int main (int argc, char **argv)
{
GetPot cl (argc, argv);
if (cl.search (2, "-h", "--help"))
{
std::cerr << help_text << std::endl;
return 0;
}
const double a = cl.follow (0.0, "-a");
const double b = cl.follow (1.0, "-b");
const unsigned int nnodes = cl.follow (100, 2, "-n", "--nnodes");
const std::string diffusion = cl.follow ("1.0", 2, "-d", "--diffusion");
const std::string forcing = cl.follow ("1.0", 2, "-f", "--forcing");
std::unique_ptr<mesh<double>> m (new mesh<double> (a, b, nnodes));
fem_1d<double> problem (std::move (m));
coeff<double> a_coeff (diffusion);
problem.set_diffusion_coefficient (a_coeff);
coeff<double> f_coeff (forcing);
problem.set_source_coefficient (f_coeff);
problem.assemble ();
problem.set_dirichlet (fem_1d<double>::left_boundary, 0.0);
problem.set_dirichlet (fem_1d<double>::right_boundary, 0.0);
problem.solve ();
for (unsigned int ii = 0; ii < nnodes; ++ii)
std::cout << problem.m->nodes[ii] << " "
<< problem.result ()(ii, 0)
<< std:: endl;
return 0;
};
int main (int argc, char *argv[])
{
const unsigned int ImageDimension = 2;
GetPot cl (argc, const_cast<char**>(argv));
if( cl.size() == 1 || cl.search (2,"--help","-h") )
{
std::cout << "Not Enough Arguments" << std::endl;
std::cout << "Generate the Gradient Table" << std::endl;
std::cout << "Usage: return -1" << std::endl;
}
const string image_n = cl.follow("NoFile",1, "-i");
const string out_n = cl.follow("NoFile",1, "-o");
typedef itk::DiffusionTensor3D<float> DiffusionTensorType;
typedef itk::Image<DiffusionTensorType, 3> ImageType;
typedef itk::ImageFileReader<ImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(image_n);
reader->Update();
ImageType::Pointer image = reader->GetOutput();
typedef itk::ImageRegionIterator<ImageType> TensorIterator;
TensorIterator itImg(image, image->GetLargestPossibleRegion());
std::ofstream file;
file.open(out_n);
for(itImg.GoToBegin(); !itImg.IsAtEnd(); ++itImg)
{
file << itImg.Get() << std::endl;
}
file.close();
return 0;
}
int main (int argc, char **argv)
{
GetPot cl (argc, argv);
if (cl.search (2, "-h", "--help"))
{
std::cerr << help_text << std::endl;
return 0;
}
const double a = cl.follow (0.0, "-a");
const double b = cl.follow (1.0, "-b");
const unsigned int nnodes = cl.follow (100, 2, "-n", "-nnodes");
mesh m (a, b, nnodes);
Eigen::MatrixXd A(nnodes, nnodes);
Eigen::Matrix2d mloc;
mloc << 0, 0, 0, 0;
for (unsigned int iel = 0; iel < m.nels; ++iel)
{
mloc << 0, 0, 0, 0;
for (unsigned int inode = 0; inode < 2; ++inode)
{
double igrad = (inode == 0 ? 1.0 / m.h : -1.0 / m.h);
for (unsigned int jnode = 0; jnode < 2; ++jnode)
{
double jgrad = (jnode == 0 ? 1.0 / m.h : -1.0 / m.h);
mloc(inode,jnode) = igrad * jgrad * m.h;
A(m.elements[iel][inode],m.elements[iel][jnode]) +=
mloc(inode,jnode);
}
}
}
Eigen::VectorXd f(nnodes);
Eigen::Vector2d vloc;
for (unsigned int iel = 0; iel < m.nels; ++iel)
{
vloc << 0, 0;
for (unsigned int inode = 0; inode < 2; ++inode)
{
vloc(inode) = m.h / 2.0;
f(m.elements[iel][inode]) += vloc(inode);
}
}
f(0) = 0;
f(nnodes - 1) = 0;
A(0,0) = 1.0;
A(nnodes-1,nnodes-1) = 1.0;
for (unsigned int ii = 1; ii < nnodes; ++ii)
{
A(0, ii) = 0.0;
A(nnodes-1, nnodes-1-ii) = 0.0;
}
Eigen::VectorXd uh = A.partialPivLu ().solve (f);
for (unsigned int ii = 0; ii < nnodes; ++ii)
std::cout << uh(ii, 0) << std:: endl;
return 0;
};
int main (int argc, char **argv)
{
GetPot cl (argc, argv);
if (cl.search (2, "-h", "--help"))
{
std::cerr << help_text << std::endl;
return 0;
}
const double a = cl.follow (0.0, "-a");
const double b = cl.follow (1.0, "-b");
const unsigned int nnodes = cl.follow (100, 2, "-n", "-nnodes");
mesh m (a, b, nnodes);
matrix A(nnodes);
matrix mloc(2);
for (unsigned int iel = 0; iel < m.nels; ++iel)
{
std::fill (mloc.get_data (),
mloc.get_data () + 4,
0.0);
for (unsigned int inode = 0; inode < 2; ++inode)
{
double igrad = (inode == 0 ? 1.0 / m.h : -1.0 / m.h);
for (unsigned int jnode = 0; jnode < 2; ++jnode)
{
double jgrad = (jnode == 0 ? 1.0 / m.h : -1.0 / m.h);
mloc(inode,jnode) = igrad * jgrad * m.h;
A(m.elements[iel][inode],m.elements[iel][jnode]) +=
mloc(inode,jnode);
}
}
}
matrix f(nnodes, 1);
matrix vloc(2, 1);
for (unsigned int iel = 0; iel < m.nels; ++iel)
{
std::fill (mloc.get_data (),
mloc.get_data () + 2,
0.0);
for (unsigned int inode = 0; inode < 2; ++inode)
{
vloc(inode, 0) = m.h / 2.0;
f(m.elements[iel][inode], 0) += vloc(inode, 0);
}
}
f(0, 0) = 0;
f(nnodes - 1, 0) = 0;
A(0,0) = 1.0;
A(nnodes-1,nnodes-1) = 1.0;
for (unsigned int ii = 1; ii < nnodes; ++ii)
{
A(0, ii) = 0.0;
A(nnodes-1, nnodes-1-ii) = 0.0;
}
matrix uh(f);
A.solve (uh);
for (unsigned int ii = 0; ii < nnodes; ++ii)
std::cout << uh(ii, 0) << std:: endl;
return 0;
};
int main (int argc, char** argv)
{
#ifdef LIFEV_HAS_HDF5
#ifdef HAVE_MPI
typedef RegionMesh<LinearTetra> mesh_Type;
MPI_Init (&argc, &argv);
boost::shared_ptr<Epetra_Comm> comm (new Epetra_MpiComm (MPI_COMM_WORLD) );
if (comm->NumProc() != 1)
{
std::cout << "This test needs to be run "
<< "with a single process. Aborting."
