/**
*
* @param FileName
* @param data
* @param nx X Dimension
* @param ny Y Dimension
* @param nz Z Dimension
*/
int ReadPHFile(QString FileName, QVector<int>& data, int& nx, int& ny, int& nz)
{
DataContainerArray::Pointer dca = DataContainerArray::New();
DataContainer::Pointer m = DataContainer::New(); /* FIXME: What Geometry do we need? */
dca->pushBack(m);
FilterManager::Pointer fm = FilterManager::Instance();
AbstractFilter::Pointer reader = fm->getFactoryForFilter("PhReader")->create();
reader->setDataContainerArray(dca);
bool propWasSet = reader->setProperty("InputFile", FileName);
if(propWasSet == false)
{
}
reader->execute();
if (reader->getErrorCondition() < 0)
{
qDebug() << "Error Reading the Ph File '" << FileName << "' Error Code:" << reader->getErrorCondition();
return -1;
}
Int32ArrayType* featureIds = Int32ArrayType::SafePointerDownCast(m->getAttributeMatrix(DREAM3D::Defaults::CellAttributeMatrixName)->getAttributeArray(DREAM3D::CellData::FeatureIds).get());
size_t count = featureIds->getNumberOfTuples();
data.resize(count);
for(size_t i = 0; i < count; ++i)
{
data[i] = featureIds->getValue(i);
}
return 0;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void LoopOnFilters()
{
FilterManager::Pointer fm = FilterManager::Instance();
FilterManager::Collection factories = fm->getFactories();
FilterManager::CollectionIterator i(factories);
int count = 0;
while (i.hasNext())
{
i.next();
std::cout << ++count << ": " << i.key().toStdString() << ": " << std::endl;
//std::cout << " public:" << std::endl;
IFilterFactory::Pointer factory = i.value();
AbstractFilter::Pointer filter = factory->create();
//if (filter->getGroupName().compare(DREAM3D::FilterGroups::StatisticsFilters) == 0)
// if(filter->getNameOfClass().compare("FindSchmids") == 0)
{
// std::cout << "" << filter->getGroupName().toStdString() << "Filters/" << filter->getNameOfClass().toStdString() << ".cpp" << std::endl;
QString cpp = findPath(filter->getGroupName(), filter->getNameOfClass(), ".cpp");
std::cout << filter << " " << cpp.toStdString() << std::endl;
}
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void PipelineViewEntry::instantiateFilter(const QString& filterClassName)
{
FilterManager::Pointer fm = FilterManager::Instance();
if(NULL == fm.get() ) { return; }
IFilterFactory::Pointer ff = fm->getFactoryForFilter(filterClassName);
if (NULL == ff.get()) { return; }
// Create an instance of the filter. Since we are dealing with the AbstractFilter interface we can not
// actually use the actual filter class. We are going to have to rely on QProperties or Signals/Slots
// to communicate changes back to the filter.
m_Filter = ff->create();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void GenerateFilterParametersCode()
{
FilterManager::Pointer fm = FilterManager::Instance();
FilterManager::Collection factories = fm->getFactories();
QMapIterator<QString, IFilterFactory::Pointer> iter(factories);
// Loop on each filter
while(iter.hasNext())
{
iter.next();
IFilterFactory::Pointer factory = iter.value();
AbstractFilter::Pointer filter = factory->create();
QString cpp = findPath(filter->getGroupName(), filter->getNameOfClass(), ".cpp");
QString h = findPath(filter->getGroupName(), filter->getNameOfClass(), ".h");
fixFile(filter, h, cpp);
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int main(int argc, char* argv[])
{
Q_ASSERT(true); // We don't want anyone to run this program.
// 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("FilterParameterTool");
std::cout << "FilterParameterTool Starting. Version " << DREAM3DLib::Version::PackageComplete().toStdString() << std::endl;
// Register all the filters including trying to load those from Plugins
FilterManager::Pointer fm = FilterManager::Instance();
DREAM3DPluginLoader::LoadPluginFilters(fm.get());
// Send progress messages from PipelineBuilder to this object for display
qRegisterMetaType<PipelineMessage>();
GenerateFilterParametersCode();
return 0;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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;
}
