void copyData(IDataArray::Pointer fromData, IDataArray::Pointer toData, size_t location)
{
typename DataArray<T>::Pointer fData = std::dynamic_pointer_cast<DataArray<T>>(fromData);
typename DataArray<T>::Pointer tData = std::dynamic_pointer_cast<DataArray<T>>(toData);
//only wanting to grab data from tuple 1 to numTuples of the fromData array,s ince the zeroth slot is a placeholder the first AM should already have
T* src = fData->getPointer(1 * fromData->getNumberOfComponents());
T* dest = tData->getPointer(location * toData->getNumberOfComponents());
size_t bytes = sizeof(T) * (fromData->getNumberOfTuples() - 1) * fromData->getNumberOfComponents();
::memcpy(dest, src, bytes);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void FlattenImage::dataCheck()
{
setErrorCondition(0);
DataArrayPath tempPath;
int32_t numImageComp = 1;
IDataArray::Pointer iDataArray = getDataContainerArray()->getPrereqIDataArrayFromPath<IDataArray, AbstractFilter>(this, getImageDataArrayPath());
if (getErrorCondition() < 0) { return; }
if (NULL != iDataArray.get())
{
numImageComp = iDataArray->getNumberOfComponents();
}
QVector<size_t> cDims(1, numImageComp);
m_ImageDataPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<uint8_t>, AbstractFilter>(this, getImageDataArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_ImageDataPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_ImageData = m_ImageDataPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
cDims[0] = 1;
tempPath.update(m_ImageDataArrayPath.getDataContainerName(), m_ImageDataArrayPath.getAttributeMatrixName(), getFlatImageDataArrayName() );
m_FlatImageDataPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<uint8_t>, AbstractFilter, uint8_t>(this, tempPath, 0, cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_FlatImageDataPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_FlatImageData = m_FlatImageDataPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
/**
* @brief
* @param parentId
* @return
*/
virtual int readH5Data(hid_t parentId)
{
int err = 0;
resize(0);
IDataArray::Pointer p = H5DataArrayReader::ReadIDataArray(parentId, getName());
if (p.get() == NULL)
{
return -1;
}
m_Array = reinterpret_cast<T*>(p->getVoidPointer(0));
m_Size = p->getSize();
m_OwnsData = true;
m_MaxId = (m_Size == 0) ? 0 : m_Size - 1;
m_IsAllocated = true;
m_Name = p->getName();
m_NumTuples = p->getNumberOfTuples();
m_CompDims = p->getComponentDimensions();
m_NumComponents = p->getNumberOfComponents();
// Tell the intermediate DataArray to release ownership of the data as we are going to be responsible
// for deleting the memory
p->releaseOwnership();
return err;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
bool ModifiedLambertProjectionArray::copyData(size_t destTupleOffset, IDataArray::Pointer sourceArray)
{
if(!m_IsAllocated) { return false; }
if(0 == m_ModifiedLambertProjectionArray.size()) { return false; }
if(destTupleOffset >= m_ModifiedLambertProjectionArray.size()) { return false; }
if(!sourceArray->isAllocated()) { return false; }
Self* source = dynamic_cast<Self*>(sourceArray.get());
if(sourceArray->getNumberOfComponents() != getNumberOfComponents()) { return false; }
if( sourceArray->getNumberOfTuples()*sourceArray->getNumberOfComponents() + destTupleOffset*getNumberOfComponents() > m_ModifiedLambertProjectionArray.size() ) { return false; }
size_t sourceNTuples = source->getNumberOfTuples();
for(size_t i = 0; i < sourceNTuples; i++)
{
m_ModifiedLambertProjectionArray[destTupleOffset + i] = (*source)[i];
}
return true;
}
/**
* @brief copyData This method copies all data from the <b>sourceArray</b> into
* the current array starting at the target destination tuple offset value.
