/** * @brief * @param parentId * @return */ virtual int readH5Data(hid_t parentId) { int err = 0; this->Resize(0); IDataArray::Pointer p = H5DataArrayReader::readIDataArray(parentId, GetName()); if (p.get() == NULL) { return -1; } this->NumberOfComponents = p->GetNumberOfComponents(); this->Size = p->GetSize(); this->MaxId = (Size == 0) ? 0 : Size -1; this->Array = reinterpret_cast<T*>(p->GetVoidPointer(0)); p->releaseOwnership(); return err; }
// ----------------------------------------------------------------------------- // // ----------------------------------------------------------------------------- void FieldDataCSVWriter::execute() { int err = 0; setErrorCondition(err); VoxelDataContainer* m = getVoxelDataContainer(); if(NULL == m) { setErrorCondition(-999); notifyErrorMessage("The DataContainer Object was NULL", -999); return; } // Make sure any directory path is also available as the user may have just typed // in a path without actually creating the full path std::string parentPath = MXAFileInfo::parentPath(m_FieldDataFile); if(!MXADir::mkdir(parentPath, true)) { std::stringstream ss; ss << "Error creating parent path '" << parentPath << "'"; notifyErrorMessage(ss.str(), -1); setErrorCondition(-1); return; } std::string filename = getFieldDataFile(); std::ofstream outFile; outFile.open(filename.c_str(), std::ios_base::binary); char space = DREAM3D::GrainData::Delimiter; // Write the total number of grains outFile << m->getNumFieldTuples()-1 << std::endl; // Get all the names of the arrays from the Data Container std::list<std::string> headers = m->getFieldArrayNameList(); std::vector<IDataArray::Pointer> data; //For checking if an array is a neighborlist NeighborList<int>::Pointer neighborlistPtr = NeighborList<int>::New(); // Print the GrainIds Header before the rest of the headers outFile << DREAM3D::GrainData::GrainID; // Loop throught the list and print the rest of the headers, ignoring those we don't want for(std::list<std::string>::iterator iter = headers.begin(); iter != headers.end(); ++iter) { // Only get the array if the name does NOT match those listed IDataArray::Pointer p = m->getFieldData(*iter); if(p->getNameOfClass().compare(neighborlistPtr->getNameOfClass()) != 0) { if (p->GetNumberOfComponents() == 1) { outFile << space << (*iter); } else // There are more than a single component so we need to add multiple header values { for(int k = 0; k < p->GetNumberOfComponents(); ++k) { outFile << space << (*iter) << "_" << k; } } // Get the IDataArray from the DataContainer data.push_back(p); } } outFile << std::endl; // Get the number of tuples in the arrays size_t numTuples = data[0]->GetNumberOfTuples(); std::stringstream ss; float threshold = 0.0f; // Skip the first grain for(size_t i = 1; i < numTuples; ++i) { if (((float)i / numTuples) * 100.0f > threshold) { ss.str(""); ss << "Writing Field Data - " << ((float)i / numTuples) * 100 << "% Complete"; notifyStatusMessage(ss.str()); threshold = threshold + 5.0f; if (threshold < ((float)i / numTuples) * 100.0f) { threshold = ((float)i / numTuples) * 100.0f; } } // Print the grain id outFile << i; // Print a row of data for( std::vector<IDataArray::Pointer>::iterator p = data.begin(); p != data.end(); ++p) { outFile << space; (*p)->printTuple(outFile, i, space); } outFile << std::endl; } if(m_WriteNeighborListData == true) { // Print the GrainIds Header before the rest of the headers // Loop throught the list and print the rest of the headers, ignoring those we don't want for(std::list<std::string>::iterator iter = headers.begin(); iter != headers.end(); ++iter) { // Only get the array if the name does NOT match those listed IDataArray::Pointer p = m->getFieldData(*iter); if(p->getNameOfClass().compare(neighborlistPtr->getNameOfClass()) == 0) { outFile << DREAM3D::GrainData::GrainID << space << DREAM3D::GrainData::NumNeighbors << space << (*iter) << std::endl; size_t numTuples = p->GetNumberOfTuples(); // float threshold = 0.0f; // Skip the first grain for(size_t i = 1; i < numTuples; ++i) { // Print the grain id outFile << i; // Print a row of data outFile << space; p->printTuple(outFile, i, space); outFile << std::endl; } } } } outFile.close(); // If there is an error set this to something negative and also set a message notifyStatusMessage("FieldDataCSVWriter Completed"); }
