// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int main(int argc, char** argv)
{
qDebug() << "Starting Ph to HDF5 Merging...";
// Instantiate the QCoreApplication that we need to get the current path and load plugins.
QCoreApplication app(argc, argv);
QCoreApplication::setOrganizationName("BlueQuartz Software");
QCoreApplication::setOrganizationDomain("bluequartz.net");
QCoreApplication::setApplicationName("PhToHDF5");
std::cout << "PhToHDF5 Starting. Version " << SIMPLib::Version::PackageComplete().toStdString() << std::endl;
// Register all the filters including trying to load those from Plugins
FilterManager::Pointer fm = FilterManager::Instance();
SIMPLibPluginLoader::LoadPluginFilters(fm.get());
// Send progress messages from PipelineBuilder to this object for display
QMetaObjectUtilities::RegisterMetaTypes();
try
{
// Handle program options passed on command line.
TCLAP::CmdLine cmd("PhToHDF5", ' ', SIMPLib::Version::Complete().toStdString());
TCLAP::ValueArg<std::string> phFileArg( "p", "phfile", "Ph Input File", true, "", "Ph Input File");
cmd.add(phFileArg);
TCLAP::ValueArg<std::string> angleFileArg( "e", "eulerfile", "Euler Angle File", false, "", "Euler Angle File");
cmd.add(angleFileArg);
TCLAP::ValueArg<std::string> h5InputFileArg( "t", "h5file", "Target HDF5 File", true, "", "Target HDF5 File");
cmd.add(h5InputFileArg);
// Parse the argv array.
cmd.parse(argc, argv);
if (argc == 1)
{
qDebug() << "PhToHDF5 program was not provided any arguments. Use the --help argument to show the help listing.";
return EXIT_FAILURE;
}
QString phFile = QString::fromStdString(phFileArg.getValue());
QString h5File = QString::fromStdString(h5InputFileArg.getValue());
QVector<int> voxels;
int nx = 0;
int ny = 0;
int nz = 0;
qDebug() << "Merging the FeatureID data from " << phFile;
qDebug() << " into";
qDebug() << "file: " << h5File;
qDebug() << "Reading the Ph data file....";
int err = ReadPHFile(phFile, voxels, nx, ny, nz);
if (err < 0)
{
return EXIT_FAILURE;
}
qDebug() << "Ph File has dimensions: " << nx << " x " << ny << " x " << nz;
qDebug() << "Now Overwriting the FeatureID data set in the HDF5 file....";
err = writePhDataToHDF5File(h5File, voxels, nz, ny, nz);
if (err < 0)
{
qDebug() << "There was an error writing the feature id data. Check other errors for possible clues.";
return EXIT_FAILURE;
}
qDebug() << "+ Done Writing the Feature ID Data.";
QMap<int, EulerSet> gidToEulerMap;
if (angleFileArg.getValue().empty() == false)
{
qDebug() << "Reading the Euler Angle Data....";
err = ReadEulerFile(QString::fromStdString(angleFileArg.getValue()), gidToEulerMap);
if (err < 0)
{
qDebug() << "Error Reading the Euler Angle File";
return EXIT_FAILURE;
}
// Over Write the Euler Angles if the Euler File was supplied
qDebug() << "Now Over Writing the Euler Angles data in the HDF5 file.....";
int totalPoints = nx * ny * nz;
int numComp = 3;
// Loop over each Voxel getting its Feature ID and then setting the Euler Angle
QVector<float> dataf(totalPoints * 3);
for (int i = 0; i < totalPoints; ++i)
{
EulerSet& angle = gidToEulerMap[voxels[i]];
dataf[i * 3] = angle.e0;
dataf[i * 3 + 1] = angle.e1;
dataf[i * 3 + 2] = angle.e2;
}
// This is going to be a 2 Dimension Table Data set.
int32_t rank = 2;
hsize_t dims[2] = {totalPoints, numComp};
err = writeEulerDataToHDF5File(h5File, dataf, numComp, rank, dims);
if (err < 0)
{
qDebug() << "There was an error writing the Euler Angle data. Check other errors for possible clues.";
return EXIT_FAILURE;
}
qDebug() << "+ Done Writing the Euler Angle Data.";
}
}
catch (TCLAP::ArgException& e) // catch any exceptions
{
std::cerr << " error: " << e.error() << " for arg " << e.argId();
return EXIT_FAILURE;
}
qDebug() << "Successfully completed the merge.";
return EXIT_SUCCESS;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int main(int argc, char **argv)
{
std::cout << "Starting Ph to HDF5 Merging..." << std::endl;
try
{
// Handle program options passed on command line.
