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|---|---|---|---|
| 1 | // -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- | ||
| 2 | // vi: set et ts=4 sw=4 sts=4: | ||
| 3 | // | ||
| 4 | // SPDX-FileCopyrightText: Copyright © DuMux Project contributors, see AUTHORS.md in root folder | ||
| 5 | // SPDX-License-Identifier: GPL-3.0-or-later | ||
| 6 | // | ||
| 7 | /*! | ||
| 8 | * \file | ||
| 9 | * \ingroup InputOutput | ||
| 10 | * \brief A vtk file reader using tinyxml2 as xml backend | ||
| 11 | */ | ||
| 12 | #ifndef DUMUX_IO_VTK_VTKREADER_HH | ||
| 13 | #define DUMUX_IO_VTK_VTKREADER_HH | ||
| 14 | |||
| 15 | #include <iostream> | ||
| 16 | #include <iterator> | ||
| 17 | #include <algorithm> | ||
| 18 | #include <memory> | ||
| 19 | #include <type_traits> | ||
| 20 | #include <unordered_map> | ||
| 21 | #include <utility> | ||
| 22 | #include <filesystem> | ||
| 23 | |||
| 24 | #include <dune/common/parallel/mpihelper.hh> | ||
| 25 | #include <dune/common/exceptions.hh> | ||
| 26 | #include <dune/grid/common/capabilities.hh> | ||
| 27 | #include <dune/grid/io/file/vtk/common.hh> | ||
| 28 | #include <dune/grid/common/gridfactory.hh> | ||
| 29 | |||
| 30 | #include <dumux/io/container.hh> | ||
| 31 | |||
| 32 | #if DUMUX_HAVE_GRIDFORMAT | ||
| 33 | |||
| 34 | #include <gridformat/gridformat.hpp> | ||
| 35 | #include <gridformat/traits/dune.hpp> | ||
| 36 | #include <gridformat/reader.hpp> | ||
| 37 | #include <gridformat/decorators/reader_polylines_subdivider.hpp> | ||
| 38 | |||
| 39 | namespace Dumux::Detail::VTKReader { | ||
| 40 | |||
| 41 | template<GridFormat::Concepts::Communicator C> | ||
| 42 | auto makeGridformatReaderFactory(const C& c) | ||
| 43 | { | ||
| 44 | return [fac = GridFormat::AnyReaderFactory<C>{c}] (const std::string& f) | ||
| 45 | -> std::unique_ptr<GridFormat::GridReader> { | ||
| 46 | // use adapter for poly data that splits polylines into segments | ||
| 47 | if (f.ends_with("vtp")) | ||
| 48 | return std::make_unique<GridFormat::ReaderDecorators::PolylinesSubdivider>(fac.make_for(f)); | ||
| 49 | return fac.make_for(f); | ||
| 50 | }; | ||
| 51 | } | ||
| 52 | |||
| 53 | } // end namespace Dumux::Detail::VTKReader | ||
| 54 | |||
| 55 | namespace Dumux { | ||
| 56 | |||
| 57 | /*! | ||
| 58 | * \ingroup InputOutput | ||
| 59 | * \brief A vtk file reader using gridformat | ||
| 60 | */ | ||
| 61 | class VTKReader | ||
| 62 | { | ||
| 63 | public: | ||
| 64 | enum class DataType { cellData, pointData, fieldData }; | ||
| 65 | |||
| 66 | //! the cell / point data type for point data read from a grid file | ||
| 67 | using Data = std::unordered_map<std::string, std::vector<double>>; | ||
| 68 | |||
| 69 | explicit VTKReader(const std::string& fileName) | ||
| 70 | : reader_(GridFormat::Reader::from(fileName, | ||
| 71 | Detail::VTKReader::makeGridformatReaderFactory( | ||
| 72 | Dune::MPIHelper::instance().getCommunicator() | ||
| 73 | ) | ||
| 74 | )) | ||
| 75 | {} | ||
| 76 | |||
| 77 | /*! | ||
| 78 | * \brief Reviews data from the vtk file to check if there is a data array with a specified name | ||
| 79 | * \param name the name attribute of the data array to read | ||
| 80 | * \param type the data array type | ||
| 81 | */ | ||
| 82 | bool hasData(const std::string& name, const DataType& type) const | ||
| 83 | { | ||
| 84 | if (type == DataType::cellData) | ||
| 85 | return std::ranges::any_of( | ||
| 86 | cell_field_names(reader_), | ||
| 87 | [&] (const auto& n) { return name == n; } | ||
| 88 | ); | ||
| 89 | else if (type == DataType::pointData) | ||
| 90 | return std::ranges::any_of( | ||
| 91 | point_field_names(reader_), | ||
| 92 | [&] (const auto& n) { return name == n; } | ||
| 93 | ); | ||
| 94 | else if (type == DataType::fieldData) | ||
| 95 | return std::ranges::any_of( | ||
| 96 | meta_data_field_names(reader_), | ||
| 97 | [&] (const auto& n) { return name == n; } | ||
| 98 | ); | ||
| 99 | else | ||
| 100 | DUNE_THROW(Dune::IOError, "Unknown data type for field '" << name << "'"); | ||
| 101 | } | ||
| 102 | |||
| 103 | /*! | ||
| 104 | * \brief read data from the vtk file to a container, e.g. std::vector<double> | ||
| 105 | * \tparam Container a container type that has begin(), end(), push_back(), e.g. std::vector<> | ||
| 106 | * \param name the name attribute of the data array to read | ||
| 107 | * \param type the data array type | ||
| 108 | */ | ||
| 109 | template<class Container> | ||
| 110 | Container readData(const std::string& name, const DataType& type) const | ||
| 111 | { | ||
| 112 | if (type == DataType::cellData) | ||
| 113 | { | ||
| 114 | Container values(reader_.number_of_cells()); | ||
| 115 | reader_.cell_field(name)->export_to(values); | ||
| 116 | return values; | ||
| 117 | } | ||
| 118 | else if (type == DataType::pointData) | ||
| 119 | { | ||
| 120 | Container values(reader_.number_of_points()); | ||
| 121 | reader_.point_field(name)->export_to(values); | ||
