kerkelae / disimpy

Massively parallel Monte Carlo diffusion MR simulator written in Python.

Disimpy

Disimpy is a Python package for generating simulated diffusion-weighted MR signals that can be useful in the development and validation of data acquisition and analysis methods. The data is generated by Monte Carlo random walk simulations that run massively parallel on Nvidia CUDA-capable GPUs. If you use Disimpy in work that leads to a scientific publication, please cite ¹, where the details about signal generation can also be found.

Requirements and installation

Follow the installation instructions.

Usage example

Read the tutorial to learn how to use Disimpy.

Validation

Disimpy's functionality has been validated by comparing its results to analytical solutions and to results from other simulators (e.g., Camino and MISST), and by automated testing (disimpy.tests). Examples of simulations used for validation are provided here. However, Disimpy is research software and some bugs undoubtedly remain. If you find any of them or encounter unexpected behaviour, please open an issue on GitHub.

Contribute

If you want to contribute to the development of Disimpy, start by reading the contributing guidelines.

Support

If you have questions or need help, open an issue on Github.

References

Sponsors

---

1. Kerkelä et al., (2020). Disimpy: A massively parallel Monte Carlo simulator for generating diffusion-weighted MRI data in Python. Journal of Open Source Software, 5(52), 2527. https://doi.org/10.21105/joss.02527↩

disimpy's Issues

Implement a simple interface for generating standard gradient arrays

separation size

Hi,

I set 'substrate = mesh', and set 'extra = true', but how to set the separation size?

Add Camino support to the docs

Fix documentation

Running Sphinx v7.2.6
making output directory... done

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/disimpy/envs/latest/lib/python3.11/site-packages/pygments/styles/__init__.py", line 45, in get_style_by_name
    mod = __import__(mod, None, None, [cls])
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'pygments.styles.stata'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/disimpy/envs/latest/lib/python3.11/site-packages/sphinx/cmd/build.py", line 293, in build_main
    app = Sphinx(args.sourcedir, args.confdir, args.outputdir,
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/disimpy/envs/latest/lib/python3.11/site-packages/sphinx/application.py", line 272, in __init__
    self._init_builder()
  File "/home/docs/checkouts/readthedocs.org/user_builds/disimpy/envs/latest/lib/python3.11/site-packages/sphinx/application.py", line 342, in _init_builder
    self.builder.init()
  File "/home/docs/checkouts/readthedocs.org/user_builds/disimpy/envs/latest/lib/python3.11/site-packages/sphinx/builders/html/__init__.py", line 220, in init
    self.init_highlighter()
  File "/home/docs/checkouts/readthedocs.org/user_builds/disimpy/envs/latest/lib/python3.11/site-packages/sphinx/builders/html/__init__.py", line 283, in init_highlighter
    self.highlighter = PygmentsBridge('html', style)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/disimpy/envs/latest/lib/python3.11/site-packages/sphinx/highlighting.py", line 99, in __init__
    style = self.get_style(stylename)
            ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/disimpy/envs/latest/lib/python3.11/site-packages/sphinx/highlighting.py", line 116, in get_style
    return get_style_by_name(stylename)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/disimpy/envs/latest/lib/python3.11/site-packages/pygments/styles/__init__.py", line 47, in get_style_by_name
    raise ClassNotFound("Could not find style module %r" % mod +
pygments.util.ClassNotFound: Could not find style module 'pygments.styles.stata'.

Exception occurred:
  File "/home/docs/checkouts/readthedocs.org/user_builds/disimpy/envs/latest/lib/python3.11/site-packages/pygments/styles/__init__.py", line 47, in get_style_by_name
    raise ClassNotFound("Could not find style module %r" % mod +
pygments.util.ClassNotFound: Could not find style module 'pygments.styles.stata'.
The full traceback has been saved in /tmp/sphinx-err-upzt0duf.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
A bug report can be filed in the tracker at <https://github.com/sphinx-doc/sphinx/issues>. Thanks!```

Update version to reflect pre-release development

Importing .ply files into disimpy

Dear disimpy creators/collaborators,

I'm trying to simulate a geometry that was originally run in Camino, however, when I try to import the .ply using meshio, I get this geometry:

I then converted the .ply into .stl file using an free online tool, which apparently fixed the problem:

However, when I simulate it, I get something close to free water diffusion, even though I set the structure as periodic.

Please let me know if you have any recommendations or suggestions.

Thanks,
T

Catch and deal with warnings

Add a list of sponsors/funders to the documentation

Add a list of papers using Disimpy to the documentation

Remove hard-coded PRNG seed

Add support for Camino scheme files

http://camino.cs.ucl.ac.uk/index.php?n=Tutorials.GenwaveTutorial

Implement permeable boundary conditions

Simulation for multiple substrates

Hi,

I want to know if it is possible to define multiple substrates in a single simulation ? ( say having multiple spheres and ellipsoids in the same simulation environment)