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unit nii_3dto4d;
{$H+}
interface
uses
{$IFDEF FPC}gzio2,{$ENDIF}
SysUtils,define_types,dicomtypes,niftiutil,prefs,classes,dialogs_msg, nifti_types;
function Stack3Dto4D(var lStr: TStringList; lOverwrite: boolean; lPrefs: TPrefs): boolean;
function ExtractNIFTIHdrs(var lStr: TStringList): boolean;
implementation
uses dialogsx;
function LeadingZeroFilename (lInX: string): string;
var
lIn: string;
lC,lnPad,lPos,lnDec,lExtPos,lLen: integer;
begin
{$IFDEF Unix}
lIn := lInX;
{$ELSE}
lIn := Lowercase(lInX);
{$ENDIF}
lnPad := 8;
lLen := length(lIn);
result := lIn;
if lLen < 1 then exit;
lExtPos := 1;
while (lExtPos <= lLen) and (lIn[lExtPos] <> '.') do
inc(lExtPos);
if lExtPos <= 1 then
exit;
//lnDec := 0;
lPos := lExtPos -1;
while (lPos > 0) and ( lIn[lPos] in ['0'..'9']) do
dec(lPos);
lnDec := (lExtPos-lPos)-1;
if (lnDec = 0) or (lnDec >= lnPad) then
exit;
result := '';
if lPos > 0 then
for lC := 1 to lPos do
result := result + lIn[lC];
for lC := 1 to (lnPad-lnDec) do
result := result + '0';
for lC := (lPos+1) to lLen do
result := result+lIn[lC];
end;
procedure SortStrPadded (var lStr: TStringList);
//file1,file2...file10 not file1,file10..file2
//may be slow: not a great sorting algorithm
//may be inefficient: not sure if strings are exchanged or only pointers...
var counter, look:integer; temp:Tstrings;
begin
if lStr.Count < 2 then exit;
temp := TStringList.Create;
for counter:=0 to lStr.Count-1 do
temp.Append(LeadingZeroFilename{LowerCase}(lStr[counter]));
for counter:=0 to temp.Count-1 do
for look:=counter+1 to temp.Count-1 do
if temp[look]<temp[counter] then begin
lStr.Exchange(look, counter);
temp.Exchange(look,counter);
end;
temp.Free;
end;
function PasStr (lStr: string): string; //removes nulls
var
i: integer;
t: string;
begin
result := '';
for i := 1 to length(lStr) do begin
if (lStr[i] <> kDel) and(lStr[i] <> kTab) and (lStr[i] <> kEsc) and (lStr[i] <> chr(10)) and (lStr[i] <> chr (13)) and (ord(lStr[i]) <> 0) then
result := result + lStr[i];
end;
result := '"'+result +'"'
end;
function NIIstr (lFileName: string; lHdr : TNIFTIhdr): string;
begin
result := lFileName
+kTab+'XYZT'+kTab+inttostr(lHdr.Dim[1])+kTab+inttostr(lHdr.Dim[2])+kTab+inttostr(lHdr.Dim[3])+kTab+inttostr(lHdr.Dim[4])
+kTab+'XYZTmm'+kTab+floattostr(lHdr.PixDim[1])+kTab+floattostr(lHdr.PixDim[2])+kTab+floattostr(lHdr.PixDim[3])+kTab+floattostr(lHdr.PixDim[4])
+kTab+'Description'+kTab+PasStr(lHdr.descrip)
+kTab+'Data_Type'+kTab+PasStr(lHdr.Data_Type)
+kTab+'db_name'+kTab+PasStr(lHdr.db_name)
+kTab+'aux_file'+kTab+PasStr(lHdr.aux_file)
+kTab+'intent_name'+kTab+PasStr(lHdr.intent_name)
;
end;
function ExtractNIFTIHdrs(var lStr: TStringList): boolean;
var
lHdrName: string;
lHdr : TNIFTIhdr;
lByteSwap: boolean;
lVol,lnVol : integer;
lO: TNIIOpts;
begin
result := false;
lnVol := lStr.Count;
if lnVol < 1 then
exit;
SortStrPadded(lStr);
for lVol := 1 to lnVol do begin
lHdrName := lStr[lVol-1];
if not NIFTIhdr_LoadHdr (lHdrName, lHdr,lO) then
dcmMsg('Unable to find '+lHdrName)
else
dcmMsg(NIIstr(lHdrName,lHdr));
//dcmMsg( inttostr(lVol)+': '+lHdrName);