| 122 | return values; | ||
| 123 | } | ||
| 124 | else if (type == DataType::fieldData) | ||
| 125 | { | ||
| 126 | DUNE_THROW(Dune::NotImplemented, "Reading meta data not yet implemented"); | ||
| 127 | } | ||
| 128 | else | ||
| 129 | DUNE_THROW(Dune::IOError, "Unknown data type for field '" << name << "'"); | ||
| 130 | } | ||
| 131 | |||
| 132 | /*! | ||
| 133 | * \brief Read a grid from a vtk/vtu/vtp file, ignoring cell and point data | ||
| 134 | * \param verbose if the output should be verbose | ||
| 135 | */ | ||
| 136 | template<class Grid> | ||
| 137 | std::unique_ptr<Grid> readGrid(bool verbose = false) const | ||
| 138 | { | ||
| 139 | Dune::GridFactory<Grid> factory; | ||
| 140 | return readGrid(factory, verbose); | ||
| 141 | } | ||
| 142 | |||
| 143 | /*! | ||
| 144 | * \brief Read a grid from a vtk/vtu/vtp file, ignoring cell and point data | ||
| 145 | * \note use this signature if the factory might be needed outside to interpret the data via the factory's insertion indices | ||
| 146 | * \param verbose if the output should be verbose | ||
| 147 | * \param factory the (empty) grid factory | ||
| 148 | */ | ||
| 149 | template<class Grid> | ||
| 150 | std::unique_ptr<Grid> readGrid(Dune::GridFactory<Grid>& factory, bool verbose = false) const | ||
| 151 | { | ||
| 152 | if (Dune::MPIHelper::instance().rank() == 0) | ||
| 153 | { | ||
| 154 | if (verbose) | ||
| 155 | std::cout << "Reading " << Grid::dimension << "d grid from vtk file " << reader_.filename() << "." << std::endl; | ||
| 156 | |||
| 157 | { | ||
| 158 | GridFormat::Dune::GridFactoryAdapter<Grid> adapter{ factory }; | ||
| 159 | reader_.export_grid(adapter); | ||
| 160 | } | ||
| 161 | } | ||
| 162 | |||
| 163 | return std::unique_ptr<Grid>(factory.createGrid()); | ||
| 164 | } | ||
| 165 | |||
| 166 | /*! | ||
| 167 | * \brief Read a grid from a vtk/vtu/vtp file, reading all cell and point data | ||
| 168 | * \note the factory will be needed outside to interpret the data via the factory's insertion indices | ||
| 169 | * \param factory the (empty) grid factory | ||
| 170 | * \param cellData the cell data arrays to be filled | ||
| 171 | * \param pointData the point data arrays to be filled | ||
| 172 | * \param verbose if the output should be verbose | ||
| 173 | */ | ||
| 174 | template<class Grid> | ||
| 175 | std::unique_ptr<Grid> readGrid(Dune::GridFactory<Grid>& factory, Data& cellData, Data& pointData, bool verbose = false) const | ||
| 176 | { | ||
| 177 | auto grid = readGrid(factory, verbose); | ||
| 178 | if (Dune::MPIHelper::instance().rank() == 0) | ||
| 179 | { | ||
| 180 | for (const auto& [name, field_ptr] : cell_fields(reader_)) | ||
| 181 | field_ptr->export_to(cellData[name]); | ||
| 182 | |||
| 183 | for (const auto& [name, field_ptr] : point_fields(reader_)) | ||
| 184 | field_ptr->export_to(pointData[name]); | ||
| 185 | } | ||
| 186 | return std::unique_ptr<Grid>(std::move(grid)); | ||
| 187 | } | ||
| 188 | |||
| 189 | private: | ||
| 190 | GridFormat::Reader reader_; | ||
| 191 | }; | ||
| 192 | |||
| 193 | } // namespace Dumux | ||
| 194 | |||
| 195 | #else // DUMUX_HAVE_GRIDFORMAT | ||
| 196 | |||
| 197 | #include <dumux/io/xml/tinyxml2.h> | ||
| 198 | // fallback to simple vtk reader using tinyxml2 | ||
| 199 | // this reader only support ascii files and limited VTK file formats | ||
| 200 | |||
| 201 | namespace Dumux::Detail::VTKReader { | ||
| 202 | |||
| 203 | /*! | ||
| 204 | * \brief Get the piece node an xml document | ||
| 205 | * \note Returns nullptr if the piece node wasn't found | ||
| 206 | * \param doc an xml document | ||
| 207 | * \param fileName a file name the doc was created from | ||
| 208 | */ | ||
| 209 | 491 | const tinyxml2::XMLElement* getPieceNode(const tinyxml2::XMLDocument& doc, const std::string& fileName) | |
| 210 | { | ||
| 211 | 491 | using namespace tinyxml2; | |
| 212 | |||
| 213 | 491 | const XMLElement* pieceNode = doc.FirstChildElement("VTKFile"); | |
| 214 |
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491 | if (pieceNode == nullptr) |
| 215 | ✗ | DUNE_THROW(Dune::IOError, "Couldn't get 'VTKFile' node in " << fileName << "."); | |
| 216 | |||
| 217 | 491 | pieceNode = pieceNode->FirstChildElement("UnstructuredGrid"); | |
| 218 |
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491 | if (pieceNode == nullptr) |
| 219 | 248 | pieceNode = doc.FirstChildElement("VTKFile")->FirstChildElement("PolyData"); | |
| 220 |
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124 | if (pieceNode == nullptr) |
| 221 | 4 | pieceNode = doc.FirstChildElement("VTKFile")->FirstChildElement("PUnstructuredGrid"); | |
| 222 |
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369 | if (pieceNode == nullptr) |
| 223 | ✗ | pieceNode = doc.FirstChildElement("VTKFile")->FirstChildElement("PPolyData"); | |
| 224 | ✗ | if (pieceNode == nullptr) | |
