eegdash 0.4.0.dev173__tar.gz → 0.4.0.dev176__tar.gz

{eegdash-0.4.0.dev173/eegdash.egg-info → eegdash-0.4.0.dev176}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eegdash
-Version: 0.4.0.dev173
+Version: 0.4.0.dev176
 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.dev173 → eegdash-0.4.0.dev176}/docs/source/_templates/autosummary/module.rst

@@ -63,3 +63,19 @@
 {% endif %}
 {%- endblock %}
 
+{% if sg_api_usage %}
+.. _sg_api_{{ fullname }}:
+
+API Usage
+---------
+
+.. raw:: html
+
+    <div class="sg-api-usage">
+
+{{ sg_api_usage }}
+
+.. raw:: html
+
+    </div>
+{% endif %}

{eegdash-0.4.0.dev173 → eegdash-0.4.0.dev176}/docs/source/conf.py

@@ -2,6 +2,7 @@ import csv
 import importlib
 import inspect
 import os
+import shutil
 import sys
 from collections import Counter
 from datetime import datetime, timezone
@@ -78,6 +79,7 @@ html_css_files = [
     "https://cdn.datatables.net/select/1.7.0/css/select.dataTables.min.css",
     "https://cdn.datatables.net/searchpanes/2.3.1/css/searchPanes.dataTables.min.css",
     "custom.css",
+    "css/treemap.css",
 ]
 html_js_files = [
     "https://code.jquery.com/jquery-3.7.1.min.js",
@@ -221,11 +223,21 @@ EX_DIR = "../../examples"  # relative to docs/source
 sphinx_gallery_conf = {
     "examples_dirs": [f"{EX_DIR}"],
     "gallery_dirs": ["generated/auto_examples"],
+    "binder": {
+        "org": "sccn",
+        "repo": "EEGDash",
+        "branch": "main",
+        "binderhub_url": "https://mybinder.org",
+        "dependencies": "binder/requirements.txt",
+        "notebooks_dir": "notebooks",
+        "use_jupyter_lab": True,
+    },
+    "capture_repr": ("_repr_html_", "__repr__"),
     "nested_sections": False,
     "backreferences_dir": "gen_modules/backreferences",
     "inspect_global_variables": True,
     "show_memory": True,
-    "show_api_usage": False,
+    "show_api_usage": True,
     "doc_module": ("eegdash", "numpy", "scipy", "matplotlib"),
     "reference_url": {"eegdash": None},
     "filename_pattern": r"/(?:plot|tutorial)_(?!_).*\.py",
@@ -602,6 +614,106 @@ def _generate_dataset_docs(app) -> None:
             continue
 
 
+def _split_tokens(value: str | None) -> set[str]:
+    tokens: set[str] = set()
+    if not value:
+        return tokens
+    for part in value.split(","):
+        cleaned = part.strip()
+        if cleaned:
+            tokens.add(cleaned)
+    return tokens
+
+
+def _compute_dataset_counter_defaults() -> dict[str, int]:
+    csv_path = Path(importlib.import_module("eegdash.dataset").__file__).with_name(
+        "dataset_summary.csv"
+    )
+    if not csv_path.exists():
+        return {}
+
+    dataset_ids: set[str] = set()
+    modalities: set[str] = set()
+    cognitive: set[str] = set()
+    subject_total = 0
+
+    with csv_path.open(encoding="utf-8") as handle:
+        filtered = (
+            line
+            for line in handle
+            if line.strip() and not line.lstrip().startswith("#")
+        )
+        reader = csv.DictReader(filtered)
+        for row in reader:
+            dataset = (row.get("dataset") or row.get("Dataset") or "").strip()
+            if dataset:
+                dataset_ids.add(dataset)
+
+            try:
+                subject_total += int(float(row.get("n_subjects", "0") or 0))
+            except (TypeError, ValueError):
+                pass
+
+            modalities.update(_split_tokens(row.get("record_modality")))
+            cognitive.update(_split_tokens(row.get("type of exp")))
+
+    return {
+        "datasets": len(dataset_ids),
+        "subjects": subject_total,
+        "modalities": len(modalities),
+        "cognitive": len(cognitive),
+    }
+
+
+_DATASET_COUNTER_DEFAULTS = _compute_dataset_counter_defaults()
+
+
+def _format_counter(key: str) -> str:
+    value = _DATASET_COUNTER_DEFAULTS.get(key, 0)
+    if isinstance(value, (int, float)):
+        if isinstance(value, float) and not value.is_integer():
+            return f"{value:,.2f}"
+        return f"{int(value):,}"
+    return str(value)
+
+
+_DATASET_COUNTER_PLACEHOLDERS = {
+    "|datasets_total|": _format_counter("datasets"),
+    "|subjects_total|": _format_counter("subjects"),
+    "|modalities_total|": _format_counter("modalities"),
+    "|cognitive_total|": _format_counter("cognitive"),
+}
+
+
+def _copy_dataset_summary(app, exception) -> None:
+    if exception is not None or not getattr(app, "builder", None):
+        return
+
+    csv_path = Path(importlib.import_module("eegdash.dataset").__file__).with_name(
+        "dataset_summary.csv"
+    )
+    if not csv_path.exists():
+        LOGGER.warning("dataset_summary.csv not found; skipping counter data copy.")
+        return
+
+    static_dir = Path(app.outdir) / "_static"
+    try:
+        static_dir.mkdir(parents=True, exist_ok=True)
+        shutil.copy2(csv_path, static_dir / "dataset_summary.csv")
+    except OSError as exc:
+        LOGGER.warning("Unable to copy dataset_summary.csv to _static: %s", exc)
+
+
+def _inject_counter_values(app, docname, source) -> None:
+    if docname != "dataset_summary":
+        return
+
+    text = source[0]
+    for token, value in _DATASET_COUNTER_PLACEHOLDERS.items():
+        text = text.replace(token, value)
+    source[0] = text
+
+
 def setup(app):
     """Create the back-references directory if it doesn't exist."""
     backreferences_dir = os.path.join(
@@ -611,6 +723,8 @@ def setup(app):
         os.makedirs(backreferences_dir)
 
