Braindecode 1.3.2__tar.gz → 1.3.2.dev167912513__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {braindecode-1.3.2/braindecode.egg-info → braindecode-1.3.2.dev167912513}/PKG-INFO +40 -8
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/README.rst +36 -6
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/braindecode/datasets/__init__.py +2 -1
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/braindecode/datasets/base.py +427 -1
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/braindecode/datasets/bids/datasets.py +10 -1
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/braindecode/datasets/mne.py +48 -4
- braindecode-1.3.2.dev167912513/braindecode/datasets/tuh.py +997 -0
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/braindecode/models/__init__.py +4 -0
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/braindecode/models/base.py +10 -1
- braindecode-1.3.2.dev167912513/braindecode/models/cbramod.py +350 -0
- braindecode-1.3.2.dev167912513/braindecode/models/eegpt.py +1424 -0
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/braindecode/models/labram.py +327 -77
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/braindecode/models/summary.csv +2 -0
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/braindecode/models/util.py +3 -1
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/braindecode/modules/__init__.py +4 -0
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/braindecode/modules/attention.py +134 -0
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/braindecode/modules/convolution.py +20 -0
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/braindecode/modules/filter.py +4 -2
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/braindecode/preprocessing/preprocess.py +17 -0
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/braindecode/preprocessing/windowers.py +350 -82
- braindecode-1.3.2.dev167912513/braindecode/version.py +1 -0
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/braindecode/visualization/gradients.py +7 -7
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513/braindecode.egg-info}/PKG-INFO +40 -8
- braindecode-1.3.2.dev167912513/braindecode.egg-info/SOURCES.txt +159 -0
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/braindecode.egg-info/requires.txt +3 -1
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/docs/api.rst +7 -0
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/docs/cite.rst +42 -4
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/docs/conf.py +1 -1
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/docs/models/models_categorization.rst +3 -3
- braindecode-1.3.2.dev167912513/docs/sg_execution_times.rst +110 -0
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/docs/whats_new.rst +46 -3
- {braindecode-1.3.2 → braindecode-1.3.2.dev167912513}/pyproject.toml +16 -14
- braindecode-1.3.2/braindecode/datasets/tuh.py +0 -591
- braindecode-1.3.2/braindecode/version.py +0 -1
- braindecode-1.3.2/braindecode.egg-info/SOURCES.txt +0 -675
- braindecode-1.3.2/docs/_build/html/_downloads/090305d06248840b75133975e5121f41/plot_sleep_staging_chambon2018.ipynb +0 -291
- braindecode-1.3.2/docs/_build/html/_downloads/0ada35f18bb95235ba2842270483081f/plot_finetune_foundation_model.ipynb +0 -237
- braindecode-1.3.2/docs/_build/html/_downloads/0f2bf063e08b7d05b80e0004fcbbb6f9/benchmark_lazy_eager_loading.ipynb +0 -183
- braindecode-1.3.2/docs/_build/html/_downloads/137d0b161de96c88644fd65258fc20b5/tutorial_create_fixed_window_length.ipynb +0 -190
- braindecode-1.3.2/docs/_build/html/_downloads/1c6590d134fa0befda654e89aa55b2ac/plot_benchmark_preprocessing.ipynb +0 -104
- braindecode-1.3.2/docs/_build/html/_downloads/1d879df548fa18be8c23d9ca0dc008d4/plot_data_augmentation.ipynb +0 -259
- braindecode-1.3.2/docs/_build/html/_downloads/2466f8ec5c733d0bd65e187b45d875cc/plot_data_augmentation_search.ipynb +0 -302
- braindecode-1.3.2/docs/_build/html/_downloads/263464a28477cf8decb861ae6e2e9be7/plot_how_train_test_and_tune.ipynb +0 -375
- braindecode-1.3.2/docs/_build/html/_downloads/3862cafd7f0d815e434319ffe525afc8/plot_bcic_iv_2a_moabb_cropped.ipynb +0 -226
- braindecode-1.3.2/docs/_build/html/_downloads/408ca4ffd0ea1f76faa9ef602734ac94/plot_tuh_eeg_corpus.ipynb +0 -187
- braindecode-1.3.2/docs/_build/html/_downloads/5030717acb00990b394b83314b0797d9/plot_bids_dataset_example.ipynb +0 -97
- braindecode-1.3.2/docs/_build/html/_downloads/66ea18b3b9cf0802bbd32bb903ab554e/plot_temporal_generalization.ipynb +0 -312
- braindecode-1.3.2/docs/_build/html/_downloads/75a73c7d94f3a671fd3dec28f4031ead/plot_regression.ipynb +0 -212
- braindecode-1.3.2/docs/_build/html/_downloads/84fbcd59a346e5e56758285122dc69e2/plot_sleep_staging_eldele2021.ipynb +0 -291
- braindecode-1.3.2/docs/_build/html/_downloads/8616a7f968141825e56ab3e3d59be449/plot_tuh_discrete_multitarget.ipynb +0 -169
- braindecode-1.3.2/docs/_build/html/_downloads/8b5ba06718764b959e8dea1dd0bb97df/plot_sleep_staging_usleep.ipynb +0 -255
- braindecode-1.3.2/docs/_build/html/_downloads/91651c9d4fde110b4a53f5775a91acc5/plot_mne_dataset_example.ipynb +0 -104
- braindecode-1.3.2/docs/_build/html/_downloads/93fdea8cbadaf0e3afa2eb2be3ebc483/bcic_iv_4_ecog_trial.ipynb +0 -376
- braindecode-1.3.2/docs/_build/html/_downloads/9a4447462c3b255ba7e5ca212bbadd52/plot_bcic_iv_2a_moabb_trial.ipynb +0 -271
- braindecode-1.3.2/docs/_build/html/_downloads/9ecad1eb1db853df0ba20dbb97303c02/plot_exca_config.ipynb +0 -439
- braindecode-1.3.2/docs/_build/html/_downloads/a2f12129facb042643a99d4b9de1886d/bcic_iv_4_ecog_cropped.ipynb +0 -345
- braindecode-1.3.2/docs/_build/html/_downloads/a39e4245738e55e0eb7084c545ed05bc/plot_hyperparameter_tuning_with_scikit-learn.ipynb +0 -257
- braindecode-1.3.2/docs/_build/html/_downloads/a6249715d3c30cb41c4af85938cca008/plot_moabb_dataset_example.ipynb +0 -140
- braindecode-1.3.2/docs/_build/html/_downloads/a868f9d41de95f5f6defc26e291cf4aa/plot_preprocessing_classes.ipynb +0 -194
- braindecode-1.3.2/docs/_build/html/_downloads/a86d0c5f3a882a069df1683a708d3e25/plot_train_in_pure_pytorch_and_pytorch_lightning.ipynb +0 -250
