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factored out uCT parameters

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This commit is contained in:
James E McClure 2018-06-06 19:00:42 -04:00
parent 4865229ae3
commit 1deabfc947
3 changed files with 15 additions and 9 deletions
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13
analysis/uCT.cpp
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@ -164,7 +164,8 @@ void solve( const Array<float>& VOL, Array<float>& Mean, Array<char>& ID,
void refine( const Array<float>& Dist_coarse, void refine( const Array<float>& Dist_coarse,
const Array<float>& VOL, Array<float>& Mean, Array<char>& ID, const Array<float>& VOL, Array<float>& Mean, Array<char>& ID,
Array<float>& Dist, Array<float>& MultiScaleSmooth, Array<float>& NonLocalMean, Array<float>& Dist, Array<float>& MultiScaleSmooth, Array<float>& NonLocalMean,
fillHalo<float>& fillFloat, const Domain& Dm, int nprocx, int level ) fillHalo<float>& fillFloat, const Domain& Dm, int nprocx, int level,
float threshold, float lamda, float sigsq, int depth)
{ {
PROFILE_SCOPED(timer,"refine"); PROFILE_SCOPED(timer,"refine");
int ratio[3] = { int(Dist.size(0)/Dist_coarse.size(0)), int ratio[3] = { int(Dist.size(0)/Dist_coarse.size(0)),
@ -175,7 +176,7 @@ void refine( const Array<float>& Dist_coarse,
// Compute the median filter on the array and segment // Compute the median filter on the array and segment
Med3D( VOL, Mean ); Med3D( VOL, Mean );
fillFloat.fill( Mean ); fillFloat.fill( Mean );
segment( Mean, ID, 0.01 ); segment( Mean, ID, threshold );
// If the ID has the wrong distance, set the distance to 0 and run a simple filter to set neighbors to 0 // If the ID has the wrong distance, set the distance to 0 and run a simple filter to set neighbors to 0
for (size_t i=0; i<ID.length(); i++) { for (size_t i=0; i<ID.length(); i++) {
char id = Dist(i)>0 ? 1:0; char id = Dist(i)>0 ? 1:0;
@ -193,11 +194,11 @@ void refine( const Array<float>& Dist_coarse,
Dist = imfilter::imfilter_separable<float>( Dist, {1,1,1}, filter_set, BC ); Dist = imfilter::imfilter_separable<float>( Dist, {1,1,1}, filter_set, BC );
fillFloat.fill( Dist ); fillFloat.fill( Dist );
// Smooth the volume data // Smooth the volume data
float lambda = 2*sqrt(double(ratio[0]*ratio[0]+ratio[1]*ratio[1]+ratio[2]*ratio[2])); float h = 2*lamda*sqrt(double(ratio[0]*ratio[0]+ratio[1]*ratio[1]+ratio[2]*ratio[2]));
smooth( VOL, Dist, lambda, MultiScaleSmooth, fillFloat ); smooth( VOL, Dist, h, MultiScaleSmooth, fillFloat );
// Compute non-local mean // Compute non-local mean
int depth = 3; // int depth = 3;
float sigsq = 0.1; // float sigsq = 0.1;
int nlm_count = NLM3D( MultiScaleSmooth, Mean, Dist, NonLocalMean, depth, sigsq); int nlm_count = NLM3D( MultiScaleSmooth, Mean, Dist, NonLocalMean, depth, sigsq);
fillFloat.fill(NonLocalMean); fillFloat.fill(NonLocalMean);
segment( NonLocalMean, ID, 0.001 ); segment( NonLocalMean, ID, 0.001 );

3
analysis/uCT.h
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@ -31,7 +31,8 @@ void removeDisconnected( Array<char>& ID, const Domain& Dm );
// Solve a level (without any coarse level information) // Solve a level (without any coarse level information)
void solve( const Array<float>& VOL, Array<float>& Mean, Array<char>& ID, void solve( const Array<float>& VOL, Array<float>& Mean, Array<char>& ID,
Array<float>& Dist, Array<float>& MultiScaleSmooth, Array<float>& NonLocalMean, Array<float>& Dist, Array<float>& MultiScaleSmooth, Array<float>& NonLocalMean,
fillHalo<float>& fillFloat, const Domain& Dm, int nprocx ); fillHalo<float>& fillFloat, const Domain& Dm, int nprocx,
float threshold, float lamda, float sigsq, int depth);
// Refine a solution from a coarse grid to a fine grid // Refine a solution from a coarse grid to a fine grid

8
tests/lbpm_uCT_pp.cpp
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@ -71,6 +71,10 @@ int main(int argc, char **argv)
int nprocz = nproc[2]; int nprocz = nproc[2];
auto InputFile=uct_db->getScalar<std::string>( "InputFile" ); auto InputFile=uct_db->getScalar<std::string>( "InputFile" );
auto rough_cutoff=uct_db->getScalar<float>( "rought_cutoff" );
auto lamda=uct_db->getScalar<float>( "lamda" );
auto nlm_sigsq=uct_db->getScalar<float>( "nlm_sigsq" );
auto nlm_depth=uct_db->getScalar<int>( "nlm_depth" );
//....................................................................... //.......................................................................
// Reading the domain information file // Reading the domain information file
@ -243,7 +247,6 @@ int main(int argc, char **argv)
} }
} }
// Fill the source data for the coarse meshes // Fill the source data for the coarse meshes
PROFILE_START("CoarsenMesh"); PROFILE_START("CoarsenMesh");
for (int i=1; i<N_levels; i++) { for (int i=1; i<N_levels; i++) {
@ -269,7 +272,8 @@ int main(int argc, char **argv)
if (rank==0) if (rank==0)
printf("Initialize full mesh\n"); printf("Initialize full mesh\n");
solve( LOCVOL[0], Mean[0], ID[0], Dist[0], MultiScaleSmooth[0], solve( LOCVOL[0], Mean[0], ID[0], Dist[0], MultiScaleSmooth[0],
NonLocalMean[0], *fillFloat[0], *Dm[0], nprocx ); NonLocalMean[0], *fillFloat[0], *Dm[0], nprocx,
rough_cutoff, lamda, nlm_sigsq, nlm_depth);
PROFILE_STOP("Solve fill mesh"); PROFILE_STOP("Solve fill mesh");
MPI_Barrier(comm); MPI_Barrier(comm);