| 225 | ✗ | DUNE_THROW(Dune::IOError, "Couldn't get 'UnstructuredGrid', 'PUnstructuredGrid', 'PolyData', or 'PPolyData' node in " << fileName << "."); | |
| 226 | |||
| 227 | 982 | return pieceNode->FirstChildElement("Piece"); | |
| 228 | } | ||
| 229 | |||
| 230 | /*! | ||
| 231 | * \brief get the vtk filename for the current processor | ||
| 232 | */ | ||
| 233 | 2 | std::string getProcessPieceFileName(const std::string& pvtkFileName) | |
| 234 | { | ||
| 235 | 2 | using namespace tinyxml2; | |
| 236 | |||
| 237 | 2 | XMLDocument pDoc; | |
| 238 |
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2 | const auto eResult = pDoc.LoadFile(pvtkFileName.c_str()); |
| 239 |
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2 | if (eResult != XML_SUCCESS) |
| 240 | ✗ | DUNE_THROW(Dune::IOError, "Couldn't open XML file " << pvtkFileName << "."); | |
| 241 | |||
| 242 | // get the first piece node | ||
| 243 |
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2 | const XMLElement* pieceNode = getPieceNode(pDoc, pvtkFileName); |
| 244 |
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2 | const auto myrank = Dune::MPIHelper::instance().rank(); |
| 245 |
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3 | for (int rank = 0; rank < myrank; ++rank) |
| 246 | { | ||
| 247 | 1 | pieceNode = pieceNode->NextSiblingElement("Piece"); | |
| 248 |
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1 | if (pieceNode == nullptr) |
| 249 |
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1 | DUNE_THROW(Dune::IOError, "Couldn't find 'Piece' node for rank " |
| 250 | << rank << " in " << pvtkFileName << "."); | ||
| 251 | } | ||
| 252 | |||
| 253 | 2 | const char *vtkFileName = pieceNode->Attribute("Source"); | |
| 254 |
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2 | if (vtkFileName == nullptr) |
| 255 | ✗ | DUNE_THROW(Dune::IOError, "Couldn't get 'Source' attribute of 'Piece' node no. " << myrank << " in " << pvtkFileName); | |
| 256 | |||
| 257 |
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4 | return vtkFileName; |
| 258 | 2 | } | |
| 259 | |||
| 260 | } // end namespace Dumux::Detail::VTKReader | ||
| 261 | |||
| 262 | namespace Dumux { | ||
| 263 | |||
| 264 | /*! | ||
| 265 | * \ingroup InputOutput | ||
| 266 | * \brief A vtk file reader using tinyxml2 as xml backend | ||
| 267 | */ | ||
| 268 | 69 | class VTKReader | |
| 269 | { | ||
| 270 | public: | ||
| 271 | /*! | ||
| 272 | * \brief The data array types | ||
| 273 | */ | ||
| 274 | enum class DataType { cellData, pointData }; | ||
| 275 | |||
| 276 | //! the cell / point data type for point data read from a grid file | ||
| 277 | using Data = std::unordered_map<std::string, std::vector<double>>; | ||
| 278 | |||
| 279 | /*! | ||
| 280 | * \brief The constructor creates a tinyxml2::XMLDocument from file | ||
| 281 | */ | ||
| 282 | 69 | explicit VTKReader(const std::string& fileName) | |
| 283 | 69 | { | |
| 284 | 69 | using namespace tinyxml2; | |
| 285 |
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138 | const auto ext = std::filesystem::path(fileName).extension().string(); |
| 286 | // If in parallel and the file to read is a parallel piece collection (pvtu/pvtp) | ||
| 287 | // read only the piece belonging to the own process. For this to work, the files | ||
| 288 | // have to have exactly the same amount of pieces than processes. | ||
| 289 |
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69 | fileName_ = Dune::MPIHelper::instance().size() > 1 && ext[1] == 'p' ? |
| 290 |
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138 | Detail::VTKReader::getProcessPieceFileName(fileName) : fileName; |
| 291 | |||
| 292 |
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69 | const auto eResult = doc_.LoadFile(fileName_.c_str()); |
| 293 |
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69 | if (eResult != tinyxml2::XML_SUCCESS) |
| 294 | ✗ | DUNE_THROW(Dune::IOError, "Couldn't open XML file " << fileName_ << "."); | |
| 295 | |||
| 296 | 138 | const XMLElement* pieceNode = getPieceNode_(); | |
| 297 |
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69 | if (pieceNode == nullptr) |
| 298 |
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69 | DUNE_THROW(Dune::IOError, "Couldn't get 'Piece' node in " << fileName_ << "."); |
| 299 | 69 | } | |
| 300 | |||
| 301 | /*! | ||
| 302 | * \brief Reviews data from the vtk file to check if there is a data array with a specified name | ||
| 303 | * \param name the name attribute of the data array to read | ||
| 304 | * \param type the data array type | ||
| 305 | */ | ||
| 306 | 273 | bool hasData(const std::string& name, const DataType& type) const | |
| 307 | { | ||
| 308 | 273 | using namespace tinyxml2; | |
| 309 | |||
| 310 | 546 | const XMLElement* pieceNode = getPieceNode_(); | |
| 311 | 273 | const XMLElement* dataNode = getDataNode_(pieceNode, type); | |
| 312 |
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273 | if (dataNode == nullptr) |
