// VERSION 2B). //
TRIANGLE* MarchingCubesLinear(float mcMinX, float mcMaxX, float mcMinY, float mcMaxY, float mcMinZ, float mcMaxZ,
int ncellsX, int ncellsY, int ncellsZ, float minValue,
FORMULA formula, int &numTriangles)
{
return MarchingCubes(mcMinX, mcMaxX, mcMinY, mcMaxY, mcMinZ, mcMaxZ, ncellsX, ncellsY, ncellsZ, minValue,
formula, LinearInterp, numTriangles);
}
// VERSION 2A). //
TRIANGLE* MarchingCubes(float mcMinX, float mcMaxX, float mcMinY, float mcMaxY, float mcMinZ, float mcMaxZ,
int ncellsX, int ncellsY, int ncellsZ, float minValue,
FORMULA formula, INTERSECTION intersection, int &numTriangles)
{
//space is already defined and subdivided, staring with step 3
//first initialize the points
mp4Vector * mcDataPoints = new mp4Vector[(ncellsX+1)*(ncellsY+1)*(ncellsZ+1)];
mpVector stepSize((mcMaxX-mcMinX)/ncellsX, (mcMaxY-mcMinY)/ncellsY, (mcMaxZ-mcMinZ)/ncellsZ);
int YtimesZ = (ncellsY+1)*(ncellsZ+1); //for extra speed
for(int i=0; i < ncellsX+1; i++) {
int ni = i*YtimesZ; //for speed
float vertX = mcMinX + i*stepSize.x;
for(int j=0; j < ncellsY+1; j++) {
int nj = j*(ncellsZ+1); //for speed
float vertY = mcMinY + j*stepSize.y;
for(int k=0; k < ncellsZ+1; k++) {
mp4Vector vert(vertX, vertY, mcMinZ + k*stepSize.z, 0);
vert.val = formula((mpVector)vert);
/*(step 3)*/ mcDataPoints[ni + nj + k] = vert;
}
}
}
//then run Marching Cubes (version 1A) on the data
return MarchingCubes(ncellsX, ncellsY, ncellsZ, minValue, mcDataPoints, intersection, numTriangles);
}
void MyWidget::paintEvent(QPaintEvent * e) {
QPainter paint(this);
memset(_bitsDest, 0, _PIC_MAX);
initFigure();
switch (_func_index) {
case 0: ScalarField();
break;
case 1: MarchingCubes();
break;
}
for (int x = 0; x < fR2; x++) {
for (int y = 0; y < fR2; y++) {
for (int z = 0; z < fR2; z++) {
_figure2D[x][y][z].free();
_figure3D[x][y][z].free();
}
}
}
paint.drawImage(QPoint(0, 0), *_imageDest);
e->accept();
}
//----------------------------------------------------------------------
System::System(RTPSSettings* set, CL* c)
{
dout<<"settings "<<set<<endl;
settings = set;
cli = c;
acquiredGL=false;
max_num = settings->GetSettingAs<unsigned int>("max_num_particles");
num = settings->GetSettingAs<unsigned int>("num_particles");
maxGravSources=settings->GetSettingAs<unsigned int>("max_gravity_sources");
activeParticle = 0;
// I should be able to not specify this, but GPU restrictions ...
//seed random
srand ( time(NULL) );
grid = Domain(settings->GetSettingAs<float4>("domain_min"),settings->GetSettingAs<float4>("domain_max"));
setupTimers();
//*** end Initialization
#ifdef CPU
dout<<"RUNNING ON THE CPU"<<endl;
#endif
#ifdef GPU
dout<<"RUNNING ON THE GPU"<<endl;
prepareSorted();
//dout<<"Here"<<endl;
//should be more cross platform
string common_source_dir = settings->GetSettingAs<string>("rtps_path") + "/" + std::string(COMMON_CL_SOURCE_DIR);
cli->addIncludeDir(common_source_dir);
//dout<<common_source_dir.c_str()<<endl;
hash = Hash(common_source_dir, cli, timers["hash_gpu"]);
gravity = Gravity(common_source_dir, cli);
bitonic = Bitonic<unsigned int>(common_source_dir, cli );
//radix = Radix<unsigned int>(common_source_dir, cli, max_num, 128);
cellindices = CellIndices(common_source_dir, cli, timers["ci_gpu"] );
permute = Permute( common_source_dir, cli, timers["perm_gpu"] );
m2p = MeshToParticles(common_source_dir, cli, timers["meshtoparticles_gpu"]);
marchingcubes = MarchingCubes(common_source_dir, cli, timers["marchingcubes_gpu"],settings->GetSettingAs<unsigned int>("color_field_res","2"));
#endif
}
/*!
