// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int EstablishShapeTypes::getPhaseCount()
{
DataContainerArray::Pointer dca = getDataContainerArray();
AttributeMatrix::Pointer inputAttrMat = dca->getAttributeMatrix(getInputPhaseTypesArrayPath());
if (NULL == inputAttrMat.get() ) { return 0; }
if (__SHOW_DEBUG_MSG__)
{
qDebug() << " data->getNumberOfTuples(): " << inputAttrMat->getTupleDimensions();
qDebug() << "Name" << inputAttrMat->getName();
}
if (inputAttrMat->getType() < DREAM3D::AttributeMatrixType::VertexEnsemble
|| inputAttrMat->getType() > DREAM3D::AttributeMatrixType::CellEnsemble )
{
return 0;
}
QVector<size_t> tupleDims = inputAttrMat->getTupleDimensions();
size_t phaseCount = 1;
for (int32_t i = 0; i < tupleDims.size(); i++)
{
phaseCount = phaseCount * tupleDims[i];
}
return phaseCount;
}
/**
*
* @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;
}
int testCase1_Execute(const QString& name, int scalarType)
{
int err = 0;
int dataArraySize = ARRAY_SIZE * N;
int junkArraySize = 0;
int skipHeaderBytes = 0;
qDebug() << "Testing case 1: " << name << " with num comps " << N;
// Allocate an array, and get the dataArray from that array
boost::shared_array<T> array(new T[dataArraySize]); // This makes sure our allocated array is deleted when we leave
T* dataArray = array.get();
// Write some data into the data array
for(size_t i = 0; i < dataArraySize; ++i)
{
dataArray[i] = static_cast<T>(i);
}
// Create junkArray and set it to NULL because there is no junk in this test case
T* junkArray = NULL;
// Create the file and write to it. If any of the information is wrong, the result will be false
bool result = createAndWriteToFile(dataArray, dataArraySize, junkArray, junkArraySize, Detail::None);
// Test to make sure that the file was created and written to successfully
DREAM3D_REQUIRED(result, == , true)
// Create the data container
VolumeDataContainer::Pointer m = VolumeDataContainer::New();
m->setName(DREAM3D::Defaults::DataContainerName);
DataContainerArray::Pointer dca = DataContainerArray::New();
dca->pushBack(m);
// Create the filter, passing in the skipHeaderBytes
RawBinaryReader::Pointer filt = createRawBinaryReaderFilter(scalarType, N, skipHeaderBytes);
filt->setDataContainerArray(dca);
// Preflight, get the error condition, and check that there are no errors
filt->preflight();
err = filt->getErrorCondition();
DREAM3D_REQUIRED(err, >= , 0)
// Execute the filter, check that there are no errors, and compare the data
filt->execute();
DREAM3D_REQUIRED(err, >= , 0)
IDataArray::Pointer iData = m->getAttributeMatrix(getCellAttributeMatrixName())->getAttributeArray("Test_Array");
T* data = reinterpret_cast<T*>(iData->getVoidPointer(0));
T d, p;
for(size_t i = 0; i < dataArraySize; ++i)
{
d = data[i];
p = dataArray[i];
DREAM3D_REQUIRE_EQUAL(d, p)
}
return err;
}
static void PopulateAttributeMatrixComboBox(AbstractFilter* filter, FilterParameter* filterParameter,
QComboBox* dcCombo, QComboBox* amCombo,
DataContainerArrayProxy& dcaProxy)
{
FilterParameterType* fp = dynamic_cast<FilterParameterType*>(filterParameter);
assert(fp != NULL);
DataContainerArray::Pointer dca = filter->getDataContainerArray();
if (NULL == dca.get()) { return; }
QString dcName = dcCombo->currentText();
// Clear the AttributeMatrix List
bool alreadyBlocked = false;
if(amCombo->signalsBlocked()) { alreadyBlocked = true; }
amCombo->blockSignals(true);
amCombo->clear();
// Loop over the data containers until we find the proper data container
QList<DataContainerProxy> containers = dcaProxy.dataContainers.values();
QListIterator<DataContainerProxy> containerIter(containers);
QVector<unsigned int> defVec = fp->getDefaultAttributeMatrixTypes();
while(containerIter.hasNext())
{
DataContainerProxy dc = containerIter.next();
if(dc.name.compare(dcName) == 0 )
{
// We found the proper Data Container, now populate the AttributeMatrix List
QMap<QString, AttributeMatrixProxy> attrMats = dc.attributeMatricies;
QMapIterator<QString, AttributeMatrixProxy> attrMatsIter(attrMats);
while(attrMatsIter.hasNext() )
{
attrMatsIter.next();
QString amName = attrMatsIter.key();
AttributeMatrix::Pointer am = dca->getAttributeMatrix(DataArrayPath(dc.name, amName, ""));
amCombo->addItem(amName);
if (NULL != am.get() && defVec.isEmpty() == false && defVec.contains(am->getType()) == false)
{
QStandardItemModel* model = qobject_cast<QStandardItemModel*>(amCombo->model());
if (NULL != model)
{
QStandardItem* item = model->item(amCombo->findText(amName));
if (NULL != item)
{
item->setFlags(item->flags() & ~Qt::ItemIsEnabled);
}
}
}
}
}
}
if(!alreadyBlocked) { // Only unblock if this function blocked the signals.
