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feat: Add HBN dataset (#576)
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prassepaul authored Sep 28, 2023
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77 changes: 77 additions & 0 deletions docs/source/bibliography.bib
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Expand Up @@ -86,3 +86,80 @@ @inproceedings{SB-SAT
publisher = {Association for Computing Machinery},
address = "Stuttgart, Germany",
}

@article{HBN,
title={An open resource for transdiagnostic research in pediatric mental health and learning disorders},
author={Alexander, Lindsay M. and
Escalera, Jasmine and
Ai, Lei and
Andreotti, Charissa and
Febre, Karina and
Mangone, Alexander and
Vega-Potler, Natan and
Langer, Nicolas and
Alexander, Alexis and
Kovacs, Meagan and
Litke, Shannon and
O'Hagan, Bridget and
Andersen, Jennifer and
Bronstein, Batya and
Bui, Anastasia and
Bushey, Marijayne and
Butler, Henry and
Castagna, Victoria and
Camacho, Nicolas and
Chan, Elisha and
Citera, Danielle and
Clucas, Jon and
Cohen, Samantha and
Dufek, Sarah and
Eaves, Megan and
Fradera, Brian and
Gardner, Judith and
Grant-Villegas, Natalie and
Green, Gabriella and
Gregory, Camille and
Hart, Emily and
Harris, Shana and
Horton, Megan and
Kahn, Danielle and
Kabotyanski, Katherine and
Karmel, Bernard and
Kelly, Simon P. and
Kleinman, Kayla and
Koo, Bonhwang and
Kramer, Eliza and
Lennon, Elizabeth and
Lord, Catherine and
Mantello, Ginny and
Margolis, Amy and
Merikangas, Kathleen R. and
Milham, Judith and
Minniti, Giuseppe and
Neuhaus, Rebecca and
Levine, Alexandra and
Osman, Yael and
Parra, Lucas C. and
Pugh, Ken R. and
Racanello, Amy and
Restrepo, Anita and
Saltzman, Tian and
Septimus, Batya and
Tobe, Russell and
Waltz, Rachel and
Williams, Anna and
Yeo, Anna and
Castellanos, Francisco X. and
Klein, Arno and
Paus, Tomas and
Leventhal, Bennett L. and
Craddock, R. Cameron and
Koplewicz, Harold S. and
Milham, Michael P.},
journal={Scientific data},
volume={4},
number={1},
pages={1--26},
year={2017},
publisher={Nature Publishing Group}
}
3 changes: 3 additions & 0 deletions src/pymovements/datasets/__init__.py
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Expand Up @@ -28,6 +28,7 @@
pymovements.datasets.GazeBase
pymovements.datasets.GazeBaseVR
pymovements.datasets.GazeOnFaces
pymovements.datasets.HBN
pymovements.datasets.JuDo1000
pymovements.datasets.SBSAT
Expand All @@ -44,6 +45,7 @@
from pymovements.datasets.gaze_on_faces import GazeOnFaces
from pymovements.datasets.gazebase import GazeBase
from pymovements.datasets.gazebasevr import GazeBaseVR
from pymovements.datasets.hbn import HBN
from pymovements.datasets.judo1000 import JuDo1000
from pymovements.datasets.sb_sat import SBSAT
from pymovements.datasets.toy_dataset import ToyDataset
Expand All @@ -54,6 +56,7 @@
'GazeBase',
'GazeBaseVR',
'GazeOnFaces',
'HBN',
'JuDo1000',
'SBSAT',
'ToyDataset',
Expand Down
151 changes: 151 additions & 0 deletions src/pymovements/datasets/hbn.py
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@@ -0,0 +1,151 @@
# Copyright (c) 2022-2023 The pymovements Project Authors
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
"""This module provides an interface to the HBN dataset."""
from __future__ import annotations

from dataclasses import dataclass
from dataclasses import field
from typing import Any

import polars as pl

from pymovements.dataset.dataset_definition import DatasetDefinition
from pymovements.dataset.dataset_library import register_dataset
from pymovements.gaze.experiment import Experiment