TCLAP::CmdLine cmd("PhToHDF5", ' ', DREAM3DLib::Version::Complete());
TCLAP::ValueArg<std::string> phFileArg( "p", "phfile", "Ph Input File", true, "", "Ph Input File");
cmd.add(phFileArg);
TCLAP::ValueArg<std::string> angleFileArg( "e", "eulerfile", "Euler Angle File", false, "", "Euler Angle File");
cmd.add(angleFileArg);
TCLAP::ValueArg<std::string> h5InputFileArg( "t", "h5file", "Target HDF5 File", true, "", "Target HDF5 File");
cmd.add(h5InputFileArg);
// Parse the argv array.
cmd.parse(argc, argv);
if (argc == 1)
{
std::cout << "PhToHDF5 program was not provided any arguments. Use the --help argument to show the help listing." << std::endl;
return EXIT_FAILURE;
}
std::string phFile = phFileArg.getValue();
std::string h5File = h5InputFileArg.getValue();
std::vector<int> voxels;
int nx = 0;
int ny = 0;
int nz = 0;
std::cout << "Merging the GrainID data from " << phFile << std::endl;
std::cout << " into" << std::endl;
std::cout << "file: " << h5File << std::endl;
std::cout << "Reading the Ph data file...." << std::endl;
int err = ReadPHFile(phFile, voxels, nx, ny, nz);
if (err < 0)
{
return EXIT_FAILURE;
}
std::cout << "Ph File has dimensions: " << nx << " x " << ny << " x " << nz << std::endl;
std::cout << "Now Overwriting the GrainID data set in the HDF5 file...." << std::endl;
err = writePhDataToHDF5File(h5File, voxels, nz, ny, nz);
if (err < 0)
{
std::cout << "There was an error writing the grain id data. Check other errors for possible clues." << std::endl;
return EXIT_FAILURE;
}
std::cout << "+ Done Writing the Grain ID Data." << std::endl;
std::map<int, EulerSet> gidToEulerMap;
if (angleFileArg.getValue().empty() == false)
{
std::cout << "Reading the Euler Angle Data...." << std::endl;
err = ReadEulerFile(angleFileArg.getValue(), gidToEulerMap);
if (err < 0)
{
std::cout << "Error Reading the Euler Angle File" << std::endl;
return EXIT_FAILURE;
}
// Over Write the Euler Angles if the Euler File was supplied
std::cout << "Now Over Writing the Euler Angles data in the HDF5 file....." << std::endl;
int totalPoints = nx * ny * nz;
int numComp = 3;
// Loop over each Voxel getting its Grain ID and then setting the Euler Angle
std::vector<float> dataf(totalPoints * 3);
for (int i = 0; i < totalPoints; ++i)
{
EulerSet& angle = gidToEulerMap[voxels[i]];
dataf[i * 3] = angle.e0;
dataf[i * 3 + 1] = angle.e1;
dataf[i * 3 + 2] = angle.e2;
}
// This is going to be a 2 Dimension Table Data set.
int32_t rank = 2;
hsize_t dims[2] = {totalPoints, numComp};
err = writeEulerDataToHDF5File(h5File, dataf, numComp, rank, dims);
if (err < 0)
{
std::cout << "There was an error writing the Euler Angle data. Check other errors for possible clues." << std::endl;
return EXIT_FAILURE;
}
std::cout << "+ Done Writing the Euler Angle Data." << std::endl;
}
}
catch (TCLAP::ArgException &e) // catch any exceptions
{
std::cerr << logTime() << " error: " << e.error() << " for arg " << e.argId() << std::endl;
return EXIT_FAILURE;
}
std::cout << "Successfully completed the merge." << std::endl;
return EXIT_SUCCESS;
}