;
GetMem(lBuffer,lVolBytes);
//Move(gMRIcroOverlay[kBGOverlayNum].ImgBuffer^,lTempBuf^,gBGImg.VOIUndoVolItems);
for lZ := 1 to lOutHdr.dim[3] do begin
lInZOffset := (lVentralCrop+lZ-1) * lInSliceSz;
for lY := 1 to lOutHdr.dim[2] do begin
lInYOffset := ((lPCrop+lY-1) * lInXSz) + lInZOffset + (lLCrop*lBPP);
for lX := 1 to lOutHdr.dim[1] do begin
for lB := 1 to lBPP do begin
inc(lOutPos);
lInPos := ((lX-1) * lBPP) + lInYOffset + lB;
lBuffer^[lOutPos] := gMRIcroOverlay[kBGOverlayNum].ImgBuffer^[lInPos];
end;
end;
end; //for Y
end; //for Z
lOutname := ChangeFilePrefix (gMRIcroOverlay[kBGOverlayNum].HdrFileName,'c');
//result := SaveNIfTICore (lOutName, lSrcBuffer, kNIIImgOffset+1, lOutHdr, lPrefs,lByteSwap);
SaveAsVOIorNIFTI (lBuffer,lOutHdr.dim[1]*lOutHdr.dim[2]*lOutHdr.dim[3], lBPP,1, false, lOutHdr, lOutname);
result := true;
Freemem(lBuffer);
end;
end.
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