// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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;
}
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 EdgeGeom::addAttributeMatrix(const QString& name, AttributeMatrix::Pointer data)
{
if (data->getType() != 0 || data->getType() != 1)
{
// EdgeGeom can only accept vertex or edge Attribute Matrices
return;
}
if (data->getType() == 0 && static_cast<int64_t>(data->getNumTuples()) != getNumberOfVertices())
{
return;
}
if (data->getType() == 1 && data->getNumTuples() != getNumberOfElements())
{
return;
}
if (data->getName().compare(name) != 0)
{
data->setName(name);
}
m_AttributeMatrices[name] = data;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void VertexGeom::addAttributeMatrix(const QString& name, AttributeMatrix::Pointer data)
{
if (data->getType() != 0)
{
// VertexGeom can only accept vertex Attribute Matrices
return;
}
if (data->getNumTuples() != getNumberOfElements())
{
return;
}
if (data->getName().compare(name) != 0)
{
data->setName(name);
}
m_AttributeMatrices[name] = data;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
DataContainerArrayProxy::DataContainerArrayProxy(DataContainerArray* dca)
{
if(NULL == dca)
{
return;
}
QList<DataContainer::Pointer> containers = dca->getDataContainers();
for(int i = 0; i < containers.size(); i++) // Loop on each Data Container
{
DataContainer::Pointer container = containers.at(i);
DataContainerProxy dcProxy(container->getName(), Qt::Checked); // Create a new DataContainerProxy
// Now loop over each AttributeMatrix in the data container that was selected
DataContainer::AttributeMatrixMap_t attrMats = container->getAttributeMatrices();
QMapIterator<QString, AttributeMatrix::Pointer> iter(attrMats);
while(iter.hasNext())
{
iter.next();
QString amName = iter.key();
AttributeMatrix::Pointer attrMat = iter.value();
AttributeMatrixProxy amProxy(amName, Qt::Checked, attrMat->getType());
QList<QString> attrArrayNames = attrMat->getAttributeArrayNames();
QListIterator<QString> attrArrayNamesIter(attrArrayNames);
while(attrArrayNamesIter.hasNext())
{
QString aaName = attrArrayNamesIter.next();
QString daPath = container->getName() + "/" + amName + "/";
IDataArray::Pointer attrArray = attrMat->getAttributeArray(aaName);
DataArrayProxy daProxy(daPath, aaName, Qt::Checked, attrArray->getTypeAsString(), attrArray->getClassVersion() );
amProxy.dataArrays.insert(aaName, daProxy);
}
dcProxy.attributeMatricies.insert(amName, amProxy); // Add the new AttributeMatrix to the DataContainerProxy
}
dataContainers.insert(dcProxy.name, dcProxy);
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ChangeResolution::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m;
if(m_SaveAsNewDataContainer == false)
{
m = getDataContainerArray()->getDataContainer(getCellAttributeMatrixPath().getDataContainerName());
}
else
{
m = getDataContainerArray()->getDataContainer(getNewDataContainerName());
}
if(m->getGeometryAs<ImageGeom>()->getXRes() == m_Resolution.x
&& m->getGeometryAs<ImageGeom>()->getYRes() == m_Resolution.y
&& m->getGeometryAs<ImageGeom>()->getZRes() == m_Resolution.z)
{
return;
}
AttributeMatrix::Pointer cellAttrMat = m->getAttributeMatrix(getCellAttributeMatrixPath().getAttributeMatrixName());
