// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void EstablishShapeTypes::dataCheck()
{
setErrorCondition(0);
DataArrayPath tempPath;
DataContainerArray::Pointer dca = getDataContainerArray();
QVector<size_t> cDims(1, 1);
m_PhaseTypesPtr = dca->getPrereqArrayFromPath<DataArray<uint32_t>, AbstractFilter>(this, getInputPhaseTypesArrayPath(), cDims);
if( NULL != m_PhaseTypesPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_PhaseTypes = m_PhaseTypesPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
// Get the DataContainer first - same as phase types
DataContainer::Pointer m = dca->getPrereqDataContainer<AbstractFilter>(this, getInputPhaseTypesArrayPath().getDataContainerName());
if(getErrorCondition() < 0) { return; }
// Now get the AttributeMatrix that the user wants to use to store the ShapeTypes array - same as phase types
AttributeMatrix::Pointer cellEnsembleAttrMat = m->getPrereqAttributeMatrix<AbstractFilter>(this, getInputPhaseTypesArrayPath().getAttributeMatrixName(), -990);
if(getErrorCondition() < 0 || NULL == cellEnsembleAttrMat.get()) { return; }
// Now create the output Shape Types Array
tempPath.update(getInputPhaseTypesArrayPath().getDataContainerName(), getInputPhaseTypesArrayPath().getAttributeMatrixName(), getShapeTypesArrayName() );
m_ShapeTypesPtr = getDataContainerArray()->createNonPrereqArrayFromPath<UInt32ArrayType, AbstractFilter>(this, tempPath, true, cDims); /* Assigns the shared_ptr<>(this, tempPath, true, dims); Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_ShapeTypesPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_ShapeTypes = m_ShapeTypesPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void RegularGridSampleSurfaceMesh::dataCheck()
{
setErrorCondition(0);
DataArrayPath tempPath;
DataContainer::Pointer m = getDataContainerArray()->createNonPrereqDataContainer<AbstractFilter>(this, getDataContainerName());
if (getErrorCondition() < 0) { return; }
ImageGeom::Pointer image = ImageGeom::CreateGeometry(DREAM3D::Geometry::ImageGeometry);
m->setGeometry(image);
// Set the Dimensions, Resolution and Origin of the output data container
m->getGeometryAs<ImageGeom>()->setDimensions(m_XPoints, m_YPoints, m_ZPoints);
m->getGeometryAs<ImageGeom>()->setResolution(m_Resolution.x, m_Resolution.y, m_Resolution.z);
m->getGeometryAs<ImageGeom>()->setOrigin(m_Origin.x, m_Origin.y, m_Origin.z);
QVector<size_t> tDims(3, 0);
tDims[0] = m_XPoints;
tDims[1] = m_YPoints;
tDims[2] = m_ZPoints;
AttributeMatrix::Pointer cellAttrMat = m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getCellAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::Cell);
if (getErrorCondition() < 0 || NULL == cellAttrMat.get()) { return; }
QVector<size_t> cDims(1, 1);
tempPath.update(getDataContainerName(), getCellAttributeMatrixName(), getFeatureIdsArrayName() );
m_FeatureIdsPtr = 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_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 */
}
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 InitializeSyntheticVolume::dataCheck()
{
setErrorCondition(0);
// Create the output Data Container
DataContainer::Pointer m = getDataContainerArray()->createNonPrereqDataContainer<AbstractFilter>(this, getDataContainerName());
if(getErrorCondition() < 0) { return; }
ImageGeom::Pointer image = ImageGeom::CreateGeometry(DREAM3D::Geometry::ImageGeometry);
m->setGeometry(image);
// Sanity Check the Dimensions and Resolution
INIT_SYNTH_VOLUME_CHECK(Dimensions.x, -5000);
INIT_SYNTH_VOLUME_CHECK(Dimensions.y, -5001);
INIT_SYNTH_VOLUME_CHECK(Dimensions.z, -5002);
INIT_SYNTH_VOLUME_CHECK(Resolution.x, -5003);
INIT_SYNTH_VOLUME_CHECK(Resolution.y, -5004);
INIT_SYNTH_VOLUME_CHECK(Resolution.z, -5005);
// Set the Dimensions, Resolution and Origin of the output data container
m->getGeometryAs<ImageGeom>()->setDimensions(m_Dimensions.x, m_Dimensions.y, m_Dimensions.z);
m->getGeometryAs<ImageGeom>()->setResolution(m_Resolution.x, m_Resolution.y, m_Resolution.z);
m->getGeometryAs<ImageGeom>()->setOrigin(m_Origin.x, m_Origin.y, m_Origin.z);
// Create our output Cell and Ensemble Attribute Matrix objects
