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unit hdr;
interface
{$H+}
uses nifti_hdr,define_types,classes;
procedure MakeStatHdr (var lBGHdr,lStatHdr: TniftiHdr; lMinIntensity,lMaxIntensity,lIntent_p1,lIntent_p2,lIntent_p3: single; lIntent_code: smallint;lIntentName: string);
procedure MakeHdr (var lBGHdr,lStatHdr: TniftiHdr);
function NIFTIhdr_SaveHdrImg (var lFilename: string; var lHdr: TNIFTIHdr; lAllowOverwrite,lSPM2,lSingleFile: boolean;var lImg: SingleP; lnVol: integer): boolean;
function NIFTIhdr_SaveHdrImg8 (var lFilename: string; var lHdr: TNIFTIHdr; lAllowOverwrite,lSPM2,lSingleFile: boolean;var lImg: ByteP; lnVol: integer): boolean;
function Files4D (lFilename: string): boolean;
function Vol4D (lFilename: string): integer;
function FileExists4D (lFilename: string): boolean;
function Filename4D(lFilename: string): string;
function FilenameVol4D (lFilename: string; var lBaseName: string; var lVol: integer): boolean;
function NIFTIhdr_HdrVolumes (lFilenameIn: string): integer;
function BPP (lDataType: integer): integer;
function CreateDecompressed4D(var lImageNames: TStrings): string;
function CheckVoxels(var lHdrNameIn : string; lMaskVoxels, lImageNumber: integer):boolean;
//function CheckVoxelsGroupX(var lG: TStrings; lMaskVoxels: integer):boolean;
function CheckVoxelsGroupX(var lG: TStrings; lMaskHdr: TMRIcroHdr): boolean;
//function CheckVoxelsGroupY(var lG: TStrings):boolean;
procedure DeleteDecompressed4D(lDecomName: string);
implementation
uses
{$IFDEF FPC} gzio2,Controls,
{$ELSE} {gzio,ZLib,}DiskSpaceKludge,gziod,{$ENDIF}
{$IFNDEF UNIX}Windows, {$ENDIF}
Dialogs ,SysUtils,StatThdsUtil,npmform;
//define_types,GraphicsMathLibrary;
{$IFDEF FPC} {$mode objfpc}{$H+} {$ENDIF}
procedure MsgX (lStr: string);
begin
//msgx
end;
procedure DeleteDecompressed4D(lDecomName: string);
begin
if lDecomName = '' then
exit;
if not fileexists(lDecomName) then
exit;
sysutils.deletefile(lDecomName);
end;
function CheckVoxels(var lHdrNameIn : string; lMaskVoxels, lImageNumber: integer):boolean;
var
lHdr: TMRIcroHdr;
lHdrName: string;
lVox: integer;
begin
result := false;
lHdrName := Filename4D(lHdrNameIn);
if not NIFTIhdr_LoadHdr(lHdrName,lHdr) then begin
MainForm.NPMmsg('Unable to load image '+lHdrName);
exit;
end;
lVox := ComputeImageDataBytes8bpp(lHdr);
if lVox <> lMaskVoxels then begin
MainForm.NPMmsg('Voxels differ for '+lHdrName+' expected '+inttostr(lMaskVoxels)+' described '+inttostr(lVox));
exit;
end;
(*if (lHdr.NIFTIhdr.bitpix <> 8) and (lHdr.NIFTIhdr.datatype <> kDT_FLOAT) and (lHdr.NIFTIhdr.datatype <> kDT_SIGNED_INT) then begin
showmessage('Error: This software can only read uncompressed images that are either 8-bit integer or 32-bit real precision.');
exit;
end; //beta *)
if UpCaseExt(lHdrName) = '.HDR' then
lHdrName := changefileext(lHdrName,'.img');
if (not GzExt(lHdrName) ) and (FSize(lHdrName) < lMaskVoxels) then begin
showmessage('The uncompressed image data should be at least '+inttostr(lMaskVoxels)+' bytes. '+lHdrName);