size_t dims[3] = { 0, 0, 0 };
m->getGeometryAs<ImageGeom>()->getDimensions(dims);
float sizex = (dims[0]) * m->getGeometryAs<ImageGeom>()->getXRes();
float sizey = (dims[1]) * m->getGeometryAs<ImageGeom>()->getYRes();
float sizez = (dims[2]) * m->getGeometryAs<ImageGeom>()->getZRes();
size_t m_XP = size_t(sizex / m_Resolution.x);
size_t m_YP = size_t(sizey / m_Resolution.y);
size_t m_ZP = size_t(sizez / m_Resolution.z);
if (m_XP == 0) { m_XP = 1; }
if (m_YP == 0) { m_YP = 1; }
if (m_ZP == 0) { m_ZP = 1; }
size_t totalPoints = m_XP * m_YP * m_ZP;
float x = 0.0f, y = 0.0f, z = 0.0f;
size_t col = 0, row = 0, plane = 0;
size_t index;
size_t index_old;
std::vector<size_t> newindicies(totalPoints);
for (size_t i = 0; i < m_ZP; i++)
{
QString ss = QObject::tr("Changing Resolution - %1 Percent Complete").arg(((float)i / m->getGeometryAs<ImageGeom>()->getZPoints()) * 100);
notifyStatusMessage(getMessagePrefix(), getHumanLabel(), ss);
for (size_t j = 0; j < m_YP; j++)
{
for (size_t k = 0; k < m_XP; k++)
{
x = (k * m_Resolution.x);
y = (j * m_Resolution.y);
z = (i * m_Resolution.z);
col = size_t(x / m->getGeometryAs<ImageGeom>()->getXRes());
row = size_t(y / m->getGeometryAs<ImageGeom>()->getYRes());
plane = size_t(z / m->getGeometryAs<ImageGeom>()->getZRes());
index_old = (plane * m->getGeometryAs<ImageGeom>()->getXPoints() * m->getGeometryAs<ImageGeom>()->getYPoints()) + (row * m->getGeometryAs<ImageGeom>()->getXPoints()) + col;
index = (i * m_XP * m_YP) + (j * m_XP) + k;
newindicies[index] = index_old;
}
}
}
QVector<size_t> tDims(3, 0);
tDims[0] = m_XP;
tDims[1] = m_YP;
tDims[2] = m_ZP;
AttributeMatrix::Pointer newCellAttrMat = AttributeMatrix::New(tDims, cellAttrMat->getName(), cellAttrMat->getType());
QList<QString> voxelArrayNames = cellAttrMat->getAttributeArrayNames();
for (QList<QString>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
{
IDataArray::Pointer p = cellAttrMat->getAttributeArray(*iter);
// Make a copy of the 'p' array that has the same name. When placed into
// the data container this will over write the current array with
// the same name. At least in theory.
IDataArray::Pointer data = p->createNewArray(p->getNumberOfTuples(), p->getComponentDimensions(), p->getName());
data->resize(totalPoints);
void* source = NULL;
void* destination = NULL;
size_t newIndicies_I = 0;
int nComp = data->getNumberOfComponents();
for (size_t i = 0; i < static_cast<size_t>(totalPoints); i++)
{
newIndicies_I = newindicies[i];
source = p->getVoidPointer((nComp * newIndicies_I));
destination = data->getVoidPointer((data->getNumberOfComponents() * i));
::memcpy(destination, source, p->getTypeSize() * data->getNumberOfComponents());
}
cellAttrMat->removeAttributeArray(*iter);
newCellAttrMat->addAttributeArray(*iter, data);
}
m->getGeometryAs<ImageGeom>()->setResolution(m_Resolution.x, m_Resolution.y, m_Resolution.z);
m->getGeometryAs<ImageGeom>()->setDimensions(m_XP, m_YP, m_ZP);
m->removeAttributeMatrix(getCellAttributeMatrixPath().getAttributeMatrixName());
m->addAttributeMatrix(getCellAttributeMatrixPath().getAttributeMatrixName(), newCellAttrMat);
// Feature Ids MUST already be renumbered.
