/
nifti.pas
executable file
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nifti.pas
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unit nifti;
{$IFDEF FPC}{$mode objfpc}{$H+}{$ENDIF}
//{$IFDEF FPC}{$mode delphi} {$H+}{$ENDIF}
{$DEFINE CUSTOMCOLORS}
interface
{$include opts.inc} //for DEFINE FASTGZ
{$DEFINE TIMER} //reports load times to stdout (Unix only)
{$IFDEF FPC}
{$DEFINE GZIP}
{$ENDIF}
//{$DEFINE PARALLEL} //for parallel Unix also edit CThreads in LPR file
{$DEFINE OPENFOREIGN} //used for q and s form as well as opening
{$DEFINE AFNI} //read Head/Brik statistics
{$IFNDEF OPENFOREIGN}{$IFDEF AFNI} error: AFNI requires OPENFOREIGN {$ENDIF} {$ENDIF}
{$DEFINE CPUGRADIENTS} //Computing volume gradients on the GPU is much faster than using the CPU
{$DEFINE CACHEUINT8} //save 8-bit data: faster requires RAM
{$DEFINE SSE}
{$DEFINE TIF} //load bitmaps, e.g. PNG, BMP, TIFFs not handled by NIfTI_TIFF
{$DEFINE BMP} //load bitmaps, e.g. PNG, BMP, TIFFs not handled by NIfTI_TIFF
{$DEFINE BZIP2}
//{$IFDEF MYTHREADS}
{$ModeSwitch nestedprocvars}
//{$ENDIF}
uses
//{$IFDEF UNIX}cthreads, cmem,{$ENDIF}
{$IFDEF AFNI}afni_fdr,{$ENDIF}
{$IFDEF BZIP2}bzip2stream,{$ENDIF}
{$IFDEF BMP} Graphics, GraphType,{$ENDIF}
{$IFDEF PARALLEL}mtprocs,mtpcpu,{$ENDIF}
{$IFDEF TIMER} DateUtils,{$ENDIF}
{$IFDEF FASTGZ}
{$IFDEF LIBDEFLATE}
libdeflate,
{$ENDIF}
SynZip,
{$ENDIF}
{$IFDEF OPENFOREIGN} nifti_foreign, {$ENDIF}
{$IFDEF CUSTOMCOLORS} colorTable, {$ENDIF}
{$IFDEF GZIP}zstream, umat, GZIPUtils, {$ENDIF} //Freepascal includes the handy zstream function for decompressing GZip files
{$IFDEF TIF} nifti_tiff, {$ENDIF}
{$IFDEF SSE}
{$IFDEF CPUAARCH64}
neon,
{$ELSE}
sse,
{$ENDIF}
{$ENDIF}
nifti_save,
sortu, strutils, dialogs, clipbrd, SimdUtils, sysutils,Classes, nifti_types, Math, VectorMath, otsuml;
//Written by Chris Rorden, released under BSD license
//This is the header NIfTI format http://nifti.nimh.nih.gov/nifti-1/
//NIfTI is popular in neuroimaging - should be compatible for Analyze format
// http://eeg.sourceforge.net/ANALYZE75.pdf
//NIfTI format images have two components:
// 1.) Header data provides image dimensions and details
// 2.) Image data
//These two components can be separate files: MRI.hdr, MRI.img
// or a single file with the header at the start MRI.nii
//Note raw image daya begins vox_offset bytes into the image data file
// For example, in a typical NII file, the header is the first 348 bytes,
// but the image data begins at byte 352 (as this is evenly divisible by 8)
(*const
kDTIno = -1; //this is NOT a DTI V1 image
kDTIscalar = 0; //this might be a DTI V1 image, but display as typical image
kDTIrgb = 1; //display as RGB V1 image
kDTIlines = 2; //display as lines *)
Type
TCluster = record
CogXYZ, PeakXYZ: TVec3; //Center of Gravity, Peak
Peak, SzMM3: single;
PeakStructure, Structure: string[248];
end;
TClusters = array of TCluster;
{$IFNDEF DYNRGBA}
TRGBA0 = array [0..MAXINT] of TRGBA;
TRGBAp = ^TRGBA0; //pointer to RGBA array
{$ENDIF}
TNIfTI = Class(TObject) // This is an actual class definition :
// Internal class field definitions - only accessible in this unit
private
fMat, fInvMat, fMatInOrient: TMat4;
fMin, fMax, fAutoBalMin, fAutoBalMax, fWindowMin, fWindowMax: single;
fOpacityPct: integer;
fScale, fCutoutLow, fCutoutHigh : TVec3;
fDim, fPermInOrient: TVec3i;
fHdr, fHdrNoRotation : TNIFTIhdr;
fKnownOrientation, fIsNativeEndian: boolean;
fFileName,fShortName, fBidsName: string;
{$IFDEF DYNRGBA}
fVolRGBA: TRGBAs;
{$ELSE}
fVolRGBA: TRGBAp;
{$ENDIF}
//fLabels: TStringList;
fhistogram: TLUT;
fisLinearReslice, fIsOverlay, fIsDrawing: boolean; //booleans do not generate 32-bit RGBA images
{$IFDEF CACHEUINT8}
fVolumesTotal, fVolumeDisplayed, fVolumesLoaded, fOpacityPctCache8: integer;
fWindowMinCache8, fWindowMaxCache8: single;
fCache8: TUInt8s;
{$ENDIF}
{$IFDEF CUSTOMCOLORS}
clut: TCLUT;
{$ELSE}
fLUT: TLUT;
{$ENDIF}
//init functions compute volume min/max and set default min/max brightness/contrast
procedure InitUInt8();
procedure InitInt16();
procedure InitFloat32();
procedure DetectV1();
//display functions apply windo min/max to generate image with desired brightness/contrast
procedure SetDisplayMinMaxRGB24();
//procedure SetDisplayMinMaxRGBV1();