QVector<size_t> tDims(3, 0);
tDims[0] = m_Dimensions.x;
tDims[1] = m_Dimensions.y;
tDims[2] = m_Dimensions.z;
AttributeMatrix::Pointer cellAttrMat = m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getCellAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::Cell);
if(getErrorCondition() < 0 && cellAttrMat.get() == NULL) { return; }
QVector<size_t> cDims(1, 1); // This states that we are looking for an array with a single component
UInt32ArrayType::Pointer phaseType = getDataContainerArray()->getPrereqArrayFromPath<UInt32ArrayType, AbstractFilter>(this, getInputPhaseTypesArrayPath(), cDims);
if(getErrorCondition() < 0 && phaseType.get() == NULL) { return; }
QVector<size_t> statsDims(1, 1);
StatsDataArray::Pointer statsPtr = getDataContainerArray()->getPrereqArrayFromPath<StatsDataArray, AbstractFilter>(this, getInputStatsArrayPath(), statsDims);
if(getErrorCondition() < 0 && statsPtr.get() == NULL) { return; }
if(m_EstimateNumberOfFeatures)
{
m_EstimatedPrimaryFeatures = estimateNumFeatures(m_Dimensions, m_Resolution);
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SineParamsSegmentFeatures::dataCheck()
{
DataArrayPath tempPath;
setErrorCondition(0);
//Set the DataContainerName for the Parent Class (SegmentFeatures) to Use
setDataContainerName(m_SineParamsArrayPath.getDataContainerName());
SegmentFeatures::dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getDataContainerName(), false);
if(getErrorCondition() < 0 || NULL == m) { return; }
QVector<size_t> tDims(1, 0);
AttributeMatrix::Pointer cellFeatureAttrMat = m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getCellFeatureAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::CellFeature);
if(getErrorCondition() < 0 || NULL == cellFeatureAttrMat.get()) { return; }
ImageGeom::Pointer image = m->getPrereqGeometry<ImageGeom, AbstractFilter>(this);
if(getErrorCondition() < 0 || NULL == image.get()) { return; }
QVector<size_t> dims(1, 3);
m_SineParamsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<float>, AbstractFilter>(this, getSineParamsArrayPath(), dims);
if( NULL != m_SineParamsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SineParams = m_SineParamsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
dims[0] = 1;
tempPath.update(getDataContainerName(), m_SineParamsArrayPath.getAttributeMatrixName(), getFeatureIdsArrayName() );
m_FeatureIdsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter, int32_t>(this, tempPath, 0, dims); /* 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 */
if(m_UseGoodVoxels == true)
{
m_GoodVoxelsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<bool>, AbstractFilter>(this, getGoodVoxelsArrayPath(), dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_GoodVoxelsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_GoodVoxels = m_GoodVoxelsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
tempPath.update(getDataContainerName(), getCellFeatureAttributeMatrixName(), getActiveArrayName() );
m_ActivePtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<bool>, AbstractFilter, bool>(this, tempPath, true, dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_ActivePtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_Active = m_ActivePtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void InsertAtoms::dataCheck()
{
setErrorCondition(0);
DataArrayPath tempPath;
TriangleGeom::Pointer triangles = getDataContainerArray()->getPrereqGeometryFromDataContainer<TriangleGeom, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath().getDataContainerName());
QVector<IDataArray::Pointer> dataArrays;
if(getErrorCondition() >= 0) { dataArrays.push_back(triangles->getTriangles()); }
DataContainer::Pointer v = getDataContainerArray()->createNonPrereqDataContainer<AbstractFilter>(this, getVertexDataContainerName());
if(getErrorCondition() < 0) { return; }
VertexGeom::Pointer vertices = VertexGeom::CreateGeometry(0, DREAM3D::Geometry::VertexGeometry);
v->setGeometry(vertices);
QVector<size_t> tDims(1, 0);