A function version of the program mc by Thomas Lewiner
see main.c in ./MarchingCubes
*/
SUMA_SurfaceObject *SUMA_MarchingCubesSurface(
SUMA_GENERIC_PROG_OPTIONS_STRUCT * Opt)
{
static char FuncName[]={"SUMA_MarchingCubesSurface"};
SUMA_SurfaceObject *SO=NULL;
int nxx, nyy, nzz, cnt, i, j, k, *FaceSetList=NULL;
float *NodeList=NULL;
SUMA_NEW_SO_OPT *nsoopt = NULL;
THD_fvec3 fv, iv;
MCB *mcp ;
SUMA_ENTRY;
if (Opt->obj_type < 0) {
nxx = DSET_NX(Opt->in_vol);
nyy = DSET_NY(Opt->in_vol);
nzz = DSET_NZ(Opt->in_vol);
if (Opt->debug) {
fprintf(SUMA_STDERR,
"%s:\nNxx=%d\tNyy=%d\tNzz=%d\n", FuncName, nxx, nyy, nzz);
}
mcp = MarchingCubes(-1, -1, -1);
set_resolution( mcp, nxx, nyy, nzz ) ;
init_all(mcp) ;
if (Opt->debug) fprintf(SUMA_STDERR,"%s:\nSetting data...\n", FuncName);
cnt = 0;
for( k = 0 ; k < mcp->size_z ; k++ ) {
for( j = 0 ; j < mcp->size_y ; j++ ) {
for( i = 0 ; i < mcp->size_x ; i++ ) {
SUMA_SET_MC_DATA ( mcp, Opt->mcdatav[cnt], i, j, k);
++cnt;
}
}
}
} else {
/* built in */
nxx = nyy = nzz = Opt->obj_type_res;
mcp = MarchingCubes(-1, -1, -1);
set_resolution( mcp, nxx, nyy, nzz) ;
init_all(mcp) ;
compute_data( *mcp , Opt->obj_type) ;
}
if (Opt->debug)
fprintf(SUMA_STDERR,"%s:\nrunning MarchingCubes...\n", FuncName);
run(mcp) ;
clean_temps(mcp) ;
if (Opt->debug > 1) {
fprintf(SUMA_STDERR,"%s:\nwriting out NodeList and FaceSetList...\n",
FuncName);
write1Dmcb(mcp);
}
if (Opt->debug) {
fprintf(SUMA_STDERR,"%s:\nNow creating SO...\n", FuncName);
}
NodeList = (float *)SUMA_malloc(sizeof(float)*3*mcp->nverts);
FaceSetList = (int *)SUMA_malloc(sizeof(int)*3*mcp->ntrigs);
if (!NodeList || !FaceSetList) {
SUMA_SL_Crit("Failed to allocate!");
SUMA_RETURN(SO);
}
nsoopt = SUMA_NewNewSOOpt();
if (Opt->obj_type < 0) {
nsoopt->LargestBoxSize = -1;
if (Opt->debug) {
fprintf(SUMA_STDERR,
"%s:\nCopying vertices, changing to DICOM \n"
"Orig:(%f %f %f) \nD:(%f %f %f)...\n",
FuncName,
DSET_XORG(Opt->in_vol),
DSET_YORG(Opt->in_vol), DSET_ZORG(Opt->in_vol),
DSET_DX(Opt->in_vol),
DSET_DY(Opt->in_vol), DSET_DZ(Opt->in_vol));
}
for ( i = 0; i < mcp->nverts; i++ ) {
j = 3*i; /* change from index coordinates to mm DICOM, next three lines are equivalent of SUMA_THD_3dfind_to_3dmm*/
fv.xyz[0] = DSET_XORG(Opt->in_vol) + mcp->vertices[i].x * DSET_DX(Opt->in_vol);
fv.xyz[1] = DSET_YORG(Opt->in_vol) + mcp->vertices[i].y * DSET_DY(Opt->in_vol);
fv.xyz[2] = DSET_ZORG(Opt->in_vol) + mcp->vertices[i].z * DSET_DZ(Opt->in_vol);