end;
end;
function Stack3Dto4D(var lStr: TStringList; lOverwrite: boolean; lPrefs: TPrefs): boolean;
//function Reorder4D(var lHdrName: string; var lHdr: TNIFTIhdr; lOverwrite: boolean; lPrefs: TPrefs): boolean;
label 123;
var
lOutBuffer,lIBuffer: byteP;
lInOffset,lnVol,l4DVolBytes,l3DVolBytes,lIn3DBytes,l4DBytes,lVol,lInPos,lOutPos,lSlice: integer;
lHdrName,lOutImgName: string;
lHdr1,lHdr2,lOutHdr : TNIFTIhdr;
lO: TNIIOpts;
lPrefs4D: TPrefs;
begin
result := false;
lnVol := lStr.Count;
if lnVol < 2 then begin
dcmMsg('Stack 3D to 4D requires >1 volume');
exit;
end;
SortStrPadded(lStr);
lHdrName := lStr[0];
NIFTIhdr_LoadHdr (lHdrName, lHdr1,lO);
for lVol := 1 to lnVol do begin
lHdrName := lStr[lVol-1];
if not NIFTIhdr_LoadHdr (lHdrName, lHdr2,lO) then begin
dcmMsg('Stack 3D to 4D unable to find '+lHdrName);
exit;
end;
if (lHdr1.dim[4] > 1) then begin
dcmMsg('Stack 3D to 4D aborted, image is already 4D: '+lHdrName );
exit;
end;
if (lHdr1.dim[1] <> lHdr2.dim[1]) or (lHdr1.dim[2] <> lHdr2.dim[2]) or
(lHdr1.dim[3] <> lHdr2.dim[3]) or (lHdr1.datatype <> lHdr2.datatype) then begin
dcmMsg('Stack 3D to 4D aborted, image dimensions/datatype vary '+lHdrName + ' <> '+lStr[0]);
exit;
end;
//dcmMsg( inttostr(lVol)+': '+lHdrName);
end;
lOutHdr := lHdr1;
lOutHdr.dim[4] := lnVol;
l3DVolBytes := lHdr1.dim[1]*lHdr1.dim[2]*lHdr1.dim[3]*(lHdr1.bitpix div 8);
l4DVolBytes := l3DVolBytes * lnVol;
GetMem(lOutBuffer,l4DVolBytes+kNIIImgOffset);
dcmMsg('Order in output file:');
lOutImgName := ChangeFilePrefix (lStr[0],'4D');
lOutPos := kNIIImgOffset + 1;
for lVol := 1 to lnVol do begin
lHdrName := lStr[lVol-1];
dcmMsg( inttostr(lVol)+': '+lHdrName);
if not NIFTIhdr_LoadImg (lHdrName, lHdr2, lIBuffer, lInOffset,lO) then begin
dcmMsg('3D -> 4D error loading image '+lHdrName);
goto 123;
end;
Move(lIBuffer^[lInOffset+1],lOutBuffer^[lOutPos],l3DVolBytes);
freemem(lIBuffer);
lOutPos := lOutPos + l3DVolBytes;
end;
lPrefs4D := lPrefs;
lPrefs4D.fourD := true;
dcmMsg('4D image '+lOutImgName);
if SaveNIfTICore (lOutImgName, lOutBuffer, kNIIImgOffset+1, lOutHdr, lPrefs4D) = '' then begin
dcmMsg('3D -> 4D Error');
goto 123;
end;
freemem(lOutBuffer);
result := true;
exit;
123:
freemem(lOutBuffer);
end;
(*function Reorder4D(var lHdrName: string; var lHdr: TNIFTIhdr; lByteSwap,lSPM2in,lSingleNIIFile,lGZ,lOverwrite: boolean): boolean;
var
lOutHdr: TNIFTIhdr;
lInName,lImgName: string;
lPos,lSlice,lVol,lInVolBytes,lSliceBytes: integer;
lBuffer: bytep;
lGZi,lSPM2: boolean;
lOutF,lInF: File;
begin
result := false;
lGZi := lGZ;
lSPM2 := lSPM2in;
if lSingleNIIFIle then
lSPM2 := false;
if (lHdr.dim[4] < 2) or (lHdr.dim[3] < 2) then
exit;
lOutHdr := lHdr;
lOutHdr.dim[4] := lHdr.dim[3];
lOutHdr.dim[3] := lHdr.dim[4];
lSliceBytes := lHdr.dim[1]*lHdr.dim[2]*(lHdr.bitpix div 8);
lInVolBytes := lSliceBytes*lHdr.dim[3];
GetMem(lBuffer,lSliceBytes);
if UpCaseExt(lHdrName) ='.HDR' then begin
if lOverwrite then
deletefile(lHdrName);
lInName := changefileext(lHdrName,'.img')
end else begin
lOutHdr.vox_offset := 352;
lInName := lHdrName;
end;
if not fileexists(lInName) then begin
