GCC Code Coverage Report

Directory: gridformat/
File: gridformat/vtk/hdf_unstructured_grid_reader.hpp
Date: 2024-11-20 14:41:59
Exec Total Coverage
Lines: 256 271 94.5%
Functions: 84 124 67.7%
Branches: 367 944 38.9%
Line Branch Exec Source
1 // SPDX-FileCopyrightText: 2022-2023 Dennis Gläser <dennis.glaeser@iws.uni-stuttgart.de>
2 // SPDX-License-Identifier: MIT
3 /*!
4 * \file
5 * \ingroup VTK
6 * \brief Reader for the VTK HDF file format for unstructured grids.
7 */
8 #ifndef GRIDFORMAT_VTK_HDF_UNSTRUCTURED_GRID_READER_HPP_
9 #define GRIDFORMAT_VTK_HDF_UNSTRUCTURED_GRID_READER_HPP_
10 #if GRIDFORMAT_HAVE_HIGH_FIVE
11
12 #include <iterator>
13 #include <optional>
14 #include <algorithm>
15 #include <type_traits>
16 #include <concepts>
17 #include <numeric>
18 #include <utility>
19 #include <cassert>
20
21 #include <gridformat/common/field.hpp>
22 #include <gridformat/common/field_transformations.hpp>
23 #include <gridformat/common/concepts.hpp>
24 #include <gridformat/common/exceptions.hpp>
25 #include <gridformat/grid/reader.hpp>
26 #include <gridformat/parallel/concepts.hpp>
27 #include <gridformat/vtk/hdf_common.hpp>
28
29 namespace GridFormat {
30
31 /*!
32 * \ingroup VTK
33 * \brief Reader for the VTK-HDF file format for unstructured grids.
34 */
35 template<Concepts::Communicator Communicator = NullCommunicator>
36 class VTKHDFUnstructuredGridReader : public GridReader {
37 using HDF5File = HDF5::File<Communicator>;
38 static constexpr std::size_t vtk_space_dim = 3;
39 static constexpr bool read_rank_piece_only = !std::is_same_v<Communicator, NullCommunicator>;
40
41 public:
42 2 explicit VTKHDFUnstructuredGridReader() requires(std::is_same_v<Communicator, NullCommunicator>)
43 2 : _comm{}
44 2 {}
45
46 72 explicit VTKHDFUnstructuredGridReader(Communicator comm)
47 72 : _comm{comm}
48 72 {}
49
50 private:
51 1 std::string _name() const override {
52
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 1 if (_is_transient())
53 ✗ return "VTKHDFUnstructuredGridReader (transient)";
54
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 2 return "VTKHDFUnstructuredGridReader";
55 }
56
57 74 void _open(const std::string& filename, typename GridReader::FieldNames& field_names) override {
58
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 74 _close();
59
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 74 _file = HDF5File{filename, _comm, HDF5File::read_only};
60
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 74 const auto type = VTKHDF::get_file_type(_file.value());
61
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 74 if (type != "UnstructuredGrid")
62 ✗ throw ValueError("Incompatible VTK-HDF type: '" + type + "', expected 'UnstructuredGrid'.");
63
64
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 74 VTKHDF::check_version_compatibility(_file.value(), {2, 0});
65
66
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 222 if (_file->exists("VTKHDF/Steps"))
67
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 146 _file->visit_attribute("VTKHDF/Steps/NSteps", [&] (auto&& field) {
68 19 _num_steps.emplace();
69 19 field.export_to(_num_steps.value());
70 19 _step_index.emplace(0);
71 });
72
73
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 74 _compute_piece_offsets();
74 192 const auto copy_names_in = [&] (const std::string& group, auto& storage) {
75
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 132 if (_file->exists(group))
76
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 120 std::ranges::copy(_file->dataset_names_in(group), std::back_inserter(storage));
77 };
78
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 148 copy_names_in("VTKHDF/CellData", field_names.cell_fields);
79
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 148 copy_names_in("VTKHDF/PointData", field_names.point_fields);
80
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 148 copy_names_in("VTKHDF/FieldData", field_names.meta_data_fields);
81 74 }
82
83 74 void _close() override {
84
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 74 _file = {};
85 74 _num_cells = 0;
86 74 _num_points = 0;
87 74 _cell_offset = 0;
88 74 _point_offset = 0;
89 74 _num_steps = {};
90 74 _step_index = {};
91 74 }
92
93 302 void _compute_piece_offsets() {
94 302 _cell_offset = 0;
95 302 _point_offset = 0;
96
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 302 _check_communicator_size();
97
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 604 const auto num_step_cells = _number_of_all_piece_entities("Cells");
98
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 302 const auto num_step_points = _number_of_all_piece_entities("Points");
99 if constexpr (read_rank_piece_only) {
100
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 232 const auto my_rank = Parallel::rank(_comm);
101
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 232 _num_cells = num_step_cells.at(my_rank);
102
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 232 _num_points = num_step_points.at(my_rank);
103 232 _cell_offset += _accumulate_until(my_rank, num_step_cells);
104 232 _point_offset += _accumulate_until(my_rank, num_step_points);
