Add muscle tutorial #471

carme-hp · 2024-02-26T08:02:40Z

This would be a potential OpenDiHu tutorial. It has one muscle and three tendons (thus multi-coupling). We have the 4 participans running in OpenDiHu. Potentially, the tendon participants could also run in deal.ii.

Note that it contains no volume coupling.

MakisH · 2024-02-28T10:46:44Z

My suggestion here regarding the distribution release: Let's aim to merge this before the distribution, as it would help citing and starting a userbase/contributing community for OpenDiHu. We anyway plan to maintain this.

For the code itself, let's not rush it.

Since this is the first tutorial of this kind, I would like to do a sanity check as well.

autopep8 --in-place --exit-code --aggressive --ignore=E402 --max-line-length=120 file.py

pip3 install --user autopep8 autopep8 --recursive --in-place --aggressive --exit-code --ignore E402 --max-line-length 120 .

- Exit on errors - Complain for undefined variables

MakisH

I went ahead and fixed most of the linting issues and some other common requirements for tutorials. In terms of general structure, it looks good.

I have not tried to run it. I will once you tell me it is ready.

I have not reviewed the code of the solvers, as I lack the expertise. I trust that they have been validated elsewhere.

See a few more suggestions and questions to continue.

MakisH · 2024-03-11T07:57:37Z

muscle-tendon-complex/.gitignore

See #477 and restrict this to the difference (let's better wait until it is merged).
Are all of these files generated with the default instructions, or are some rules only as "just in case"?

Sorry I don't understand. Which default instructions are you referring to?

Sorry, I meant "are all these rules to ignore files that will actually be generated when I try to run the tutorial?".

yes! Some when building and some when running

MakisH · 2024-03-11T10:12:49Z

muscle-tendon-complex/README.md

+
+The muscle and tendon meshes are obtained from patient imaging. The interfaces of the tendons and the muscle do not perfectly match, which is a quite common issue due to the limitations of imaging methods and postprocessing tools. Nonetheless, preCICE coupling methods are robust and can handle meshes that do not perfectly match.
+
+TODO: Explain how is the muscle activated!


Isn't this already covered later on by the following?

The electrical signal triggers chemical reactions which lead to the contraction of sarcomeres, the smallest contraction unit in the muscle.

I tried to make it clear in a new commit.

muscle-tendon-complex/README.md

MakisH · 2024-03-11T10:52:24Z

muscle-tendon-complex/muscle-opendihu/variables/variables.py

+end_time = 1000.0                   # [ms] end time of the simulation
+# [ms^-1] sampling frequency of stimuli in firing_times_file, in stimulations per ms, number before 1e-3 factor is in Hertz.
+stimulation_frequency = 100 * 1e-3


Long comments have been moved to new lines, as a result of the aggressive option (I think) of the autopep8 and the column limit (120). Consider shortening or splitting some of these comments.

MakisH · 2024-03-11T10:56:00Z

muscle-tendon-complex/precice-config.xml

Just for review purposes, this is how this config looks like:

MakisH · 2024-03-11T11:06:50Z

muscle-tendon-complex/README.md

+
+   - Download input files for OpenDiHu
+
+      OpenDiHu requires input files hosted in [Zenodo](https://zenodo.org/records/4705982) which include CellML files (containing model equations) and mesh files. Downloading these files is necessary to simulate muscles and/or tendons with OpenDiHu. You can [directly download the necessary files](https://zenodo.org/record/4705982/files/input.tgz?download=1). Extract the files and place them in the `opendihu/examples/electrophysiology/` directory.


Do they really need to be downloaded into the opendihu source directory? What if that is a system directory? What if it is generally a frozen installation?

Can we move these to a local path, or to an OPENDIHU_EXAMPLES directory?

I'm not sure I understand your point.
Would path/to/opendihu/examples/electrophysiology/ be better?
Or OPENDIHU_HOME/examples/electrophysiology/.

No, I mean that it is strange to first get OpenDiHu (imagine in the future a sudo apt install opendihu) and then copy the examples into the installation directory (similarly to sudo apt install opendihu-examples).

What I suggest is to decouple them from the actual installation (for the tutorial) and be able to use them from any directory.

mmh I think you mean the input files and not the examples. The input files are downloaded separately because they are 1.5 GB and thus too big for GitHub.
Alternatives I see instead of moving the downloaded files are

option 1: user has to define OPENDIHU_INPUT_DIR

# input files # ----------- import os input_dir = os.environ.get('OPENDIHU_INPUT_DIR') fiber_file = input_dir + "/left_biceps_brachii_9x9fibers.bin"

option 2: user has to edit variables.py

# input files # ----------- input_dir = path/to/input fiber_file = input_dir + "/left_biceps_brachii_9x9fibers.bin"

I think that option 2 is more intuitive for the user, while option 1 is better for scripting/automation.

Anything is fine, as long as this path if configurable.

okay, I decided for option 2, because I think this is something I could generally do in OpenDiHu.

MakisH · 2024-03-11T11:08:51Z

muscle-tendon-complex/tendon-top-B-opendihu/variables/variables.py

Side-effect of having configuration files in Python script format (see opendihu/opendihu#44): How can I know if all variable names exist / are defined / are not misspelled / are needed?

