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unit voismooth;
{$mode objfpc}{$H+}
interface
uses
Classes, SysUtils, LResources, Forms, Controls, Graphics, Dialogs, StdCtrls,
Buttons, Spin,define_types;
type
{ Tvoismoothform }
Tvoismoothform = class(TForm)
CancelBtn: TSpeedButton;
Label37: TLabel;
Label38: TLabel;
OKBtn: TSpeedButton;
ScaleSides: TComboBox;
HelpBtn: TSpeedButton;
XROIfwhm: TSpinEdit;
xROIoutput: TComboBox;
XROIthresh: TFloatSpinEdit;
procedure FormCreate(Sender: TObject);
procedure SmoothOpenVOI(Sender: TObject);
procedure BtnClick(Sender: TObject);
procedure FormShow(Sender: TObject);
procedure HelpBtnClick(Sender: TObject);
procedure SmoothVOI_SPM5masks;
private
{ private declarations }
public
{ public declarations }
end;
var
voismoothform: Tvoismoothform;
implementation
uses nifti_img_view,nifti_img;
{ Tvoismoothform }
procedure Tvoismoothform.HelpBtnClick(Sender: TObject);
begin
Showmessage('The Full Width Half Maximum [FWHM] defines the width of the smoothing Gaussian. '+
'The threshold defines a binary cutoff boundary - signals greater than the threshold will be included in the output. '+
'A threshold of 0 will create an continuous 8-bit output (0..200 for signal 0..1)');
end;
procedure Tvoismoothform.SmoothOpenVOI(Sender: TObject);
var
lScaleXY,lOK,lResliceNotMask: boolean;
lYOutra,lROIrealRA: SingleP;
lIncX,lMissing,lZPos,lYPos,lSliceSz,lXt,lYt,lZt,lX,lY,lZ,lXoffset,lYOffset,lZOffset,lI,lI2,lImgSz,lcutoffvoxx,lcutoffvoxy,lcutoffvoxz: integer;
lScale,lThreshComp,lExpd,lThresh,lSig,lXmm,lYmm,lZmm,lcumgauss: single;//double;
lxra,lyra,lzra,lzraScaled,lxCutra,lyCutra,lzCutra:SingleP0;//x0P;
lStartTime,lEndTime: DWord;
lXDim,lYDim,lZDim,lPlanes,lMinX,lMaxX,lMinY,lMaxY,lMinZ,lMaxZ: integer;
begin
lXDim := gBGImg.ScrnDim[1];
lYDim := gBGImg.ScrnDim[2];
lZDim := gBGImg.ScrnDim[3];
lXmm := gBGImg.ScrnMM[1];
lYmm := gBGImg.ScrnMM[2];
lZmm := gBGImg.ScrnMM[3];
lResliceNotMask := false;
if not IsVOIOpen then begin
ShowMessage('You have not created or opened a region of interest.');
exit;
end;
if (gBGImg.ScrnMM[1] = 0) or (lXmm = 0) or (lYmm = 0) or (lZmm =0) or (XROIfwhm.value=0) then begin
ShowMessage('At least one of the images ''size [mm]'' settings or the ''FWHM [mm]'' is zero. Smoothing requires the image size to be specified.');
Exit;
end;
if ScaleSides.itemindex = 1 then
lScaleXY := true
else
lScaleXY := false;
lOK := true;
if lScaleXY then begin
lsig := (XROIfwhm.value / lXmm)/sqrt(8*ln(2)); // % FWHM -> sigma
lcutoffvoxX := round(6*lsig);
if (lcutoffvoxX *2) >= lXdim then lOK := false;
lsig := (XROIfwhm.value / lYmm)/sqrt(8*ln(2)); // % FWHM -> sigma
lcutoffvoxY := round(6*lsig);
if (lcutoffvoxY *2) >= lYdim then lOK := false;