procedure LoadRGBVector();
procedure DisplayLabel2Uint8();
//procedure SetDisplayMinMaxFloat32();
//procedure SetDisplayMinMaxInt16();
//procedure SetDisplayMinMaxUint8();
{$IFDEF PARALLEL}
//procedure SetDisplayMinMaxParallel(Index: PtrInt; Data: Pointer; Item: TMultiThreadProcItem);
{$ENDIF}
procedure ConvertUint16Int16();
procedure Convert2Float();
procedure Convert2RGB(); //convert RGBA -> RGB
procedure Convert2UInt8(); //convert int8 -> int16
procedure VolumeReslice(tarMat: TMat4; tarDim: TVec3i; isLinearReslice: boolean);
procedure VolumeReorient();
//procedure ApplyVolumeReorient(perm: TVec3i; outR: TMat4);
function OpenNIfTI(): boolean;
procedure MakeBorg(voxelsPerDimension: integer);
procedure initHistogram(Histo: TUInt32s = nil);
procedure ApplyCutout();
function loadForeign(FileName : AnsiString; var rawData: TUInt8s; var lHdr: TNIFTIHdr): boolean;// Load 3D data
function LoadRaw(FileName : AnsiString; out isNativeEndian: boolean): boolean;
//function SaveBVox(bVoxFileName: string; var hdr: TNIFTIhdr; var img8: TUInt8s): boolean;
//function SaveOsp(OspFileName: string; var hdr: TNIFTIhdr; var img8: TUInt8s): boolean;
//function SaveNii(niftiFileName: string): boolean; overload;
//function SaveFormatBasedOnExt(fnm: string; var hdr: TNIFTIhdr; var img8: TUInt8s): boolean; overload;
//function SaveNii(fnm: string; var hdr: TNIFTIhdr; var img8: TUInt8s): boolean; overload;
{$IFDEF GZIP}
//function SaveGz(niftiFileName: string; var hdr: TNIFTIhdr; var img8: TUInt8s): boolean;
{$IFDEF FASTGZ}function LoadFastGz(FileName : AnsiString; out isNativeEndian: boolean): boolean;{$ENDIF}
function LoadGz(FileName : AnsiString; out isNativeEndian: boolean): boolean;
{$ENDIF}
function skipVox(): int64; //if fVolumeDisplayed > 0, skip this many VOXELS for first byte of data
//function skipBytes(): int64; //if fVolumeDisplayed > 0, skip this many BYTES for first byte of data
//function skipRawVolBytes(): TUInt8s;
function VoiDescriptivesLabels(VoiRawBytes: TUInt8s): TStringList;
//function CenterOfMass(idx: integer; out sizeMM3: single): TVec3;
//procedure GenerateAtlasClusters8bit;
procedure GenerateAtlasClusters;
function rawAtlasMax: integer;
function mm3toVox(mm3: single) : integer; //e.g. if 3x3x3mm voxels (27mm) and input is 28, return 2
//procedure robustMinMax(var rMin, rMax: single);
public
RefreshCount: integer;
fLabels: TStringList;
fLabelMask: TUInt8s;
fRawVolBytes: TUInt8s;
LoadFewVolumes: boolean;
SortClustersBySize : boolean;
HiddenByCutout: boolean;
//fDTImode: integer; //kDTIno, kDTIscalar,kDTIrgb,kDTIlines
IsShrunken : boolean;
IsFightInterpolationBleeding: boolean;
IsInterpolated : boolean;
ZeroIntensityInvisible: boolean;
MaxTexMb: integer; //maximum number of voxels in any dimension
isAntiAliasHugeTexMb: boolean;
MaxMM: single; //maximum mm in any dimension
{$IFDEF AFNI}
afnis: TAFNIs;
{$ENDIF}
clusters: TClusters;
clusterNotes: string[128]; //interpolated, label map, etc
property InputReorientPermute: TVec3i read fPermInOrient;
property IsNativeEndian: boolean read fIsNativeEndian;
property VolumeDisplayed: integer read fVolumeDisplayed; //indexed from 0 (0..VolumesLoaded-1)
property VolumesLoaded: integer read fVolumesLoaded; //1 for 3D data, for 4D 1..hdr.dim[4] depending on RAM
property VolumesTotal: integer read fVolumesTotal; //1 for 3D data, for 4D 1..hdr.dim[4] depending on RAM
property KnownOrientation: boolean read fKnownOrientation;
{$IFDEF CUSTOMCOLORS}
function GetColorTable: TLUT;
//property ColorTable: TLUT read clut.fLUT write clut.fLUT;
function FullColorTable: TCLUTrec;
property CX: TCLUT read clut write clut;
{$ELSE}
property ColorTable: TLUT read fLUT write fLUT;
{$ENDIF}
//procedure SmoothMaskedImages();
property Drawing: boolean read fIsDrawing;
function AsFloats(): TFloat32s;
procedure SortClusters;
function NotZero(): TInt16s; //volume where voxels non-zero voxels are set to 1, voxels with intensity zero set to 0
function NeedsUpdate(): boolean;
function DisplayMinMax2Uint8(isForceRefresh: boolean = false): TUInt8s;
procedure SaveRotated(fnm: string; perm: TVec3i);
function RemoveSmallClusters(thresh, mm: double; NeighborMethod: integer = 1): single; //returns surviving mm3
function SaveCropped(fnm: string; crop: TVec6i; cropVols: TPoint): boolean;
