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mesh.pas
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unit mesh;
{$Include opts.inc}
{$mode objfpc}{$H+}
interface
//{$DEFINE TIMER} //defined in opts.inc
{$DEFINE TREFOIL} //use Trefoil Knot as default object (instead of pyramid)
uses
//nifti_foreign,
{$IFDEF DGL} dglOpenGL, {$ELSE DGL} {$IFDEF COREGL}glcorearb, {$ELSE} gl, glext,{$ENDIF} {$ENDIF DGL}
{$IFDEF CTM} ctm_loader, {$ENDIF}
Classes, SysUtils, Forms, Controls, Graphics, Dialogs, strutils, DateUtils,
base64, zstream, LcLIntf, nifti_loader, colorTable, matmath, math,
define_types, nifti_types, fileutil;
const
kMinOverlayIndex = 1;
kMaxOverlays = 256;
kLUTinvisible = 0;
kLUTtranslucent = 50;
kLUTopaque = 100;
type
TSphere = packed record
X: single;
Y: single;
Z: single;
Clr: single;
Radius: single;
end;
TOverlay = record
LUTinvert, AOmap: boolean;
PaintMode: integer;
OpacityPercent: integer;
//LUTvisible: integer; //0=invisible, 1=translucent, 2=opaque
LUTindex,atlasMaxIndex, volumes, CurrentVolume : integer;
LUT: TLUT;
minIntensity, maxIntensity, windowScaledMin, windowScaledMax: single;
filename: string;
isBinary: boolean;
intensity: TFloats;
//next: if loaded as mesh...
faces : TFaces;
vertices: TVertices;
vertexRGBA : TVertexRGBA; //array of TRGBA;
vertexAtlas: TInts; //what atlas regions does this vertex belong to, e.g. [7, 8, 17...] the 3rd vertex belongs to region 17
atlasTransparentFilter: TBools;
atlasHideFilter: TInts; //atlas show these atlas regions, e.g. if [7, 8, 22] then only regions 7,8 and 22 will be visible
end;
TNodePrefs = record //preferences for nodes
minEdge, maxEdge, maxEdgeAbs, minEdgeThresh, maxEdgeThresh, minNodeColor, maxNodeColor, minNodeSize, maxNodeSize,
minNodeThresh, maxNodeThresh, scaleNodeSize, scaleEdgeSize, thresholdNodeFrac: single;
nodeLUTindex , edgeLUTindex: integer;
isNodeThresholdBySize, isNoNegEdge, isNoPosEdge, isNoLeftNodes,isNoRightNodes,isNoNodeWithoutEdge, isNodeColorVaries, isEdgeColorVaries, isEdgeSizeVaries, isEdgeShowNeg, isEdgeShowPos : boolean;
layerName: array[0..kMaxOverlays] of string[32];
end;
type
TMesh = class
scale, vertexRgbaSaturation, vertexRgbaAlpha : single;
origin, mxV, mnV : TPoint3f;
nFacesOverlay, nFaces: integer;
{$IFDEF COREGL}
vao, vbo, vaoOverlay, vboOverlay: GLuint;
{$ELSE}
{$IFDEF LEGACY_INDEXING}
index_vbo, vertex_vbo, index_vboOverlay, vertex_vboOverlay: GLuint;
{$ELSE}
displayList, displayListOverlay : GLuint;
{$ENDIF}
{$ENDIF}
isZDimIsUp, isRebuildList, isBusy, isNode, isFreeSurferMesh, isVisible, isAdditiveOverlay : boolean;
OpenOverlays, OverlayTransparency, AtlasMaxIndex : integer;
overlay: array [kMinOverlayIndex..kMaxOverlays] of TOverlay;
nodes: array of TSphere;
edges: array of array of Single;
edgeLayers: array of single;
faces : array of TPoint3i;
vertices: array of TPoint3f;
vertexRGBA : array of TRGBA;
vertexAtlas: TInts; //what atlas regions does this vertex belong to, e.g. [7, 8, 17...] the 3rd vertex belongs to region 17
atlasTransparentFilter: TBools;
atlasHideFilter: TInts; //atlas show these atlas regions, e.g. if [7, 8, 22] then only regions 7,8 and 22 will be visible
tempIntensityLUT : TFloats; //only used to load without external files - flushed after LoadOverlay
shortName, errorString: string;
//overlay: array of single;
private
//procedure DBug();
function FindBorderVertices(): TUInt8s;
function CheckMesh: boolean;
function CheckNodes: boolean;
function CheckEdges: boolean;
procedure SetOverlayDescriptives(lOverlayIndex: integer);
procedure MinMaxPct(lOverlayIndex, num_v: integer; var mx, mn: single; isExcludeZero: boolean);
procedure SetDescriptives;
{$IFDEF TREFOIL} procedure MakeTrefoil; {$ENDIF}
procedure MakeSphere;
function SetLutIndex(layer:integer): integer;
procedure BuildListCore(Clr: TRGBA; var f: TFaces; var v: TVertices; var vtxRGBA: TVertexRGBA; vRemap: TInts = nil; isWriteToGPU: boolean = true);
//procedure BuildListCore(Clr: TRGBA; var f: TFaces; var v: TVertices; var vtxRGBA: TVertexRGBA; vRemap: TInts = nil);
procedure BuildListPartialAtlas(Clr: TRGBA; vtxRGBA: TVertexRGBA);
procedure BuildList(Clr: TRGBA);
procedure FilterOverlay(c: integer; var f: TFaces; var v: TVertices; var vRGBA: TVertexRGBA);
procedure BuildListOverlay(Clr: TRGBA);
function Load1D(const FileName: string; lOverlayIndex: integer): boolean;
function Load3Do(const FileName: string): boolean;
function Load3ds(const FileName: string): boolean;
function LoadAc(const FileName: string): boolean;
function LoadByu(const FileName: string): boolean;
function LoadAnnot(const FileName: string): boolean;
function LoadNiml(const FileName: string): boolean;
function LoadNimlNodeEdge(const FileName: string): boolean;
function loadCifti(fnm: string; lOverlayIndex, lSeriesIndex: integer; isLoadCortexLeft: boolean): integer;
function LoadDae(const FileName: string): boolean; //only subset!