AttributeMatrix::Pointer vertexAttrMat = v->createNonPrereqAttributeMatrix<AbstractFilter>(this, getVertexAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::Vertex);
if(getErrorCondition() < 0 || NULL == vertexAttrMat.get()) { return; }
QVector<size_t> cDims(1, 2);
m_SurfaceMeshFaceLabelsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFaceLabelsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFaceLabels = m_SurfaceMeshFaceLabelsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if(getErrorCondition() >= 0) { dataArrays.push_back(m_SurfaceMeshFaceLabelsPtr.lock()); }
cDims[0] = 4;
m_AvgQuatsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<float>, AbstractFilter>(this, getAvgQuatsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_AvgQuatsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_AvgQuats = m_AvgQuatsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
cDims[0] = 1;
tempPath.update(getVertexDataContainerName(), getVertexAttributeMatrixName(), getAtomFeatureLabelsArrayName() );
m_AtomFeatureLabelsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter, int32_t>(this, tempPath, -301, cDims); /* Assigns the shared_ptr<>(this, tempPath, -301, dims); Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_AtomFeatureLabelsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_AtomFeatureLabels = m_AtomFeatureLabelsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
getDataContainerArray()->validateNumberOfTuples<AbstractFilter>(this, dataArrays);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SharedFeatureFaceFilter::dataCheck()
{
setErrorCondition(0);
DataArrayPath tempPath;
getDataContainerArray()->getPrereqGeometryFromDataContainer<TriangleGeom, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath().getDataContainerName());
DataContainer::Pointer sm = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName(), false);
if(getErrorCondition() < 0) { return; }
QVector<size_t> tDims(1, 0);
AttributeMatrix::Pointer facefeatureAttrMat = sm->createNonPrereqAttributeMatrix<AbstractFilter>(this, getFaceFeatureAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::FaceFeature);
if(getErrorCondition() < 0 || NULL == facefeatureAttrMat.get()) { return; }
QVector<size_t> cDims(1, 2);
m_SurfaceMeshFaceLabelsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFaceLabelsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFaceLabels = m_SurfaceMeshFaceLabelsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
cDims[0] = 1;
tempPath.update(m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName(), m_SurfaceMeshFaceLabelsArrayPath.getAttributeMatrixName(), getSurfaceMeshFeatureFaceIdsArrayName() );
m_SurfaceMeshFeatureFaceIdsPtr = 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_SurfaceMeshFeatureFaceIdsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFeatureFaceIds = m_SurfaceMeshFeatureFaceIdsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
tempPath.update(m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName(), getFaceFeatureAttributeMatrixName(), getSurfaceMeshFeatureFaceNumTrianglesArrayName() );
m_SurfaceMeshFeatureFaceNumTrianglesPtr = 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_SurfaceMeshFeatureFaceNumTrianglesPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFeatureFaceNumTriangles = m_SurfaceMeshFeatureFaceNumTrianglesPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
cDims[0] = 2;
tempPath.update(m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName(), getFaceFeatureAttributeMatrixName(), getSurfaceMeshFeatureFaceLabelsArrayName() );
m_SurfaceMeshFeatureFaceLabelsPtr = 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_SurfaceMeshFeatureFaceLabelsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFeatureFaceLabels = m_SurfaceMeshFeatureFaceLabelsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void YSChoiAbaqusReader::dataCheck()
{
DataArrayPath tempPath;
setErrorCondition(0);
DataContainer::Pointer m = getDataContainerArray()->createNonPrereqDataContainer<AbstractFilter>(this, getDataContainerName());
if(getErrorCondition() < 0) { return; }
ImageGeom::Pointer image = ImageGeom::CreateGeometry(DREAM3D::Geometry::ImageGeometry);