function SaveAs8Bit(fnm: string; Lo,Hi: single): boolean;
function SaveRescaled(fnm: string; xFrac, yFrac, zFrac: single; OutDataType, Filter: integer; isAllVolumes: boolean): boolean;
procedure SaveAsSourceOrient(NiftiOutName: string; rawVolBytes: TUInt8s); overload;
procedure SaveAsSourceOrient(NiftiOutName, HdrDescrip, IntentName: string; rawVolBytes: TUInt8s; dataType: integer; intentCode: integer = 0; mn: single = 0; mx: single = 0);
function FracToSlice(Frac: TVec3): TVec3i; //given volume fraction return zero-indexed slice
function FracShiftSlice(Frac: TVec3; sliceMove: TVec3i): TVec3; //move a desired number of slices
function FracMM(Frac: TVec3): TVec3; //return mm coordinates given volume fraction
function MMFrac(MM: TVec3): TVec3; //return frac coordinates given volume mm
function VoiDescriptives(VoiRawBytes: TUInt8s): TStringList;
function VoxMM3: single; //voxel volume of resliced data
function VoxIntensityString(vox: int64): string; overload;
function VoxIntensityString(vox: TVec3i): string; overload;
function VoxIntensity(vox: int64): single; overload; //return intensity of voxel at coordinate
function VoxIntensity(vox: TVec3i): single; overload; //return intensity of voxel at coordinate
function VoxIntensityArray(vox: TVec3i): TFloat32s; overload;
function VoxIntensityArray(roi: TUInt8s): TFloat32s; overload;
function EdgeMap(isSmooth: boolean): TFloat32s;
function SeedCorrelationMap(vox: TVec3i; isZ: boolean): TFloat32s; overload;
function SeedCorrelationMap(roi: TUInt8s; isZ: boolean): TFloat32s; overload;
function SeedCorrelationMap(vSeed: TFloat32s; isZ: boolean): TFloat32s; overload;
property OpacityPercent: integer read fOpacityPct write fOpacityPct; //0=transparent, 50=translucent, 100=opaque
property Histogram: TLUT read fhistogram;
property VolumeMin: single read fMin; //darkest voxel in volume
property VolumeMax: single read fMax; //brightest voxel in volume
property SuggestedDisplayMin: single read fAutoBalMin;
property SuggestedDisplayMax: single read fAutoBalMax;
property DisplayMin: single read fWindowMin; //write warning: changes only isplayed if you call SetDisplayMinMax()
property DisplayMax: single read fWindowMax; //write warning: changes only isplayed if you call SetDisplayMinMax()
property Header: TNIFTIhdr read fhdr;
property HeaderNoRotation: TNIfTIhdr read fHdrNoRotation;
property Scale: TVec3 read fScale;
property ShortName: String read fShortName;
property Mat: TMat4 read fMat;
property InvMat: TMat4 read fInvMat;
property Dim: TVec3i read fDim;
{$IFDEF DYNRGBA}
property VolRGBA: TRGBAs read fVolRGBA;
{$IFDEF CPUGRADIENTS}
procedure CreateGradientVolume (rData: TRGBAs; Xsz,Ysz,Zsz: integer; out Vol : TRGBAs);
function GenerateGradientVolume: TRGBAs; overload;
{$ENDIF}
{$ELSE}
property VolRGBA: TRGBAp read fVolRGBA;
{$IFDEF CPUGRADIENTS}
procedure CreateGradientVolume (rData: TRGBAp; Xsz,Ysz,Zsz: integer; out Vol : TRGBAp);
function GenerateGradientVolume: TRGBAp; overload;
{$ENDIF}
{$ENDIF}
property VolRawBytes: TUInt8s read fRawVolBytes;
property Filename: String read fFileName;
property BidsName: String read fBidsName;
procedure Sharpen();
procedure Smooth(Mask: TUInt8s = nil);
procedure Mask(MaskingVolume: TUInt8s; isPreserveMask: boolean);
procedure RemoveHaze(isSmoothEdges: boolean = true; isSingleObject: boolean = true; OtsuLevels : integer = 5);
procedure GPULoadDone();
function SaveFormatBasedOnExt(fnm: string): boolean; overload; //filename determines format.nii, .tif, .bvox, .nrrd, .nhdr etc...
function Load(niftiFileName: string): boolean; overload;
function Load(niftiFileName: string; tarMat: TMat4; tarDim: TVec3i; isInterpolate: boolean; hdr: TNIFTIhdr; img: TFloat32s): boolean; overload;
function Load(niftiFileName: string; tarMat: TMat4; tarDim: TVec3i; isInterpolate: boolean; volumeNumber: integer = 0; isKeepContrast: boolean = false): boolean; overload;
procedure SetDisplayMinMax(newMin, newMax: single); overload;
procedure SetDisplayMinMax(isForceRefresh: boolean = false); overload;
procedure SetDisplayMinMaxNoUpdate(newMin, newMax: single); overload;
procedure SetCutoutNoUpdate(CutoutLow, CutoutHigh: TVec3);
