// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void VisualizeGBCDPoleFigure::dataCheck()
{
setErrorCondition(0);
getDataContainerArray()->getPrereqGeometryFromDataContainer<TriangleGeom, AbstractFilter>(this, getGBCDArrayPath().getDataContainerName());
if (getOutputFile().isEmpty() == true)
{
QString ss = QObject::tr( "The output file must be set");
setErrorCondition(-1000);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
QFileInfo fi(getOutputFile());
QDir parentPath = fi.path();
if (parentPath.exists() == false && getInPreflight())
{
QString ss = QObject::tr( "The directory path for the output file does not exist. DREAM.3D will attempt to create this path during execution of the filter");
notifyWarningMessage(getHumanLabel(), ss, -1);
}
if (fi.suffix().compare("") == 0)
{
setOutputFile(getOutputFile().append(".vtk"));
}
QVector<size_t> cDims(1, 1);
m_CrystalStructuresPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<unsigned int>, AbstractFilter>(this, getCrystalStructuresArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if (NULL != m_CrystalStructuresPtr.lock().get()) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{
m_CrystalStructures = m_CrystalStructuresPtr.lock()->getPointer(0);
} /* Now assign the raw pointer to data from the DataArray<T> object */
IDataArray::Pointer tmpGBCDPtr = getDataContainerArray()->getPrereqIDataArrayFromPath<IDataArray, AbstractFilter>(this, getGBCDArrayPath());
if(getErrorCondition() < 0) { return; }
if (NULL != tmpGBCDPtr.get())
{
QVector<size_t> cDims = tmpGBCDPtr->getComponentDimensions();
m_GBCDPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<double>, AbstractFilter>(this, getGBCDArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_GBCDPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_GBCD = m_GBCDPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
if (NULL != m_GBCDPtr.lock().get() && getPhaseOfInterest() >= m_GBCDPtr.lock()->getNumberOfTuples())
{
QString ss = QObject::tr("The phase index is larger than the number of Ensembles").arg(ClassName());
setErrorCondition(-1);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void RegularizeZSpacing::dataCheck()
{
setErrorCondition(0);
if (getNewZRes() <= 0)
{
QString ss = QObject::tr("The new Z resolution Y (%1) must be positive").arg(getNewZRes());
setErrorCondition(-5555);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
std::ifstream inFile;
inFile.open(m_InputFile.toLatin1().data());
if (!inFile.good())
{
QString ss = QObject::tr("Unable to open input file with name '%1'").arg(getInputFile());
setErrorCondition(-5556);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
ImageGeom::Pointer image = getDataContainerArray()->getPrereqGeometryFromDataContainer<ImageGeom, AbstractFilter>(this, getCellAttributeMatrixPath().getDataContainerName());
AttributeMatrix::Pointer cellAttrMat = getDataContainerArray()->getPrereqAttributeMatrixFromPath<AbstractFilter>(this, getCellAttributeMatrixPath(), -301);
if(getErrorCondition() < 0) {
return;
}
float zval = 0.0f;
for (size_t iter = 0; iter < image->getZPoints() + 1; iter++)
{
inFile >> zval;
}
size_t zP = static_cast<size_t>(zval / getNewZRes());
if(zP == 0) {
zP = 1;
}
if (getInPreflight())
{
image->setDimensions(image->getXPoints(), image->getYPoints(), zP);
QVector<size_t> tDims(3, 0);
tDims[0] = image->getXPoints();
tDims[1] = image->getYPoints();
tDims[2] = zP;
cellAttrMat->resizeAttributeArrays(tDims);
}
inFile.close();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void DataContainerReader::readData(bool preflight, DataContainerArrayProxy& proxy, DataContainerArray::Pointer dca)
{
setErrorCondition(0);
QString ss;
int32_t err = 0;
QString m_FileVersion;
float fVersion = 0.0f;
bool check = false;
// qDebug() << "DataContainerReader::readData() " << m_InputFile;
// Read the Meta Data and Array names from the file
hid_t fileId = QH5Utilities::openFile(m_InputFile, true); // Open the file Read Only
if (fileId < 0)
{
ss = QObject::tr("Error opening input file '%1'").arg(m_InputFile);
setErrorCondition(-150);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
// This will make sure if we return early from this method that the HDF5 File is properly closed.