105 } else {
106 70 _num_cells = _accumulate_until(num_step_cells.size(), num_step_cells);
107 70 _num_points = _accumulate_until(num_step_points.size(), num_step_points);
108 }
109 302 }
110
111 1661 std::size_t _get_part_offset() const {
112 1661 return _is_transient()
113
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 7618 ? _access_file().template read_dataset_to<std::size_t>(
114 "/VTKHDF/Steps/PartOffsets",
115 HDF5::Slice{
116
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 1432 .offset = {_step_index.value()},
117 .count = {1}
118 })
119
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 7389 }
121
122 926 std::size_t _get_step_cells_offset() const {
123 926 return _is_transient()
124
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 5052 ? _access_file().template read_dataset_to<std::size_t>(
125 "VTKHDF/Steps/CellOffsets",
126 HDF5::Slice{
127
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 800 .offset = {_step_index.value(), 0},
128 .count = {1, 1}
129 })
130
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 3326 }
132
133 227 std::size_t _get_step_points_offset() const {
134 227 return _is_transient()
135
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 1024 ? _access_file().template read_dataset_to<std::size_t>(
136 "VTKHDF/Steps/PointOffsets",
137 HDF5::Slice{
138
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 190 .offset = {_step_index.value()},
139 .count = {1}
140 })
141
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 454 : std::size_t{0};
142
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 987 }
143
144 463 std::size_t _get_connectivity_id_offset() const {
145 463 return _is_transient()
146
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 2526 ? _access_file().template read_dataset_to<std::size_t>(
147 "VTKHDF/Steps/ConnectivityIdOffsets",
148 HDF5::Slice{
149
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 400 .offset = {_step_index.value(), 0},
150 .count = {1, 1}
151 })
152
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 1663 }
154
155 1152 std::size_t _get_cell_data_offset(std::string_view name) const {
156 1152 return _is_transient()
157
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158
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 3072 "VTKHDF/Steps/CellDataOffsets/" + std::string{name},
159 HDF5::Slice{
160
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 960 .offset = {_step_index.value()},
161 .count = {1}
162 })
163
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 4992 }
165
166 1162 std::size_t _get_point_data_offset(std::string_view name) const {
167 1162 return _is_transient()
168
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 4244 ? _access_file().template read_dataset_to<std::size_t>(
169
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 3082 "VTKHDF/Steps/PointDataOffsets/" + std::string{name},
170 HDF5::Slice{
171
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 960 .offset = {_step_index.value()},
172 .count = {1}
173 })
174
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 5002 }
176
177 150 std::size_t _get_field_data_offset(std::string_view name) const {
178 150 return _is_transient()
179
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 600 ? _access_file().template read_dataset_to<std::size_t>(
180
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 450 "VTKHDF/Steps/FieldDataOffsets/" + std::string{name},
181 HDF5::Slice{
182
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 150 .offset = {_step_index.value()},
183 .count = {1}
184 })
185
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 300 : std::size_t{0};
186
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 750 }
187
188 45 bool _is_sequence() const override {
189 45 return _is_transient();
190 }
191
192 542 std::size_t _number_of_steps() const override {
193
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 542 if (!_num_steps)
194 ✗ throw ValueError("No step information available");
195 542 return _num_steps.value();
196 }
197
198 160 double _time_at_step(std::size_t step_idx) const override {
199
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 160 if (step_idx >= _number_of_steps())
200 ✗ throw ValueError("Only " + as_string(_number_of_steps()) + " available");
201
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 640 return _access_file().template read_dataset_to<double>("/VTKHDF/Steps/Values", HDF5::Slice{
202 .offset = {step_idx},
203 .count = {1}
204 320 });
205
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 640 }
206
207 260 void _set_step(std::size_t step_idx, typename GridReader::FieldNames&) override {
208
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 260 if (step_idx >= _number_of_steps())
209 ✗ throw ValueError("Only " + as_string(_number_of_steps()) + " available");
210
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 260 if (step_idx != _step_index.value()) {
211 228 _compute_piece_offsets();
212 228 _step_index = step_idx;
213 }
214 260 }
215
216 367 std::size_t _number_of_cells() const override {
217 367 return _num_cells;
218 }