| 313 | return false; | ||
| 314 | |||
| 315 | 273 | const XMLElement* dataArray = findDataArray_(dataNode, name); | |
| 316 |
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273 | if (dataArray == nullptr) |
| 317 | return false; | ||
| 318 | |||
| 319 | return true; | ||
| 320 | } | ||
| 321 | |||
| 322 | /*! | ||
| 323 | * \brief read data from the vtk file to a container, e.g. std::vector<double> | ||
| 324 | * \tparam Container a container type that has begin(), end(), push_back(), e.g. std::vector<> | ||
| 325 | * \param name the name attribute of the data array to read | ||
| 326 | * \param type the data array type | ||
| 327 | */ | ||
| 328 | template<class Container> | ||
| 329 | 139 | Container readData(const std::string& name, const DataType& type) const | |
| 330 | { | ||
| 331 | using namespace tinyxml2; | ||
| 332 | |||
| 333 | 139 | const XMLElement* pieceNode = getPieceNode_(); | |
| 334 | 139 | const XMLElement* dataNode = getDataNode_(pieceNode, type); | |
| 335 |
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139 | if (dataNode == nullptr) |
| 336 | ✗ | DUNE_THROW(Dune::IOError, "Couldn't get 'PointData' or 'CellData' node in " << fileName_ << "."); | |
| 337 | |||
| 338 | 139 | const XMLElement* dataArray = findDataArray_(dataNode, name); | |
| 339 |
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139 | if (dataArray == nullptr) |
| 340 | ✗ | DUNE_THROW(Dune::IOError, "Couldn't find the data array " << name << "."); | |
| 341 | |||
| 342 | 139 | return parseDataArray_<Container>(dataArray); | |
| 343 | } | ||
| 344 | |||
| 345 | /*! | ||
| 346 | * \brief Read a grid from a vtk/vtu/vtp file, ignoring cell and point data | ||
| 347 | * \param verbose if the output should be verbose | ||
| 348 | */ | ||
| 349 | template<class Grid> | ||
| 350 | std::unique_ptr<Grid> readGrid(bool verbose = false) const | ||
| 351 | { | ||
| 352 | static_assert(!Dune::Capabilities::isCartesian<Grid>::v, "Grid reader only supports unstructured grid implementations"); | ||
| 353 | |||
| 354 | // make a grid factory | ||
| 355 | Dune::GridFactory<Grid> factory; | ||
| 356 | |||
| 357 | // only read on rank 0 | ||
| 358 | if (Dune::MPIHelper::instance().rank() == 0) | ||
| 359 | { | ||
| 360 | if (verbose) | ||
| 361 | std::cout << "Reading " << Grid::dimension << "d grid from vtk file " << fileName_ << "." << std::endl; | ||
| 362 | readGrid_(factory, verbose); | ||
| 363 | } | ||
| 364 | |||
| 365 | return std::unique_ptr<Grid>(factory.createGrid()); | ||
| 366 | } | ||
| 367 | |||
| 368 | /*! | ||
| 369 | * \brief Read a grid from a vtk/vtu/vtp file, ignoring cell and point data | ||
| 370 | * \note use this signature if the factory might be needed outside to interpret the data via the factory's insertion indices | ||
| 371 | * \param verbose if the output should be verbose | ||
| 372 | * \param factory the (empty) grid factory | ||
| 373 | */ | ||
| 374 | template<class Grid> | ||
| 375 | std::unique_ptr<Grid> readGrid(Dune::GridFactory<Grid>& factory, bool verbose = false) const | ||
| 376 | { | ||
| 377 | static_assert(!Dune::Capabilities::isCartesian<Grid>::v, "Grid reader only supports unstructured grid implementations"); | ||
| 378 | |||
| 379 | if (Dune::MPIHelper::instance().rank() == 0) | ||
| 380 | { | ||
| 381 | if (verbose) | ||
| 382 | std::cout << "Reading " << Grid::dimension << "d grid from vtk file " << fileName_ << "." << std::endl; | ||
| 383 | readGrid_(factory, verbose); | ||
| 384 | } | ||
| 385 | |||
| 386 | return std::unique_ptr<Grid>(factory.createGrid()); | ||
| 387 | } | ||
| 388 | |||
| 389 | /*! | ||
| 390 | * \brief Read a grid from a vtk/vtu/vtp file, reading all cell and point data | ||
| 391 | * \note the factory will be needed outside to interpret the data via the factory's insertion indices | ||
| 392 | * \param factory the (empty) grid factory | ||
| 393 | * \param cellData the cell data arrays to be filled | ||
| 394 | * \param pointData the point data arrays to be filled | ||
| 395 | * \param verbose if the output should be verbose | ||
| 396 | */ | ||
| 397 | template<class Grid> | ||
| 398 | 13 | std::unique_ptr<Grid> readGrid(Dune::GridFactory<Grid>& factory, Data& cellData, Data& pointData, bool verbose = false) const | |
| 399 | { | ||
| 400 | static_assert(!Dune::Capabilities::isCartesian<Grid>::v, "Grid reader only supports unstructured grid implementations"); | ||
| 401 | |||
| 402 |
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13 | if (Dune::MPIHelper::instance().rank() == 0) |
| 403 | { | ||
| 404 |
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11 | if (verbose) |
| 405 | 11 | std::cout << "Reading " << Grid::dimension << "d grid from vtk file " << fileName_ << "." << std::endl; | |
| 406 | 11 | readGrid_(factory, verbose); | |
| 407 | 11 | readGridData_(cellData, pointData, verbose); | |
| 408 | } | ||
| 409 | |||
