Allow specifying attribute name when reading meshtag #3257

mleoni-pf · 2024-06-06T14:20:40Z

If no attribute_name is provided, read the first attribute. Otherwise, read the attribute with the provided name or throw an error if it couldn't be found.

garth-wells · 2024-06-07T10:43:18Z

python/dolfinx/io/utils.py

        return MeshTags(mt)

+    def read_meshtags(self, mesh, name, xpath="/Xdmf/Domain"):


Needs docs.

garth-wells · 2024-06-07T10:43:56Z

python/dolfinx/io/utils.py

@@ -276,10 +276,13 @@ def read_mesh(
        )
        return Mesh(msh, domain)

-    def read_meshtags(self, mesh, name, attribute_name="", xpath="/Xdmf/Domain"):
-        mt = super().read_meshtags(mesh._cpp_object, name, attribute_name, xpath)
+    def read_meshtags_by_name(self, mesh, name, attribute_name, xpath="/Xdmf/Domain"):


Would it be better as one function and using default arg attribute_name=None?

I remember that you don't like having two default arguments in one function but I'm guessing that's only for C++, right?

Not good for C++, fine with Python if it's simple (which this is) and doesn't introduce complicated conditional handling.

garth-wells · 2024-06-07T10:46:31Z

cpp/dolfinx/io/XDMFFile.cpp

-    const mesh::Mesh<double>& mesh, const std::string name,
-    const std::string attribute_name, const std::string xpath)
+mesh::MeshTags<std::int32_t>
+XDMFFile::read_meshtags_by_name(const mesh::Mesh<double>& mesh,


Let's change name -> label in the function name. 'name' is ambiguous.

garth-wells

The code is XDMFFile.cpp looks to me more complicated than it needs to be. I've left some suggestions as a first pass. I can look again once it's been simplified some more.

garth-wells · 2024-06-08T09:01:12Z

cpp/dolfinx/io/XDMFFile.h

@@ -164,6 +164,16 @@ class XDMFFile
                      const mesh::Geometry<T>& x, std::string geometry_xpath,
                      std::string xpath = "/Xdmf/Domain");

+  /// Read MeshTags by name
+  /// @param[in] mesh The Mesh that the data is defined on
+  /// @param[in] name


What is name? Can you add a doctstring?

Done, but for the record this was already undocumented.

cpp/dolfinx/io/XDMFFile.cpp

garth-wells · 2024-06-08T09:03:43Z

cpp/dolfinx/io/XDMFFile.cpp

+  if (not attribute_label.empty())
+  {
+    bool found = false;
+    for (; attribute_node;


This looks weird and is hard to read. Should it be while loop?

garth-wells · 2024-06-08T09:07:08Z

cpp/dolfinx/io/XDMFFile.cpp

+    {
+      pugi::xml_attribute hint;
+      pugi::xml_attribute name = attribute_node.attribute("Name", hint);
+      if (std::string(name.value()) == attribute_label)


Creating the string is a bit clumsy, maybe use https://en.cppreference.com/w/cpp/string/char_traits/compare.

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?

I think name.value() == attribute_label might work, see https://en.cppreference.com/w/cpp/string/basic_string/operator_cmp.

garth-wells · 2024-06-08T09:07:36Z

cpp/dolfinx/io/XDMFFile.cpp

+    for (; attribute_node;
+         attribute_node = attribute_node.next_sibling("Attribute"))
+    {
+      pugi::xml_attribute hint;


What is this for?

It's something that pugixml requires, like a hint to try to speed-up the search of a node.

The hint is not set or re-used - does the code compile without it?

cpp/dolfinx/io/XDMFFile.cpp

python/dolfinx/wrappers/io.cpp

garth-wells · 2024-07-17T04:07:04Z

cpp/test/mesh/Domain.xdmf

@@ -0,0 +1,26 @@
+<Xdmf Version="3.0">


Can we avoid adding data files? Can it be created by the test rather than added to the repo?

I can convert the file to ascii, add it to the source code and have the code write it to /dev/shm, then read it back. How about that? :)

On second though, that's really just the same thing as adding a file with the ascii content, which is what I do now XD
Please advise!

Ok, never mind... I turned on my brain and found a solution.

…nx into mleoni/readNamedMeshtags

garth-wells · 2024-09-12T08:39:47Z

cpp/dolfinx/io/XDMFFile.h

@@ -164,9 +164,21 @@ class XDMFFile
                      const mesh::Geometry<T>& x, std::string geometry_xpath,
                      std::string xpath = "/Xdmf/Domain");

+  /// Read MeshTags by name


This is a bit confusing - the docstring says "Read MeshTags by name" but the function name is "read_meshtags_by_label". Is it by name or by label?

garth-wells · 2024-09-12T08:46:39Z

cpp/dolfinx/io/XDMFFile.cpp

+    for (; attribute_node;
+         attribute_node = attribute_node.next_sibling("Attribute"))
+    {
+      pugi::xml_attribute hint;


The hint is not set or re-used - does the code compile without it?

garth-wells · 2024-09-12T08:47:30Z

cpp/dolfinx/io/XDMFFile.cpp

+  if (!attribute_label.empty())
+  {
+    bool found = false;
+    while (!found and attribute_node)


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.

garth-wells · 2024-09-12T08:52:38Z

cpp/dolfinx/io/XDMFFile.cpp

+    {
+      pugi::xml_attribute hint;
+      pugi::xml_attribute name = attribute_node.attribute("Name", hint);
+      if (std::string(name.value()) == attribute_label)


I think name.value() == attribute_label might work, see https://en.cppreference.com/w/cpp/string/basic_string/operator_cmp.

mleoni-pf added 2 commits June 6, 2024 16:18

Allow to specify attribute name when reading meshtag

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Add python interface

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mleoni-pf changed the title ~~Allow to specify attribute name when reading meshtag~~ Allow specifying attribute name when reading meshtag Jun 6, 2024

mleoni-pf added 2 commits June 7, 2024 09:55

Disambiguate functions

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Fix Python wrapper

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Only one function in the python wrapper and interface

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Merge branch 'main' into mleoni/readNamedMeshtags

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mleoni-pf requested a review from garth-wells June 21, 2024 08:03

garth-wells and others added 5 commits June 26, 2024 07:08

Merge branch 'main' into mleoni/readNamedMeshtags

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mleoni-pf and others added 6 commits July 17, 2024 10:00

Using ASCII file to circumvent CI issue

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Merge branch 'mleoni/readNamedMeshtags' of github.com:mleoni-pf/dolfi…

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…nx into mleoni/readNamedMeshtags

Specify ASCII encoding

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Fix a bug and create mesh within test

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Dodge issue 3316

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Allow specifying attribute name when reading meshtag #3257

Allow specifying attribute name when reading meshtag #3257

mleoni-pf commented Jun 6, 2024

garth-wells Jun 7, 2024

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garth-wells Sep 12, 2024

		return MeshTags(mt)

		def read_meshtags(self, mesh, name, xpath="/Xdmf/Domain"):

Allow specifying attribute name when reading meshtag #3257

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Allow specifying attribute name when reading meshtag #3257

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