eegdash 0.4.0.dev150__tar.gz → 0.4.0.dev162__tar.gz

{eegdash-0.4.0.dev150/eegdash.egg-info → eegdash-0.4.0.dev162}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eegdash
-Version: 0.4.0.dev150
+Version: 0.4.0.dev162
 Summary: EEG data for machine learning
 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>
 License-Expression: GPL-3.0-only

eegdash-0.4.0.dev162/docs/source/_templates/autosummary/module.rst

@@ -0,0 +1,65 @@
+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :member-order: bysource
+
+   {% block attributes %}
+   {%- if attributes %}
+   .. rubric:: {{ _('Module Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {%- endblock %}
+
+   {%- block functions %}
+   {%- if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {%- endblock %}
+
+   {%- block classes %}
+   {%- if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {%- endblock %}
+
+   {%- block exceptions %}
+   {%- if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {%- endblock %}
+
+{%- block modules %}
+{%- if modules %}
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :recursive:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{%- endblock %}
+

{eegdash-0.4.0.dev150 → eegdash-0.4.0.dev162}/docs/source/api/api_core.rst

@@ -76,4 +76,4 @@ API Reference
    hbn
    mongodb
    paths
-   utils
+   utils

{eegdash-0.4.0.dev150 → eegdash-0.4.0.dev162}/docs/source/conf.py

@@ -12,13 +12,15 @@ from sphinx.util import logging
 from sphinx_gallery.sorting import ExplicitOrder, FileNameSortKey
 from tabulate import tabulate
 
+sys.path.insert(0, os.path.abspath(".."))
+
 import eegdash
 
 # -- Project information -----------------------------------------------------
 
 project = "EEG Dash"
 copyright = f"2025–{datetime.now(tz=timezone.utc).year}, {project} Developers"
-author = "Arnaud Delorme"
+author = "Bruno Aristimunha and Arnaud Delorme"
 release = eegdash.__version__
 version = ".".join(release.split(".")[:2])
 
@@ -44,6 +46,7 @@ extensions = [
     "sphinx_sitemap",
     "sphinx_copybutton",
     "sphinx.ext.graphviz",
+    "sphinx_time_estimation",
 ]
 
 templates_path = ["_templates"]
@@ -103,8 +106,8 @@ html_theme_options = {
     "navbar_end": ["theme-switcher", "navbar-icon-links"],
     "footer_start": ["copyright"],
     "logo": {
-        "image_light": "_static/eegdash_long.png",
-        "image_dark": "_static/eegdash_long.png",
+        "image_light": "_static/eegdash_long_white.svg",
+        "image_dark": "_static/eegdash_long_dark.svg",
         "alt_text": "EEG Dash Logo",
     },
     "external_links": [
@@ -293,6 +296,14 @@ EEGDash currently exposes **{dataset_count} OpenNeuro EEG datasets** that are
 registered dynamically from mongo database. The table below summarises
 the distribution by experimental type as tracked in the summary file.
 
+Base Dataset API
+----------------
+
+.. toctree::
+   :maxdepth: 1
+
+   eegdash.dataset.EEGChallengeDataset
+
 .. list-table:: Dataset counts by experimental type
    :widths: 60 20
    :header-rows: 1
@@ -314,6 +325,22 @@ All Datasets
 """
 
 
+BASE_DATASET_TEMPLATE = """{notice}.. _api_eegdash_challenge_dataset:
+
+.. currentmodule:: eegdash.dataset
+
+EEGChallengeDataset
+===================
+
+.. autoclass:: eegdash.dataset.EEGChallengeDataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :member-order: bysource
+
+"""
+
+
 def _write_if_changed(path: Path, content: str) -> bool:
     """Write ``content`` to ``path`` if it differs from the current file."""
     existing = path.read_text(encoding="utf-8") if path.exists() else None
@@ -540,6 +567,11 @@ def _generate_dataset_docs(app) -> None:
     if _write_if_changed(index_path, index_content):
         LOGGER.info("[dataset-docs] Updated %s", index_path.relative_to(app.srcdir))
 