m->setGeometry(image);
QVector<size_t> tDims(3, 0);
AttributeMatrix::Pointer cellAttrMat = m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getCellAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::Cell);
if(getErrorCondition() < 0 || NULL == cellAttrMat.get()) { return; }
tDims.resize(1);
tDims[0] = 0;
AttributeMatrix::Pointer cellFeatureAttrMat = m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getCellFeatureAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::CellFeature);
if(getErrorCondition() < 0 || NULL == cellFeatureAttrMat.get()) { return; }
AttributeMatrix::Pointer cellEnsembleAttrMat = m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getCellEnsembleAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::CellEnsemble);
if(getErrorCondition() < 0 || NULL == cellEnsembleAttrMat.get()) { return; }
QFileInfo fi(getInputFile());
if (getInputFile().isEmpty() == true)
{
QString ss = QObject::tr("%1 needs the Input File Set and it was not.").arg(ClassName());
setErrorCondition(-387);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
else if (fi.exists() == false)
{
QString ss = QObject::tr("The input file does not exist");
setErrorCondition(-388);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
else
{
bool ok = false;
//const unsigned int size(1024);
// Read header from data file to figure out how many points there are
QFile in(getInputFile());
if (!in.open(QIODevice::ReadOnly | QIODevice::Text))
{
QString msg = QObject::tr("Abaqus file could not be opened: %1").arg(getInputFile());
setErrorCondition(-100);
notifyErrorMessage(getHumanLabel(), "", getErrorCondition());
return;
}
QString word;
bool headerdone = false;
int xpoints, ypoints, zpoints;
float resx, resy, resz;
while (headerdone == false)
{
QByteArray buf = in.readLine();
if (buf.startsWith(DIMS))
{
QList<QByteArray> tokens = buf.split(' ');
xpoints = tokens[1].toInt(&ok, 10);
ypoints = tokens[2].toInt(&ok, 10);
zpoints = tokens[3].toInt(&ok, 10);
size_t dims[3] = { static_cast<size_t>(xpoints), static_cast<size_t>(ypoints), static_cast<size_t>(zpoints) };
m->getGeometryAs<ImageGeom>()->setDimensions(dims);
m->getGeometryAs<ImageGeom>()->setOrigin(0, 0, 0);
}
if (RES == word)
{
QList<QByteArray> tokens = buf.split(' ');
resx = tokens[1].toInt(&ok, 10);
resy = tokens[2].toInt(&ok, 10);
resz = tokens[3].toInt(&ok, 10);
float res[3] = {resx, resy, resz};
m->getGeometryAs<ImageGeom>()->setResolution(res);
}
}
}
QVector<size_t> dims(1, 3);
tempPath.update(getDataContainerName(), getCellAttributeMatrixName(), getCellEulerAnglesArrayName() );
m_CellEulerAnglesPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<float>, AbstractFilter, float>(this, tempPath, 0, dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_CellEulerAnglesPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_CellEulerAngles = m_CellEulerAnglesPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
dims[0] = 4;
tempPath.update(getDataContainerName(), getCellAttributeMatrixName(), getQuatsArrayName() );
m_QuatsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<float>, AbstractFilter, float>(this, tempPath, 0, dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_QuatsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_Quats = m_QuatsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
tempPath.update(getDataContainerName(), getCellFeatureAttributeMatrixName(), getAvgQuatsArrayName() );
m_AvgQuatsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<float>, AbstractFilter, float>(this, tempPath, 0, dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_AvgQuatsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_AvgQuats = m_AvgQuatsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
dims[0] = 1;
tempPath.update(getDataContainerName(), getCellAttributeMatrixName(), getCellPhasesArrayName() );
m_CellPhasesPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter, int32_t>(this, tempPath, 1, dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_CellPhasesPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_CellPhases = m_CellPhasesPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
