mne-tools / mne-nirs

Process Near-Infrared Spectroscopy Data in MNE
https://mne.tools/mne-nirs/
BSD 3-Clause "New" or "Revised" License
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read_snirf_aux_data() / _decode_name() fails when name of aux channel is string scalar #557

Open kdarti opened 2 months ago

kdarti commented 2 months ago

Describe the bug

According to the snirf spec strings should be stored as as scalars, not as 1x1 arrays.

image

The example aux dataset used in the aux tutorial has strings in 1x1 array.

image

The read_snirf_aux_data() function works fine with this dataset that has strings in 1x1 array, but when the name of aux channel is scalar the _decode_name() function fails.

https://github.com/mne-tools/mne-nirs/blob/2fdddfe9962ad000ebe60d71d0f9794d1800acbd/mne_nirs/io/snirf/_aux.py#L62-L63 image

To properly retrieve the scalar string,

Steps to reproduce

Can use this file (ignore other possible issues with the file): 04_single.zip

import mne
import mne_nirs

snirf_file = r"04_single.snirf"
raw = mne.io.read_raw_snirf(snirf_file)
raw_od = mne.preprocessing.nirs.optical_density(raw)
raw_haemo = mne.preprocessing.nirs.beer_lambert_law(raw_od, ppf=0.1)
aux_df = mne_nirs.io.snirf.read_snirf_aux_data(snirf_file,raw_haemo)

Expected results

Should work since strings are stored as scalar, in accordance with snirf spec.

Actual results

Fail since _decode_name() only works on arrays

Additional information

Could add conditional to check if it's a scalar, and in that case handle it as such, e.g.:

def _decode_name(key): if key.shape == (): return key[()].decode() else: return np.array(key)[0].decode()

kdarti commented 2 months ago

I got a little confused during testing becuase the official snirf samples are also incorrect, in their own way, c..f. https://github.com/fNIRS/snirf-samples/issues/9

Given I'm reading the snirf spec correctly the example file I provided should have the correct string format.