procedure GenerateClusters(thresh, smallestClusterMM3: single; NeighborMethod: integer = 1; isDarkAndBright: boolean = false); overload;
//thresh, mm: double; NeighborMethod: integer
procedure GenerateClusters(LabelMap: TNIfTI; thresh, smallestClusterMM3: single; NeighborMethod: integer = 1; isDarkAndBright: boolean = false); overload;
function DisplayRGBGreen(): TUInt8s;
procedure DisplayRGB();
procedure SetDisplayColorScheme(clutFileName: string; cTag: integer);
procedure SetDisplayVolume(newDisplayVolume: integer);
//procedure SetLabelMask(Idx: integer; isMasked: boolean);
procedure ForceUpdate;
procedure SetClusters(c: TClusters; notes: string);
constructor Create(); overload; //empty volume
constructor Create(niftiFileName: string; backColor: TRGBA; tarMat: TMat4; tarDim: TVec3i; isInterpolate: boolean; hdr: TNIFTIhdr; img: TFloat32s); overload;
constructor Create(niftiFileName: string; backColor: TRGBA; lLoadFewVolumes: boolean; lMaxTexMb: integer; out isOK: boolean); overload; //background
constructor Create(niftiFileName: string; backColor: TRGBA; tarMat: TMat4; tarDim: TVec3i; isInterpolate: boolean; out isOK: boolean; lLoadFewVolumes: boolean = true; lMaxTexMb: integer = 640); overload; //overlay
constructor Create(tarMat: TMat4; tarDim: TVec3i); overload; //blank drawing
procedure SetIsLabels(b: boolean);
function IsLabels: boolean; //e.g. template map: should be drawn nearest neighbor (border of area 19 and 17 is NOT 18)
destructor Destroy; override;
end;
{$IFDEF CPUGRADIENTS}
{$IFDEF DYNRGBA}
procedure CreateGradientVolumeX (rData: TUInt8s; Xsz,Ysz,Zsz, isRGBA: integer; out VolRGBA : TRGBAs);
{$ELSE}
procedure CreateGradientVolumeX (rData: TUInt8s; Xsz,Ysz,Zsz, isRGBA: integer; out VolRGBA : TRGBAp);
procedure SetLengthP(var S: TRGBAp; Len: SizeInt);
{$ENDIF}
{$ENDIF}
function extractfileextX(fnm: string): string;
implementation
uses nifti_resize;
//uses reorient;
(*procedure TNIfTI.SetLabelMask(Idx: integer; isMasked: boolean);
var
i: integer;
begin
if fLabels.Count < 1 then exit;
if fLabelMask = nil then begin
SetLength(fLabelMask, fLabels.Count );
for i := 0 to fLabels.Count - 1 do
fLabelMask[i] := 0;
end;
end;*)
{$IFDEF CUSTOMCOLORS}
function TNIfTI.GetColorTable: TLUT;
begin
result := clut.LUT;
end;
{$ENDIF}
FUNCTION specialsingle (var s:single): boolean; inline;
//returns true if s is Infinity, NAN or Indeterminate
CONST kSpecialExponent = 255 shl 23;
VAR Overlay: LongInt ABSOLUTE s;
BEGIN
IF ((Overlay AND kSpecialExponent) = kSpecialExponent) THEN
RESULT := true
ELSE
RESULT := false;
END; //specialsingle()
procedure TNIfTI.SetClusters(c: TClusters; notes: string);
begin
clusterNotes := notes+ 'From AFNI: volume in voxels, peak intensity not reported';
setlength(clusters, length(c));
if length(c) < 1 then exit;
clusters := copy(c, 0, maxint);
end;
procedure Coord(var lV: TVec4; lMat: TMat4);
//transform X Y Z by matrix
var
lXi,lYi,lZi: single;
begin
lXi := lV[0]; lYi := lV[1]; lZi := lV[2];
lV[0] := (lXi*lMat[0,0]+lYi*lMat[0,1]+lZi*lMat[0,2]+lMat[0,3]);
lV[1] := (lXi*lMat[1,0]+lYi*lMat[1,1]+lZi*lMat[1,2]+lMat[1,3]);
lV[2] := (lXi*lMat[2,0]+lYi*lMat[2,1]+lZi*lMat[2,2]+lMat[2,3]);
end;
function voxelCenter(frac: single; dim: integer): single;
//if 3 voxels span 0..1 then centers are at 0.25/0.5/0.75 - voxels frac is 1/(n+1)
//if 4 voxels, centers 0.125, 0.375. 0.625. 0.875
// so val 0..0.33 will return 0.25
var
sliceFrac: double;
slice: integer;
begin
if (dim < 2) then exit(0.5);
sliceFrac := 1/dim;
slice := trunc(frac/sliceFrac);
if (slice >= dim) then slice := dim - 1; //e.g. frac 1.0 = top slice
if (slice < 0) then slice := 0; //only with negative fraction!
result := (sliceFrac * (slice+0.5));
end;
function frac2slice(frac: single; dim: integer): integer;
var
sliceFrac: double;
begin
if (dim < 2) then exit(0);
sliceFrac := 1/dim;
result := trunc(frac/sliceFrac);
if (result >= dim) then result := dim - 1; //e.g. frac 1.0 = top slice
if (result < 0) then result := 0; //only with negative fraction!
end;
function SliceMM(vox0: TVec3; Mat: TMat4): TVec3;
var
v4: TVec4;
begin
v4 := Vec4(vox0.x, vox0.y, vox0.z, 1.0); //Vec4(X-1,Y-1,Z-1, 1); //indexed from 0, use -1 if indexed from 1
Coord(v4, Mat);
result := Vec3(v4.x, v4.y, v4.z);
end;
function TNIfTI.skipVox(): int64;
begin
