NiWrap 
NiWrap is an extensive collection of neuroimaging command line tool metadata used for generating modern, ideomatic Python wrappers.
Metadata is partly hand-written and partly extracted from the source code of the tools themselves. NiWrap is based on the Boutiques Descriptor Schema and powered by the Styx Boutiques-to-Python compiler.
Supported frameworks
| Framework | Approach | Status | API Coverage |
|---|---|---|---|
| AFNI | Manual | In progress | 22/621 (3.5%) |
| ANTs | Manual | In progress | 9/120 (7.5%) |
| Connectome Workbench | Source extraction | Testing | 202/202 (100% 🎉) |
| Convert3D | Manual | In progress | 2/4 (50.0%) |
| FSL | Manual | In progress | 221/376 (58.8%) |
| FreeSurfer | Manual | In progress | 2/104 (1.9%) |
| MRTrix3 | Source extraction | Testing | 112/125 (89.6%) |
| NiftyReg | Manual | In progress | 7/7 (100% 🎉) |
[!NOTE] API Coverage is defined as the percentage of individual binaries for which a descriptor is available in NiWrap. This is not a measure of the completeness of the descriptors themselves nor is reaching 100% strictly necessary as e.g. FSL and AFNI contain many small utilities for which Python offers much easier standard library functions. One way to increase coverage is to mark known-irrelevant binaries as
"status": "ignore"inframeworks/.
Repository structure
| Directory | Description |
|---|---|
/descriptors |
Boutiques descriptors |
/schemas |
JSON schema for Boutiques descriptors |
/python |
Generated niwrap Python package |
/extraction |
Source metadata extraction |
/frameworks |
Framework-specific metadata |
Python package
Install the niwrap Python package to use the generated Python wrappers.
See the niwrap Python package README for installation instructions and usage information.
Contributing
See the CONTRIBUTING.md file for information on how to contribute to NiWrap.