*
* For example if the DataArray has 10 tuples and the destTupleOffset = 5 then
* then source data will be copied into the destination array starting at
* destination tuple 5. In psuedo code it would be the following:
* @code
* destArray[5] = sourceArray[0];
* destArray[6] = sourceArray[1];
* .....
* @endcode
* @param destTupleOffset
* @param sourceArray
* @return
*/
bool copyData(size_t destTupleOffset, IDataArray::Pointer sourceArray)
{
if(destTupleOffset >= m_Array.size()) { return false; }
if(!sourceArray->isAllocated()) { return false; }
if(sourceArray->getNumberOfComponents() != getNumberOfComponents()) { return false; }
Self* source = dynamic_cast<Self*>(sourceArray.get());
size_t sourceNTuples = source->getNumberOfTuples();
for(size_t i = 0; i < sourceNTuples; i++)
{
m_Array[destTupleOffset + i] = source->getValue(i);
}
return true;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
QString AttributeMatrix::writeXdmfAttributeData(IDataArray::Pointer array, const QString& centering, const QString& dataContainerName, const QString& hdfFileName, const uint8_t gridType)
{
QString xdmfText;
QTextStream out(&xdmfText);
int precision = 0;
QString xdmfTypeName;
array->getXdmfTypeAndSize(xdmfTypeName, precision);
if (0 == precision)
{
out << "<!-- " << array->getName() << " has unkown type or unsupported type or precision for XDMF to understand" << " -->" << "\n";
return xdmfText;
}
int numComp = array->getNumberOfComponents();
QString attrType = "";
if(numComp == 1)
{
attrType = "Scalar";
}
//we are assuming a component of 2 is for scalars on either side of a single object (ie faceIds)
if(numComp == 2)
{
attrType = "Scalar";
}
if(numComp == 3)
{
attrType = "Vector";
}
if(numComp == 6)
{
attrType = "Vector";
}
// if(numComp == 6) { attrType = "Tensor6"; }
if(numComp == 9)
{
attrType = "Tensor";
}
QString block = writeXdmfAttributeDataHelper(numComp, attrType, dataContainerName, array, centering, precision, xdmfTypeName, hdfFileName, gridType);
out << block;
return xdmfText;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 WarpRegularGrid::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()); }
AttributeMatrix::Pointer cellAttrMat = m->getAttributeMatrix(getCellAttributeMatrixPath().getAttributeMatrixName());
AttributeMatrix::Pointer newCellAttrMat = cellAttrMat->deepCopy();
size_t dims[3] = { 0, 0, 0 };
m->getGeometryAs<ImageGeom>()->getDimensions(dims);
float res[3] = { 0.0f, 0.0f, 0.0f };
m->getGeometryAs<ImageGeom>()->getResolution(res);
size_t totalPoints = m->getGeometryAs<ImageGeom>()->getNumberOfElements();
float x = 0.0f, y = 0.0f, z = 0.0f;
float newX = 0.0f, newY = 0.0f;
int col = 0.0f, row = 0.0f, plane = 0.0f;
size_t index;
size_t index_old;
std::vector<size_t> newindicies(totalPoints);
std::vector<bool> goodPoint(totalPoints, true);
for (size_t i = 0; i < dims[2]; i++)
{
QString ss = QObject::tr("Warping Data - %1 Percent Complete").arg(((float)i / dims[2]) * 100);
notifyStatusMessage(getMessagePrefix(), getHumanLabel(), ss);
for (size_t j = 0; j < dims[1]; j++)
{
for (size_t k = 0; k < dims[0]; k++)
{
x = static_cast<float>((k * res[0]));
y = static_cast<float>((j * res[1]));
z = static_cast<float>((i * res[2]));
index = (i * dims[0] * dims[1]) + (j * dims[0]) + k;
determine_warped_coordinates(x, y, newX, newY);
col = newX / res[0];