amCombo->blockSignals(false);
}
}
void testCase6_Execute(const QString& name, int scalarType)
{
int dataArraySize = 0;
int junkArraySize = ARRAY_SIZE * N;
int skipHeaderBytes = junkArraySize * sizeof(T);
int err = 0;
qDebug() << "Testing case 6: " << name << " with num comps " << N;
// Allocate an array, and get the dataArray from that array
boost::shared_array<T> array(new T[dataArraySize]); // This makes sure our allocated array is deleted when we leave
T* dataArray = array.get();
// Write some data into the data array
for(size_t i = 0; i < dataArraySize; ++i)
{
dataArray[i] = static_cast<T>(i);
}
// Create junkArray
T* junkArray = new T[junkArraySize];
// Write a pattern into junkArray
for(size_t i = 0; i < junkArraySize; ++i)
{
junkArray[i] = (unsigned)0xAB;
}
// Create the file and write to it. If any of the information is wrong, the result will be false
bool result = createAndWriteToFile(dataArray, dataArraySize, junkArray, junkArraySize, Detail::Start);
// Test to make sure that the file was created and written to successfully
DREAM3D_REQUIRED(result, == , true)
// Create the data container
VolumeDataContainer::Pointer m = VolumeDataContainer::New();
m->setName(DREAM3D::Defaults::DataContainerName);
DataContainerArray::Pointer dca = DataContainerArray::New();
dca->pushBack(m);
// Create the filter, passing in the skipHeaderBytes
RawBinaryReader::Pointer filt = createRawBinaryReaderFilter(scalarType, N, skipHeaderBytes);
filt->setDataContainerArray(dca);
// Preflight, get error condition, and check that the "file too small" error has occurred
filt->preflight();
err = filt->getErrorCondition();
DREAM3D_REQUIRED(err, == , RBRT_FILE_TOO_SMALL)
// Execute, get error condition, and check that there are errors
filt->execute();
err = filt->getErrorCondition();
DREAM3D_REQUIRED(err, < , 0)
}
static void PopulateDataContainerComboBox(AbstractFilter* filter, FilterParameter* filterParameter,
QComboBox* dcCombo, DataContainerArrayProxy& dcaProxy)
{
FilterParameterType* fp = dynamic_cast<FilterParameterType*>(filterParameter);
assert(fp != NULL);
DataContainerArray::Pointer dca = filter->getDataContainerArray();
// Populate the DataContainerArray Combo Box with all the DataContainers
QList<DataContainerProxy> dcList = dcaProxy.dataContainers.values();
QListIterator<DataContainerProxy> iter(dcList);
dcCombo->clear();
QVector<unsigned int> defVec = fp->getDefaultGeometryTypes();
while(iter.hasNext() )
{
DataContainerProxy dcProxy = iter.next();
DataContainer::Pointer dc = dca->getDataContainer(dcProxy.name);
IGeometry::Pointer geom = IGeometry::NullPointer();
uint32_t geomType = 999;
if (NULL != dc.get()) { geom = dc->getGeometry(); }
if (NULL != geom.get()) { geomType = geom->getGeometryType(); }
dcCombo->addItem(dcProxy.name);
if (defVec.isEmpty() == false)
{
if (defVec.contains(geomType) == false)
{
QStandardItemModel* model = qobject_cast<QStandardItemModel*>(dcCombo->model());
if (NULL != model)
{
QStandardItem* item = model->item(dcCombo->findText(dcProxy.name));
if (NULL != item)
{
item->setFlags(item->flags() & ~Qt::ItemIsEnabled);
}
}
}
}
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void DataContainerArrayProxyWidget::beforePreflight()
{
if (m_DidCausePreflight == false)
{
// qDebug() << getFilter()->getNameOfClass() << " DataContainerArrayProxyWidget::beforePreflight()";
// Get the DataContainerArray from the Filter instance. This will have what will become the choices for the user
// to select from.