if (m_RenumberFeatures == true)
{
totalPoints = m->getGeometryAs<ImageGeom>()->getNumberOfElements();
AttributeMatrix::Pointer cellFeatureAttrMat = m->getAttributeMatrix(getCellFeatureAttributeMatrixPath().getAttributeMatrixName());
size_t totalFeatures = cellFeatureAttrMat->getNumTuples();
QVector<bool> activeObjects(totalFeatures, false);
if (0 == totalFeatures)
{
notifyErrorMessage(getHumanLabel(), "The number of Features is 0 and should be greater than 0", -600);
return;
}
updateCellInstancePointers();
// Find the unique set of feature ids
for (size_t i = 0; i < totalPoints; ++i)
{
activeObjects[m_FeatureIds[i]] = true;
}
cellFeatureAttrMat->removeInactiveObjects(activeObjects, m_FeatureIdsPtr.lock());
}
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void CombineAttributeMatrices::dataCheck()
{
setErrorCondition(0);
DataArrayPath tempPath;
DataContainer::Pointer m = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getFirstAttributeMatrixPath().getDataContainerName(), false);
if (getErrorCondition() < 0 || NULL == m.get()) { return; }
if (getFirstAttributeMatrixPath().getDataContainerName().compare(getSecondAttributeMatrixPath().getDataContainerName()) != 0)
{
QString ss = QObject::tr("The selected attribute matrices must be in the same data container and currently are not");
setErrorCondition(-5557);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
if (getFirstAttributeMatrixPath().getAttributeMatrixName().compare(getSecondAttributeMatrixPath().getAttributeMatrixName()) == 0)
{
QString ss = QObject::tr("The selected attribute matrices must be different and currently are the same");
setErrorCondition(-5558);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
AttributeMatrix::Pointer firstAttrMat = m->getPrereqAttributeMatrix(this, getFirstAttributeMatrixPath().getAttributeMatrixName(), -301);
AttributeMatrix::Pointer secondAttrMat = m->getPrereqAttributeMatrix(this, getSecondAttributeMatrixPath().getAttributeMatrixName(), -301);
if (getErrorCondition() < 0) { return; }
if (firstAttrMat->getType() != secondAttrMat->getType())
{
QString ss = QObject::tr("The selected attribute matrices must be of the same type (ie Feature) and currently are not");
setErrorCondition(-5559);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
if (getErrorCondition() < 0) { return; }
//Note that the minus 1 in the totalTuples calculation is to account for the fact that the zeroth tuple in the two attribute matrices should only be counted once, not twice.
//All Feature or Ensemble AMs should start from 1 and the zeroth tuple can be combined in the two AMs
size_t totalTuples = firstAttrMat->getNumTuples() + secondAttrMat->getNumTuples() - 1;
QVector<size_t> tDims(1, totalTuples);
m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getCombinedAttributeMatrixName(), tDims, firstAttrMat->getType());
if (getErrorCondition() < 0) { return; }
AttributeMatrix::Pointer combinedAttrMat = m->getAttributeMatrix(getCombinedAttributeMatrixName());
QVector<size_t> cDims(1, 1);
m_FirstIndexPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getFirstIndexArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if (NULL != m_FirstIndexPtr.lock().get()) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{
m_FirstIndex = m_FirstIndexPtr.lock()->getPointer(0);
} /* Now assign the raw pointer to data from the DataArray<T> object */
if (getErrorCondition() < 0) { return; }
m_SecondIndexPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getSecondIndexArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if (NULL != m_SecondIndexPtr.lock().get()) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{