dcmMsg('4Dclip Error: Unable to find '+lInName);
exit;
end;
if FSize (lInName) < ( (lInVolBytes*lHdr.dim[4])+round(lHdr.vox_offset)) then begin
dcmMsg('4Dclip Error: File smaller than expected (can not convert compressed) '+lInName);
exit;
end;
dcmMsg('Reordering image');
if not lSingleNiiFile then begin
lHdrName := changefileext(lHdrName,'.hdr');
lImgName := changefileext(lHdrName,'.img');
lGZi := false;
end else begin
lHdrName := changefileext(lHdrName,'.nii');
lImgName := changefileext(lHdrName,'.nii');
end;
if lOverwrite then begin
renamefile(lInName,changefileext(lInName,'.tmp'));
lInName := changefileext(lInName,'.tmp');
end else begin
lHdrName := ChangeFilePrefixExt (lHdrName,'x');
lImgName := ChangeFilePrefixExt (lImgName,'x');
dcmMsg('saving as '+lHdrName);
end;
AssignFile(lInF, lInName);
Reset(lInF,1);
Seek(lInF,round(lHdr.vox_offset));
SaveHdr (lHdrName,lOutHdr,lByteSwap{ false},lSPM2);
AssignFile(lOutF, lImgName);
if lSingleNIIFile then begin
Reset(lOutF,1);
Seek(lOutF,352);
end else
Rewrite(lOutF,1);
for lVol := 1 to lOutHdr.dim[4] do begin
lPos := ((lVol-1)*lSliceBytes) + round(lHdr.vox_offset);
for lSlice := 1 to lOutHdr.dim[3] do begin
Filemode := 0; //ReadONly
seek(lInF,lPos);
BlockRead(lInF, lBuffer^, lSliceBytes);
Filemode := 2;
BlockWrite(lOutF, lBuffer^, lSliceBytes);
lPos := lPos + lInVolBytes;
end;//for lslice
end; //for lvol
CloseFile(lInF);
CloseFile(lOutF);
Freemem(lBuffer);
if lOverwrite then
DeleteFile(lInName);
if lGZi then
GZipFile(lImgName,lImgName+'.gz',true);
result := true;
end; *)
(*function Clip4D(var lHdrName: string; var lHdr: TNIFTIhdr; lByteSwap,lSPM2in, lSingleNIIFile,lGZ,lOverwrite: boolean; lStartIn,lEndIn: integer ): string;
var
lOutHdr: TNIFTIhdr;
lInName,lImgName: string;
lVol,lVolBytes,lStart,lEnd: integer;
lBuffer: bytep;
lGZi,lSPM2 : boolean;
lOutF,lInF: File;
begin
result := '';
lGZi := lGZ;
lSPM2 := lSPM2in;
if lSingleNIIFIle then
lSPM2 := false;
lStart := lStartIn;
if lStart < 0 then
lStart := 0;
lEnd := lEndIn;
if lEnd < 0 then
lEnd := 0;
lOutHdr := lHdr;
lOutHdr.dim[4] := lOutHdr.dim[4]-lStart-lEnd;
if lOutHdr.dim[4] < 1 then
exit;
lVolBytes := lOutHdr.dim[1]*lOutHdr.dim[2]*lOutHdr.dim[3]*(lOutHdr.bitpix div 8);
GetMem(lBuffer,lVolBytes);
if UpCaseExt(lHdrName) ='.HDR' then begin
if lOverwrite then
deletefile(lHdrName);
lInName := changefileext(lHdrName,'.img')
end else begin
lOutHdr.vox_offset := 352;
lInName := lHdrName;
end;
if not fileexists(lInName) then begin
dcmMsg('4Dclip Error: Unable to find '+lInName);
exit;
end;
if FSize (lInName) < ( (lVolBytes*lHdr.dim[4])+round(lHdr.vox_offset)) then begin
dcmMsg('4Dclip Error: File smaller than expected (can not convert compressed) '+lInName);
exit;
end;
if (lStart > 0) or (lEnd > 0) then
dcmMsg('4D clip - removing first '+inttostr(lStart)+' and last '+inttostr(lEnd) +' volumes')
else
dcmMsg('Formatting image');
if not lSingleNiiFile then begin
lGZi := false;
lHdrName := changefileext(lHdrName,'.hdr');
lImgName := changefileext(lHdrName,'.img');
end else begin
lHdrName := changefileext(lHdrName,'.nii');
lImgName := changefileext(lHdrName,'.nii');
end;