- braindecode-1.3.2/docs/_build/html/_downloads/aa8426d97090e7b3062c4e4732c3214a/plot_relative_positioning.ipynb +0 -266
- braindecode-1.3.2/docs/_build/html/_downloads/b9d19304ecd233ea7a79d4365316ea49/plot_load_save_datasets.ipynb +0 -176
- braindecode-1.3.2/docs/_build/html/_downloads/cb62940d13f700ed2b9e813705e9d437/plot_moabb_benchmark.ipynb +0 -122
- braindecode-1.3.2/docs/_build/html/_downloads/cd24c95e5e6c988ebb6ece50ac672ab5/plot_bcic_iv_2a_eegprep_cleaning.ipynb +0 -260
- braindecode-1.3.2/docs/_build/html/_downloads/f158ead3e4720f6f4685ff1d3f48dc15/plot_hub_integration.ipynb +0 -201
- braindecode-1.3.2/docs/_build/html/_downloads/f3c89d39e947a121c7920b4d415413a2/plot_split_dataset.ipynb +0 -180
- braindecode-1.3.2/docs/_build/html/_downloads/f7b38cac92c078838442753121efc297/plot_custom_dataset_example.ipynb +0 -140
- braindecode-1.3.2/docs/_build/html/_downloads/fff46913db5173d3ae22c1113acffb45/plot_basic_training_epochs.ipynb +0 -237
- braindecode-1.3.2/docs/auto_examples/advanced_training/bcic_iv_4_ecog_cropped.ipynb +0 -345
- braindecode-1.3.2/docs/auto_examples/advanced_training/bcic_iv_4_ecog_cropped.rst +0 -626
- braindecode-1.3.2/docs/auto_examples/advanced_training/index.rst +0 -173
- braindecode-1.3.2/docs/auto_examples/advanced_training/plot_data_augmentation.ipynb +0 -259
- braindecode-1.3.2/docs/auto_examples/advanced_training/plot_data_augmentation.rst +0 -1990
- braindecode-1.3.2/docs/auto_examples/advanced_training/plot_data_augmentation_search.ipynb +0 -302
- braindecode-1.3.2/docs/auto_examples/advanced_training/plot_data_augmentation_search.rst +0 -2219
- braindecode-1.3.2/docs/auto_examples/advanced_training/plot_exca_config.ipynb +0 -439
- braindecode-1.3.2/docs/auto_examples/advanced_training/plot_exca_config.rst +0 -1002
- braindecode-1.3.2/docs/auto_examples/advanced_training/plot_finetune_foundation_model.ipynb +0 -237
- braindecode-1.3.2/docs/auto_examples/advanced_training/plot_finetune_foundation_model.rst +0 -611
- braindecode-1.3.2/docs/auto_examples/advanced_training/plot_moabb_benchmark.ipynb +0 -122
- braindecode-1.3.2/docs/auto_examples/advanced_training/plot_moabb_benchmark.rst +0 -319
- braindecode-1.3.2/docs/auto_examples/advanced_training/plot_relative_positioning.ipynb +0 -266
- braindecode-1.3.2/docs/auto_examples/advanced_training/plot_relative_positioning.rst +0 -875
- braindecode-1.3.2/docs/auto_examples/advanced_training/plot_temporal_generalization.ipynb +0 -312
- braindecode-1.3.2/docs/auto_examples/advanced_training/plot_temporal_generalization.rst +0 -944
- braindecode-1.3.2/docs/auto_examples/advanced_training/sg_execution_times.rst +0 -58
- braindecode-1.3.2/docs/auto_examples/applied_examples/bcic_iv_4_ecog_trial.ipynb +0 -376
- braindecode-1.3.2/docs/auto_examples/applied_examples/bcic_iv_4_ecog_trial.rst +0 -581
- braindecode-1.3.2/docs/auto_examples/applied_examples/index.rst +0 -137
- braindecode-1.3.2/docs/auto_examples/applied_examples/plot_sleep_staging_chambon2018.ipynb +0 -291
- braindecode-1.3.2/docs/auto_examples/applied_examples/plot_sleep_staging_chambon2018.rst +0 -2091
- braindecode-1.3.2/docs/auto_examples/applied_examples/plot_sleep_staging_eldele2021.ipynb +0 -291
- braindecode-1.3.2/docs/auto_examples/applied_examples/plot_sleep_staging_eldele2021.rst +0 -2185
- braindecode-1.3.2/docs/auto_examples/applied_examples/plot_sleep_staging_usleep.ipynb +0 -255
- braindecode-1.3.2/docs/auto_examples/applied_examples/plot_sleep_staging_usleep.rst +0 -2096
- braindecode-1.3.2/docs/auto_examples/applied_examples/plot_tuh_eeg_corpus.ipynb +0 -187
- braindecode-1.3.2/docs/auto_examples/applied_examples/plot_tuh_eeg_corpus.rst +0 -497
- braindecode-1.3.2/docs/auto_examples/applied_examples/sg_execution_times.rst +0 -52
- braindecode-1.3.2/docs/auto_examples/applied_examples/tutorial_create_fixed_window_length.ipynb +0 -190
- braindecode-1.3.2/docs/auto_examples/applied_examples/tutorial_create_fixed_window_length.rst +0 -365
- braindecode-1.3.2/docs/auto_examples/datasets_io/benchmark_lazy_eager_loading.ipynb +0 -183
- braindecode-1.3.2/docs/auto_examples/datasets_io/benchmark_lazy_eager_loading.rst +0 -504
- braindecode-1.3.2/docs/auto_examples/datasets_io/index.rst +0 -209
- braindecode-1.3.2/docs/auto_examples/datasets_io/plot_benchmark_preprocessing.ipynb +0 -104
- braindecode-1.3.2/docs/auto_examples/datasets_io/plot_benchmark_preprocessing.rst +0 -588
- braindecode-1.3.2/docs/auto_examples/datasets_io/plot_bids_dataset_example.ipynb +0 -97
- braindecode-1.3.2/docs/auto_examples/datasets_io/plot_bids_dataset_example.rst +0 -230
- braindecode-1.3.2/docs/auto_examples/datasets_io/plot_custom_dataset_example.ipynb +0 -140
- braindecode-1.3.2/docs/auto_examples/datasets_io/plot_custom_dataset_example.rst +0 -323
- braindecode-1.3.2/docs/auto_examples/datasets_io/plot_hub_integration.ipynb +0 -201
- braindecode-1.3.2/docs/auto_examples/datasets_io/plot_hub_integration.rst +0 -720
- braindecode-1.3.2/docs/auto_examples/datasets_io/plot_load_save_datasets.ipynb +0 -176
- braindecode-1.3.2/docs/auto_examples/datasets_io/plot_load_save_datasets.rst +0 -494
- braindecode-1.3.2/docs/auto_examples/datasets_io/plot_mne_dataset_example.ipynb +0 -104
- braindecode-1.3.2/docs/auto_examples/datasets_io/plot_mne_dataset_example.rst +0 -351
- braindecode-1.3.2/docs/auto_examples/datasets_io/plot_moabb_dataset_example.ipynb +0 -140
- braindecode-1.3.2/docs/auto_examples/datasets_io/plot_moabb_dataset_example.rst +0 -320
- braindecode-1.3.2/docs/auto_examples/datasets_io/plot_split_dataset.ipynb +0 -180
- braindecode-1.3.2/docs/auto_examples/datasets_io/plot_split_dataset.rst +0 -656
- braindecode-1.3.2/docs/auto_examples/datasets_io/plot_tuh_discrete_multitarget.ipynb +0 -169
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- braindecode-1.3.2/docs/auto_examples/index.rst +0 -697
- braindecode-1.3.2/docs/auto_examples/model_building/index.rst +0 -191
- braindecode-1.3.2/docs/auto_examples/model_building/plot_basic_training_epochs.ipynb +0 -237