<< std::endl;
return (EXIT_FAILURE);
}
GetPot commandLine (argc, argv);
string dataFileName = commandLine.follow ("data", 2, "-f", "--file");
GetPot dataFile (dataFileName);
const UInt numElements (dataFile ("mesh/nelements", 10) );
const UInt numParts (dataFile ("test/num_parts", 4) );
const std::string partsFileName (dataFile ("test/hdf5_file_name", "cube.h5") );
const std::string ioClass (dataFile ("test/io_class", "new") );
std::cout << "Number of elements in mesh: " << numElements << std::endl;
std::cout << "Number of parts: " << numParts << std::endl;
std::cout << "Name of HDF5 container: " << partsFileName << std::endl;
boost::shared_ptr<mesh_Type> fullMeshPtr (new mesh_Type ( comm ) );
regularMesh3D (*fullMeshPtr, 1, numElements, numElements, numElements,
false, 2.0, 2.0, 2.0, -1.0, -1.0, -1.0);
MeshPartitioner<mesh_Type> meshPart;
meshPart.setup (numParts, comm);
meshPart.attachUnpartitionedMesh (fullMeshPtr);
meshPart.doPartitionGraph();
meshPart.doPartitionMesh();
// Release the original mesh from the MeshPartitioner object and
// delete the RegionMesh object
meshPart.releaseUnpartitionedMesh();
fullMeshPtr.reset();
// Write mesh parts to HDF5 container
if (! ioClass.compare ("old") )
{
ExporterHDF5Mesh3D<mesh_Type> HDF5Output (dataFile,
meshPart.meshPartition(),
partsFileName,
comm->MyPID() );
HDF5Output.addPartitionGraph (meshPart.elementDomains(), comm);
HDF5Output.addMeshPartitionAll (meshPart.meshPartitions(), comm);
HDF5Output.postProcess (0);
HDF5Output.closeFile();
}
else
{
boost::shared_ptr<Epetra_MpiComm> mpiComm =
boost::dynamic_pointer_cast<Epetra_MpiComm> (comm);
PartitionIO<mesh_Type> partitionIO (partsFileName, mpiComm);
partitionIO.write (meshPart.meshPartitions() );
}
MPI_Finalize();
#else
std::cout << "This test needs MPI to run. Aborting." << std::endl;
return (EXIT_FAILURE);
#endif /* HAVE_MPI */
#else
std::cout << "This test needs HDF5 to run. Aborting." << std::endl;
return (EXIT_FAILURE);
#endif /* LIFEV_HAS_HDF5 */
return (EXIT_SUCCESS);
}
void Server::parseConfig(GetPot &config)
{
// this variable is needed for setting up the partial loading part when the features
// are loaded for the very first time at fire start up
string partialLoadingString="empty";
if(config.search(2,"-F","--filter"))
{
string unparsed = config.follow("empty",2,"-F","--filter");
if (parseFilter(unparsed.c_str()))
{
retriever_.setFilterApply(true);
DBG(10) << "Using filter " << unparsed << " for retrieval" << endl;
}
else
{
retriever_.setFilterApply(false);
retriever_.clearFilter();
DBG(10) << "Error in filter String " << unparsed << endl;
DBG(10) << "Aborting filtering and using normal retrieval settings" << endl;
}
}
if(config.search(2,"-q","--queryCombiner")) {
retriever_.setQueryCombiner(config.follow("adding:POS=1.0:NEG=0.833",2,"-q","--queryCombiner"));
}
if(config.search("--reRanker")) {
retriever_.setReranking(config.follow("cluster:CONS=100:RR=20:CLUSTERS=5","--reRanker"));
}
if(config.search(2,"-U","--defdontload"))
{
partialLoadingString="default";
retriever_.setPartialLoadingApply(true);
}
if(config.search(2,"-u","--dontload"))
{
string unparsed=config.follow("empty",2,"-u","--dontload");
if(unparsed!="empty")
{
// the parsing is not possible here, because the amount of different features
// is not known yet
// but a sanity check is possible
const char* str = unparsed.c_str();
bool errformat = false;
// note it is not checked if there are two or more : present in a row
while(*str != '\0' && !errformat)
{
if(!isdigit(*str) && *str!=':')
{
errformat=true;
DBG(10) << "Error in format string " << unparsed << " following -u/--dontload option" << endl;
DBG(10) << "format string must start with a digit; aborting partial feature loading" << endl;
}
str++;
}
if(!errformat && retriever_.setPartialLoadingApply(true))
{
partialLoadingString=unparsed;
}
else
{
ERR << "-u/--dontload was used without -F/--filter option or there are illegal characters in the format string" << endl;
ERR << "ignoring -u/--dontload option, loading all features" << endl;
}
}
else
{
retriever_.setPartialLoadingApply(false);
ERR << "Error after -u/--dontload option: No featureindexsequence given" << endl;
//DBG(10) << "Aborting partial loading for filtered retrieval and loading all features" << endl;
}
}
if(config.search(2,"-f","--filelist"))
{
string filelistname=config.follow("list.txt",2,"-f","--filelist");
string result=retriever_.filelist(filelistname,partialLoadingString);
if(result=="filelist FAILURE")
{
ERR << "Error in filelist. Please correct it and start again." << endl;
exit(1);
}
DBG(10) << result << endl;
}
if(config.search(2,"-R","--relevancefile"))
{
relevanceFile_=config.follow("",2,"-R","--relevancefile");
}
retriever_.setScoring("linear");
log_=LogFile(config.follow("",2,"-l","--logfile"));
if(config.search(2,"-D","--defaultdists"))
{
for(uint i=0;i<retriever_.numberOfSuffices();++i)
{
retriever_.dist(i,distanceMaker_.getDefaultDistance(retriever_.featureType(i)));
retriever_.weight(i,1.0);
DBG(10) << "default dist[" << i << "]=" << retriever_.dist(i)->name() << endl;
}
}
config.init_multiple_occurrence(); // can have multiple distances
while(config.search(2,"-d","--dist"))
{
uint idx=config.follow(0,2,"-d","--dist");
string distname=config.next("basedist"); // default distance measure (dummy!)