function LoadDfs(const FileName: string): boolean;
function LoadDxf(const FileName: string): boolean;
function LoadGcs(const FileName: string): boolean;
function LoadGii(const FileName: string; lOverlayIndex, lOverlayItem: integer; var HasOverlays: boolean): integer;
function LoadGts(const FileName: string): boolean;
function LoadIdtf(const FileName: string): boolean;
function LoadJson(const FileName: string): boolean;
function LoadLwo(const FileName: string): boolean;
function LoadMesh(const FileName: string): boolean;
function LoadMeshAscii(const FileName: string): boolean;
function LoadVoxel2Vertex(const FileName: string; lOverlayIndex: integer): boolean;
function LoadMs3d(const FileName: string): boolean;
//function LoadVbo(const FileName: string): boolean;
function LoadMz3(const FileName: string; lOverlayIndex : integer): boolean;
function LoadPrwm(const FileName: string): boolean;
function LoadObjMni(const FileName: string): boolean;
function LoadOff(const FileName: string): boolean;
function LoadOffBin(const FileName: string): boolean;
function LoadPly2(const FileName: string): boolean;
function CullUnusedVertices(): boolean;
function LoadSrf(const FileName: string): boolean;
function LoadSurf(const FileName: string): boolean;
function LoadTri(const FileName: string): boolean;
function LoadVrml(const FileName: string): boolean;
function LoadWfr(const FileName: string): boolean; //EMSE wireframe
function LoadAsc_Srf(const FileName: string): boolean;
function LoadAsc_Sparse(const FileName: string): boolean;
procedure LoadCtm(const FileName: string);
function LoadDpv(const FileName: string; lOverlayIndex: integer): boolean;
function LoadCol(const FileName: string; lOverlayIndex, lOverlayItem: integer): integer; //AFNI https://afni.nimh.nih.gov/afni/community/board/read.php?1,44391,44410
function LoadAtlasMapCore(lOverlayIndex: integer; intensityLUT: TFloats): string;
function LoadAtlasMap(const FileName: string; lOverlayIndex: integer): boolean;
procedure LoadCurv(const FileName: string; lOverlayIndex: integer);
procedure LoadMeshAsOverlay(const FileName: string; lOverlayIndex: integer);
procedure LoadNii(const FileName: string; lOverlayIndex: integer; lLoadSmooth: boolean);
procedure Overlay2Atlas();
function LoadCluster(const FileName: string): boolean;
function LoadNodeTxt(const FileName: string): boolean;
procedure LoadNode(const FileName: string; out isEmbeddedEdge: boolean);
procedure LoadNv(const FileName: string);
procedure LoadObj(const FileName: string);
//procedure LoadFreeSurferQuad(const FileName: string);
procedure LoadPial(const FileName: string);
procedure LoadPly(const FileName: string);
procedure LoadStl(const FileName: string);
procedure LoadStlAscii(const FileName: string);
function LoadVtkTxt(const FileName: string):boolean;
procedure LoadVtk(const FileName: string);
procedure LoadW(const FileName: string; lOverlayIndex: integer);
public
bilateralOffset: single;
nodePrefs: TNodePrefs;
isBilateral: boolean;
OverlappingOverlaysOverwrite: boolean;
procedure MakePyramid;
function SetEdgeLayer(layer: integer): boolean;
//function AtlasStatMapCore(AtlasName, StatName: string; Indices: TInts; Intensities: TFloats): string;
//function AtlasMaxIndex: integer;
procedure DrawGL (Clr: TRGBA; clipPlane: TPoint4f; isFlipMeshOverlay: boolean);
procedure Node2Mesh;
procedure ReverseFaces;
procedure CenterOrigin;
procedure SwapYZ;
procedure SwapZY;
function LoadFromFile(const FileName: string): boolean;
function LoadEdge(const FileName: string; isEmbeddedEdge: boolean): boolean;