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- braindecode-1.3.2/docs/auto_examples/model_building/plot_bcic_iv_2a_eegprep_cleaning.ipynb +0 -260
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- braindecode-1.3.2/docs/auto_examples/model_building/plot_bcic_iv_2a_moabb_cropped.ipynb +0 -226
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- braindecode-1.3.2/docs/auto_examples/model_building/plot_how_train_test_and_tune.ipynb +0 -375
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learning with EEG recordings. Please use the following reference:
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@@ -16,7 +16,7 @@ from .nmt import NMT
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from .siena import SIENA
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from .sleep_physio_challe_18 import SleepPhysionetChallenge2018
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from .sleep_physionet import SleepPhysionet
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from .tuh import TUH, TUHAbnormal
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from .tuh import TUH, TUHAbnormal, TUHEvents
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from .xy import create_from_X_y
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__all__ = [
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@@ -34,6 +34,7 @@ __all__ = [
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"create_from_mne_epochs",
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"TUH",
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"TUHAbnormal",
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"TUHEvents",
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"SIENA",
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"NMT",
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"CHBMIT",
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@@ -11,11 +11,13 @@
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from __future__ import annotations
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import bisect
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import html as _html
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import json
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import os
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import shutil
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import warnings
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from abc import abstractmethod
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from collections import Counter
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from collections.abc import Callable
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from glob import glob
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from typing import Any, Generic, Iterable, no_type_check
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@@ -42,6 +44,256 @@ def _create_description(description) -> pd.Series:
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return description
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def _html_row(label, value):
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"""Generate a single HTML table row."""
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label = _html.escape(str(label))
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value = _html.escape(str(value))
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return f"<tr><td><b>{label}</b></td><td>{value}</td></tr>"
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_METADATA_INTERNAL_COLS = {
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"i_window_in_trial",
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"i_start_in_trial",
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"i_stop_in_trial",
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"target",
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}
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def _metadata_summary(metadata):
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"""Summarize window metadata into a dict.
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Returns a dict with keys: n_windows, target_info, extra_columns,
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window_info, is_lazy.
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"""
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is_lazy = not isinstance(metadata, pd.DataFrame)
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if is_lazy:
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n_windows = len(metadata)
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columns = list(metadata.columns) if hasattr(metadata, "columns") else []
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extra_columns = [str(c) for c in columns if c not in _METADATA_INTERNAL_COLS]
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return {
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"n_windows": n_windows,
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"target_info": None,
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"extra_columns": extra_columns,
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"window_info": None,
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"is_lazy": True,
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}
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n_windows = len(metadata)
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extra_columns = [
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str(c) for c in metadata.columns if c not in _METADATA_INTERNAL_COLS
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]
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target_info = None
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if "target" in metadata.columns:
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targets = metadata["target"]
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n_unique = targets.nunique()
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if n_unique <= 10:
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counts = targets.value_counts().sort_index().to_dict()