m_SecondIndex = m_SecondIndexPtr.lock()->getPointer(0);
} /* Now assign the raw pointer to data from the DataArray<T> object */
if (getErrorCondition() < 0) { return; }
// Create arrays on the reference grid to hold data present on the sampling grid
QList<QString> fArrayNames = firstAttrMat->getAttributeArrayNames();
for (QList<QString>::iterator iter = fArrayNames.begin(); iter != fArrayNames.end(); ++iter)
{
tempPath.update(getFirstAttributeMatrixPath().getDataContainerName(), getCombinedAttributeMatrixName(), *iter);
IDataArray::Pointer tmpDataArray = firstAttrMat->getPrereqIDataArray<IDataArray, AbstractFilter>(this, *iter, -90001);
if (getErrorCondition() >= 0)
{
QVector<size_t> cDims = tmpDataArray->getComponentDimensions();
TemplateHelpers::CreateNonPrereqArrayFromArrayType()(this, tempPath, cDims, tmpDataArray);
}
}
QList<QString> sArrayNames = secondAttrMat->getAttributeArrayNames();
for (QList<QString>::iterator iter = sArrayNames.begin(); iter != sArrayNames.end(); ++iter)
{
tempPath.update(getSecondAttributeMatrixPath().getDataContainerName(), getCombinedAttributeMatrixName(), *iter);
IDataArray::Pointer tmpDataArray = secondAttrMat->getPrereqIDataArray<IDataArray, AbstractFilter>(this, *iter, -90001);
if (getErrorCondition() >= 0)
{
if (fArrayNames.contains(*iter) == false)
{
QVector<size_t> cDims = tmpDataArray->getComponentDimensions();
TemplateHelpers::CreateNonPrereqArrayFromArrayType()(this, tempPath, cDims, tmpDataArray);
}
}
}
tempPath.update(getFirstIndexArrayPath().getDataContainerName(), getFirstIndexArrayPath().getAttributeMatrixName(), getNewIndexArrayName());
m_NewIndexPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter, int32_t>(this, tempPath, 0, cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if (NULL != m_NewIndexPtr.lock().get()) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{
m_NewIndex = m_NewIndexPtr.lock()->getPointer(0);
} /* Now assign the raw pointer to data from the DataArray<T> object */
if (getErrorCondition() < 0) { return; }
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int DataContainer::writeXdmf(QTextStream& out, QString hdfFileName)
{
if (NULL == m_Geometry.get())
{
return -1;
}
m_Geometry->writeXdmf(out, getName(), hdfFileName);
unsigned int geomType = m_Geometry->getGeometryType();
// Get all of our AttributeMatrices
AttributeMatrixMap_t amMap = getAttributeMatrices();
// Loop over each AttributeMatrix and write the meta data to the Xdmf file
QString xdmfCenter = "";
for(QMap<QString, AttributeMatrix::Pointer>::iterator iter = amMap.begin(); iter != amMap.end(); ++iter)
{
xdmfCenter = "";
AttributeMatrix::Pointer attrMat = iter.value();
uint32_t amType = attrMat->getType();
switch(geomType)
{
case DREAM3D::GeometryType::VertexGeometry:
switch(amType)
{
//FIXME: There are more AttributeMatrix Types that should be implemented
case DREAM3D::AttributeMatrixType::Vertex:
xdmfCenter = DREAM3D::XdmfCenterType::Node;
break;
default:
break;
}
case DREAM3D::GeometryType::EdgeGeometry:
switch(amType)
{
//FIXME: There are more AttributeMatrix Types that should be implemented
case DREAM3D::AttributeMatrixType::Vertex:
xdmfCenter = DREAM3D::XdmfCenterType::Node;
break;
case DREAM3D::AttributeMatrixType::Edge:
xdmfCenter = DREAM3D::XdmfCenterType::Cell;
break;
default:
break;
}
case DREAM3D::GeometryType::TriangleGeometry:
switch(amType)
{
//FIXME: There are more AttributeMatrix Types that should be implemented
case DREAM3D::AttributeMatrixType::Vertex:
xdmfCenter = DREAM3D::XdmfCenterType::Node;
break;
