SNIRF loader not working with the official samples

[HanBnrd]

Describe the bug

The function read_raw_snirf returns errors with the official samples from https://github.com/fNIRS/snirf-samples/.

Steps to reproduce

With Simple_Probe.snirf:

from mne.io import read_raw_snirf

snirf_intensity = read_raw_snirf('Simple_Probe.snirf')

With minimum_example.snirf:

from mne.io import read_raw_snirf

snirf_intensity = read_raw_snirf('minimum_example.snirf')

Expected results

Loading Simple_Probe.snirf

and

Loading minimum_example.snirf

respectively.

Actual results

Loading Simple_Probe.snirf
...\snirf.py:3: RuntimeWarning: Non uniform sampled data not supported.
  snirf_intensity = read_raw_snirf('Simple_Probe.snirf')
...\snirf.py:3: RuntimeWarning: Unable to extract sample rate from SNIRF file.
  snirf_intensity = read_raw_snirf('Simple_Probe.snirf')
Traceback (most recent call last):
  File "...\snirf.py", line 3, in <module>
    snirf_intensity = read_raw_snirf('Simple_Probe.snirf')
  File "...\mne-python\mne\io\snirf\_snirf.py", line 43, in read_raw_snirf
    return RawSNIRF(fname, preload, verbose)
  File "<decorator-gen-248>", line 24, in __init__
  File "...\mne-python\mne\io\snirf\_snirf.py", line 112, in __init__
    sources = [s.decode('UTF-8') for s in sources]
  File "...\mne-python\mne\io\snirf\_snirf.py", line 112, in <listcomp>
    sources = [s.decode('UTF-8') for s in sources]
AttributeError: 'numpy.ndarray' object has no attribute 'decode'

and

Loading minimum_example.snirf
...\snirf.py:3: RuntimeWarning: Non uniform sampled data not supported.
  snirf_intensity = read_raw_snirf('minimum_example.snirf')
...\snirf.py:3: RuntimeWarning: Unable to extract sample rate from SNIRF file.
  snirf_intensity = read_raw_snirf('minimum_example.snirf')
Traceback (most recent call last):
  File "...\snirf.py", line 3, in <module>
    snirf_intensity = read_raw_snirf('minimum_example.snirf')
  File "...\mne-python\mne\io\snirf\_snirf.py", line 43, in read_raw_snirf
    return RawSNIRF(fname, preload, verbose)
  File "<decorator-gen-248>", line 24, in __init__
  File "...\mne-python\mne\io\snirf\_snirf.py", line 112, in __init__
    sources = [s.decode('UTF-8') for s in sources]
TypeError: iteration over a 0-d array

respectively.

Additional information

This tutorial from MNE-NIRS works fine on my machine.

[HanBnrd]

Hi, just pinging @rob-luke. I will try to have a look at it ASAP.

[HanBnrd]

I created a separate issue for the sourcePos3D problem: #9308

[rob-luke]

We should ensure we follow the SNIRF standard. However, from memory not all files in the examples repo do. What specific part of our reader is diverging from the standard?

[HanBnrd]

Thanks @rob-luke, you are right, my bad. Both files do not pass the snirf_validator.py.

Some modifications of the samples are planned according to https://github.com/fNIRS/snirf/issues/44, so maybe better to close this issue. Sorry about that.

[rob-luke]

That's good to know. Thanks for checking this. I probably wouldn't trust that validator either. Just the spec is valid

[rob-luke]

I just received some SNIRF files from NIRx. So I will test and ensure these load in to our reader.