// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int VertexGeom::writeXdmf(QTextStream& out, QString dcName, QString hdfFileName)
{
herr_t err = 0;
// Always start the grid
out << " <!-- *************** START OF " << dcName << " *************** -->" << "\n";
out << " <Grid Name=\"" << dcName << "\" GridType=\"Uniform\">" << "\n";
#if 0
DataArrayPath dap = getTemporalDataPath();
if(dap.isValid())
{
IDataArray::Pointer timeValues = getAttributeMatrix(dap.getAttributeMatrixName())->getAttributeArray(dap.getDataArrayName());
Int32ArrayType::Pointer timeValuePtr = boost::dynamic_pointer_cast<Int32ArrayType>(timeValues);
out << " <Time TimeType=\"Single\" Value=\"" << timeValuePtr->getValue(0) << "\"/>\n";
}
#endif
out << " <Topology TopologyType=\"Polyvertex\" NumberOfElements=\"" << getNumberOfVertices() << "\">" << "\n";
out << " <DataItem Format=\"HDF\" NumberType=\"Int\" Dimensions=\"" << getNumberOfVertices() << "\">" << "\n";
out << " " << hdfFileName << ":/DataContainers/" << dcName << "/" << DREAM3D::Geometry::Geometry << "/" << "Verts" << "\n";
out << " </DataItem>" << "\n";
out << " </Topology>" << "\n";
out << " <Geometry Type=\"XYZ\">" << "\n";
out << " <DataItem Format=\"HDF\" Dimensions=\"" << getNumberOfVertices() << " 3\" NumberType=\"Float\" Precision=\"4\">" << "\n";
out << " " << hdfFileName << ":/DataContainers/" << dcName << "/" << DREAM3D::Geometry::Geometry << "/" << DREAM3D::Geometry::SharedVertexList << "\n";
out << " </DataItem>" << "\n";
out << " </Geometry>" << "\n";
out << "" << "\n";
return err;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
AttributeMatrix::Pointer DataContainer::getAttributeMatrix(const DataArrayPath& path)
{
QMap<QString, AttributeMatrix::Pointer>::iterator it;
it = m_AttributeMatrices.find(path.getAttributeMatrixName());
if (it == m_AttributeMatrices.end())
{
return AttributeMatrix::NullPointer();
}
return it.value();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
QString InitializeSyntheticVolume::estimateNumFeatures(IntVec3_t dims, FloatVec3_t res)
{
float totalvol = 0.0f;
int32_t phase = 0;
totalvol = (dims.x * res.x) * (dims.y * res.y) * (dims.z * res.z);
if (totalvol == 0.0)
{
return "-1";
}
DataContainerArray::Pointer dca = getDataContainerArray();
// Get the PhaseTypes - Remember there is a Dummy PhaseType in the first slot of the array
QVector<size_t> cDims(1, 1); // This states that we are looking for an array with a single component
UInt32ArrayType::Pointer phaseType = dca->getPrereqArrayFromPath<UInt32ArrayType, AbstractFilter>(NULL, getInputPhaseTypesArrayPath(), cDims);
if (phaseType.get() == NULL)
{
QString ss = QObject::tr("Phase types array could not be downcast using std::dynamic_pointer_cast<T> when estimating the number of grains. The path is %1").arg(getInputPhaseTypesArrayPath().serialize());
setErrorCondition(-11002);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return "0";
}
QVector<size_t> statsDims(1, 1);
StatsDataArray::Pointer statsPtr = dca->getPrereqArrayFromPath<StatsDataArray, AbstractFilter>(this, getInputStatsArrayPath(), statsDims);
if (statsPtr.get() == NULL)
{
QString ss = QObject::tr("Statistics array could not be downcast using std::dynamic_pointer_cast<T> when estimating the number of grains. The path is %1").arg(getInputStatsArrayPath().serialize());
notifyErrorMessage(getHumanLabel(), ss, -11001);
return "0";
}
if (!phaseType->isAllocated())
{
if (getInputStatsFile().isEmpty())
{
QString ss = QObject::tr("Phase types array has not been allocated and the input statistics file is empty");
setErrorCondition(-1000);
notifyWarningMessage(getHumanLabel(), ss, getErrorCondition());
return "-1";
}
QFileInfo fi(getInputStatsFile());
if (fi.exists() == false)
{
QString ss = QObject::tr("Phase types array has not been allocated and the input statistics file does not exist at '%1'").arg(fi.absoluteFilePath());
setErrorCondition(-1001);
notifyWarningMessage(getHumanLabel(), ss, getErrorCondition());
return "-1";
}
hid_t fileId = -1;
herr_t err = 0;
// open the file
fileId = H5Utilities::openFile(getInputStatsFile().toLatin1().constData(), true);
// This will make sure if we return early from this method that the HDF5 File is properly closed.