case DREAM3D::AttributeMatrixType::Edge:
xdmfCenter = DREAM3D::XdmfCenterType::Cell;
break;
case DREAM3D::AttributeMatrixType::Face:
xdmfCenter = DREAM3D::XdmfCenterType::Cell;
break;
case DREAM3D::AttributeMatrixType::Cell:
xdmfCenter = DREAM3D::XdmfCenterType::Cell;
break;
default:
break;
}
case DREAM3D::GeometryType::QuadGeometry:
switch(amType)
{
//FIXME: There are more AttributeMatrix Types that should be implemented
case DREAM3D::AttributeMatrixType::Vertex:
xdmfCenter = DREAM3D::XdmfCenterType::Node;
break;
case DREAM3D::AttributeMatrixType::Edge:
xdmfCenter = DREAM3D::XdmfCenterType::Cell;
break;
case DREAM3D::AttributeMatrixType::Face:
xdmfCenter = DREAM3D::XdmfCenterType::Cell;
break;
case DREAM3D::AttributeMatrixType::Cell:
xdmfCenter = DREAM3D::XdmfCenterType::Cell;
break;
default:
break;
}
case DREAM3D::GeometryType::ImageGeometry:
switch(amType)
{
//FIXME: There are more AttributeMatrix Types that should be implemented
case DREAM3D::AttributeMatrixType::Vertex:
xdmfCenter = DREAM3D::XdmfCenterType::Node;
break;
case DREAM3D::AttributeMatrixType::Edge:
xdmfCenter = DREAM3D::XdmfCenterType::Cell;
break;
case DREAM3D::AttributeMatrixType::Face:
xdmfCenter = DREAM3D::XdmfCenterType::Cell;
break;
case DREAM3D::AttributeMatrixType::Cell:
xdmfCenter = DREAM3D::XdmfCenterType::Cell;
break;
default:
break;
}
}
if(xdmfCenter.isEmpty() == false)
{
QString xdmfText = attrMat->generateXdmfText(xdmfCenter, getName(), hdfFileName, m_Geometry->getXdmfGridType());
out << xdmfText;
}
}
writeXdmfFooter(out);
return 0;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void CropImageGeometry::dataCheck()
{
if(getErrorCondition() < 0) { return; }
setErrorCondition(0);
// Validate the incoming DataContainer, Geometry, and AttributeMatrix ; bail if any do not exist since we plan on using them later on in the dataCheck
// Error messages are handled by the getPrereq functions
DataContainer::Pointer srcCellDataContainer = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getCellAttributeMatrixPath().getDataContainerName());
ImageGeom::Pointer image = getDataContainerArray()->getPrereqGeometryFromDataContainer<ImageGeom, AbstractFilter>(this, getCellAttributeMatrixPath().getDataContainerName());
AttributeMatrix::Pointer srcCellAttrMat = getDataContainerArray()->getPrereqAttributeMatrixFromPath<AbstractFilter>(this, getCellAttributeMatrixPath(), -301);
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer destCellDataContainer = srcCellDataContainer;
AttributeMatrix::Pointer destCellAttrMat;
if (m_SaveAsNewDataContainer == true)
{
float ox = 0.0f, oy = 0.0f, oz = 0.0f, rx = 0.0f, ry = 0.0f, rz = 0.0f;
size_t dx = 0, dy = 0, dz = 0;
image->getOrigin(ox, oy, oz);
image->getResolution(rx, ry, rz);
image->getDimensions(dx, dy, dz);
destCellDataContainer = getDataContainerArray()->createNonPrereqDataContainer<AbstractFilter>(this, getNewDataContainerName());
if(NULL == destCellDataContainer.get() || getErrorCondition() < 0)
{
return;
}
IGeometry::Pointer imageCopy = image->deepCopy();
destCellDataContainer->setGeometry(imageCopy);
destCellAttrMat = srcCellAttrMat->deepCopy();
destCellDataContainer->addAttributeMatrix(destCellAttrMat->getName(), destCellAttrMat);
}
else
{
destCellAttrMat = srcCellAttrMat;
}
if(NULL == destCellDataContainer.get() || NULL == destCellAttrMat.get() || getErrorCondition() < 0)
{
return;
}
if (getXMax() < getXMin())
{
QString ss = QObject::tr("X Max (%1) less than X Min (%2)").arg(getXMax()).arg(getXMin());
notifyErrorMessage(getHumanLabel(), ss, -5550);
setErrorCondition(-5550);
}
if (getYMax() < getYMin())
{