end; {scaleXY}
lsig := (XROIfwhm.value / lZmm)/sqrt(8*ln(2)); // % FWHM -> sigma
lcutoffvoxZ := round(6*lsig);
if (lcutoffvoxZ *2) >= lZdim then lOK := false;
if not lOK then begin
showmessage('Unable to smooth image: image dimensions are too small for such a broad smoothing. Reduce the FWHM');
exit;
end;
if xROIoutput.itemindex <> 1 then
lResliceNotMask := true;
lImgSz := gMRIcroOverlay[kVOIOverlayNum].ScrnBufferItems;
if lImgSz < 1 then exit;
CreateUndoVol;//create gBGImg.VOIUndoVol
Move(gMRIcroOverlay[kVOIOverlayNum].ScrnBuffer^,gBGImg.VOIUndoVol^,gBGImg.VOIUndoVolItems);
if lResliceNotMask then begin //reslice
for lI := 1 to lImgSz do
if gBGImg.VOIUndoVol^[lI] <> 0 then
gBGImg.VOIUndoVol^[lI] := 1;
end else begin //create mask: invert
for lI := 1 to lImgSz do
if gBGImg.VOIUndoVol^[lI] = 0 then
gBGImg.VOIUndoVol^[lI] := 1
else
gBGImg.VOIUndoVol^[lI] := 0;
end; //create mask
lSliceSz := lXdim * lYdim;
//lZXi := lZdim*lXdim; //for swizzle
lPlanes := 0;
ImgForm.ProgressBar1.Position := 0;
ImgForm.ProgressBar1.Min := 0;
ImgForm.ProgressBar1.Max := lZdim * 3;
ImgForm.StatusLabel.caption := 'Smoothing slice data: X-plane';
//lStartTime := GetTickCount;
lThresh := XRoiThresh.value;
lsig := (XROIfwhm.value / lXmm)/sqrt(8*ln(2)); // % FWHM -> sigma
if lsig = 0 then begin
Showmessage('Unable to compute gaussian with current FWHM');
exit;
end;
lcutoffvoxx := round(6*lsig); // % highest / lowest voxel to go out to
getmem(lxra,(lcutoffvoxx+1)*sizeof(double {was extended}));
getmem(lxCutra,(lcutoffvoxx+1)*sizeof(double {was extended}));
lexpd := 2*lsig*lsig;
lCumGauss := 0;
for lI := 0 to lcutoffvoxx do begin
lxra^[lI] := exp(-1*(lI*lI)/lexpd) ;
lCumGauss := lCumGauss + lxra^[lI];
end;
lCumGauss := 2*lCumGauss - lxra^[0];
if lCumGauss <> 0 then
for lI := 0 to lcutoffvoxx do begin
lxra^[lI] := lxra^[lI]/lCumGauss;
end;
for lI := 1 to lcutoffvoxX do begin
lCumGauss := 0;
for lI2 := (lcutoffvoxX - lI) downto -lcutoffvoxX do
lCumGauss := lCumGauss + lXra^[abs(lI2)];
if lCumGauss <> 0 then
lXCutra^[lI] := 1/lCumGauss;
end;
lXCutra^[0] := 1;
lsig := (XROIfwhm.value / lYmm)/sqrt(8*ln(2)); // % FWHM -> sigma
if lsig = 0 then begin
Showmessage('Unable to compute gaussian with current FWHM');
exit;
end;
lcutoffvoxY := round(6*lsig); // % highest / lowest voxel to go out to
getmem(lYra,(lcutoffvoxY+1)*sizeof(double {was extended}));
getmem(lYCutra,(lcutoffvoxY+1)*sizeof(double {was extended}));
lexpd := 2*lsig*lsig;
lCumGauss := 0;
for lI := 0 to lcutoffvoxY do begin
lYra^[lI] := exp(-1*(lI*lI)/lexpd) ;
lCumGauss := lCumGauss + lYra^[lI];
end;
lCumGauss := 2*lCumGauss - lYra^[0];
if lCumGauss <> 0 then
for lI := 0 to lcutoffvoxY do begin
lYra^[lI] := lYra^[lI]/lCumGauss;
end;