if (fVolumeDisplayed <= 0) or (fIsOverlay) then exit(0);
result := prod(fDim) * fVolumeDisplayed;
end;
procedure TNIfTI.ForceUpdate;
begin
fWindowMinCache8 := infinity;
end;
procedure TNIfTI.SetIsLabels(b: boolean);
var
i: smallint;
begin
//see todo in main unit
i := fHdr.intent_code;
if b then
fHdr.intent_code := kNIFTI_INTENT_LABEL
else if fHdrNoRotation.intent_code = kNIFTI_INTENT_LABEL then
fHdr.intent_code := kNIFTI_INTENT_NONE
else
fHdr.intent_code := fHdrNoRotation.intent_code;
if (i <> fHdr.intent_code ) then
fWindowMinCache8 := infinity; //force update
end;
function TNIfTI.IsLabels: boolean;
//return TRUE for neurolabels
begin
result := (fHdr.intent_code= kNIFTI_INTENT_LABEL);
end;
function TNIfTI.VoiDescriptivesLabels(VoiRawBytes: TUInt8s): TStringList;
const
kTab = chr(9);
var
i, j, nVox, nVoi, sumTotal : int64;
sumVois, sumVoisNot0: TUInt32s;
frac: single;
begin
result := TStringList.Create();
if fLabels.Count < 1 then exit;
nVox := length(VoiRawBytes);
nVoi := fLabels.Count;
if (nVox <> (dim.x * dim.y * dim.z)) then exit;
setlength(sumVois, nVoi);
setlength(sumVoisNot0, nVoi);
for i := 0 to (nVoi -1) do begin
sumVois[i] := 0;
sumVoisNot0[i] := 0;
end;
sumTotal := 0;
for i := 0 to (nVox -1) do begin
j := round(VoxIntensity(i));
if j = 0 then continue;
sumVois[j] := sumVois[j] + 1;
if (VoiRawBytes[i] = 0) then continue;
sumTotal := sumTotal + 1;
if (j >= nVox) then continue;
sumVoisNot0[j] := sumVoisNot0[j] + 1;
end;
result.Add('Background image: '+ShortName);
result.Add(format('Regions: ', [nVoi]));
result.Add(format('TotalVoxelsNotZero%s%d', [kTab, sumTotal]));
result.Add('Background image: '+ShortName);
result.Add('Index'+kTab+'Name'+kTab+'numVox'+kTab+'numVoxNotZero'+kTab+'fracVoxNotZero');
for i := 0 to (fLabels.Count -1) do begin
if sumVoisNot0[i] < 1 then continue;
if sumVois[i] < 1 then continue;
frac := sumVoisNot0[i] / sumVois[i];
if fLabels[i] = '' then
result.Add(format('%d%s<%d>%s%d%s%d%s%g', [i,kTab, i, kTab, sumVois[i], kTab, sumVoisNot0[i],kTab,frac]))
else
result.Add(format('%d%s"%s"%s%d%s%d%s%g', [i,kTab, fLabels[i], kTab, sumVois[i], kTab, sumVoisNot0[i],kTab,frac]));
end;
sumVois := nil;
sumVoisNot0 := nil;
end;
function RealToStr(lR: double {was extended}; lDec: integer): string;
begin
result := FloatToStrF(lR, ffFixed,7,lDec);
end;
function TNIfTI.VoiDescriptives(VoiRawBytes: TUInt8s): TStringList;
const
kTab = ' ';//chr(9);
var
x, y, z, lInc, i, nVox, nVoi : int64;
lROIVol: array [1..3] of int64;
lROISum,lROISumSqr,lROImin,lROImax:array [1..3] of double;
lCC,lVal,lSD,lROImean: double;
lLabelStr, lStr: string;
mm: TVec3;
procedure AddVal( lRA: integer);
begin
inc(lROIVol[lRA]);
lROISum[lRA] := lROISum[lRA]+lVal;
lROISumSqr[lRA] := lROISumSqr[lRA] + sqr(lVal);
if lVal > lROImax[lRA] then
lROImax[lRA] := lVal;
if lVal < lROImin[lRA] then
lROImin[lRA] := lVal;
end;//nested AddVal()
begin
if fLabels.Count > 0 then begin
result := VoiDescriptivesLabels(VoiRawBytes);
exit;
end;
lLabelStr := 'Drawing ';
result := TStringList.Create();
result.Add('Background image: '+ShortName);
nVox := length(VoiRawBytes);
if (nVox <> (dim.x * dim.y * dim.z)) then exit;
//center of mass
for i := 1 to 3 do
lROISum[i] := 0;
i := 0;
nVoi := 0;
for z := 0 to (dim.z-1) do
for y := 0 to (dim.y-1) do
for x := 0 to (dim.x-1) do begin
if (VoiRawBytes[i] > 0) then begin
nVoi := nVoi + 1;
lROISum[1] := lROISum[1] + x;
lROISum[2] := lROISum[2] + y;
lROISum[3] := lROISum[3] + z;
end;
i := i + 1;
end;
if (nVoi = 0) then begin
result.Add('Drawing empty');
exit;
end;
lROISum[1] := lROISum[1] / nVoi;
lROISum[2] := lROISum[2] / nVoi;
lROISum[3] := lROISum[3] / nVoi;
//mm := FracMM(Vec3(lROISum[1],lROISum[2],lROISum[3]));
result.Add('Drawing Center of mass XYZvox '+RealToStr(lROISum[1],2)+'x'+RealToStr(lROISum[2],2)+'x'+RealToStr(lROISum[3],2));
mm := SliceMM(Vec3(lROISum[1],lROISum[2],lROISum[3]), Mat);
result.Add('Drawing Center of mass XYZmm '+RealToStr(mm.x,2)+'x'+RealToStr(mm.y,2)+'x'+RealToStr(mm.z,2));
//statistics
for i := 1 to 3 do begin
lROIVol[i] := 0;
lROISum[i] := 0;
lROISumSqr[i] := 0;
lROImax[i] := NegInfinity;
lROImin[i] := Infinity;
end;
for i := 0 to (nVox -1) do begin
if (VoiRawBytes[i] = 0) then continue;
lVal := VoxIntensity(i);
AddVal(1);
if lVal <> 0 then
AddVal(2);