function LoadOverlay(const FileName: string; lLoadSmooth: boolean): boolean;
procedure LoadDummyOverlay(layer: integer; ov: TOverlay);
procedure CloseOverlaysCore;
procedure CloseOverlays;
function Contours(OverlayIndex: integer): boolean;
function Mesh2Node(const FileName: string; isAppend: boolean = true):boolean;
function Atlas2Node(const FileName: string; isAppend: boolean = true):boolean;
procedure Close;
constructor Create;
(*procedure SaveVrml(const FileName: string; MeshColor: TColor = clWhite);
procedure SaveMz3(const FileName: string; MeshColor: TColor = clWhite);
procedure SaveGii(const FileName: string);
procedure SaveObj(const FileName: string);
procedure SavePly(const FileName: string; MeshColor: TColor = clWhite);*)
procedure SaveMesh(const FileName: string; MeshColor: TColor = clWhite);
procedure SaveOverlay(const FileName: string; OverlayIndex: integer);
destructor Destroy; override;
end;
function isNimlNodes(fnm: string): boolean;
implementation
uses
mainunit, {$IFDEF FASTGZ}SynZip, {$ENDIF}
meshify_simplify,shaderu, {$IFDEF COREGL} gl_core_3d {$ELSE} gl_legacy_3d {$ENDIF};
procedure printf(s: string);
begin
{$IFDEF UNIX}writeln(s);{$ENDIF}
end;
procedure ShowMessageX(str: string);
begin
printf(str);
showmessage(str);
end;
function isNimlNodes(fnm: string): boolean;
//some .niml.dset are per-vertex scalars, others are node maps, the latter have "Graph_Bucket_data"
label
123;
var
f: TextFile;
st: string;
begin
result := false;
AssignFile(f, fnm);
FileMode := fmOpenRead;
reset(f);
while not eof(f) do begin
readln(f, st);
if (AnsiContainsText(st, '"Graph_Bucket"')) then begin
result := true;
goto 123;
end;
if (AnsiContainsText(st, '"Node_Bucket"')) or (AnsiContainsText(st, '"Node_Label"')) or (AnsiContainsText(st, '>')) then
goto 123;
end;
123:
closefile(f);
end;
(*function TMesh.Atlas2Node(const FileName: string):boolean;
const
kT = chr(9);
label
123;
var
xROI, yROI, zROI, maxRoiDxIdx, nVert, maxROI, nFace, roi, nroiEdges, nroiVerts, nCOGs: integer;
roiEdges, roiVerts: TInts;
isEdge, isVert: TInts;
roiDx, maxRoiDx: double;
COGs: array of TPoint4f; //center of gravity
j, i : integer;
txt: TextFile;
begin
result := false;
nVert := length(vertices);
nFace := length(faces);
maxROI := AtlasMaxIndex;
if (nFace < 1) or (nVert < 3) or (maxROI < 1) or (length(vertexAtlas) <> nVert) then exit;
setlength(COGs, maxROI+1);
setlength(roiEdges, nVert); //list of vertices on edge of ROI
setlength(roiVerts, nVert); //list all vertices in ROI
setlength(isEdge, nVert);
setlength(isVert, nVert);
for i := 0 to maxROI do
COGs[i] := pt4f(0,0,0,0);
nCOGs := 0;
for roi := 0 to maxROI do begin
nroiEdges := 0;
for i := 0 to nVert -1 do begin
isEdge[i] := 0;
isVert[i] := 0;
end;
//fillChar(isEdge,sizeOf(isEdge),0);
//fillChar(isVert,sizeOf(isVert),0);
for i := 0 to (nFace-1) do begin
xROI := vertexAtlas[Faces[i].X];
yROI := vertexAtlas[Faces[i].Y];
zROI := vertexAtlas[Faces[i].Z];
if (xROI <> roi) and (yROI <> roi) and (zROI <> roi) then continue; //this vertex not member of ROI
//roiVerts[nroiVerts] := i;
if (xROI = roi) then isVert[Faces[i].X] := 1;
if (yROI = roi) then isVert[Faces[i].Y] := 1;
if (zROI = roi) then isVert[Faces[i].Z] := 1;
if (xROI = yROI) and (xROI = zROI) then continue; //all members of same ROI
if (xROI = roi) then isEdge[Faces[i].X] := 1;
if (yROI = roi) then isEdge[Faces[i].Y] := 1;
if (zROI = roi) then isEdge[Faces[i].Z] := 1;
nroiEdges := nroiEdges + 1;
end;
if nroiEdges < 1 then continue; //no edges found!
//compute total number of edges, faces...