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target_info = f"{n_unique} unique ({counts})"
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else:
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target_info = f"{n_unique} unique targets"
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window_info = None
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if "i_start_in_trial" in metadata.columns and "i_stop_in_trial" in metadata.columns:
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sizes = metadata["i_stop_in_trial"] - metadata["i_start_in_trial"]
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if len(sizes) == 0:
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pass
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elif (min_s := int(sizes.min())) == (max_s := int(sizes.max())):
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window_info = {"min": min_s, "max": max_s, "uniform": True}
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else:
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window_info = {"min": min_s, "max": max_s, "uniform": False}
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return {
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"n_windows": n_windows,
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"target_info": target_info,
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"extra_columns": extra_columns,
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"window_info": window_info,
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"is_lazy": False,
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}
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def _concat_metadata_summary(datasets):
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"""Aggregate metadata summary across datasets without full concatenation.
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Returns a dict with keys: window_info, target_info, extra_columns.
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"""
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overall_min = None
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overall_max = None
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target_counts = Counter()
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extra_cols = set()
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for ds in datasets:
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if hasattr(ds, "windows"):
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md = ds.windows.metadata
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elif hasattr(ds, "metadata"):
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md = ds.metadata
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else:
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continue
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if md is None or len(md) == 0:
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continue
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extra_cols.update(
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str(c) for c in md.columns if c not in _METADATA_INTERNAL_COLS
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)
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if "i_start_in_trial" in md.columns and "i_stop_in_trial" in md.columns:
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sizes = md["i_stop_in_trial"] - md["i_start_in_trial"]
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if len(sizes) > 0:
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ds_min, ds_max = int(sizes.min()), int(sizes.max())
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overall_min = (
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ds_min if overall_min is None else min(overall_min, ds_min)
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)
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overall_max = (
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ds_max if overall_max is None else max(overall_max, ds_max)
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)
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if "target" in md.columns:
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target_counts.update(md["target"].value_counts().to_dict())
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window_info = None
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if overall_min is not None:
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window_info = {
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"min": overall_min,
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"max": overall_max,
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"uniform": overall_min == overall_max,
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}
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target_info = None
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if target_counts:
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n_unique = len(target_counts)
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if n_unique <= 10:
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sorted_counts = dict(sorted(target_counts.items()))
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target_info = f"{n_unique} unique ({sorted_counts})"
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else:
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target_info = f"{n_unique} unique targets"
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return {
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"window_info": window_info,
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"target_info": target_info,
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"extra_columns": sorted(extra_cols),
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}
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def _channel_info(mne_obj):
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"""Extract channel summary from an mne object.
