sappelhoff/brainvision-validator

Validator for BrainVision EEG file triplets

Hi there 👋

I am a postdoctoral researcher in cognitive neuroscience at the Max Planck Institute for Human Development in Berlin.

You can learn more about me on my personal website!

Here are a few open source projects that I work on (see more under "pinned repositories" below):

• The Brain Imaging Data Structure (BIDS)
  • BIDS Specification
  • BIDS website
• MNE-Python
  • Website
  • MNE-BIDS subproject

brainvision-validator's Issues

Use issue_list.js and integer issue codes

instead of specifying error strings in index.js and pushing them to the issues if a validator function returns false, do the following:

• validator functions return integer codes
  • e.g., a 1 if a file was not read, a 2 if internal links were wrong, ...
• the new issue_list.js exports a dictionary mapping these issue codes to issue messages
• index.js gets the issue code, uses it to get the issue message ... and add that to the issues.

With that approach, a single validator function can potentially raise more than one issue. E.g. when checking for link consistency within the file triplet, it might happen that a file cannot be opened ... so we can return the more specific issue code 1

Add more validation checks

Add more checks in validator.js, put adequate tests into test_validator.js ... and then add these checks to the validateBrainVision function in index.js.

Some ideas:

• check if file size of .eeg, .vmrk, .vhdr is adequately big
• make sure .eeg is binary (e.g., using https://github.com/bevry/istextorbinary)
• estimate filesize of .eeg using SamplingInterval and nChannels
• check if files are readable
• check if all mandatory sections are present, such as [Binary Infos], [Common Infos], ...
• within the mandatory sections are all non-default fields present? Such as SamplingInterval
• check the first line of vhdr: is it the header? --> which version of BrainVision format?
• check that links (file pointers) are relative and do not contain idiosyncratic paths because that will make copying the files troublesome (e.g., not /home/stefan/Desktop/test.vhdr but simply test.vhdr)

the more sensible checks, the merrier.

Better to make them fine-grained, so that meaningful issue messages can be pushed in index.js

check if all mandatory sections are present

such as [Binary infos]

check if any of the file triplets is empty

if any of the three files is a 0kb file ... raise an error

make utils.js

wrapping up repeated functions in a utils.js module

e.g.,
--> parsing sections and key-value pairs ... make available in dictionary like datatype

--> get all paths as a dictionary ... so "filepaths.vhdr" or "filepaths.eeg" ...

make sure .eeg is binary

(e.g., using https://github.com/bevry/istextorbinary)

Add more documentation

Include the Brain Products BrainVision Core spec pdf file.

fix extracting index from unmatched regexp (=null)

x@y:~/Desktop/brainvision-validator/test/data$ brainvision-validator test.vmrk
/usr/lib/node_modules/brainvision-validator/validator.js:40
        var vmrkBaseName = vhdrContent.match(vmrkRe)[1];
                                                    ^

TypeError: Cannot read property '1' of null
    at Object.assertBVTriplet (/usr/lib/node_modules/brainvision-validator/validator.js:40:53)
    at validateBrainVision (/usr/lib/node_modules/brainvision-validator/index.js:25:38)
    at module.exports (/usr/lib/node_modules/brainvision-validator/cli.js:7:18)
    at Object.<anonymous> (/usr/lib/node_modules/brainvision-validator/bin/brainvision-validator:19:21)
    at Module._compile (module.js:652:30)
    at Object.Module._extensions..js (module.js:663:10)
    at Module.load (module.js:565:32)
    at tryModuleLoad (module.js:505:12)
    at Function.Module._load (module.js:497:3)
    at Function.Module.runMain (module.js:693:10)

check file links for correct format

check that links (file pointers) are relative and do not contain idiosyncratic paths because that will make copying the files troublesome (e.g., not /home/stefan/Desktop/test.vhdr but simply test.vhdr)

allow ignoring certain errors

within the command line, allow for an option that specifies an array of "keys" ... these keys map to certain issues to be ignored.

also requires that issue keys are printed together with the issue text upon validation

estimate size that eeg would need to have and assert

minimum size of eeg should be determined with nchannels and ntimepoints together with data encoding

assert that minimum file size is achieved

Integrate into bids-validator

BrainVision files are part of the EEG extension for the Brain Imaging Data Structure (BIDS).

To Do before integration:

• #6
• #9
• #14

It would be good to use this tool as a validation for BV files, see: bids-standard/bids-validator#475

check if all non-default fields are present

such as SamplingInterval

check version of BrainVision file and assert its 1.0