if lOverwrite then begin
renamefile(lInName,changefileext(lInName,'.tmp'));
lInName := changefileext(lInName,'.tmp');
end else begin
lHdrName := ChangeFilePrefixExt (lHdrName,'x');
lImgName := ChangeFilePrefixExt (lImgName,'x');
dcmMsg('Saving clipped as '+lHdrName);
end;
AssignFile(lInF, lInName);
Reset(lInF,1);
Seek(lInF,round(lHdr.vox_offset));
SaveHdr (lHdrName,lOutHdr, lByteSwap{false},lSPM2);
AssignFile(lOutF, lImgName);
if lSingleNIIFile then begin
Reset(lOutF,1);
Seek(lOutF,352);
end else
Rewrite(lOutF,1);
for lVol := 1 to (lHdr.dim[4]-lEnd) do begin
//1st - save header
Filemode := 0; //ReadONly
BlockRead(lInF, lBuffer^, lVolBytes);
if (lVol > lStart) then begin
Filemode := 2;
BlockWrite(lOutF, lBuffer^, lVolBytes);
end;
end;
CloseFile(lInF);
CloseFile(lOutF);
Freemem(lBuffer);
if lOverwrite then
DeleteFile(lInName);
if lGZi then begin
lHdrName := lImgName+'.gz';
GZipFile(lImgName,lHdrName,true);
end;
result := lHdrName;
end;
function Convert4Dto3D(var lHdrName: string; var lHdr: TNIFTIhdr; lByteSwap, lSPM2in,lSingleNIIFile,lGZ: boolean ): boolean;
var
lOutHdr: TNIFTIhdr;
lOutName,lImgName: string;
lVol,lVolBytes: integer;
lBuffer: bytep;
lSPM2,lGZi: boolean;
lOutF,lInF: File;
begin
result := false;
lSPM2 := lSPM2in;
if lSingleNIIFIle then
lSPM2 := false;
lGZi := lGZ;
if lHdr.dim[4] < 2 then
exit;
lOutHdr := lHdr;
lOutHdr.dim[0] := 3;//3D
lOutHdr.dim[4] := 1;
lVolBytes := lOutHdr.dim[1]*lOutHdr.dim[2]*lOutHdr.dim[3]*(lOutHdr.bitpix div 8);
GetMem(lBuffer,lVolBytes);
//lSingleNIIFile := true;
if UpCaseExt(lHdrName) ='.HDR' then begin
//lSingleNIIFile := false;
lImgName := changefileext(lHdrName,'.img')
end else
lImgName := lHdrName;
if not fileexists(lImgName) then begin
dcmMsg('4D->3D Error: Unable to find '+lImgName);
exit;
end;
if FSize (lImgName) < ( (lVolBytes*lHdr.dim[4])+round(lHdr.vox_offset)) then begin
dcmMsg('4D->3D Error: File smaller than expected (can not convert compressed) '+lImgName);
exit;
end;
//dcmMsg(inttostr(round(lHdr.vox_offset)));
AssignFile(lInF, lImgName);
Reset(lInF,1);
Seek(lInF,round(lHdr.vox_offset));
if not lSingleNiiFile then begin
lGZi := false;
lHdrName := changefileext(lHdrName,'.hdr');
lImgName := changefileext(lHdrName,'.img');
end else begin
lHdrName := changefileext(lHdrName,'.nii');
lImgName := changefileext(lHdrName,'.nii');
end;
for lVol := 1 to lHdr.dim[4] do begin
//1st - save header
lOutName := AddFileNum(lVol,lHdr.dim[4],lHdrName);
SaveHdr (lOutName,lOutHdr,lByteSwap {false},lSPM2);
Filemode := 0; //ReadONly
BlockRead(lInF, lBuffer^, lVolBytes);
lOutName := AddFileNum(lVol,lHdr.dim[4],lImgName);
Filemode := 2;
AssignFile(lOutF, lOutName);
if (lSingleNIIFile) and (not lSPM2) then begin
Reset(lOutF,1);
Seek(lOutF,352);
end else
Rewrite(lOutF,1);
BlockWrite(lOutF, lBuffer^, lVolBytes);
CloseFile(lOutF);
if lGZi then begin
GZipFile(lOutName,lOutName+'.gz',true);
//DeleteFile(lOutName);
end;
end;
CloseFile(lInF);
Freemem(lBuffer);
//if lDeleteOrig then begin
DeleteFile(lHdrName);
if not lSingleNIIFile then
DeleteFile(lImgName);
//end;
end; *)
end.
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