DataContainerArray::Pointer dca = getFilter()->getDataContainerArray();
DataContainerArrayProxy incomingProxy = DataContainerArrayProxy(dca.get() );
incomingProxy.setAllFlags(m_FilterParameter->getDefaultFlagValue());
//incomingProxy.print("BeforePreflight INCOMING");
//Now the idea becomes to save the selections that the user has made and transfer those changes to the incoming
// proxy object
updateProxyFromProxy(m_DcaProxy, incomingProxy);
//proxy.print("'proxy' beforePreflight AFTER updateProxyFromProxy()");
m_DcaProxy = incomingProxy;
// Now that the proxy was updated with our selections, make the updated incoming proxy into our cache
// Now update the Model
updateModelFromProxy(m_DcaProxy);
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 testCase4_Execute(const QString& name, int scalarType)
{
int dataArraySize = ARRAY_SIZE * N;
int junkArraySize = 5;
int skipHeaderBytes = junkArraySize * sizeof(T);
int err = 0;
qDebug() << "Testing case 4: " << name << " with num comps " << N;
// Allocate an array, and get the dataArray from that array
boost::shared_array<T> array(new T[dataArraySize]); // This makes sure our allocated array is deleted when we leave
T* dataArray = array.get();
// Write some data into the data array
for(size_t i = 0; i < dataArraySize; ++i)
{
dataArray[i] = static_cast<T>(i);
}
// Create junkArray
T* junkArray = new T[junkArraySize];
// Write a pattern into junkArray
for(size_t i = 0; i < junkArraySize; ++i)
{
junkArray[i] = (unsigned)0xAB;
}
// Create the file and write to it. If any of the information is wrong, the result will be false
bool result = createAndWriteToFile(dataArray, dataArraySize, junkArray, junkArraySize, Detail::Start);
// Test to make sure that the file was created and written to successfully
DREAM3D_REQUIRED(result, == , true)
// Create the data container
VolumeDataContainer::Pointer m = VolumeDataContainer::New();
m->setName(DREAM3D::Defaults::DataContainerName);
DataContainerArray::Pointer dca = DataContainerArray::New();
dca->pushBack(m);
// Create the filter, passing in the skipHeaderBytes
RawBinaryReader::Pointer filt = createRawBinaryReaderFilter(scalarType, N, skipHeaderBytes);
filt->setDataContainerArray(dca);
// Preflight, get error condition, and check that there are no errors
filt->preflight();
err = filt->getErrorCondition();
DREAM3D_REQUIRED(err, >= , 0)
// Execute, get error condition, check that there are no errors, and compare the data
filt->execute();
err = filt->getErrorCondition();
DREAM3D_REQUIRED(err, >= , 0)
IDataArray::Pointer iData = m->getAttributeMatrix(getCellAttributeMatrixName())->getAttributeArray("Test_Array");
T* data = reinterpret_cast<T*>(iData->getVoidPointer(0));
T d, p;
for(size_t i = 0; i < dataArraySize; ++i)
{
d = data[i];
p = dataArray[i];
DREAM3D_REQUIRE_EQUAL(d, p)
}
/*
* SUBTEST: Test when skipHeaderBytes is larger than expected
*/
// Create another data container
VolumeDataContainer::Pointer m2 = VolumeDataContainer::New();
m2->setName(DREAM3D::Defaults::DataContainerName);
DataContainerArray::Pointer dca2 = DataContainerArray::New();
dca2->pushBack(m2);
// Create another filter, passing in the skipHeaderBytes + 1
RawBinaryReader::Pointer filt2 = createRawBinaryReaderFilter(scalarType, N, skipHeaderBytes + 1);
filt2->setDataContainerArray(dca2);
// Preflight, get error condition, and check that there are errors
filt2->preflight();
err = filt2->getErrorCondition();
DREAM3D_REQUIRED(err, < , 0)
// Execute, get error condition, and check that the "file too small" error occurred
filt2->execute();
err = filt2->getErrorCondition();
DREAM3D_REQUIRED(err, == , RBRT_FILE_TOO_SMALL)
}
static void PopulateAttributeArrayList(AbstractFilter* filter, FilterParameter* filterParameter,
QComboBox* dcCombo, QComboBox* amCombo, WidgetType* attributeArraysWidget,
DataContainerArrayProxy& dcaProxy,