tempPath.update(getDataContainerName(), getCellFeatureAttributeMatrixName(), getSurfaceFeaturesArrayName() );
m_SurfaceFeaturesPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<bool>, AbstractFilter, bool>(this, tempPath, false, dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceFeaturesPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceFeatures = m_SurfaceFeaturesPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
tempPath.update(getDataContainerName(), getCellAttributeMatrixName(), getFeatureIdsArrayName() );
m_FeatureIdsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter, int32_t>(this, tempPath, 0, dims); /* 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 */
//typedef DataArray<unsigned int> XTalStructArrayType;
tempPath.update(getDataContainerName(), getCellEnsembleAttributeMatrixName(), getCrystalStructuresArrayName() );
m_CrystalStructuresPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<uint32_t>, AbstractFilter, uint32_t>(this, tempPath, Ebsd::CrystalStructure::Cubic_High, dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_CrystalStructuresPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_CrystalStructures = m_CrystalStructuresPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void MultiEmmpmFilter::dataCheck()
{
setErrorCondition(0);
if (DataArrayPath::ValidateVector(getInputDataArrayVector()) == false)
{
setErrorCondition(-62000);
QString ss = QObject::tr("All Attribute Arrays must belong to the same Data Container and Attribute Matrix");
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
QVector<size_t> cDims(1, 1); // We need a single component, gray scale image
#if 0
m_InputImagePtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<uint8_t>, AbstractFilter>(this, getInputDataArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if (NULL != m_InputImagePtr.lock().get()) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{
m_InputImage = m_InputImagePtr.lock()->getPointer(0);
} /* Now assign the raw pointer to data from the DataArray<T> object */
if (getErrorCondition() < 0) { return; }
ImageGeom::Pointer image = getDataContainerArray()->getDataContainer(getInputDataArrayPath().getDataContainerName())->getPrereqGeometry<ImageGeom, AbstractFilter>(this);
if (getErrorCondition() < 0 || NULL == image.get()) { return; }
m_OutputImagePtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<uint8_t>, AbstractFilter, uint8_t>(this, getOutputDataArrayPath(), 0, cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if (NULL != m_OutputImagePtr.lock().get()) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{
m_OutputImage = m_OutputImagePtr.lock()->getPointer(0);
} /* Now assign the raw pointer to data from the DataArray<T> object */
#endif
if (getOutputArrayPrefix().isEmpty())
{
setErrorCondition(-62002);
QString message = QObject::tr("Using a prefix (even a single alphanumeric value) is required so that the output Xdmf files can be written correctly");
notifyErrorMessage(getHumanLabel(), message, getErrorCondition());
}
if (getInputDataArrayVector().isEmpty())
{
setErrorCondition(-62003);
QString message = QObject::tr("At least one Attribute Array must be selected");
notifyErrorMessage(getHumanLabel(), message, getErrorCondition());
return;
}
DataArrayPath inputAMPath = DataArrayPath::GetAttributeMatrixPath(getInputDataArrayVector());
AttributeMatrix::Pointer inAM = getDataContainerArray()->getPrereqAttributeMatrixFromPath<AbstractFilter>(this, inputAMPath, -301);
if(getErrorCondition() < 0 || NULL == inAM.get()) { return; }
// Now create our output attributeMatrix which will contain all of our segmented images
QVector<size_t> tDims = inAM->getTupleDimensions();
AttributeMatrix::Pointer outAM = getDataContainerArray()->getDataContainer(inputAMPath.getDataContainerName())->createNonPrereqAttributeMatrix<AbstractFilter>(this, getOutputAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::Cell);
if(getErrorCondition() < 0 || NULL == outAM.get()) { return; }
