[DRAFT] Redesign/datasets ICA addition #56
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Implement in-memory caching for speed
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Move this to the other PR. |
Drew-Wagner
requested changes
Mar 18, 2025
benchmarks/MOABB/dataio/ica.py
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| def process( | ||
| self, raw: mne.io.RawArray, raw_path: Union[str, Path] | ||
| ) -> mne.io.RawArray: | ||
| """Process raw data with ICA, computing or loading from cache.""" | ||
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| ica_path = self.get_ica_path(raw_path) | ||
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| if not ica_path.exists(): | ||
| ica = self.compute_ica(raw, ica_path) | ||
| else: | ||
| ica = mne.preprocessing.read_ica(ica_path, verbose="ERROR") | ||
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| # Create a copy of the raw data before applying ICA | ||
| raw_ica = raw.copy() | ||
| ica.apply(raw_ica) | ||
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| return raw_ica |
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Suggested change
| def process( | |
| self, raw: mne.io.RawArray, raw_path: Union[str, Path] | |
| ) -> mne.io.RawArray: | |
| """Process raw data with ICA, computing or loading from cache.""" | |
| ica_path = self.get_ica_path(raw_path) | |
| if not ica_path.exists(): | |
| ica = self.compute_ica(raw, ica_path) | |
| else: | |
| ica = mne.preprocessing.read_ica(ica_path, verbose="ERROR") | |
| # Create a copy of the raw data before applying ICA | |
| raw_ica = raw.copy() | |
| ica.apply(raw_ica) | |
| return raw_ica | |
| @property | |
| def dynamic_item(self): | |
| @takes("raw", "fpath") | |
| @provides("raw", "ica_path") | |
| def process( | |
| raw: mne.io.RawArray, fpath: Union[str, Path] | |
| ): | |
| """Process raw data with ICA, computing or loading from cache.""" | |
| ica_path = self.get_ica_path(fpath) | |
| if not ica_path.exists(): | |
| ica = self.compute_ica(raw, ica_path) | |
| else: | |
| ica = mne.preprocessing.read_ica(ica_path, verbose="ERROR") | |
| # Create a copy of the raw data before applying ICA | |
| raw_ica = raw.copy() | |
| ica.apply(raw_ica) | |
| yield raw_ica | |
| yield ica_path | |
| return process |
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function inside one function is not super nice
Co-authored-by: Drew Wagner <[email protected]>
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| bids_path.root = bids_path.root / ".." / "derivatives" / folder_name | ||
| # Keep the same base entities: | ||
| bids_path.update( | ||
| suffix="eeg", # override or confirm suffix | ||
| extension=".fif", | ||
| description=desc, # <-- This sets a desc=ica entity | ||
| check=True, # If you do not want BIDSPath to fail on derivative checks | ||
| ) |
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Suggested change
| bids_path.root = bids_path.root / ".." / "derivatives" / folder_name | |
| # Keep the same base entities: | |
| bids_path.update( | |
| suffix="eeg", # override or confirm suffix | |
| extension=".fif", | |
| description=desc, # <-- This sets a desc=ica entity | |
| check=True, # If you do not want BIDSPath to fail on derivative checks | |
| ) | |
| ica_path = bids_path.update( | |
| processing="ica", suffix="ica" | |
| ) |
| check=True, # If you do not want BIDSPath to fail on derivative checks | ||
| ) | ||
| # Make sure the folder is created | ||
| bids_path.fpath.parent.mkdir(parents=True, exist_ok=True) |
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Suggested change
| bids_path.fpath.parent.mkdir(parents=True, exist_ok=True) | |
| ica_path.mkdir(parents=True, exist_ok=True) |
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| ica_path = bids_path.fpath | ||
| metadata_path = ica_path.with_suffix(".json") |
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Suggested change
| ica_path = bids_path.fpath | |
| metadata_path = ica_path.with_suffix(".json") | |
| metadata_path = bids_path.update( | |
| suffix="metaica", extension=".json" | |
| ) |
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| if self.filter_params is not None: | ||
| # Apply high-pass filter only if filter parameters are provided | ||
| raw_filtered = raw.copy() | ||
| raw_filtered.filter(**self.filter_params) | ||
| else: | ||
| # Use raw data directly if no filtering is needed | ||
| raw_filtered = raw |
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Suggested change
| if self.filter_params is not None: | |
| # Apply high-pass filter only if filter parameters are provided | |
| raw_filtered = raw.copy() | |
| raw_filtered.filter(**self.filter_params) | |
| else: | |
| # Use raw data directly if no filtering is needed | |
| raw_filtered = raw | |
| raw.info['h_freq'] |
| n_components=self.n_components, | ||
| method=self.method, | ||
| random_state=self.random_state, | ||
| **self.fit_params, |
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| **self.fit_params, | |
| **self._fit_params, |
| @@ -95,10 +95,12 @@ def __init__( | |||
| data, | |||
| preload=False, | |||
| verbose=None, | |||
| # ica_processor: Optional[ICAProcessor] = None, | |||
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Suggested change
| # ica_processor: Optional[ICAProcessor] = None, |
description update Co-authored-by: Bru <[email protected]>
description update 2 Co-authored-by: Bru <[email protected]>
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added ica as dynamic item to preprocessing pipeline. uses BIDSPath and exposes method and other features. still has issues with the use of caching.