Handling data with 3D locations for sources and detectors

[rob-luke]

Hi all,

Thanks for the great package. I have been converting my data to snirf and run in to what I believe is a bug. Could you please let me know if this is an issue or if it is expected behaviour?

I have converted my data from a NIRX device to .nirs using the HomerOfflineConverter provided on the NIRX website. I then load this data using the code snippet from the README of this repo. I then save and load the data as described in the README. The .nirs data that I read has 3 dimensional locations for the source and detect positions. However, the snirf data is written as 2 dimensional data, so when I read it back I only have two of the three dimensions I started with.

I have provided a minimum working example below. The raw NIRX data I am using can be downloaded from https://osf.io/dj3eh/

nirs = load('Participant-1/NIRS-2019-11-02_002.nirs','-mat')

snirf1 = SnirfClass(nirs)
snirf1.Save('Participant-1.snirf')
snirf1.Info()

snirf2 = SnirfClass();
snirf2.Load('Participant-1.snirf');
snirf2.Info();

>> snirf1.probe.sourcePos2D
ans =

   -2.4810    1.0702    4.3366
   -6.4240    4.8954    4.8502
   -6.6257   -2.4181    4.3792
  -10.3412    1.6660    4.0343
    2.3877    1.2580    4.3585
    6.4382    5.0176    4.7415
    6.4641   -2.3230    4.6840
   10.2646    1.7367    4.1666


>> snirf2.probe.sourcePos2D
ans =

   -2.4810    1.0702         0
   -6.4240    4.8954         0
   -6.6257   -2.4181         0
  -10.3412    1.6660         0
    2.3877    1.2580         0
    6.4382    5.0176         0
    6.4641   -2.3230         0
   10.2646    1.7367         0

[dboas]

@fangq or @jayd1860 or maybe Stephen, can you look at this pull request and accept it if you agree. I just talked with Rob and I think this is consistent with our idea of 2D versus 3D probe positions.

[rob-luke]

Is there anything I can do to make this issue and pull request clearer/better? Or is there some code clash this causes that I'm unaware of? I'm happy to help work through any issues together.