QVector<DataArrayPath> selectedPaths)
{
FilterParameterType* fp = dynamic_cast<FilterParameterType*>(filterParameter);
assert(fp != NULL);
DataContainerArray::Pointer dca = filter->getDataContainerArray();
if (NULL == dca.get()) { return; }
attributeArraysWidget->blockSignals(true);
attributeArraysWidget->clear();
// Get the selected Data Container Name from the DataContainerList Widget
QString currentDCName = dcCombo->currentText();
QString currentAttrMatName = amCombo->currentText();
// Loop over the data containers until we find the proper data container
QList<DataContainerProxy> containers = dcaProxy.dataContainers.values();
QListIterator<DataContainerProxy> containerIter(containers);
QVector<QString> daTypes = fp->getDefaultAttributeArrayTypes();
QVector< QVector<size_t> > cDims = fp->getDefaultComponentDimensions();
while (containerIter.hasNext())
{
DataContainerProxy dc = containerIter.next();
if (dc.name.compare(currentDCName) == 0)
{
// We found the proper Data Container, now populate the AttributeMatrix List
QMap<QString, AttributeMatrixProxy> attrMats = dc.attributeMatricies;
QMapIterator<QString, AttributeMatrixProxy> attrMatsIter(attrMats);
while (attrMatsIter.hasNext())
{
attrMatsIter.next();
QString amName = attrMatsIter.key();
if (amName.compare(currentAttrMatName) == 0)
{
// Clear the list of arrays from the QListWidget
attributeArraysWidget->clear();
// We found the selected AttributeMatrix, so loop over this attribute matrix arrays and populate the list widget
AttributeMatrixProxy amProxy = attrMatsIter.value();
QMap<QString, DataArrayProxy> dataArrays = amProxy.dataArrays;
QMapIterator<QString, DataArrayProxy> dataArraysIter(dataArrays);
while (dataArraysIter.hasNext())
{
dataArraysIter.next();
QString daName = dataArraysIter.key();
QListWidgetItem* daItem = new QListWidgetItem(daName);
daItem->setCheckState(Qt::Unchecked);
for (int i = 0; i < selectedPaths.size(); i++)
{
if (selectedPaths.at(i).getDataArrayName() == daName)
{
daItem->setCheckState(Qt::Checked);
}
}
IDataArray::Pointer da = dca->getPrereqIDataArrayFromPath<IDataArray, AbstractFilter>(NULL, DataArrayPath(dc.name, amProxy.name, daName));
attributeArraysWidget->addItem(daItem);
if (NULL != da.get() && ((daTypes.isEmpty() == false && daTypes.contains(da->getTypeAsString()) == false) || (cDims.isEmpty() == false && cDims.contains(da->getComponentDimensions()) == false)))
{
QList<QListWidgetItem*> rejectList = attributeArraysWidget->findItems(daName, Qt::MatchRecursive);
for (int i = 0; i < rejectList.size(); i++)
{
QListWidgetItem* item = rejectList[i];
item->setFlags(item->flags() & ~Qt::ItemIsEnabled);
}
}
}
}
}
}
}
attributeArraysWidget->blockSignals(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; }
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int main(int argc, char** argv)
{
std::cout << "Starting Conversion of H5Voxel to VTK with Feature ID and IPF Colors" << std::endl;
if (argc < 3)
{
std::cout << "This program takes 2 arguments: Input .h5voxel file and output vtk file." << std::endl;
return EXIT_FAILURE;
}
QString iFile = argv[1];
int err = 0;
DataContainerArray::Pointer dca = DataContainerArray::New();
VolumeDataContainer::Pointer m = VolumeDataContainer::New();
dca->pushBack(m);
DataContainerReader::Pointer h5Reader = DataContainerReader::New();
h5Reader->setInputFile(iFile);
h5Reader->setDataContainerArray(dca);
size_t dcDims[3];
float spacing[3];
float origin[3];
h5Reader->execute();
err = h5Reader->getErrorCondition();
if (err < 0)
{
setErrorCondition(err);
// addErrorMessages(h5Reader->getErrorMessages());
return EXIT_FAILURE;
}
m->getDimensions(dcDims);
m->getResolution(spacing);
m->getOrigin(origin);
int64_t dims[3] = {dcDims[0], dcDims[1], dcDims[2]};
/* Sanity check what we are trying to load to make sure it can fit in our address space.
