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Open Source Science

https://github.com/brainlesion/gliomoda

https://github.com/brainlesion/gliomoda

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.3%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: BrainLesion
  • Language: Python
  • Default Branch: main
  • Size: 126 KB
Statistics
  • Stars: 3
  • Watchers: 0
  • Forks: 1
  • Open Issues: 1
  • Releases: 0
Created over 1 year ago · Last pushed about 1 year ago
Metadata Files
Readme Contributing

README.md

GlioMODA

Python Versions Stable Version Documentation Status tests codecov License

Features

Installation

With a Python 3.10+ environment, you can install gliomoda directly from PyPI:

bash pip install gliomoda

Use Cases and Tutorials

A minimal example to create a segmentation could look like this:

```python from gliomoda import Inferer

inferer = Inferer()

Save NIfTI files

inferer.infer( t1c="path/to/t1c.nii.gz", t2f="path/to/t2f.nii.gz", t1n="path/to/t1n.nii.gz", t2w="path/to/t2w.nii.gz", segmentation_file="path/to/segmentation.nii.gz", )

Or directly use pre-loaded NumPy data. (Both works as well)

segmentationnp = inferer.infer( t1c=t1cnp, t2f=t2fnp, t1n=t1nnp, t2w=t2w_np, ) ```

[!NOTE] If you're interested in the GlioMODA package, the BraTS Adult Glioma Segmentation may also be of interest.

Citation

If you use GlioMODA in your research, please cite it to support the development!

TODO: citation will be added asap

Trouble shoot

Multiprocessing error If you get an error related to something like this:
``` RuntimeError: An attempt has been made to start a new process before the current process has finished its bootstrapping phase. This probably means that you are not using fork to start your child processes and you have forgotten to use the proper idiom in the main module: if __name__ == '__main__': freeze_support() ... The "freeze_support()" line can be omitted if the program is not going to be frozen to produce an executable. To fix this issue, refer to the "Safe importing of main module" section in https://docs.python.org/3/library/multiprocessing.html ``` Please ensure you properly wrap your script: ```python if __name__ == "__main__": inferer = Inferer() ... ```

Contributing

We welcome all kinds of contributions from the community!

Reporting Bugs, Feature Requests and Questions

Please open a new issue here.

Code contributions

Nice to have you on board! Please have a look at our CONTRIBUTING.md file.

Owner

  • Name: BrainLesion
  • Login: BrainLesion
  • Kind: organization

GitHub Events

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Last Year
  • Create event: 5
  • Release event: 2
  • Issues event: 8
  • Watch event: 1
  • Delete event: 5
  • Issue comment event: 6
  • Push event: 16
  • Pull request review comment event: 3
  • Pull request review event: 11
  • Pull request event: 12
  • Fork event: 1