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basic vis for uCT

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This commit is contained in:
James E McClure 2018-06-06 15:00:55 -04:00
parent f461bb4852
commit 1479a13ab2
2 changed files with 61 additions and 21 deletions
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32
example/uCT/eos-uCT.pbs Normal file
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@ -0,0 +1,32 @@
#!/bin/bash
#PBS -A GEO106
#PBS -N uCT
#PBS -j oe
##PBS -l walltime=02:30:00,nodes=20
#PBS -l walltime=00:10:00,nodes=20
##PBS -l gres=widow2%widow3
##PBS -q killable
#PBS -q debug
#cd /tmp/work/$USER
date
cd $PBS_O_WORKDIR
#LBPM_WIA_INSTALL_DIR=/lustre/atlas/proj-shared/geo106/build-eos-LBPM-WIA
LBPM_WIA_INSTALL_DIR=/ccs/proj/geo106/eos/LBPM-WIA
#echo "PBS_O_WORKDIR: `echo $PBS_O_WORKDIR`"
source $MODULESHOME/init/bash
module swap PrgEnv-intel PrgEnv-gnu
export LD_LIBRARY_PATH=${CRAY_LD_LIBRARY_PATH}:${LD_LIBRARY_PATH}
# generate distance map from the binary image
# input files are ID.xxxxx
# output files are SignDist.xxxxx
NUMPROCS=320
aprun -n $NUMPROCS $LBPM_WIA_INSTALL_DIR/bin/lbpm_uCT_pp input.db
exit;

50
tests/lbpm_uCT_pp.cpp
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@ -141,6 +141,7 @@ int main(int argc, char **argv)
MultiScaleSmooth[i].fill(0);
Mean[i].fill(0);
NonLocalMean[i].fill(0);
fillDouble[i].reset(new fillHalo<double>(Dm[i]->Comm,Dm[i]->rank_info,{Nx[i],Ny[i],Nz[i]},{1,1,1},0,1) );
fillFloat[i].reset(new fillHalo<float>(Dm[i]->Comm,Dm[i]->rank_info,{Nx[i],Ny[i],Nz[i]},{1,1,1},0,1) );
fillChar[i].reset(new fillHalo<char>(Dm[i]->Comm,Dm[i]->rank_info,{Nx[i],Ny[i],Nz[i]},{1,1,1},0,1) );
}
@ -229,6 +230,7 @@ int main(int argc, char **argv)
if (rank==0) printf(" Region 1 mean (+): %f, Region 2 mean (-): %f \n",mean_plus, mean_minus);
MPI_Barrier(comm);
// Scale the source data to +-1.0
for (size_t i=0; i<LOCVOL[0].length(); i++) {
if (MASK(i) < 0.f){
@ -245,7 +247,7 @@ int main(int argc, char **argv)
// Fill the source data for the coarse meshes
PROFILE_START("CoarsenMesh");
PROFILE_START("CoarsenMesh");
for (int i=1; i<N_levels; i++) {
Array<float> filter(ratio[0],ratio[1],ratio[2]);
filter.fill(1.0f/filter.length());
@ -277,19 +279,20 @@ int main(int argc, char **argv)
NonLocalMean[i], *fillFloat[i], *Dm[i], nprocx, i );
}
PROFILE_STOP("Refine distance");
// Perform a final filter
// Perform a final filter
PROFILE_START("Filtering final domains");
if (rank==0)
printf("Filtering final domains\n");
Array<float> filter_Mean, filter_Dist1, filter_Dist2;
filter_final( ID[0], Dist[0], *fillFloat[0], *Dm[0], filter_Mean, filter_Dist1, filter_Dist2 );
PROFILE_STOP("Filtering final domains");
//removeDisconnected( ID[0], *Dm[0] );
// Write the distance function to a netcdf file
/*
// Write the distance function to a netcdf file
const char* netcdf_filename = "Distance.nc";
{
RankInfoStruct info( rank, nprocx, nprocy, nprocz );
@ -301,33 +304,35 @@ int main(int argc, char **argv)
netcdf::write( fid, "Distance", dims, data, info );
netcdf::close( fid );
}
*/
// Write the results to visit
if (rank==0) printf("Writing output \n");
std::vector<IO::MeshDataStruct> meshData(N_levels);
for (size_t i=0; i<Nx.size(); i++) {
if (rank==0) printf("Setting up visualization structure \n");
// std::vector<IO::MeshDataStruct> meshData(N_levels);
std::vector<IO::MeshDataStruct> meshData(1);
// for (size_t i=0; i<Nx.size(); i++) {
// Mesh
meshData[i].meshName = "Level " + std::to_string(i+1);
meshData[i].mesh = std::shared_ptr<IO::DomainMesh>( new IO::DomainMesh(Dm[i]->rank_info,Nx[i],Ny[i],Nz[i],Lx,Ly,Lz) );
meshData[0].meshName = "image";
meshData[0].mesh = std::shared_ptr<IO::DomainMesh>( new IO::DomainMesh(Dm[0]->rank_info,Nx[0],Ny[0],Nz[0],Lx,Ly,Lz) );
// Source data
std::shared_ptr<IO::Variable> OrigData( new IO::Variable() );
OrigData->name = "Source Data";
OrigData->type = IO::VariableType::VolumeVariable;
OrigData->dim = 1;
OrigData->data.resize(Nx[i],Ny[i],Nz[i]);
meshData[i].vars.push_back(OrigData);
fillDouble[i]->copy( LOCVOL[i], OrigData->data );
OrigData->data.resize(Nx[0],Ny[0],Nz[0]);
meshData[0].vars.push_back(OrigData);
fillDouble[0]->copy( LOCVOL[0], OrigData->data );
// Non-Local Mean
std::shared_ptr<IO::Variable> NonLocMean( new IO::Variable() );
NonLocMean->name = "Non-Local Mean";
NonLocMean->type = IO::VariableType::VolumeVariable;
NonLocMean->dim = 1;
NonLocMean->data.resize(Nx[i],Ny[i],Nz[i]);
meshData[i].vars.push_back(NonLocMean);
fillDouble[i]->copy( NonLocalMean[i], NonLocMean->data );
// Segmented Data
std::shared_ptr<IO::Variable> SegData( new IO::Variable() );
NonLocMean->data.resize(Nx[0],Ny[0],Nz[0]);
meshData[0].vars.push_back(NonLocMean);
fillDouble[0]->copy( NonLocalMean[0], NonLocMean->data );
/*// Segmented Data
std::shared_ptr<IO::Variable> SegData( new IO::Variable() );
SegData->name = "Segmented Data";
SegData->type = IO::VariableType::VolumeVariable;
SegData->dim = 1;
@ -350,8 +355,9 @@ int main(int argc, char **argv)
SmoothData->data.resize(Nx[i],Ny[i],Nz[i]);
meshData[i].vars.push_back(SmoothData);
fillDouble[i]->copy( MultiScaleSmooth[i], SmoothData->data );
}
#if 0
#if 0
std::shared_ptr<IO::Variable> filter_Mean_var( new IO::Variable() );
filter_Mean_var->name = "Mean";
filter_Mean_var->type = IO::VariableType::VolumeVariable;
@ -374,7 +380,9 @@ int main(int argc, char **argv)
meshData[0].vars.push_back(filter_Dist2_var);
fillDouble[0]->copy( filter_Dist2, filter_Dist2_var->data );
#endif
*/
MPI_Barrier(comm);
if (rank==0) printf("Writing output \n");
// Write visulization data
IO::writeData( 0, meshData, comm );
if (rank==0) printf("Finished. \n");