HDF5ScopedFileSentinel scopedFileSentinel(&fileId, true);
DataArrayPath dap = getInputPhaseTypesArrayPath();
// Generate the path to the AttributeMatrix
QString hPath = DREAM3D::StringConstants::DataContainerGroupName + "/" + dap.getDataContainerName() + "/" + dap.getAttributeMatrixName();
// Open the AttributeMatrix Group
hid_t amGid = H5Gopen(fileId, hPath.toLatin1().data(), H5P_DEFAULT );
scopedFileSentinel.addGroupId(&amGid);
err = phaseType->readH5Data(amGid);
if (err < 0)
{
QString ss = QObject::tr("Error reading phase type data");
setErrorCondition(-1003);
notifyWarningMessage(getHumanLabel(), ss, getErrorCondition());
return "-1";
}
if (!phaseType->isAllocated())
{
QString ss = QObject::tr("Phase types Array was not allocated due to an error reading the data from the statistics file %1").arg(fi.absoluteFilePath());
setErrorCondition(-1002);
notifyWarningMessage(getHumanLabel(), ss, getErrorCondition());
return "-1";
}
}
// Create a Reference Variable so we can use the [] syntax
StatsDataArray& statsDataArray = *(statsPtr.get());
std::vector<int32_t> primaryphases;
std::vector<double> primaryphasefractions;
double totalprimaryfractions = 0.0;
// find which phases are primary phases
for (size_t i = 1; i < phaseType->getNumberOfTuples(); ++i)
{
if (phaseType->getValue(i) == DREAM3D::PhaseType::PrimaryPhase)
{
PrimaryStatsData* pp = PrimaryStatsData::SafePointerDownCast(statsDataArray[i].get());
primaryphases.push_back(i);
primaryphasefractions.push_back(pp->getPhaseFraction());
totalprimaryfractions = totalprimaryfractions + pp->getPhaseFraction();
}
}
// scale the primary phase fractions to total to 1
for (int32_t i = 0; i < primaryphasefractions.size(); i++)
{
primaryphasefractions[i] = primaryphasefractions[i] / totalprimaryfractions;
}
SIMPL_RANDOMNG_NEW()
// generate the Features
int32_t gid = 1;
float currentvol = 0.0f;
float vol = 0.0f;
float diam = 0.0f;
bool volgood = false;
for (int32_t j = 0; j < primaryphases.size(); ++j)
{
float curphasetotalvol = totalvol * primaryphasefractions[j];
while (currentvol < curphasetotalvol)
{
volgood = false;
phase = primaryphases[j];
PrimaryStatsData* pp = PrimaryStatsData::SafePointerDownCast(statsDataArray[phase].get());
if (NULL == pp)
{
QString ss = QObject::tr("Tried to cast a statsDataArray[%1].get() to a PrimaryStatsData* "
"pointer but this resulted in a NULL pointer.\n")
.arg(phase).arg(phase);
setErrorCondition(-666);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return "-1";
}
while (volgood == false)
{
volgood = true;
if (pp->getFeatureSize_DistType() == DREAM3D::DistributionType::LogNormal)
{
float avgdiam = pp->getFeatureSizeDistribution().at(0)->getValue(0);
float sddiam = pp->getFeatureSizeDistribution().at(1)->getValue(0);
diam = rg.genrand_norm(avgdiam, sddiam);
diam = expf(diam);
if (diam >= pp->getMaxFeatureDiameter()) { volgood = false; }
if (diam < pp->getMinFeatureDiameter()) { volgood = false; }
vol = (4.0f / 3.0f) * (M_PI) * ((diam * 0.5f) * (diam * 0.5f) * (diam * 0.5f));
}
}
currentvol = currentvol + vol;
gid++;
}
}
return QString::number(gid);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void PhaseTypeSelectionWidget::populateComboBoxes()
{
// std::cout << "void PhaseTypeSelectionWidget::populateComboBoxesWithSelection()" << std::endl;
// Now get the DataContainerArray from the Filter instance
// We are going to use this to get all the current DataContainers
DataContainerArray::Pointer dca = getFilter()->getDataContainerArray();
if(NULL == dca.get()) { return; }
// Grab what is currently selected
QString curDcName = dataContainerCombo->currentText();
QString curAmName = attributeMatrixCombo->currentText();
// Check to see if we have any DataContainers to actually populate drop downs with.
