Improve find_ch_adjacency and read_ch_adjacency #12293
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mscheltienne
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drammock,
agramfort,
dengemann and
jasmainak
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mscheltienne
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Dec 13, 2023
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| # TODO: This test is strange, raw and bti148 adjacency matrix do not have the same | ||
| # channel names. Previously, it was loading the bti148 adjacency matrix without the | ||
| # 'mag' channel selection confirming the existence of the channel names in the raw | ||
| # object, and asserting: | ||
| # assert 'A1' in ch_names # returned by find_ch_adjacency | ||
| # while in practice, 'A1' is not in raw.ch_names | ||
| bti_fname = testing_path / "BTi" / "erm_HFH" / "c,rfDC" | ||
| bti_config_name = testing_path / "BTi" / "erm_HFH" / "config" | ||
| raw = read_raw_bti(bti_fname, bti_config_name, None) | ||
| _, ch_names = find_ch_adjacency(raw.info, "mag") | ||
| assert "A1" in ch_names | ||
| with pytest.raises(ValueError, match="could not be interpreted as channel names"): | ||
| find_ch_adjacency(raw.info, "mag") | ||
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| # TODO: same as above, with 'assert "MLC11" in ch_names'. | ||
| ctf_fname = testing_path / "CTF" / "testdata_ctf_short.ds" | ||
| raw = read_raw_ctf(ctf_fname) | ||
| _, ch_names = find_ch_adjacency(raw.info, "mag") | ||
| assert "MLC11" in ch_names | ||
| with pytest.raises(ValueError, match="could not be interpreted as channel names"): | ||
| _, ch_names = find_ch_adjacency(raw.info, "mag") |
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Channel names in raw and adjacency matrix do not match. What should be the correct and tested behavior here?
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Can you try it with read_raw_bti(..., rename_channels=False)? If so I think we might need to detect somehow the BTi-ness of the data (probably by MEG coil type) and internally be willing to tolerate the renaming to MEGXXX-style naming when rename_channels=True.
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Fixes #12292
This PR:
ch_typeinfind_ch_adjacencyin favor ofpicksinforead_ch_adjacency: thepicksargument can not be a list of indices and can not interact with an non-existinginfo["bads"]list.IMO, the test
test_find_ch_adjacencyhas something wrong with thebtiandctfsegments. It loads adjacency matrix with different channel names than theraw recording. Changes to pass the test highlighted below, any input would be welcome as I am unfamiliar with those 2 MEG systems.