exit;
end;
result := true;
//gBitPixRA[lImageNumber] := lHdr.NIFTIhdr.bitpix;
gDataTypeRA[lImageNumber] := lHdr.NIFTIhdr.datatype;
gOffsetRA[lImageNumber] := lHdr.NIFTIhdr.vox_offset;
gScaleRA[lImageNumber] := lHdr.NIFTIhdr.scl_slope;
gInterceptRA[lImageNumber] := lHdr.NIFTIhdr.scl_inter;
end;
(*function CheckVoxelsGroup(var lG: TStrings; lMaskVoxels: integer):boolean;
var
lC: integer;
lHdrName : string;
begin
result := false;
if lG.count < 1 then exit;
for lC := 1 to lG.count do begin
lHdrName:= lG[lC-1];
result := CheckVoxels(lHdrName, lMaskVoxels,lC);
end;
end;*)
(*function CheckVoxelsGroup(var lG: TStrings; lMaskVoxels: integer):boolean;
var
lC: integer;
lHdrName : string;
begin
result := false;
if lG.count < 1 then exit;
for lC := 1 to lG.count do begin
lHdrName:= lG[lC-1];
if not CheckVoxels(lHdrName, lMaskVoxels,lC) then begin
if not fileexists (lHdrName) then
MainForm.NPMmsg('File not found "'+lHdrName+'"')
else
MainForm.NPMmsg('Problem with "'+lHdrName+'" expected '+inttostr(lMaskVoxels));
exit;
end;
end;
result := true;
end;*)
function SameTransform (A,B:TNIFTIhdr): boolean;
var
lDim: integer;
begin
result := false;
for lDim := 0 to 3 do begin
if A.srow_x[lDim] <> B.srow_x[lDim] then
exit;
if A.srow_y[lDim] <> B.srow_y[lDim] then
exit;
if A.srow_z[lDim] <> B.srow_z[lDim] then
exit;
end;
result := true;
end;
function TransformTxt (A:TNIFTIhdr): string;
var
lDim: integer;
begin
result := '[';
for lDim := 0 to 3 do
result := result + ' '+floattostr(A.srow_x[lDim]);
result := result + ';';
for lDim := 0 to 3 do
result := result + ' '+floattostr(A.srow_y[lDim]);
result := result + ';';
for lDim := 0 to 3 do
result := result + ' '+floattostr(A.srow_z[lDim]);
result := result + ']';
end;
function CheckVoxelsX(var lHdrNameIn : string; lMaskHdr: TMRIcroHdr; lImageNumber: integer):boolean;
var
lHdr: TMRIcroHdr;
lHdrName: string;
lDim: integer;
begin
result := false;
lHdrName := Filename4D(lHdrNameIn);
if not NIFTIhdr_LoadHdr(lHdrName,lHdr) then begin
MainForm.NPMmsg('Unable to load image '+lHdrName+' Possible solution: make sure VAL file and images are in the same folder');
exit;
end;
(*lVox := ComputeImageDataBytes8bpp(lHdr);
lMaskVoxels := ComputeImageDataBytes8bpp(lMaskHdr);
if lVox <> lMaskVoxels then begin
MainForm.NPMmsg('Voxels differ for '+lHdrName+' expected '+inttostr(lMaskVoxels)+' described '+inttostr(lVox));
exit;
end; *)
for lDim := 1 to 3 do begin
if (lHdr.NIFTIhdr.dim[lDim] <> lMaskHdr.NIFTIhdr.dim[lDim]) then begin
MainForm.NPMmsg('Dimension '+inttostr(lDim)+' of '+lHdrName+' does not match '+lMaskHdr.HdrFileName);
exit;
end;
end;
if (not lHdr.NIfTItransform) then
MainForm.NPMmsg('Warning: no spatial transform for '+lHdrName+' (Analyze not NIfTI). Please ensure images are coregistered.')
else if (not lMaskHdr.NIfTItransform) then
MainForm.NPMmsg('Warning: no spatial transform for '+lMaskHdr.HdrFileName+' (Analyze not NIfTI). Please ensure images are coregistered.')