* Note that this does not guarantee the user has enough left, just that the
* size of the volume can fit in the address space of the program
*/
#if (CMP_SIZEOF_SSIZE_T==4)
int64_t max = std::numeric_limits<size_t>::max();
#else
int64_t max = std::numeric_limits<int64_t>::max();
#endif
if (dims[0] * dims[1] * dims[2] > max )
{
err = -1;
std::stringstream s;
s << "The total number of elements '" << (dims[0] * dims[1] * dims[2])
<< "' is greater than this program can hold. Try the 64 bit version.";
setErrorCondition(err);
setErrorMessage(s.str());
return EXIT_FAILURE;
}
if (dims[0] > max || dims[1] > max || dims[2] > max)
{
err = -1;
std::stringstream s;
s << "One of the dimensions is greater than the max index for this sysem. Try the 64 bit version.";
s << " dim[0]=" << dims[0] << " dim[1]=" << dims[1] << " dim[2]=" << dims[2];
setErrorCondition(err);
setErrorMessage(s.str());
return EXIT_FAILURE;
}
/* ************ End Sanity Check *************************** */
std::stringstream ss;
std::cout << "Writing VTK file" << std::endl;
FILE* f = fopen(argv[2], "wb");
WRITE_STRUCTURED_POINTS_HEADER("ASCII", m)
// VoxelIPFColorScalarWriter<VolumeDataContainer> ipfWriter(m.get());
// ipfWriter.m_WriteBinaryFiles = false;
// ipfWriter.writeScalars(f);
int64_t totalPoints = m->getTotalPoints();
int32_t* m_FeatureIds = NULL;
m_FeatureIds = m->getCellDataSizeCheck<int32_t, Int32ArrayType, AbstractFilter>(SIMPL::CellData::FeatureIds, totalPoints, 1, NULL);
if (0 == m_FeatureIds )
{
ss << "Filter " << getNameOfClass() << " requires the data array '" <<
"DREAM3D" << "::" << "CellData" << "::" << "FeatureIds" << "' to already be created prior to execution." << std::endl;
setErrorCondition(-300);
}
WRITE_VTK_GRAIN_IDS_ASCII(m, SIMPL::CellData::FeatureIds, m_FeatureIds)
fclose(f);
std::cout << "Done Converting" << std::endl;
return EXIT_SUCCESS;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 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; }
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int DataContainerReader::readDataContainerBundles(hid_t fileId, DataContainerArray::Pointer dca)
{
herr_t err = 0;
hid_t dcbGroupId = H5Gopen(fileId, DREAM3D::StringConstants::DataContainerBundleGroupName.toLatin1().constData(), H5P_DEFAULT);
if (dcbGroupId < 0)
{
// NO Bundles are available to read so just return.
// QString ss = QObject::tr("Error opening HDF5 Group '%1' ").arg(DREAM3D::StringConstants::DataContainerBundleGroupName);
// setErrorCondition(-75);
// notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return 0;
}
HDF5ScopedGroupSentinel sentinel(&dcbGroupId, false);
QList<QString> groupNames;
err = QH5Utilities::getGroupObjects(dcbGroupId, H5Utilities::H5Support_GROUP, groupNames);
if (err < 0)
{
QString ss = QObject::tr("Error getting group objects from HDF5 group '%1' ").arg(DREAM3D::StringConstants::DataContainerBundleGroupName);
setErrorCondition(-76);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return err;
}
char sep = 0x1E;
QListIterator<QString> iter(groupNames);
while (iter.hasNext() )
{
QString bundleName = iter.next();
DataContainerBundle::Pointer bundle = DataContainerBundle::New(bundleName);
hid_t bundleId = H5Gopen(dcbGroupId, bundleName.toLatin1().constData(), H5P_DEFAULT);
sentinel.addGroupId(&bundleId); // Make sure this group gets closed
// Read in the Data Container Names
QString dcNames;
err = QH5Lite::readStringDataset(bundleId, DREAM3D::StringConstants::DataContainerNames, dcNames);
if (err < 0)
{
QString ss = QObject::tr("Error reading DataContainer group names from HDF5 group '%1' ").arg(bundleName);
setErrorCondition(-75);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return err;