if lVal > 0 then
AddVal(3);
end;
result.Add('Background image: '+ShortName);
for lInc := 1 to 3 do begin
if lROIVol[lInc] > 1 then begin
lSD := (lROISumSqr[lInc] - ((Sqr(lROISum[lInc]))/lROIVol[lInc]));
if (lSD > 0) then
lSD := Sqrt ( lSD/(lROIVol[lInc]-1))
else
lSD := 0;
end else
lSD := 0;
//next compute mean
if lROIVol[lInc] > 0 then begin
lROImean := lROISum[lInc]/lROIVol[lInc];
end else begin //2/2008
lROImin[lInc] := 0;
lROImax[lInc] := 0;
lROImean := 0;
end;
lcc := ((lROIVol[lInc]/1000)*fHdr.pixdim[1]*fHdr.pixdim[2]*fHdr.pixdim[3]);
case lInc of
3: lStr := 'VOI >0 ';
2: lStr := 'VOI <>0 ';
else lStr := 'VOI ';
end;
lStr := lStr+' nvox(cc)=min/mean/max=SD: '+inttostr(round(lROIVol[lInc]))+kTab+RealToStr(lCC,2)+kTab+'='+kTab+RealToStr(lROIMin[lInc],4)+kTab+realToStr(lROIMean,4)+kTab+realToStr(lROIMax[lInc],4)+kTab+'='+kTab+realtostr(lSD,4);
result.Add(lLabelStr+ lStr);
end;
end;
function isStat(statCode: integer): boolean;
begin
result := (statCode = kFUNC_ZT_TYPE) or (statCode = kFUNC_TT_TYPE) or (statCode = kFUNC_FT_TYPE) or (statCode = kFUNC_CT_TYPE) ;
end;
function TNIfTI.VoxIntensityString(vox: int64): string; overload;//return intensity or label of voxel at coordinate
var
f, q : single;
i: integer;
begin
if fHdr.datatype = kDT_RGB then begin
i := vox * 3;
result := format('%d,%d,%d',[fRawVolBytes[i],fRawVolBytes[i+1],fRawVolBytes[i+2]]);
exit;
end;
f := VoxIntensity(vox);
{$IFDEF AFNI}
if (f <> 0) and (length(AFNIs) > 0) and (fVolumeDisplayed < length(AFNIs)) and (isStat(AFNIs[fVolumeDisplayed].jv) ) then begin
q := VoxelIntensity2q(AFNIs[fVolumeDisplayed].FDRcurv, f);
q := max(q, 0.0001);
result := format(' %3.6g (q<%.4f)', [f,q]);
exit;
end;
{$ENDIF}
if IsLabels then begin
i := round(f);
if (i >= 0) and (i < fLabels.Count) then
result := fLabels[i]
else
result := inttostr(i);//''; //todo
end else
result := format(' %3.6g', [f]);
end;
function TNIfTI.VoxIntensityString(vox: TVec3i): string; overload;//return intensity of voxel at coordinate
var
i: int64;
begin
i := vox.x + (vox.y * dim.x) + (vox.z * (dim.x * dim.y));
result := '';
if (i < 0) or (i >= (dim.x * dim.y * dim.z)) then exit;
result := VoxIntensityString(i);
end;
procedure printf (str: AnsiString);
begin
{$IFNDEF WINDOWS}
writeln(str);
{$ELSE}
if IsConsole then writeln(str);
{$ENDIF}
end;
//{$DEFINE FASTCORREL}
{$IFDEF FASTCORREL} //~10% faster, but may be less precise for large values.
function correl(var v: TFloat32s): double;
var
i, n: int64;
sum, mn: double;
begin
n := length(v);
if n < 2 then exit(0); //avoid div by zero
//compute mean for seed
sum := 0.0;
for i := 0 to (n - 1) do
sum := sum + v[i];
mn := sum / n;
result := 0.0;
for i := 0 to (n - 1) do begin
v[i] := (v[i]-mn);
result := result + sqr(v[i]);
end;
end;
function TNIfTI.SeedCorrelationMap(vox: TVec3i): TFloat32s;
//Based on Numerical Recipes. One suspects this might have poor precision for large values
// https://www.johndcook.com/blog/2008/11/05/how-to-calculate-pearson-correlation-accurately/
var
vx, nVx, vol, nVol, volBytes: int64;
vol8: TUInt8s;
vol16: TInt16s;
x, y, vol32: TFloat32s;
sxx, syy, sxy: double;
r: double;
{$IFDEF TIMER}StartTime: TDateTime;{$ENDIF}
begin
setlength(result, 0);
if IsLabels then exit;
if volumesLoaded < 2 then exit;
if fHdr.bitpix = 24 then exit;
{$IFDEF TIMER}startTime := now;{$ENDIF}
nVx := fHdr.Dim[1]*fHdr.Dim[2]*fHdr.Dim[3];
volBytes := nVx * (fHdr.bitpix shr 3);
nVol := length(fRawVolBytes) div volBytes;
if nVol <> fVolumesLoaded then exit;
vx := vox.x + (vox.y * dim.x) + (vox.z * (dim.x * dim.y));
if (vx < 0) or (vx >= nVx) then exit;
setlength(result, nVx);
setlength(x, nVol);
setlength(y, nVol);
vol8 := fRawVolBytes;
vol16 := TInt16s(vol8);
vol32 := TFloat32s(vol8);
//load values for seed
if fHdr.datatype = kDT_UINT8 then begin
for vol := 0 to (nVol - 1) do
x[vol] := vol8[vx + (vol * nVx)];
end else if fHdr.datatype = kDT_INT16 then begin
for vol := 0 to (nVol - 1) do
x[vol] := vol16[vx + (vol * nVx)];
end else if fHdr.datatype = kDT_FLOAT then begin
for vol := 0 to (nVol - 1) do
x[vol] := vol32[vx + (vol * nVx)];
end;
sxx := correl(x);
//compute correlation for each voxel
for vx := 0 to (nVx - 1) do begin
if fHdr.datatype = kDT_UINT8 then begin
for vol := 0 to (nVol - 1) do
