snirf2bids 0.1.20

To convert snirf file to bids format.

Table of Contents

• Introduction

• Features

  • Create BIDS Compliant Structures

• Code Generation

• Maintainers

• Contributors

snirf2BIDS

Conveniently generate BIDS structure from .snirf files.
Developed by BU BME Senior Design Group 3 (2022): Christian Arthur, Jeonghoon Choi, Jiazhen Liu, Juncheng Zhang.
Will be maintained by Boston University Neurophotonics Center(BUNPC).
snirf2BIDS requires Python >3 and h5py >3.6.

Features

Create BIDS-compliant Structures

def snirf_to_bids(inputpath: str, outputpath: str, participants: dict = None) creates a BIDS structure from a SNIRF file.
Inputpath: The file path to the reference SNIRF file
Outputpath: The file path/directory for the created BIDS metadata files
Participants: A dictionary with participant information

      def snirf_to_bids(inputpath: str, outputpath: str, participants: dict = None):
      
        subj = Subject(inputpath)
        subj.export('Folder', outputpath)
        _compliancy_check(subj)
        fname = outputpath + '/participants.tsv'

Create BIDS-compliant Metadata Files

def export(self, outputFormat: str = 'Folder', fpath: str = None) creats BIDS-compliant metadata files based on information stored in subject class.

OutputFormat: The target destination and indirectly, the output format of the metadata file. The default value is Folder, which outputs the metadata file to a specific file directory specified by the user.The other option is Text, which outputs the files and data as a string (JSON-like format)
fpath: The file path that points to the folder where we intend to save the metadata files in.

        def export(self, outputFormat: str = 'Folder', fpath: str = None):

        if outputFormat == 'Folder':
            self.coordsystem.save_to_json(self.subinfo, fpath)
            self.optodes.save_to_tsv(self.subinfo, fpath)
            self.optodes.export_sidecar(self.subinfo, fpath)
            self.channel.save_to_tsv(self.subinfo, fpath)
            self.channel.export_sidecar(self.subinfo, fpath)
            self.sidecar.save_to_json(self.subinfo, fpath)
            self.events.save_to_tsv(self.subinfo, fpath)
            self.events.export_sidecar(self.subinfo, fpath)
            return 0
        else:
            subj = {}
            if self.subinfo['ses-'] is None:
                subj = {'name': 'sub-' + self.get_subj(), 'filenames': self.pull_fnames(), 'sessions': self.get_ses()}

            out = json.dumps(subj)
            if fpath is None:
                return out
            else: 
                open(fpath + '/snirf.json', 'w').write(out)
                return 0

Code Generation

The fields and descriptions in JSON files are generated based on the latest Brain Imaging Data Structure v1.7.1-dev and SNIRF specification.

Maintainers

@Christian Arthur :melon:
@Juncheng Zhang :tangerine:
@Jeonghoon Choi :pineapple:
@Jiazhen Liu :grapes:
Boston University Neurophotonics Center(BUNPC)

Contributors

This project exsists thanks to all people who contribute.