row = newY / res[1];
plane = i;
index_old = (plane * dims[0] * dims[1]) + (row * dims[0]) + col;
newindicies[index] = index_old;
if (col > 0 && col < dims[0] && row > 0 && row < dims[1]) { goodPoint[index] = true; }
else { goodPoint[index] = false; }
}
}
}
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];
if(goodPoint[i] == true)
{
source = p->getVoidPointer((nComp * newIndicies_I));
destination = data->getVoidPointer((data->getNumberOfComponents() * i));
::memcpy(destination, source, p->getTypeSize() * data->getNumberOfComponents());
}
else
{
int var = 0;
data->initializeTuple(i, &var);
}
}
cellAttrMat->removeAttributeArray(*iter);
newCellAttrMat->addAttributeArray(*iter, data);
}
m->removeAttributeMatrix(getCellAttributeMatrixPath().getAttributeMatrixName());
m->addAttributeMatrix(getCellAttributeMatrixPath().getAttributeMatrixName(), newCellAttrMat);
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
QString AttributeMatrix::writeXdmfAttributeDataHelper(int numComp, const QString& attrType,
const QString& dataContainerName,
IDataArray::Pointer array,
const QString& centering,
int precision, const QString& xdmfTypeName, const QString& hdfFileName, const uint8_t gridType)
{
QString buf;
QTextStream out(&buf);
QString tupleStr;
for(int i = m_TupleDims.size() - 1; i >= 0 ; i--)
{
tupleStr = tupleStr + QString::number(m_TupleDims[i]) + QString(" ");
}
QString dimStr = tupleStr + QString::number(array->getNumberOfComponents());
QString dimStrHalf = tupleStr + QString::number(array->getNumberOfComponents() / 2);
if(numComp == 1 || numComp == 3 || numComp == 9)
// if(numComp == 1 || numComp == 3 || numComp == 6 || numComp == 9)
{
out << " <Attribute Name=\"" << array->getName() << "\" ";
out << "AttributeType=\"" << attrType << "\" ";
out << "Center=\"" << centering << "\">" << "\n";
// Open the <DataItem> Tag
out << " <DataItem Format=\"HDF\" Dimensions=\"" << dimStr << "\" ";
out << "NumberType=\"" << xdmfTypeName << "\" " << "Precision=\"" << precision << "\" >" << "\n";
out << " " << hdfFileName << ":/DataContainers/" << dataContainerName << "/" << getName() << "/" << array->getName() << "\n";
out << " </DataItem>" << "\n";
out << " </Attribute>" << "\n";
}
else if(numComp == 2 || numComp == 6)
// else if(numComp == 2)
{
//First Slab
out << " <Attribute Name=\"" << array->getName() << " (Feature 0)\" ";
out << "AttributeType=\"" << attrType << "\" ";
out << "Center=\"" << centering << "\">" << "\n";
// Open the <DataItem> Tag
out << " <DataItem ItemType=\"HyperSlab\" Dimensions=\"" << dimStrHalf << "\" ";
out << "Type=\"HyperSlab\" " << "Name=\"" << array->getName() << " (Feature 0)\" >" << "\n";
out << " <DataItem Dimensions=\"3 2\" " << "Format=\"XML\" >" << "\n";
out << " 0 0" << "\n";
out << " 1 1" << "\n";
out << " " << dimStrHalf << " </DataItem>" << "\n";
out << "\n";
out << " <DataItem Format=\"HDF\" Dimensions=\"" << dimStr << "\" " << "NumberType=\"" << xdmfTypeName << "\" " << "Precision=\"" << precision << "\" >" << "\n";
out << " " << hdfFileName << ":/DataContainers/" << dataContainerName << "/" << getName() << "/" << array->getName() << "\n";
out << " </DataItem>" << "\n";
out << " </DataItem>" << "\n";
out << " </Attribute>" << "\n" << "\n";
//Second Slab
out << " <Attribute Name=\"" << array->getName() << " (Feature 1)\" ";