nroiEdges := 0;
for i := 0 to (nVert-1) do
if isEdge[i] > 0 then begin
roiEdges[nroiEdges] := i;
nroiEdges := nroiEdges + 1;
end;
nroiVerts := 0;
for i := 0 to (nVert-1) do
if isVert[i] > 0 then begin
roiVerts[nroiVerts] := i;
nroiVerts := nroiVerts + 1;
end;
maxRoiDx := -infinity;
maxRoiDxIdx := 0;
for i := 0 to (nroiVerts -1) do begin //compute cost function for each vertex - furtherst from edges
roiDx := 0;
for j := 0 to (nroiEdges - 1) do
roiDx := roiDx + DistanceBetween(vertices[roiVerts[i]], vertices[roiEdges[j]]);
if (roiDx <= maxRoiDx) then continue;
maxRoiDx := roiDx;
maxRoiDxIdx := roiVerts[i];
end;
COGs[nCOGs].x := vertices[maxRoiDxIdx].x;
COGs[nCOGs].y := vertices[maxRoiDxIdx].y;
COGs[nCOGs].z := vertices[maxRoiDxIdx].z;
COGs[nCOGs].w := roi+1;
nCOGs := nCOGs + 1;
end;
if nCOGs < 1 then goto 123;
result := true;
AssignFile(txt, FileName);
rewrite(txt);
for i := 0 to nCOGs-1 do begin
if COGs[i].w < 1 then continue; //label not present
writeln(txt, format('%g%s%g%s%g%s%d%s1', [COGs[i].x,kT,COGs[i].y,kT,COGs[i].z,kT,round(COGs[i].w),kT ]));
end;
CloseFile(txt);
123:
roiEdges := nil;
roiEdges := nil;
COGs := nil;
isVert := nil;
isEdge := nil;
nearestNode := nil;
end; *)
{$DEFINE FXR}
{$IFDEF FXR}
function DistanceBetween(var a,b: TPoint3f): single;
begin
result := sqrt(sqr(a.x-b.x)+sqr(a.y-b.y)+sqr(a.z-b.z));
end;
function AddPt3f(var a,b: TPoint3f): TPoint3f; //create float vector
begin
result.X := a.X + b.X;
result.Y := a.Y + b.Y;
result.Z := a.Z + b.Z;
end;
(*procedure TMesh.dBug();
var
mn, mx, i, nVert, nFace: integer;
begin
nVert := length(vertices);
nFace := length(faces);
if (nFace < 1) or (nVert < 3) or (length(vertexAtlas) <> nVert) then exit;
mn := vertexAtlas[0];
mx := mn;
for i := 0 to (nVert -1) do begin
mn := min(mn, vertexAtlas[i]);
mx := max(mx, vertexAtlas[i]);
end;
printf(format('>>>> %d..%d', [mn, mx]));
end; *)
function TMesh.FindBorderVertices(): TUInt8s;
var
isEdge: TUInt8s;
prefixSum, loCount, hiVs: TInts;
nVert, nFace, i, j, k, lov, repeats: integer;
procedure addV(x, y: integer);
var
lo, hi: integer;
begin
lo := min(x,y);
hi := max(x,y);
prefixSum[lo] -= 1;
hiVs[prefixSum[lo]] := hi;
end;
begin
result := nil;
//For triangular mesh, a "border vertex" has at least one edge
// that is used by only one face (triangle)
nVert := length(vertices);
nFace := length(faces);
if (nFace < 2) or (nVert < 3) then exit(nil);
printf(format('Find borders. face %d vert %d', [nFace, nVert]));
//each face (triangle) has 3 vertices (x,y,z)
setlength(loCount, nVert);
//first pass: bucket size
for i := 0 to (nFace-1) do begin
loCount[min(faces[i].X, faces[i].Y)] += 1;
loCount[min(faces[i].X, faces[i].Z)] += 1;
loCount[min(faces[i].Y, faces[i].Z)] += 1;
end;
//create prefix sum
setlength(prefixSum, nVert);
prefixSum := Copy(loCount, Low(loCount), Length(loCount));
for i := 1 to (nVert -1) do
prefixSum[i] += prefixSum[i-1];
setlength(hiVs, nFace * 3);
//second pass: load high value
for i := 0 to (nFace-1) do begin
addV(faces[i].X, faces[i].Y);
addV(faces[i].X, faces[i].Z);
addV(faces[i].Y, faces[i].Z);
end;
prefixSum := nil;
//finally: identify vertices that have singleton lines
setlength(isEdge, nVert);
//test
(*i := 0;
for lov := 0 to (nVert -1) do
i += loCount[lov];
printf(format(' lines %d %d', [i, nFace * 3]));
i := 0;
for lov := 0 to (nVert -1) do begin
if loCount[lov] < 1 then continue;
//printf(format('%d %d', [loCount[lov], lov]));
for j := 0 to (loCount[lov]-1) do begin
printf(format('%d line %d %d', [i+j, lov, hiVs[i+j]]));
end;
i += loCount[lov];
end; *)
//done
i := 0;
for lov := 0 to (nVert -1) do begin
if loCount[lov] < 1 then continue;
//printf(format('%d %d', [loCount[lov], lov]));
for j := 0 to (loCount[lov]-1) do begin
repeats := 0;
for k := 0 to (loCount[lov]-1) do
if hiVs[i+j] = hiVs[i+k] then
repeats += 1;
if repeats > 1 then continue;
//border edge found - set both vertices of edge as "border"
isEdge[lov] := 1;
isEdge[hiVs[i+j]] := 1;
end;
i += loCount[lov];
end;
hiVs := nil;
loCount := nil;
//test if watertight
j := 0;
for i := 0 to (nVert -1) do
if isEdge[i] > 0 then
j += 1;
if (j = 0) then begin
printf(format('This is a watertight mesh: none of the %d vertices are on the border', [nVert]));
isEdge := nil;
exit;
end else
printf(format('%d of %d vertices are on the border', [j, nVert]));
result := isEdge;
end;
function TMesh.Mesh2Node(const FileName: string; isAppend: boolean = true): boolean;
label
123;
const
kT = chr(9);
var
borderVertices: TUInt8s; //binary for all vertices [0 0 1 0 1]
borderIdxs: TInts; //indices for edges [2 4]
nVert, nEdge, i, j, maxIdx: integer;
vert, cog: TPoint3f;
cogDx, maxCogDX, maxEdgeDx, dx: single;
txt: TextFile;
begin
result := false;
nVert := length(vertices);
if nVert < 3 then exit;
borderVertices := FindBorderVertices;
if borderVertices = nil then begin
printf('Finding vertex closest to center-of-gravity');
cog := ptf(0,0,0);
for i := 0 to (nVert -1) do
cog := AddPt3f(cog, vertices[i]);
cog.x := cog.x / nVert;
cog.y := cog.y / nVert;
cog.z := cog.z / nVert;
maxCogDX := infinity;
maxIdx := 0;
for i := 0 to (nVert -1) do begin
cogDx := DistanceBetween(vertices[i], cog);
if (cogDx > maxCogDx) then continue;
maxCogDx := cogDx;
maxIdx := i;
end;
goto 123; //e.g. watertight mesh
end;
//
setlength(borderIdxs, nVert); //worst case scenario: all edges
nEdge := 0;
for i := 0 to (nVert -1) do
if borderVertices[i] <> 0 then begin
borderIdxs[nEdge] := i;
nEdge += 1;
end;
setlength(borderIdxs, nEdge); //reduce memory
if nEdge = 0 then exit;
//find center of gravity for whole mesh (tie breaker);
cog := ptf(0,0,0);
for i := 0 to (nVert -1) do
cog := AddPt3f(cog, vertices[i]);
cog.x := cog.x / nVert;
cog.y := cog.y / nVert;
cog.z := cog.z / nVert;
maxCogDX := infinity;
maxEdgeDx := -infinity;
maxIdx := 0;
for i := 0 to (nVert -1) do begin
//compute cost function for each vertex - furtherst from edges
// who on the island has the longest walk to the beach?
if (maxEdgeDx > 0) and (borderVertices[i] = 1) then continue; //this vertex is on the edge, only useful if all vertices edge
dx := infinity;
vert := vertices[i];
for j := 0 to (nEdge - 1) do //find closest distance to edge
dx := min(dx, DistanceBetween(vert, vertices[borderIdxs[j]]));
if (dx < maxEdgeDx) then continue; //a previous vertex is closer to edge
cogDx := DistanceBetween(vert, cog);
if (dx = maxEdgeDx) then begin //we have a tie - is this closer to the center of gravity
if (cogDx > maxCogDx) then continue;
end;
maxCogDx := cogDx;
maxEdgeDx := dx;
maxIdx := i;
end;
borderVertices := nil;
borderIdxs := nil;
123:
result := true;
printf(format('xyz %g %g %g', [vertices[maxIdx].x, vertices[maxIdx].y, vertices[maxIdx].z]));
AssignFile(txt, FileName);
if (isAppend) and (FileExists(FileName)) then
append(txt)
else
rewrite(txt);
writeln(txt, format('%g%s%g%s%g%s%d%s1', [vertices[maxIdx].x,kT,vertices[maxIdx].y,kT,vertices[maxIdx].z,kT,round(123),kT ]));
CloseFile(txt);
end;
function TMesh.Atlas2Node(const FileName: string; isAppend: boolean = true):boolean;
const
kT = chr(9);
label
123;
var
xROI, yROI, zROI, maxRoiDxIdx, nVert, maxROI, nFace, roi, nroiEdges, nroiVerts, nCOGs: integer;
roiEdges, roiVerts: TInts;
isEdge, isVert: TUInt8s;
cogDx, maxCogDX, roiDx, maxRoiDx, dx: single;
vert, cog: TPoint3f;
COGs: array of TPoint4f; //center of gravity
j, i : integer;
txt: TextFile;
isOverlayAsAtlas: boolean = false;
borderVertices: TUInt8s; //binary for all vertices [0 0 1 0 1]
{$IFDEF TIMER}startTime : TDateTime;{$ENDIF}
begin
{$IFDEF TIMER}startTime := Now;{$ENDIF}
result := false;
nVert := length(vertices);
nFace := length(faces);
maxROI := AtlasMaxIndex;
//GLForm1.OverlayBox.Caption := 'a'+inttostr(maxROI);
if (nFace < 1) or (nVert < 3) then exit;
if (maxROI < 1) and (OpenOverlays > 0) and (length(overlay[kMinOverlayIndex].intensity) = nVert) then begin
maxROI := 0;
isOverlayAsAtlas := true;
setlength(vertexAtlas, nVert);
for i := 0 to nVert -1 do begin
vertexAtlas[i] := round(overlay[kMinOverlayIndex].intensity[i]);
maxROI := max(vertexAtlas[i], maxROI);
end;
if maxROI < 1 then
vertexAtlas := nil
else
printf(format('Overlay is %d discrete parcels', [maxROI]));
end;
if (maxROI < 1) or (length(vertexAtlas) <> nVert) then begin
//find single node most representative of whole mesh
result := Mesh2Node(FileName);
exit;
end;
// for i := 0 to (nVert -1) do
// sumV += vertexAtlas[i];
setlength(COGs, maxROI+1);
setlength(roiEdges, nVert); //list of vertices on edge of ROI
setlength(roiVerts, nVert); //list all vertices in ROI
setlength(isEdge, nVert);
setlength(isVert, nVert);
//GLForm1.OverlayBox.Caption := 'b'+inttostr(maxROI);
for i := 0 to maxROI do
COGs[i] := pt4f(0,0,0,0);
nCOGs := 0;
borderVertices := FindBorderVertices; //find border vertices that have no neighbors - these are boundary for a region
for roi := 0 to maxROI do begin
for i := 0 to nVert -1 do begin
isEdge[i] := 0;
isVert[i] := 0;
end;
nroiVerts := 0;
for i := 0 to (nFace-1) do begin
if maxROI < 1 then begin
xROI := 0;
yROI := 0;
zROI := 0;
end else begin
xROI := vertexAtlas[Faces[i].X];
yROI := vertexAtlas[Faces[i].Y];
zROI := vertexAtlas[Faces[i].Z];
end;
if (xROI <> roi) and (yROI <> roi) and (zROI <> roi) then continue; //this vertex not member of ROI
//roiVerts[nroiVerts] := i;
nroiVerts += 1;
if (xROI = roi) then isVert[Faces[i].X] := 1;
if (yROI = roi) then isVert[Faces[i].Y] := 1;
if (zROI = roi) then isVert[Faces[i].Z] := 1;
if (xROI = yROI) and (xROI = zROI) then continue; //all members of same ROI
if (xROI = roi) then isEdge[Faces[i].X] := 1;