y[vol] := vol8[vx + (vol * nVx)];
end else if fHdr.datatype = kDT_INT16 then begin
for vol := 0 to (nVol - 1) do
y[vol] := vol16[vx + (vol * nVx)];
end else if fHdr.datatype = kDT_FLOAT then begin
for vol := 0 to (nVol - 1) do
y[vol] := vol32[vx + (vol * nVx)];
end;
syy := correl(y);
sxy := 0.0;
for vol := 0 to (nVol-1) do
sxy := sxy + (x[vol] * y[vol]);
r := sxy / sqrt(sxx*syy);
result[vx] := r;
end;
{$IFDEF TIMER}printf(format('Correl time %d',[MilliSecondsBetween(Now,startTime)]));{$ENDIF}
end;
{$ELSE}
//{$DEFINE ONEPASSCORREL}
{$IFDEF ONEPASSCORREL}
function correl(var v: TFloat32s): double;
//stable one-pass method: extra divisions mean this is slower than 2 pass
//http://jonisalonen.com/2013/deriving-welfords-method-for-computing-variance/
//aka Welford’s method for computing variance
//https://www.strchr.com/standard_deviation_in_one_pass
var
i, n: int64;
sd, mn, delta: double;
begin
n := length(v);
if n < 2 then exit(0.0); //avoid div by zero
//compute mean for seed
sd := 0.0;
mn := v[0];
for i := 1 to (n - 1) do begin
delta := v[i] - mn;
mn := mn + delta / (i+1);
sd := sd + delta*(v[i]- mn);
end;
sd := sqrt(sd / (n - 1));
if (sd = 0.0) then exit; //no variance
sd := 1/sd;
for i := 0 to (n - 1) do
v[i] := (v[i]-mn)*sd;
result := sd;
end;
{$ELSE}
function correl(var v: TFloat32s): double;
var
i, n: int64;
sd, sum, mn: double;
begin
n := length(v);
if n < 2 then exit(0.0); //avoid div by zero
//compute mean for seed
sd := 0.0;
sum := 0.0;
for i := 0 to (n - 1) do
sum := sum + v[i];
mn := sum / n;
for i := 0 to (n - 1) do
sd := sd + sqr(v[i] - mn);
sd := sqrt(sd / (n - 1));
if (sd = 0.0) then exit(0.0); //no variance
sd := 1/sd;
for i := 0 to (n - 1) do
v[i] := (v[i]-mn)*sd;
result := sd;
end;
{$ENDIF}//ONEPASSCORREL
{$DEFINE FASTCORREL2}
{$IFDEF FASTCORREL2}
function correlR(var x, y: TFloat32s): single;
//assumes X already processed with correl()
// about 10% faster in practice than running correl() twice
var
i, n: int64;
r, sum, mn, sd: double;
begin
n := length(x);
if (n < 2) or (n <> length(y)) then exit(0.0); //avoid div by zero
sum := 0.0;
for i := 0 to (n - 1) do
sum := sum + y[i];
mn := sum / n;
sd := 0.0;
for i := 0 to (n - 1) do
sd := sd + sqr(y[i] - mn);
sd := sqrt(sd / (n - 1));
if (sd = 0) then exit(0.0);
sd := 1/sd;
r := 0.0;
for i := 0 to (n - 1) do begin
r := r + (x[i] * ((y[i]-mn)*sd));
end;
r := r / (n - 1);
exit(r);
end;
{$ENDIF} //FASTCORREL2
function TNIfTI.EdgeMap(isSmooth: boolean): TFloat32s;
//https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/programs/3dedge3_sphx.html
//https://en.wikipedia.org/wiki/Sobel_operator#Extension_to_other_dimensions
var
x, y, z, vx, nXYZ, nXY, nX, nY, nZ: int64;
llh, mlh, hlh, lmh, mmh, hmh, lhh, mhh, hhh, //voxel neighbors: slice above (high)
llm, mlm, hlm, lmm, hmm, lhm, mhm, hhm, //voxel neighbors: same slice (middle)
lll, mll, hll, lml, mml, hml, lhl, mhl, hhl, //voxel neighbors: slice below (low)
gx, gy, gz, mn, mx, unityScale: single;
vol8: TUInt8s;
vol16: TInt16s;
v, vol32: TFloat32s;
begin
setlength(result, 0);
if IsLabels then exit;
if fHdr.bitpix = 24 then exit;
nX := fHdr.Dim[1];
nY := fHdr.Dim[2];
nZ := fHdr.Dim[3];
if (nX < 3) or (nY < 3) or (nZ < 3) then exit;
nXY := nX * nY;
nXYZ := nXY * nZ;
setlength(result, nXYZ);
setlength(v, nXYZ);
vol8 := fRawVolBytes;
vol16 := TInt16s(vol8);
vol32 := TFloat32s(vol8);
if fHdr.datatype = kDT_UINT8 then begin
for vx := 0 to (nXYZ - 1) do
v[vx] := vol8[vx];
end else if fHdr.datatype = kDT_INT16 then begin
for vx := 0 to (nXYZ - 1) do
v[vx] := vol16[vx];
end else if fHdr.datatype = kDT_FLOAT then begin
for vx := 0 to (nXYZ - 1) do
v[vx] := vol32[vx];
end;
vx := -1;
for z := 1 to nZ do
for y := 1 to nY do
for x := 1 to nX do begin
vx += 1;
if (z = 1) or (z = nZ) or (y = 1) or (y = nY) or (x = 1) or (x = nX) then begin
result[vx] := 0.0;
continue;
end;
//slice above (high)
llh := v[vx - 1 - nX + nXY];
mlh := v[vx - 0 - nX + nXY] * 2;
hlh := v[vx + 1 - nX + nXY];
lmh := v[vx - 1 - 0 + nXY] * 2;
mmh := v[vx - 0 - 0 + nXY] * 4;
hmh := v[vx + 1 - 0 + nXY] * 2;
lhh := v[vx - 1 + nX + nXY];
mhh := v[vx - 0 + nX + nXY] * 2;
hhh := v[vx + 1 + nX + nXY];
//same slice (middle)
llm := v[vx - 1 - nX + 0] * 2;
mlm := v[vx - 0 - nX + 0] * 4;