}
QStringList dcNameList = dcNames.split(QString(sep));
QStringListIterator nameIter(dcNameList);
while(nameIter.hasNext() )
{
QString dcName = nameIter.next();
DataContainer::Pointer dc = dca->getDataContainer(dcName);
if (NULL == dc.get() )
{
qDebug() << "Data Container '" << dcName << "' was NULL" << " " << __FILE__ << "(" << __LINE__ << ")";
}
bundle->addDataContainer(dc);
}
QString metaArrays;
err = QH5Lite::readStringDataset(bundleId, DREAM3D::StringConstants::MetaDataArrays, metaArrays);
if (err < 0)
{
QString ss = QObject::tr("Error reading DataContainerBundle meta data arrays from HDF5 group '%1' ").arg(bundleName);
setErrorCondition(-76);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return err;
}
QStringList metaNameList = metaArrays.split(QString(sep));
bundle->setMetaDataArrays(metaNameList);
dca->addDataContainerBundle(bundle);
}
H5Gclose(dcbGroupId);
dcbGroupId = -1;
return err;
}
static void PopulateAttributeArrayComboBox(AbstractFilter* filter, FilterParameter* filterParameter,
QComboBox* dcCombo, QComboBox* amCombo, QComboBox* aaCombo,
DataContainerArrayProxy& dcaProxy)
{
FilterParameterType* fp = dynamic_cast<FilterParameterType*>(filterParameter);
assert(fp != NULL);
DataContainerArray::Pointer dca = filter->getDataContainerArray();
if (NULL == dca.get()) { return; }
bool alreadyBlocked = false;
if(aaCombo->signalsBlocked()) { alreadyBlocked = true; }
aaCombo->blockSignals(true);
aaCombo->clear();
// Get the selected Data Container Name from the DataContainerList Widget
QString currentDCName = dcCombo->currentText();
QString currentAttrMatName = amCombo->currentText();
// Loop over the data containers until we find the proper data container
QList<DataContainerProxy> containers = dcaProxy.dataContainers.values();
QListIterator<DataContainerProxy> containerIter(containers);
QVector<QString> daTypes = fp->getDefaultAttributeArrayTypes();
QVector< QVector<size_t> > cDims = fp->getDefaultComponentDimensions();
while (containerIter.hasNext())
{
DataContainerProxy dc = containerIter.next();
if (dc.name.compare(currentDCName) == 0)
{
// We found the proper Data Container, now populate the AttributeMatrix List
QMap<QString, AttributeMatrixProxy> attrMats = dc.attributeMatricies;
QMapIterator<QString, AttributeMatrixProxy> attrMatsIter(attrMats);
while (attrMatsIter.hasNext())
{
attrMatsIter.next();
QString amName = attrMatsIter.key();
if (amName.compare(currentAttrMatName) == 0)
{
// Clear the list of arrays from the QListWidget
aaCombo->clear();
// We found the selected AttributeMatrix, so loop over this attribute matrix arrays and populate the list widget
AttributeMatrixProxy amProxy = attrMatsIter.value();
QMap<QString, DataArrayProxy> dataArrays = amProxy.dataArrays;
QMapIterator<QString, DataArrayProxy> dataArraysIter(dataArrays);
while (dataArraysIter.hasNext())
{
dataArraysIter.next();
//DataArrayProxy daProxy = dataArraysIter.value();
QString daName = dataArraysIter.key();
IDataArray::Pointer da = dca->getPrereqIDataArrayFromPath<IDataArray, AbstractFilter>(NULL, DataArrayPath(dc.name, amProxy.name, daName));
aaCombo->addItem(daName);
if (NULL != da.get() && ((daTypes.isEmpty() == false && daTypes.contains(da->getTypeAsString()) == false) || (cDims.isEmpty() == false && cDims.contains(da->getComponentDimensions()) == false)))
{
QStandardItemModel* model = qobject_cast<QStandardItemModel*>(aaCombo->model());
if (NULL != model)
{
QStandardItem* item = model->item(aaCombo->findText(daName));
if (NULL != item)
{
item->setFlags(item->flags() & ~Qt::ItemIsEnabled);
}
}
}
}
}
}
}
aaCombo->setCurrentIndex(-1);
if(alreadyBlocked == false)
{
aaCombo->blockSignals(false);
}
}
}