if (yROI = roi) then isEdge[Faces[i].Y] := 1;
if (zROI = roi) then isEdge[Faces[i].Z] := 1;
end;
//add border vertices that are part of region but have no neighbors
if (borderVertices <> nil) then begin //if mesh is not water tight
for i := 0 to nVert -1 do begin
if (isVert[i] = 1) and (borderVertices[i] = 1) then
isEdge[i] := 1;
end;
end;
//count
nroiEdges := 0;
for i := 0 to nVert -1 do
if (isEdge[i] = 1) then
nroiEdges := nroiEdges + 1;
//printf(roi, ' has ', nroiVerts, ' vertices and ', nroiEdges, ' edges' );
if nroiVerts < 1 then continue;
//compute total number of edges, faces...
nroiEdges := 0;
for i := 0 to (nVert-1) do
if isEdge[i] > 0 then begin
roiEdges[nroiEdges] := i;
nroiEdges := nroiEdges + 1;
end;
nroiVerts := 0;
for i := 0 to (nVert-1) do
if isVert[i] > 0 then begin
roiVerts[nroiVerts] := i;
nroiVerts := nroiVerts + 1;
end;
//find center of mass
cog := ptf(0,0,0);
for i := 0 to (nroiVerts -1) do
cog := AddPt3f(cog, vertices[roiVerts[i]]);
cog.x := cog.x / nroiVerts;
cog.y := cog.y / nroiVerts;
cog.z := cog.z / nroiVerts;
maxCogDX := infinity;
maxRoiDx := -infinity;
maxRoiDxIdx := 0;
//if no edges, center of gravity is our only metric
if nroiEdges < 1 then begin
printf(format('Region %d has no edges (%d vertices, CoG %g %g %g)',[roi,nroiVerts, cog.x, cog.y, cog.z ]));
for i := 0 to (nroiVerts -1) do begin
cogDx := DistanceBetween(vertices[roiVerts[i]], cog);
if (cogDx > maxCogDx) then continue;
maxCogDx := cogDx;
maxRoiDxIdx := roiVerts[i];
end;
COGs[nCOGs].x := vertices[maxRoiDxIdx].x;
COGs[nCOGs].y := vertices[maxRoiDxIdx].y;
COGs[nCOGs].z := vertices[maxRoiDxIdx].z;
COGs[nCOGs].w := roi+1;
nCOGs := nCOGs + 1;
continue; //no edges found: only use CoG
end;
for i := 0 to (nroiVerts -1) do begin
//compute cost function for each vertex - furtherst from edges
// who on the island has the longest walk to the beach?
roiDx := infinity;
vert := vertices[roiVerts[i]];
for j := 0 to (nroiEdges - 1) do begin
dx := DistanceBetween(vert, vertices[roiEdges[j]]);
if dx < roiDx then
roiDx := dx;
end;
if (roiDx < maxRoiDx) then continue; //a previous vertex is closer to edge
cogDx := DistanceBetween(vert, cog);
if (roiDx = maxRoiDx) then begin //we have a tie - is this closer to the center of gravity
if (cogDx > maxCogDx) then continue;
end;
maxCogDx := cogDx;
maxRoiDx := roiDx;
maxRoiDxIdx := roiVerts[i];
end;
//maxRoiDxIdx := roiVerts[random(nroiVerts)];
//maxRoiDxIdx := roiEdges[random(nroiEdges)];
COGs[nCOGs].x := vertices[maxRoiDxIdx].x;
COGs[nCOGs].y := vertices[maxRoiDxIdx].y;
COGs[nCOGs].z := vertices[maxRoiDxIdx].z;
COGs[nCOGs].w := roi+1;
nCOGs := nCOGs + 1;
end;
if isOverlayAsAtlas then
vertexAtlas := nil;
if nCOGs < 1 then goto 123;
//GLForm1.Caption := 'nCOGs'+inttostr(nCOGs);
result := true;
AssignFile(txt, FileName);
if (isAppend) and (FileExists(FileName)) then
append(txt)
else
rewrite(txt);
for i := 0 to nCOGs-1 do begin
if COGs[i].w < 1 then continue; //label not present
writeln(txt, format('%g%s%g%s%g%s%d%s1', [COGs[i].x,kT,COGs[i].y,kT,COGs[i].z,kT,round(COGs[i].w),kT ]));
end;
CloseFile(txt);
//if result then GLForm1.Caption := 'nCOGs'+inttostr(nCOGs);
{$IFDEF TIMER}GLForm1.Caption := inttostr(MilliSecondsBetween(Now,StartTime)); {$ENDIF}
123:
roiEdges := nil;
borderVertices := nil;
roiEdges := nil;
COGs := nil;
isVert := nil;
isEdge := nil;
//nearestNode := nil;
end;
{$ELSE}
function TMesh.Atlas2Node(const FileName: string):boolean;
const
kT = chr(9);
label
123;
var
nVert, maxROI: integer;
COGs, nearestNode: array of TPoint4f; //center of gravity
i, idx : integer;
dx: single;
txt: TextFile;
begin
result := false;
nVert := length(vertices);