for lI := 1 to lcutoffvoxY do begin
lCumGauss := 0;
for lI2 := (lcutoffvoxY - lI) downto -lcutoffvoxY do
lCumGauss := lCumGauss + lYra^[abs(lI2)];
if lCumGauss <> 0 then
lYCutra^[lI] := 1/lCumGauss;
end;
lYCutra^[0] := 1;
lsig := (XROIfwhm.value / lZmm)/sqrt(8*ln(2)); // % FWHM -> sigma
if lsig = 0 then begin
Showmessage('Unable to compute gaussian with current FWHM');
exit;
end;
lcutoffvoxZ := round(6*lsig); // % highest / lowest voxel to go out to
getmem(lZra,(lcutoffvoxZ+1)*sizeof(double {was extended}));
getmem(lZraScaled,(lcutoffvoxZ+lcutoffvoxZ+1)*sizeof(double {was extended}));
getmem(lZCutra,(lcutoffvoxZ+1)*sizeof(double {was extended}));
lexpd := 2*lsig*lsig;
lCumGauss := 0;
for lI := 0 to lcutoffvoxZ do begin
lZra^[lI] := exp(-1*(lI*lI)/lexpd );
lCumGauss := lCumGauss + lZra^[lI];
end;
lCumGauss := 2*lCumGauss - lZra^[0];
if lCumGauss <> 0 then
for lI := 0 to lcutoffvoxZ do begin
lZra^[lI] := lZra^[lI]/lCumGauss;
end;
for lI := 1 to lcutoffvoxZ do begin
lCumGauss := 0;
for lI2 := (lcutoffvoxZ - lI) downto -lcutoffvoxZ do
lCumGauss := lCumGauss + lZra^[abs(lI2)];
if lCumGauss <> 0 then
lZCutra^[lI] := 1/lCumGauss;
end;
lZCutra^[0] := 1;(**)
GetMem ( lROIrealRA , sizeof(single)*lImgSz);
GetMem (lYOutRA, sizeof(single) * lYdim);
if lResliceNotMask then
for lI := 1 to lImgSz do
lROIrealRA^[lI] := 0
else
for lI := 1 to lImgSz do
lROIrealRA^[lI] := 1;
//X-direction
for lZ := 1 to lZdim do begin
lZPos := (lZ-1)*lSliceSz;
for lY := 1 to lYdim do begin
lyPos := (lY-1)*lXdim;
for lX := 1 to lXdim do begin
lMinX := lX - lCutoffVoxX;
if lMinX < 1 then lMinX := 1;
lMaxX := lX + lCutoffVoxX;
if lMaxX > lXdim then lMaxX := lXdim;
lMissing := (2*lCutOffVoxX)-(lMaxX-lMinX);
if lScaleXY then
lScale := lXCutRA^[lMissing]
else
lScale := lXCutRA^[0];
lCumGauss := 0;
for lXt := lMinX to lMaxX do begin
//SSE optimization?
if (gBGImg.VOIUndoVol^[lXt+lYPos+lZpos] <> 0) then
lCumGauss := lCumGauss + lScale*lXra^[abs(lX-lXt)] (*{kSmoothImg}*(gROIEXport[lXt+lYPos+lZpos]/255)*);
end; {for each position}
lROIrealRA^[lX+lYPos+lZpos] := lCumGauss;
end; {lX}
end; {lY}
Application.ProcessMessages;
inc(lPlanes);
ImgForm.ProgressBar1.Position := lPLanes;
end; {lZ loop for X-plane}
ImgForm.StatusLabel.caption := 'Smoothing slice data: Y-plane';
for lZ := 1 to lZdim do begin {Z loop for Y plane}
lZPos := (lZ-1)*lSliceSz;
for lX := 1 to lXdim do begin
for lY := 1 to lYdim do begin
lMinY := lY - lCutoffVoxY;
if lMinY < 1 then lMinY := 1;
lMaxY := lY + lCutoffVoxY;
if lMaxY > lYdim then lMaxY := lYdim;
lMissing := (2*lCutOffVoxY)-(lMaxY-lMinY);
if lScaleXY then
lScale := lYCutRA^[lMissing]
else
lScale := lYCutRA^[0];
lCumGauss := 0;
for lYt := lMinY to lMaxY do begin
//SSE optimization?