retriever_.weight(idx,1.0); // set default weight for configured distances
retriever_.dist(idx,distanceMaker_.makeDistance(distname));
DBG(10) << "dist[" << idx << "]=" << retriever_.dist(idx)->name() << endl;
}
config.init_multiple_occurrence(); // can have multiple weights
while(config.search(2,"-w","--weight"))
{
uint idx=config.follow(0,2,"-w","--weight");
double w=config.next(1.0);
retriever_.weight(idx,w);
DBG(10) << "weight[" << idx << "]=" << w << endl;
}
retriever_.setScoring(config.follow("linear",2,"-C","--scoring"));
if(config.search(2,"-I","--interactor"))
{
retriever_.setInteractor(config.follow("",2,"-I","--interactor"));
}
config.enable_loop(); // enable returning to the beginning of command line (was disabled for multiplicity before)
if(config.search(2,"-S","--startAfterInit"))
{
startAfterInit_=config.follow("echo \"No program defined\"",2,"-S","--startAfterInit");
}
if(config.search(2,"-P","--proxy"))
{
proxyhost_=config.follow("localhost",2,"-P","--proxy");
proxyport_=config.next(12963);
DBG(10) << "Will notify proxy at " << proxyhost_ << ":"<<proxyport_ << " about my existence." << endl;
}
if(config.search(2,"-r","--results"))
{
retriever_.results(config.follow(9,2,"-r","--results"));
DBG(10) << "results=" << retriever_.results() << endl;
}
if(config.search(2,"-l","--log"))
{
logfile_=config.follow("log.txt",2,"-l","--log");
DBG(10) << "logfile="<< logfile_ << endl;
}
if(config.search(2,"-s","--server"))
{
port_=config.follow(12961,2,"-s","--server");
DBG(10) << "port="<< port_ << endl;
}
if(config.search(2,"-B","--batch"))
{
batchfile_=config.follow("batch",2,"-B","--batch");
DBG(10) << "batchfile="<< batchfile_ << endl;
}
if(config.search("--cache")) {
retriever_.setCache(config.follow("cache.sqlite3.db","--cache"));
}
if(config.search(2,"-e","--expansion"))
{
retriever_.extensions(config.follow(2,2,"-e","--expansion"));
DBG(10) << "expansions=" << config.follow(2,2,"-e","--expansion") << endl;
}
if(config.search(2,"-p","--password"))
{
password_=config.follow("",2,"-p","--password");
DBG(10) << "password necessary for changing settings: " << password_ << endl;
}
if(config.search(2,"-t","--type2bin"))
{
t2bpath=config.follow("",2,"-t","--type2bin");
DBG(10) << "type2bin-file has been reset to: " << t2bpath << endl;
}
}
int
main ( int argc, char** argv )
{
#ifdef LIFEV_HAS_HDF5
#ifdef HAVE_MPI
MPI_Init (&argc, &argv);
boost::shared_ptr<Epetra_MpiComm> comm (new Epetra_MpiComm (MPI_COMM_WORLD) );
const bool verbose (comm->MyPID() == 0);
// Read first the data needed
if (verbose)
{
std::cout << " -- Reading the data ... " << std::flush;
}
// GetPot dataFile ( "data" );
if (verbose)
{
std::cout << " done ! " << std::endl;
}
GetPot cl (argc, argv);
// partitionerType should be MeshPartitioner, MeshPartitionTool_ParMETIS or
// MeshPartitionTool_Zoltan
const std::string partitionerType = cl.follow ("MeshPartitioner",
"--partitioner-type");
std::string partsFile;
partsFile.reserve (50);
partsFile += "cube_";
partsFile += partitionerType;
partsFile += ".h5";
boost::shared_ptr<mesh_Type> mesh;
{
PartitionIO<RegionMesh<LinearTetra> > partitionIO (partsFile, comm);
partitionIO.read (mesh);
}
// Build the FESpaces
if (verbose)
{
std::cout << " -- Building FESpaces ... " << std::flush;
}
std::string uOrder ("P1");
std::string bOrder ("P1");
boost::shared_ptr<FESpace<mesh_Type, MapEpetra> >
uFESpace (new FESpace<mesh_Type, MapEpetra> (mesh, uOrder, 1, comm) );
boost::shared_ptr<FESpace<mesh_Type, MapEpetra> >
betaFESpace (new FESpace<mesh_Type, MapEpetra> (mesh, bOrder, 3, comm) );
if (verbose)
{
std::cout << " done ! " << std::endl;
}
if (verbose) std::cout << " ---> Dofs: "
<< uFESpace->dof().numTotalDof() << std::endl;
// Build the assembler and the matrices
if (verbose)
{
std::cout << " -- Building assembler ... " << std::flush;
}
ADRAssembler<mesh_Type, matrix_Type, vector_Type> adrAssembler;
if (verbose)
{
std::cout << " done! " << std::endl;
}
if (verbose)
{
std::cout << " -- Setting up assembler ... " << std::flush;
}
adrAssembler.setup (uFESpace, betaFESpace);
if (verbose)
{
std::cout << " done! " << std::endl;
}
if (verbose)
{
std::cout << " -- Defining the matrix ... " << std::flush;
}
boost::shared_ptr<matrix_Type>
systemMatrix (new matrix_Type (uFESpace->map() ) );
*systemMatrix *= 0.0;
if (verbose)
{
std::cout << " done! " << std::endl;
}
// Perform the assembly of the matrix
if (verbose)
{
std::cout << " -- Adding the diffusion ... " << std::flush;
}
adrAssembler.addDiffusion (systemMatrix, 1);
if (verbose)
{
std::cout << " done! " << std::endl;
}
if (verbose) std::cout << " Time needed : "
<< adrAssembler.diffusionAssemblyChrono().diffCumul()
<< std::endl;
if (verbose)
{
std::cout << " -- Closing the matrix ... " << std::flush;
}
systemMatrix->globalAssemble();
if (verbose)
{
std::cout << " done ! " << std::endl;
}
Real matrixNorm (systemMatrix->normFrobenius() );
if (verbose)
{
std::cout << " ---> Norm 2 : " << matrixNorm << std::endl;
}
if (std::fabs (matrixNorm - 35.908) > 1e-3)
{
std::cout << " <!> Matrix has changed !!! <!> " << std::endl;
return EXIT_FAILURE;
}
if (verbose)
{
std::cout << "End Result: TEST PASSED" << std::endl;
}
MPI_Finalize();
#else
std::cout << "This test needs MPI to run. Aborting." << std::endl;
return (EXIT_FAILURE);
#endif /* HAVE_MPI */
#else
std::cout << "This test needs HDF5 to run. Aborting." << std::endl;
return (EXIT_FAILURE);
#endif /* LIFEV_HAS_HDF5 */
return ( EXIT_SUCCESS );
}
int main (int argc, char *argv[])
{
GetPot cl (argc, const_cast<char**>(argv));
if( cl.size() == 1 || cl.search (2,"--help","-h") )
{
std::cout << "Not Enough Arguments" << std::endl;
std::cout << "Scales the tensors with a scalar factor" << std::endl;
std::cout << "Usage: -trueB0 <true B0> -m <MaskImage> -true <True Tensors> -f <flag for extended gradient> -t <initial tensor estimate> -g <gradient> -o <Output File> -s <Sigma> -nm <Noise Model> -Sim <intelligent COnvergence>" << std::endl;
return -1;
}
const string image_n =cl.follow("NoFile", 1, "-i");
const string out_n = cl.follow("NoFile", 1, "-o");
const int idx = cl.follow(0, 1, "-ix");
const int idy = cl.follow(0, 1, "-iy");
const int idz = cl.follow(0, 1, "-iz");
const int sx = cl.follow(0, 1, "-sx");
const int sy = cl.follow(0, 1, "-sy");
const int sz = cl.follow(0, 1, "-sz");
typedef itk::Image< float, 3> ImageType;
typedef itk::ImageFileReader<ImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(image_n);
reader->Update();
ImageType::Pointer image = reader->GetOutput();
ImageType::SizeType size;
ImageType::IndexType id;
id[0] = idx; id[1] = idy; id[2] = idz;
size[0] = sx; size[1] = sy; size[2] =sz;
ImageType::RegionType region(id, size);
typedef itk::ExtractImageFilter<ImageType, ImageType> FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetExtractionRegion(region);
filter->SetInput(image);
filter->SetDirectionCollapseToIdentity();
filter->Update();
ImageType::Pointer exImage = filter ->GetOutput();
typedef itk::ImageFileWriter<ImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(out_n);
writer->SetInput(exImage);
writer->Update();