if(dca->getDataContainers().size() == 0)
{
dataContainerCombo->clear();
attributeMatrixCombo->clear();
return;
}
// Cache the DataContainerArray Structure for our use during all the selections
m_DcaProxy = DataContainerArrayProxy(dca.get());
// Populate the DataContainerArray Combo Box with all the DataContainers
QList<DataContainerProxy> dcList = m_DcaProxy.dataContainers.values();
QListIterator<DataContainerProxy> iter(dcList);
dataContainerCombo->clear();
while(iter.hasNext() )
{
DataContainerProxy dc = iter.next();
dataContainerCombo->addItem(dc.name);
}
// Get what is in the filter
PhaseTypeSelectionFilterParameter* p = dynamic_cast<PhaseTypeSelectionFilterParameter*>(getFilterParameter());
QVariant qvSelectedPath = getFilter()->property(p->getAttributeMatrixPathProperty().toLatin1().constData());
DataArrayPath selectedPath = qvSelectedPath.value<DataArrayPath>();
QString filtDcName = selectedPath.getDataContainerName();
QString filtAmName = selectedPath.getAttributeMatrixName();
QString dcName;
QString amName;
// If EVERYTHING is empty, then try the default value
if(filtDcName.isEmpty() && filtAmName.isEmpty()
&& curDcName.isEmpty() && curAmName.isEmpty() )
{
DataArrayPath daPath = getFilterParameter()->getDefaultValue().value<DataArrayPath>();
dcName = daPath.getDataContainerName();
amName = daPath.getAttributeMatrixName();
}
else
{
// Now to figure out which one of these to use. If this is the first time through then what we picked up from the
// gui will be empty strings because nothing is there. If there is something in the filter then we should use that.
// If there is something in both of them and they are NOT equal then we have a problem. Use the flag m_DidCausePreflight
// to determine if the change from the GUI should over ride the filter or vice versa. there is a potential that in future
// versions that something else is driving DREAM3D and pushing the changes to the filter and we need to reflect those
// changes in the GUI, like a testing script?
dcName = checkStringValues(curDcName, filtDcName);
if( !dca->doesDataContainerExist(dcName) ) { dcName = ""; }
amName = checkStringValues(curAmName, filtAmName);
if( !dca->doesAttributeMatrixExist(DataArrayPath(dcName, amName, "") ) ) { amName = ""; }
}
bool didBlock = false;
if (!dataContainerCombo->signalsBlocked()) { didBlock = true; }
dataContainerCombo->blockSignals(true);
int dcIndex = dataContainerCombo->findText(dcName);
dataContainerCombo->setCurrentIndex(dcIndex);
populateAttributeMatrixList();
if(didBlock) { dataContainerCombo->blockSignals(false); didBlock = false; }
if(!attributeMatrixCombo->signalsBlocked()) { didBlock = true; }
attributeMatrixCombo->blockSignals(true);
if (dcIndex < 0)
{
attributeMatrixCombo->setCurrentIndex(-1);
}
else
{
int amIndex = attributeMatrixCombo->findText(amName);
attributeMatrixCombo->setCurrentIndex(amIndex);
}
if(didBlock) { attributeMatrixCombo->blockSignals(false); didBlock = false; }
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AttributeMatrixCreationWidget::populateComboBoxes()
{
// std::cout << "void AttributeMatrixCreationWidget::populateComboBoxesWithSelection()" << std::endl;
// Now get the DataContainerArray from the Filter instance
// We are going to use this to get all the current DataContainers
DataContainerArray::Pointer dca = getFilter()->getDataContainerArray();
if (NULL == dca.get()) { return; }
// Check to see if we have any DataContainers to actually populate drop downs with.
