eegdash 0.3.3.dev178374711__tar.gz → 0.3.4.dev69__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.
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- eegdash-0.3.4.dev69/MANIFEST.in +7 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/PKG-INFO +1 -1
- eegdash-0.3.4.dev69/docs/Makefile +31 -0
- eegdash-0.3.4.dev69/docs/source/conf.py +142 -0
- eegdash-0.3.4.dev69/docs/source/dataset_summary.rst +80 -0
- eegdash-0.3.4.dev69/docs/source/index.rst +56 -0
- eegdash-0.3.4.dev69/docs/source/install/install.rst +77 -0
- eegdash-0.3.4.dev69/docs/source/install/install_pip.rst +19 -0
- eegdash-0.3.4.dev69/docs/source/install/install_source.rst +80 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/__init__.py +1 -1
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/data_utils.py +12 -1
- eegdash-0.3.4.dev69/eegdash/dataset_summary.csv +255 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash.egg-info/PKG-INFO +1 -1
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash.egg-info/SOURCES.txt +9 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/pyproject.toml +4 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/LICENSE +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/README.md +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/api.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/data_config.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/dataset.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/features/__init__.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/features/datasets.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/features/decorators.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/features/extractors.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/features/feature_bank/__init__.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/features/feature_bank/complexity.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/features/feature_bank/connectivity.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/features/feature_bank/csp.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/features/feature_bank/dimensionality.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/features/feature_bank/signal.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/features/feature_bank/spectral.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/features/feature_bank/utils.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/features/inspect.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/features/serialization.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/features/utils.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/mongodb.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/preprocessing.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/registry.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash/utils.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash.egg-info/dependency_links.txt +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash.egg-info/requires.txt +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/eegdash.egg-info/top_level.txt +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/setup.cfg +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/tests/test_correctness.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/tests/test_dataset.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/tests/test_dataset_registration.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/tests/test_eegdash.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/tests/test_functional.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/tests/test_init.py +0 -0
- {eegdash-0.3.3.dev178374711 → eegdash-0.3.4.dev69}/tests/test_mongo_connection.py +0 -0
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Metadata-Version: 2.4
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Name: eegdash
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Version: 0.3.
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Version: 0.3.4.dev69
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Summary: EEG data for machine learning
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Author-email: Young Truong <dt.young112@gmail.com>, Arnaud Delorme <adelorme@gmail.com>, Aviv Dotan <avivd220@gmail.com>, Oren Shriki <oren70@gmail.com>, Bruno Aristimunha <b.aristimunha@gmail.com>
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License-Expression: GPL-3.0-only
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# Minimal makefile for Sphinx documentation
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SPHINXOPTS ?=
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SPHINXBUILD ?= sphinx-build
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SOURCEDIR = source
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BUILDDIR = build
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PKG ?= eegdash
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APIDIR := $(SOURCEDIR)/api
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help:
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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.PHONY: apidoc
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apidoc:
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@sphinx-apidoc -o "$(APIDIR)" "../$(PKG)" -f -e -M
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# Standard build runs examples
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html: apidoc
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# Fast build: do NOT execute examples (sphinx-gallery)
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.PHONY: html-noplot
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html-noplot: apidoc
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@python prepare_summary_tables.py ../eegdash/ $(BUILDDIR)
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@$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(BUILDDIR)" \
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$(SPHINXOPTS) -D sphinx_gallery_conf.plot_gallery=0 $(O)
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.PHONY: help apidoc
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Makefile: ;
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%: Makefile
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@python prepare_summary_tables.py ../eegdash/ $(BUILDDIR)
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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import os
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from datetime import datetime, timezone
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from sphinx_gallery.sorting import ExplicitOrder, FileNameSortKey
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import eegdash
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# -- Project information -----------------------------------------------------
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project = "EEG Dash"
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copyright = f"2025–{datetime.now(tz=timezone.utc).year}, {project} Developers"
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author = "Arnaud Delorme"
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release = eegdash.__version__
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version = ".".join(release.split(".")[:2])
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# -- General configuration ---------------------------------------------------
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extensions = [
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"sphinx.ext.autodoc",
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"sphinx.ext.autosummary",
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"sphinx.ext.doctest",
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"sphinx.ext.todo",
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"sphinx.ext.coverage",
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"sphinx.ext.mathjax",
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"sphinx.ext.ifconfig",
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"sphinx.ext.intersphinx",
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"sphinx.ext.githubpages",
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"sphinx.ext.napoleon",
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"sphinx_design",
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# "autoapi.extension",
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"numpydoc",
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"sphinx_gallery.gen_gallery",
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]
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templates_path = ["_templates"]
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exclude_patterns = ["build", "Thumbs.db", ".DS_Store"]
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# -- Options for HTML output -------------------------------------------------
