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?

I don't think it can because hint is also an output parameter of the function.

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?

The issue comes from the following fact: mesh tags are identified by "a word", so it is natural that this word be called the "name" of the mesh tag. The problem is that there is already another name parameter which refers to the name of the mesh node in the same file. I picked the word "label" to distinguish the two internally, in the code implementation, but a user should not be concerned with this implementation detail: a user saved a mesh tag giving it a "name" and wants to read it back by the same "name".
The fact remains that the user still needs to call a function whose name includes the word "label", not "name", which is indeed a bit confusing. I will change everything to be called more consistently, the code shouldn't become too unintelligible on the development side.

By the way, re-reading this conversation I noticed that in the first review, four months ago, you asked me to change the method name to avoid the word "name" in favour of "label". I had forgotten about that and, based on your comment, I reverted the change. Which one should I keep? To a user, a mesh tag's "label" means presumably very little...

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.

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 using next_attribute I 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].

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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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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Merge branch 'main' into mleoni/readNamedMeshtags

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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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mleoni-pf requested a review from garth-wells September 26, 2024 16:27

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Fix missing renaming

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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

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		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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