     app.connect("builder-inited", _generate_dataset_docs)
+    app.connect("build-finished", _copy_dataset_summary)
+    app.connect("source-read", _inject_counter_values)
 
 
 # Configure sitemap URL format (omit .html where possible)

eegdash-0.4.0.dev176/docs/source/dataset_summary/treemap.rst

@@ -0,0 +1,19 @@
+.. title:: Dataset treemap
+
+.. rubric:: Dataset treemap
+
+.. raw:: html
+
+   <figure class="eegdash-figure" style="margin: 0 0 1.25rem 0;">
+
+.. raw:: html
+   :file: ../_static/dataset_generated/dataset_treemap.html
+
+.. raw:: html
+
+   <figcaption class="eegdash-caption">
+     Figure: Treemap of EEG Dash datasets. The top level groups population type,
+     the second level breaks down experimental modality, and leaves list individual datasets.
+     Tile area encodes the total number of subjects; hover to view aggregated hours (or records when unavailable).
+   </figcaption>
+   </figure>

eegdash-0.4.0.dev176/docs/source/dataset_summary.rst

@@ -0,0 +1,99 @@
+:hide_sidebar: true
+:html_theme.sidebar_secondary.remove: true
+:html_theme.sidebar_primary.remove: true
+
+.. _data_summary:
+
+.. raw:: html
+
+   <script>document.documentElement.classList.add('dataset-summary-page');</script>
+
+.. rst-class:: dataset-summary-article
+
+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.
+
+.. raw:: html
+
+   <section class="dataset-counter-grid">
+     <article class="dataset-counter-card">
+       <div class="dataset-counter-icon" aria-hidden="true">
+         <svg class="dataset-counter-svg" viewBox="0 0 24 24" role="presentation" fill="none" stroke="currentColor" stroke-width="1.6" stroke-linecap="round" stroke-linejoin="round">
+           <ellipse cx="12" cy="5" rx="7" ry="3"></ellipse>
+           <path d="M5 5v10c0 1.66 3.13 3 7 3s7-1.34 7-3V5"></path>
+           <path d="M5 12c0 1.66 3.13 3 7 3s7-1.34 7-3"></path>
+         </svg>
+       </div>
+       <div class="dataset-counter-body">
+         <span class="dataset-counter-label">Datasets</span>
+         <span class="dataset-counter-value">|datasets_total|</span>
+       </div>
+     </article>
+     <article class="dataset-counter-card">
+       <div class="dataset-counter-icon" aria-hidden="true">
+         <svg class="dataset-counter-svg" viewBox="0 0 24 24" role="presentation" fill="none" stroke="currentColor" stroke-width="1.6" stroke-linecap="round" stroke-linejoin="round">
+           <circle cx="8" cy="9" r="3"></circle>
+           <circle cx="16" cy="9" r="3"></circle>
+           <path d="M4 19c0-3 2.24-5 4-5s4 2 4 5"></path>
+           <path d="M12 19c0-3 2.24-5 4-5s4 2 4 5"></path>
+         </svg>
+       </div>
+       <div class="dataset-counter-body">
+         <span class="dataset-counter-label">Subjects</span>
+         <span class="dataset-counter-value">|subjects_total|</span>
+       </div>
+     </article>
+     <article class="dataset-counter-card">
+       <div class="dataset-counter-icon" aria-hidden="true">
+         <svg class="dataset-counter-svg" viewBox="0 0 24 24" role="presentation" fill="none" stroke="currentColor" stroke-width="1.6" stroke-linecap="round" stroke-linejoin="round">
+           <path d="M3 15c2.5 0 2.5-6 5-6s2.5 6 5 6 2.5-6 5-6 2.5 6 5 6"></path>
+           <path d="M3 9c2.5 0 2.5-5 5-5s2.5 5 5 5 2.5-5 5-5 2.5 5 5 5"></path>
+         </svg>
+       </div>
+       <div class="dataset-counter-body">
+         <span class="dataset-counter-label">Experiment Modalities</span>
+         <span class="dataset-counter-value">|modalities_total|</span>
+       </div>
+     </article>
+     <article class="dataset-counter-card">
+       <div class="dataset-counter-icon" aria-hidden="true">
+         <svg class="dataset-counter-svg" viewBox="0 0 24 24" role="presentation" fill="none" stroke="currentColor" stroke-width="1.6" stroke-linecap="round" stroke-linejoin="round">
+           <path d="M12 4c-3.5 0-7 2-7 6 0 3.5 2.5 6 6 6v4l3-2 3 2v-4c2.5 0 4-2 4-5 0-3.5-2.5-7-9-7z"></path>
+         </svg>
+       </div>
+       <div class="dataset-counter-body">
+         <span class="dataset-counter-label">Cognitive Domains</span>
+         <span class="dataset-counter-value">|cognitive_total|</span>
+       </div>
+     </article>
+   </section>
+
+.. raw:: html
+
+   <script src="https://cdn.plot.ly/plotly-3.1.0.min.js"></script>
+
+.. tab-set::
+
+   .. tab-item:: Dataset Table
+
+      .. include:: dataset_summary/table.rst
+
+   .. tab-item:: Participant Distribution
+
+      .. include:: dataset_summary/kde.rst
+
+   .. tab-item:: Dataset Flow
+
+      .. include:: dataset_summary/sankey.rst
+
+   .. tab-item:: Dataset Treemap
+
+      .. include:: dataset_summary/treemap.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.dev173 → eegdash-0.4.0.dev176}/eegdash/__init__.py

@@ -18,4 +18,4 @@ _init_mongo_client()
 
 __all__ = ["EEGDash", "EEGDashDataset", "EEGChallengeDataset", "preprocessing"]
 
-__version__ = "0.4.0.dev173"
+__version__ = "0.4.0.dev176"

{eegdash-0.4.0.dev173 → eegdash-0.4.0.dev176}/eegdash/features/datasets.py

@@ -18,6 +18,11 @@ from braindecode.datasets.base import (
 
 from ..logging import logger
 
+__all__ = [
+    "FeaturesDataset",
+    "FeaturesConcatDataset",
+]
+
 
 class FeaturesDataset(EEGWindowsDataset):
     """A dataset of features extracted from EEG windows.

{eegdash-0.4.0.dev173 → eegdash-0.4.0.dev176}/eegdash/features/decorators.py

@@ -10,6 +10,14 @@ from .extractors import (
     _get_underlying_func,
 )
 
+__all__ = [
+    "bivariate_feature",
+    "FeatureKind",
+    "FeaturePredecessor",
+    "multivariate_feature",
+    "univariate_feature",
+]
+
 
 class FeaturePredecessor:
     """A decorator to specify parent extractors for a feature function.

{eegdash-0.4.0.dev173 → eegdash-0.4.0.dev176}/eegdash/features/extractors.py

@@ -8,6 +8,15 @@ from typing import Dict
 import numpy as np
 from numba.core.dispatcher import Dispatcher
 
+__all__ = [
+    "BivariateFeature",
+    "DirectedBivariateFeature",
+    "FeatureExtractor",
+    "MultivariateFeature",
+    "TrainableFeature",
+    "UnivariateFeature",
+]
+
 
 def _get_underlying_func(func: Callable) -> Callable:
     """Get the underlying function from a potential wrapper.

{eegdash-0.4.0.dev173 → eegdash-0.4.0.dev176}/eegdash/features/feature_bank/signal.py

@@ -8,20 +8,21 @@ from ..extractors import FeatureExtractor
 
 __all__ = [
     "HilbertFeatureExtractor",
-    "signal_mean",
-    "signal_variance",
-    "signal_skewness",
+    "SIGNAL_PREDECESSORS",
+    "signal_decorrelation_time",
+    "signal_hjorth_activity",
+    "signal_hjorth_complexity",
+    "signal_hjorth_mobility",
     "signal_kurtosis",
-    "signal_std",
-    "signal_root_mean_square",
+    "signal_line_length",
+    "signal_mean",
     "signal_peak_to_peak",
     "signal_quantile",
+    "signal_root_mean_square",
+    "signal_skewness",
+    "signal_std",
+    "signal_variance",
     "signal_zero_crossings",
-    "signal_line_length",
-    "signal_hjorth_activity",
-    "signal_hjorth_mobility",
-    "signal_hjorth_complexity",
-    "signal_decorrelation_time",
 ]
 
 

{eegdash-0.4.0.dev173 → eegdash-0.4.0.dev176}/eegdash/features/feature_bank/utils.py

@@ -1,5 +1,13 @@
 import numpy as np
 
+__all__ = [
+    "DEFAULT_FREQ_BANDS",
+    "get_valid_freq_band",
+    "reduce_freq_bands",
+    "slice_freq_band",
+]
+
+
 DEFAULT_FREQ_BANDS = {
     "delta": (1, 4.5),
     "theta": (4.5, 8),

{eegdash-0.4.0.dev173 → eegdash-0.4.0.dev176}/eegdash/features/inspect.py

@@ -6,6 +6,14 @@ from collections.abc import Callable
 from . import extractors, feature_bank
 from .extractors import FeatureExtractor, MultivariateFeature, _get_underlying_func
 
+__all__ = [
+    "get_all_feature_extractors",
+    "get_all_feature_kinds",
+    "get_all_features",
+    "get_feature_kind",
+    "get_feature_predecessors",
+]
+
 
 def get_feature_predecessors(feature_or_extractor: Callable) -> list:
     """Get the dependency hierarchy for a feature or feature extractor.

{eegdash-0.4.0.dev173 → eegdash-0.4.0.dev176}/eegdash/features/serialization.py

@@ -2,7 +2,7 @@
 
 See Also
 --------
-https://github.com/braindecode/braindecode//blob/master/braindecode/datautil/serialization.py#L165-L229
+https://github.com/braindecode/braindecode/blob/master/braindecode/datautil/serialization.py#L165-L229
 
 """
 
@@ -18,6 +18,10 @@ from braindecode.datautil.serialization import _load_kwargs_json
 
 from .datasets import FeaturesConcatDataset, FeaturesDataset
 
+__all__ = [
+    "load_features_concat_dataset",
+]
+
 
 def load_features_concat_dataset(
     path: str | Path, ids_to_load: list[int] | None = None, n_jobs: int = 1

{eegdash-0.4.0.dev173 → eegdash-0.4.0.dev176}/eegdash/features/utils.py

@@ -17,6 +17,11 @@ from braindecode.datasets.base import (
 from .datasets import FeaturesConcatDataset, FeaturesDataset
 from .extractors import FeatureExtractor
 
+__all__ = [
+    "extract_features",
+    "fit_feature_extractors",
+]
+
 
 def _extract_features_from_windowsdataset(
     win_ds: EEGWindowsDataset | WindowsDataset,

{eegdash-0.4.0.dev173 → eegdash-0.4.0.dev176/eegdash.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eegdash
-Version: 0.4.0.dev173
+Version: 0.4.0.dev176
 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.dev173 → eegdash-0.4.0.dev176}/eegdash.egg-info/SOURCES.txt

@@ -16,6 +16,7 @@ docs/source/dataset_summary/bubble.rst
 docs/source/dataset_summary/kde.rst
 docs/source/dataset_summary/sankey.rst
 docs/source/dataset_summary/table.rst
+docs/source/dataset_summary/treemap.rst
 docs/source/install/install.rst
 docs/source/install/install_pip.rst
 docs/source/install/install_source.rst

eegdash-0.4.0.dev173/docs/source/dataset_summary.rst

@@ -1,40 +0,0 @@
-:hide_sidebar: true
-:html_theme.sidebar_secondary.remove: true
-:html_theme.sidebar_primary.remove: true
-
-.. _data_summary:
-
-.. raw:: html
-
-   <script>document.documentElement.classList.add('dataset-summary-page');</script>
-
-.. rst-class:: dataset-summary-article
-
-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.
-
-.. raw:: html
-
-   <script src="https://cdn.plot.ly/plotly-3.1.0.min.js"></script>
-
-.. tab-set::
-
-   .. tab-item:: Dataset Table
-
-      .. include:: dataset_summary/table.rst
-
-   .. tab-item:: Participant Distribution
-
-      .. include:: dataset_summary/kde.rst
-
-   .. 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.