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Returns (n_ch, type_str, sfreq).
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"""
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info = mne_obj.info
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n_ch = info["nchan"]
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sfreq = info["sfreq"]
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ch_types = mne_obj.get_channel_types()
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type_counts = Counter(ch_types)
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type_str = ", ".join(f"{cnt} {t.upper()}" for t, cnt in sorted(type_counts.items()))
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return n_ch, type_str, sfreq
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def _window_info(crop_inds, sfreq):
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"""Extract window size from crop indices.
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Returns (win_samples, win_secs) or None if crop_inds is empty.
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"""
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if len(crop_inds) == 0:
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return None
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first = crop_inds[0]
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win_samples = int(first[2] - first[1])
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win_secs = win_samples / sfreq
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return win_samples, win_secs
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class _ReprBuilder:
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"""Lightweight builder that renders both text and HTML from the same data."""
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def __init__(self, cls_name, type_display=None):
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self._cls_name = cls_name
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self._type_display = type_display or cls_name
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self._header_parts = []
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self._header_rows = []
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self._items = []
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def add_header(self, header_text, label, value):
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"""Add to both the compact ``<ClassName | ...>`` line and an HTML row."""
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self._header_parts.append(header_text)
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self._header_rows.append((label, value))
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return self
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def add_row(self, label, value):
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"""Add a detail row (text: `` label: value``, HTML: ``<tr>``)."""
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self._items.append(("row", label, value))
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return self
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def add_footnote(self, text):
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"""Add a footnote (text: `` (text)``, HTML: italic ``<td colspan=2>``)."""
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self._items.append(("footnote", text, None))
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return self
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def to_repr(self):
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if self._header_parts:
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parts = " | ".join(self._header_parts)
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lines = [f"<{self._cls_name} | {parts}>"]
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else:
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lines = [f"<{self._cls_name}>"]
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for kind, label, value in self._items:
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if kind == "row":
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lines.append(f" {label}: {value}")
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else:
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lines.append(f" ({label})")
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return "\n".join(lines)
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def to_html(self):
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rows = [_html_row("Type", self._type_display)]
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for label, value in self._header_rows:
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rows.append(_html_row(label, value))
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for kind, label, value in self._items:
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if kind == "row":
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html_label = label[0].upper() + label[1:]
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rows.append(_html_row(html_label, value))
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else:
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rows.append(
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f"<tr><td colspan='2'><i>{_html.escape(str(label))}</i></td></tr>"
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)
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table_rows = "\n".join(rows)
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esc_name = _html.escape(str(self._cls_name))
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return (
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f"<table border='1' class='dataframe'>\n"
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f" <thead><tr><th colspan='2'>{esc_name}</th></tr></thead>\n"
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f" <tbody>\n{table_rows}\n </tbody>\n</table>"
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)
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def _build_windowed_repr(
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cls_name, n_windows, mne_obj, crop_inds, description, metadata
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):
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"""Build repr for EEGWindowsDataset and WindowsDataset."""
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b = _ReprBuilder(cls_name)
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270
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n_ch, type_str, sfreq = _channel_info(mne_obj)
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271
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b.add_header(f"{n_windows} windows", "Windows", n_windows)
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272
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b.add_header(f"{n_ch} ch ({type_str})", "Channels", f"{n_ch} ({type_str})")
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273
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wi = _window_info(crop_inds, sfreq)
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274
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if wi is not None:
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+
win_samples, win_secs = wi
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276
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+
b.add_header(
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277
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f"{win_samples} samples/win ({win_secs:.3f} s)",
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278
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"Window size",
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279
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f"{win_samples} samples ({win_secs:.3f} s)",
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280
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)
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281
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b.add_header(f"{sfreq:.1f} Hz", "Sfreq", f"{sfreq:.1f} Hz")
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282
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+
if description is not None:
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283
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desc_items = ", ".join(f"{k}={v}" for k, v in description.items())
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284
|
+
b.add_row("description", desc_items)
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285
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+
if metadata is not None:
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286
|
+
summary = _metadata_summary(metadata)
|
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287
|
+
if summary["is_lazy"]:
|
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288
|
+
b.add_row("metadata", f"lazy ({summary['n_windows']} windows)")
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289
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+
else:
|
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290
|
+
if summary["target_info"]:
|
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291
|
+
b.add_row("targets", summary["target_info"])
|
|
292
|
+
if summary["extra_columns"]:
|
|
293
|
+
b.add_row("extra metadata", ", ".join(summary["extra_columns"]))
|
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294
|
+
return b
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295
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+
|
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296
|
+
|
|
45
297
|
class RecordDataset(Dataset[tuple[np.ndarray, int | str, tuple[int, int, int]]]):
|
|
46
298
|
def __init__(
|
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47
299
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self,
|
|
@@ -94,6 +346,15 @@ class RecordDataset(Dataset[tuple[np.ndarray, int | str, tuple[int, int, int]]])
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|
|
94
346
|
raise ValueError("Transform needs to be a callable.")