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html_theme = "pydata_sphinx_theme"
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html_static_path = ["_static"]
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html_logo = "_static/eegdash_icon.svg"
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html_favicon = "_static/eegdash_icon.png"
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html_title = "EEG Dash"
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html_short_title = "EEG Dash"
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html_css_files = ["custom.css"]
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html_theme_options = {
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"icon_links_label": "External Links", # for screen reader
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"use_edit_page_button": False,
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"navigation_with_keys": False,
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"collapse_navigation": False,
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"header_links_before_dropdown": 6,
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"navigation_depth": 6,
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"show_toc_level": 1,
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"navbar_end": ["theme-switcher", "navbar-icon-links"],
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"footer_start": ["copyright"],
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"logo": {
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"image_light": "_static/eegdash_long.png",
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"image_dark": "_static/eegdash_long.png",
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"alt_text": "EEG Dash Logo",
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},
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"external_links": [
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{"name": "EEG2025 competition", "url": "https://eeg2025.github.io/"},
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],
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"icon_links": [
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{
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"name": "GitHub",
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"url": "https://github.com/sccn/EEGDash",
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"icon": "fa-brands fa-github",
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"type": "fontawesome",
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},
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{
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"name": "PyPI",
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"url": "https://pypi.org/project/eegdash/",
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"icon": "fa-solid fa-box",
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"type": "fontawesome",
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},
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{
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"name": "Docs (Stable)",
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"url": "https://sccn.github.io/EEGDash",
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"icon": "fa-solid fa-book",
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"type": "fontawesome",
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},
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{
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"name": "Discord",
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"url": "https://discord.gg/8jd7nVKwsc",
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"icon": "fa-brands fa-discord",
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"type": "fontawesome",
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},
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],
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}
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html_sidebars = {"api": [], "dataset_summary": [], "installation": []}
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# -- Extension configurations ------------------------------------------------
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# Numpydoc
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numpydoc_show_class_members = False
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# Sphinx Gallery
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EX_DIR = "../../examples" # relative to docs/source
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sphinx_gallery_conf = {
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"examples_dirs": [EX_DIR],
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"gallery_dirs": ["generated/auto_examples"],
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"nested_sections": False,
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"backreferences_dir": "gen_modules/backreferences",
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"inspect_global_variables": True,
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"show_memory": True,
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"show_api_usage": True,
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"doc_module": ("eegdash", "numpy", "scipy", "matplotlib"),
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"reference_url": {"eegdash": None},
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"filename_pattern": r"/(?:plot|tutorial)_(?!_).*\.py",
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"matplotlib_animations": True,
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"first_notebook_cell": (
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"# For tips on running notebooks in Google Colab:\n"
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"# `pip install eegdash`\n"
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"%matplotlib inline"
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),
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"subsection_order": ExplicitOrder(
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[
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f"{EX_DIR}/core",
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f"{EX_DIR}/eeg2025",
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"*",
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]
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),
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"within_subsection_order": FileNameSortKey,
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}
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# -- Custom Setup Function to fix the error -----------------------------------
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def setup(app):
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"""Create the back-references directory if it doesn't exist."""
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backreferences_dir = os.path.join(
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app.srcdir, sphinx_gallery_conf["backreferences_dir"]
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)
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if not os.path.exists(backreferences_dir):
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os.makedirs(backreferences_dir)
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.. meta::
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:hide_sidebar: true
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:html_theme.sidebar_secondary.remove:
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:html_theme.sidebar_primary.remove:
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.. _data_summary:
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.. automodule:: eegdash.dataset
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.. currentmodule:: eegdash.dataset
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EEG Dash Datasets
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==================
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Columns definitions:
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- **dataset**: Name of the dataset.
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- **n_records**: Number of EEG records in the dataset.
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- **n_subjects**: Number of subjects in the dataset.
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- **n_tasks**: Number of experimental tasks in the dataset.
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- **nchans_set**: Set of EEG channel counts used in the dataset.
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- **sampling_freqs**: Set of sampling frequencies used in the dataset.
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- **duration_hours_total**: Total duration of all recordings in hours.