if (dca->getDataContainers().size() == 0)
{
return;
}
// Cache the DataContainerArray Structure for our use during all the selections
m_DcaProxy = DataContainerArrayProxy(dca.get());
// Populate the DataContainer ComboBox
FilterPararameterWidgetUtils::PopulateDataContainerComboBox<AttributeMatrixCreationFilterParameter>(getFilter(), getFilterParameter(), dataContainerCombo, m_DcaProxy);
// Grab what is currently selected
QString curDcName = dataContainerCombo->currentText();
QString curAmName = attributeMatrixName->text();
// Get what is in the filter
DataArrayPath selectedPath = getFilter()->property(PROPERTY_NAME_AS_CHAR).value<DataArrayPath>();
// Split the path up to make sure we have a valid path separated by the "|" character
QString filtDcName = selectedPath.getDataContainerName();
QString filtAmName = selectedPath.getAttributeMatrixName();
// Now to figure out which one of these to use. If this is the first time through then what we picked up from the
// gui will be empty strings because nothing is there. If there is something in the filter then we should use that.
// If there is something in both of them and they are NOT equal then we have a problem. Use the flag m_DidCausePreflight
// to determine if the change from the GUI should over ride the filter or vice versa. there is a potential that in future
// versions that something else is driving SIMPLView and pushing the changes to the filter and we need to reflect those
// changes in the GUI, like a testing script?
QString dcName = checkStringValues(curDcName, filtDcName);
if (!dca->doesDataContainerExist(dcName)) { dcName = ""; }
bool didBlock = false;
if (!dataContainerCombo->signalsBlocked()) { didBlock = true; }
dataContainerCombo->blockSignals(true);
int dcIndex = dataContainerCombo->findText(dcName);
dataContainerCombo->setCurrentIndex(dcIndex);
if (didBlock) { dataContainerCombo->blockSignals(false); didBlock = false; }
if (!attributeMatrixName->signalsBlocked()) { didBlock = true; }
attributeMatrixName->blockSignals(true);
QString amName = checkStringValues(curAmName, filtAmName);
attributeMatrixName->setText(amName);
if (didBlock) { attributeMatrixName->blockSignals(false); didBlock = false; }
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void DataArraySelectionWidget::populateComboBoxes()
{
//qDebug() << "-----------------------------------------------";
//qDebug() << getFilter()->getHumanLabel() << " " << getFilterParameter()->getHumanLabel() << " DataArraySelectionWidget::populateComboBoxes()";
// Now get the DataContainerArray from the Filter instance
// We are going to use this to get all the current DataContainers
DataContainerArray::Pointer dca = getFilter()->getDataContainerArray();
if(NULL == dca.get()) { return; }
//qDebug() << getFilter()->getHumanLabel() << " " << getFilterParameter()->getHumanLabel();
// Grab what is currently selected
QString curDcName = dataContainerCombo->currentText();
QString curAmName = attributeMatrixCombo->currentText();
QString curDaName = attributeArrayCombo->currentText();
//qDebug() << "Current ComboBox Value: " << curDcName << "::" << curAmName << "::" << curDaName;
// Check to see if we have any DataContainers to actually populate drop downs with.