else begin
if not SameTransform (lHdr.NIFTIhdr, lMaskHdr.NIFTIhdr) then begin
MainForm.NPMmsg('Warning: spatial transforms differ for '+lHdrName+' and '+lMaskHdr.HdrFileName);
MainForm.NPMmsg(TransformTxt(lHdr.NIFTIhdr)+' <> '+ TransformTxt(lMaskHdr.NIFTIhdr));
end;
end;
(*if (lHdr.NIFTIhdr.bitpix <> 8) and (lHdr.NIFTIhdr.datatype <> kDT_FLOAT) and (lHdr.NIFTIhdr.datatype <> kDT_SIGNED_INT) then begin
showmessage('Error: This software can only read uncompressed images that are either 8-bit integer or 32-bit real precision.');
exit;
end; //beta *)
if UpCaseExt(lHdrName) = '.HDR' then
lHdrName := changefileext(lHdrName,'.img');
if (not GzExt(lHdrName) ) and (FSize(lHdrName) < (lHdr.NIFTIhdr.dim[1]*lHdr.NIFTIhdr.dim[2]*lHdr.NIFTIhdr.dim[3])) then begin
showmessage('The file size appears too small '+lHdrName);
exit;
end;
result := true;
//gBitPixRA[lImageNumber] := lHdr.NIFTIhdr.bitpix;
gDataTypeRA[lImageNumber] := lHdr.NIFTIhdr.datatype;
gOffsetRA[lImageNumber] := lHdr.NIFTIhdr.vox_offset;
gScaleRA[lImageNumber] := lHdr.NIFTIhdr.scl_slope;
gInterceptRA[lImageNumber] := lHdr.NIFTIhdr.scl_inter;
end;
function CheckVoxelsGroupX(var lG: TStrings; lMaskHdr: TMRIcroHdr):boolean;
var
lC: integer;
lHdrName : string;
begin
result := false;
if lG.count < 1 then exit;
for lC := 1 to lG.count do begin
lHdrName:= lG[lC-1];
if not CheckVoxelsX(lHdrName, lMaskHdr,lC) then begin
if not fileexists (lHdrName) then
MainForm.NPMmsg('File not found "'+lHdrName+'". Possible solution: make sure VAL file and images are in the same folder')
else
MainForm.NPMmsg('Problem with "'+lHdrName);
exit;
end;
end;
result := true;
end;
(*function CheckVoxelsGroupY(var lG: TStrings):boolean;
var
lMaskHdr: TMRIcroHdr;
lS: string;
begin
result := false;
if lG.count < 1 then exit;
lS := lG[0];
if not NIFTIhdr_LoadHdr(lS,lMaskHdr) then begin
MainForm.NPMmsg('Unable to load image '+lS);
exit;
end;
result := CheckVoxelsGroupX(lG,lMaskHdr);
end; *)
function BPP (lDataType: integer): integer;
begin
result := 0;
case lDataType of
kDT_UNSIGNED_CHAR: result := 1;
kDT_SIGNED_SHORT: result := 2; // signed short (16 bits/voxel)
kDT_SIGNED_INT : result := 4; // signed int (32 bits/voxel)
kDT_FLOAT : result := 4; // float (32 bits/voxel)
kDT_COMPLEX : result := 8; // complex (64 bits/voxel)
end;
end;
function NIFTIhdr_HdrVolumes (lFilenameIn: string): integer;
var
lFilename: string;
lHdr: TMRIcroHdr;
begin
result := 0;
lFilename := lFilenameIn;
if not NIFTIhdr_LoadHdr (lFilename, lHdr)then exit;
result := lHdr.niftiHdr.dim[4];
end;
function FileExists4D (lFilename: string): boolean;
var
lBaseName: string; var lVol: integer;
begin
FilenameVol4D (lFilename, lBasename,lVol);
result := fileexists(lBasename);
end;
function FilenameVol4D (lFilename: string; var lBaseName: string; var lVol: integer): boolean;
//4D files end with the image index number c:\dir\filename:1
//returns true if 4D file (with lVol = volume), otherwise returns false with lvol = 1
var
lLen,lP: integer;
lNumStr: string;
begin
lVol := 1;
lBasename := lFilename;
result := false;
lLen := length(lFilename);
if lLen < 1 then exit;
lP := lLen;
lNumStr := '';
while (lP > 0) and (lFilename[lP] in ['0'..'9']) do begin