lCumGauss := lCumGauss+ lScale*(lROIrealRA^[lX+((lYt-1)*lXdim)+lZpos])*lYra^[abs(lY-lYt)];
end; {for each position}
lYOutRA^[lY] := lCumGauss;
end; {lY}
for lY := 1 to lYdim do begin
//SSE optimization
lROIrealRA^[lX+((lY-1)*lXdim)+lZpos] := lYOutRA^[lY];
end;
end; {lX}
Application.ProcessMessages;
inc(lPlanes);
ImgForm.ProgressBar1.Position := lPlanes;
end; {Z loop for Y plane}
(*if (not lScaleXY) then begin
//lOrigZPos := (lFirstEmptySlice-1)*lSliceSz;
for lZ := lFirstEmptySlice to lZi do begin
if (lROIonSliceRA[lZ]=0) then begin
lZPos := (lZ-1)*lSliceSz;
for lX := 1 to lSliceSz do
//SSE optimization?
lROIrealRA[lX+lZPos] := lROIrealRA[lX+lOrigZPos];
Application.ProcessMessages;
end; {no ROI on this slice}
end; {for n slices}
end; {not scaled} *)
lThreshComp := 1 - lThresh;
ImgForm.StatusLabel.caption := 'Smoothing slice data: Z-plane';
lI := 0;
for lZ := 1 to lZdim do begin
lMinZ := lZ - lCutoffVoxZ;
if lMinZ < 1 then lMinZ := 1;
lMaxZ := lZ + lCutoffVoxZ;
if lMaxZ > lZdim then lMaxZ := lZdim;
lScale := 1;
lMissing := (2*lCutOffVoxZ)-(lMaxZ-lMinZ);
if (lMissing >= 0) and (lMissing <= lCutOffVoxZ) then
lScale := lZCutRA^[lMissing];
if lThreshComp <> 1 then begin
if lResliceNotMask then begin
for lIncX := 1 to lcutoffvoxZ do
lZraScaled^[lcutoffvoxZ-lIncX] := lZra^[lIncX]*lScale;
for lIncX := 0 to lcutoffvoxZ do
lZraScaled^[lcutoffvoxZ+lIncX] := lZra^[lIncX]*lScale;
lZOffset := lcutoffvoxZ + lZ;
for lY := 1 to lYdim do begin
lyPos := (lY-1)*lXdim;
for lX := 1 to lXdim do begin
lCumGauss := 0;
lIncX := ((lMinZ-1)*lSliceSz)+lX+lYPos;
for lZt := lMinZ to lMaxZ do begin
lCumGauss := lCumGauss + lROIrealRA^[lIncX]*lZraScaled^[(lZoffset-lZt)];
lIncX := lIncX+ lSliceSz
//SSE optimization
//lCumGauss := lCumGauss + lROIrealRA[lX+lYPos+(lZt-1)*lSliceSz]*lZra[abs(lZ-lZt)]*lScale;
end;
inc(lI);
if (lCumGauss < (1-lThreshComp)) then
gBGImg.VOIUndoVol^[lI] := 100
else
gBGImg.VOIUndoVol^[lI] := 0;
end; {lX}
end; {lY}
end else begin //this is a mask -> unrolled loop means faster processing
for lY := 1 to lYdim do begin
lyPos := (lY-1)*lXdim;
for lX := 1 to lXdim do begin
lCumGauss := 0;
for lZt := lMinZ to lMaxZ do
lCumGauss := lCumGauss + lROIrealRA^[lX+lYPos+(lZt-1)*lSliceSz]*lZra^[abs(lZ-lZt)]*lScale;
inc(lI);
if lCumGauss > lThreshComp then
gBGImg.VOIUndoVol^[lI] := 0
else
gBGImg.VOIUndoVol^[lI] := 100;
end; {lX}
end; {lY}
end;
end else begin //threshcomp = 1 analogua output
for lY := 1 to lYdim do begin
lyPos := (lY-1)*lXdim;
for lX := 1 to lXdim do begin
lCumGauss := 0;
for lZt := lMinZ to lMaxZ do
//SSE optimization?
