Allow specifying attribute name when reading meshtag #3257
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@@ -322,8 +322,9 @@ template void XDMFFile::write_meshtags(const mesh::MeshTags<std::int32_t>&, | |
| /// @endcond | ||
| //----------------------------------------------------------------------------- | ||
| mesh::MeshTags<std::int32_t> | ||
| XDMFFile::read_meshtags_by_label(const mesh::Mesh<double>& mesh, | ||
| std::string name, std::string attribute_label, | ||
| std::string xpath) | ||
| { | ||
| spdlog::info("XDMF read meshtags ({})", name); | ||
| pugi::xml_node node = _xml_doc->select_node(xpath.c_str()).node(); | ||
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@@ -336,8 +337,28 @@ XDMFFile::read_meshtags(const mesh::Mesh<double>& mesh, std::string name, | |
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| const auto [entities, eshape] = read_topology_data(name, xpath); | ||
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| pugi::xml_node attribute_node = grid_node.child("Attribute"); | ||
| pugi::xml_node values_data_node = attribute_node.child("DataItem"); | ||
| if (!attribute_label.empty()) | ||
| { | ||
| bool found = false; | ||
| while (!found and attribute_node) | ||
| { | ||
| pugi::xml_attribute hint; | ||
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There was a problem hiding this comment. It's something that There was a problem hiding this comment. The hint is not set or re-used - does the code compile without it? There was a problem hiding this comment. I don't think it can because |
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| pugi::xml_attribute name = attribute_node.attribute("Name", hint); | ||
| if (std::string(name.value()) == attribute_label) | ||
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There was a problem hiding this comment. Creating the string is a bit clumsy, maybe use https://en.cppreference.com/w/cpp/string/char_traits/compare. There was a problem hiding this comment. Using the function you suggested requires providing a number of characters to compare, so it would have to be something like if (auto len = std::max(std::strlen(name.value()), attribute_label.size());
std::char_traits<char>::compare(name.value(), attribute_label.c_str(),
len) == 0)right? There was a problem hiding this comment. I think |
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| { | ||
| values_data_node = attribute_node.child("DataItem"); | ||
| found = true; | ||
| } | ||
| attribute_node = attribute_node.next_sibling("Attribute"); | ||
| } | ||
| if (!found) | ||
| { | ||
| throw std::runtime_error("Attribute with name '" + attribute_label | ||
| + "' not found."); | ||
| } | ||
| } | ||
| const std::vector values = xdmf_utils::get_dataset<std::int32_t>( | ||
| _comm.comm(), values_data_node, _h5_id); | ||
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@@ -376,6 +397,13 @@ XDMFFile::read_meshtags(const mesh::Mesh<double>& mesh, std::string name, | |
| return meshtags; | ||
| } | ||
| //----------------------------------------------------------------------------- | ||
| mesh::MeshTags<std::int32_t> | ||
| XDMFFile::read_meshtags(const mesh::Mesh<double>& mesh, std::string name, | ||
| std::string xpath) | ||
| { | ||
| return read_meshtags_by_label(mesh, name, std::string(), xpath); | ||
| } | ||
| //----------------------------------------------------------------------------- | ||
| std::pair<mesh::CellType, int> XDMFFile::read_cell_type(std::string grid_name, | ||
| std::string xpath) | ||
| { | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,91 @@ | ||
| // Copyright (C) 2024 Massimiliano Leoni | ||
| // | ||
| // This file is part of DOLFINx (https://www.fenicsproject.org) | ||
| // | ||
| // SPDX-License-Identifier: LGPL-3.0-or-later | ||
| // | ||
| // Unit tests for reading meshtags by name | ||
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| #include <catch2/catch_template_test_macros.hpp> | ||
| #include <catch2/catch_test_macros.hpp> | ||
| #include <dolfinx/common/IndexMap.h> | ||
| #include <dolfinx/common/MPI.h> | ||
| #include <dolfinx/io/XDMFFile.h> | ||
| #include <dolfinx/la/Vector.h> | ||
| #include <dolfinx/mesh/MeshTags.h> | ||
| #include <dolfinx/mesh/generation.h> | ||
| #include <dolfinx/mesh/utils.h> | ||