| 410 | 13 | return std::unique_ptr<Grid>(factory.createGrid()); | |
| 411 | } | ||
| 412 | |||
| 413 | private: | ||
| 414 | /*! | ||
| 415 | * \brief Read a grid from a vtk/vtu/vtp file | ||
| 416 | * \param factory the (empty) grid factory | ||
| 417 | * \param verbose if the output should be verbose | ||
| 418 | */ | ||
| 419 | template<class Grid> | ||
| 420 | 11 | void readGrid_(Dune::GridFactory<Grid>& factory, bool verbose = false) const | |
| 421 | { | ||
| 422 | using namespace tinyxml2; | ||
| 423 | |||
| 424 | 11 | const XMLElement* pieceNode = getPieceNode_(); | |
| 425 | 22 | const XMLElement* pointsNode = pieceNode->FirstChildElement("Points")->FirstChildElement("DataArray"); | |
| 426 |
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11 | if (pointsNode == nullptr) |
| 427 | ✗ | DUNE_THROW(Dune::IOError, "Couldn't get data array of points in " << fileName_ << "."); | |
| 428 | |||
| 429 | using Point3D = Dune::FieldVector<double, 3>; | ||
| 430 |
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11 | std::vector<Point3D> points3D; |
| 431 |
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22 | std::stringstream dataStream(pointsNode->GetText()); |
| 432 |
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11 | std::istream_iterator<Point3D> it(dataStream); |
| 433 |
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11 | std::copy(it, std::istream_iterator<Point3D>(), std::back_inserter(points3D)); |
| 434 | |||
| 435 | // adapt point dimensions if grid dimension is smaller than 3 | ||
| 436 |
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11 | auto points = adaptPointDimension_<Grid::dimensionworld>(std::move(points3D)); |
| 437 | |||
| 438 |
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17 | if (verbose) std::cout << "Found " << points.size() << " vertices." << std::endl; |
| 439 | |||
| 440 | // insert vertices to the grid factory | ||
| 441 |
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18400 | for (auto&& point : points) |
| 442 |
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18389 | factory.insertVertex(std::move(point)); |
| 443 | |||
| 444 | 11 | const XMLElement* cellsNode = pieceNode->FirstChildElement("Cells"); | |
| 445 | 11 | const XMLElement* linesNode = pieceNode->FirstChildElement("Lines"); | |
| 446 |
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11 | if (cellsNode) |
| 447 | { | ||
| 448 |
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8 | const XMLElement* connectivityNode = findDataArray_(cellsNode, "connectivity"); |
| 449 |
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8 | const XMLElement* offsetsNode = findDataArray_(cellsNode, "offsets"); |
| 450 |
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8 | const XMLElement* typesNode = findDataArray_(cellsNode, "types"); |
| 451 | |||
| 452 |
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8 | const auto connectivity = parseDataArray_<std::vector<unsigned int>>(connectivityNode); |
| 453 |
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8 | const auto offsets = parseDataArray_<std::vector<unsigned int>>(offsetsNode); |
| 454 |
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8 | const auto types = parseDataArray_<std::vector<unsigned int>>(typesNode); |
| 455 | |||
| 456 |
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16 | if (verbose) std::cout << "Found " << offsets.size() << " elements." << std::endl; |
| 457 | |||
| 458 | unsigned int lastOffset = 0; | ||
| 459 |
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18835 | for (unsigned int i = 0; i < offsets.size(); ++i) |
| 460 | { | ||
| 461 |
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18827 | const auto geomType = vtkToDuneGeomType_(types[i]); |
| 462 |
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18827 | unsigned int offset = offsets[i]; |
| 463 |
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18827 | std::vector<unsigned int> corners; corners.resize(offset-lastOffset); |
| 464 |
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96288 | for (unsigned int j = 0; j < offset-lastOffset; ++j) |
| 465 | 77461 | corners[Dune::VTK::renumber(geomType, j)] = connectivity[lastOffset+j]; | |
| 466 |
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18827 | factory.insertElement(geomType, std::move(corners)); |
| 467 |
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18827 | lastOffset = offset; |
| 468 | } | ||
| 469 | 13 | } | |
| 470 | // for poly data | ||
| 471 |
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3 | else if (linesNode) |
| 472 | { | ||
| 473 | // sanity check | ||
| 474 | if (Grid::dimension != 1) | ||
| 475 |
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3 | DUNE_THROW(Dune::IOError, "Grid expects dimension " << Grid::dimension |
| 476 | << " but " << fileName_ << " contains a 1D grid."); | ||
| 477 | |||
| 478 |
