snirf2bids 0.3.0

To convert snirf file to bids format.

Installation

pip install snirf2bids

Table of Contents

• Introduction

• Features

  • Create BIDS Structures
  • Create BIDS Metadata Directory
  • Create BIDS Metadata Files in JSON Format

• BIDS implementation

• Contributors

snirf2BIDS

Conveniently generate BIDS structures from SNIRF files.

snirf2BIDS requires Python >3 and h5py >3.6.

Features

Create BIDS Structures

def snirf2bids(inputpath: str, outputpath: str = 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.

def snirf2bids(inputpath: str, outputpath: str = None):
     if os.path.isfile(inputpath):
        subj = Subject(inputpath)
    else:
        return ValueError('Invalid directory to SNIRF file.')

    if outputpath is None:  # if output directory is not specified, it will be same as input
        outputpath = os.path.dirname(inputpath)

    if os.path.isdir(outputpath):
        subjpath = 'sub' + str(subj.subinfo['sub-'])
        outputpath = os.path.join(outputpath, subjpath)
        if not os.path.exists(outputpath):
            os.mkdir(outputpath)

        if subj.subinfo['ses-'] is not None:
            sespath = 'ses' + str(subj.subinfo['ses-'])
            outputpath = os.path.join(outputpath, sespath)
            if not os.path.exists(outputpath):
                os.mkdir(outputpath)

        outputpath = os.path.join(outputpath, 'nirs')
        if not os.path.exists(outputpath):
            os.mkdir(outputpath)
    else:
        return ValueError('Invalid directory to build BIDS folder.')

    subj.directory_export(outputpath)

    # re-create source snirf file
    snirfoutput = os.path.join(outputpath,os.path.basename(inputpath))
    if not os.path.isfile(snirfoutput):
        subj.SNIRF.save(snirfoutput)

    # This will probably work only with a single SNIRF file for now
    fname = outputpath + '/participants.tsv'
    with open(fname, 'w', newline='') as f:
        writer = csv.DictWriter(f, fieldnames=list(subj.participants.keys()), delimiter="\t", quotechar='"')
        writer.writeheader()
        writer.writerow(subj.participants)
    f.close()

    # scans.tsv output, same thing as participants for scans
    fname = outputpath + '/scans.tsv'
    with open(fname, 'w', newline='') as f:
        writer = csv.DictWriter(f, fieldnames=list(subj.scans.keys()), delimiter="\t", quotechar='"')
        writer.writeheader()
        writer.writerow(subj.scans)
    f.close()

Create BIDS Metadata Directory

def directory_export(self, fpath: str): creates BIDS-compliant metadata text files based on information stored in subject class.
fpath: The file path that points to the folder where we intend to save the metadata files in.

        def directory_export(self, fpath: str):

        self.coordsystem.save_to_json(self.subinfo, fpath)
        self.optodes.save_to_tsv(self.subinfo, fpath)
        self.optodes.export_sidecar(self.subinfo, fpath)
        self.channels.save_to_tsv(self.subinfo, fpath)
        self.channels.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)

Create BIDS Metadata Files in JSON Format

def json_export(self): creats BIDS-compliant metadata files in JSON format. Returns a string containing the metadata file names and its content.

       def json_export(self):
        subj = self.subinfo
        subjnames= self.pull_fnames()

        # coordsystem.json
        name = 'coordsystem'
        temp = self.coordsystem.get_all_fields()
        subj[subjnames[name]] = temp

        # optodes.tsv + json sidecar
        name = 'optodes'
        fieldnames, valfiltered, temp = self.optodes.get_all_fields()
        subj[subjnames[name]] = temp

        sidecarname = _make_filename(name, subj, 'sidecar')
        subj[sidecarname] = self.optodes._sidecar

        # channels.tsv + json sidecar
        name = 'channels'
        fieldnames, valfiltered, temp = self.channels.get_all_fields()
        subj[subjnames[name]] = temp

        sidecarname = _make_filename(name, subj, 'sidecar')
        subj[sidecarname] = self.channels._sidecar

        # nirs sidecar
        name = 'sidecar'
        temp = self.sidecar.get_all_fields()
        subj[subjnames[name]] = temp

        # event.tsv + json sidecar
        name = 'events'
        fieldnames, valfiltered, temp = self.events.get_all_fields()
        subj[subjnames[name]] = temp

        sidecarname = _make_filename(name, subj, 'sidecar')
        subj[sidecarname] = self.events._sidecar

        # participant.tsv
        fields = self.participants
        text = _tsv_to_json(fields)
        subj['participants.tsv'] = text

        # scans.tsv
        fields = self.scans
        text = _tsv_to_json(fields)
        subj['scans.tsv'] = text

        text = json.dumps(subj)
        return text

BIDS implementation

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

Contributors

Developed by BU BME Senior Design Group 3 (2022): Christian Arthur, Jeonghoon Choi, Jiazhen Liu, Juncheng Zhang and the Boston University Neurophotonics Center. @Christian Arthur :melon:
@Juncheng Zhang :tangerine:
@Jeonghoon Choi :pineapple:
@Jiazhen Liu :grapes:

This project exists thanks to: