Allow specifying attribute name when reading meshtag by mleoni-pf · Pull Request #3257 · FEniCS/dolfinx

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

+        mt = super().read_meshtags_by_name(mesh._cpp_object, name, attribute_name, xpath)
        return MeshTags(mt)

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


Needs docs.

garth-wells · 2024-06-07T10:43:56Z


-    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

-    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 · 2024-09-12T08:39:47Z

                      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...

jorgensd · 2024-11-08T22:31:59Z

@garth-wells
@mleoni-pf and I sat down and looked through the pugixml docs today.
The new solution is much cleaner and much closer to what we use in general in DOLFINx (i.e. lambda function for search predicate).
This is a very neat function to have, as it will allow storing multiple data arrays within the same grid (for instance material parameters.

jorgensd · 2024-11-11T10:13:21Z

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


Do we really want a separate function for this in C++? Couldn't we just put the attribute name as a fourth argument (optional) argument.

I don't see the added value of a constructor for handling one optional value to have a backwards compatible C++ interface. @garth-wells

Agree, one function would be better. Would is make sense to use std::optional for attribute_name?

Related to this, we should not pass empty strings as 'null' - use std::optional.

garth-wells · 2024-11-12T10:06:40Z

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


Agree, one function would be better. Would is make sense to use std::optional for attribute_name?

Related to this, we should not pass empty strings as 'null' - use std::optional.

garth-wells · 2024-11-12T10:11:05Z

+  std::iota(std::begin(indices), std::end(indices), 0);
+
+  std::vector<std::int32_t> domain_values(n_cells);
+  std::ranges::fill(domain_values, domain_value);


Just use std::vector<std::int32_t> domain_values(n_cells, domain_value);

garth-wells · 2024-11-12T10:11:14Z

+  std::vector<std::int32_t> domain_values(n_cells);
+  std::ranges::fill(domain_values, domain_value);
+
+  std::vector<std::int32_t> material_values(n_cells);


See above comment.

garth-wells · 2024-11-12T10:12:57Z


-    def read_meshtags(self, mesh, name, xpath="/Xdmf/Domain"):
-        mt = super().read_meshtags(mesh._cpp_object, name, xpath)
+    def read_meshtags(self, mesh, name, attribute_label=None, xpath="/Xdmf/Domain"):


Follow the Google docs style with Arguments, etc. There are quite a few examples in the code.

garth-wells · 2024-11-12T12:21:32Z

@garth-wells @mleoni-pf and I sat down and looked through the pugixml docs today. The new solution is much cleaner and much closer to what we use in general in DOLFINx (i.e. lambda function for search predicate). This is a very neat function to have, as it will allow storing multiple data arrays within the same grid (for instance material parameters.

Nice - looking good.

jorgensd

LGTM!

Co-authored-by: Jørgen Schartum Dokken <dokken92@gmail.com>

garth-wells

I've pushed some fixes to the code. Last things that is missing is a Python test. @massimiliano-leoni can you add a Python test?

mleoni-pf · 2024-11-22T09:29:56Z

@garth-wells Python test added!

* Safe default value for unbound variables in dolfinx.conf * Allow to specify attribute name when reading meshtag * Add python interface * Disambiguate functions * Fix Python wrapper * Applying review changes * Linting * Only one function in the python wrapper and interface * Applied code review changes * Added unit test * Fix comments * Removed unused variables * Using ASCII file to circumvent CI issue * Specify ASCII encoding * Fix a bug and create mesh within test * Dodge issue 3316 * Applied review suggestions * Fix missing renaming * Fix python wrapper * Simplify code * Update cpp/dolfinx/io/XDMFFile.h Co-authored-by: Jørgen Schartum Dokken <dokken92@gmail.com> * Update cpp/dolfinx/io/XDMFFile.h Co-authored-by: Jørgen Schartum Dokken <dokken92@gmail.com> * Sprinkling some const * Apply revision * Fix doc * Fix doc * Ruff format * Const and ref fixes * Ruff fixes * Update python/dolfinx/io/utils.py Co-authored-by: Jørgen Schartum Dokken <dokken92@gmail.com> * Add type hints * Fix dispatch * Fixes * Add missing include * Tidy cmake order * Minor fixes * Added test * Ruff fixes * Ruff fixes --------- Co-authored-by: Jørgen Schartum Dokken <dokken92@gmail.com> Co-authored-by: Garth N. Wells <gnw20@cam.ac.uk>