/* change mm to RAI coords */
iv = SUMA_THD_3dmm_to_dicomm( Opt->in_vol->daxes->xxorient, Opt->in_vol->daxes->yyorient, Opt->in_vol->daxes->zzorient, fv );
NodeList[j ] = iv.xyz[0];
NodeList[j+1] = iv.xyz[1];
NodeList[j+2] = iv.xyz[2];
}
for ( i = 0; i < mcp->ntrigs; i++ ) {
j = 3*i;
FaceSetList[j ] = mcp->triangles[i].v3;
FaceSetList[j+1] = mcp->triangles[i].v2;
FaceSetList[j+2] = mcp->triangles[i].v1;
}
} else {
nsoopt->LargestBoxSize = 100;
/* built in */
for ( i = 0; i < mcp->nverts; i++ ) {
j = 3*i;
NodeList[j ] = mcp->vertices[i].x;
NodeList[j+1] = mcp->vertices[i].y;
NodeList[j+2] = mcp->vertices[i].z;
}
for ( i = 0; i < mcp->ntrigs; i++ ) {
j = 3*i;
FaceSetList[j ] = mcp->triangles[i].v3;
FaceSetList[j+1] = mcp->triangles[i].v2;
FaceSetList[j+2] = mcp->triangles[i].v1;
}
}
SO = SUMA_NewSO(&NodeList, mcp->nverts, &FaceSetList, mcp->ntrigs, nsoopt);
if (Opt->obj_type < 0) {
/* not sure if anything needs to be done here ...*/
} else {
if (Opt->obj_type == 0) SO->normdir = 1;
else SO->normdir = -1;
}
if (Opt->debug) {
fprintf(SUMA_STDERR,"%s:\nCleaning mcp...\n", FuncName);
}
clean_all(mcp) ;
free(mcp);
nsoopt=SUMA_FreeNewSOOpt(nsoopt);
SUMA_RETURN(SO);
}
// VERSION 1B). //
TRIANGLE* MarchingCubesLinear(int ncellsX, int ncellsY, int ncellsZ, float minValue,
mp4Vector * points, int &numTriangles)
{
return MarchingCubes(ncellsX, ncellsY, ncellsZ, minValue, points, LinearInterp, numTriangles);
}
void ElPoly::IsoSurf(int NSample,double *IsoLevel,int NIso){
int NPairF = NFile[1]-NFile[0];
double OldPos[3] = {pNanoPos(0,0),pNanoPos(0,1),pNanoPos(0,2)};
double DensEl = CUB(NSample)/(pVol()*NPairF);
double Dens = 13.3;
FILE *FNano = fopen("NanoPos.txt","w");
//IsoLevel *= NPairF;
for(int ff=NFile[0];ff<NFile[1];ff+=NPairF){
double *Plot = (double *)calloc(CUBE(NSample),sizeof(double));
double Min = 0.;
double Max = 0.;
VAR_TRIANGLE *Triang = NULL;
double Pos[3];
for(int f=ff;f<ff+NPairF&&f<NFile[1];f++){
Processing(f);
if(OpenRisk(cFile[f],BF_PART))return;
for(int b=0;b<pNBlock();b++){
for(int p=Block[b].InitIdx;p<Block[b].EndIdx;p++){
if(pType(p) != 0)continue;
for(int d=0;d<3;d++){
Pos[d] = pPos(p,d) - (pNanoPos(0,d)-.5*pEdge(d));
Pos[d] -= floor(Pos[d]*pInvEdge(d))*pEdge(d);
}
int sx = (int)(Pos[0]*pInvEdge(0)*NSample);
int sy = (int)(Pos[1]*pInvEdge(1)*NSample);
int sz = (int)(Pos[2]*pInvEdge(2)*NSample);
int sTot = (sx*NSample+sy)*NSample+sz;
Plot[sTot] += DensEl;
if(Max < Plot[sTot]) Max = Plot[sTot];