219
220 721 std::size_t _number_of_points() const override {
221 721 return _num_points;
222 }
223
224 28 std::size_t _number_of_pieces() const override {
225 28 return _number_of_current_pieces_in_file();
226 }
227
228 2028 std::size_t _number_of_current_pieces_in_file() const {
229
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 2028 if (_is_transient())
230 1734 return _number_of_pieces_in_file_at_step(_step_index.value());
231 294 return _total_number_of_pieces();
232 }
233
234 294 std::size_t _total_number_of_pieces() const {
235
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 588 auto ncells = _access_file().get_dimensions("/VTKHDF/NumberOfCells");
236
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 294 if (!ncells) throw IOError("Missing dataset at '/VTKHDF/NumberOfCells'");
237
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 294 if (ncells->size() != 1) throw IOError("Unexpected dimension of '/VTKHDF/NumberOfCells'");
238
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 588 return ncells->at(0);
239 294 }
240
241 2554 std::size_t _number_of_pieces_in_file_at_step(std::size_t step) const {
242
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 2554 if (!_is_transient())
243 ✗ throw InvalidState("Step data only available in transient files");
244
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 7662 if (const auto& file = _access_file(); file.exists("/VTKHDF/Steps/NumberOfParts"))
245
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 7662 return file.template read_dataset_to<std::vector<std::size_t>>("/VTKHDF/Steps/NumberOfParts").at(step);
246
247 // all steps have the same number of parts
248 ✗ if (_total_number_of_pieces()%_num_steps.value() != 0)
249 ✗ throw IOError(
250 "Cannot deduce the number of pieces. "
251 "The dataset '/VTKHDF/Steps/NumberOfParts' is not available, "
252 "but the total number of pieces is not divisble by the number of steps"
253 );
254 ✗ return _total_number_of_pieces()/_num_steps.value();
255 }
256
257 302 void _check_communicator_size() const {
258 if constexpr (!std::is_same_v<Communicator, NullCommunicator>)
259
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 232 if (_number_of_current_pieces_in_file() != static_cast<std::size_t>(Parallel::size(_comm)))
260 ✗ throw SizeError(
261 "Can only read the file in parallel if the size of the communicator matches the size "
262 "of that used when writing the file. Please read in the file sequentially on one process "
263 "and distribute the grid yourself, or restart the parallel run with "
264 ✗ + std::to_string(_number_of_current_pieces_in_file()) + " processes."
265 );
266 302 }
267
268 439 void _visit_cells(const typename GridReader::CellVisitor& visitor) const override {
269 if constexpr (read_rank_piece_only)
270 332 _visit_cells_for_rank(Parallel::rank(_comm), 0, visitor);
271 else
272
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 107 std::ranges::for_each(
273
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 107 std::views::iota(std::size_t{0}, _number_of_current_pieces_in_file()),
274 107 [&] (int rank) mutable {
275
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 321 const auto [_, base_offset] = _number_of_entities_and_offset_at_rank(rank, "Points");
276
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 107 _visit_cells_for_rank(rank, base_offset, visitor);
277 }
278 );
279 439 }
280
281 463 void _visit_cells_for_rank(int piece_rank,
282 std::size_t point_base_offset,
283 const typename GridReader::CellVisitor& visitor) const {
284
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 463 const auto& file = _access_file();
285
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 926 const auto [my_num_cells, my_cell_offset] = _number_of_entities_and_offset_at_rank(piece_rank, "Cells");
286
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 926 const auto num_connectivity_ids = file.template read_dataset_to<std::vector<std::size_t>>(
287 "VTKHDF/NumberOfConnectivityIds",
288 HDF5::Slice{
289
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 463 .offset = {_get_part_offset()},
290 926 .count = {_number_of_current_pieces_in_file()}
291 }
292 );
293 926 const auto my_num_connectivity_ids = num_connectivity_ids.at(piece_rank);
294 463 const auto my_id_offset = std::accumulate(
295 num_connectivity_ids.begin(),
296 463 num_connectivity_ids.begin() + piece_rank,
297 std::size_t{0}
298 );
299
300
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 926 auto offsets = file.template read_dataset_to<std::vector<std::size_t>>("VTKHDF/Offsets", {{
301 // offsets have length num_cells+1, so we need to add +1 per rank to the cell offsets
302 .offset = {
303
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 463 _get_step_cells_offset() + _accumulate_over_pieces_until_step(_step_index.value_or(0), 1) // offset from step
304 463 + my_cell_offset + piece_rank // offset from this piece in the pieces of the current step
305 },
306 463 .count = {my_num_cells + 1}
307 }});
308
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 926 auto types = file.template read_dataset_to<std::vector<std::uint_least8_t>>(