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3 | const XMLElement* connectivityNode = findDataArray_(linesNode, "connectivity"); |
| 479 |
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3 | const XMLElement* offsetsNode = findDataArray_(linesNode, "offsets"); |
| 480 | |||
| 481 |
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3 | const auto connectivity = parseDataArray_<std::vector<unsigned int>>(connectivityNode); |
| 482 |
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3 | const auto offsets = parseDataArray_<std::vector<unsigned int>>(offsetsNode); |
| 483 | |||
| 484 |
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6 | if (verbose) std::cout << "Found " << offsets.size() << " polylines." << std::endl; |
| 485 | |||
| 486 | unsigned int lastOffset = 0; | ||
| 487 |
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3482 | for (unsigned int i = 0; i < offsets.size(); ++i) |
| 488 | { | ||
| 489 | // a polyline can have many points in the VTK format | ||
| 490 | // split the line in segments with two points | ||
| 491 | 3479 | unsigned int offset = offsets[i]; | |
| 492 |
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6975 | for (unsigned int j = 0; j < offset-lastOffset-1; ++j) |
| 493 |
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3496 | factory.insertElement(Dune::GeometryTypes::line, |
| 494 |
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6992 | std::vector<unsigned int>({ connectivity[lastOffset+j], connectivity[lastOffset+j+1] })); |
| 495 | 3479 | lastOffset = offset; | |
| 496 | } | ||
| 497 | 4 | } | |
| 498 | else | ||
| 499 |
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|
7 | DUNE_THROW(Dune::IOError, "No Cells or Lines element found in " << fileName_); |
| 500 | 27 | } | |
| 501 | |||
| 502 | /*! | ||
| 503 | * \brief Read a grid data from a vtk/vtu/vtp file | ||
| 504 | * \param cellData the cell data arrays to be filled | ||
| 505 | * \param pointData the point data arrays to be filled | ||
| 506 | * \param verbose if the output should be verbose | ||
| 507 | */ | ||
| 508 | 11 | void readGridData_(Data& cellData, Data& pointData, bool verbose = false) const | |
| 509 | { | ||
| 510 | 11 | using namespace tinyxml2; | |
| 511 | |||
| 512 | 22 | const XMLElement* pieceNode = getPieceNode_(); | |
| 513 | 11 | const XMLElement* cellDataNode = getDataNode_(pieceNode, DataType::cellData); | |
| 514 |
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11 | if (cellDataNode != nullptr) |
| 515 | { | ||
| 516 | 11 | const XMLElement* cellsNode = pieceNode->FirstChildElement("Cells"); | |
| 517 | 11 | const XMLElement* linesNode = pieceNode->FirstChildElement("Lines"); | |
| 518 | |||
| 519 |
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11 | if (cellsNode) |
| 520 | { | ||
| 521 | 8 | const XMLElement* dataArray = cellDataNode->FirstChildElement("DataArray"); | |
| 522 |
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54 | for (; dataArray != nullptr; dataArray = dataArray->NextSiblingElement("DataArray")) |
| 523 | { | ||
| 524 | 23 | const char *attributeText = dataArray->Attribute("Name"); | |
| 525 | |||
| 526 |
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23 | if (attributeText == nullptr) |
| 527 | ✗ | DUNE_THROW(Dune::IOError, "Couldn't get Name attribute of a cell data array."); | |
| 528 | |||
| 529 |
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46 | cellData[std::string(attributeText)] = parseDataArray_<std::vector<double>>(dataArray); |
| 530 | |||
| 531 |
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23 | if (verbose) |
| 532 | 23 | std::cout << "Read cell data field " << attributeText << std::endl; | |
| 533 | } | ||
| 534 | } | ||
| 535 | // for poly data | ||
| 536 |
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3 | else if (linesNode) |
| 537 | { | ||
| 538 | // first parse all the cell data (each cell in this sense can be a polyline) | ||
| 539 | 3 | const XMLElement* dataArray = cellDataNode->FirstChildElement("DataArray"); | |
| 540 |
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3 | if (dataArray) |
| 541 | { | ||
| 542 | 3 | Data polyLineCellData; | |
| 543 |
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13 | for (; dataArray != nullptr; dataArray = dataArray->NextSiblingElement("DataArray")) |
| 544 | { | ||
| 545 | 7 | const char *attributeText = dataArray->Attribute("Name"); | |
| 546 | |||
| 547 |
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7 | if (attributeText == nullptr) |
| 548 | ✗ | DUNE_THROW(Dune::IOError, "Couldn't get Name attribute of a cell data array."); | |
| 549 | |||
| 550 |
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14 | polyLineCellData[std::string(attributeText)] = parseDataArray_<std::vector<double>>(dataArray); |
| 551 | |||
| 552 |
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7 | if (verbose) |
| 553 |
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7 | std::cout << "Read cell data field " << attributeText << std::endl; |
