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Added tests/TestSegDist.cpp to test parallel converseion for segemented data to signed distance function

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This commit is contained in:
James E McClure 2015-06-03 17:55:25 -04:00
parent e7eb11f228
commit ae9b848296
2 changed files with 186 additions and 35 deletions
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113
tests/TestComputeSignDist.cpp
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@ -11,13 +11,13 @@
#include <fstream>
#include <Array.h>
inline void SSO(DoubleArray &Distance, IntArray &ID, int timesteps){
inline void SSO(DoubleArray &Distance, char *ID, int timesteps){
int Q=26;
int q,i,j,k;
int Nx = ID.m;
int Ny = ID.n;
int Nz = ID.o;
int q,i,j,k,n;
int Nx = Distance.m;
int Ny = Distance.n;
int Nz = Distance.o;
const static int D3Q27[26][3]={{1,0,0},{-1,0,0},{0,1,0},{0,-1,0},{0,0,1},{0,0,-1},
{1,1,0},{-1,-1,0},{1,-1,0},{-1,1,0},{1,0,1},{-1,0,-1},{1,0,-1},{-1,0,1},
{0,1,1},{0,-1,-1},{0,1,-1},{0,-1,1},{1,1,1},{-1,-1,-1},{1,1,-1},{-1,-1,1},
@ -30,40 +30,58 @@ inline void SSO(DoubleArray &Distance, IntArray &ID, int timesteps){
}
// Initialize the Distance from ID
for (i=0; i<Nx*Ny*Nz; i++) Distance.data[i] = -0.5;
for (k=1;k<Nz-1;k++){
for (j=1;j<Ny-1;j++){
for (i=1;i<Nx-1;i++){
// for (i=0; i<Nx*Ny*Nz; i++) Distance.data[i] = -0.5;
for (k=0;k<Nz;k++){
for (j=0;j<Ny;j++){
for (i=0;i<Nx;i++){
n=k*Nx*Ny+j*Nx+i;
// Initialize distance to +/- 1
Distance(i,j,k) = 1.0*ID(i,j,k)-0.5;
Distance(i,j,k) = 1.0*ID[n]-0.5;
}
}
}
int count = 0;
double dt=1.0;
int n,in,jn,kn,nn;
double dt=0.1;
int in,jn,kn,nn;
double Dqx,Dqy,Dqz,Dx,Dy,Dz,W;
double nx,ny,nz,Cqx,Cqy,Cqz,sign,norm;
double f1,f2,f3,f4,f5,f6,f7,f8,f9,f10,f11,f12,f13,f14,f15,f16,f17,f18;
printf("Number of timesteps is %i \n",timesteps);
printf("Mesh is %i,%i,%i \n",Nx,Ny,Nz);
while (count < timesteps){
for (k=1;k<Nz-1;k++){
for (j=1;j<Ny-1;j++){
for (i=1;i<Nx-1;i++){
printf("count=%i \n",count);
for (k=0;k<Nz;k++){
for (j=0;j<Ny;j++){
for (i=0;i<Nx;i++){
n = k*Nx*Ny + j*Nx + i;
sign = Distance.data[n] / fabs(Distance.data[n]);
//............Compute the Gradient...................................
