doc: clarify ica.apply include and exclude params by sappelhoff · Pull Request #10086 · mne-tools/mne-python

sappelhoff · 2021-12-03T16:53:20Z

That's how I understand it (and the code looks like it in the source and when running it) ... so I thought I'd add this to the docstring to clear things up.

The relevant things happen here:

mne-python/mne/preprocessing/ica.py

Lines 1796 to 1801 in c3ff05c

    
           def _pick_sources(self, data, include, exclude, n_pca_components): 
        
               """Aux function.""" 
        
               if n_pca_components is None: 
        
                   n_pca_components = self.n_pca_components 
        
               data = self._pre_whiten(data) 
        
               exclude = self._check_exclude(exclude)

where _check_exclude does this (either union of ica.exclude and exclude, or just ica.exclude, if exclude is "n/a"):

mne-python/mne/preprocessing/ica.py

Lines 1726 to 1731 in c3ff05c

    
           def _check_exclude(self, exclude): 
        
               if exclude is None: 
        
                   return list(set(self.exclude)) 
        
               else: 
        
                   # Allow both self.exclude and exclude to be array-like: 
        
                   return list(set(self.exclude).union(set(exclude)))

include is handled a few lines below in _pick_sources:

mne-python/mne/preprocessing/ica.py

Lines 1820 to 1824 in c3ff05c

    
           sel_keep = np.arange(self.n_components_) 
        
           if include not in (None, []): 
        
               sel_keep = np.unique(include) 
        
           elif exclude not in (None, []): 
        
               sel_keep = np.setdiff1d(np.arange(self.n_components_), exclude)

i.e., all are included if None ... else the specific selection specified ... and then idxs are removed from it using exclude as previously triaged

mne/preprocessing/ica.py

* upstream/main: Use fixes._compare_version for version checks everywhere (mne-tools#10091) Fast annotation from mask (mne-tools#10089) fix trace offsets in butterfly mode (mne-tools#10087) fix plot_compare_evokeds topo legend axes placement (mne-tools#9927) doc: clarify ica.apply include and exclude params (mne-tools#10086) MRG: Make y a required parameter in CSP.fit_transform() (mne-tools#10084) Add scrollbar to report tag dropdown menu (mne-tools#10082)

doc: clarify ica.apply include and exclude params

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sappelhoff commented Dec 3, 2021

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agramfort approved these changes Dec 3, 2021

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drammock approved these changes Dec 3, 2021

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drammock merged commit d7202b4 into mne-tools:main Dec 3, 2021

sappelhoff deleted the doc/ica/exclude branch December 3, 2021 21:12

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doc: clarify ica.apply include and exclude params#10086

doc: clarify ica.apply include and exclude params#10086
drammock merged 2 commits intomne-tools:mainfrom
sappelhoff:doc/ica/exclude

sappelhoff commented Dec 3, 2021

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	def _pick_sources(self, data, include, exclude, n_pca_components):
	"""Aux function."""
	if n_pca_components is None:
	n_pca_components = self.n_pca_components
	data = self._pre_whiten(data)
	exclude = self._check_exclude(exclude)

	def _check_exclude(self, exclude):
	if exclude is None:
	return list(set(self.exclude))
	else:
	# Allow both self.exclude and exclude to be array-like:
	return list(set(self.exclude).union(set(exclude)))

	sel_keep = np.arange(self.n_components_)
	if include not in (None, []):
	sel_keep = np.unique(include)
	elif exclude not in (None, []):
	sel_keep = np.setdiff1d(np.arange(self.n_components_), exclude)

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sappelhoff commented Dec 3, 2021

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