309 "VTKHDF/Types",
310 926 {{.offset = {_get_step_cells_offset() + my_cell_offset}, .count = {my_num_cells}}}
311 );
312
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 926 auto connectivity = file.template read_dataset_to<std::vector<std::size_t>>(
313 "VTKHDF/Connectivity",
314 926 {{.offset = {_get_connectivity_id_offset() + my_id_offset}, .count = {my_num_connectivity_ids}}}
315 );
316
317 463 std::vector<std::size_t> corners;
318
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 6299 for (std::size_t i = 0; i < types.size(); ++i) {
319
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 5836 assert(i < offsets.size() - 1);
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 5836 assert(offsets.at(i+1) > offsets.at(i));
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 5836 const auto p0_offset = offsets.at(i);
322
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 5836 const auto num_corners = offsets.at(i+1) - p0_offset;
323
324
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 5836 corners.resize(num_corners);
325
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 29180 for (std::size_t c = 0; c < num_corners; ++c)
326
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 23344 corners[c] = connectivity.at(p0_offset + c) + point_base_offset;
327
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 5836 visitor(VTK::cell_type(types.at(i)), corners);
328 }
329
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 6945 }
330
331 227 FieldPtr _points() const override {
332
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 227 const std::string path = "VTKHDF/Points";
333
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 681 return make_field_ptr(VTKHDF::DataSetField{
334 _file.value(),
335
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 227 MDLayout{{_num_points, vtk_space_dim}},
336
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 227 _file.value().get_precision(path).value(),
337
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 454 _serialization_callback(path, HDF5::Slice{
338
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 227 .offset = {_point_offset + _get_step_points_offset(), 0},
339 227 .count = {_num_points, vtk_space_dim}
340 })
341
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 454 });
342
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 908 }
343
344 1152 FieldPtr _cell_field(std::string_view name) const override {
345
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 1152 const std::string path = "VTKHDF/CellData/" + std::string{name};
346
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 1152 const auto slice = _get_slice(path, _num_cells, _cell_offset + _get_cell_data_offset(name));
347
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 3456 return make_field_ptr(VTKHDF::DataSetField{
348 _file.value(),
349 MDLayout{slice.count},
350
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 1152 _file.value().get_precision(path).value(),
351
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 2304 _serialization_callback(path, slice)
352
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 2304 });
353 1152 }
354
355 1162 FieldPtr _point_field(std::string_view name) const override {
356
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 1162 const std::string path = "VTKHDF/PointData/" + std::string{name};
357
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 1162 const auto slice = _get_slice(path, _num_points, _point_offset + _get_point_data_offset(name));
358
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 3486 return make_field_ptr(VTKHDF::DataSetField{
359 _file.value(),
360 MDLayout{slice.count},
361
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 1162 _file.value().get_precision(path).value(),
362
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 2324 _serialization_callback(path, slice)
363
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 2324 });
364 1162 }
365
366 180 FieldPtr _meta_data_field(std::string_view name) const override {
367
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 180 const auto path = "VTKHDF/FieldData/" + std::string{name};
368
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 180 const auto dims = _file.value().get_dimensions(path).value();
369
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 180 if (dims.size() == 1)
370
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 30 return make_field_ptr(VTKHDF::DataSetField{_file.value(), path});
371
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 150 if (dims.size() != 2)
372 ✗ throw SizeError("Unexpected field data array size");
373
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 150 auto offset = dims;
374
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 150 auto count = offset;
375
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 150 count.at(0) = 1;
376
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 150 std::ranges::fill(offset, 0);
377
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 150 offset.at(0) = _get_field_data_offset(name);
378
