Can't open snirf file

[ansleykunnath]

Describe the bug

"write_raw_snirf" and "read_raw_snirf" are not working with my .snirf files from fNIRS recordings with the Kernel Flow system. I am able to use the following code to plot other .snirf sample files found online, but not the .snirf files produced from my fNIRS system.

Steps to reproduce

from mne_nirs.io import write_raw_snirf
from mne.io import read_raw_snirf

snirf_intensity = read_raw_snirf('Kernel_Flow_Recording.snirf').load_data()
snirf_intensity.load_data()
write_raw_snirf(snirf_intensity, 'Kernel_Flow_Recording.snirf')
snirf_intensity.plot(duration=2, show_scrollbars=False)

The file Kernel_Flow_Recording.snirf can be found here: https://github.com/ansleykunnath/fnirs.git

Expected results

I expected a plot to pop up displaying the recordings for each channel over time. (This happens with the online sample .snirf files.)

Actual results

Python 3.10.4 (v3.10.4:9d38120e33, Mar 23 2022, 17:29:05) [Clang 13.0.0 (clang-1300.0.29.30)] Type 'copyright', 'credits' or 'license' for more information IPython 8.3.0 -- An enhanced Interactive Python. Type '?' for help. PyDev console: using IPython 8.3.0 Python 3.10.4 (v3.10.4:9d38120e33, Mar 23 2022, 17:29:05) [Clang 13.0.0 (clang-1300.0.29.30)] on darwin runfile('/Users/ansle/PycharmProjects/test1/open_snirf_file.py', wdir='/Users/ansle/PycharmProjects/test1') Backend MacOSX is interactive backend. Turning interactive mode on. Loading /Users/ansle/PycharmProjects/test1/Kernel_Flow_Recording.snirf Reading 0 ... 16 = 0.000 ... 2.242 secs... Traceback (most recent call last): File "/Users/ansle/PycharmProjects/test1/venv/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 3397, in run_code exec(code_obj, self.user_global_ns, self.user_ns) File "", line 1, in <cell line: 1> runfile('/Users/ansle/PycharmProjects/test1/open_snirf_file.py', wdir='/Users/ansle/PycharmProjects/test1') File "/Applications/PyCharm CE.app/Contents/plugins/python-ce/helpers/pydev/_pydev_bundle/pydev_umd.py", line 198, in runfile pydev_imports.execfile(filename, global_vars, local_vars) # execute the script File "/Applications/PyCharm CE.app/Contents/plugins/python-ce/helpers/pydev/_pydev_imps/_pydev_execfile.py", line 18, in execfile exec(compile(contents+"\n", file, 'exec'), glob, loc) File "/Users/ansle/PycharmProjects/test1/open_snirf_file.py", line 17, in write_raw_snirf(snirf_intensity, 'Kernel_Flow_Recording.snirf') File "/Users/ansle/PycharmProjects/test1/venv/lib/python3.10/site-packages/mne_nirs/io/snirf/_snirf.py", line 29, in write_raw_snirf picks = _picks_to_idx(raw.info, 'fnirs_cw_amplitude', exclude=[]) File "/Users/ansle/PycharmProjects/test1/venv/lib/python3.10/site-packages/mne/io/pick.py", line 1047, in _picks_to_idx picks = _picks_str_to_idx(info, picks, exclude, with_ref_meg, File "/Users/ansle/PycharmProjects/test1/venv/lib/python3.10/site-packages/mne/io/pick.py", line 1160, in _picks_str_to_idx raise ValueError( ValueError: picks ('fnirs_cw_amplitude') could not be interpreted as channel names (no channel "['fnirs_cw_amplitude']"), channel types (no type "None"), or a generic type (just "all" or "data")

Additional information

Platform: macOS-12.3.1-arm64-arm-64bit Python: 3.10.4 (v3.10.4:9d38120e33, Mar 23 2022, 17:29:05) [Clang 13.0.0 (clang-1300.0.29.30)] Executable: /Users/ansle/PycharmProjects/test1/venv/bin/python CPU: arm: 8 cores Memory: Unavailable (requires "psutil" package) mne: 1.0.3 numpy: 1.22.3 {} scipy: 1.8.0 matplotlib: 3.5.2 {backend=MacOSX} sklearn: 1.1.0 numba: Not found nibabel: 3.2.2 nilearn: 0.9.1 dipy: Not found cupy: Not found pandas: 1.4.2 pyvista: Not found pyvistaqt: Not found ipyvtklink: Not found vtk: Not found PyQt5: Not found ipympl: Not found pooch: v1.6.0 mne_bids: Not found mne_nirs: 0.2.1 mne_features: Not found mne_qt_browser: 0.3.1 mne_connectivity: Not found

[welcome[bot]]

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

[larsoner]

Cc @rob-luke , I'll try to look in the coming days

[rob-luke]

Your data is in "hbo"/"hbr" type. According to the write_raw_snirf documentation "Data to write to file. Must contain only fnirs_cw_amplitude type."

So the write_raw_snirfrequires data in fnirs_cw_amplitude type. It does not support writing other types yet. Would you be willing to open a PR to add support for exporting hbo/hbr?

We should also make the error more informative than it is now

[ansleykunnath]

Created a pull request. Thank you for the information!