Validator Finds Fatal Errors in Normal SNIRF Datasets

[emmaspeh]

Hello,

I have a set of SNIRF files formatted according to the latest SNIRF specifications, and I would like to ensure that they pass the pysnirf2 validator before sharing them with others in the community. I created the SNIRF files using jsnirfy https://github.com/fangq/jsnirfy/tree/4140f1535e11470d2a63c3bfcff90f5cf447993c) in Matlab, and my SNIRF files can be loaded and used as expected in Matlab with the loadsnirf function from jsnirfy.

When I run the SNIRF validator on any of the SNIRF files I created, there are a large number of fatal errors. Each error has the same message, pictured below, and it occurs for all fields in the measurementList, metaDataTags, and aux. I checked the formatting of the measurementList against the SNIRF specifications, and it is formatted as an array of structs. For the metaDataTags, I also checked to ensure that they were saved as string variables. I also tried down-grading NumPy to <2.0.0 as mentioned in the current PR (#50), but I still get the same fatal errors.

Is this a known bug with the validator, or does this indicate that I did something wrong on my end when creating the SNIRF files?

(Windows 11, Python 3.9.13, snirf 0.8.0)

Best,
Emma

[sstucker]

Hi Emma,

Thanks for your post. This is seemingly not an issue with your files, but an issue with jsnirfy saving your strings as a type of HDF5 dataset that the pysnirf validator does not accept.

I will look into where this is going wrong. In the meantime, you can manually overwrite the strings using the sample code in the SNIRF specification appendix, or simply filter out these messages

[emmaspeh]

Hi,

Thank you for looking into this! For now, I will try overwriting the strings to be the correct type.

[sstucker]

If this works, let me know here. Thanks

[emmaspeh]

Hello,

I used the code in the SNIRF specification appendix to manually overwrite the strings in my SNIRF file, and that did not resolve the fatal errors in the pysnirf2 validator, unfortunately.

[Edouard2laire]

Hi.

Have you tried updating jsnirfy and all the dependancy ? (https://github.com/NeuroJSON/jsnirfy) it seems that the newest version of jsnirfy / easyh5 are able to produce valid snirf file.