if(dca->getDataContainers().size() == 0)
{
dataContainerCombo->clear();
attributeMatrixCombo->clear();
attributeArrayCombo->clear();
return;
}
// Cache the DataContainerArray Structure for our use during all the selections
m_DcaProxy = DataContainerArrayProxy(dca.get());
// Populate the DataContainerArray Combo Box with all the DataContainers
QList<DataContainerProxy> dcList = m_DcaProxy.dataContainers.values();
QListIterator<DataContainerProxy> iter(dcList);
dataContainerCombo->clear();
while(iter.hasNext() )
{
DataContainerProxy dc = iter.next();
dataContainerCombo->addItem(dc.name);
// if(dataContainerCombo->findText(dc.name) == -1 )
// {
// int index = dataContainerCombo->currentIndex();
// dataContainerCombo->addItem(dc.name);
// dataContainerCombo->setCurrentIndex(index);
// }
}
// Get what is in the filter
DataArrayPath selectedPath = getFilter()->property(PROPERTY_NAME_AS_CHAR).value<DataArrayPath>();
// Split the path up to make sure we have a valid path separated by the "|" character
QString filtDcName = selectedPath.getDataContainerName();
QString filtAmName = selectedPath.getAttributeMatrixName();
QString filtDaName = selectedPath.getDataArrayName();
QString dcName;
QString amName;
QString daName;
// If EVERYTHING is empty, then try the default value
if(filtDcName.isEmpty() && filtAmName.isEmpty() && filtDaName.isEmpty()
&& curDcName.isEmpty() && curAmName.isEmpty() && curDaName.isEmpty() )
{
DataArrayPath daPath = getFilterParameter()->getDefaultValue().value<DataArrayPath>();
dcName = daPath.getDataContainerName();
amName = daPath.getAttributeMatrixName();
daName = daPath.getDataArrayName();
}
else
{
// Now to figure out which one of these to use. If this is the first time through then what we picked up from the
// gui will be empty strings because nothing is there. If there is something in the filter then we should use that.
// If there is something in both of them and they are NOT equal then we have a problem. Use the flag m_DidCausePreflight
// to determine if the change from the GUI should over ride the filter or vice versa. there is a potential that in future
// versions that something else is driving DREAM3D and pushing the changes to the filter and we need to reflect those
// changes in the GUI, like a testing script?
dcName = checkStringValues(curDcName, filtDcName);
if( !dca->doesDataContainerExist(dcName) ) { dcName = ""; }
amName = checkStringValues(curAmName, filtAmName);
if ( !dca->doesAttributeMatrixExist(DataArrayPath(dcName, amName, "") ) ) { amName = ""; }
daName = checkStringValues(curDaName, filtDaName);
if ( !dca->doesAttributeArrayExist(DataArrayPath(dcName, amName, daName) )) { daName = ""; }
}
bool didBlock = false;
if (!dataContainerCombo->signalsBlocked()) { didBlock = true; }
dataContainerCombo->blockSignals(true);
int dcIndex = dataContainerCombo->findText(dcName);
dataContainerCombo->setCurrentIndex(dcIndex);
populateAttributeMatrixList();
if(didBlock) { dataContainerCombo->blockSignals(false); didBlock = false; }
if(!attributeMatrixCombo->signalsBlocked()) { didBlock = true; }
attributeMatrixCombo->blockSignals(true);
int amIndex = -1;
if (dcIndex < 0)
{
attributeMatrixCombo->setCurrentIndex(-1);
attributeArrayCombo->setCurrentIndex(-1);
}
else
{
amIndex = attributeMatrixCombo->findText(amName);
attributeMatrixCombo->setCurrentIndex(amIndex);
populateAttributeArrayList();
}
if(didBlock) { attributeMatrixCombo->blockSignals(false); didBlock = false; }
if(!attributeArrayCombo->signalsBlocked()) { didBlock = true; }
attributeArrayCombo->blockSignals(true);
if (amIndex < 0)
{
attributeArrayCombo->setCurrentIndex(-1);
}
else
{
int daIndex = attributeArrayCombo->findText(daName);
// The DataArray Name was empty, lets instantiate the filter and get the default value and try that
if (daIndex < 0)
{
QVariant var = getFilterParameter()->getDefaultValue();
DataArrayPath path = var.value<DataArrayPath>();
daName = path.getDataArrayName(); // Pick up the DataArray Name from a Default instantiation of the filter
daIndex = attributeArrayCombo->findText(daName);
}
attributeArrayCombo->setCurrentIndex(daIndex); // we set the selection but we are NOT triggering anything so we should
}
if(didBlock) { attributeArrayCombo->blockSignals(false); didBlock = false; }// not be triggering an infinte recursion of preflights
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void DataContainerSelectionWidget::populateComboBoxes()
{
// std::cout << "void DataContainerSelectionWidget::populateComboBoxesWithSelection()" << std::endl;
// Now get the DataContainerArray from the Filter instance
// We are going to use this to get all the current DataContainers
DataContainerArray::Pointer dca = getFilter()->getDataContainerArray();
if(NULL == dca.get()) { return; }
// Check to see if we have any DataContainers to actually populate drop downs with.