out << "AttributeType=\"" << attrType << "\" ";
out << "Center=\"" << centering << "\">" << "\n";
// Open the <DataItem> Tag
out << " <DataItem ItemType=\"HyperSlab\" Dimensions=\"" << dimStrHalf << "\" ";
out << "Type=\"HyperSlab\" " << "Name=\"" << array->getName() << " (Feature 1)\" >" << "\n";
out << " <DataItem Dimensions=\"3 2\" " << "Format=\"XML\" >" << "\n";
out << " 0 " << (array->getNumberOfComponents() / 2) << "\n";
out << " 1 1" << "\n";
out << " " << dimStrHalf << " </DataItem>" << "\n";
out << "\n";
out << " <DataItem Format=\"HDF\" Dimensions=\"" << dimStr << "\" " << "NumberType=\"" << xdmfTypeName << "\" " << "Precision=\"" << precision << "\" >" << "\n";
out << " " << hdfFileName << ":/DataContainers/" << dataContainerName << "/" << getName() << "/" << array->getName() << "\n";
out << " </DataItem>" << "\n";
out << " </DataItem>" << "\n";
out << " </Attribute>" << "\n";
}
return buf;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void RotateSampleRefFrame::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getCellAttributeMatrixPath().getDataContainerName());
float rotAngle = m_RotationAngle * SIMPLib::Constants::k_Pi / 180.0;
int64_t xp = 0, yp = 0, zp = 0;
float xRes = 0.0f, yRes = 0.0f, zRes = 0.0f;
int64_t xpNew = 0, ypNew = 0, zpNew = 0;
float xResNew = 0.0f, yResNew = 0.0f, zResNew = 0.0f;
RotateSampleRefFrameImplArg_t params;
xp = static_cast<int64_t>(m->getGeometryAs<ImageGeom>()->getXPoints());
xRes = m->getGeometryAs<ImageGeom>()->getXRes();
yp = static_cast<int64_t>(m->getGeometryAs<ImageGeom>()->getYPoints());
yRes = m->getGeometryAs<ImageGeom>()->getYRes();
zp = static_cast<int64_t>(m->getGeometryAs<ImageGeom>()->getZPoints());
zRes = m->getGeometryAs<ImageGeom>()->getZRes();
params.xp = xp;
params.xRes = xRes;
params.yp = yp;
params.yRes = yRes;
params.zp = zp;
params.zRes = zRes;
size_t col = 0, row = 0, plane = 0;
float rotMat[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
float coords[3] = { 0.0f, 0.0f, 0.0f };
float newcoords[3] = { 0.0f, 0.0f, 0.0f };
float xMin = std::numeric_limits<float>::max();
float xMax = std::numeric_limits<float>::min();
float yMin = std::numeric_limits<float>::max();
float yMax = std::numeric_limits<float>::min();
float zMin = std::numeric_limits<float>::max();
float zMax = std::numeric_limits<float>::min();
FOrientArrayType om(9);
FOrientTransformsType::ax2om(FOrientArrayType(m_RotationAxis.x, m_RotationAxis.y, m_RotationAxis.z, rotAngle), om);
om.toGMatrix(rotMat);
for (int32_t i = 0; i < 8; i++)
{
if (i == 0) { col = 0, row = 0, plane = 0; }
if (i == 1) { col = xp - 1, row = 0, plane = 0; }
if (i == 2) { col = 0, row = yp - 1, plane = 0; }
if (i == 3) { col = xp - 1, row = yp - 1, plane = 0; }
if (i == 4) { col = 0, row = 0, plane = zp - 1; }
if (i == 5) { col = xp - 1, row = 0, plane = zp - 1; }
if (i == 6) { col = 0, row = yp - 1, plane = zp - 1; }
if (i == 7) { col = xp - 1, row = yp - 1, plane = zp - 1; }
coords[0] = static_cast<float>(col * xRes);
coords[1] = static_cast<float>(row * yRes);
coords[2] = static_cast<float>(plane * zRes);
MatrixMath::Multiply3x3with3x1(rotMat, coords, newcoords);
if (newcoords[0] < xMin) { xMin = newcoords[0]; }
if (newcoords[0] > xMax) { xMax = newcoords[0]; }
if (newcoords[1] < yMin) { yMin = newcoords[1]; }
if (newcoords[1] > yMax) { yMax = newcoords[1]; }