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 450 return make_field_ptr(VTKHDF::DataSetField{
379 _file.value(),
380
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 150 MDLayout{count | std::views::drop(1)},
381
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 150 _file.value().get_precision(path).value(),
382
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 318 [p=path, o=offset, c=count] (const HDF5File& f) {
383 60 return f.visit_dataset(p, [&] <typename F> (F&& field) {
384
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 18 return FlattenedField{make_field_ptr(std::move(field))}.serialized();
385
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 54 }, HDF5::Slice{.offset = o, .count = c});
386 }
387
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 150 });
388 180 }
389
390 template<Concepts::Scalar T>
391 T _read_rank_scalar(const std::string& path, const std::size_t base_offset = 0) const {
392 T result;
393 _file.value().visit_dataset(
394 path,
395 [&] (auto&& field) { field.export_to(result); },
396 HDF5::Slice{
397 .offset = {base_offset + static_cast<std::size_t>(Parallel::rank(_comm))},
398 .count = {1}
399 }
400 );
401 return result;
402 }
403
404 2314 HDF5::Slice _get_slice(const std::string& path,
405 std::size_t count,
406 std::size_t offset) const {
407
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 2314 auto ds_size = _file.value().get_dimensions(path).value();
408
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 2314 auto ds_offset = ds_size;
409
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 2314 std::ranges::fill(ds_offset, std::size_t{0});
410
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 2314 ds_size.at(0) = count;
411
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 2314 ds_offset.at(0) = offset;
412 2314 return {.offset = ds_offset, .count = ds_size};
413
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 2314 }
414
415 2541 auto _serialization_callback(std::string path, std::optional<HDF5::Slice> slice = {}) const {
416 3477 return [_p=std::move(path), _s=std::move(slice)] (const HDF5File& file) {
417
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418
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 3159 return file.visit_dataset(_p, [&] <typename F> (F&& f) { return f.serialized(); }, _s.value());
419 ✗ return file.visit_dataset(_p, [&] <typename F> (F&& f) { return f.serialized(); });
420 2541 };
421 }
422
423 10691 bool _is_transient() const {
424 10691 return static_cast<bool>(_num_steps);
425 }
426
427 9561 const HDF5File& _access_file() const {
428
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 9561 if (!_file.has_value())
429 ✗ throw InvalidState("No file has been read");
430 9561 return _file.value();
431 }
432
433 1198 std::vector<std::size_t> _number_of_all_piece_entities(const std::string& entity_type) const {
434
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 3594 return _access_file().template read_dataset_to<std::vector<std::size_t>>("/VTKHDF/NumberOf" + entity_type, {{
435
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 1198 .offset = {_get_part_offset()},
436 2396 .count = {_number_of_current_pieces_in_file()}
437
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 2396 }});
438
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 4792 }
439
440 template<std::integral T>
441 594 std::array<std::size_t, 2> _number_of_entities_and_offset_at_rank(T rank, const std::string& entity_type) const {
442
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 594 const auto entities = _number_of_all_piece_entities(entity_type);
443
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 1188 return std::array{entities.at(rank), _accumulate_until(rank, entities)};
444 594 }
445
446 template<typename T>
447 1480 T _accumulate_until(std::integral auto rank, const std::vector<T>& values) const {
448 1480 return std::accumulate(values.begin(), values.begin() + rank, T{0});
449 }
450
451 273 std::size_t _accumulate_over_pieces_until_step(std::size_t step, std::size_t count_per_piece) const {
452
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 273 if (step == 0)
453 83 return 0;
454
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 190 if (!_is_transient())
455 ✗ throw InvalidState("Step data only available in transient files");
456
457 190 std::size_t result = 0;
458
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 862 std::ranges::for_each(std::views::iota(std::size_t{0}, step), [&] (std::size_t step_idx) {
459 484 const auto num_step_pieces = _number_of_pieces_in_file_at_step(step_idx);
460 484 result += count_per_piece*num_step_pieces;
461 });
462 190 return result;
463 }
464
465 Communicator _comm;
466 std::optional<HDF5File> _file;
467 std::size_t _num_cells = 0;
468 std::size_t _num_points = 0;
469 std::size_t _cell_offset = 0;
470 std::size_t _point_offset = 0;
471 std::optional<std::size_t> _num_steps;
472 std::optional<std::size_t> _step_index;
473 };
474
475 } // namespace GridFormat
476
477 #endif // GRIDFORMAT_HAVE_HIGH_FIVE
478 #endif // GRIDFORMAT_VTK_HDF_UNSTRUCTURED_GRID_READER_HPP_
479