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| #include <numeric> | ||
| #include <string> | ||
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| using namespace dolfinx; | ||
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| namespace | ||
| { | ||
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| void test_read_named_meshtags() | ||
| { | ||
| const std::string mesh_file = "Domain.xdmf"; | ||
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| constexpr std::int32_t domain_value = 1; | ||
| constexpr std::int32_t material_value = 2; | ||
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| // Create mesh | ||
| auto part = mesh::create_cell_partitioner(mesh::GhostMode::none); | ||
| auto mesh = std::make_shared<mesh::Mesh<double>>( | ||
| mesh::create_rectangle(MPI_COMM_WORLD, {{{0.0, 0.0}, {1.0, 1.0}}}, {3, 3}, | ||
| mesh::CellType::triangle, part)); | ||
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| const std::int32_t n_cells = mesh->topology()->index_map(2)->size_local(); | ||
| std::vector<std::int32_t> indices(n_cells); | ||
| std::iota(std::begin(indices), std::end(indices), 0); | ||
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| std::vector<std::int32_t> domain_values(n_cells); | ||
| std::ranges::fill(domain_values, domain_value); | ||
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| std::vector<std::int32_t> material_values(n_cells); | ||
| std::ranges::fill(material_values, material_value); | ||
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| mesh::MeshTags<std::int32_t> mt_domains(mesh->topology(), 2, indices, | ||
| domain_values); | ||
| mt_domains.name = "domain"; | ||
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| mesh::MeshTags<std::int32_t> mt_materials(mesh->topology(), 2, indices, | ||
| material_values); | ||
| mt_materials.name = "material"; | ||
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| io::XDMFFile file(mesh->comm(), mesh_file, "w", io::XDMFFile::Encoding::HDF5); | ||
| file.write_mesh(*mesh); | ||
| file.write_meshtags(mt_domains, mesh->geometry(), | ||
| "/Xdmf/Domain/mesh/Geometry"); | ||
| file.write_meshtags(mt_materials, mesh->geometry(), | ||
| "/Xdmf/Domain/Grid/Geometry"); | ||
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| file.close(); | ||
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| io::XDMFFile meshFile(MPI_COMM_WORLD, mesh_file, "r", | ||
| io::XDMFFile::Encoding::HDF5); | ||
| mesh = std::make_shared<mesh::Mesh<double>>(meshFile.read_mesh( | ||
| fem::CoordinateElement<double>(mesh::CellType::triangle, 1), | ||
| mesh::GhostMode::none, "mesh")); | ||
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| const auto mt_domain = meshFile.read_meshtags_by_label( | ||
| *mesh, "domain", "domain", "/Xdmf/Domain"); | ||
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| CHECK(mt_domain.values().front() == domain_value); | ||
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| const auto mt_material = meshFile.read_meshtags_by_label( | ||
| *mesh, "material", "material", "/Xdmf/Domain"); | ||
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| CHECK(mt_material.values().front() == material_value); | ||
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| CHECK_THROWS(meshFile.read_meshtags_by_label(*mesh, "mesh", "missing")); | ||
| } | ||
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| } // namespace | ||
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| TEST_CASE("Read meshtag by name", "[read_meshtag_by_name]") | ||
| { | ||
| CHECK_NOTHROW(test_read_named_meshtags()); | ||
| } |
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Is this just iterating through the attributes? If yes, can it be made simpler using pugixml functionality, see https://pugixml.org/docs/manual.html#access.basic.
The code is hard to follow - at a minimum it needs a comment on what it is doing.
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I remember looking at this. The problem was, if I recall correctly, that I am searching for an attribute by the name of
"Name"and the "basic functionality" functions do not allow to search for a name. If I wanted to loop usingnext_attributeI would then need to check if the attribute's name is"Name"and, if not,continue.I will add documentation but the code doesn't look to exotic to me [because I wrote it, of course XD].