[](https://pypi.org/project/snirf2bids/)
[](https://github.com/BUNPC/snirf2bids/actions/workflows/test.yml)
[](https://zenodo.org/badge/latestdoi/478632378)
# snirf2BIDS
Conveniently generate [BIDS files](https://bids-specification--802.org.readthedocs.build/en/802/04-modality-specific-files/11-functional-near-infrared-spectroscopy.html) from [SNIRF files](https://github.com/fnirs/snirf).
## Installation
### `pip install snirf2bids`
snirf2bids requires Python > 3.
## Usage
SNIRF files with [valid BIDS names](https://bids-specification.readthedocs.io/en/stable/02-common-principles.html#file-name-structure) can be converted into BIDS metadata text files.
For use with snirf2bids, a SNIRF file name must include at least the `sub-` and `task-` entitites and end in `_nirs.snirf`, i.e. `sub-01_task-tapping_nirs.snirf`.
### Generate BIDS text files from a SNIRF file
If the list_files parameter is empty, snirf2bids replaces all existing BIDS files with newly generated ones; otherwise, it replaces only the files specified in list_files. The parameter retain_old_info, with a default value of True, ensures that information in the existing scans and participants files is retained whenever a conflict occurs.
```python
snirf2bids.snirf2bids('<path to snirf file>', 'outputpath = <folder to generate files in>', 'list_files =<list of BIDS files to replace>' , 'retain_old_info=True')
```
### Generate BIDS text files from a SNIRF file or from all SNIRF files within a directory and its subdirectories
If the list_files parameter is empty, snirf2bids replaces all existing BIDS files with newly generated ones; otherwise, it replaces only the files specified in list_files. The parameter retain_old_info, with a default value of True, ensures that information in the existing scans and participants files is retained whenever a conflict occurs.
```python
snirf2bids.snirf2bids_recurse('<path to a directiory or path to snirf file>', 'list_files =<list of BIDS files to replace>', 'retain_old_info=True')
```
### Export BIDS text files in JSON Format
```python
s = snirf2bids.snirf2json('<path to snirf file>') # Returns serialized JSON in which keys are filenames and values are their contents
```
## Contributors
Developed by BU BME Senior Design Group 3 (2022): Christian Arthur, Jeonghoon Choi, Jiazhen Liu, Juncheng Zhang and the [Boston University Neurophotonics Center](https://github.com/BUNPC).
[@Christian Arthur :melon:](https://github.com/chrsthur)<br>
[@Juncheng Zhang :tangerine:](https://github.com/andyzjc)<br>
[@Jeonghoon Choi :pineapple:](https://github.com/jeonghoonchoi)<br>
[@Jiazhen Liu :grapes:](https://github.com/ELISALJZ)<br>
This project exists thanks to:
<br>
<center class= "half">
<a href="https://github.com/sstucker">
<img src="https://github.com/sstucker.png" width="50" height="50">
</a>
<a href="https://github.com/rob-luke">
<img src="https://github.com/rob-luke.png" width="50" height="50">
</a>
<a href="https://github.com/chrsthur">
<img src="https://github.com/chrsthur.png" width="50" height="50">
</a>
<a href="https://github.com/andyzjc">
<img src="https://github.com/andyzjc.png" width="50" height="50">
</a>
<a href="https://github.com/jeonghoonchoi">
<img src="https://github.com/jeonghoonchoi.png" width="50" height="50">
</a>
<a href="https://github.com/ELISALJZ">
<img src="https://github.com/ELISALJZ.png" width="50" height="50">
</a>
<a href="https://github.com/dboas">
<img src="https://github.com/dboas.png" width="50" height="50">
</a>
</center>
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