Fair point, at the moment there's no way to check that.

muscle-tendon-complex/solver-opendihu/src/tendon-solver.cpp

muscle-tendon-complex/solver-opendihu/src/muscle-solver.cpp

muscle-tendon-complex/muscle-opendihu/settings-muscle.py

Co-authored-by: Gerasimos Chourdakis <[email protected]>

…nto add-muscle-tutorial

MakisH · 2024-03-11T17:57:03Z

muscle-tendon-complex/README.md


-   - Setup `$OPENDIHU_HOME` to your `.bashrc` file
+   - Setup `$OPENDIHU_HOME` and `$OPENDIHU_INPUT_DIR` in your `.bashrc` file


Just a general terminology thing: When I see "input files", I understand configuration files for a specific simulation. How do these differ that the files included in this repository?

If they are specific to this tutorial, they could also be downloaded directly into this directory (and specified in the .gitignore).

What in opendihu we call input file are not what I understand as configuration files. They are files that specify meshes, i.e., geometry, and cellml models, i.e., equations. In the configuration files (the ones included in the tutorial, we give the parameters and user settings to use this files.

carme-hp added 2 commits February 26, 2024 08:37

Create tutorial structure

822cb19

Add sample structure for an opendihu participant

cc8b43c

carme-hp requested a review from davidscn February 26, 2024 08:02

carme-hp added 3 commits February 27, 2024 23:24

Move src code to opendihu-solver folder

feef2d0

Complete opendihu participants

cfbe718

Update README

3eb5bb0

MakisH self-requested a review February 28, 2024 10:44

carme-hp and others added 21 commits February 29, 2024 20:16

Get muscle participant to run

b559c85

Add check for OPENDIHU_HOME

1b4f1fe

Rename meshName to preciceMeshName

0cb1947

Fix rename

bcbc6fd

Fix paths, variables and add scripts

ff5ed78

Add remove precice-run to clean.sh

a80cfaa

Fix bc errors

b383782

Setup exchange directory and remove comments

0bdcb05

Add information about OpenDiHu

c6091ae

Add .gitignore

1d31091

Merge branch 'develop' into add-muscle-tutorial

f555039

Fix Markdown linting issues in muscle tutorial README

6bfa0a9

Fix Markdown linting issues in muscle tutorial README

5459862

Remove unrelated results image - fix check.sh

c3b4db8

Mark shell scripts as executable

b24c63d

Fix shellcheck errors

50333ef

Format with autopep8

0a5858a

autopep8 --in-place --exit-code --aggressive --ignore=E402 --max-line-length=120 file.py

Bump GItHub Action autopep8 from v1 to v2

e3bd5e2

Format more files with autopep8

83f7597

pip3 install --user autopep8 autopep8 --recursive --in-place --aggressive --exit-code --ignore E402 --max-line-length 120 .

Double --aggressive autopep8

dcd7a3f

Double --aggressive autopep8

f9325f3

MakisH mentioned this pull request Mar 11, 2024

Input file format opendihu/opendihu#44

Open

MakisH added 8 commits March 11, 2024 11:10

Minor fixes in muscle tutorial README

bbfa73e

Add a clean_opendihu function, adjust cleaning scripts

9660161

Rename opendihu-solver to solver-opendihu

13ccd83

solver-opendihu scripts: set -e -u

d9141f5

- Exit on errors - Complain for undefined variables

Fix clean_opendihu call to clean_precice_logs

9ec1cdb

Further fixes in solver-opendihu/clean.sh

b3602f0

Apply set -e -u to more shell scripts

e908415

Format precice-config.xml

b7e9272

MakisH reviewed Mar 11, 2024

View reviewed changes

carme-hp and others added 8 commits March 11, 2024 12:46

Update muscle-tendon-complex/README.md

2e6dc39

Co-authored-by: Gerasimos Chourdakis <[email protected]>

Update muscle-tendon-complex/solver-opendihu/src/tendon-solver.cpp

09d53d6

Co-authored-by: Gerasimos Chourdakis <[email protected]>

Update muscle-tendon-complex/solver-opendihu/src/muscle-solver.cpp

37233da

Co-authored-by: Gerasimos Chourdakis <[email protected]>

Explain activation and add citation

76b5a0f

Use pre-commit

db6820e

Use pre-commit

535342f

Merge branch 'add-muscle-tutorial' of github.com:carme-hp/tutorials i…

75c09ff

…nto add-muscle-tutorial

Add automatically generated folder to gitignore

755c3e4

MakisH reviewed Mar 11, 2024

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Add muscle tutorial #471

Add muscle tutorial #471

carme-hp commented Feb 26, 2024

MakisH commented Feb 28, 2024

MakisH left a comment

MakisH Mar 11, 2024

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MakisH Mar 11, 2024

carme-hp Mar 11, 2024


		The muscle and tendon meshes are obtained from patient imaging. The interfaces of the tendons and the muscle do not perfectly match, which is a quite common issue due to the limitations of imaging methods and postprocessing tools. Nonetheless, preCICE coupling methods are robust and can handle meshes that do not perfectly match.

		TODO: Explain how is the muscle activated!


		- Download input files for OpenDiHu

		OpenDiHu requires input files hosted in [Zenodo](https://zenodo.org/records/4705982) which include CellML files (containing model equations) and mesh files. Downloading these files is necessary to simulate muscles and/or tendons with OpenDiHu. You can [directly download the necessary files](https://zenodo.org/record/4705982/files/input.tgz?download=1). Extract the files and place them in the `opendihu/examples/electrophysiology/` directory.


		- Setup `$OPENDIHU_HOME` to your `.bashrc` file
		- Setup `$OPENDIHU_HOME` and `$OPENDIHU_INPUT_DIR` in your `.bashrc` file

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carme-hp commented Feb 26, 2024

MakisH commented Feb 28, 2024

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