// Get the list of checked array names from the input data arrays list
QList<QString> arrayNames = DataArrayPath::GetDataArrayNames(getInputDataArrayVector());
for (int32_t i = 0; i < arrayNames.size(); i++ )
{
QString daName = arrayNames.at(i);
QString newName = getOutputArrayPrefix() + arrayNames.at(i);
inputAMPath.setDataArrayName(daName);
getDataContainerArray()->getPrereqArrayFromPath<DataArray<uint8_t>, AbstractFilter>(this, inputAMPath, cDims);
if (getErrorCondition() < 0) { return; }
outAM->createAndAddAttributeArray<UInt8ArrayType, AbstractFilter, uint8_t>(this, newName, 0, cDims);
}
// The EM/MPM Library has a hard coded MAX Classes of 16
if (getNumClasses() > 15)
{
setErrorCondition(-62000);
QString ss = QObject::tr("The maximum number of classes is 15");
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
// It does not make any sense if we want anything less than 2 classes
if (getNumClasses() < 2)
{
setErrorCondition(-62001);
QString ss = QObject::tr("The minimum number of classes is 2");
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void EstablishMatrixPhase::dataCheck()
{
setErrorCondition(0);
DataArrayPath tempPath;
getDataContainerArray()->getPrereqGeometryFromDataContainer<ImageGeom, AbstractFilter>(this, getOutputCellAttributeMatrixPath().getDataContainerName());
QVector<size_t> cDims(1, 1);
m_PhaseTypesPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<uint32_t>, AbstractFilter>(this, getInputPhaseTypesArrayPath(), cDims);
if( NULL != m_PhaseTypesPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_PhaseTypes = m_PhaseTypesPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
m_StatsDataArray = getDataContainerArray()->getPrereqArrayFromPath<StatsDataArray, AbstractFilter>(this, getInputStatsArrayPath(), cDims);
if(m_StatsDataArray.lock() == NULL)
{
QString ss = QObject::tr("Statistics array is not initialized correctly. The path is %1").arg(getInputStatsArrayPath().serialize());
setErrorCondition(-308);
notifyErrorMessage(getHumanLabel(), ss, -308);
}
cDims[0] = 1;
// Cell Data
tempPath.update(getOutputCellAttributeMatrixPath().getDataContainerName(), getOutputCellAttributeMatrixPath().getAttributeMatrixName(), getFeatureIdsArrayName() );
m_FeatureIdsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter, int32_t>(this, tempPath, -1, cDims); /* Assigns the shared_ptr<>(this, tempPath, -1, dims); 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 */
tempPath.update(getOutputCellAttributeMatrixPath().getDataContainerName(), getOutputCellAttributeMatrixPath().getAttributeMatrixName(), getCellPhasesArrayName() );
m_CellPhasesPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter, int32_t>(this, tempPath, 0, cDims); /* Assigns the shared_ptr<>(this, tempPath, 0, dims); Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_CellPhasesPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_CellPhases = m_CellPhasesPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if (m_UseMask == true)
{
m_MaskPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<bool>, AbstractFilter>(this, getMaskArrayPath(), cDims);
if (NULL != m_MaskPtr.lock().get()) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_Mask = m_MaskPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getOutputCellAttributeMatrixPath().getDataContainerName());
QVector<size_t> tDims(1, 0);
AttributeMatrix::Pointer cellFeatureAttrMat = m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getOutputCellFeatureAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::CellFeature);
if(getErrorCondition() < 0 || NULL == cellFeatureAttrMat.get()) { return; }
tDims[0] = m_PhaseTypesPtr.lock()->getNumberOfTuples();
AttributeMatrix::Pointer cellEnsembleAttrMat = m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getOutputCellEnsembleAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::CellEnsemble);
if(getErrorCondition() < 0 || NULL == cellEnsembleAttrMat.get()) { return; }
// Feature Data
tempPath.update(getOutputCellAttributeMatrixPath().getDataContainerName(), getOutputCellFeatureAttributeMatrixName(), getFeaturePhasesArrayName() );