return 0;
}
int main(int argc, char *argv[])
{
GetPot cl (argc, const_cast<char**>(argv));
if( cl.size() == 1 || cl.search (2,"--help","-h") )
{
std::cout << "Not Enough Arguments" << std::endl;
std::cout << "Generate the Gradient Table" << std::endl;
std::cout << "Usage: return -1" << std::endl;
}
// One idea is to apply the rotation matrix
const string Linear_trans_n = cl.follow("NoFile",1,"-t");
const string ref_Image_n = cl.follow("NoFile",1, "-r");
const string out_n = cl.follow("NoFile",1,"-o");
const string B0_n =cl.follow("NoFile",1,"-B0");
const string T1_n =cl.follow("NoFile",1,"-T1");
typedef itk::Image<float, 3> ImageType;
typedef itk::ImageFileReader<ImageType> ImageReaderType;
ImageReaderType::Pointer imageReaderB0 = ImageReaderType::New();
imageReaderB0->SetFileName(B0_n);
imageReaderB0->Update();
std::cout << imageReaderB0->GetOutput()->GetDirection() << std::endl;
ImageReaderType::Pointer imageReaderT1 = ImageReaderType::New();
imageReaderT1->SetFileName(B0_n);
imageReaderT1->Update();
std::cout << imageReaderT1->GetOutput()->GetDirection() << std::endl;
// typedef itk::TransformFileReader TransformFileReaderType;
// typedef TransformFileReaderType::TransformListType TransformListType;
// typedef itk::TransformBase TransformBaseType;
// typedef itk::AffineTransform<double, 3> AffineTransformType;
//
// typedef itk::Image<float, 3> ImageType;
// typedef itk::ImageFileReader<ImageType> ImageReaderType;
// ImageReaderType::Pointer imageReader = ImageReaderType::New();
//
// imageReader->SetFileName(ref_Image_n);
// imageReader->Update();
// ImageType::Pointer refImage = imageReader->GetOutput();
//
//
//
// TransformFileReaderType::Pointer readerTransform = TransformFileReaderType::New();
// readerTransform->SetFileName(Linear_trans_n);
// readerTransform -> Update();
// TransformListType *list = readerTransform->GetTransformList();
// TransformBaseType * transform = list->front().GetPointer();
// TransformBaseType::ParametersType parameters = transform->GetParameters();
// AffineTransformType::Pointer transform_fwd = AffineTransformType::New();
// transform_fwd->SetParameters(parameters);
//
// std::cout << transform_fwd->GetParameters() << std::endl;
// typedef itk::Vector< float, 3 > VectorPixelType;
// typedef itk::Image< VectorPixelType, 3 > DisplacementFieldImageType;
//
//
// typedef itk::TransformToDisplacementFieldFilter<DisplacementFieldImageType, double> DisplacementFieldGeneratorType;
// DisplacementFieldGeneratorType::Pointer dispfieldGenerator = DisplacementFieldGeneratorType::New();
//
// dispfieldGenerator->UseReferenceImageOn();
// dispfieldGenerator->SetReferenceImage( refImage );
// dispfieldGenerator->SetTransform( transform_fwd );
// dispfieldGenerator->Update();
// DisplacementFieldImageType::Pointer dispField = dispfieldGenerator->GetOutput();
//
// typedef itk::ImageFileWriter<DisplacementFieldImageType> DispFieldWriterType;
// DispFieldWriterType::Pointer writer = DispFieldWriterType::New();
// writer->SetFileName(out_n);
// writer->SetInput(dispField);
// writer->Update();
return 0;
}
int main (int argc, char *argv[])
{
GetPot cl (argc, const_cast<char**>(argv));
if( cl.size() == 1 || cl.search (2,"--help","-h") )
{
std::cout << "Not Enough Arguments" << std::endl;
std::cout << "Scales the tensors with a scalar factor" << std::endl;
std::cout << "Usage: -trueB0 <true B0> -m <MaskImage> -true <True Tensors> -f <flag for extended gradient> -t <initial tensor estimate> -g <gradient> -o <Output File> -s <Sigma> -nm <Noise Model> -Sim <intelligent COnvergence>" << std::endl;
return -1;
}
const string file_g_n = cl.follow("NoFile",1, "-g");
const string fileIn = cl.follow("NoFile",1,"-i");
const string fileIn_HR = cl.follow("NoFile",1,"-iHR");
const string B0_n = cl.follow("NoFile", 1, "-B0");
const string mask_LR_n = cl.follow("NoFile",1, "-mLR");
const int numOfIter = cl.follow(1,1, "-n");
const float kappa_L = cl.follow(0.05, 1, "-k");
const float lambda_L = cl.follow(0.25, 1, "-lamb_L");
const string B0Image_HR_n = cl.follow("NoFile", 1, "-B0HR");
const string dispField_n = cl.follow("NoFile",1,"-d");
const string T1Image_n = cl.follow("NoFile",1,"-T1");
const string mask_HR_n = cl.follow("NoFile", 1, "-mHR");
// Usual Typedefs
typedef float RealType;
const int ImageDim =3;
typedef itk::Image<RealType, ImageDim> ScalarImageType;
typedef itk::Vector<double, ImageDim> VectorType;
typedef itk::Image<VectorType, ImageDim> DeformationFieldType;
typedef itk::Image<VectorType, ImageDim> VectorImageType;
typedef itk::ImageFileReader<ScalarImageType> ScalarImageReaderType;
typedef itk::ImageFileWriter<ScalarImageType> ScalarImageWriterType;
//Read T1 image
ScalarImageReaderType::Pointer scalarReader = ScalarImageReaderType::New();
scalarReader->SetFileName(T1Image_n.c_str());
scalarReader->Update();
ScalarImageType::Pointer T1_image = scalarReader->GetOutput();
// Read LR ImageList
typedef std::vector<ScalarImageType::Pointer> ImageListType;
ImageListType DWIList;
std::ifstream file(fileIn.c_str());
int numOfImages = 0;
file >> numOfImages;
for (int i=0; i < numOfImages ; i++) // change of numOfImages
{
char filename[256];
file >> filename;
ScalarImageReaderType::Pointer myReader=ScalarImageReaderType::New();
myReader->SetFileName(filename);
std::cout << "Reading.." << filename << std::endl; // add a try catch block
myReader->Update();
DWIList.push_back( myReader->GetOutput() ); //using push back to create a stack of diffusion images
}
// Read deformation field
typedef itk::ImageFileReader<DeformationFieldType> DeformationFieldReaderType;
DeformationFieldReaderType::Pointer deformationFieldReader = DeformationFieldReaderType::New();
deformationFieldReader->SetFileName(dispField_n.c_str());
deformationFieldReader->Update();
DeformationFieldType::Pointer defField = deformationFieldReader->GetOutput();
// Read Mask Image Spatial
typedef itk::ImageMaskSpatialObject<ImageDim> MaskSpatialObjectType;
typedef MaskSpatialObjectType::ImageType MaskSpatialImageType;
typedef itk::ImageFileReader<MaskSpatialImageType> MaskSpatialImageReaderType;
MaskSpatialImageReaderType::Pointer spatialReader = MaskSpatialImageReaderType::New();
spatialReader->SetFileName(mask_LR_n.c_str());
spatialReader->Update();
MaskSpatialImageType::Pointer maskSpatialImage_LR = spatialReader->GetOutput();
//Read Mask Image Normal
ScalarImageReaderType::Pointer maskImageReader = ScalarImageReaderType::New();
maskImageReader->SetFileName(mask_LR_n.c_str());
maskImageReader->Update();
ScalarImageType::Pointer maskImage_LR = maskImageReader->GetOutput();
// Resample diffusion Images
/* typedef itk::WarpImageFilter<ScalarImageType, ScalarImageType, DeformationFieldType> WarpImageFilterType;
typedef itk::ImageFileWriter<ScalarImageType> ScalarImageWriterType;
for (int i =0; i < numOfImages; i++)
{
WarpImageFilterType::Pointer warpImageFilter = WarpImageFilterType::New();
warpImageFilter->SetOutputSpacing(T1_image->GetSpacing());
warpImageFilter->SetOutputOrigin(T1_image->GetOrigin());
warpImageFilter->SetDisplacementField(defField);