maxROI := AtlasMaxIndex;
if (nVert < 3) or (maxROI < 1) or (length(vertexAtlas) <> nVert) then exit;
//vertexAtlas: TInts; //what atlas regions does this vertex belong to, e.g. [7, 8, 17...] the 3rd vertex belongs to region 17
//setlength(mass, maxROI+1);
setlength(COGs, maxROI+1);
for i := 0 to maxROI do
COGs[i] := pt4f(0,0,0,0);
for i := 0 to (nVert -1) do begin
idx := vertexAtlas[i];
COGs[idx].w := COGs[idx].w + 1;
COGs[idx].x := COGs[idx].x + vertices[i].x;
COGs[idx].y := COGs[idx].y + vertices[i].y;
COGs[idx].z := COGs[idx].z + vertices[i].z;
end;
//set center of gravity = mean
for i := 0 to maxROI do begin
COGs[i].x := COGs[i].x / COGs[i].w;
COGs[i].y := COGs[i].y / COGs[i].w;
COGs[i].z := COGs[i].z / COGs[i].w;
end;
//initialize nearest node - infinitely far away from COG
setlength(nearestNode, maxROI+1);
for i := 0 to maxROI do
nearestNode[i] := pt4f(0,0,0,Infinity);
//for each vertex - see if this is closest to COG
for i := 0 to (nVert -1) do begin
idx := vertexAtlas[i];
dx := sqrt( sqr(COGs[idx].x-vertices[i].x) + sqr(COGs[idx].y-vertices[i].y) + sqr(COGs[idx].z-vertices[i].z) );
if (dx >= nearestNode[idx].w) then continue;
nearestNode[idx] := pt4f(vertices[i].x, vertices[i].y, vertices[i].z, dx);
result := true; //at least one node survives
end;
if not result then goto 123;
AssignFile(txt, FileName);
rewrite(txt);
for i := 0 to maxROI do begin
if COGs[i].w < 1 then continue; //label not present
writeln(txt, format('%g%s%g%s%g%s%d%s1', [nearestNode[i].x,kT,nearestNode[i].y,kT,nearestNode[i].z,kT,i,kT ]));
end;
CloseFile(txt);
123:
COGs := nil;
nearestNode := nil;
end;
{$ENDIF}
{$IFDEF FASTGZ}
function ExtractGz(fnm: string; var mStream : TMemoryStream; magic: word = 0): boolean;
//if magic <> 0, then a file that starts with magic will assume to uncompressed
//if magic = 0, a file will be assumed to be uncompressed if first two bytes are not $8B1F
var
gz: TGZRead;
sig: word;
F : File Of byte;
src : array of byte;
cSz : int64; //uncompressed, compressed size
begin
if not fileexists(fnm) then exit(false);
FileMode := fmOpenRead;
Assign (F, fnm);
Reset (F);
cSz := FileSize(F);
sig := 0; //only to hide compiler warning
blockread(F, sig, SizeOf(sig) );
seek(F,0);
//n.b. GZ header/footer is ALWAYS little-endian
{$IFDEF ENDIAN_BIG}
sig := Swap(sig);
{$ENDIF}
if ( ((magic = 0) and (sig <> $8B1F)) or ((magic <> 0) and (sig = magic)) ) then begin //hex: 1F 8B : gzip specific: will reject zlib format
Close (F);
mStream.LoadFromFile(fnm);
exit(true);
end;
setlength(src, cSz);
blockread(f, src[0], cSz );
CloseFile(f);
result := gz.Init(@src[0], cSz);
if not result then begin
src := nil;
exit;
end;
gz.ToStream(mStream, cSz);
src := nil;
gz.ZStreamDone;
end;
{$ELSE}
function ExtractGz(fnm: string; var mStream : TMemoryStream; magic: word = 0): boolean;
const
kChunkSize = 65535;
var
zStream : TGZFileStream;
bytes : array of byte;
i: integer;
begin
zStream := TGZFileStream.create(fnm, gzopenread);
result := (zStream <> nil);
setlength(bytes, kChunkSize);
repeat
i := zStream.read(bytes[0],kChunkSize);
mStream.Write(bytes[0],i) ;
until i < kChunkSize;
zStream.Free;
end;
{$ENDIF}
//{$IFDEF COREGL}
function mixRGBA(c1, c2: TRGBA; frac2: single): TRGBA;
var
frac1: single;
begin
frac2 := ((c2.a * frac2 )/255.0);
frac1 := 1 - frac2;
result.R := round(c1.R*frac1 + c2.R*frac2) ;
result.G := round(c1.G*frac1 + c2.G*frac2);
result.B := round(c1.B*frac1 + c2.B*frac2);
end;
//{$ENDIF}
procedure AddPt4f(var v: TPoint4f; c1,c2,c3: TRGBA); //create float vector
begin
v.X := v.X + c1.r+ c2.r+ c3.r;
v.Y := v.Y + c1.g+ c2.g+ c3.g;
