[MRG] PCA flip for volumetric source estimates #13092
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Extension of PCA flip in volumetric setting. Underlying logic is pretty much identical to cortical case with respect to flip vector creation and PCA itself Added a check in PCA flip in case the flip is None or number of vertices is below 2, in which case PCA will return a trivial estimate of the signal Complete with its own unit test case
Shrecki
requested review from
drammock,
agramfort and
dengemann
as code owners
Shrecki
changed the title
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I belive this PR is ready for review :) (although I do not know why pip pre is failing on Windows) |
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Found some cruft, can you take a look at the diff on GitHub and make sure I found all of it?
Also with enhancements it's nice to see the effect in some example. Maybe you could modify this:
https://mne.tools/1.8/auto_examples/inverse/compute_mne_inverse_epochs_in_label.html
which comes from examples/inverse/compute_mne_inverse_epochs_in_label.py could be modified to add a volume example to show its flip modes as well? Or maybe some other example like tutorials/inverse/60_visualize_stc.py or examples/inverse/label_source_activations.py?
| # logger.info("Selected mode: " + mode) | ||
| # print("Entering _prepare_label_extraction") | ||
| # print("Selected mode: " + mode) |
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Cruft, should be removed. But really to help next time:
| # logger.info("Selected mode: " + mode) | |
| # print("Entering _prepare_label_extraction") | |
| # print("Selected mode: " + mode) | |
| logger.debug(f"Selected mode: {mode}") |
then if you run with verbose='debug' you will see the statement
| @@ -3445,6 +3456,7 @@ def _prepare_label_extraction(stc, labels, src, mode, allow_empty, use_sparse): | |||
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| bad_labels = list() | |||
| for li, label in enumerate(labels): | |||
| # print("Mode: " + mode + " li: " + str(li) + " label: " + str(label)) | |||
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| # print("Mode: " + mode + " li: " + str(li) + " label: " + str(label)) |
| # print(f"src: {src[:2]}") | ||
| # print(f"len(src): {len(src[:2])}") | ||
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| # print(f"src: {src[:2]}") | |
| # print(f"len(src): {len(src[:2])}") |
| @@ -1460,22 +1460,47 @@ def label_sign_flip(label, src): | |||
| flip : array | |||
| Sign flip vector (contains 1 or -1). | |||
| """ | |||
| if len(src) != 2: | |||
| raise ValueError("Only source spaces with 2 hemisphers are accepted") | |||
| if len(src) > 2 or len(src) == 0: | |||
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A better / more modern check would be something like:
_validate_type(src, SourceSpaces, "src")
_check_option("source space kind", src.kind, ("volume", "surface"))
if src.kind == "volume" and len(src) != 1:
raise ValueError("Only single-segment volumes, are supported, got labelized volume source space")
And incidentally I think eventually we could add support for segmented volume source spaces, as well as mixed source spaces (once surface + volume are fully supported, mixed isn't too bad after that). But probably not as part of this PR!
| if isbi_hemi: | ||
| lh_id = 0 | ||
| rh_id = 1 | ||
| lh_vertno = src[0]["vertno"] | ||
| rh_vertno = src[1]["vertno"] | ||
| elif label.hemi == "lh": | ||
| lh_vertno = src[0]["vertno"] | ||
| elif label.hemi == "rh": | ||
| rh_id = 0 | ||
| rh_vertno = src[0]["vertno"] | ||
| else: | ||
| raise Exception(f'Unknown hemisphere type "{label.hemi}"') |
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I don't totally follow this logic. It's a surface source space if and only if it's bihemi, and it's volume source space if and only if it's a single-element list. I think it would be cleaner to triage based on source space type probably...
| # if flip is None: # Happens if fewer than 2 vertices in the label | ||
| # if this_data.shape[] | ||
| # label_tc[i] = 0 | ||
| # else: |
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| # if flip is None: # Happens if fewer than 2 vertices in the label | |
| # if this_data.shape[] | |
| # label_tc[i] = 0 | |
| # else: |
| @@ -1469,7 +1613,7 @@ def objective(x): | |||
| assert_allclose(directions, want_nn, atol=2e-6) | |||
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| @testing.requires_testing_data | |||
| # @testing.requires_testing_data | |||
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| # @testing.requires_testing_data | |
| @testing.requires_testing_data |
| modes = ("mean", "max") if vector else ("mean", "max") | ||
| for mode in modes: |
What does this implement/fix?
This PR implements PCA flip in volumetric source estimates.
To do so, it relies on using the already existing _pca_flip method. _pca_flip has been slighly modified to check if at least two vertices are available within a label. If that is not the case, it returns trivially the original signal, as PCA is ill-defined in this case.
Additional information
Feel free to have a look and - of course - double-check for correctness!