// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void InitializeData::readFilterParameters(AbstractFilterParametersReader* reader, int index)
{
reader->openFilterGroup(this, index);
setCellAttributeMatrixPath( reader->readDataArrayPath("CellAttributeMatrixPath", getCellAttributeMatrixPath() ) );
setXMin( reader->readValue("XMin", getXMin()) );
setYMin( reader->readValue("YMin", getYMin()) );
setZMin( reader->readValue("ZMin", getZMin()) );
setXMax( reader->readValue("XMax", getXMax()) );
setYMax( reader->readValue("YMax", getYMax()) );
setZMax( reader->readValue("ZMax", getZMax()) );
reader->closeFilterGroup();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void InitializeData::readFilterParameters(AbstractFilterParametersReader* reader, int index)
{
reader->openFilterGroup(this, index);
setCellAttributeMatrixPaths( reader->readDataArrayPathVector("CellAttributeMatrixPaths", getCellAttributeMatrixPaths() ) );
setXMin( reader->readValue("XMin", getXMin()) );
setYMin( reader->readValue("YMin", getYMin()) );
setZMin( reader->readValue("ZMin", getZMin()) );
setXMax( reader->readValue("XMax", getXMax()) );
setYMax( reader->readValue("YMax", getYMax()) );
setZMax( reader->readValue("ZMax", getZMax()) );
setInitType(reader->readValue("InitType", getInitType()));
setInitValue(reader->readValue("InitValue", getInitValue()));
setInitRange(reader->readPairOfDoubles("InitRange", getInitRange()));
reader->closeFilterGroup();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void CropImageGeometry::readFilterParameters(AbstractFilterParametersReader* reader, int index)
{
reader->openFilterGroup(this, index);
setNewDataContainerName( reader->readString("NewDataContainerName", getNewDataContainerName() ) );
setCellAttributeMatrixPath( reader->readDataArrayPath("CellAttributeMatrixPath", getCellAttributeMatrixPath() ) );
setCellFeatureAttributeMatrixPath( reader->readDataArrayPath("CellFeatureAttributeMatrixPath", getCellFeatureAttributeMatrixPath() ) );
setFeatureIdsArrayPath(reader->readDataArrayPath("FeatureIdsArrayPath", getFeatureIdsArrayPath() ) );
setXMin( reader->readValue("XMin", getXMin()) );
setYMin( reader->readValue("YMin", getYMin()) );
setZMin( reader->readValue("ZMin", getZMin()) );
setXMax( reader->readValue("XMax", getXMax()) );
setYMax( reader->readValue("YMax", getYMax()) );
setZMax( reader->readValue("ZMax", getZMax()) );
setRenumberFeatures( reader->readValue("RenumberFeatures", getRenumberFeatures()) );
setSaveAsNewDataContainer( reader->readValue("SaveAsNewDataContainer", getSaveAsNewDataContainer()) );
setUpdateOrigin( reader->readValue("UpdateOrigin", getUpdateOrigin()) );
reader->closeFilterGroup();
}
void setupInitialConditions()
{
relVelocity_ = 1e-1;
setName("AdhesiveForceUnitTest_ParticleWallInteractionWithPlasticForces");
setSystemDimensions(3);
setParticleDimensions(3);
setGravity(Vec3D(0,0,0));
species->setDensity(2000.0);
species->setStiffness(1e2);
species->setAdhesionStiffness(1e2);
species->setAdhesionForceMax(1e-5*species->getAdhesionStiffness());
Mdouble R = 1e-3;
species->setSlidingStiffness(1.2e1);
species->setSlidingFrictionCoefficient(0.01);
setTimeStep(5e-6 / 2.0);
setXMax( 2*R);
setYMax( R);
setZMax( R);
setXMin(0);
setYMin(-R);
setZMin(-R);
particleHandler.clear();
BaseParticle P;
P.setRadius(R);
P.setPosition(Vec3D(R+species->getInteractionDistance()*1/3,0,0));
P.setVelocity(Vec3D(-relVelocity_/2,0,0));
particleHandler.copyAndAddObject(P);
wallHandler.clear();
InfiniteWall w;
w.set(Vec3D(-1, 0, 0), Vec3D(getXMin(), 0, 0));
wallHandler.copyAndAddObject(w);
setTimeMax(getTimeStep()*250*4);
setFileType(FileType::ONE_FILE);
setSaveCount(1);
}
void setupInitialConditions()
{
setParticleDimensions(3);
setXMax(2);
setYMax(2);
setZMax(2);
setSystemDimensions(3);
species->setDensity(6.0 / constants::pi);
setGravity(Vec3D(0.0, 0.0, 0.0));
species->setCollisionTimeAndRestitutionCoefficient(0.01, 1.0, 1.0);
setTimeStep(0.0002);
setTimeMax(1.0);
setSaveCount(helpers::getSaveCountFromNumberOfSavesAndTimeMaxAndTimestep(20, getTimeMax(), getTimeStep()));
//set particles
particle->setRadius(0.5);
particle->setPosition(Vec3D(1.0, 1.0, 1.0));
particle->setVelocity(Vec3D(0.0, 0.0, -1.0));
//set walls
wall->setNormal(Vec3D(0.0, 0.0, -1.0));
}
void setupInitialConditions()
{
if (particleHandler.getNumberOfObjects() != N)
{
particleHandler.clear();
boundaryHandler.clear();
double VP = constants::pi * 4.0 / 3.0;
L = pow(N * VP * DistInt(1, omega) / nu, 1.0 / 3.0);
setXMin(0);
setYMin(0);
setZMin(0);
setXMax(L);
setYMax(L);
setZMax(L);
PeriodicBoundary b0;
b0.set(Vec3D(1, 0, 0), getXMin(), getXMax());
boundaryHandler.copyAndAddObject(b0);
b0.set(Vec3D(0, 1, 0), getYMin(), getYMax());
boundaryHandler.copyAndAddObject(b0);
b0.set(Vec3D(0, 0, 1), getZMin(), getZMax());
boundaryHandler.copyAndAddObject(b0);
particleHandler.setStorageCapacity(2 * N);
BaseParticle p0;
p0.setVelocity(Vec3D(0.0, 0.0, 0.0));
double V = 0;
//Use at least particles with maximum and minimum size
p0.setRadius(1.0);
Vec3D position;
position.Z = random.getRandomNumber(0, getZMax());
position.Y = random.getRandomNumber(0, getYMax());
position.X = random.getRandomNumber(0, getXMax());
p0.setPosition(position);
particleHandler.copyAndAddObject(p0);
V += VP * pow(p0.getRadius(), 3);
p0.setRadius(omega);
position.Z = random.getRandomNumber(0, getZMax());
position.Y = random.getRandomNumber(0, getYMax());
position.X = random.getRandomNumber(0, getXMax());
p0.setPosition(position);
particleHandler.copyAndAddObject(p0);
V += VP * pow(p0.getRadius(), 3);
//For other particles use a random distribution
for (unsigned int i = 2; i < N; i++)
{
p0.setRadius(RandomRadius());
position.Z = random.getRandomNumber(0, getZMax());
position.Y = random.getRandomNumber(0, getYMax());
position.X = random.getRandomNumber(0, getXMax());
p0.setPosition(position);
particleHandler.copyAndAddObject(p0);
V += VP * pow(p0.getRadius(), 3);
}
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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());
}
}