lNumStr := lFilename[lP]+lNumStr;
dec(lP);
end;
//showmessage(lNumStr + '*'+lFilename[lP]);
if (lNumStr = '') or (lP < 2) or (lFilename[lP] <> ':') then exit;
lVol := strtoint(lNumStr);
lLen := lP -1;
lBasename := '';
for lP := 1 to lLen do
lBasename := lBasename + lFilename[lP];
result := true;
end;
function Filename4D(lFilename: string): string;
var lVol: integer;
begin
FilenameVol4D (lFilename, result,lVol);
end;
function Vol4D (lFilename: string): integer;
var
lBaseName: string;
begin
FilenameVol4D (lFilename, lBasename,result);
end;
function Files4D (lFilename: string): boolean;
var
lBaseName: string; var lVol: integer;
begin
result := FilenameVol4D (lFilename, lBasename,lVol);
end;
function CreateDecompressed4D(var lImageNames: TStrings): string;
//returns temp filename if all imagenames are a single compressed 4D datafile
//this means that a nii.gz file is only decompressed once, instead of once per volume*plank
var
lP: integer;
lFilename : string;
begin
result := '';
if lImageNames.Count < 2 then
exit;
if not Files4D(lImageNames.Strings[0]) then exit;
lFilename := Filename4D(lImageNames.Strings[0]);
if not Fileexists(lFilename) then
exit;
if not GzExt(lFilename) then
exit; //not a decompressed file
//see if single 4D image
for lP := 2 to lImageNames.Count do
if not Files4D(lImageNames.Strings[lP-1]) then
exit;
for lP := 2 to lImageNames.Count do
if lFilename <> Filename4D(lImageNames.Strings[lP-1]) then
exit;
//find unique filename for extracted file
result := lFilename +'.nii';
while fileexists(result) do //make sure we do not overwrite anything
result := lFilename +inttostr(random(9999))+'.nii';
//unzip
Msgx('Decompressing 4D image '+lFilename+ ' -> '+result);
Gunzip(lFilename,result);
//set image names to point to uncompressed volume
for lP := 1 to lImageNames.Count do
lImageNames.Strings[lP-1] := result +':'+inttostr(Vol4D(lImageNames.Strings[lP-1]) );
end;
procedure MakeStatHdr (var lBGHdr,lStatHdr: TniftiHdr; lMinIntensity,lMaxIntensity,lIntent_p1,lIntent_p2,lIntent_p3: single; lIntent_code: smallint;lIntentName: string);
var lIntentNameLen,lPos: integer;
lStr: string;
begin
move(lBGHdr,lStatHdr,sizeof(TniftiHdr));
with lStatHdr do begin
magic :=kNIFTI_MAGIC_SEPARATE_HDR;
bitpix := 32; //32-bit real data
datatype := kDT_FLOAT;
scl_slope:= 1;
scl_inter:= 0;
glmin := round(lMinIntensity);
glmax := round(lMaxIntensity);
intent_code := lIntent_Code;// kNIFTI_INTENT_ESTIMATE;
intent_p1 := lIntent_p1;
intent_p2 := lIntent_p2;
intent_p3 := lIntent_p3;
lIntentNameLen := length(lIntentName);
descrip[1] := 'N';
descrip[2] := 'P';
descrip[3] := 'M';
if lIntent_code=kNIFTI_INTENT_TTEST then begin
descrip[4] := 't' ;
lStr := inttostr(trunc(lIntent_p1));
for lPos := 1 to length (lStr) do
descrip[4+lPos] := lStr[lPos] ;
end else
descrip[4] := 'z';
if lIntentNameLen > sizeof(intent_name) then
lIntentNameLen := sizeof(intent_name);
if lIntentNameLen > 0 then
for lPos := 1 to lIntentNameLen do
intent_name[lPos] := lIntentName[lPos];
end;
end;
procedure SaveAsVOIorNIFTIcore (var lFilename: string; var lNiftiHdr: TNIFTIHdr; var lImg: SingleP; lnVolIn,lImgBufferBPP: integer);
const
kImgOffset = 352; //header is 348 bytes, but 352 is divisible by 8...
