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"); }