lCumGauss := lCumGauss + lROIrealRA^[lX+lYPos+(lZt-1)*lSliceSz]*lZra^[abs(lZ-lZt)]*lScale;
inc(lI);
gBGImg.VOIUndoVol^[lI] := round(200 * lCumGauss);
end; {lX}
end; {lY}
end; //threshcomp=1 analogue output
Application.ProcessMessages;
inc(lPlanes);
ImgForm.ProgressBar1.Position := lPlanes;
end; {lZ loop}
//lEndTime := GetTickCOunt;
// ImgForm.StatusLabel.caption :=('Smoothing time(ms): '+inttostr(lEndTime-lStartTime));
FreeMem (lROIrealRA);
FreeMem (lYOutRA);
Freemem(lXra);
Freemem(lYra);
Freemem(lZra);
Freemem(lZraScaled);
Freemem(lXCutra);
Freemem(lYCutra);
Freemem(lZCutra);
if (lThreshComp = 1) then begin //analogue output
//gGlMaxUnscaledS := 200;
//Scale.value := 0.0050000;
for lI := 1 to lImgSz do
gBGImg.VOIUndoVol^[lI] := 200 - gBGImg.VOIUndoVol^[lI];
end else begin //threshcomp <> 1
//gGlMaxUnscaledS := 100;
//Scale.value := 0.0100000;
for lI := 1 to lImgSz do
if gBGImg.VOIUndoVol^[lI] = 0 then
gBGImg.VOIUndoVol^[lI] := kVOI8bit
else
gBGImg.VOIUndoVol^[lI] := 0;
end; //Threshcomp <> 1 so digital output
lResliceNotMask := false;
gBGImg.VOIchanged := true;
ImgForm.ProgressBar1.Position := 0;
ImgForm.Undo1Click(nil); //show smoothed buffer
end;
procedure Tvoismoothform.FormCreate(Sender: TObject);
begin
XROIthresh.value := 0.5;
XROIfwhm.value := 8;
ScaleSides.ItemIndex := 0;
xROIoutput.ItemIndex := 0;
end;
procedure Tvoismoothform.BtnClick(Sender: TObject);
begin
if (Sender as TSpeedButton).tag = 1 then
SmoothOpenVOI(Sender);
voismoothform.Close;
end;
procedure Tvoismoothform.FormShow(Sender: TObject);
begin
// voismoothform.ModalResult := mrCancel;
end;
procedure VOIinvert;
var
lI,lImgSz: integer;
begin
lImgSz := gMRIcroOverlay[kVOIOverlayNum].ScrnBufferItems;
if lImgSz < 1 then exit;
CreateUndoVol;
Move(gMRIcroOverlay[kVOIOverlayNum].ScrnBuffer^,gBGImg.VOIUndoVol^,gBGImg.VOIUndoVolItems);
for lI := 1 to lImgSz do
if gBGImg.VOIUndoVol^[lI] = 0 then
gBGImg.VOIUndoVol^[lI] := 1
else
gBGImg.VOIUndoVol^[lI] := 0;
gBGImg.VOIchanged := true;
ImgForm.Undo1Click(nil); //show smoothed buffer
end;
procedure Tvoismoothform.SmoothVOI_SPM5masks;
var
lBGname,lmaskname,llesionname: string;
lorigFWHM ,
lorigThresh : single;
lorigSS,lOrigOut: integer;
begin
if not IsVOIOpen then begin
ShowMessage('You have not created or opened a region of interest.');
exit;
end;
lBGname := gMRIcroOverlay[kBGOverlayNum].HdrFileName;