nx = 0.5*(Distance(i+1,j,k) - Distance(i-1,j,k));
ny = 0.5*(Distance(i,j+1,k) - Distance(i,j-1,k));
nz = 0.5*(Distance(i,j,k+1) - Distance(i,j,k-1));
if (!(i+1<Nx)) nx=0.5*Distance(i,j,k);
else nx=0.5*Distance(i+1,j,k);;
if (!(j+1<Ny)) ny=0.5*Distance(i,j,k);
else ny=0.5*Distance(i,j+1,k);
if (!(k+1<Nz)) nz=0.5*Distance(i,j,k);
else nz=0.5*Distance(i,j,k+1);
if (i<1) nx-=0.5*Distance(i,j,k);
else nx-=0.5*Distance(i-1,j,k);
if (j<1) ny-=0.5*Distance(i,j,k);
else ny-=0.5*Distance(i,j-1,k);
if (k<1) nz-=0.5*Distance(i,j,k);
else nz-=0.5*Distance(i,j,k-1);
// nx = 0.5*(Distance(i+1,j,k) - Distance(i-1,j,k));
// ny = 0.5*(Distance(i,j+1,k) - Distance(i,j-1,k));
// nz = 0.5*(Distance(i,j,k+1) - Distance(i,j,k-1));
W = 0.0; Dx = Dy = Dz = 0.0;
if (nx*nx+ny*ny+nz*nz > 0.0){
for (q=0; q<27; q++){
for (q=0; q<26; q++){
Cqx = 1.0*D3Q27[q][0];
Cqy = 1.0*D3Q27[q][1];
Cqz = 1.0*D3Q27[q][2];
@ -72,12 +90,19 @@ inline void SSO(DoubleArray &Distance, IntArray &ID, int timesteps){
jn = j + D3Q27[q][1];
kn = k + D3Q27[q][2];
// make sure the neighbor is in the domain (periodic BC)
if (in < 0 ) in +=Nx;
/* if (in < 0 ) in +=Nx;
if (jn < 0 ) jn +=Ny;
if (kn < 0 ) kn +=Nz;
if (!(in < Nx) ) in -=Nx;
if (!(jn < Ny) ) jn -=Ny;
if (!(kn < Nz) ) kn -=Nz;
*/ // symmetric boundary
if (in < 0 ) in = i;
if (jn < 0 ) jn = j;
if (kn < 0 ) kn = k;
if (!(in < Nx) ) in = i;
if (!(jn < Ny) ) jn = k;
if (!(kn < Nz) ) kn = k;
// 1-D index
nn = kn*Nx*Ny + jn*Nx + in;
@ -103,20 +128,18 @@ inline void SSO(DoubleArray &Distance, IntArray &ID, int timesteps){
norm = sqrt(Dx*Dx+Dy*Dy+Dz*Dz);
}
else{
norm = 0.7;
norm = 0.0;
}
Distance.data[n] += dt*sign*(1.0 - norm);
// Disallow any change in phase position
if (Distance.data[n]*ID.data[n] < 0) Distance.data[n] = -Distance.data[n];
// Disallow any change in phase
if (Distance.data[n]*2.0*(ID[n]-1.0) < 0) Distance.data[n] = -Distance.data[n];
}
}
}
count++;
}
}
int main(){
@ -136,28 +159,31 @@ int main(){
double fxm,fym,fzm,fxp,fyp,fzp;
double fxy,fXy,fxY,fXY,fxz,fXz,fxZ,fXZ,fyz,fYz,fyZ,fYZ;
double nx,ny,nz;
int ip,im,jp,jm,kp,km;
int count = 0;
double sign;
double dt=0.01;
double dt=1.0;
printf("Nx=%i, Ny=%i, Nz= %i, \n",Nx,Ny,Nz);
short int *id;
char *id;
#ifdef READMEDIA
Nx = 347;
Ny = 347;
Nz = 235;
Nx = 512;
Ny = 512;
Nz = 512;
N = Nx*Ny*Nz;
id = new short int [N];
FILE *INPUT = fopen("Solid.dat",'rb');
fread(id,4,N*,Ny*Nz,INPUT)
id = new char [N];
FILE *INPUT = fopen("Solid.dat","rb");
fread(id,1,Nx*Ny*Nz,INPUT);
fclose(INPUT);
#else
id = new short int [N];
id = new char [N];
double BubbleRadius = 5;
// Initialize the bubble
for (k=0;k<Nz;k++){
@ -176,6 +202,21 @@ int main(){
}
#endif
DoubleArray Distance(Nx,Ny,Nz);
// Initialize the signed distance function
for (k=0;k<Nz;k++){
for (j=0;j<Ny;j++){
for (i=0;i<Nx;i++){
n=k*Nx*Ny+j*Nx+i;
// Initialize distance to +/- 1
Distance(i,j,k) = 2.0*ID[n]-1.0;
}
}
}
printf("Initialized! Converting to Signed Distance function \n");
SSO(Distance,id,20);
/* double *f,*f_old,*f_new;
f = new double[N];
f_old = new double[N];
@ -184,9 +225,11 @@ int main(){
