Add Riemannian Potato Field #142

qbarthelemy · 2021-09-22T06:37:17Z

This PR:

adds the class PotatoField,
adds an animated example in the gallery, on artifact detection by Riemannian Potato Field , compared with Riemannian Potato.

Q. Barthélemy, L. Mayaud, D. Ojeda, M. Congedo, "The Riemannian potato field: a tool for online signal quality index of EEG", IEEE TNSRE, 2019, link to pdf.

agramfort · 2021-09-26T13:02:44Z

examples/artifacts/plot_detect_riemannian_potato_field_EEG.py

+# -----------------------
+#
+# Riemannian potato field (RPF) [1]_ combines several potatoes of low dimension
+# , each one being designed to capture specific artifact typically affecting


breaking , here is weird

agramfort · 2021-09-26T13:03:28Z

examples/artifacts/plot_detect_riemannian_potato_field_EEG.py

+Online Artifact Detection with Riemannian Potato Field
+===============================================================================
+
+Example of Riemannian Potato Field [1]_ applied on EEG time-series to detect


Suggested change

Example of Riemannian Potato Field [1]_ applied on EEG time-series to detect

Example of Riemannian Potato Field (RPF) [1]_ applied on EEG time-series to detect

as you use the acronym below

agramfort · 2021-09-26T13:03:52Z

examples/artifacts/plot_detect_riemannian_potato_field_EEG.py

+#
+# Detect artifacts/outliers on test set, with an animation to imitate an online
+# acquisition, processing and artifact detection of EEG time-series.
+# Remak that all these potatoes are semi-dynamic: they are updated when EEG is


Suggested change

# Remak that all these potatoes are semi-dynamic: they are updated when EEG is

# Remark that all these potatoes are semi-dynamic: they are updated when EEG is

agramfort · 2021-09-26T13:04:28Z

examples/artifacts/plot_detect_riemannian_potato_field_EEG.py

+###############################################################################
+
+# Plot online detection (a dynamic display is required)


Suggested change

###############################################################################

# Plot online detection (a dynamic display is required)

###############################################################################

# Plot online detection (a dynamic display is required)

agramfort · 2021-09-26T13:05:01Z

pyriemann/clustering.py

+class PotatoField(BaseEstimator, TransformerMixin, ClassifierMixin):
+


Suggested change

class PotatoField(BaseEstimator, TransformerMixin, ClassifierMixin):

class PotatoField(BaseEstimator, TransformerMixin, ClassifierMixin):

agramfort · 2021-09-26T13:07:58Z

pyriemann/clustering.py

+
+        Returns
+        -------
+        z : ndarray, shape (n_potatoes, n_trials)


Suggested change

z : ndarray, shape (n_potatoes, n_trials)

z : ndarray, shape (n_trials, n_potatoes)

would be more natural

agramfort · 2021-09-26T13:08:49Z

tests/test_clustering.py

@@ -221,3 +260,57 @@ def test_Potato_specific_labels(get_covmats):
    assert_array_equal(np.unique(pt.predict(covmats)), [2, 7])
    # fit with custom positive label
    pt.fit(covmats, y=[2] * n_trials)
+
+
+def test_PotatoField_fit(get_covmats):


Suggested change

def test_PotatoField_fit(get_covmats):

def test_potato_field_fit(get_covmats):

agramfort · 2021-09-26T13:08:59Z

tests/test_clustering.py

+        pf.fit([covmats1, covmats2[:1]])
+
+
+def test_PotatoField_partialfit(get_covmats):


Suggested change

def test_PotatoField_partialfit(get_covmats):

def test_potato_field_partial_fit(get_covmats):

agramfort · 2021-09-26T13:09:13Z

tests/test_clustering.py

+        pf.partial_fit([covmats1, covmats2[:1]])
+
+
+def test_PotatoField_transform(get_covmats):


Suggested change

def test_PotatoField_transform(get_covmats):

def test_potato_field_transform(get_covmats):

agramfort · 2021-09-26T13:09:22Z

tests/test_clustering.py

+        pf.transform([covmats1, covmats2[:1]])
+
+
+def test_PotatoField_predictproba(get_covmats):


Suggested change

def test_PotatoField_predictproba(get_covmats):

def test_potato_field_predict_proba(get_covmats):

sylvchev · 2021-09-27T13:15:52Z

examples/artifacts/plot_detect_riemannian_potato_field_EEG.py

+ax[1].set_ylim([-1.5, 8.5])
+ax[1].legend(loc='upper left')
+axp = ax[1].twinx()
+axp.set(ylabel='RPF probability of being clean')