if (newcoords[2] < zMin) { zMin = newcoords[2]; }
if (newcoords[2] > zMax) { zMax = newcoords[2]; }
}
float xAxis[3] = {1, 0, 0};
float yAxis[3] = {0, 1, 0};
float zAxis[3] = {0, 0, 1};
float xAxisNew[3] = { 0.0f, 0.0f, 0.0f };
float yAxisNew[3] = { 0.0f, 0.0f, 0.0f };
float zAxisNew[3] = { 0.0f, 0.0f, 0.0f };
MatrixMath::Multiply3x3with3x1(rotMat, xAxis, xAxisNew);
MatrixMath::Multiply3x3with3x1(rotMat, yAxis, yAxisNew);
MatrixMath::Multiply3x3with3x1(rotMat, zAxis, zAxisNew);
float closestAxis = 0.0f;
xResNew = xRes;
closestAxis = fabs(GeometryMath::CosThetaBetweenVectors(xAxis, xAxisNew));
if (fabs(GeometryMath::CosThetaBetweenVectors(yAxis, xAxisNew)) > closestAxis) { xResNew = yRes, closestAxis = fabs(GeometryMath::CosThetaBetweenVectors(yAxis, xAxisNew)); }
if (fabs(GeometryMath::CosThetaBetweenVectors(zAxis, xAxisNew)) > closestAxis) { xResNew = zRes, closestAxis = fabs(GeometryMath::CosThetaBetweenVectors(zAxis, xAxisNew)); }
yResNew = yRes;
closestAxis = fabs(GeometryMath::CosThetaBetweenVectors(yAxis, yAxisNew));
if (fabs(GeometryMath::CosThetaBetweenVectors(xAxis, yAxisNew)) > closestAxis) { yResNew = xRes, closestAxis = fabs(GeometryMath::CosThetaBetweenVectors(xAxis, yAxisNew)); }
if (fabs(GeometryMath::CosThetaBetweenVectors(zAxis, yAxisNew)) > closestAxis) { yResNew = zRes, closestAxis = fabs(GeometryMath::CosThetaBetweenVectors(zAxis, yAxisNew)); }
zResNew = zRes;
closestAxis = fabs(GeometryMath::CosThetaBetweenVectors(zAxis, zAxisNew));
if (fabs(GeometryMath::CosThetaBetweenVectors(xAxis, zAxisNew)) > closestAxis) { zResNew = xRes, closestAxis = fabs(GeometryMath::CosThetaBetweenVectors(xAxis, zAxisNew)); }
if (fabs(GeometryMath::CosThetaBetweenVectors(yAxis, zAxisNew)) > closestAxis) { zResNew = yRes, closestAxis = fabs(GeometryMath::CosThetaBetweenVectors(yAxis, zAxisNew)); }
xpNew = static_cast<int64_t>(nearbyint((xMax - xMin) / xResNew) + 1);
ypNew = static_cast<int64_t>(nearbyint((yMax - yMin) / yResNew) + 1);
zpNew = static_cast<int64_t>(nearbyint((zMax - zMin) / zResNew) + 1);
params.xpNew = xpNew;
params.xResNew = xResNew;
params.xMinNew = xMin;
params.ypNew = ypNew;
params.yResNew = yResNew;
params.yMinNew = yMin;
params.zpNew = zpNew;
params.zResNew = zResNew;
params.zMinNew = zMin;
int64_t newNumCellTuples = params.xpNew * params.ypNew * params.zpNew;
DataArray<int64_t>::Pointer newIndiciesPtr = DataArray<int64_t>::CreateArray(newNumCellTuples, "_INTERNAL_USE_ONLY_RotateSampleRef_NewIndicies");
newIndiciesPtr->initializeWithValue(-1);
int64_t* newindicies = newIndiciesPtr->getPointer(0);
#ifdef SIMPLib_USE_PARALLEL_ALGORITHMS
tbb::task_scheduler_init init;
bool doParallel = true;
#endif
#ifdef SIMPLib_USE_PARALLEL_ALGORITHMS
if (doParallel == true)
{
tbb::parallel_for(tbb::blocked_range3d<int64_t, int64_t, int64_t>(0, params.zpNew, 0, params.ypNew, 0, params.xpNew),
RotateSampleRefFrameImpl(newIndiciesPtr, ¶ms, rotMat, m_SliceBySlice), tbb::auto_partitioner());
}
else
#endif
{
RotateSampleRefFrameImpl serial(newIndiciesPtr, ¶ms, rotMat, m_SliceBySlice);
serial.convert(0, params.zpNew, 0, params.ypNew, 0, params.xpNew);
}
// This could technically be parallelized also where each thread takes an array to adjust. Except
// that the DataContainer is NOT thread safe or re-entrant so that would actually be a BAD idea.