| 554 | } | ||
| 555 | |||
| 556 | // a polyline can have many points in the VTK format | ||
| 557 | // we split the line in segments with two points | ||
| 558 | // so we also need to duplicate the cell data to fit the increased line number | ||
| 559 |
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3 | const XMLElement* offsetsNode = findDataArray_(linesNode, "offsets"); |
| 560 |
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3 | const auto offsets = parseDataArray_<std::vector<unsigned int>>(offsetsNode); |
| 561 | |||
| 562 |
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3 | if (offsets.size() != polyLineCellData.begin()->second.size()) |
| 563 | ✗ | DUNE_THROW(Dune::IOError, "Expected the same number of cell data entries (is " | |
| 564 | << polyLineCellData.begin()->second.size() | ||
| 565 | << ") as polylines (" << offsets.size() << ")!"); | ||
| 566 | |||
| 567 | // count the number of Dune cells to be able to resize the data vectors | ||
| 568 | unsigned int lastOffset = 0; | ||
| 569 | std::size_t numCells = 0; | ||
| 570 |
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3482 | for (unsigned int i = 0; i < offsets.size(); ++i) |
| 571 | { | ||
| 572 | 3479 | unsigned int offset = offsets[i]; | |
| 573 |
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6975 | for (unsigned int j = 0; j < offset-lastOffset-1; ++j) |
| 574 | 3496 | ++numCells; | |
| 575 | 3479 | lastOffset = offset; | |
| 576 | } | ||
| 577 | |||
| 578 | // create the data arrays | ||
| 579 |
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10 | for (const auto& dArray : polyLineCellData) |
| 580 | { | ||
| 581 |
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7 | cellData[dArray.first] = std::vector<double>(numCells); |
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7 | auto& cd = cellData[dArray.first]; |
| 583 | const auto& pd = dArray.second; | ||
| 584 | |||
| 585 | lastOffset = 0; | ||
| 586 | std::size_t cellIdx = 0; | ||
| 587 |
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8703 | for (unsigned int i = 0; i < offsets.size(); ++i) |
| 588 | { | ||
| 589 | 8696 | unsigned int offset = offsets[i]; | |
| 590 |
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17426 | for (unsigned int j = 0; j < offset-lastOffset-1; ++j) |
| 591 | 8730 | cd[cellIdx++] = pd[i]; | |
| 592 | 8696 | lastOffset = offset; | |
| 593 | } | ||
| 594 | } | ||
| 595 | 3 | } | |
| 596 | } | ||
| 597 | else | ||
| 598 | ✗ | DUNE_THROW(Dune::IOError, "No Cells or Lines element found in " << fileName_); | |
| 599 | } | ||
| 600 | |||
| 601 | 11 | const XMLElement* pointDataNode = getDataNode_(pieceNode, DataType::pointData); | |
| 602 |
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11 | if (pointDataNode != nullptr) |
| 603 | { | ||
| 604 | 7 | const XMLElement* dataArray = pointDataNode->FirstChildElement("DataArray"); | |
| 605 |
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39 | for (; dataArray != nullptr; dataArray = dataArray->NextSiblingElement("DataArray")) |
| 606 | { | ||
| 607 | 16 | const char *attributeText = dataArray->Attribute("Name"); | |
| 608 | |||
| 609 |
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16 | if (attributeText == nullptr) |
| 610 | ✗ | DUNE_THROW(Dune::IOError, "Couldn't get Name attribute of a point data array."); | |
| 611 | |||
| 612 |
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32 | pointData[std::string(attributeText)] = parseDataArray_<std::vector<double>>(dataArray); |
| 613 | |||
| 614 |
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16 | if (verbose) |
| 615 | 16 | std::cout << "Read point data field " << attributeText << std::endl; | |
| 616 | } | ||
| 617 | } | ||
| 618 | 11 | } | |
| 619 | |||
| 620 | /*! | ||
| 621 | * \brief Get the piece node of the XMLDocument | ||
| 622 | * \note Returns nullptr if the piece node wasn't found | ||
| 623 | */ | ||
| 624 | 489 | const tinyxml2::XMLElement* getPieceNode_() const | |
| 625 |
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489 | { return Detail::VTKReader::getPieceNode(doc_, fileName_); } |
| 626 | |||
| 627 | /*! | ||
| 628 | * \brief Get the piece node of the XMLDocument | ||
| 629 | * \param pieceNode the pieceNode of the vtk file | ||
| 630 | * \param type the vtk data type (cell data or point data) | ||
| 631 | * \note Returns nullptr if the data node wasn't found | ||
| 632 | */ | ||
| 633 | 420 | const tinyxml2::XMLElement* getDataNode_(const tinyxml2::XMLElement* pieceNode, const DataType& type) const | |
| 634 | { | ||
| 635 | 420 | using namespace tinyxml2; | |
| 636 | |||
| 637 | 420 | const XMLElement* dataNode = nullptr; | |
| 638 |
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420 | if (type == DataType::pointData) |
| 639 | 132 | dataNode = pieceNode->FirstChildElement("PointData"); | |
| 640 |
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288 | else if (type == DataType::cellData) |