+    base_content = BASE_DATASET_TEMPLATE.format(notice=AUTOGEN_NOTICE)
+    base_path = dataset_dir / "eegdash.dataset.EEGChallengeDataset.rst"
+    if _write_if_changed(base_path, base_content):
+        LOGGER.info("[dataset-docs] Updated %s", base_path.relative_to(app.srcdir))
+
     generated_paths: set[Path] = set()
     for name in dataset_names:
         title = f"eegdash.dataset.{name}"

{eegdash-0.4.0.dev150 → eegdash-0.4.0.dev162}/docs/source/dataset_summary/bubble.rst

@@ -1,3 +1,7 @@
+.. title:: Dataset landscape
+
+.. rubric:: Dataset landscape
+
 .. raw:: html
 
    <figure class="eegdash-figure" style="margin: 0 0 1.25rem 0;">

{eegdash-0.4.0.dev150 → eegdash-0.4.0.dev162}/docs/source/dataset_summary/kde.rst

@@ -1,3 +1,7 @@
+.. title:: Participant Distribution by Modality
+
+.. rubric:: Distribution of Sample Sizes Varies by Experimental Modality
+
 .. raw:: html
 
    <figure class="eegdash-figure" style="margin: 0 0 1.25rem 0;">

eegdash-0.4.0.dev162/docs/source/dataset_summary/sankey.rst

@@ -0,0 +1,20 @@
+.. title:: Dataset flow
+
+.. rubric:: Sankey diagrams of EEGDash Datasets by Population, Modality, and Cognitive Domain
+
+.. raw:: html
+
+   <figure class="eegdash-figure" style="margin: 0 0 1.25rem 0;">
+
+.. raw:: html
+   :file: ../_static/dataset_generated/dataset_sankey.html
+
+.. raw:: html
+
+   <figcaption class="eegdash-caption">
+     Figure: Dataset flow across population, modality, and cognitive domain.
+     Link thickness is proportional to the total number of subjects, and the tooltip
+     reports both subject and dataset counts. Hover and click legend entries to
+     explore specific segments.
+   </figcaption>
+   </figure>

eegdash-0.4.0.dev162/docs/source/dataset_summary/table.rst

@@ -0,0 +1,27 @@
+.. title:: EEG Datasets Table
+
+.. rubric:: EEG Datasets Table
+
+The data in EEG-DaSh originates from a collaboration involving 25 laboratories, encompassing 27,053 participants. This extensive collection includes M-EEG data, which is a combination of EEG and MEG signals. The data is sourced from various studies conducted by these labs,
+involving both healthy subjects and clinical populations with conditions such as ADHD, depression, schizophrenia, dementia, autism, and psychosis. Additionally, data spans different mental states like sleep, meditation, and cognitive tasks.
+
+In addition, EEG-DaSh will incorporate a subset of the data converted from `NEMAR <https://nemar.org/>`__, which includes 330 MEEG BIDS-formatted datasets, further expanding the archive with well-curated, standardized neuroelectromagnetic data.
+
+.. raw:: html
+
+   <figure class="eegdash-figure" style="margin: 0 0 1.25rem 0;">
+
+.. raw:: html
+   :file: ../_static/dataset_generated/dataset_summary_table.html
+
+.. raw:: html
+
+   <figcaption class="eegdash-caption">
+     Table: Sortable catalogue of EEG‑DaSh datasets. Use the “Filters” button to open column filters;
+     click a column header to jump directly to a filter pane. The Total row is pinned at the bottom.
+     * means that we use the median value across multiple recordings in the dataset, and empty cells
+     when the metainformation is not extracted yet.
+   </figcaption>
+   </figure>
+
+Pathology, modality, and dataset type now surface as consistent color-coded tags so you can scan the table at a glance.