var
lHdr: TNIFTIhdr;
lBuff: ByteP;
lF: File;
lCompressedFilename,lExt: string;
lnVol,lC,lFSize: integer;
lImgBuffer: ByteP; lImgBufferItems{, lImgBufferBPP}: integer;
begin
lnVol := lnVolIn;
move(lNiftiHdr,lHdr,sizeof(lHdr));
lImgBufferItems := lHdr.dim[1]*lHdr.dim[2]*lHdr.dim[3];
//lImgBufferBPP:= 4;
lImgBuffer := ByteP(lImg);
lExt := UpCaseExt(lFileName);
if DiskFreeEx(lFilename) < (kImgOffset+(lImgBufferItems*lImgBufferBPP*lnVol)) then begin
case MessageDlg('Very little space on the selected drive. Attempt to save to this disk?', mtConfirmation,
[mbYes, mbCancel], 0) of
{$IFDEF FPC}mrCancel: exit; {$ELSE} id_Cancel: exit;{$ENDIF}
end; //case
end;
if FileExistsEX(lFileName) then begin
case MessageDlg('Overwrite the file named '+lFileName+'?', mtConfirmation,
[mbYes, mbCancel], 0) of
{$IFDEF FPC}mrCancel: exit; {$ELSE} id_Cancel: exit;{$ENDIF} //requires Uses Controls
end; //case
end; //file exists
if (lExt='.VOI') then begin
lHdr.intent_name[1] := 'B';//Binary
lHdr.scl_slope := 1/kVOI8bit;
lHdr.scl_inter := 0;
end;
if lnVol < 2 then begin
lHdr.dim[0] := 3;//3D july2006
lHdr.dim[4] := 1;//3D Aug 2007
lnVol := 1;
end else begin
lHdr.dim[0] := 4;//3D july2006
lHdr.dim[4] := lnVol;//3D july2006
end;
(*if not (lImgBufferItems = (lHdr.dim[1]*lHdr.dim[2]*lHdr.dim[3])) then begin //july2006
lHdr.sform_code := 1;
WriteNiftiMatrix ( lHdr, //must match MAGMA in nifti_hdr
gBGImg.ScrnMM[1],0,0,(gBGImg.ScrnOri[1]-1)*-gBGImg.ScrnMM[1],
0,gBGImg.ScrnMM[2],0,(gBGImg.ScrnOri[2]-1)*-gBGImg.ScrnMM[2],
0,0,gBGImg.ScrnMM[3],(gBGImg.ScrnOri[3]-1)*-gBGImg.ScrnMM[3]);
end;*)
if not IsNifTiMagic(lHdr) then begin
{lHdr.sform_code := 1;
WriteNiftiMatrix ( lHdr, //must match MAGMA in nifti_hdr
gBGImg.ScrnMM[1],0,0,(gBGImg.ScrnOri[1]-1)*-gBGImg.ScrnMM[1],
0,gBGImg.ScrnMM[2],0,(gBGImg.ScrnOri[2]-1)*-gBGImg.ScrnMM[2],
0,0,gBGImg.ScrnMM[3],(gBGImg.ScrnOri[3]-1)*-gBGImg.ScrnMM[3]);
}
end;
case lImgBufferBPP of
4: begin
lHdr.bitpix := 32;
lHdr.datatype := kDT_FLOAT;//note 32-bit integers saved internally as 32-bit float
end;
2: begin
lHdr.bitpix := 16;
lHdr.datatype := kDT_SIGNED_SHORT;
end;
1: begin
lHdr.bitpix := 8;
lHdr.datatype := kDT_UNSIGNED_CHAR;
//lHdr.scl_inter := lHdr.WindowScaledMin;
//lHdr.scl_slope := (lHdr.WindowScaledMax-lHdr.WindowScaledMin) /255;
end;
else begin
showmessage('Error: Unsupported bytes per voxel: '+inttostr(lImgBufferBPP));
exit;
end;
end;
if (lExt='.IMG') or (lExt ='.HDR') then begin
//done previously lHdr.magic := kNIFTI_MAGIC_SEPARATE_HDR;
lHdr.vox_offset := 0;
Filemode := 1;
//next write header data as .hdr
lFilename := changeFileExt(lFilename,'.hdr');
AssignFile(lF, lFileName);
Rewrite(lF,sizeof(TNIFTIhdr));
BlockWrite(lF,lHdr, 1);
CloseFile(lF);
//next write image data as .img
lFilename := changeFileExt(lFilename,'.img');
AssignFile(lF, lFileName); {WIN}
Rewrite(lF,lImgBufferItems*lImgBufferBPP*lnVol);
BlockWrite(lF,lImgBuffer^,1);
CloseFile(lF);