warpImageFilter->SetInput(DWIList[i]);
warpImageFilter->Update();
ScalarImageType::Pointer imageDWI = warpImageFilter->GetOutput();
std::ostringstream num_con;
num_con << i ;
std::string result = num_con.str() + ".nii.gz";
ScalarImageWriterType::Pointer writer = ScalarImageWriterType::New();
writer->SetFileName(result);
writer->SetInput(imageDWI);
writer->Update();
std::cout<< i << "Done" << std::endl;
}*/
// Read Gradient List ScalarValues
typedef itk::Vector<double, 3> VectorDoubleType;
typedef std::vector<VectorDoubleType> GradientListType;
GradientListType GradientList;
std::ifstream fileg(file_g_n.c_str());
int numOfGrads =0;
fileg >> numOfGrads;
for (int i=0; i < numOfGrads ; i++)
{
VectorType g;
fileg >> g[0]; fileg >> g[1]; fileg >> g[2];
GradientList.push_back(g);
}
// Transform gradients
// Read the HR diffusion images,
typedef std::vector<ScalarImageType::Pointer> ImageListType;
ImageListType DWIList_HR;
std::ifstream fileHR(fileIn_HR.c_str());
int numOfImagesHR = 0;
fileHR >> numOfImagesHR;
/* for (int i=0; i < numOfImagesHR ; i++) // change of numOfImages
{
char filename[256];
fileHR >> filename;
ScalarImageReaderType::Pointer myReader=ScalarImageReaderType::New();
myReader->SetFileName(filename);
myReader->Update();
std::cout << "Reading.." << filename << std::endl; // add a try catch block
DWIList_HR.push_back(myReader->GetOutput());
}
*/
// Read HR mask image spatial
MaskSpatialImageReaderType::Pointer spatialReader_HR = MaskSpatialImageReaderType::New();
spatialReader_HR->SetFileName(mask_HR_n.c_str());
spatialReader_HR->Update();
MaskSpatialImageType::Pointer maskSpatial_HR = spatialReader_HR->GetOutput();
//Read HR mask image Normal
ScalarImageReaderType::Pointer maskImage_HR_reader = ScalarImageReaderType::New();
maskImage_HR_reader->SetFileName(mask_HR_n.c_str());
maskImage_HR_reader->Update();
ScalarImageType::Pointer maskImage_HR = maskImage_HR_reader->GetOutput();
// Read B0 HR image
ScalarImageReaderType::Pointer B0Image_HR_reader = ScalarImageReaderType::New();
B0Image_HR_reader->SetFileName(B0Image_HR_n.c_str());
B0Image_HR_reader->Update();
ScalarImageType::Pointer B0Image_HR = B0Image_HR_reader->GetOutput();
//Read B0 LR image
ScalarImageReaderType::Pointer B0_image_LR_reader = ScalarImageReaderType::New();
B0_image_LR_reader->SetFileName(B0_n.c_str());
B0_image_LR_reader->Update();
ScalarImageType::Pointer B0_image_LR = B0_image_LR_reader->GetOutput();
// ComputeGradientImages
/* TransformGradients transformGradients;
transformGradients.ReadMaskImage(maskImage_HR);
transformGradients.ReadDeformationField(defField);
transformGradients.ReadGradients(GradientList);
transformGradients.ComputeGradients();
typedef std::vector<VectorImageType::Pointer> GradientImageListType;
GradientImageListType GradientImageList;
GradientImageList = transformGradients.GetGradientImages();
std::cout << "Transformed all Gradients... Done." << std::endl;
typedef itk::ImageFileWriter<VectorImageType> GradientImageWriterType;
for (int i=0; i < numOfGrads; i++)
{
GradientImageWriterType::Pointer gradientImageWriter = GradientImageWriterType::New();
std::ostringstream c;
c << i;
std::string tempName;
tempName = "Gradient_" + c.str() + ".nii.gz";
gradientImageWriter->SetFileName(tempName);
gradientImageWriter->SetInput(GradientImageList[i]);
gradientImageWriter->Update();
}
*/
//Read GradientImages
const string file_gradImage_n = cl.follow("NoFile", 1, "-fG");
std::ifstream fileGImg(file_gradImage_n.c_str());
int numOfGradImages = 0;
fileGImg >> numOfGradImages;
typedef itk::ImageFileReader<VectorImageType> GradientImageReaderType;
typedef std::vector<VectorImageType::Pointer> GradientImageListType;
GradientImageListType gradientImageList;
/* for (int i=0; i < numOfGradImages; i++)
{
char filename[25];
fileGImg >> filename;
VectorImageType::Pointer gradientImage = VectorImageType::New();
GradientImageReaderType::Pointer gradientImageReader = GradientImageReaderType::New();
gradientImageReader->SetFileName(filename);
gradientImageReader->Update();
gradientImageList.push_back(gradientImageReader->GetOutput()) ;
std::cout << "Reading...." << filename << std::endl;
}*/
// Compute the matrix
MapFilterLR2HRDisp filter;
filter.ReadFixedImage(T1_image); //
filter.ReadMovingImage(B0_image_LR);
filter.ReadDeformationField(defField);
filter.ReadMaskImage(maskSpatial_HR);
filter.ComputeMapWithDefField();
vnl_sparse_matrix<float> MapLR2HR, MapHR2LR;
MapLR2HR = filter.GetLR2HRMatrix();
MapHR2LR = filter.GetHR2LRMatrix();
std::cout << "Computing Map done " << std::endl;
std::cout << B0_image_LR->GetLargestPossibleRegion().GetSize() << std::endl;
//
// ComposeImageFilter composeFilter;
// composeFilter.GetHRImage(T1_image);
// composeFilter.GetLRImage(B0_image_LR);
// composeFilter.ReadMatrix(MapLR2HR);
//
// ScalarImageType::Pointer tempImage1 = composeFilter.ComposeIt();
// std::cout << "Composing done " << std::endl;
//
// typedef itk::ImageFileWriter<ScalarImageType> ScalarWriterType;
// ScalarWriterType::Pointer scalarWriter = ScalarWriterType::New();
// scalarWriter->SetFileName("TempImage.nii.gz");
// scalarWriter->SetInput(tempImage1);
// scalarWriter->Update();
/* UnweightedLeastSquaresTensorEstimation UnWeightedTensorEstimator;
UnWeightedTensorEstimator.ReadDWIList(DWIList_HR);
UnWeightedTensorEstimator.ReadMask(maskImage_HR);
UnWeightedTensorEstimator.ReadBVal(1.0);
UnWeightedTensorEstimator.ReadGradientList(gradientImageList);
UnWeightedTensorEstimator.ReadB0Image(B0Image_HR);
typedef itk::DiffusionTensor3D<RealType> DiffusionTensorType;
typedef itk::Image<DiffusionTensorType, ImageDim> TensorImageType;
TensorImageType::Pointer tensorImage_init = UnWeightedTensorEstimator.Compute();
typedef itk::ImageFileWriter<TensorImageType> TensorWriterType;
TensorWriterType::Pointer tensorWriter = TensorWriterType::New();
tensorWriter->SetFileName("TensorImage.nii.gz");
tensorWriter->SetInput(tensorImage_init);
tensorWriter->Update();
//Compute Sigma
vnl_vector<RealType> Sigma;
// Compute Joint Estimation
// JointTensorEstimation jTestimation;
// jTestimation.ReadBVal(1.0);
// jTestimation.ReadDWIList(DWIList_HR);
// jTestimation.ReadMaskImage(maskImage_HR);
// jTestimation.ReadB0Image(B0Image_HR);
// jTestimation.ReadGradientList(gradientImageList);
// jTestimation.ReadInitialTensorImage(tensorImage_init);
// jTestimation.ReadKappa(kappa_L);
*/
return 0;
}
int main (int argc, char **argv)
{
GetPot cl (argc, argv);
if (cl.search (2, "-h", "--help"))
{
std::cerr << help_text << std::endl;
return 0;
}
const double a =
cl.follow (0.0, "-a");
const double b =
cl.follow (1.0, "-b");
const unsigned int nnodes =
cl.follow (100, 2, "-n", "--nnodes");
const std::string diffusion =
cl.follow ("1.0", 2, "-d", "--diffusion");
const std::string forcing =
cl.follow ("1.0", 2, "-f", "--forcing");
coeff f_coeff (forcing);
coeff a_coeff (diffusion);
const std::string quadrature =
cl.follow ("trapezoidal.so",
2, "-q", "--quadrature-rule");
std::function <void ()> r_r;
void * handle = dlopen (quadrature.c_str (), RTLD_NOW);
if (! handle)
{
std::cerr << "fem1d: cannot load dynamic object!"
