Description of the problem
Hi,
I'm trying to produce SNIRF files that can be read by MNE, using the PySnirf2 package. It seems that MNE has a particular dislike against the DateOfBirth metadata tag, throwing an exception when I try to import a file with it added (see code for minimal SNIRF sample below). I tried valid dates and gibberish - the result is the same, as long as the tag exists. Other custom string tags work just fine.
Of course, there's a chance that PySnirf2 does something special to that particular field, but I cannot see anything special about it when I check the contents, and I'm unsure how to debug further.
Steps to reproduce
1. Use code below in _Link to Data_ to create minimal SNIRF file. Requires PySnirf2 package.
2.
import mne
mne.io.read_raw_snirf("test.snirf", verbose=True)Link to data
import snirf
import numpy as np
from datetime import datetime
a = snirf.Snirf("test.snirf", "w")
a.nirs.appendGroup()
a.nirs[0].data.appendGroup()
a.nirs[0].data[0].dataTimeSeries = np.zeros((2, 2))
a.nirs[0].data[0].time = [0, 1]
for i in range(2):
a.nirs[0].data[0].measurementList.appendGroup()
a.nirs[0].data[0].measurementList[i].sourceIndex = 1
a.nirs[0].data[0].measurementList[i].detectorIndex = 1
a.nirs[0].data[0].measurementList[i].wavelengthIndex = 1
a.nirs[0].data[0].measurementList[i].dataType = 99999
a.nirs[0].data[0].measurementList[i].dataTypeIndex = 0
a.nirs[0].data[0].measurementList[0].dataTypeLabel = "HbO"
a.nirs[0].data[0].measurementList[1].dataTypeLabel = "HbR"
a.nirs[0].metaDataTags.SubjectID = "0"
a.nirs[0].metaDataTags.MeasurementDate = "1950-01-01"
a.nirs[0].metaDataTags.MeasurementTime = "00:00"
a.nirs[0].metaDataTags.LengthUnit = "m"
a.nirs[0].metaDataTags.TimeUnit = "s"
a.nirs[0].metaDataTags.FrequencyUnit = "Hz"
a.nirs[0].metaDataTags.add("DateOfBirth", "1950-01-01") # ERROR
# field content can be invalid date, or any string as far as I can tell
a.nirs[0].probe.wavelengths = [0, 0]
a.nirs[0].probe.sourcePos3D = np.zeros((1, 3))
a.nirs[0].probe.detectorPos3D = np.zeros((1, 3))
a.save()
a.close()Expected results
no output = file imported without errors
Actual results
Loading C:\test\test.snirf
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\Users\d\Virtualenvs\f\Lib\site-packages\mne\io\snirf\_snirf.py", line 54, in read_raw_snirf
return RawSNIRF(fname, optode_frame, preload, verbose)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<decorator-gen-318>", line 10, in __init__
File "C:\Users\d\Virtualenvs\f\Lib\site-packages\mne\io\snirf\_snirf.py", line 441, in __init__
str_birth = np.array((dat.get("/nirs/metaDataTags/" "DateOfBirth")))[
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: too many indices for array: array is 0-dimensional, but 1 were indexed
Additional information
Platform Windows-10-10.0.22621-SP0
Python 3.11.4 (tags/v3.11.4:d2340ef, Jun 7 2023, 05:45:37) [MSC v.1934 64 bit (AMD64)]
Executable C:\Users\d\Virtualenvs\f\Scripts\python.exe
CPU AMD64 Family 25 Model 68 Stepping 1, AuthenticAMD (16 cores)
Memory 30.8 GB
Core
├☑ mne 1.4.2
├☑ numpy 1.24.3 (OpenBLAS 0.3.21 with 16 threads)
├☑ scipy 1.10.1
├☑ matplotlib 3.7.1 (backend=QtAgg)
├☑ pooch 1.7.0
└☑ jinja2 3.1.2
Numerical (optional)
├☑ sklearn 1.2.2
├☑ numba 0.57.0
├☑ nibabel 5.1.0
├☑ nilearn 0.10.1
├☑ dipy 1.7.0
C:\Users\d\Virtualenvs\f\Lib\site-packages\cupy\_environment.py:214: UserWarning: CUDA path could not be detected. Set CUDA_PATH environment variable if CuPy fails to load.
warnings.warn(
├☑ pandas 2.0.2
└☐ unavailable openmeeg, cupy
Visualization (optional)
├☑ pyvista 0.39.1 (OpenGL 4.6.0 Compatibility Profile Context 22.20.44.50.230329 via AMD Radeon(TM) Graphics)
├☑ pyvistaqt 0.10.0
├☑ vtk 9.2.6
├☑ qtpy 2.3.1 (PySide6=6.5.1)
├☑ pyqtgraph 0.13.3
├☑ mne-qt-browser 0.5.1
└☐ unavailable ipyvtklink, ipympl
Ecosystem (optional)
├☑ mne-nirs 0.5.0
└☐ unavailable mne-bids, mne-features, mne-connectivity, mne-icalabel, mne-bids-pipeline
Description of the problem
Hi,
I'm trying to produce SNIRF files that can be read by MNE, using the
PySnirf2package. It seems that MNE has a particular dislike against theDateOfBirthmetadata tag, throwing an exception when I try to import a file with it added (see code for minimal SNIRF sample below). I tried valid dates and gibberish - the result is the same, as long as the tag exists. Other custom string tags work just fine.Of course, there's a chance that
PySnirf2does something special to that particular field, but I cannot see anything special about it when I check the contents, and I'm unsure how to debug further.Steps to reproduce
Link to data
Expected results
no output = file imported without errors
Actual results
Additional information