if(dca->getDataContainers().size() == 0)
{
return;
}
// Cache the DataContainerArray Structure for our use during all the selections
m_DcaProxy = DataContainerArrayProxy(dca.get());
// Populate the DataContainerArray Combo Box with all the DataContainers
QList<DataContainerProxy> dcList = m_DcaProxy.dataContainers.values();
QListIterator<DataContainerProxy> iter(dcList);
dataContainerCombo->clear();
while(iter.hasNext() )
{
DataContainerProxy dc = iter.next();
dataContainerCombo->addItem(dc.name);
// if(dataContainerCombo->findText(dc.name) == -1 )
// {
// int index = dataContainerCombo->currentIndex();
// dataContainerCombo->addItem(dc.name);
// dataContainerCombo->setCurrentIndex(index);
// }
}
//remove items in the combo that are NOT in the Data Container Array
// int count = dataContainerCombo->count();
// for(int i = count - 1; i >= 0; i--)
// {
// QString str0 = dataContainerCombo->itemText(i);
// iter.toFront();
// bool boo = false;
// while(iter.hasNext() )
// {
// DataContainerProxy dc = iter.next();
// if(dc.name.compare(str0) == 0)
// {
// boo = true; // found in the list
// }
// }
// if(boo == false)
// {
// dataContainerCombo->removeItem(i);
// }
// }
// Grab what is currently selected
QString curDcName = dataContainerCombo->currentText();
// Get what is in the filter
QString filtDcName;
QString filtAmName;
QVariant qvSelectedPath = getFilter()->property(PROPERTY_NAME_AS_CHAR);
if( QString("QString").compare(qvSelectedPath.typeName()) == 0 )
{
filtDcName = qvSelectedPath.toString();
}
else if( QString("DataArrayPath").compare(qvSelectedPath.typeName()) == 0 )
{
DataArrayPath selectedPath = qvSelectedPath.value<DataArrayPath>();
filtDcName = selectedPath.getDataContainerName();
filtAmName = selectedPath.getAttributeMatrixName();
}
// Now to figure out which one of these to use. If this is the first time through then what we picked up from the
// gui will be empty strings because nothing is there. If there is something in the filter then we should use that.
// If there is something in both of them and they are NOT equal then we have a problem. Use the flag m_DidCausePreflight
// to determine if the change from the GUI should over ride the filter or vice versa. there is a potential that in future
// versions that something else is driving DREAM3D and pushing the changes to the filter and we need to reflect those
// changes in the GUI, like a testing script?
QString dcName = checkStringValues(curDcName, filtDcName);
if( !dca->doesDataContainerExist(dcName) ) { dcName = ""; }
bool didBlock = false;
if (!dataContainerCombo->signalsBlocked()) { didBlock = true; }
dataContainerCombo->blockSignals(true);
int dcIndex = dataContainerCombo->findText(dcName);
if(dcIndex < 0 && dcName.isEmpty() == false)
{
dataContainerCombo->addItem(dcName);
}
else
{
dataContainerCombo->setCurrentIndex(dcIndex);
}
if(didBlock) { dataContainerCombo->blockSignals(false); didBlock = false; }
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
QDebug operator<<(QDebug out, const DataArrayPath& v)
{
out << v.getDataContainerName() << "|" << v.getAttributeMatrixName() << "|" << v.getDataArrayName();
return out;
}