m_FeaturePhasesPtr = 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_FeaturePhasesPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_FeaturePhases = m_FeaturePhasesPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
// Ensemble Data
tempPath.update(getOutputCellAttributeMatrixPath().getDataContainerName(), getOutputCellEnsembleAttributeMatrixName(), getNumFeaturesArrayName() );
m_NumFeaturesPtr = 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_NumFeaturesPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_NumFeatures = m_NumFeaturesPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void CropImageGeometry::execute()
{
setErrorCondition(0);
/* Normally, filters call dataCheck during the execute to reuse code. Unfortunately, this cannot happen for this filter, because calling dataCheck
would destroy an Attribute Matrix that we need during the execute. Do not uncomment the code, and be careful when reusing code from either of
these functions. Make sure you understand how this works before you reuse any code. */
//dataCheck();
//if(getErrorCondition() < 0) { return; }
DataContainer::Pointer srcCellDataContainer = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getCellAttributeMatrixPath().getDataContainerName());
AttributeMatrix::Pointer cellAttrMat = srcCellDataContainer->getAttributeMatrix(getCellAttributeMatrixPath().getAttributeMatrixName());
DataContainer::Pointer destCellDataContainer = srcCellDataContainer;
if (m_SaveAsNewDataContainer == true)
{
float ox = 0.0f, oy = 0.0f, oz = 0.0f, rx = 0.0f, ry = 0.0f, rz = 0.0f;
srcCellDataContainer->getGeometryAs<ImageGeom>()->getOrigin(ox, oy, oz);
srcCellDataContainer->getGeometryAs<ImageGeom>()->getResolution(rx, ry, rz);
destCellDataContainer = getDataContainerArray()->createNonPrereqDataContainer<AbstractFilter>(this, getNewDataContainerName());
ImageGeom::Pointer image = ImageGeom::CreateGeometry(DREAM3D::Geometry::ImageGeometry);
destCellDataContainer->setGeometry(image);
destCellDataContainer->getGeometryAs<ImageGeom>()->setOrigin(ox, oy, oz);
destCellDataContainer->getGeometryAs<ImageGeom>()->setResolution(rx, ry, rz);
AttributeMatrix::Pointer cellAttrMatCopy = cellAttrMat->deepCopy();
destCellDataContainer->addAttributeMatrix(cellAttrMatCopy->getName(), cellAttrMatCopy);
cellAttrMat = destCellDataContainer->getAttributeMatrix(getCellAttributeMatrixPath().getAttributeMatrixName());
}
if(NULL == destCellDataContainer.get() || NULL == cellAttrMat.get() || getErrorCondition() < 0)
{
return;
}
// No matter where the AM is (same DC or new DC), we have the correct DC and AM pointers...now it's time to crop
int64_t totalPoints = cellAttrMat->getNumTuples();
size_t udims[3] =
{ 0, 0, 0 };
srcCellDataContainer->getGeometryAs<ImageGeom>()->getDimensions(udims);
#if (CMP_SIZEOF_SIZE_T == 4)
typedef int32_t DimType;
#else
typedef int64_t DimType;
#endif
DimType dims[3] =
{ static_cast<DimType>(udims[0]), static_cast<DimType>(udims[1]), static_cast<DimType>(udims[2]), };
// Check to see if the dims have actually changed.
if(dims[0] == (m_XMax - m_XMin) && dims[1] == (m_YMax - m_YMin) && dims[2] == (m_ZMax - m_ZMin))
{
return;
}
// Get current origin
float oldOrigin[3] = {0.0f, 0.0f, 0.0f};
destCellDataContainer->getGeometryAs<ImageGeom>()->getOrigin(oldOrigin);
// Check to make sure the new dimensions are not "out of bounds" and warn the user if they are
if (dims[0] <= m_XMax)
{
QString ss = QObject::tr("The Max X value (%1) is greater than the Image Geometry X entent (%2)."
" This may lead to junk data being filled into the extra space.").arg(m_XMax).arg(dims[0]);
setErrorCondition(-950);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
if (dims[1] <= m_YMax)
{
QString ss = QObject::tr("The Max Y value (%1) is greater than the Image Geometry Y entent (%2)."
" This may lead to junk data being filled into the extra space.").arg(m_YMax).arg(dims[1]);
setErrorCondition(-951);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
if (dims[2] <= m_ZMax)
{
QString ss = QObject::tr("The Max Z value (%1) is greater than the Image Geometry Z entent (%2)."