QString attrMatName = getCellAttributeMatrixPath().getAttributeMatrixName();
QList<QString> voxelArrayNames = m->getAttributeMatrix(attrMatName)->getAttributeArrayNames();
// resize attribute matrix
QVector<size_t> tDims(3);
tDims[0] = params.xpNew;
tDims[1] = params.ypNew;
tDims[2] = params.zpNew;
m->getAttributeMatrix(attrMatName)->resizeAttributeArrays(tDims);
for (QList<QString>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
{
IDataArray::Pointer p = m->getAttributeMatrix(attrMatName)->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.
IDataArray::Pointer data = p->createNewArray(newNumCellTuples, p->getComponentDimensions(), p->getName());
void* source = NULL;
void* destination = NULL;
int64_t newIndicies_I = 0;
int32_t nComp = data->getNumberOfComponents();
for (size_t i = 0; i < static_cast<size_t>(newNumCellTuples); i++)
{
newIndicies_I = newindicies[i];
if(newIndicies_I >= 0)
{
source = p->getVoidPointer((nComp * newIndicies_I));
if (NULL == source)
{
QString ss = QObject::tr("The index is outside the bounds of the source array");
setErrorCondition(-11004);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
destination = data->getVoidPointer((data->getNumberOfComponents() * i));
::memcpy(destination, source, p->getTypeSize() * data->getNumberOfComponents());
}
else
{
data->initializeTuple(i, 0);
}
}
m->getAttributeMatrix(attrMatName)->addAttributeArray(*iter, data);
}
m->getGeometryAs<ImageGeom>()->setResolution(params.xResNew, params.yResNew, params.zResNew);
m->getGeometryAs<ImageGeom>()->setDimensions(params.xpNew, params.ypNew, params.zpNew);
m->getGeometryAs<ImageGeom>()->setOrigin(xMin, yMin, zMin);
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void NearestPointFuseRegularGrids::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer refDC = getDataContainerArray()->getDataContainer(m_ReferenceCellAttributeMatrixPath.getDataContainerName());
DataContainer::Pointer sampleDC = getDataContainerArray()->getDataContainer(m_SamplingCellAttributeMatrixPath.getDataContainerName());
AttributeMatrix::Pointer refAttrMat = refDC->getAttributeMatrix(m_ReferenceCellAttributeMatrixPath.getAttributeMatrixName());
AttributeMatrix::Pointer sampleAttrMat = sampleDC->getAttributeMatrix(m_SamplingCellAttributeMatrixPath.getAttributeMatrixName());
// Get dimensions and resolutions of two grids
size_t _refDims[3] = { 0, 0, 0 };
size_t _sampleDims[3] = { 0, 0, 0 };
float refRes[3] = { 0.0f, 0.0f, 0.0f };
float sampleRes[3] = { 0.0f, 0.0f, 0.0f };
float refOrigin[3] = { 0.0f, 0.0f, 0.0f };
float sampleOrigin[3] = { 0.0f, 0.0f, 0.0f };
refDC->getGeometryAs<ImageGeom>()->getDimensions(_refDims);
sampleDC->getGeometryAs<ImageGeom>()->getDimensions(_sampleDims);
refDC->getGeometryAs<ImageGeom>()->getResolution(refRes);
sampleDC->getGeometryAs<ImageGeom>()->getResolution(sampleRes);
refDC->getGeometryAs<ImageGeom>()->getOrigin(refOrigin);
sampleDC->getGeometryAs<ImageGeom>()->getOrigin(sampleOrigin);