|
|
95
347
|
self._transform = value
|
|
96
348
|
|
|
349
|
+
def _build_repr(self):
|
|
350
|
+
return _ReprBuilder(type(self).__name__)
|
|
351
|
+
|
|
352
|
+
def __repr__(self):
|
|
353
|
+
return self._build_repr().to_repr()
|
|
354
|
+
|
|
355
|
+
def _repr_html_(self):
|
|
356
|
+
return self._build_repr().to_html()
|
|
357
|
+
|
|
97
358
|
|
|
98
359
|
# Type of the datasets contained in BaseConcatDataset
|
|
99
360
|
T = TypeVar("T", bound=RecordDataset)
|
|
@@ -148,6 +409,23 @@ class RawDataset(RecordDataset):
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|
|
148
409
|
def __len__(self):
|
|
149
410
|
return len(self.raw)
|
|
150
411
|
|
|
412
|
+
def _build_repr(self):
|
|
413
|
+
b = _ReprBuilder(type(self).__name__)
|
|
414
|
+
n_ch, type_str, sfreq = _channel_info(self.raw)
|
|
415
|
+
n_times = len(self.raw.times)
|
|
416
|
+
duration = n_times / sfreq
|
|
417
|
+
b.add_header(f"{n_ch} ch ({type_str})", "Channels", f"{n_ch} ({type_str})")
|
|
418
|
+
b.add_header(f"{sfreq:.1f} Hz", "Sfreq", f"{sfreq:.1f} Hz")
|
|
419
|
+
b.add_header(
|
|
420
|
+
f"{n_times} samples ({duration:.1f} s)",
|
|
421
|
+
"Samples",
|
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f"{n_times} ({duration:.1f} s)",
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)
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if self.description is not None:
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desc_items = ", ".join(f"{k}={v}" for k, v in self.description.items())
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b.add_row("description", desc_items)
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return b
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+
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def _target_name(self, target_name):
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if target_name is not None and not isinstance(target_name, (str, tuple, list)):
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raise ValueError("target_name has to be None, str, tuple or list")
|
|
@@ -291,6 +569,16 @@ class EEGWindowsDataset(RecordDataset):
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def __len__(self):
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return len(self.crop_inds)
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def _build_repr(self):
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return _build_windowed_repr(
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type(self).__name__,
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len(self),
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self.raw,
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self.crop_inds,
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self.description,
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self.metadata,
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+
)
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+
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@register_dataset
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class WindowsDataset(RecordDataset):
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@@ -329,6 +617,15 @@ class WindowsDataset(RecordDataset):
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last_target_only: bool = True,
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):
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super().__init__(description, transform)
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+
self._fast_disk = self._can_use_fast_get_epoch_from_raw(windows)
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if not (self._fast_disk or windows.preload):
|
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+
warnings.warn(
|
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"The provided mne.Epochs object does not meet the requirements for "
|
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+
"fast epoch access. This may lead to slow data loading from disk. "
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+
"Consider preloading the epochs or checking the conditions in "
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+
"WindowsDataset._can_use_fast_get_epoch_from_raw.",
|
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+
UserWarning,
|
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+
)
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self.windows = windows
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self.last_target_only = last_target_only
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if targets_from not in ("metadata", "channels"):
|
|
@@ -345,6 +642,20 @@ class WindowsDataset(RecordDataset):
|
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self.raw_preproc_kwargs: list[dict[str, Any]] = []
|
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|
self.window_preproc_kwargs: list[dict[str, Any]] = []
|
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644
|
|
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+
@staticmethod
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|
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|
+
def _can_use_fast_get_epoch_from_raw(epochs: mne.BaseEpochs) -> bool:
|
|
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|
+
"""Check if we can use the fast _get_epoch_from_raw method,
|
|
648
|
+
or if we need to use the slow get_data method."""
|
|
649
|
+
return (
|
|
650
|
+
not epochs.preload
|
|
651
|
+
and epochs._bad_dropped
|
|
652
|
+
and epochs.detrend is None
|
|
653
|
+
and not epochs._do_baseline # baseline is None
|
|
654
|
+
and (epochs._decim == 1)
|
|
655
|
+
and epochs._offset is None
|
|
656
|
+
and epochs._projector is None
|
|
657
|
+
)
|
|
658
|
+
|
|
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|
def __getitem__(self, index: int):
|
|
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660
|
"""Get a window and its target.