if(Min > Plot[sTot]) Min = Plot[sTot];
}
}
}
Matrice Mask(3,3,3);
Mask.FillGaussian(.5,3.);
Mask.Print();
int NDim = 3;
int IfMinImConv = 1;
Mask.ConvoluteMatrix(Plot,NSample,NDim,IfMinImConv);
Mask.ConvoluteMatrix(Plot,NSample,NDim,IfMinImConv);
// ConvoluteMatrix(Plot,NSample,&Mask,3);
// ConvoluteMatrix(Plot,NSample,&Mask,3);
char FString[256];
sprintf(FString,"IsoSurf%05d.dat",ff);
FILE *F2Write = fopen(FString,"w");
fprintf(F2Write,"#l(%lf %lf %lf) v[%d] d[polygon]\n",pEdge(0),pEdge(1),pEdge(2),NSample);
HeaderNano(F2Write);
int NTri = 0;
for(int i=0;i<NIso;i++){
printf("Min %lf Max %lf IsoLevel %lf DensEl %lf\n",Min,Max,IsoLevel[i],DensEl);
Triang = MarchingCubes(Plot,NSample,IsoLevel[i],&NTri);
for(int t=0;t<NTri;t++){
for(int i=0;i<3;i++){
int l1 = t*3 + (i+1)%3;
int l2 = t*3 + (i+2)%3;
for(int d=0;d<3;d++) Pos[d] = Triang[t].p[i].x[d];
int sx = (int)(Pos[0]*pInvEdge(0)*NSample);
int sy = (int)(Pos[1]*pInvEdge(1)*NSample);
int sz = (int)(Pos[2]*pInvEdge(2)*NSample);
int sTot = (sx*NSample+sy)*NSample+sz;
fprintf(F2Write,"{t[%d %d %d] ",sTot,t,0);
fprintf(F2Write,"x(%lf %lf %lf) ",Pos[0],Pos[1],Pos[2]);
fprintf(F2Write,"v(%lf %lf %lf) ",Triang[t].n[i].x[0],Triang[t].n[i].x[1],Triang[t].n[i].x[2]);
fprintf(F2Write,"l[%d] l[%d]}\n",l1,l2);
}
}
}
fclose(F2Write);
free(Plot);
free(Triang);continue;
int NVertex = CUBE(2*NSample-1);
double *WeightL = (double *) calloc(NVertex,sizeof(double));
NormalWeight(Triang,WeightL,NSample,NTri);
double CmStalk[3] = {0.,0.,0.};//OldPos[0],OldPos[1],OldPos[2]};
double CountStalk = 0.;
for(int t=0;t<NTri;t++){
for(int v=0;v<3;v++){
int vRef = Triang[t].v[v];
for(int d=0;d<3;d++){
CmStalk[d] = Triang[t].p[v].x[d]*WeightL[vRef];
}
CountStalk += WeightL[vRef];
}
}
free(WeightL);
free(Triang);
if(CountStalk <= 0.) CountStalk = 1.;
for(int d=0;d<3;d++){
CmStalk[d] /= CountStalk;
}
pPos(CmStalk);
SetNNano(1);
for(int d=0;d<3;d++){
Nano->Pos[d] = CmStalk[d];
OldPos[d] = Nano->Pos[d];
}
SetNanoBkf(0);
Nano->Axis[0] = 0.;
Nano->Axis[1] = 0.;
Nano->Axis[2] = 1.;
Nano->Rad = .5;
Nano->Height = 4.;
Nano->Hamaker = 1.;
Nano->OffSet = 1.;
Nano->Shape = SHAPE_STALK;
for(int f=ff;f<ff+NPairF&&f<NFile[1];f++){
char String[120];
StringNano(String,0);
fprintf(FNano,"sed '/Rigid/c\\%s' %s > Ciccia.dat\n",String,cFile[f]);
fprintf(FNano,"mv Ciccia.dat %s\n",cFile[f]);
//command("chmod u+x %s\n","NanoPos.txt");
//SubNanoHeader(cFile[f]);
}
printf("\n");
}
fclose(FNano);
}