v.Z := v.Z + c1.b+ c2.b+ c3.b;
v.W := v.W + c1.a+ c2.a+ c3.a;
end;
procedure invertDarken(var c: TRGBA; v, mn,mx: single);
var
frac: single;
begin
if (v <= mn) then exit;
if (v >= mx) then begin
c.R := 0;
c.G := 0;
c.B := 0;
exit;
end;
frac := 1.0 - ((v-mn)/(mx-mn));
c.R := round(c.R * frac);
c.G := round(c.G * frac);
c.B := round(c.B * frac);
end;
procedure darken(var c: TRGBA; v, mn,mx: single);
var
frac: single;
begin
if (v >= mx) then exit;
if (v <= mn) then begin
c.R := 0;
c.G := 0;
c.B := 0;
exit;
end;
frac := (v-mn)/(mx-mn);
c.R := round(c.R * frac);
c.G := round(c.G * frac);
c.B := round(c.B * frac);
end;
procedure TMesh.BuildListCore(Clr: TRGBA; var f: TFaces; var v: TVertices; var vtxRGBA: TVertexRGBA; vRemap: TInts = nil; isWriteToGPU: boolean = true);
var
i,volInc, c: integer;
mn, mx, frac: single;
rgb, rgb0: TRGBA;
vRGBA, vRGBAmx :TVertexRGBA;
vNumNeighbor: array of integer;
vSumRGBBA: array of TPoint4f;
isOverlayPainting : boolean = false;
begin
nFaces := length(f);
if (length(f) < 1) or (length(v) < 3) then exit;
volInc := 0;
isOverlayPainting := false;
if (OpenOverlays > 0) then //ignore overlays if they are all meshes rather than vertex colors
for c := OpenOverlays downto 1 do
if (overlay[c].OpacityPercent <> kLUTinvisible) and (length(overlay[c].intensity) >= length(v)) then
isOverlayPainting := true;
if (isOverlayPainting) or (length(vtxRGBA) = length(v)) then begin
rgb := RGBA(Clr.R, Clr.G, Clr.B, 0);
setlength(vRGBA, length(v));
if (length(vtxRGBA) = length(v)) then begin
c := round(vertexRgbaAlpha * 255);
if vertexRgbaSaturation >= 1 then begin
for i := 0 to (length(v)-1) do begin
vRGBA[i].r := vtxRGBA[i].r;
vRGBA[i].g := vtxRGBA[i].g;
vRGBA[i].b := vtxRGBA[i].b;
if vtxRGBA[i].a > 0 then begin
c := round(vertexRgbaAlpha * vtxRGBA[i].a);
vRGBA[i].a := c
end else begin
vRGBA[i] := Clr; //Catani2020
vRGBA[i].a := 0; //Catani
end;
end;
end else begin
for i := 0 to (length(v)-1) do
vRGBA[i] := desaturateRGBA ( vtxRGBA[i], vertexRgbaSaturation, C);
end;
//2019: required only when no overlays open - try adjusting transparency of Altas
if (OpenOverlays < 1) and (vertexRGBAAlpha < 1.0) then
for i := 0 to (length(v)-1) do
vRGBA[i] := mixRGBA( Clr, vRGBA[i], vertexRGBAAlpha);
end else begin
for i := 0 to (length(v)-1) do
vRGBA[i] := rgb;
end;
if (OpenOverlays > 0) then begin
if isAdditiveOverlay then begin
setlength(vRGBAmx, length(v));
rgb0 := RGBA(0,0,0,0);
for i := 0 to (length(v)-1) do
vRGBAmx[i] := rgb0;
for c := OpenOverlays downto 1 do begin
if isFreeSurferLUT(overlay[c].LUTindex) then continue; //curve files ALWAYs darken
volInc := length(v) * (overlay[c].currentVolume - 1);
if (not overlay[c].aoMap) and (overlay[c].OpacityPercent <> kLUTinvisible) and (length(overlay[c].intensity) >= length(v)) then begin
frac := overlay[c].OpacityPercent/100;
if (frac > 1) or (frac < 0) then frac := 1;
if overlay[c].windowScaledMax > overlay[c].windowScaledMin then begin
mn := overlay[c].windowScaledMin;
mx := overlay[c].windowScaledMax;
end else begin
mx := overlay[c].windowScaledMin;
mn := overlay[c].windowScaledMax;
end;
if vRemap <> nil then begin //filtered atlas: vertices have been decimated
for i := 0 to (length(v)-1) do begin
rgb := inten2rgb(overlay[c].intensity[vRemap[i]+volInc], mn, mx, overlay[c].LUT, overlay[c].PaintMode);
rgb.A := round(rgb.A * frac);
vRGBAmx[i] := maxRGBA(vRGBAmx[i], rgb);
end; //for i
end else begin
for i := 0 to (length(v)-1) do begin
rgb := inten2rgb(overlay[c].intensity[i+volInc], mn, mx, overlay[c].LUT, overlay[c].PaintMode);
rgb.A := round(rgb.A * frac);
vRGBAmx[i] := maxRGBA(vRGBAmx[i], rgb);
end; //for i