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unit clustering;
//USED by stats to select only regions with a given number of connected/contiguous voxels
interface
uses define_types,dialogs,SysUtils,nifti_hdr,nifti_img;
//procedure FindClusters (lMultiBuf: SingleP; lXdim, lYDim, lZDim, lThreshClusterSz: integer; lMinNeg, lMinPos: single);
function ClusterFilterScrnImg (var lHdr: TMRIcroHdr; lThreshClusterSz: integer; lThresh: double ): boolean;
implementation
procedure FindClusters (var lHdr: TMRIcroHdr; lXdim, lYDim, lZDim, lThreshClusterSz: integer; lThresh: double);
var
lThreshClusterSzM1,lScaledThresh,lClusterSign,lClusterSz,lClusterFillValue,lQTail,lQHead,lSliceSz,lQSz,lInc,lVolSz: integer;
lClusterBuff, lQra: LongIntP;
lBuffIn32 : SingleP;
lBuffIn16 : SmallIntP;
lScaledThreshFloat: double;
//lFdata: file;//abba - test
const
kFillValue = -2;
Procedure IncQra(var lVal, lQSz: integer);
begin
inc(lVal);
if lVal >= lQSz then
lVal := 1;
end;
procedure Check(lPixel: integer);
begin
//if lClusterFillValue = kFillvalue then showmessage(inttostr(lPixel)+'@');
if (lClusterBuff^[lPixel]=lClusterSign) then begin//add item
//if lClusterFillValue = kFillvalue then showmessage(inttostr(lPixel));
incQra(lQHead,lQSz);
inc(lClusterSz);
lClusterBuff^[lPixel] := lClusterFillValue;
lQra^[lQHead] := lPixel;
end;
end;
PROCEDURE RetirePixel; //FIFO cleanup , 1410: added 18-voxel check
VAR
lXDimM,lVal,lValX,lXPos,lYPos,lZPos: integer;
BEGIN
lVal := lQra^[lQTail];
if lVal = 0 then begin
//should never happen: unmarked voxel = increment lQTail so not infinite loop
incQra(lQTail,lQSz); //done with this pixel
exit;
end;
lXpos := lVal mod lXdim;
if lXpos = 0 then lXPos := lXdim;
lYpos := (1+((lVal-1) div lXdim)) mod lYDim;
if lYPos = 0 then lYPos := lYdim;
lZpos := ((lVal-1) div lSliceSz)+1;
if (lXPos <= 1) or (lXPos >= lXDim) or
(lYPos <= 1) or (lYPos >= lYDim) or
(lZPos <= 1) or (lZPos >= lZDim) then
// retire and exit
else begin
lXDimM := lXDim;
Check(lVal-1); //left
Check(lVal+1); //right
Check(lVal-lXDimM); //up
Check(lVal+lXDimM); //down
Check(lVal-lSliceSz); //up
Check(lVal+lSliceSz); //down
//check plane above
lValX := lVal + lSLiceSz;
Check(lValX-1); //left
Check(lValX+1); //right
Check(lValX-lXDimM); //up
Check(lValX+lXDimM); //down
//check plane below
lValX := lVal - lSLiceSz;
Check(lValX-1); //left
Check(lValX+1); //right
Check(lValX-lXDimM); //up
Check(lValX+lXDimM); //down
//check diagonals of current plane
Check(lVal-lXDimM-1); //up, left
Check(lVal-lXDimM+1); //up, right
Check(lVal+lXDimM-1); //down, left
Check(lVal+lXDimM+1); //down, right
end;{} //not edge
incQra(lQTail,lQSz); //done with this pixel
END;
procedure FillStart (lPt: integer); {FIFO algorithm: keep memory VERY low}
var lI: integer;
begin
if (lClusterBuff^[lPt]<>lClusterSign) then exit;
for lI := 1 to lQsz do
lQra^[lI] := 0;
lQHead := 0;
lQTail := 1;
Check(lPt);
RetirePixel;
// check that there was anything in the cluster at all
//showmessage('head'+inttostr(lQHead)+'.'+inttostr(lQTail));
//if lQHead > 2 then begin
// and do the recursion to get rid of it
while ((lQHead+1) <> lQTail) do begin//complete until all voxels in buffer have been tested
RetirePixel;
if (lQHead = lQSz) and (lQTail = 1) then
exit; //break condition: avoids possible infinite loop where QTail is being incremented but QHead is stuck at maximum value
end;
//end;
//showmessage('alldone');
end;
procedure SelectClusters (lSign: integer);
var lInc: integer;