|
|
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661
|
|
|
@@ -362,7 +673,10 @@ class WindowsDataset(RecordDataset):
|
|
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362
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|
np.ndarray
|
|
363
674
|
Crop indices.
|
|
364
675
|
"""
|
|
365
|
-
|
|
676
|
+
if self._fast_disk:
|
|
677
|
+
X = self.windows._get_epoch_from_raw(index).astype("float32")
|
|
678
|
+
else:
|
|
679
|
+
X = self.windows.get_data(item=index)[0].astype("float32")
|
|
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680
|
if self.transform is not None:
|
|
367
681
|
X = self.transform(X)
|
|
368
682
|
if self.targets_from == "metadata":
|
|
@@ -383,6 +697,16 @@ class WindowsDataset(RecordDataset):
|
|
|
383
697
|
def __len__(self) -> int:
|
|
384
698
|
return len(self.windows.events)
|
|
385
699
|
|
|
700
|
+
def _build_repr(self):
|
|
701
|
+
return _build_windowed_repr(
|
|
702
|
+
type(self).__name__,
|
|
703
|
+
len(self),
|
|
704
|
+
self.windows,
|
|
705
|
+
self.crop_inds,
|
|
706
|
+
self.description,
|
|
707
|
+
self.windows.metadata,
|
|
708
|
+
)
|
|
709
|
+
|
|
386
710
|
|
|
387
711
|
@register_dataset
|
|
388
712
|
class BaseConcatDataset(ConcatDataset, HubDatasetMixin, Generic[T]):
|
|
@@ -533,8 +857,12 @@ class BaseConcatDataset(ConcatDataset, HubDatasetMixin, Generic[T]):
|
|
|
533
857
|
If a dict then each key will be used in the returned
|
|
534
858
|
splits dict and each value should be a list of int.
|
|
535
859
|
property : str
|
|
860
|
+
:bdg-warning:`Deprecated`
|
|
861
|
+
|
|
536
862
|
Some property which is listed in the info DataFrame.
|
|
537
863
|
split_ids : list | dict
|
|
864
|
+
:bdg-warning:`Deprecated`
|
|
865
|
+
|
|
538
866
|
List of indices to be combined in a subset.
|
|
539
867
|
It can be a list of int or a list of list of int.
|
|
540
868
|
|
|
@@ -883,3 +1211,101 @@ class BaseConcatDataset(ConcatDataset, HubDatasetMixin, Generic[T]):
|
|
|
883
1211
|
target_file_path = os.path.join(sub_dir, "target_name.json")
|
|
884
1212
|
with open(target_file_path, "w") as f:
|
|
885
1213
|
json.dump({"target_name": ds.target_name}, f)
|
|
1214
|
+
|
|
1215
|
+
@staticmethod
|
|
1216
|
+
def _signal_summary(ds):
|
|
1217
|
+
"""Return (mne_obj, is_windowed) from a dataset."""
|
|
1218
|
+
if hasattr(ds, "windows"):
|
|
1219
|
+
mne_obj = ds.windows
|
|
1220
|
+
elif hasattr(ds, "raw"):
|
|
1221
|
+
mne_obj = ds.raw
|
|
1222
|
+
else:
|
|
1223
|
+
return None, False
|
|
1224
|
+
is_windowed = hasattr(ds, "crop_inds")
|
|
1225
|
+
return mne_obj, is_windowed
|
|
1226
|
+
|
|
1227
|
+
def _build_repr(self):
|
|
1228
|
+
n_ds = len(self.datasets)
|
|
1229
|
+
b = _ReprBuilder("BaseConcatDataset")
|
|
1230
|
+
if n_ds == 0:
|
|
1231
|
+
b.add_header("0 datasets", "Recordings", 0)
|
|
1232
|
+
return b
|
|
1233
|
+
|
|
1234
|
+
n_total = len(self)
|
|
1235
|
+
ds_type = type(self.datasets[0]).__name__
|
|
1236
|
+
first_ds = self.datasets[0]
|
|
1237
|
+
mne_obj, is_windowed = self._signal_summary(first_ds)
|
|
1238
|
+
|
|
1239
|
+
b._type_display = f"BaseConcatDataset of {ds_type}"
|
|
1240
|
+
b.add_header(f"{n_ds} {ds_type}(s)", "Recordings", n_ds)
|
|
1241
|
+
b.add_header(f"{n_total} total samples", "Total samples", n_total)
|
|
1242
|
+
|
|
1243
|
+
if mne_obj is not None:
|
|
1244
|
+
n_ch, type_str, sfreq = _channel_info(mne_obj)
|
|
1245
|
+