<< std::endl;
std::cerr << dlerror ()
<< std::endl;
return (-1);
}
void * sym = dlsym (handle, "register_rules");
if (! sym)
{
std::cerr << "fem1d: cannot load symbol!"
<< std::endl;
std::cerr << dlerror ()
<< std::endl;
return (-1);
}
r_r = reinterpret_cast <void (*) ()> (sym);
r_r ();
auto & the_factory = quadrature_factory::instance ();
auto integrate = the_factory.create ("trapezoidal");
if (! integrate)
{
std::cerr << "rule name unknown" << std::endl;
return (-1);
}
mesh m (a, b, nnodes);
Eigen::SparseMatrix<double> A(nnodes, nnodes);
Eigen::Matrix2d mloc;
mloc << 0, 0, 0, 0;
for (unsigned int iel = 0; iel < m.nels; ++iel)
{
mloc << 0, 0, 0, 0;
for (unsigned int inode = 0; inode < 2; ++inode)
{
auto igrad = [=, &m] (double x) -> double
{
return basisfungrad
(x, m.nodes[m.elements[iel][0]],
m.nodes[m.elements[iel][1]],
inode == 0 ? 1.0 : 0.0,
inode == 1 ? 1.0 : 0.0);
};
for (unsigned int jnode = 0; jnode < 2; ++jnode)
{
auto jgrad = [=, &m] (double x) -> double
{
return basisfungrad
(x, m.nodes[m.elements[iel][0]],
m.nodes[m.elements[iel][1]],
jnode == 0 ? 1.0 : 0.0,
jnode == 1 ? 1.0 : 0.0);
};
mloc(inode,jnode) +=
(*integrate) ([=, &m, &igrad, &jgrad, &a_coeff]
(double x) -> double
{
return (igrad (x) *
jgrad (x) *
a_coeff (x));
},
m.nodes[m.elements[iel][0]],
m.nodes[m.elements[iel][1]]);
A.coeffRef(m.elements[iel][inode],
m.elements[iel][jnode]) +=
mloc(inode,jnode);
}
}
}
Eigen::VectorXd f(nnodes);
for (unsigned int ii = 0; ii < nnodes; ++ii)
f(ii) = 0.0;
Eigen::Vector2d vloc;
for (unsigned int iel = 0; iel < m.nels; ++iel)
{
vloc << 0, 0;
for (unsigned int inode = 0; inode < 2; ++inode)
{
auto ifun = [=, &m] (double x) -> double
{
return basisfun
(x, m.nodes[m.elements[iel][0]],
m.nodes[m.elements[iel][1]],
inode == 0 ? 1.0 : 0.0,
inode == 1 ? 1.0 : 0.0);
};
vloc(inode) +=
(*integrate) ([=, &m, &ifun, &f_coeff]
(double x) -> double
{
return (ifun (x) *
f_coeff (x));
},
m.nodes[m.elements[iel][0]],
m.nodes[m.elements[iel][1]]);
f(m.elements[iel][inode]) += vloc(inode);
}
}
f(0) = 0;
f(nnodes - 1) = 0;
A.coeffRef(0,0) = 1.0e10;
A.coeffRef(nnodes-1,nnodes-1) = 1.0e10;
for (unsigned int ii = 1; ii < nnodes; ++ii)
{
A.coeffRef(0, ii) = 0.0;
A.coeffRef(nnodes-1, nnodes-1-ii) = 0.0;
}
Eigen::SparseLU<Eigen::SparseMatrix<double>> solver;
A.makeCompressed ();
solver.analyzePattern(A);
solver.factorize(A);
Eigen::VectorXd uh = solver.solve (f);
for (unsigned int ii = 0; ii < nnodes; ++ii)
std::cout << m.nodes[ii] << " "
<< uh(ii, 0)
<< std:: endl;
return 0;
};
int main (int argc, char *argv[])
{
const unsigned int ImageDimension = 2;
GetPot cl (argc, const_cast<char**>(argv));
if( cl.size() == 1 || cl.search (2,"--help","-h") )
{
std::cout << "Not Enough Arguments" << std::endl;
std::cout << "Generate the Gradient Table" << std::endl;
std::cout << "Usage: return -1" << std::endl;
}
const string image_n = cl.follow("NoFile",1, "-i");
const string mask_n = cl.follow("NoFile", 1, "-m");
const string out_n = cl.follow("NoFile",1, "-o");
typedef itk::DiffusionTensor3D<float> DiffusionTensorType;
typedef itk::Image<DiffusionTensorType, 3> TensorImageType;
typedef itk::ImageFileReader<TensorImageType> TensorReaderType;
TensorReaderType::Pointer reader = TensorReaderType::New();
reader->SetFileName(image_n.c_str());
reader->Update();
TensorImageType::Pointer image = reader->GetOutput();
typedef itk::Image<float, 3> ScalarImageType;
typedef itk::ImageFileReader<ScalarImageType> ScalarReaderType;
ScalarReaderType::Pointer scalarReader = ScalarReaderType::New();
scalarReader->SetFileName(mask_n.c_str());
scalarReader->Update();
ScalarImageType::Pointer maskImage = scalarReader->GetOutput();
typedef itk::ImageRegionIterator<TensorImageType> TensorIterator;
typedef itk::ImageRegionIterator<ScalarImageType> ScalarIterator;
ScalarIterator itMask(maskImage, maskImage->GetLargestPossibleRegion());
TensorUtilities utilsTensor;
TensorImageType::Pointer logTensorImage = utilsTensor.LogTensorImageFilter(image, maskImage);
typedef itk::ImageFileWriter<TensorImageType> TensorImageWriterType;
TensorImageWriterType::Pointer tensorImageWriter = TensorImageWriterType::New();
tensorImageWriter->SetFileName("LogTensorImage_stupid.nii.gz");
tensorImageWriter->SetInput(logTensorImage);
tensorImageWriter->Update();
std::ofstream file;
file.open(out_n);
ScalarImageType::Pointer TraceImage = ScalarImageType::New();
CopyImage cpImage;
cpImage.CopyScalarImage(maskImage, TraceImage);
ScalarIterator itTr(TraceImage, TraceImage->GetLargestPossibleRegion());
TensorIterator itImg(logTensorImage, logTensorImage->GetLargestPossibleRegion());
for(itImg.GoToBegin(), itMask.GoToBegin(), itTr.GoToBegin(); !itTr.IsAtEnd(), !itImg.IsAtEnd(), !itMask.IsAtEnd(); ++itTr, ++itImg, ++itMask)
{
file << itImg.Get().GetTrace() << std::endl;
itTr.Set(itImg.Get().GetTrace()) ;
}
typedef itk::ImageFileWriter<ScalarImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName("LogTense_Trace.nii.gz");
writer->SetInput(TraceImage);
writer->Update();
file.close();
return 0;
}
int main (int argc, char **argv)
{
GetPot cl (argc, argv);
if (cl.search (2, "-h", "--help"))
{
std::cerr << help_text << std::endl;
return 0;
}
const double a = cl.follow (double (0.0), "-a");
const double b = cl.follow (double (1.0), "-b");
const unsigned int nnodes = cl.follow (100, 2, "-n", "--nnodes");
const unsigned int nel = nnodes - 1;