HDF5ScopedFileSentinel scopedFileSentinel(&fileId, true);
// Check to see if version of .dream3d file is prior to new data container names
err = QH5Lite::readStringAttribute(fileId, "/", DREAM3D::HDF5::FileVersionName, m_FileVersion);
fVersion = m_FileVersion.toFloat(&check);
if (fVersion < 5.0 || err < 0)
{
QH5Utilities::closeFile(fileId);
fileId = QH5Utilities::openFile(m_InputFile, false); // Re-Open the file as Read/Write
err = H5Lmove(fileId, "VoxelDataContainer", fileId, DREAM3D::Defaults::DataContainerName.toLatin1().data(), H5P_DEFAULT, H5P_DEFAULT);
err = H5Lmove(fileId, "SurfaceMeshDataContainer", fileId, DREAM3D::Defaults::DataContainerName.toLatin1().data(), H5P_DEFAULT, H5P_DEFAULT);
err = QH5Lite::writeStringAttribute(fileId, "/", DREAM3D::HDF5::FileVersionName, "5.0");
QH5Utilities::closeFile(fileId);
fileId = QH5Utilities::openFile(m_InputFile, true); // Re-Open the file as Read Only
}
if (fVersion < 7.0)
{
ss = QObject::tr("File unable to be read - file structure older than 7.0");
setErrorCondition(-250);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
hid_t dcaGid = H5Gopen(fileId, DREAM3D::StringConstants::DataContainerGroupName.toLatin1().data(), 0);
if (dcaGid < 0)
{
setErrorCondition(-1923123);
QString ss = QObject::tr("Error attempting to open the HDF5 Group '%1'").arg(DREAM3D::StringConstants::DataContainerGroupName);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
scopedFileSentinel.addGroupId(&dcaGid);
err = dca->readDataContainersFromHDF5(preflight, dcaGid, proxy, this);
if (err < 0)
{
setErrorCondition(err);
QString ss = QObject::tr("Error trying to read the DataContainers from the file '%1'").arg(getInputFile());
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
err = H5Gclose(dcaGid);
dcaGid = -1;
err = readDataContainerBundles(fileId, dca);
if (err < 0)
{
setErrorCondition(err);
QString ss = QObject::tr("Error trying to read the DataContainerBundles from the file '%1'").arg(getInputFile());
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
if (!getInPreflight())
{
err = readExistingPipelineFromFile(fileId);
if(err < 0)
{
setErrorCondition(err);
QString ss = QObject::tr("Error trying to read the existing pipeline from the file '%1'").arg(getInputFile());
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void DataContainerReader::dataCheck()
{
// Sync the file proxy and cached proxy if the time stamps are different
QFileInfo fi(getInputFile());
if (getInputFile() == getLastFileRead() && getLastRead() < fi.lastModified())
{
syncProxies();
}
QString ss;
if (getInputFile().isEmpty() == true)
{
ss = QObject::tr("The input file must be set");
setErrorCondition(-387);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
else if (fi.exists() == false)
{
ss = QObject::tr("The input file does not exist");
setErrorCondition(-388);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
if(getErrorCondition())
{
// something has gone wrong and errors were logged alread so just return
return;
}
DataContainerArray::Pointer dca = getDataContainerArray();
// Create a new DataContainerArray to read the file data into
DataContainerArray::Pointer tempDCA = DataContainerArray::New();
// Read either the structure or all the data depending on the preflight status
readData(getInPreflight(), m_InputFileDataContainerArrayProxy, tempDCA);
QList<DataContainer::Pointer>& tempContainers = tempDCA->getDataContainers();
QListIterator<DataContainer::Pointer> iter(tempContainers);
while (iter.hasNext())
{
DataContainer::Pointer container = iter.next();
if (getOverwriteExistingDataContainers() == true )
{
if (dca->doesDataContainerExist(container->getName()) == true)
{
dca->removeDataContainer(container->getName());
}
dca->addDataContainer(container);
}
else
{
if (dca->doesDataContainerExist(container->getName()) == true)
{
ss = QObject::tr("The input file has a DataContainer with a name (%1) that already exists in the current DataContainerArray structure").arg(container->getName());
setErrorCondition(-390);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
else
{
dca->addDataContainer(container);
}
}
}
QMap<QString, IDataContainerBundle::Pointer> bundles = tempDCA->getDataContainerBundles();
dca->setDataContainerBundles(bundles);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ConvertData::dataCheck()
{
setErrorCondition(0);
DataContainer::Pointer m = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getSelectedCellArrayPath().getDataContainerName(), false);
QString ss;
if (m_OutputArrayName.isEmpty() == true)
{
ss = QObject::tr("The output array name must be set");
setErrorCondition(-398);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
if (getInPreflight())
{
AttributeMatrix::Pointer cellAttrMat = getDataContainerArray()->getPrereqAttributeMatrixFromPath<AbstractFilter>(this, m_SelectedCellArrayPath, -301);
if(getErrorCondition() < 0) { return; }
IDataArray::Pointer p = getDataContainerArray()->getPrereqIDataArrayFromPath<IDataArray, AbstractFilter>(this, getSelectedCellArrayPath());
if(getErrorCondition() < 0) { return; }
QVector<size_t> dims = p->getComponentDimensions();
size_t voxels = cellAttrMat->getNumTuples();
if (m_ScalarType == Detail::Int8)
{
p = Int8ArrayType::CreateArray(voxels, dims, m_OutputArrayName);
}
else if (m_ScalarType == Detail::UInt8)
{
p = UInt8ArrayType::CreateArray(voxels, dims, m_OutputArrayName);
}
else if (m_ScalarType == Detail::Int16)
{
p = Int16ArrayType::CreateArray(voxels, dims, m_OutputArrayName);
}
else if (m_ScalarType == Detail::UInt16)
{
p = UInt16ArrayType::CreateArray(voxels, dims, m_OutputArrayName);
}
else if (m_ScalarType == Detail::Int32)
{
p = Int32ArrayType::CreateArray(voxels, dims, m_OutputArrayName);
}
else if (m_ScalarType == Detail::UInt32)
{
p = UInt32ArrayType::CreateArray(voxels, dims, m_OutputArrayName);
}
else if (m_ScalarType == Detail::Int64)
{
p = Int64ArrayType::CreateArray(voxels, dims, m_OutputArrayName);
}
else if (m_ScalarType == Detail::UInt64)
{
p = UInt64ArrayType::CreateArray(voxels, dims, m_OutputArrayName);
}
else if (m_ScalarType == Detail::Float)
{
p = FloatArrayType::CreateArray(voxels, dims, m_OutputArrayName);
}
else if (m_ScalarType == Detail::Double)
{
p = DoubleArrayType::CreateArray(voxels, dims, m_OutputArrayName);
}
cellAttrMat->addAttributeArray(p->getName(), p);
}
}