b.add_row("Sfreq*", f"{sfreq:.1f} Hz")
|
|
1246
|
+
b.add_row("Channels*", f"{n_ch} ({type_str})")
|
|
1247
|
+
|
|
1248
|
+
ch_names = mne_obj.info["ch_names"]
|
|
1249
|
+
if len(ch_names) <= 10:
|
|
1250
|
+
ch_str = ", ".join(ch_names)
|
|
1251
|
+
else:
|
|
1252
|
+
ch_str = (
|
|
1253
|
+
", ".join(ch_names[:10]) + f", ... (+{len(ch_names) - 10} more)"
|
|
1254
|
+
)
|
|
1255
|
+
b.add_row("Ch. names*", ch_str)
|
|
1256
|
+
|
|
1257
|
+
montage = mne_obj.get_montage()
|
|
1258
|
+
if montage is not None:
|
|
1259
|
+
b.add_row("Montage*", montage.get_positions()["coord_frame"])
|
|
1260
|
+
|
|
1261
|
+
if not is_windowed:
|
|
1262
|
+
n_times = len(mne_obj.times)
|
|
1263
|
+
duration = n_times / sfreq
|
|
1264
|
+
b.add_row("Duration*", f"{duration:.1f} s")
|
|
1265
|
+
|
|
1266
|
+
b.add_footnote("* from first recording")
|
|
1267
|
+
|
|
1268
|
+
desc = self.description
|
|
1269
|
+
if desc is not None and not desc.empty:
|
|
1270
|
+
col_str = ", ".join(str(c) for c in desc.columns)
|
|
1271
|
+
b.add_row(
|
|
1272
|
+
"Description",
|
|
1273
|
+
f"{desc.shape[0]} recordings × {desc.shape[1]} columns [{col_str}]",
|
|
1274
|
+
)
|
|
1275
|
+
|
|
1276
|
+
if is_windowed:
|
|
1277
|
+
try:
|
|
1278
|
+
summary = _concat_metadata_summary(self.datasets)
|
|
1279
|
+
if summary["window_info"] is not None and mne_obj is not None:
|
|
1280
|
+
wi = summary["window_info"]
|
|
1281
|
+
if wi["uniform"]:
|
|
1282
|
+
win_secs = wi["min"] / sfreq
|
|
1283
|
+
b.add_row(
|
|
1284
|
+
"Window",
|
|
1285
|
+
f"{wi['min']} samples ({win_secs:.3f} s)",
|
|
1286
|
+
)
|
|
1287
|
+
else:
|
|
1288
|
+
min_secs = wi["min"] / sfreq
|
|
1289
|
+
max_secs = wi["max"] / sfreq
|
|
1290
|
+
b.add_row(
|
|
1291
|
+
"Window",
|
|
1292
|
+
f"{wi['min']}-{wi['max']} samples"
|
|
1293
|
+
f" ({min_secs:.3f}-{max_secs:.3f} s)",
|
|
1294
|
+
)
|
|
1295
|
+
if summary["target_info"]:
|
|
1296
|
+
b.add_row("Targets", summary["target_info"])
|
|
1297
|
+
if summary["extra_columns"]:
|
|
1298
|
+
b.add_row(
|
|
1299
|
+
"Extra meta",
|
|
1300
|
+
", ".join(summary["extra_columns"]),
|
|
1301
|
+
)
|
|
1302
|
+
except (TypeError, AttributeError):
|
|
1303
|
+
pass
|
|
1304
|
+
|
|
1305
|
+
return b
|
|
1306
|
+
|
|
1307
|
+
def __repr__(self):
|
|
1308
|
+
return self._build_repr().to_repr()
|
|
1309
|
+
|
|
1310
|
+
def _repr_html_(self):
|
|
1311
|
+
return self._build_repr().to_html()
|
|
@@ -137,6 +137,10 @@ class BIDSDataset(BaseConcatDataset):
|
|
|
137
137
|
)
|
|
138
138
|
datatypes: str | list[str] | None = None
|
|
139
139
|
check: bool = False
|
|
140
|
+
# Loading arguments for mne_bids.read_raw_bids:
|
|
141
|
+
extra_params: dict | None = None
|
|
142
|
+
on_ch_mismatch: str = "raise"
|
|
143
|
+
# Other arguments:
|
|
140
144
|
preload: bool = False
|
|
141
145
|
n_jobs: int = 1
|
|
142
146
|
|
|
@@ -182,7 +186,12 @@ class BIDSDataset(BaseConcatDataset):
|
|
|
182
186
|
|
|
183
187
|
def _get_dataset(self, bids_path: mne_bids.BIDSPath) -> RawDataset:
|
|
184
188
|
description = _description_from_bids_path(bids_path)
|
|
185
|
-
raw = mne_bids.read_raw_bids(
|
|
189
|
+
raw = mne_bids.read_raw_bids(
|
|
190
|
+
bids_path,
|
|
191
|
+
verbose=False,
|
|
192
|
+
on_ch_mismatch=self.on_ch_mismatch,
|
|
193
|
+
extra_params=self.extra_params,
|
|
194
|
+
)
|
|
186
195
|
if self.preload:
|
|
187
196
|
raw.load_data()
|
|
188
197
|
return RawDataset(raw, description)
|