| 641 | 288 | dataNode = pieceNode->FirstChildElement("CellData"); | |
| 642 | else | ||
| 643 | ✗ | DUNE_THROW(Dune::IOError, "Only cell and point data are supported."); | |
| 644 | |||
| 645 | 420 | return dataNode; | |
| 646 | } | ||
| 647 | |||
| 648 | /*! | ||
| 649 | * \brief Find a data array with a specific name | ||
| 650 | * \param dataNode a cell or point data node | ||
| 651 | * \param name the name of the data array to be found | ||
| 652 | * \note Returns nullptr if the data array wasn't found | ||
| 653 | */ | ||
| 654 | 431 | const tinyxml2::XMLElement* findDataArray_(const tinyxml2::XMLElement* dataNode, const std::string& name) const | |
| 655 | { | ||
| 656 | 431 | using namespace tinyxml2; | |
| 657 | |||
| 658 | // loop over XML node siblings to find the correct data array | ||
| 659 | 431 | const XMLElement* dataArray = dataNode->FirstChildElement("DataArray"); | |
| 660 |
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5183 | for (; dataArray != nullptr; dataArray = dataArray->NextSiblingElement("DataArray")) |
| 661 | { | ||
| 662 | 2805 | const char *attributeText = dataArray->Attribute("Name"); | |
| 663 | |||
| 664 |
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2805 | if (attributeText == nullptr) |
| 665 | ✗ | DUNE_THROW(Dune::IOError, "Couldn't get Name attribute of a data array."); | |
| 666 | |||
| 667 |
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2805 | if (attributeText == name) |
| 668 | break; | ||
| 669 | } | ||
| 670 | |||
| 671 | 431 | return dataArray; | |
| 672 | } | ||
| 673 | |||
| 674 | /*! | ||
| 675 | * \brief Parses the text of a data array into a container | ||
| 676 | * \tparam Container a container type that has begin(), end(), push_back(), e.g. std::vector<double> | ||
| 677 | * \param dataArray the data array node to be parsed | ||
| 678 | */ | ||
| 679 | template<class Container> | ||
| 680 | 297 | Container parseDataArray_(const tinyxml2::XMLElement* dataArray) const | |
| 681 | { | ||
| 682 |
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297 | std::stringstream dataStream(dataArray->GetText()); |
| 683 |
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594 | return readStreamToContainer<Container>(dataStream); |
| 684 | 297 | } | |
| 685 | |||
| 686 | /*! | ||
| 687 | * \brief Return the Dune::GeometryType for a given VTK geometry type | ||
| 688 | * \param vtkCellType the vtk cell type | ||
| 689 | */ | ||
| 690 | 18827 | Dune::GeometryType vtkToDuneGeomType_(unsigned int vtkCellType) const | |
| 691 | { | ||
| 692 |
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18827 | switch (vtkCellType) |
| 693 | { | ||
| 694 | ✗ | case Dune::VTK::GeometryType::vertex: return Dune::GeometryTypes::vertex; | |
| 695 | ✗ | case Dune::VTK::GeometryType::line: return Dune::GeometryTypes::line; | |
| 696 | 10639 | case Dune::VTK::GeometryType::triangle: return Dune::GeometryTypes::triangle; | |
| 697 | 4990 | case Dune::VTK::GeometryType::quadrilateral: return Dune::GeometryTypes::quadrilateral; | |
| 698 | ✗ | case Dune::VTK::GeometryType::tetrahedron: return Dune::GeometryTypes::tetrahedron; | |
| 699 | 3198 | case Dune::VTK::GeometryType::hexahedron: return Dune::GeometryTypes::hexahedron; | |
| 700 | ✗ | case Dune::VTK::GeometryType::prism: return Dune::GeometryTypes::prism; | |
| 701 | ✗ | case Dune::VTK::GeometryType::pyramid: return Dune::GeometryTypes::pyramid; | |
| 702 | ✗ | default: DUNE_THROW(Dune::NotImplemented, "VTK cell type " << vtkCellType); | |
| 703 | } | ||
| 704 | } | ||
| 705 | |||
| 706 | template<int dim, std::enable_if_t<(dim < 3), int> = 0> | ||
| 707 | std::vector<Dune::FieldVector<double, dim>> | ||
| 708 | 6 | adaptPointDimension_(std::vector<Dune::FieldVector<double, 3>>&& points3D) const | |
| 709 | { | ||
| 710 | 6 | std::vector<Dune::FieldVector<double, dim>> points(points3D.size()); | |
| 711 |
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10496 | for (std::size_t i = 0; i < points.size(); ++i) |
| 712 |
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31470 | for (int j = 0; j < dim; ++j) |
| 713 | 20980 | points[i][j] = points3D[i][j]; | |
| 714 | 6 | return points; | |
| 715 | } | ||
| 716 | |||
| 717 | template<int dim, std::enable_if_t<(dim == 3), int> = 0> | ||
| 718 | std::vector<Dune::FieldVector<double, dim>> | ||
| 719 |
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5 | adaptPointDimension_(std::vector<Dune::FieldVector<double, 3>>&& points3D) const |
| 720 |
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5 | { return std::move(points3D); } |
| 721 | |||
| 722 | std::string fileName_; //!< the vtk file name | ||
| 723 | tinyxml2::XMLDocument doc_; //!< the xml document created from file with name fileName_ | ||
| 724 | }; | ||
| 725 | |||
| 726 | } // end namespace Dumux | ||
| 727 | |||
| 728 | #endif // DUMUX_HAVE_GRIDFORMAT | ||
| 729 | |||
| 730 | #endif | ||
| 731 |