{eegdash-0.4.0.dev150 → eegdash-0.4.0.dev162}/docs/source/dataset_summary.rst

@@ -10,13 +10,11 @@
 
 .. rst-class:: dataset-summary-article
 
-Datasets 
-=========
+Datasets Catalog
+================
 
 To leverage recent and ongoing advancements in large-scale computational methods and to ensure the preservation of scientific data generated from publicly funded research, the EEG-DaSh data archive will create a data-sharing resource for MEEG (EEG, MEG) data contributed by collaborators for machine learning (ML) and deep learning (DL) applications.
 
-The archive is currently still in :bdg-danger:`beta testing` mode, so be kind. 
-
 .. raw:: html
 
    <script src="https://cdn.plot.ly/plotly-3.1.0.min.js"></script>
@@ -27,10 +25,16 @@ The archive is currently still in :bdg-danger:`beta testing` mode, so be kind.
 
       .. include:: dataset_summary/table.rst
 
-   .. tab-item:: Participant KDE
+   .. tab-item:: Participant Distribution
 
       .. include:: dataset_summary/kde.rst
 
-   .. tab-item:: Landscape
+   .. tab-item:: Dataset Flow
+
+      .. include:: dataset_summary/sankey.rst
+
+   .. tab-item:: Scatter of Sample Size vs. Recording Duration
 
       .. include:: dataset_summary/bubble.rst
+
+The archive is currently still in :bdg-danger:`beta testing` mode, so be kind. 

eegdash-0.4.0.dev162/docs/source/index.rst

@@ -0,0 +1,86 @@
+:html_theme.sidebar_secondary.remove: true
+
+EEGDASH Homepage
+=================
+
+.. title:: EEG Dash
+
+
+EEG Dash Homepage
+==================
+
+.. raw:: html
+
+   <style type="text/css">h1 {display:none;}</style>
+
+.. raw:: html
+
+   <h1 class="eegdash-hero__title">EEG Dash</h1>
+
+
+.. image:: _static/logos/eegdash.svg
+    :alt: EEG Dash Logo
+    :class: logo mainlogo only-dark
+    :align: center
+    :scale: 50%
+
+.. image:: _static/logos/eegdash.svg
+    :alt: EEG Dash Logo
+    :class: logo mainlogo only-light
+    :align: center
+    :scale: 50%
+
+.. rst-class:: h4 text-center font-weight-light my-4
+
+   The EEG-DaSh data archive is a data-sharing resource for MEEG (EEG, MEG) data, enabling 
+   large-scale computational advancements to preserve and share scientific data from publicly funded 
+   research for machine learning and deep learning applications.
+
+.. rst-class:: text-center
+
+    The "DaSh" in EEG-DaSh stands for **Data Share**.
+
+    The EEG-DaSh data archive is a collaborative effort led by the University of California, San Diego (UCSD) and Ben-Gurion University of the Negev (BGU) and partially funded by the National Science Foundation (NSF). All are welcome to contribute to the https://github.com/sccn/EEGDash project.
+
+    The archive is currently still in :bdg-danger:`beta testing` mode, so be kind. 
+
+.. raw:: html
+
+    <h2 style="text-align: center;">Institutions</h2>
+
+
+.. image:: _static/logos/ucsd_white.svg
+    :alt: UCSD
+    :class: logo mainlogo only-dark flex-logo
+    :width: 45%
+    :align: left
+
+    
+.. image:: _static/logos/ucsd_dark.svg
+    :alt: UCSD
+    :class: logo mainlogo only-light flex-logo
+    :align: left
+    :width: 45%
+    
+
+.. image:: _static/logos/bgu_dark.svg
+    :alt: Ben-Gurion University of the Negev (BGU)
+    :class: logo mainlogo only-dark flex-logo
+    :align: right
+    :width: 40%
+
+.. image:: _static/logos/bgu_white.svg
+    :alt: Ben-Gurion University of the Negev (BGU)
+    :class: logo mainlogo only-light flex-logo
+    :align: right
+    :width: 40%
+
+
+.. toctree::
+   :hidden:
+
+   Installing <install/install>
+   User Guide <user_guide>
+   API <api/api>
+   Dataset Catalog <dataset_summary>
+   Examples <generated/auto_examples/index>