" This may lead to junk data being filled into the extra space.").arg(m_ZMax).arg(dims[2]);
setErrorCondition(-952);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
int64_t XP = ( (m_XMax - m_XMin) + 1 );
int64_t YP = ( (m_YMax - m_YMin) + 1 );
int64_t ZP = ( (m_ZMax - m_ZMin) + 1 );
int64_t col = 0, row = 0, plane = 0;
int64_t colold = 0, rowold = 0, planeold = 0;
int64_t index = 0;
int64_t index_old = 0;
QList<QString> voxelArrayNames = cellAttrMat->getAttributeArrayNames();
for (int64_t i = 0; i < ZP; i++)
{
QString ss = QObject::tr("Cropping Volume - Slice %1 of %2 Complete").arg(i).arg(ZP);
notifyStatusMessage(getMessagePrefix(), getHumanLabel(), ss);
planeold = (i + m_ZMin) * (srcCellDataContainer->getGeometryAs<ImageGeom>()->getXPoints() * srcCellDataContainer->getGeometryAs<ImageGeom>()->getYPoints());
plane = (i * XP * YP);
for (int64_t j = 0; j < YP; j++)
{
rowold = (j + m_YMin) * srcCellDataContainer->getGeometryAs<ImageGeom>()->getXPoints();
row = (j * XP);
for (int64_t k = 0; k < XP; k++)
{
colold = (k + m_XMin);
col = k;
index_old = planeold + rowold + colold;
index = plane + row + col;
for (QList<QString>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
{
IDataArray::Pointer p = cellAttrMat->getAttributeArray(*iter);
p->copyTuple(index_old, index);
}
}
}
}
destCellDataContainer->getGeometryAs<ImageGeom>()->setDimensions(static_cast<size_t>(XP), static_cast<size_t>(YP), static_cast<size_t>(ZP));
totalPoints = destCellDataContainer->getGeometryAs<ImageGeom>()->getNumberOfElements();
QVector<size_t> tDims(3, 0);
tDims[0] = XP;
tDims[1] = YP;
tDims[2] = ZP;
cellAttrMat->setTupleDimensions(tDims); // THIS WILL CAUSE A RESIZE of all the underlying data arrays.
if (m_RenumberFeatures == true)
{
totalPoints = destCellDataContainer->getGeometryAs<ImageGeom>()->getNumberOfElements();
// This just sanity checks to make sure there were existing features before the cropping
AttributeMatrix::Pointer cellFeatureAttrMat = srcCellDataContainer->getAttributeMatrix(getCellFeatureAttributeMatrixPath().getAttributeMatrixName());
size_t totalFeatures = cellFeatureAttrMat->getNumTuples();
QVector<bool> activeObjects(totalFeatures, false);
if (0 == totalFeatures)
{
setErrorCondition(-600);
notifyErrorMessage(getHumanLabel(), "The number of Features is 0 and should be greater than 0", getErrorCondition());
return;
}
//QVector<size_t> cDims(1, 1);
DataArrayPath dap = getFeatureIdsArrayPath();
if(getSaveAsNewDataContainer())
{
dap.setDataContainerName(getNewDataContainerName());
}
m_FeatureIdsPtr = cellAttrMat->getAttributeArrayAs<Int32ArrayType>(dap.getDataArrayName()); /* 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 */
else
{
setErrorCondition(-601);
QString ss = QObject::tr("The FeatureIds array with name '%1' was not found in the destination DataContainer. The expected path was '%2'")
.arg(dap.getDataArrayName()).arg(dap.serialize("/"));
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
// Find the unique set of feature ids
for (int64_t i = 0; i < totalPoints; ++i)
{
int32_t currentFeatureId = m_FeatureIds[i];
if (currentFeatureId < totalFeatures)
{
activeObjects[currentFeatureId] = true;
}
else
{
setErrorCondition(-601);
QString ss = QObject::tr("The total number of Features from %1 is %2, but a value of %3 was found in DataArray %4.").arg(cellFeatureAttrMat->getName()).arg(totalFeatures).arg(currentFeatureId).arg(getFeatureIdsArrayPath().serialize("/"));
qDebug() << ss;
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
}
cellFeatureAttrMat->removeInactiveObjects(activeObjects, m_FeatureIdsPtr.lock());
}
if(m_UpdateOrigin == true)
{
float resolution[3] = {0.0f, 0.0f, 0.0f};
destCellDataContainer->getGeometryAs<ImageGeom>()->getResolution(resolution);
float origin[3] = {0.0f, 0.0f, 0.0f};
destCellDataContainer->getGeometryAs<ImageGeom>()->getOrigin(origin);
origin[0] = m_XMin * resolution[0] + oldOrigin[0];
origin[1] = m_YMin * resolution[1] + oldOrigin[1];
origin[2] = m_ZMin * resolution[2] + oldOrigin[2];
destCellDataContainer->getGeometryAs<ImageGeom>()->setOrigin(origin);
}
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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());
}
}