// Further down we divide by sampleRes, so here check to make sure that no components of the resolution are 0
// This would be incredible unusual behavior if it were to occur, hence why we don't spend the time
// doing the validation up in the dataCheck
bool zeroRes = false;
for (size_t i = 0; i < 3; i++)
{
if (sampleRes[i] == 0.0f)
{
zeroRes = true;
break;
}
}
if (zeroRes == true)
{
QString ss = QObject::tr("A component of the resolution for the Image Geometry associated with DataContainer '%1' is 0. This would result in a division by 0 operation").arg(m_SamplingCellAttributeMatrixPath.getDataContainerName());
setErrorCondition(-5555);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
int64_t refDims[3] = { 0, 0, 0 };
int64_t sampleDims[3] = { 0, 0, 0 };
for (size_t i = 0; i < 3; i++)
{
refDims[i] = static_cast<int64_t>(_refDims[i]);
sampleDims[i] = static_cast<int64_t>(_sampleDims[i]);
}
int64_t numRefTuples = refDims[0] * refDims[1] * refDims[2];
float x = 0.0f, y = 0.0f, z = 0.0f;
int64_t col = 0, row = 0, plane = 0;
int64_t refIndex = 0;
int64_t sampleIndex = 0;
int64_t planeComp = 0, rowComp = 0;
// Create arrays on the reference grid to hold data present on the sampling grid
QList<QString> voxelArrayNames = sampleAttrMat->getAttributeArrayNames();
for (QList<QString>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
{
IDataArray::Pointer p = sampleAttrMat->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(numRefTuples, p->getComponentDimensions(), p->getName());
refAttrMat->addAttributeArray(p->getName(), data);
}
bool outside = false;
for (int64_t i = 0; i < refDims[2]; i++)
{
planeComp = i * refDims[0] * refDims[1];
for (int64_t j = 0; j < refDims[1]; j++)
{
rowComp = j * refDims[0];
for (int64_t k = 0; k < refDims[0]; k++)
{
outside = false;
x = (k * refRes[0] + refOrigin[0]);
y = (j * refRes[1] + refOrigin[1]);
z = (i * refRes[2] + refOrigin[2]);
if ((x - sampleOrigin[0]) < 0) { outside = true; }
else { col = int64_t((x - sampleOrigin[0]) / sampleRes[0]); }
if ((y - sampleOrigin[1]) < 0) { outside = true; }
else { row = int64_t((y - sampleOrigin[1]) / sampleRes[1]); }
if ((z - sampleOrigin[2]) < 0) { outside = true; }
else { plane = int64_t((z - sampleOrigin[2]) / sampleRes[2]); }
if (col > sampleDims[0] || row > sampleDims[1] || plane > sampleDims[2]) { outside = true; }
if (outside == false)
{
sampleIndex = (plane * sampleDims[0] * sampleDims[1]) + (row * sampleDims[0]) + col;
refIndex = planeComp + rowComp + k;
for (QList<QString>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
{
IDataArray::Pointer p = sampleAttrMat->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 = refAttrMat->getAttributeArray(*iter);
void* source = NULL;
void* destination = NULL;
int nComp = data->getNumberOfComponents();
source = p->getVoidPointer((nComp * sampleIndex));
destination = data->getVoidPointer((nComp * refIndex));
::memcpy(destination, source, p->getTypeSize() * nComp);
}
}
}
}
}
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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");
}