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Add support for dictionary-type ref_channels in set_eeg_reference() #12366

Merged
merged 72 commits into from
Sep 24, 2024
Merged

Add support for dictionary-type ref_channels in set_eeg_reference() #12366

merged 72 commits into from
Sep 24, 2024

Commits on Jan 16, 2024

  1. init the PR draft

    @qian-chu
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  2. Merge branch 'main' into dict_ref

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  4. Create 12366.newfeature.rst

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Commits on Jan 17, 2024

  1. Update 12366.newfeature.rst

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Commits on May 2, 2024

  1. Merge branch 'mne-tools:main' into dict_ref

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Commits on May 3, 2024

  1. Add custom reference based on dict 

    The current implementation is based on a dictionary mapping a list to each channel. The list contains the channels to average and take as reference for the respective channel.
I have also implemented an assertion to make sure that the channels in the dict correspond to the channels in the instance.
We might want to implement something about bad channels. If bad channels are present in the mapping, they should probably be skipped
    Alex Lepauvre committed May 3, 2024
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  3. BF: use isintance to check if dict

    Alex Lepauvre committed May 3, 2024
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  4. BF: remove extra copy of data

    Alex Lepauvre committed May 3, 2024
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  5. Add custom reference

    Alex Lepauvre committed May 3, 2024
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  6. change doc (add Alex)

    Qian Chu committed May 3, 2024
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  7. Add warning if bad channels in re-referencing scheme

    Alex Lepauvre committed May 3, 2024
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  8. Merge branch 'dict_ref' of https://github.com/qian-chu/mne-python int… 

    …o dict_ref
    Alex Lepauvre committed May 3, 2024
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  9. add _check_before_dict_reference and enrich set_eeg_reference_see_als… 

    …o_notes
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Commits on May 31, 2024

  1. Update reference.py

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  3. Update test_reference.py

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Commits on Jun 3, 2024

  1. Update reference.py

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  3. Update test_reference.py

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  5. formatting

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Commits on Jun 5, 2024

  1. dict does not accept repeated keys, no need to test

    @qian-chu
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  2. add test for warnings and raises

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  3. Update test_reference.py

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  4. Update docs.py

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  5. Merge branch 'mne-tools:main' into dict_ref

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Commits on Jun 7, 2024

  1. Data check test 

    Check that the data that were not referenced are untouched and that the data that were referenced were referenced correctly
    @AlexLepauvre
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  3. Add check of reference flag and bug correction

    @AlexLepauvre
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  5. Add tests for epochs object

    @AlexLepauvre
    AlexLepauvre committed Jun 7, 2024
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  6. Merge branch 'dict_ref' of https://github.com/qian-chu/mne-python int… 

    …o dict_ref
    @AlexLepauvre
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  8. Merge branch 'main' into dict_ref

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Commits on Jun 10, 2024

  1. formatting

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Commits on Jun 19, 2024

  1. Add warning for re-referencing electrode by itself

    @AlexLepauvre
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  3. Refactorize tests of epochs and raws

    @AlexLepauvre
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  5. Apply suggestions from code review 

    Co-authored-by: Daniel McCloy <[email protected]>
    @qian-chu @drammock
    qian-chu and drammock authored Jun 19, 2024
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  6. Re-organize warnings and errors

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Commits on Jun 21, 2024

  1. Merge branch 'main' into dict_ref

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Commits on Jul 2, 2024

  1. Merge branch 'main' into dict_ref

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Commits on Jul 3, 2024

  1. new dict check function as suggested

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  2. Merge branch 'main' into dict_ref

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Commits on Jul 9, 2024

  1. simplify (now that we guarantee list-like dict vals)

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  2. warn when keys (not just vals) are bad chs

    @drammock
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  3. clearer var name; only compute mismatch pairs if needed

    @drammock
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  4. refactor: convert to ch indices in helper func

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  5. return None (like REST/proj references) instead of copy of inst data

    @drammock
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  6. slightly less misleading docstring

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Commits on Jul 29, 2024

  1. modularize check_ssp and adds the check to dict-based reference

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  2. Merge branch 'main' into dict_ref

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Commits on Jul 30, 2024

  1. doc improvement

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  2. Merge branch 'main' into dict_ref

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Commits on Aug 10, 2024

  1. Merge branch 'main' into dict_ref

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Commits on Aug 23, 2024

  1. Alex not new contributor now

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  2. Merge branch 'main' into dict_ref

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  3. Merge branch 'dict_ref' of https://github.com/qian-chu/mne-python int… 

    …o dict_ref
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  4. Update 12366.newfeature.rst

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  5. Update 12366.newfeature.rst

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Commits on Sep 13, 2024

  1. Merge branch 'main' into dict_ref

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Commits on Sep 20, 2024

  1. MAINT: Reorder

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  2. Merge branch 'main' into dict_ref

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Commits on Sep 21, 2024

  1. Merge branch 'main' into dict_ref

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Commits on Sep 24, 2024

  1. Merge branch 'main' into dict_ref

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