if not gMRIcroOverlay[kBGOverlayNum].NIfTItransform then begin
//need to save BG as NIfTI
lBGName := ChangeFilePrefix(lBGname,'x');
SaveAsVOIorNIFTIcore(lBGName,gMRIcroOverlay[kBGOverlayNum].ImgBuffer,gMRIcroOverlay[kBGOverlayNum].ImgBufferItems,gMRIcroOverlay[kBGOverlayNum].ImgBufferBPP,1,gMRIcroOverlay[kBGOverlayNum].NiftiHdr);
end;
lmaskname := ChangeFilePrefix(lBGname,'m');
lmaskname := changefileextx(lmaskname, '.nii');
llesionname := ChangeFilePrefix(lBGname,'l');
llesionname := changefileextx(llesionname, '.nii');
if (fileexists(lmaskname)) or (fileexists(llesionname)) then begin
showmessage ('Files already exist named '+lmaskname+' '+llesionname);
exit;
end;
//init
lorigFWHM := XROIfwhm.value;
lorigThresh := XROIthresh.value;
lorigSS := voismoothform.ScaleSides.itemindex;
lorigOut := xROIoutput.itemindex;
//compute mask
//XROIfwhm.value := 8;
XROIfwhm.value := gBGImg.LesionDilate;
XROIthresh.value := 0.001;
ScaleSides.itemindex:=(1);
xROIoutput.itemindex:=(1);
if gBGImg.LesionDilate <= 0 then
VOIinvert
else
SmoothOpenVOI(nil);
if (gBGImg.VOIUndoSlice < 1) or (gBGImg.VOIUndoOrient <> 4) then begin //should be impossible - smoothVOI creates undovol
showmessage('Serious error.');
exit;
end;
ImgForm.StatusLabel.caption := 'Smoothed :'+lMaskName;
gMRIcroOverlay[kVOIOverlayNum].HdrFileName := lmaskname;
ImgForm.SaveVOIcore(false);//12/2010 //unmirrors image
//12/2010 SaveAsVOIorNIFTIcore (lmaskname, gMRIcroOverlay[kVOIOverlayNum].ScrnBuffer,gMRIcroOverlay[kVOIOverlayNum].ScrnBufferItems, 1,1,gMRIcroOverlay[kBGOverlayNum].NiftiHdr);
//compute lesion
UndoVolVOI;
XROIfwhm.value := gBGImg.LesionSmooth;
XROIthresh.value := 0.5;
//ScaleSides.setitemindex(0);
xROIoutput.itemindex:=(0);
SmoothOpenVOI(nil);
gMRIcroOverlay[kVOIOverlayNum].HdrFileName := llesionname;
ImgForm.SaveVOIcore(false);//12/2010 //unmirrors image
gMRIcroOverlay[kVOIOverlayNum].HdrFileName := lmaskname;
//SaveAsVOIorNIFTIcore (llesionname, gMRIcroOverlay[kVOIOverlayNum].ScrnBuffer,gMRIcroOverlay[kVOIOverlayNum].ScrnBufferItems, 1,1,gMRIcroOverlay[kBGOverlayNum].NiftiHdr);
//re-init
UndoVolVOI;
XROIfwhm.value := round(lorigFWHM);
XROIthresh.value := lorigThresh;
ScaleSides.itemindex:=(lOrigSS);
xROIoutput.itemindex:=(lOrigOut);
end;
initialization
{$I voismooth.lrs}
end.
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