const std::string diffusion = cl.follow ("1.0", 2, "-d", "--diffusion");
const std::string forcing = cl.follow ("1.0", 2, "-f", "--forcing");
const double tol = 1e-6;
const unsigned int maxit = 43;
const unsigned int overlap = 3;
const double L = b - a;
const int mpi_size = 3;
const double L_loc = L / double (mpi_size);
const double h = L_loc / ceil (double(nel) / double(mpi_size));
std::vector<double> a_loc (mpi_size);
std::vector<double> b_loc (mpi_size);
std::vector<unsigned int> nel_loc (mpi_size);
std::vector<unsigned int> ndof_loc (mpi_size);
std::vector<fem_1d<double>*> subproblems (mpi_size);
coeff<double> a_coeff (diffusion);
coeff<double> f_coeff (forcing);
int mpi_rank;
for (mpi_rank = 0; mpi_rank < mpi_size; ++mpi_rank)
{
a_loc[mpi_rank] = a + mpi_rank * L_loc;
b_loc[mpi_rank] = a_loc[mpi_rank] + L_loc;
nel_loc[mpi_rank] = ceil (double(nel) / double(mpi_size));
if (mpi_rank > 0)
{
a_loc[mpi_rank] -= overlap * h;
nel_loc[mpi_rank] += overlap;
}
if (mpi_rank < mpi_size - 1)
{
b_loc[mpi_rank] += overlap * h;
nel_loc[mpi_rank] += overlap;
}
ndof_loc[mpi_rank] = nel_loc[mpi_rank] + 1;
fem_1d<double>* tmp = new fem_1d<double>(new mesh<double>
(a_loc[mpi_rank],
b_loc[mpi_rank],
ndof_loc[mpi_rank]));
subproblems[mpi_rank] = tmp;
subproblems[mpi_rank]->set_diffusion_coefficient (a_coeff);
subproblems[mpi_rank]->set_source_coefficient (f_coeff);
subproblems[mpi_rank]->assemble ();
subproblems[mpi_rank]->set_dirichlet (fem_1d<double>::left_boundary, 0.0);
subproblems[mpi_rank]->set_dirichlet (fem_1d<double>::right_boundary, 0.0);
subproblems[mpi_rank]->solve ();
};
for (unsigned int it = 0; it < maxit; ++it)
for (mpi_rank = 0; mpi_rank < mpi_size; ++mpi_rank)
{
if (mpi_rank > 0)
subproblems[mpi_rank]->set_dirichlet
(fem_1d<double>::left_boundary,
subproblems[mpi_rank-1]->result ()
[ndof_loc[mpi_rank-1]-1-2*overlap]);
else
subproblems[mpi_rank]->set_dirichlet
(fem_1d<double>::left_boundary, 0.0);
if (mpi_rank < mpi_size - 1)
subproblems[mpi_rank]->set_dirichlet
(fem_1d<double>::right_boundary,
subproblems[mpi_rank+1]->result ()
[2*overlap]);
else
subproblems[mpi_rank]->set_dirichlet
(fem_1d<double>::right_boundary, 0.0);
subproblems[mpi_rank]->solve ();
}
for (mpi_rank = 0; mpi_rank < mpi_size; ++mpi_rank)
for (unsigned int ii = 0; ii < ndof_loc[mpi_rank]; ++ii)
std::cout << subproblems[mpi_rank]->m->nodes[ii] << " "
<< subproblems[mpi_rank]->result ()(ii, 0)
<< std::endl;
return 0;
};
int main (int argc, char **argv)
{
MPI_Init (&argc, &argv);
GetPot cl (argc, argv);
if (cl.search (2, "-h", "--help"))
{
std::cerr << help_text << std::endl;
return 0;
}
const double a = cl.follow (double (0.0), "-a");
const double b = cl.follow (double (1.0), "-b");
const unsigned int nnodes = cl.follow (100, 2, "-n", "--nnodes");
const unsigned int nel = nnodes - 1;
const std::string diffusion = cl.follow ("1.0", 2, "-d", "--diffusion");
const std::string forcing = cl.follow ("1.0", 2, "-f", "--forcing");
const double L = b - a;
constexpr double tol = 1e-6;
constexpr unsigned int maxit = 100;
constexpr unsigned int overlap = 100;
MPI_Status status;
int mpi_size, mpi_rank, tag;
MPI_Comm_size (MPI_COMM_WORLD, &mpi_size);
MPI_Comm_rank (MPI_COMM_WORLD, &mpi_rank);
const double L_loc = L / double(mpi_size);
const double h = L_loc / ceil (double(nel) / double(mpi_size));
double a_loc = .0;
double lval = .0;
double b_loc = .0;
double rval = .0;
double buffer = .0;
unsigned int nel_loc = 0;
unsigned int ndof_loc = 1;
fem_1d<double> *subproblems;
coeff<double> a_coeff (diffusion);
coeff<double> f_coeff (forcing);
a_loc = a + mpi_rank * L_loc;
b_loc = a_loc + L_loc;
nel_loc = ceil (double(nel) / double(mpi_size));
if (mpi_rank > 0)
{
a_loc -= overlap * h;
nel_loc += overlap;
}
if (mpi_rank < mpi_size - 1)
{
b_loc += overlap * h;
nel_loc += overlap;
}
ndof_loc = nel_loc + 1;
subproblems = new fem_1d<double>
(new mesh<double> (a_loc, b_loc, ndof_loc));
subproblems->set_diffusion_coefficient (a_coeff);
subproblems->set_source_coefficient (f_coeff);
subproblems->assemble ();
subproblems->set_dirichlet (fem_1d<double>::left_boundary, 0.0);
subproblems->set_dirichlet (fem_1d<double>::right_boundary, 0.0);
subproblems->solve ();
for (unsigned int it = 0; it < maxit; ++it)
{
// With the following implementation
// communication will occur sequentailly
// left to right first then right to left
// Receive from left neighbour
if (mpi_rank > 0)
{
std::cerr << "rank " << mpi_rank
<< " receiving lval from rank "
<< mpi_rank - 1
<< std::endl;
MPI_Recv (&buffer, 1, MPI_DOUBLE, mpi_rank - 1, MPI_ANY_TAG,
MPI_COMM_WORLD, &status);
std::cerr << "rank " << mpi_rank
<< " received lval from rank "
<< mpi_rank - 1
<< std::endl;
lval = buffer;
}
tag = 10*mpi_rank;
// Send to right neighbour
if (mpi_rank < mpi_size - 1)
{
buffer = subproblems->result ()
[ndof_loc - 1 - 2*overlap];
std::cerr << "rank " << mpi_rank
<< " sending lval to rank "
<< mpi_rank + 1
<< std::endl;
MPI_Send (&buffer, 1, MPI_DOUBLE, mpi_rank + 1, tag,
MPI_COMM_WORLD);
std::cerr << "rank " << mpi_rank
<< " sent lval to rank "
<< mpi_rank + 1
<< std::endl;
}
// Receive from right neighbour
if (mpi_rank < mpi_size - 1)
{
std::cerr << "rank " << mpi_rank
<< " receiving rval from rank "
<< mpi_rank + 1
<< std::endl;
MPI_Recv (&buffer, 1, MPI_DOUBLE, mpi_rank + 1, MPI_ANY_TAG,
MPI_COMM_WORLD, &status);