hlm := v[vx + 1 - nX + 0] * 2;
lmm := v[vx - 1 - 0 + 0] * 4;
//mmm := v[vx - 0 - 0 + 0];
hmm := v[vx + 1 - 0 + 0] * 4;
lhm := v[vx - 1 + nX + 0] * 2;
mhm := v[vx - 0 + nX + 0] * 4;
hhm := v[vx + 1 + nX + 0] * 2;
//slice below (low)
lll := v[vx - 1 - nX - nXY];
mll := v[vx - 0 - nX - nXY] * 2;
hll := v[vx + 1 - nX - nXY];
lml := v[vx - 1 - 0 - nXY] * 2;
mml := v[vx - 0 - 0 - nXY] * 4;
hml := v[vx + 1 - 0 - nXY] * 2;
lhl := v[vx - 1 + nX - nXY];
mhl := v[vx - 0 + nX - nXY] * 2;
hhl := v[vx + 1 + nX - nXY];
gx := (hlh + hmh + hhh + hlm + hmm + hhm + hll + hml + hhl) - (llh + lmh + lhh + llm + lmm + lhm + lll + lml + lhl);
gy := (lhh + mhh + hhh + lhm + mhm + hhm + lhl + mhl + hhl) - (llh + mlh + hlh + llm + mlm + hlm + lll + mll + hll);
gz := (llh + mlh + hlh + lmh + mmh + hmh + lhh + mhh + hhh) - (lll + mll + hll + lml + mml + hml + lhl + mhl + hhl);
result[vx] += sqrt( sqr(gx) + sqr(gy) + sqr(gz));
end;
setlength(v, 0); //free memory
//scale 0..1
mn := infinity;
mx := -infinity;
for vx := 0 to (nXYZ - 1) do begin
if specialsingle(result[vx]) then continue;
mn := min(mn, result[vx]);
mx := max(mx, result[vx]);
end;
if (mn >= mx) then begin
setlength(result, 0);
exit;
end;
unityScale := 1.0 / (mx - mn);
for vx := 0 to (nXYZ - 1) do
result[vx] := unityScale * (result[vx] - mn);
end;
function TNIfTI.SeedCorrelationMap(vSeed: TFloat32s; isZ: boolean): TFloat32s; overload;
//https://www.johndcook.com/blog/2008/11/05/how-to-calculate-pearson-correlation-accurately/
var
vx, nVx, vol, nVol, volBytes: int64;
vol8: TUInt8s;
vol16: TInt16s;
v, vol32: TFloat32s;
r: double;
{$IFDEF TIMER}StartTime: TDateTime;{$ENDIF}
begin
setlength(result, 0);
if IsLabels then exit;
if volumesLoaded < 2 then exit;
if fHdr.bitpix = 24 then exit;
{$IFDEF TIMER}startTime := now;{$ENDIF}
nVx := fHdr.Dim[1]*fHdr.Dim[2]*fHdr.Dim[3];
volBytes := nVx * (fHdr.bitpix shr 3);
nVol := length(fRawVolBytes) div volBytes;
if nVol <> fVolumesLoaded then exit;
if length(vSeed) <> nVol then exit;
if (correl(vSeed) = 0.0) then exit; //no variance in seed
vol8 := fRawVolBytes;
vol16 := TInt16s(vol8);
vol32 := TFloat32s(vol8);
setlength(v, nVol);
setlength(result, nVx);
//compute correlation for each voxel
for vx := 0 to (nVx - 1) do begin
if fHdr.datatype = kDT_UINT8 then begin
for vol := 0 to (nVol - 1) do
v[vol] := vol8[vx + (vol * nVx)];
end else if fHdr.datatype = kDT_INT16 then begin
for vol := 0 to (nVol - 1) do
v[vol] := vol16[vx + (vol * nVx)];
end else if fHdr.datatype = kDT_FLOAT then begin
for vol := 0 to (nVol - 1) do
v[vol] := vol32[vx + (vol * nVx)];
end;
{$IFDEF FASTCORREL2} //FastCorrel2 about 10% faster
result[vx] := CorrelR(vSeed, v);
{$ELSE}
if (correl(v) = 0.0) then begin //no variance at this voxel
result[vx] := 0;
continue;
end;
r := 0.0;
for vol := 0 to (nVol - 1) do
r := r + (v[vol] * vSeed[vol]);
r := r / (nVol - 1);
result[vx] := r;
{$ENDIF}
end;
if isZ then begin
//https://www.statisticshowto.datasciencecentral.com/fisher-z/
//z’ = .5[ln(1+r) – ln(1-r)]
for vx := 0 to (nVx - 1) do begin
r := result[vx];
if (r >= 1.0) or (r <= -1.0) then
result[vx] := 10.0
else
result[vx] := 0.5 * ln((1+r)/(1-r));
//result[vx] := arctanh(r);
//result[vx] := 0.5 * (ln(1+r) - ln(1-r));
//Matlab check: these generate same values
// atanh(r)
// 0.5 * (log(1+r)-log(1-r))
// log((1+r)/(1-r))*0.5
//result[vx] := 0.5*(ln(1+r) – ln(1-r));
end;
end;
setlength(v, 0);
{$IFDEF TIMER}printf(format('Correl time %d',[MilliSecondsBetween(Now,startTime)]));{$ENDIF}
end;
//VolRawBytes: TUInt8s
function TNIfTI.SeedCorrelationMap(roi: TUInt8s; isZ: boolean): TFloat32s; overload;
//https://www.johndcook.com/blog/2008/11/05/how-to-calculate-pearson-correlation-accurately/
var
nROI, vx, nVx, vol, nVol, volBytes: int64;
vol8: TUInt8s;
vol16: TInt16s;
vSeed, vol32: TFloat32s;
begin
result := nil;
if IsLabels then exit;
if volumesLoaded < 2 then exit;
if fHdr.bitpix = 24 then exit;
nVx := fHdr.Dim[1]*fHdr.Dim[2]*fHdr.Dim[3];
volBytes := nVx * (fHdr.bitpix shr 3);
nVol := length(fRawVolBytes) div volBytes;
if nVol <> fVolumesLoaded then exit;
if nVx <> length(roi) then exit;
nROI := 0;
for vx := 0 to (nVx-1) do
if roi[vx] <> 0 then nROI := nROI + 1;
if (nROI < 1) then exit; //no images in mask
setlength(vSeed, nVol);
vol8 := fRawVolBytes;