Suggested change

axp.set(ylabel='RPF probability of being clean')

axp.set(ylabel='RPF probability of clean EEG')

examples/artifacts/plot_detect_riemannian_potato_field_EEG.py

pyriemann/clustering.py

plcrodrigues · 2021-09-29T15:19:28Z

pyriemann/clustering.py

+        X : list of n_potatoes ndarray of shape (n_trials, n_channels,
+                n_channels), with same n_trials but different n_channels
+            list of ndarray of SPD matrices.


Same as above.

pyriemann/clustering.py

plcrodrigues · 2021-09-29T15:29:45Z

pyriemann/clustering.py

+    p_threshold : float (default 0.01)
+        Threshold on probability to being clean, in (0, 1).


Can you be more precise?

Ok, I complete the doc.

Co-authored-by: Pedro L. C. Rodrigues <pedro.rodrigues01@gmail.com>

nbara · 2021-10-01T11:55:25Z

Hi @qbarthelemy, one of the figures is empty in the docs :

https://pyriemann.readthedocs.io/en/latest/auto_examples/artifacts/plot_detect_riemannian_potato_field_EEG.html#sphx-glr-auto-examples-artifacts-plot-detect-riemannian-potato-field-eeg-py

Is that normal?

qbarthelemy · 2021-10-01T17:45:03Z

Yes, it's normal: since it is an online processing, a dynamic display is required.
In you want to see the animation, run the example from a shell.

That being said, I have tried to plot the animation in the html documentation, but I have not found the way to do not display it twice. See #133 (comment) .
Your ideas are welcome!

* adding the sampling.py feature and two examples related to it * cleaning up * correcting pep8 issues * getting rid of the tqdm dependency * Update examples/sampling/plot_riemannian_gaussian.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update examples/sampling/plot_toy_classification.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update pyriemann/sampling.py Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> * Update pyriemann/sampling.py Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> * Update pyriemann/sampling.py Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> * Remove ignored files * Update examples/sampling/plot_toy_classification.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update examples/sampling/plot_toy_classification.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update examples/sampling/plot_toy_classification.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update pyriemann/datasets.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update examples/sampling/plot_riemannian_gaussian.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update pyriemann/sampling.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update pyriemann/sampling.py Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> * Update pyriemann/sampling.py Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> * Update pyriemann/sampling.py Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> * Update pyriemann/sampling.py Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> * Update pyriemann/sampling.py Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> * Update pyriemann/sampling.py Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> * taking into account agramfort and qbarthelemy comments * more updates * adding make_outliers function * putting make_* functions into simulated.py for consistency * including corrections and comments * ... * further corrections * ... * flake8 * adding a few tests * flake8 * including reviews; adding a new test * ... * adding warnings * trying to edit API.rst * Add Riemannian Potato Field (#142) * add PotatoField and improve Potato * add example on PotatoField and clean example on Potato * add tests and complete api * minor corrections * minor modifs * commit suggestions * complete doc * complete doc again * Apply suggestions from code review Co-authored-by: Pedro L. C. Rodrigues <pedro.rodrigues01@gmail.com> * complete doc Co-authored-by: Pedro L. C. Rodrigues <pedro.rodrigues01@gmail.com> * remove class templates in api.rst for new functionns * adding things to whatsnew.rst * ... * adding the sampling.py feature and two examples related to it * cleaning up * correcting pep8 issues * getting rid of the tqdm dependency * Update examples/sampling/plot_riemannian_gaussian.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update examples/sampling/plot_toy_classification.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update pyriemann/sampling.py Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> * Update pyriemann/sampling.py Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> * Update pyriemann/sampling.py Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> * Remove ignored files * Update examples/sampling/plot_toy_classification.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update examples/sampling/plot_toy_classification.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update examples/sampling/plot_toy_classification.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update pyriemann/datasets.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update examples/sampling/plot_riemannian_gaussian.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update pyriemann/sampling.py Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> * Update pyriemann/sampling.py Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> * Update pyriemann/sampling.py Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> * Update pyriemann/sampling.py Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> * Update pyriemann/sampling.py Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> * Update pyriemann/sampling.py Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> * Update pyriemann/sampling.py Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> * taking into account agramfort and qbarthelemy comments * more updates * adding make_outliers function * putting make_* functions into simulated.py for consistency * including corrections and comments * ... * further corrections * ... * flake8 * adding a few tests * flake8 * including reviews; adding a new test * ... * adding warnings * trying to edit API.rst * remove class templates in api.rst for new functionns * adding things to whatsnew.rst * ... * adding ValueError tests * solving problem coming from conftest.py * ... * ... * trying to make tests pass? * flake8 * re-add init file * move is_* functions into pyriemann to be reused by pyriemann methods * remove pytest import from utils.test * re-add tests for raise errors * refactor test * revert changes on doc/conf.py * complete tests * updating api.rst * fix whatsnew.rst * Update doc/whatsnew.rst Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org> Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com>