begin
for lInc := 1 to lVolSz do begin
if lClusterBuff^[lInc] = lSign then begin
// measure size of the cluster and fill it with kFillValue
lClusterSz := 0;
lClusterSign := lSign;
lClusterFillValue := kFillValue;
FillStart(lInc);
// now fill the cluster with its size (=1 if the voxel was isolated)
lClusterFillValue := lClusterSz;
lClusterSign := kFillValue;
//if lClusterSz > 1 then ShowMessage(inttostr(lClusterSz)+'@'+inttostr(lInc));
if lClusterSz > 1 then
FillStart(lInc)
else
lClusterBuff^[lInc] := 1; //fill all voxels in cluster with size of voxel
end;
end;
end;
begin
lVolSz := lXdim*lYdim*lZdim;
lSliceSz := lXdim * lYdim;
if (lXDim < 4) or (lYDim < 4) or (lZDim < 4) or (lVolSz < 1) then exit;
GetMem(lClusterBuff, lVolSz* sizeof(LongInt));
for lInc := 1 to lVolSz do
lClusterBuff^[lInc] := 0;
if lHdr.ImgBufferBPP = 4 then begin
lBuffIn32 := SingleP(lHdr.ImgBuffer);
lScaledThreshFloat := Scaled2RawIntensity (lHdr, lThresh);
for lInc := 1 to lVolSz do
if lBuffIn32^[lInc] > lScaledThreshFloat then
lClusterBuff^[lInc] := 1;
lScaledThreshFloat := Scaled2RawIntensity (lHdr, -lThresh);
for lInc := 1 to lVolSz do
if lBuffIn32^[lInc] < lScaledThreshFloat then
lClusterBuff^[lInc] := -1;
end else if lHdr.ImgBufferBPP = 2 then begin //not 32bit - if 16bit input
lBuffIn16 := SmallIntP(lHdr.ImgBuffer);
lScaledThresh := round(Scaled2RawIntensity (lHdr, lThresh));
for lInc := 1 to lVolSz do
if lBuffIn16^[lInc] > lScaledThresh then
lClusterBuff^[lInc] := 1;
lScaledThresh := round(Scaled2RawIntensity (lHdr, -lThresh));
for lInc := 1 to lVolSz do
if lBuffIn16^[lInc] < lScaledThresh then
lClusterBuff^[lInc] := -1;
end else begin //not 16 or 32 bit input
lScaledThresh := round(Scaled2RawIntensity (lHdr, lThresh));
for lInc := 1 to lVolSz do
if lHdr.ImgBuffer^[lInc] > lScaledThresh then
lClusterBuff^[lInc] := 1;
lScaledThresh := round(Scaled2RawIntensity (lHdr, -lThresh));
for lInc := 1 to lVolSz do
if lHdr.ImgBuffer^[lInc] < lScaledThresh then
lClusterBuff^[lInc] := -1;
end; //8-bit input
lThreshClusterSzM1 := lThreshClusterSz;
if lThreshClusterSzM1 < 1 then
lThreshClusterSzM1 := 1;
if (lThreshClusterSzM1 > 1) then begin
//Next - START count cluster size
lQSz := (lVolSz div 4)+8;
GetMem(lQra,lQsz * sizeof(longint) );
//check positive clusters....
SelectClusters(1);
//Check negative clusters
SelectClusters(-1);
Freemem(lQra);
//END check clusters
end; //only count clusters if minimum size > 1, otherwise simple intensity threshold...
//NEXT: mask image data with cluster size
if lHdr.ImgBufferBPP = 4 then begin
lBuffIn32 := SingleP(lHdr.ImgBuffer);
for lInc := 1 to lVolSz do
if lClusterBuff^[lInc] < lThreshClusterSzM1 then
lBuffIn32^[lInc] := 0;
end else if lHdr.ImgBufferBPP = 2 then begin
lBuffIn16 := SmallIntP(lHdr.ImgBuffer);
for lInc := 1 to lVolSz do
if lClusterBuff^[lInc] < lThreshClusterSzM1 then
lBuffIn16^[lInc] := 0;
end else begin
for lInc := 1 to lVolSz do
if lClusterBuff^[lInc] < lThreshClusterSzM1 then
lHdr.ImgBuffer^[lInc] := 0;
end;
Freemem(lClusterBuff);
end;
function ClusterFilterScrnImg (var lHdr: TMRIcroHdr; lThreshClusterSz: integer; lThresh: double ): boolean;
var
lX,lY,lZ: integer;
begin
result := false;
lX := lHdr.NIFTIhdr.Dim[1];
lY := lHdr.NIFTIhdr.Dim[2];
lZ := lHdr.NIFTIhdr.Dim[3];
if (lHdr.ImgBufferItems < (lX*lY*lZ)) then
exit;
FindClusters (lHdr, lX, lY, lZ, lThreshClusterSz, lThresh);
result := true;
end;
end.
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