Filemode := 2;
exit;
end; //separate header
lHdr.magic := kNIFTI_MAGIC_EMBEDDED_HDR;
lHdr.vox_offset := kImgOffset;//352 bytes
lFSize := kImgOffset+(lImgBufferItems*lImgBufferBPP*lnVol);
getmem(lBuff,lFSize);
move(lHdr,lBuff^,sizeof(lHdr));
//Next: NIfTI 1.1 requires bytes 349..352 set to zero when no XML information
lC := kImgOffset;
lBuff^[lC-3] := 0;
lBuff^[lC-2] := 0;
lBuff^[lC-1] := 0;
lBuff^[lC] := 0;
lC := kImgOffset+1;
move(lImgBuffer^[1],lBuff^[lC],lImgBufferItems*lImgBufferBPP*lnVol);
if (lExt='.NII') then begin
Filemode := 1;
AssignFile(lF, lFileName);
Rewrite(lF,lFSize);
BlockWrite(lF,lBuff^,1);
CloseFile(lF);
Filemode := 2;
exit;
end; //uncompressed
if (lExt<>'.VOI') then
lCompressedFilename := changefileextX(lFilename,'.nii.gz')
else
lCompressedFilename := lFilename;
//FX(lFSize);
GZipBuffer(lCompressedFilename,lBuff,lFSize,false);
freemem(lBuff);
end;
procedure MakeHdr (var lBGHdr,lStatHdr: TniftiHdr);
//lIntent kNIFTI_INTENT_CHISQ lIntent_p1 = DOF
//lIntent kNIFTI_INTENT_ZSCORE no params
//lIntent kNIFTI_INTENT_TTEST lIntent_p1 = DOF
begin
move(lBGHdr,lStatHdr,sizeof(TniftiHdr));
with lStatHdr do begin
magic :=kNIFTI_MAGIC_SEPARATE_HDR;
bitpix := 32; //32-bit real data
datatype := kDT_FLOAT;
scl_slope:= 1;
scl_inter:= 0;
descrip[1] := 'X';//can not be npm
end;
end;
function NIFTIhdr_SaveHdrImg (var lFilename: string; var lHdr: TNIFTIHdr; lAllowOverwrite,lSPM2,lSingleFile: boolean;var lImg: SingleP; lnVol: integer): boolean;
var
lOutNameMod: string;
lSPM2output: boolean;
begin
lOutNameMod := lFilename;
lOutNameMod := changefileextX(lOutNameMod,'.hdr');
lSPM2output := lSPM2;
//fx(lHdr.srow_x[3],lHdr.srow_y[3],lHdr.srow_z[3]);
(*if not IsNifTiMagic(lHdr) then
lSPM2output := true;*)
if (lSingleFile) and (not lSPM2output) then begin
lHdr.magic := kNIFTI_MAGIC_EMBEDDED_HDR;
lOutNameMod := changefileextX(lOutNameMod,'.nii.gz');
end else if (not lSPM2output) then
lHdr.magic := kNIFTI_MAGIC_SEPARATE_HDR
else //the nifti_hdr reader converts the Analyze to NIfTI, so we need to save as NIfTI with NPM
lHdr.magic := kNIFTI_MAGIC_SEPARATE_HDR;
//lHdr.magic := 1984;
SaveAsVOIorNIFTIcore (lOutNameMod, lHdr, lImg,lnVol,4);
end;
function NIFTIhdr_SaveHdrImg8 (var lFilename: string; var lHdr: TNIFTIHdr; lAllowOverwrite,lSPM2,lSingleFile: boolean;var lImg: ByteP; lnVol: integer): boolean;
var
lOutNameMod: string;
begin
lOutNameMod := lFilename;
if IsVOIExt (lOutNameMod) then begin
lHdr.magic := kNIFTI_MAGIC_EMBEDDED_HDR;
end else begin
lOutNameMod := changefileextX(lOutNameMod,'.hdr');
if (lSingleFile) and (not lSPM2) then begin
lHdr.magic := kNIFTI_MAGIC_EMBEDDED_HDR;
lOutNameMod := changefileextX(lOutNameMod,'.nii.gz');
end else if (not lSPM2) then
lHdr.magic := kNIFTI_MAGIC_SEPARATE_HDR
else
lHdr.magic := 1984;
end;
SaveAsVOIorNIFTIcore (lOutNameMod, lHdr, SingleP(lImg),lnVol,1);
end;
end.
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