QString ss = QObject::tr("Y Max (%1) less than Y Min (%2)").arg(getYMax()).arg(getYMin());
notifyErrorMessage(getHumanLabel(), ss, -5550);
setErrorCondition(-5550);
}
if (getZMax() < getZMin())
{
QString ss = QObject::tr("Z Max (%1) less than Z Min (%2)").arg(getZMax()).arg(getZMin());
notifyErrorMessage(getHumanLabel(), ss, -5550);
setErrorCondition(-5550);
}
if (getXMin() < 0)
{
QString ss = QObject::tr("X Min (%1) less than 0").arg(getXMin());
notifyErrorMessage(getHumanLabel(), ss, -5550);
setErrorCondition(-5550);
}
if (getYMin() < 0)
{
QString ss = QObject::tr("Y Min (%1) less than 0").arg(getYMin());
notifyErrorMessage(getHumanLabel(), ss, -5550);
setErrorCondition(-5550);
}
if (getZMin() < 0)
{
QString ss = QObject::tr("Z Min (%1) less than 0").arg(getZMin());
notifyErrorMessage(getHumanLabel(), ss, -5550);
setErrorCondition(-5550);
}
if (getXMax() > (static_cast<int64_t>(destCellDataContainer->getGeometryAs<ImageGeom>()->getXPoints()) - 1))
{
QString ss = QObject::tr("The X Max (%1) is greater than the Image Geometry X extent (%2)").arg(getXMax()).arg(static_cast<int64_t>(destCellDataContainer->getGeometryAs<ImageGeom>()->getXPoints()) - 1);
notifyErrorMessage(getHumanLabel(), ss, -5550);
setErrorCondition(-5550);
}
if (getYMax() > (static_cast<int64_t>(destCellDataContainer->getGeometryAs<ImageGeom>()->getYPoints()) - 1))
{
QString ss = QObject::tr("The Y Max (%1) is greater than the Image Geometry Y extent (%2)").arg(getYMax()).arg(static_cast<int64_t>(destCellDataContainer->getGeometryAs<ImageGeom>()->getYPoints()) - 1);
notifyErrorMessage(getHumanLabel(), ss, -5550);
setErrorCondition(-5550);
}
if (getZMax() > (static_cast<int64_t>(destCellDataContainer->getGeometryAs<ImageGeom>()->getZPoints()) - 1))
{
QString ss = QObject::tr("The Z Max (%1) is greater than the Image Geometry Z extent (%2)").arg(getZMax()).arg(static_cast<int64_t>(destCellDataContainer->getGeometryAs<ImageGeom>()->getZPoints()) - 1);
notifyErrorMessage(getHumanLabel(), ss, -5550);
setErrorCondition(-5550);
}
QVector<size_t> tDims(3, 0);
if (getXMax() - getXMin() < 0) { setXMax(getXMin() + 1); }
if (getYMax() - getYMin() < 0) { setYMax(getYMin() + 1); }
if (getZMax() - getZMin() < 0) { setZMax(getZMin() + 1); }
tDims[0] = (getXMax() - getXMin()) + 1;
tDims[1] = (getYMax() - getYMin()) + 1;
tDims[2] = (getZMax() - getZMin()) + 1;
destCellDataContainer->getGeometryAs<ImageGeom>()->setDimensions(tDims[0], tDims[1], tDims[2]);
// If any of the sanity checks fail above then we should NOT attempt to go any further.
if (getErrorCondition() < 0) { return; }
size_t totalPoints = 1;
for(int i = 0; i < 3; i++) {
if(tDims[i] != 0) { totalPoints *= tDims[i]; }
}
AttributeMatrix::Pointer newCellAttrMat = AttributeMatrix::New(tDims, destCellAttrMat->getName(), destCellAttrMat->getType());
QList<QString> voxelArrayNames = destCellAttrMat->getAttributeArrayNames();
for (QList<QString>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
{
IDataArray::Pointer p = destCellAttrMat->getAttributeArray(*iter);
//
IDataArray::Pointer data = p->createNewArray(totalPoints, p->getComponentDimensions(), p->getName(), false);
destCellAttrMat->removeAttributeArray(*iter);
newCellAttrMat->addAttributeArray(*iter, data);
}
destCellDataContainer->removeAttributeMatrix(destCellAttrMat->getName());
destCellDataContainer->addAttributeMatrix(newCellAttrMat->getName(), newCellAttrMat);
if(m_RenumberFeatures == true)
{
QVector<size_t> cDims(1, 1);
m_FeatureIdsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getFeatureIdsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_FeatureIdsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{