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

garth-wells requested changes Jun 7, 2024

View reviewed changes

jorgensd added the io label Jun 7, 2024

garth-wells requested changes Jun 8, 2024

View reviewed changes

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

garth-wells reviewed Jul 17, 2024

View reviewed changes

Comment thread cpp/test/mesh/Domain.xdmf Outdated

mleoni-pf requested a review from garth-wells July 31, 2024 16:17

mscroggs added this to the 0.9.0 milestone Sep 3, 2024

garth-wells reviewed Sep 12, 2024

View reviewed changes

garth-wells requested changes Sep 12, 2024

View reviewed changes

Comment thread cpp/dolfinx/io/XDMFFile.cpp Outdated

Comment thread cpp/dolfinx/io/XDMFFile.cpp Outdated

Comment thread cpp/dolfinx/io/XDMFFile.cpp Outdated

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

garth-wells modified the milestones: 0.9.0, 0.10.0 Oct 4, 2024

Safe default value for unbound variables in dolfinx.conf

35a65b4

jorgensd reviewed Nov 8, 2024

View reviewed changes

Comment thread cpp/dolfinx/io/XDMFFile.h Outdated

jorgensd reviewed Nov 8, 2024

View reviewed changes

Comment thread cpp/dolfinx/io/XDMFFile.h Outdated

jorgensd reviewed Nov 8, 2024

View reviewed changes

Comment thread cpp/dolfinx/io/XDMFFile.cpp

jorgensd reviewed Nov 11, 2024

View reviewed changes

garth-wells requested changes Nov 12, 2024

View reviewed changes

jorgensd reviewed Nov 21, 2024

View reviewed changes

Comment thread python/dolfinx/io/utils.py Outdated

mleoni-pf requested review from garth-wells and jorgensd November 21, 2024 14:29

jorgensd approved these changes Nov 21, 2024

View reviewed changes

mleoni-pf and others added 5 commits November 21, 2024 17:40

Merge branch 'FEniCS:main' into main

dfca9ce

Allow to specify attribute name when reading meshtag

7cd17dc

Add python interface

b416660

Disambiguate functions

7ea0982

Fix Python wrapper

bcf71e4

mleoni-pf and others added 9 commits November 21, 2024 17:43

Apply revision

1511b27

Fix doc

d524140

Fix doc

c38ba2a

Ruff format

33e775a

Const and ref fixes

6310419

Ruff fixes

a1b75bd

Update python/dolfinx/io/utils.py

b4f2e88

Co-authored-by: Jørgen Schartum Dokken <dokken92@gmail.com>

Add type hints

0f4251f

Fix dispatch

d348efa

mleoni-pf force-pushed the mleoni/readNamedMeshtags branch from 64ad359 to d348efa Compare November 21, 2024 16:43

garth-wells added 3 commits November 21, 2024 20:37

Fixes

1c23594

Add missing include

b2d4b9c

Tidy cmake order

6f059d6

garth-wells requested changes Nov 21, 2024

View reviewed changes

mleoni-pf and others added 4 commits November 22, 2024 09:47

Merge branch 'main' into mleoni/readNamedMeshtags

8396c05

Minor fixes

4b8978a

Added test

dd877c4

Ruff fixes

4583604

mleoni-pf requested a review from garth-wells November 22, 2024 10:19

garth-wells approved these changes Nov 22, 2024

View reviewed changes

garth-wells added this pull request to the merge queue Nov 22, 2024

github-merge-queue Bot removed this pull request from the merge queue due to no response for status checks Nov 22, 2024

mleoni-pf and others added 2 commits November 22, 2024 13:19

Merge branch 'main' into mleoni/readNamedMeshtags

599c86f

Ruff fixes

80c0216

jorgensd added this pull request to the merge queue Nov 22, 2024

Merged via the queue into FEniCS:main with commit 13bc37f Nov 22, 2024

mleoni-pf deleted the mleoni/readNamedMeshtags branch November 25, 2024 08:42

Uh oh!

Uh oh!

Conversation

mleoni-pf commented Jun 6, 2024

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

garth-wells left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

jorgensd commented Nov 8, 2024

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

garth-wells commented Nov 12, 2024

Uh oh!

Uh oh!

jorgensd left a comment

Choose a reason for hiding this comment

Uh oh!

garth-wells left a comment

Choose a reason for hiding this comment

Uh oh!

mleoni-pf commented Nov 22, 2024

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development