qbarthelemy added 3 commits September 22, 2021 08:34

add PotatoField and improve Potato

4b6cdae

add example on PotatoField and clean example on Potato

d1d67ac

add tests and complete api

fd89d78

qbarthelemy requested review from sylvchev, agramfort and lkorczowski September 22, 2021 06:37

minor corrections

4cc9788

qbarthelemy requested a review from plcrodrigues September 22, 2021 06:50

minor modifs

993fd2e

agramfort reviewed Sep 26, 2021

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sylvchev approved these changes Sep 27, 2021

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qbarthelemy added 2 commits September 27, 2021 21:54

commit suggestions

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complete doc

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agramfort approved these changes Sep 28, 2021

View reviewed changes

complete doc again

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plcrodrigues reviewed Sep 29, 2021

View reviewed changes

qbarthelemy and others added 2 commits September 29, 2021 18:30

Apply suggestions from code review

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Co-authored-by: Pedro L. C. Rodrigues <pedro.rodrigues01@gmail.com>

complete doc

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plcrodrigues approved these changes Sep 29, 2021

View reviewed changes

qbarthelemy merged commit b35873b into pyRiemann:master Sep 29, 2021

qbarthelemy deleted the rpf branch September 29, 2021 17:33

qbarthelemy mentioned this pull request Jan 19, 2022

Display animated figures in the documentation #161

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Add Riemannian Potato Field #142

Add Riemannian Potato Field #142

qbarthelemy commented Sep 22, 2021 •

edited

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plcrodrigues Sep 29, 2021

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qbarthelemy Sep 29, 2021

nbara commented Oct 1, 2021 •

edited

qbarthelemy commented Oct 1, 2021 •

edited

	Example of Riemannian Potato Field [1]_ applied on EEG time-series to detect
	Example of Riemannian Potato Field (RPF) [1]_ applied on EEG time-series to detect

	# Remak that all these potatoes are semi-dynamic: they are updated when EEG is
	# Remark that all these potatoes are semi-dynamic: they are updated when EEG is

		###############################################################################

		# Plot online detection (a dynamic display is required)

		class PotatoField(BaseEstimator, TransformerMixin, ClassifierMixin):

	z : ndarray, shape (n_potatoes, n_trials)
	z : ndarray, shape (n_trials, n_potatoes)

	def test_PotatoField_fit(get_covmats):
	def test_potato_field_fit(get_covmats):

		pf.fit([covmats1, covmats2[:1]])


		def test_PotatoField_partialfit(get_covmats):

	def test_PotatoField_partialfit(get_covmats):
	def test_potato_field_partial_fit(get_covmats):

		pf.partial_fit([covmats1, covmats2[:1]])


		def test_PotatoField_transform(get_covmats):

	def test_PotatoField_transform(get_covmats):
	def test_potato_field_transform(get_covmats):

		pf.transform([covmats1, covmats2[:1]])


		def test_PotatoField_predictproba(get_covmats):

	def test_PotatoField_predictproba(get_covmats):
	def test_potato_field_predict_proba(get_covmats):

	axp.set(ylabel='RPF probability of being clean')
	axp.set(ylabel='RPF probability of clean EEG')

		p_threshold : float (default 0.01)
		Threshold on probability to being clean, in (0, 1).

Add Riemannian Potato Field #142

Add Riemannian Potato Field #142

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qbarthelemy commented Sep 22, 2021 • edited

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nbara commented Oct 1, 2021 • edited

qbarthelemy commented Oct 1, 2021 • edited

qbarthelemy commented Sep 22, 2021 •

edited

nbara commented Oct 1, 2021 •

edited

qbarthelemy commented Oct 1, 2021 •

edited