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Datasets
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======================
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.. csv-table::
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:file: ../build/dataset_summary.csv
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:header-rows: 1
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:class: sortable
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.. raw:: html
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<style>
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/* Make this page full-width and remove side padding */
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:root {
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--pst-page-max-width: 100%;
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--pst-content-max-width: 100%;
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}
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.bd-main .bd-content .bd-article-container {
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max-width: 100%;
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padding-left: 0;
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padding-right: 0;
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}
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/* Ensure the DataTable uses the full width */
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table.sortable { width: 100% !important; }
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</style>
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EEGDASH Documentation
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=====================
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.. title:: EEG Dash
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EEG Dash Homepage
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==================
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.. image:: _static/logos/eegdash.png
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:alt: EEG Dash Logo
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.. rst-class:: h4 text-center font-weight-light my-4
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The EEG-DaSh data archive will establish a data-sharing resource for MEEG (EEG, MEG) data, enabling
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large-scale computational advancements to preserve and share scientific data from publicly funded
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research for machine learning and deep learning applications.
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:width: 100%
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* - .. image:: _static/logos/ucsd_white.png
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:alt: University of California, San Diego (UCSD)
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- .. image:: _static/logos/bgu_white.png
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:alt: Ben-Gurion University of the Negev (BGU)
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:width: 100%
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.. toctree::
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:hidden:
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Install <install/install>
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API <api/modules.rst>
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Dataset Summary <dataset_summary>
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Examples <generated/auto_examples/index>
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.. _installation:
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================
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Installation
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================
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EEGDash is written in Python 3, specifically for version 3.8 or above.
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The package is distributed via Python package index (`PyPI <eegdash-pypi_>`_), and you can access the
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source code via `Github <eegdash-github_>`_ repository.
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There are different ways to install EEGDash, depending on your needs and:
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Install via ``pip``
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.. rst-class:: card-subtitle text-muted mt-0
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For Beginners
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. image:: /_static/eegdash_install.gif
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:alt: EEGDash Installer with pip
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+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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.. button-ref:: install_pip
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:shadow:
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Installing from PyPI
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.. grid-item-card::
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:text-align: center
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.. rst-class:: font-weight-bold mb-0
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Building from source code
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.. rst-class:: card-subtitle text-muted mt-0
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For Advanced Users
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. image:: https://mne.tools/stable/_images/mne_installer_console.png
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:alt: Terminal Window
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**Already familiar with Python?**
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Follow our setup instructions for building from Github and start to contribute!
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+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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.. button-ref:: install_source
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:ref-type: ref
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From Source Code
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.. toctree::
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:hidden:
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install_pip
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install_source
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.. _install_pip:
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Installing from PyPI
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~~~~~~~~~~~~~~~~~~~~
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EEGDash can be installed via pip from `PyPI <eegdash-pypi_>`_.
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.. note::
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We recommend the most updated version of pip to install from PyPI.
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Below are the installation commands for the most common use cases.
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.. code-block:: bash
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pip install eegdash
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This will install the eegdash package and its dependencies.
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.. include:: /links.inc
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.. _install_source:
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Installing from sources
|
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~~~~~~~~~~~~~~~~~~~~~~~
|
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|
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If you want to test features under development or contribute to the library, or if you want to test the new tools that have been tested in EEGDash and not released yet, this is the right tutorial for you!
|
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|
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.. note::
|
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If you are only trying to install EEGDash, we recommend the :doc:`Installing from PyPI </install/install_pip>` section for details on that.
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Install preview version from PyPI
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----------------------------------
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.. code-block:: bash
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pip install --pre eegdash
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You should will install the version of `eegdash` that is currently under development at main branch, which may not be stable.
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Install directly from repository from GitHub
|
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--------------------------------------------
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Let's suppose that you want to install EEGDash from the source. The first thing you should do is clone the EEGDash repository to your computer and enter inside the repository.
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.. code-block:: bash
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git clone https://github.com/sccn/EEGDash && cd EEGDash
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You should now be in the root directory of the EEGDash repository.