m_FeatureIds = m_FeatureIdsPtr.lock()->getPointer(0);
} /* Now assign the raw pointer to data from the DataArray<T> object */
AttributeMatrix::Pointer cellFeatureAttrMat = srcCellDataContainer->getAttributeMatrix(getCellFeatureAttributeMatrixPath().getAttributeMatrixName());
if(NULL == cellFeatureAttrMat.get()) { return; }
QVector<bool> activeObjects(cellFeatureAttrMat->getNumTuples(), true);
cellFeatureAttrMat->removeInactiveObjects(activeObjects, m_FeatureIdsPtr.lock());
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void RegularizeZSpacing::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) {
return;
}
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getCellAttributeMatrixPath().getDataContainerName());
size_t dims[3];
m->getGeometryAs<ImageGeom>()->getDimensions(dims);
std::ifstream inFile;
inFile.open(m_InputFile.toLatin1().data());
float zval = 0.0f;
std::vector<float> zboundvalues(dims[2] + 1, 0.0);
for (size_t iter = 0; iter < dims[2] + 1; iter++)
{
inFile >> zval;
zboundvalues[iter] = zval;
}
inFile.close();
float xRes = m->getGeometryAs<ImageGeom>()->getXRes();
float yRes = m->getGeometryAs<ImageGeom>()->getYRes();
float sizez = zboundvalues[dims[2]];
size_t m_XP = dims[0];
size_t m_YP = dims[1];
size_t m_ZP = static_cast<size_t>(sizez / m_NewZRes);
if (m_ZP == 0) {
m_ZP = 1;
}
size_t totalPoints = m_XP * m_YP * m_ZP;
size_t index = 0, oldindex = 0;
size_t plane = 0;
std::vector<size_t> newindicies(totalPoints, 0);
for (size_t i = 0; i < m_ZP; i++)
{
plane = 0;
for (size_t iter = 1; iter < dims[2]; iter++)
{
if ((i * m_NewZRes) > zboundvalues[iter]) {
plane = iter;
}
}
for (size_t j = 0; j < m_YP; j++)
{
for (size_t k = 0; k < m_XP; k++)
{
oldindex = (plane * dims[0] * dims[1]) + (j * dims[0]) + k;
index = (i * dims[0] * dims[1]) + (j * dims[0]) + k;
newindicies[index] = oldindex;
}
}
}
AttributeMatrix::Pointer cellAttrMat = m->getAttributeMatrix(getCellAttributeMatrixPath().getAttributeMatrixName());
QVector<size_t> tDims(3, 0);
tDims[0] = m_XP;
tDims[1] = m_YP;
tDims[2] = m_ZP;
AttributeMatrix::Pointer newCellAttrMat = AttributeMatrix::New(tDims, cellAttrMat->getName(), cellAttrMat->getType());
QList<QString> voxelArrayNames = cellAttrMat->getAttributeArrayNames();
for (QList<QString>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
{
IDataArray::Pointer p = cellAttrMat->getAttributeArray(*iter);
// Make a copy of the 'p' array that has the same name. When placed into
// the data container this will over write the current array with
// the same name. At least in theory
IDataArray::Pointer data = p->createNewArray(p->getNumberOfTuples(), p->getComponentDimensions(), p->getName());
data->resize(totalPoints);
void* source = NULL;
void* destination = NULL;
size_t newIndicies_I = 0;
int nComp = data->getNumberOfComponents();
for (size_t i = 0; i < static_cast<size_t>(totalPoints); i++)
{
newIndicies_I = newindicies[i];
source = p->getVoidPointer((nComp * newIndicies_I));
destination = data->getVoidPointer((data->getNumberOfComponents() * i));
::memcpy(destination, source, p->getTypeSize() * data->getNumberOfComponents());
}
cellAttrMat->removeAttributeArray(*iter);
newCellAttrMat->addAttributeArray(*iter, data);
}
m->getGeometryAs<ImageGeom>()->setResolution(xRes, yRes, m_NewZRes);
m->getGeometryAs<ImageGeom>()->setDimensions(m_XP, m_YP, m_ZP);
m->removeAttributeMatrix(getCellAttributeMatrixPath().getAttributeMatrixName());
m->addAttributeMatrix(getCellAttributeMatrixPath().getAttributeMatrixName(), newCellAttrMat);
notifyStatusMessage(getHumanLabel(), "Complete");
}