for (int n=0; n<N; n++) Distance.data[n] = 0.5*(id[n]-1);
for (int n=0; n<N; n++) f_old[n] = Distance.data[n];
for (int n=0; n<N; n++) f_new[n] = Distance.data[n];
for (int n=0; n<N; n++) f[n] = Distance.data[n];
count=0;
while (count < 10000 && dt > 1.0e-6){
dt=1.0;
while (count < 10 && dt > 1.0e-6){
err = 0.0;
for (k=0;k<Nz;k++){
@ -306,7 +349,7 @@ int main(){
f_y = 0.5*(f[k*Nx*Ny + jp*Nx + i] - f[k*Nx*Ny + jm*Nx + i]);
f_z = 0.5*(f[kp*Nx*Ny + j*Nx + i] - f[km*Nx*Ny + j*Nx + i]);
if (id[n] > 0){
if (id[n] < 0){
if ( nx > 0.0) f_x = fxp;
else f_x = fxm;
if ( ny > 0.0) f_y = fyp;
@ -348,8 +391,8 @@ int main(){
count++;
}
*/
*/
FILE *DIST;
DIST = fopen("SignDist","wb");
fwrite(Distance.data,8,N,DIST);

108
tests/TestSegDist.cpp Normal file
View File

@ -0,0 +1,108 @@
// Compute the signed distance from a digitized image
// Two phases are present
// Phase 1 has value -1
// Phase 2 has value 1
// this code uses the segmented image to generate the signed distance
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <iostream>
#include <fstream>
#include <Array.h>
int main(int argc, char **argv)
{
// Initialize MPI
int rank, nprocs;
MPI_Init(&argc,&argv);
MPI_Comm_rank(MPI_COMM_WORLD,&rank);
MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
int i,j,k,n,nn;
int nx,ny,nz;
int Nx, Ny, Nz, N;
Nx = Ny = Nz = 50;
N = Nx*Ny*Nz;
if (nprocs != 8){
ERROR("TestSegDist: Number of MPI processes must be equal to 8");
}
//.......................................................................
// Reading the domain information file
//.......................................................................
int nprocx, nprocy, nprocz, nx, ny, nz, nspheres;
double Lx, Ly, Lz;
ifstream domain("Domain.in");
domain >> nprocx;
domain >> nprocy;
domain >> nprocz;
domain >> nx;
domain >> ny;
domain >> nz;
domain >> nspheres;
domain >> Lx;
domain >> Ly;
domain >> Lz;
nprocx=nprocy=nprocz=2;
if (nprocx !=2 || nprocz !=2 || nprocy !=2 ){
ERROR("TestSegDist: MPI process grid must be 2x2x2");
}
int BC=0;
// Get the rank info
Domain Dm(nx,ny,nz,rank,nprocx,nprocy,nprocz,Lx,Ly,Lz,BC);
nx+=2; ny+=2; nz+=2;
int count = 0;
char *id;
id = new char [N];
double BubbleRadius = 5;
// Initialize the bubble
int x,y,z;
for (k=1;k<nz-1;k++){
for (j=1;j<ny-1;j++){
for (i=1;i<nx-1;i++){
x = (nx-2)*iproc+i;
y = (ny-2)*jproc+i;
z = (nz-2)*kproc+i;
// Initialize phase positions
if ((x-nx+1)*(x-nx+1)+(y-ny+1)*(y-ny+1)+(z-nz+1)*(z-nz+1) < BubbleRadius*BubbleRadius){
id[n] = 0;
}
else{
id[n]=1;
}
}
}
}
DoubleArray Distance(Nx,Ny,Nz);
// Initialize the signed distance function
for (k=0;k<Nz;k++){
for (j=0;j<Ny;j++){
for (i=0;i<Nx;i++){
n=k*Nx*Ny+j*Nx+i;
// Initialize distance to +/- 1
Distance(i,j,k) = 2.0*id[n]-1.0;
}
}
}
printf("Initialized! Converting to Signed Distance function \n");
SSO(Distance,id,Dm,10);
char LocalRankFilename[40];
sprintf(LocalRankFilename,"Dist.%05i",rank);
FILE *DIST = fopen(LocalRankFilename,"wb");
fwrite(Distance.get(),8,Distance.length(),DIST);
fclose(DIST);
MPI_Barrier(MPI_COMM_WORLD);
MPI_Finalize();
return 0;
}