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Installing EEGDash from the source with pip
|
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-------------------------------------------
|
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|
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If you want to only install EEGDash from source once and not do any development
|
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work, then the recommended way to build and install is to use ``pip``
|
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|
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For the latest development version, directly from GitHub:
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.. code-block:: bash
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pip install git+https://github.com/sccn/EEGDash.git
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If you have a local clone of the EEGDash git repository:
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.. code-block:: bash
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pip install -e .
|
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This will install EEGDash in editable mode, i.e., changes to the source code could be used
|
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directly in python.
|
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|
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You could also install optional dependency, like to import datasets from `test` and `docs`.
|
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pip install -e .[test,docs,dev]
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There is also optional dependencies for unit testing and building documentation, you could install
|
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them if you want to contribute to EEGDash.
|
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.. code-block:: bash
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pip install -e .[all]
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Testing if your installation is working
|
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
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|
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To verify that EEGDash is installed and running correctly, run the following command:
|
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|
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.. code-block:: console
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python -m "import eegdash; eegdash.__version__"
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.. include:: /links.inc
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@@ -2,10 +2,12 @@ import json
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from typing import Any
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import mne_bids
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@@ -174,7 +176,16 @@ class EEGDashBaseDataset(BaseDataset):
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self._download_s3()
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if self._raw is None:
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-
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# capturing any warnings
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# to-do: remove this once is fixed on the mne-bids side.
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with warnings.catch_warnings(record=True) as w:
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self._raw = mne_bids.read_raw_bids(
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bids_path=self.bidspath, verbose="ERROR"
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)
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for warning in w:
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logger.warning(
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f"Warning while reading BIDS file: {warning.message}"
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)
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# === BaseDataset and PyTorch Dataset interface ===
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dataset,n_records,n_subjects,n_tasks,nchans_set,sampling_freqs,duration_hours_total
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ds002718,18,18,1,74,250,14.844
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ds005505,1342,136,10,129,500,125.366
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ds004745,6,6,1,,1000,0.0
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ds005514,2885,295,10,129,500,213.008
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ds005512,2320,257,10,129,500,196.205
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ds005510,1227,135,10,129,500,112.464
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ds005511,3100,381,10,"6,129",500,285.629
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ds005509,3326,330,10,129,500,274.559
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ds005508,3342,324,10,129,500,269.281
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ds005507,1812,184,10,129,500,168.649
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ds005506,1405,150,10,129,500,127.896
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ds004854,1,1,1,64,128,0.535
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ds004853,1,1,1,64,128,0.535
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ds004844,68,17,1,64,1024,21.252
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ds004843,92,14,1,64,256,29.834
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ds004842,102,14,1,64,256,20.102
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ds004852,1,1,1,64,128,0.535
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ds004851,1,1,1,64,128,0.535
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ds004850,1,1,1,64,128,0.535
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ds004855,1,1,1,64,128,0.535
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ds004849,1,1,1,64,128,0.535
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ds004841,147,20,1,64,256,29.054
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ds004661,17,17,1,64,128,10.137
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ds004660,42,21,1,32,"2048,512",23.962
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ds004657,119,24,1,64,"1024,8192",27.205
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ds004362,1526,109,1,64,"128,160",48.592
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ds004010,24,24,1,64,1000,26.457
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ds002181,226,226,1,125,500,7.676
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ds004554,16,16,1,99,1000,0.024
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ds005697,50,50,1,"65,69",1000,77.689
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ds004350,240,24,5,64,256,41.265
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ds004785,17,17,1,32,500,0.019
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ds004504,88,88,1,19,500,19.608
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ds004635,55,55,1,129,1000,20.068
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ds005787,448,19,1,"64,66","1000,500",23.733
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ds005079,60,1,15,65,500,3.25
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ds005342,32,32,1,17,250,33.017
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ds005034,100,25,2,129,1000,37.525
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40
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ds003710,48,13,1,32,5000,9.165
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Author-email: Young Truong <dt.young112@gmail.com>, Arnaud Delorme <adelorme@gmail.com>, Aviv Dotan <avivd220@gmail.com>, Oren Shriki <oren70@gmail.com>, Bruno Aristimunha <b.aristimunha@gmail.com>
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+
docs/source/install/install_source.rst
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4
12
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eegdash/__init__.py
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5
13
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eegdash/api.py
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eegdash/data_config.py
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7
15
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eegdash/data_utils.py
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8
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eegdash/dataset.py
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+
eegdash/dataset_summary.csv
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9
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eegdash/mongodb.py
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eegdash/preprocessing.py
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eegdash/registry.py
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@@ -100,6 +100,7 @@ all = [
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101
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[tool.setuptools]
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py-modules = []
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+
include-package-data = true
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[tool.setuptools.dynamic]
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version = {attr = "eegdash.__version__"}
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@@ -110,6 +111,9 @@ include = ["eegdash*"]
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exclude = []
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namespaces = false
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+
[tool.setuptools.package-data]
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+
eegdash = ["dataset_summary.csv"]
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+
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[tool.ruff]
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lint.ignore-init-module-imports = true
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