std::cerr << "rank " << mpi_rank
<< " received rval from rank "
<< mpi_rank + 1
<< std::endl;
rval = buffer;
}
tag = 10*mpi_rank + 1;
// Send to right neighbour
if (mpi_rank > 0)
{
buffer = subproblems->result () [2*overlap];
std::cerr << "rank " << mpi_rank
<< " sending rval to rank "
<< mpi_rank - 1
<< std::endl;
MPI_Send (&buffer, 1, MPI_DOUBLE, mpi_rank - 1, tag,
MPI_COMM_WORLD);
std::cerr << "rank " << mpi_rank
<< " sent rval to rank "
<< mpi_rank - 1
<< std::endl;
}
subproblems->set_dirichlet
(fem_1d<double>::left_boundary, lval);
subproblems->set_dirichlet
(fem_1d<double>::right_boundary, rval);
subproblems->solve ();
}
for (int rank = 0; rank < mpi_size; ++rank)
{
if (rank == mpi_rank)
for (unsigned int ii = 0; ii < ndof_loc; ++ii)
std::cout << subproblems->m->nodes[ii] << " "
<< subproblems->result ()(ii, 0)
<< std::endl;
MPI_Barrier (MPI_COMM_WORLD);
}
MPI_Finalize ();
return 0;
};
Int
main ( Int argc, char** argv )
{
//Setup main communicator
boost::shared_ptr< Epetra_Comm > comm;
//Setup MPI variables
Int numberOfProcesses (1);
Int rank (0);
#ifdef HAVE_MPI
MPI_Init ( &argc, &argv );
MPI_Comm_size ( MPI_COMM_WORLD, &numberOfProcesses );
MPI_Comm_rank ( MPI_COMM_WORLD, &rank );
#endif
if ( rank == 0 )
{
std::cout << std::endl;
std::cout << "$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$" << std::endl;
std::cout << " THE ZERO DIMENSIONAL SOLVER IS AN ALPHA VERSION UNDER STRONG DEVELOPMENT" << std::endl;
std::cout << "$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$" << std::endl << std::endl;
std::cout << "MPI Processes: " << numberOfProcesses << std::endl;
}
#ifdef HAVE_MPI
if ( numberOfProcesses > 1 )
{
if ( rank == 0 )
{
std::cout << "test_ZeroDimensional not enabled in parallel, failing gracefully." << std::endl;
std::cout << "MPI Finalization" << std::endl;
}
MPI_Finalize();
return EXIT_FAILURE;
}
#endif
#ifdef EPETRA_MPI
if ( rank == 0 )
{
std::cout << "MPI Epetra Initialization ... " << std::endl;
}
comm.reset ( new Epetra_MpiComm ( MPI_COMM_WORLD ) );
#else
std::cout << "SERIAL Epetra Initialization ... " << std::endl;
comm.reset ( new Epetra_SerialComm() );
#endif
bool exitFlag = EXIT_SUCCESS;
#if ( defined(HAVE_NOX_THYRA) && defined(HAVE_TRILINOS_RYTHMOS) )
// Command line parameters
GetPot commandLine ( argc, argv );
const bool check = commandLine.search ( 2, "-c", "--check" );
string fileName = commandLine.follow ( "data", 2, "-f", "--file" );
// SetupData
GetPot dataFile ( fileName + ".dat" );
std::string circuitDataFile = dataFile ( "0D_Model/CircuitDataFile", "./inputFile.dat" );
BCInterface0D< ZeroDimensionalBCHandler, ZeroDimensionalData > zeroDimensionalBC;
zeroDimensionalBC.createHandler();
zeroDimensionalBC.fillHandler ( circuitDataFile, "Files" );
boost::shared_ptr< ZeroDimensionalData > zeroDimensionalData ( new ZeroDimensionalData );
zeroDimensionalData->setup ( dataFile, zeroDimensionalBC.handler() );
boost::shared_ptr< ZeroDimensionalSolver > zeroDimensionalSolver ( new ZeroDimensionalSolver ( zeroDimensionalData->unknownCounter(), comm, zeroDimensionalData->circuitData() ) );
zeroDimensionalSolver->setup ( zeroDimensionalData->solverData() );
zeroDimensionalData->showMe();
// SetupModel
zeroDimensionalData->dataTime()->setInitialTime (0);
zeroDimensionalData->initializeSolution();
// Create output folder
if ( comm->MyPID() == 0 )
{
mkdir ( "output", 0777 );
}
// Save initial solution
zeroDimensionalData->saveSolution();
zeroDimensionalData->dataTime()->updateTime();
zeroDimensionalData->dataTime()->setInitialTime (zeroDimensionalData->dataTime()->time() );
// Definitions for the time loop
LifeChrono chronoTotal;
LifeChrono chronoSystem;
LifeChrono chronoIteration;
Int count = 0;
chronoTotal.start();
for ( ; zeroDimensionalData->dataTime()->canAdvance() ; zeroDimensionalData->dataTime()->updateTime(), ++count )
{
std::cout << std::endl << "--------- Iteration " << count << " time = " << zeroDimensionalData->dataTime()->time() << std::endl;
chronoIteration.start();
chronoSystem.start();
zeroDimensionalSolver->takeStep ( zeroDimensionalData->dataTime()->previousTime(), zeroDimensionalData->dataTime()->time() );
chronoSystem.stop();
//Save solution
zeroDimensionalData->saveSolution();
chronoIteration.stop();
std::cout << " System solved in " << chronoSystem.diff() << " s, (total time " << chronoIteration.diff() << " s)." << std::endl;
}
chronoTotal.stop();
std::cout << std::endl << " Simulation ended successfully in " << chronoTotal.diff() << " s" << std::endl;
// Final check
if ( check )
{
bool ok = true;
ok = ok && checkValue ( 0.001329039627, zeroDimensionalData->circuitData()->Nodes()->nodeListAt (1)->voltage() );
ok = ok && checkValue ( 0.000787475119, zeroDimensionalData->circuitData()->Elements()->elementListAt (1)->current() );
if (ok)
{
std::cout << " Test succesful" << std::endl;
exitFlag = EXIT_SUCCESS;
}
else
{
std::cout << " Test unsuccesful" << std::endl;
exitFlag = EXIT_FAILURE;
}
}
#else
std::cout << "ZeroDimensional requires configuring Trilinos with Rythmos/NOX/Thyra. Skipping test." << std::endl;
exitFlag = EXIT_SUCCESS;
#endif /* HAVE_NOX_THYRA && HAVE_TRILINOS_RYTHMOS */
if (rank == 0)
{
std::cout << "End Result: TEST PASSED" << std::endl;
}
#ifdef HAVE_MPI
if ( rank == 0 )
{
std::cout << "MPI Finalization" << std::endl;
}
MPI_Finalize();
#endif
return exitFlag;
}
