API error in 'write_raw_bids': channel type mappings description is not correct. KeyError: 'grad'

dasdiptyajit commented 1 year ago

Description of the problem

We have a Neuromag-122 system which is equipped with 61 dual-channel planar first-order gradiometers. I am trying to convert our local meg files to MNE-BIDS format using write_raw_bids API. The API prompts the following error.

Steps to reproduce

***Error description*:**

Traceback (most recent call last):
  File "/media/dip_linux/18F80D53F80D3094/Auditory_P3/x_Dip_p300/auditory_code/regression_model/MNE_BIDs.py", line 99, in <module>
    write_raw_bids(
  File "<decorator-gen-627>", line 12, in write_raw_bids
  File "/home/dip_linux/anaconda3/envs/mne/lib/python3.10/site-packages/mne_bids/write.py", line 1865, in write_raw_bids
    _channels_tsv(raw, channels_path.fpath, overwrite)
  File "/home/dip_linux/anaconda3/envs/mne/lib/python3.10/site-packages/mne_bids/write.py", line 126, in _channels_tsv
    ch_type.append(map_chs[_channel_type])
KeyError: 'grad'

# It seems channel type mappings description is not correct. 
Currently its written as: 
# line 90: 
map_desc.update(meggradaxial='Axial Gradiometer',
                        megrefgradaxial='Axial Gradiometer Reference',
                        meggradplanar='Planar Gradiometer',
                        megmag='Magnetometer',
                        megrefmag='Magnetometer Reference',
                        stim='Trigger',
                        eeg='ElectroEncephaloGram',
                        ecog='Electrocorticography',
                        seeg='StereoEEG',
                        ecg='ElectroCardioGram',
                        eog='ElectroOculoGram',
                        emg='ElectroMyoGram',
                        misc='Miscellaneous',
                        bio='Biological',
                        ias='Internal Active Shielding',
                        dbs='Deep Brain Stimulation',
                        fnirs_cw_amplitude='Near Infrared Spectroscopy '
                                           '(continuous wave)',
                        resp='Respiration',
                        gsr='Galvanic skin response (electrodermal activity, EDA)',
                        temperature='Temperature',)

    # get the manufacturer from the file in the Raw object
    _, ext = _parse_ext(raw.filenames[0])
    manufacturer = MANUFACTURERS.get(ext, '')
    ignored_channels = IGNORED_CHANNELS.get(manufacturer, list())

    status, ch_type, description = list(), list(), list()
    for idx, ch in enumerate(raw.info['ch_names']):
        status.append('bad' if ch in raw.info['bads'] else 'good')
        _channel_type = channel_type(raw.info, idx)
        if _channel_type in get_specific:
            _channel_type = coil_type(raw.info, idx, _channel_type)
        ch_type.append(map_chs[_channel_type])    
        description.append(map_desc[_channel_type])   # error prompt line 126

Expected results

current system outputs:

map_desc output is:

defaultdict(<function _channels_tsv.. at 0x7f7705bcadd0>, {'meggradaxial': 'Axial Gradiometer', 'megrefgradaxial': 'Axial Gradiometer Reference', 'meggradplanar': 'Planar Gradiometer', 'megmag': 'Magnetometer', 'megrefmag': 'Magnetometer Reference', 'stim': 'Trigger', 'eeg': 'ElectroEncephaloGram', 'ecog': 'Electrocorticography', 'seeg': 'StereoEEG', 'ecg': 'ElectroCardioGram', 'eog': 'ElectroOculoGram', 'emg': 'ElectroMyoGram', 'misc': 'Miscellaneous', 'bio': 'Biological', 'ias': 'Internal Active Shielding', 'dbs': 'Deep Brain Stimulation', 'fnirs_cw_amplitude': 'Near Infrared Spectroscopy (continuous wave)', 'resp': 'Respiration', 'gsr': 'Galvanic skin response (electrodermal activity, EDA)', 'temperature': 'Temperature'})

_channel_type output is: 'grad'

Actual results

######### error line 126 ch_type.append(map_chs[_channel_type]) map_chs[_channel_type] expects the key word 'meggradplanar' instead of 'grad'

Additional information

Platform: Linux-5.15.0-52-generic-x86_64-with-glibc2.31 Python: 3.10.6 | packaged by conda-forge | (main, Aug 22 2022, 20:35:26) [GCC 10.4.0] Executable: /home/dip_linux/anaconda3/envs/mne/bin/python3.10 CPU: x86_64: 8 cores Memory: 15.3 GB

mne: 1.2.3 numpy: 1.22.4 {OpenBLAS 0.3.21 with 8 threads} scipy: 1.9.1 matplotlib: 3.6.0 {backend=QtAgg}

sklearn: 1.1.2 numba: 0.55.2 nibabel: 4.0.2 nilearn: 0.9.2 dipy: 1.5.0 openmeeg: Not found cupy: Not found pandas: 1.5.0 pyvista: 0.36.1 {OpenGL 3.3 (Core Profile) Mesa 21.2.6 via Mesa Intel(R) UHD Graphics (CML GT2)} pyvistaqt: 0.9.0 ipyvtklink: 0.2.2 vtk: 9.1.0 qtpy: 2.2.0 {PyQt5=5.12.10} ipympl: Not found pyqtgraph: 0.12.4 pooch: v1.6.0

mne_bids: 0.12.dev0 mne_nirs: Not found mne_features: Not found mne_qt_browser: 0.3.2 mne_connectivity: 0.4.0 mne_icalabel: Not found

welcome[bot] commented 1 year ago

Hello! 👋 Thanks for opening your first issue here! ❤️ We will try to get back to you soon. 🚴🏽‍♂️

agramfort commented 1 year ago

https://github.com/mne-tools/mne-bids/pull/1110 should fix your problem @dasdiptyajit

thanks for the bug report

mne-tools / mne-bids