{eegdash-0.4.0.dev150 → eegdash-0.4.0.dev162}/docs/source/user_guide.rst

@@ -1,16 +1,21 @@
 .. _user_guide:
 
+:html_theme.sidebar_secondary.remove: true
+
+.. currentmodule:: eegdash.api
+
+
 User Guide
 ==========
 
-This guide provides a comprehensive overview of the ``eegdash`` library, focusing on its core data access object, ``EEGDashDataset``. You will learn how to use this object to find, access, and manage EEG data for your research and analysis tasks.
+This guide provides a comprehensive overview of the :mod:`eegdash` library, focusing on its core data access object, :class:`~eegdash.api.EEGDashDataset`. You will learn how to use this object to find, access, and manage EEG data for your research and analysis tasks.
 
 The EEGDash Object
 ------------------
 
-While :class:`~eegdash.EEGDashDataset` is the main tool for loading data for machine learning, the :class:`~eegdash.EEGDash` object provides a lower-level interface for directly interacting with the metadata database. It is useful for exploring the available data, performing complex queries, or managing metadata records.
+While :class:`~eegdash.api.EEGDashDataset` is the main tool for loading data for machine learning, the :class:`~eegdash.api.EEGDash` object provides a lower-level interface for directly interacting with the metadata database. It is useful for exploring the available data, performing complex queries, or managing metadata records.
 
-Initializing ``EEGDash``
+Initializing EEGDash
 ~~~~~~~~~~~~~~~~~~~~~~~~
 
 You can create a client to connect to the public database like this:
@@ -38,25 +43,25 @@ The ``find()`` method allows you to query the database for records matching spec
     records_advanced = eegdash.find(query)
     print(f"Found {len(records_advanced)} records with advanced query.")
 
-``EEGDash`` vs. ``EEGDashDataset``
+EEGDash vs. EEGDashDataset
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 It's important to understand the distinction between these two objects:
 
--   **EEGDash**: Use this for querying and managing metadata. It returns a list of dictionaries, where each dictionary is a record from the database.
--   **EEGDashDataset**: Use this when you need to load EEG data for analysis or machine learning. It returns a PyTorch-compatible dataset object where each item can load the actual EEG signal.
+-   :class:`~eegdash.api.EEGDash`: Use this for querying and managing metadata. It returns a list of dictionaries, where each dictionary is a record from the database.
+-   :class:`~eegdash.api.EEGDashDataset`: Use this when you need to load EEG data for analysis or machine learning. It returns a PyTorch-compatible dataset object where each item can load the actual EEG signal.
 
-In general, you will use ``EEGDashDataset`` for most of your data loading needs.
+In general, you will use :class:`~eegdash.api.EEGDashDataset` for most of your data loading needs.
 
 The EEGDashDataset Object
 -------------------------
 
-The :class:`~eegdash.EEGDashDataset` is the primary entry point for working with EEG recordings in ``eegdash``. It acts as a high-level interface that allows you to query a metadata database and load corresponding EEG data, either from a remote source or from a local cache.
+The :class:`~eegdash.api.EEGDashDataset` is the primary entry point for working with EEG recordings in :mod:`eegdash`. It acts as a high-level interface that allows you to query a metadata database and load corresponding EEG data, either from a remote source or from a local cache.
 
-Initializing ``EEGDashDataset``
+Initializing EEGDashDataset
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-To get started, you need to create an instance of ``EEGDashDataset``. The two most important parameters are ``cache_dir`` and ``dataset``.
+To get started, you need to create an instance of :class:`~eegdash.api.EEGDashDataset`. The two most important parameters are ``cache_dir`` and ``dataset``.
 
 - ``cache_dir``: This is the local directory where ``eegdash`` will store downloaded data.
 - ``dataset``: The identifier of the dataset you want to work with (e.g., ``"ds002718"``).
@@ -80,7 +85,7 @@ This will create a dataset object containing all recordings from ``ds002718``. T
 Querying for Specific Data
 --------------------------
 
-``EEGDashDataset`` offers powerful filtering capabilities, allowing you to select a subset of recordings based on various criteria. You can filter by task, subject, session, or run.
+:class:`~eegdash.api.EEGDashDataset` offers powerful filtering capabilities, allowing you to select a subset of recordings based on various criteria. You can filter by task, subject, session, or run.
 
 Filtering by Task
 ~~~~~~~~~~~~~~~~~
@@ -162,11 +167,11 @@ For more complex queries, you can pass a MongoDB-style query dictionary directly
 Working with Local Data (Offline Mode)
 --------------------------------------
 