// ----------------------------------------------------------------------------- // // ----------------------------------------------------------------------------- void FindFaceAverage::dataCheckSurfaceMesh(bool preflight, size_t voxels, size_t fields, size_t ensembles) { setErrorCondition(0); std::stringstream ss; SurfaceMeshDataContainer* sm = getSurfaceMeshDataContainer(); if(NULL == sm) { addErrorMessage(getHumanLabel(), "SurfaceMeshDataContainer is missing", -383); setErrorCondition(-383); } else { // We MUST have Triangles defined. if(sm->getFaces().get() == NULL) { addErrorMessage(getHumanLabel(), "SurfaceMesh DataContainer missing Triangles", -385); setErrorCondition(-385); } else { GET_PREREQ_DATA(sm, DREAM3D, FaceData, SurfaceMeshGrainFaceId, ss, -387, int32_t, Int32ArrayType, fields, 1) if(1==m_AverageMethod) { GET_PREREQ_DATA(sm, DREAM3D, FaceData, SurfaceMeshTriangleAreas, ss, -387, double, DoubleArrayType, fields, 1) } if(m_SelectedFaceArrayName.empty() == true) { setErrorCondition(-11000); addErrorMessage(getHumanLabel(), "An array from the Face Data Container must be selected.", getErrorCondition()); } else if(preflight) { IDataArray::Pointer inputData = sm->getFaceData(m_SelectedFaceArrayName); if (NULL == inputData.get()) { ss.str(""); ss << "Selected array '" << m_SelectedFaceArrayName << "' does not exist in the Surface Mesh Data Container. Was it spelled correctly?"; setErrorCondition(-11001); notifyErrorMessage(ss.str(), getErrorCondition()); return; } int numberOfComponents = inputData->GetNumberOfComponents(); std::string dType = inputData->getTypeAsString(); IDataArray::Pointer p = IDataArray::NullPointer(); if (dType.compare("int8_t") == 0) { p = Int8ArrayType::CreateArray(1, numberOfComponents, m_SelectedFaceArrayName); } else if (dType.compare("uint8_t") == 0) { p = UInt8ArrayType::CreateArray(1, numberOfComponents, m_SelectedFaceArrayName); } else if (dType.compare("int16_t") == 0) { p = Int16ArrayType::CreateArray(1, numberOfComponents, m_SelectedFaceArrayName); } else if (dType.compare("uint16_t") == 0) { p = UInt16ArrayType::CreateArray(1, numberOfComponents, m_SelectedFaceArrayName); } else if (dType.compare("int32_t") == 0) { p = Int32ArrayType::CreateArray(1, numberOfComponents, m_SelectedFaceArrayName); } else if (dType.compare("uint32_t") == 0) { p = UInt32ArrayType::CreateArray(1, numberOfComponents, m_SelectedFaceArrayName); } else if (dType.compare("int64_t") == 0) { p = Int64ArrayType::CreateArray(1, numberOfComponents, m_SelectedFaceArrayName); } else if (dType.compare("uint64_t") == 0) { p = UInt64ArrayType::CreateArray(1, numberOfComponents, m_SelectedFaceArrayName); } else if (dType.compare("float") == 0) { p = FloatArrayType::CreateArray(1, numberOfComponents, m_SelectedFaceArrayName); } else if (dType.compare("double") == 0) { p = DoubleArrayType::CreateArray(1, numberOfComponents, m_SelectedFaceArrayName); } else if (dType.compare("bool") == 0) { p = BoolArrayType::CreateArray(1, numberOfComponents, m_SelectedFaceArrayName); } sm->addFieldData(p->GetName(), p); } } }
// ----------------------------------------------------------------------------- // // ----------------------------------------------------------------------------- void ChangeResolution::execute() { int err = 0; setErrorCondition(err); DREAM3D_RANDOMNG_NEW() VoxelDataContainer* m = getVoxelDataContainer(); if(NULL == m) { setErrorCondition(-999); notifyErrorMessage("The DataContainer Object was NULL", -999); return; } setErrorCondition(0); if (getErrorCondition() < 0) { return; } if(m->getXRes() == m_Resolution.x && m->getYRes() == m_Resolution.y && m->getZRes() == m_Resolution.z) { return; } size_t dims[3]; m->getDimensions(dims); float sizex = (dims[0])*m->getXRes(); float sizey = (dims[1])*m->getYRes(); float sizez = (dims[2])*m->getZRes(); int m_XP = int(sizex / m_Resolution.x); int m_YP = int(sizey / m_Resolution.y); int m_ZP = int(sizez / m_Resolution.z); int64_t totalPoints = m_XP*m_YP*m_ZP; float x, y, z; int col, row, plane; int index; int index_old; std::vector<size_t> newindicies; newindicies.resize(totalPoints); for (int i = 0; i < m_ZP; i++) { std::stringstream ss; ss << "Changing Resolution - " << ((float)i/m->getZPoints())*100 << " Percent Complete"; notifyStatusMessage(ss.str()); for (int j = 0; j < m_YP; j++) { for (int k = 0; k < m_XP; k++) { x = (k * m_Resolution.x); y = (j * m_Resolution.y); z = (i * m_Resolution.z); col = int(x / m->getXRes()); row = int(y / m->getYRes()); plane = int(z / m->getZRes()); index_old = (plane * m->getXPoints() * m->getYPoints()) + (row * m->getXPoints()) + col; index = (i * m_XP * m_YP) + (j * m_XP) + k; newindicies[index] = index_old; } } } std::list<std::string> voxelArrayNames = m->getCellArrayNameList(); for (std::list<std::string>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter) { std::string name = *iter; IDataArray::Pointer p = m->getCellData(*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->GetNumberOfComponents(), 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()); } m->addCellData(*iter, data); } m->setResolution(m_Resolution.x, m_Resolution.y, m_Resolution.z); m->setDimensions(m_XP, m_YP, m_ZP); notifyStatusMessage("Complete"); }
// ----------------------------------------------------------------------------- // // ----------------------------------------------------------------------------- std::string SurfaceMeshDataContainerWriter::writeXdmfAttributeDataHelper(int numComp, const std::string &attrType, const std::string &groupName, IDataArray::Pointer array, const std::string ¢ering, int precision, const std::string &xdmfTypeName) { std::stringstream out; std::stringstream dimStr; std::stringstream dimStr1; std::stringstream dimStr1half; std::stringstream dimStr2; std::stringstream dimStr2half; if((numComp%2) == 1) { out << " <Attribute Name=\"" << array->GetName() << "\" "; out << "AttributeType=\"" << attrType << "\" "; dimStr << array->GetNumberOfTuples() << " " << array->GetNumberOfComponents(); out << "Center=\"" << centering << "\">" << std::endl; // Open the <DataItem> Tag out << " <DataItem Format=\"HDF\" Dimensions=\"" << dimStr.str() << "\" "; out << "NumberType=\"" << xdmfTypeName << "\" " << "Precision=\"" << precision << "\" >" << std::endl; ssize_t nameSize = H5Fget_name(m_HdfFileId, NULL, 0) + 1; std::vector<char> nameBuffer(nameSize, 0); nameSize = H5Fget_name(m_HdfFileId, &(nameBuffer.front()), nameSize); std::string hdfFileName(&(nameBuffer.front()), nameSize); hdfFileName = MXAFileInfo::filename(hdfFileName); out << " " << hdfFileName << ":/SurfaceMeshDataContainer/" << groupName << "/" << array->GetName() << std::endl; out << " </DataItem>" << std::endl; out << " </Attribute>" << std::endl << std::endl; } else { //First Slab out << " <Attribute Name=\"" << array->GetName() << " (Field 0)\" "; out << "AttributeType=\"" << attrType << "\" "; dimStr1 << array->GetNumberOfTuples() << " " << array->GetNumberOfComponents(); dimStr1half << array->GetNumberOfTuples() << " " << (array->GetNumberOfComponents()/2); out << "Center=\"" << centering << "\">" << std::endl; // Open the <DataItem> Tag out << " <DataItem ItemType=\"HyperSlab\" Dimensions=\"" << dimStr1half.str() << "\" "; out << "Type=\"HyperSlab\" " << "Name=\"" << array->GetName() << " (Field 0)\" >" << std::endl; out << " <DataItem Dimensions=\"3 2\" " << "Format=\"XML\" >" << std::endl; out << " 0 0" << std::endl; out << " 1 1" << std::endl; out << " " << dimStr1half.str() << " </DataItem>" << std::endl; out << std::endl; out << " <DataItem Format=\"HDF\" Dimensions=\"" << dimStr1.str() << "\" " << "NumberType=\"" << xdmfTypeName << "\" " << "Precision=\"" << precision << "\" >" << std::endl; ssize_t nameSize = H5Fget_name(m_HdfFileId, NULL, 0) + 1; std::vector<char> nameBuffer(nameSize, 0); nameSize = H5Fget_name(m_HdfFileId, &(nameBuffer.front()), nameSize); std::string hdfFileName(&(nameBuffer.front()), nameSize); hdfFileName = MXAFileInfo::filename(hdfFileName); out << " " << hdfFileName << ":/SurfaceMeshDataContainer/" << groupName << "/" << array->GetName() << std::endl; out << " </DataItem>" << std::endl; out << " </DataItem>" << std::endl; out << " </Attribute>" << std::endl << std::endl; //Second Slab out << " <Attribute Name=\"" << array->GetName() << " (Field 1)\" "; out << "AttributeType=\"" << attrType << "\" "; dimStr2 << array->GetNumberOfTuples() << " " << array->GetNumberOfComponents(); dimStr2half << array->GetNumberOfTuples() << " " << (array->GetNumberOfComponents()/2); out << "Center=\"" << centering << "\">" << std::endl; // Open the <DataItem> Tag out << " <DataItem ItemType=\"HyperSlab\" Dimensions=\"" << dimStr2half.str() << "\" "; out << "Type=\"HyperSlab\" " << "Name=\"" << array->GetName() << " (Field 1)\" >" << std::endl; out << " <DataItem Dimensions=\"3 2\" " << "Format=\"XML\" >" << std::endl; out << " 0 " << (array->GetNumberOfComponents()/2) << std::endl; out << " 1 1" << std::endl; out << " " << dimStr2half.str() << " </DataItem>" << std::endl; out << std::endl; out << " <DataItem Format=\"HDF\" Dimensions=\"" << dimStr2.str() << "\" " << "NumberType=\"" << xdmfTypeName << "\" " << "Precision=\"" << precision << "\" >" << std::endl; ssize_t nameSize2 = H5Fget_name(m_HdfFileId, NULL, 0) + 1; std::vector<char> nameBuffer2(nameSize2, 0); nameSize2 = H5Fget_name(m_HdfFileId, &(nameBuffer2.front()), nameSize2); std::string hdfFileName2(&(nameBuffer2.front()), nameSize2); hdfFileName2 = MXAFileInfo::filename(hdfFileName2); out << " " << hdfFileName2 << ":/SurfaceMeshDataContainer/" << groupName << "/" << array->GetName() << std::endl; out << " </DataItem>" << std::endl; out << " </DataItem>" << std::endl; out << " </Attribute>" << std::endl << std::endl; } return out.str(); }
// ----------------------------------------------------------------------------- // // ----------------------------------------------------------------------------- void ConvertData::dataCheck(bool preflight, size_t voxels, size_t fields, size_t ensembles) { setErrorCondition(0); std::stringstream ss; VoxelDataContainer* m = getVoxelDataContainer(); if(m_SelectedCellArrayName.empty() == true) { ss.str(""); ss << "The Input Voxel Cell Array Name is blank (empty) and a value must be filled in for the pipeline to complete."; setErrorCondition(-397); addErrorMessage(getHumanLabel(), ss.str(), getErrorCondition()); } if(m_OutputArrayName.empty() == true) { ss.str(""); ss << "The Output Array Name is blank (empty) and a value must be filled in for the pipeline to complete."; setErrorCondition(-398); addErrorMessage(getHumanLabel(), ss.str(), getErrorCondition()); } int numberOfComponents = 0; IDataArray::Pointer iArray = m->getCellData(m_SelectedCellArrayName); if (NULL != iArray) { numberOfComponents = iArray->GetNumberOfComponents(); } if (true == preflight) { IDataArray::Pointer p = IDataArray::NullPointer(); if (m_ScalarType == Detail::Int8) { p = Int8ArrayType::CreateArray(voxels, numberOfComponents, m_OutputArrayName); } else if (m_ScalarType == Detail::UInt8) { p = UInt8ArrayType::CreateArray(voxels, numberOfComponents, m_OutputArrayName); } else if (m_ScalarType == Detail::Int16) { p = Int16ArrayType::CreateArray(voxels, numberOfComponents, m_OutputArrayName); } else if (m_ScalarType == Detail::UInt16) { p = UInt16ArrayType::CreateArray(voxels, numberOfComponents, m_OutputArrayName); } else if (m_ScalarType == Detail::Int32) { p = Int32ArrayType::CreateArray(voxels, numberOfComponents, m_OutputArrayName); } else if (m_ScalarType == Detail::UInt32) { p = UInt32ArrayType::CreateArray(voxels, numberOfComponents, m_OutputArrayName); } else if (m_ScalarType == Detail::Int64) { p = Int64ArrayType::CreateArray(voxels, numberOfComponents, m_OutputArrayName); } else if (m_ScalarType == Detail::UInt64) { p = UInt64ArrayType::CreateArray(voxels, numberOfComponents, m_OutputArrayName); } else if (m_ScalarType == Detail::Float) { p = FloatArrayType::CreateArray(voxels, numberOfComponents, m_OutputArrayName); } else if (m_ScalarType == Detail::Double) { p = DoubleArrayType::CreateArray(voxels, numberOfComponents, m_OutputArrayName); } m->addCellData(p->GetName(), p); } }