load in source detector locations and compute channel locations

[kylemath]

need to load in source detector locations from .elp file use .mtg file to find used locations get their location and write them into the MNE raw object

raw.info['dig'] - has the .elp information in it raw.info['chs'] - has a 3d location for each channel

[kylemath]

These are the same locations that we would digitize into the .elp file for each participant

[kylemath]

>>> raw_intensity.info['chs'][0]
{
'loc': array([-4.01877067e-02,  4.46422957e-02,  1.23576592e-01, -4.16132047e-02,
        2.67997753e-02,  1.29904394e-01, -3.76195887e-02,  6.32285163e-02,
        1.15728028e-01,  7.60000000e+02,             nan,             nan]), 
'unit_mul': 0, 
'range': 1.0, 
'cal': 1.0, 
'kind': 1100 (FIFFV_FNIRS_CH), 
'coil_type': 302 (FIFFV_COIL_FNIRS_RAW), 
'unit': 107 (FIFF_UNIT_V), 
'coord_frame': 0 (FIFFV_COORD_UNKNOWN), 
'ch_name': 'S1_D1 760', 
'scanno': 1, 
'logno': 1}```

        # Store channel, source, and detector locations
        # The channel location is stored in the first 3 entries of loc.
        # The source location is stored in the second 3 entries of loc.
        # The detector location is stored in the third 3 entries of loc.
        # NIRx NIRSite uses MNI coordinates.

[kylemath]

good start to this in https://github.com/kylemath/pyoptical/pull/12, still working

[kylemath]

here is the pull request in which they made the nirx loader: https://github.com/mne-tools/mne-python/pull/6674/files/b02600eba9e46d7b6738153d3753c4bfbc447d44

[kylemath]

Note that the meg and fnirs parameters of pick_types() accept strings as well as boolean values, to allow selecting only magnetometer or gradiometer channels (via meg='mag' or meg='grad') or to pick only oxyhemoglobin or deoxyhemoglobin channels (via fnirs='hbo' or fnirs='hbr', respectively).

-https://mne.tools/dev/auto_tutorials/intro/plot_30_info.html#sphx-glr-auto-tutorials-intro-plot-30-info-py

[kylemath]

A third way to pick channels from an Info object is to apply regular expression matching to the channel names using mne.pick_channels_regexp(). Here the ^ represents the beginning of the string and . character matches any single character, so both EEG and EOG channels will be selected:

print(mne.pick_channels_regexp(info['ch_names'], '^E.G'))

[kylemath]

gonna keep this open so we can test on the head plots

[kylemath]

@kuziekj - i think you've already solved this but check this out: https://mne.tools/dev/overview/implementation.html#dig-formats

[kylemath]

https://mne.tools/dev/auto_tutorials/source-modeling/plot_source_alignment.html#plot-source-alignment

[kylemath]

https://mne.tools/dev/auto_examples/visualization/plot_montage.html https://mne.tools/dev/auto_examples/visualization/plot_eeg_on_scalp.html

[kuziekj]

continuing discussion in https://github.com/kylemath/pyoptical/issues/16