-``eegdash`` also supports working with local data that you have already downloaded or manage separately. By setting ``download=False``, you can instruct ``EEGDashDataset`` to use local BIDS-compliant data instead of accessing the database or remote storage.
+:mod:`eegdash` also supports working with local data that you have already downloaded or manage separately. By setting ``download=False``, you can instruct :class:`~eegdash.api.EEGDashDataset` to use local BIDS-compliant data instead of accessing the database or remote storage.
 
 To use this feature, your data must be organized in a BIDS-like structure within your ``cache_dir``. For example, if your ``cache_dir`` is ``./eeg_data`` and your dataset is ``ds002718``, the files should be located at ``./eeg_data/ds002718/``.
 
-Here is how to use ``EEGDashDataset`` in offline mode:
+Here is how to use :class:`~eegdash.api.EEGDashDataset` in offline mode:
 
 .. code-block:: python
 
@@ -179,12 +184,12 @@ Here is how to use ``EEGDashDataset`` in offline mode:
 
     print(f"Found {len(local_dataset)} local recordings.")
 
-When ``download=False``, ``eegdash`` will scan the specified directory for EEG files and construct the dataset from the local file system. This is useful for environments without internet access or when you want to work with your own curated datasets.
+When ``download=False``, :mod:`eegdash` will scan the specified directory for EEG files and construct the dataset from the local file system. This is useful for environments without internet access or when you want to work with your own curated datasets.
 
 Accessing Data from the Dataset
 -------------------------------
 
-Once you have your ``EEGDashDataset`` object, you can access individual recordings as if it were a list. Each item in the dataset is an ``EEGDashBaseDataset`` object, which contains the metadata and methods to load the actual EEG data.
+Once you have your :class:`~eegdash.api.EEGDashDataset` object, you can access individual recordings as if it were a list. Each item in the dataset is an :class:`~eegdash.data_utils.EEGDashBaseDataset` object, which contains the metadata and methods to load the actual EEG data.
 
 .. code-block:: python
 
@@ -199,4 +204,4 @@ Once you have your ``EEGDashDataset`` object, you can access individual recordin
         print(f"Sampling frequency: {raw.info['sfreq']} Hz")
         print(f"Number of channels: {len(raw.ch_names)}")
 
-This provides a powerful and flexible way to integrate ``eegdash`` into your data analysis pipelines, whether you are working with remote or local data.
+This provides a powerful and flexible way to integrate ``eegdash`` into your data analysis pipelines, whether you are working with remote or local data.

{eegdash-0.4.0.dev150 → eegdash-0.4.0.dev162}/eegdash/__init__.py

@@ -18,4 +18,4 @@ _init_mongo_client()
 
 __all__ = ["EEGDash", "EEGDashDataset", "EEGChallengeDataset", "preprocessing"]
 
-__version__ = "0.4.0.dev150"
+__version__ = "0.4.0.dev162"