@dataclass
@register_dataset
class HBN(DatasetDefinition):
"""HBN dataset :cite:p:`HBN`.
This dataset consists of recordings from children
watching four different age-appropriate videos: (1) an
educational video clip (Fun with Fractals), (2) a short animated
film (The Present), (3) a short clip of an animated film (Despicable Me),
and (4) a trailer for a feature-length movie (Diary of a Wimpy Kid).
The eye gaze was recorded at a sampling rate of 120 Hz.
Check the respective paper for details :cite:p:`HBN`.
Attributes
----------
name : str
The name of the dataset.
mirrors : tuple[str, ...]
A tuple of mirrors of the dataset. Each entry must be of type `str` and end with a '/'.
resources : tuple[dict[str, str], ...]
A tuple of dataset resources. Each list entry must be a dictionary with the following keys:
- `resource`: The url suffix of the resource. This will be concatenated with the mirror.
- `filename`: The filename under which the file is saved as.
- `md5`: The MD5 checksum of the respective file.
experiment : Experiment
The experiment definition.
filename_format : str
Regular expression which will be matched before trying to load the file. Namedgroups will
appear in the `fileinfo` dataframe.
filename_format_dtypes : dict[str, type], optional
If named groups are present in the `filename_format`, this makes it possible to cast
specific named groups to a particular datatype.
column_map : dict[str, str]
The keys are the columns to read, the values are the names to which they should be renamed.
custom_read_kwargs : dict[str, Any], optional
If specified, these keyword arguments will be passed to the file reading function.
Examples
--------
Initialize your :py:class:`~pymovements.PublicDataset` object with the
:py:class:`~pymovements.HBN` definition:
>>> import pymovements as pm
>>>
>>> dataset = pm.Dataset("HBN", path='data/HBN')
Download the dataset resources resources:
>>> dataset.download()# doctest: +SKIP
Load the data into memory:
>>> dataset.load()# doctest: +SKIP
"""

# pylint: disable=similarities
# The PublicDatasetDefinition child classes potentially share code chunks for definitions.

name: str = 'HBN'

mirrors: tuple[str, ...] = (
'https://files.osf.io/v1/resources/qknuv/providers/osfstorage/',
)

resources: tuple[dict[str, str], ...] = (
{
'resource': '651190031e76a453918a9971',
'filename': 'data.zip',
'md5': '2c523e911022ffc0eab700e34e9f7f30',
},
)

experiment: Experiment = Experiment(
screen_width_px=800,
screen_height_px=600,
screen_width_cm=33.8,
screen_height_cm=27.0,
distance_cm=63.5,
origin='center',
sampling_rate=120,
)

filename_format: str = r'{subject_id:12}_{video_id}.csv'

filename_format_dtypes: dict[str, type] = field(
default_factory=lambda: {
'subject_id': str,
'video_id': str,
},
)

trial_columns: list[str] = field(default_factory=lambda: ['video_id'])

time_column: str = 'time'

pixel_columns: list[str] = field(default_factory=lambda: ['x_pix', 'y_pix'])

column_map: dict[str, str] = field(default_factory=lambda: {})

custom_read_kwargs: dict[str, Any] = field(
default_factory=lambda: {
'separator': ',',
'columns': [
'time', 'x_pix', 'y_pix',
],
'dtypes': [
pl.Float64, pl.Float64, pl.Float64,
],
},
)
2 changes: 1 addition & 1 deletion src/pymovements/datasets/sb_sat.py
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Expand Up @@ -17,7 +17,7 @@
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
"""This module provides an interface to the GazeOnFaces dataset."""
"""This module provides an interface to the SB-SAT dataset."""
from __future__ import annotations

from dataclasses import dataclass
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2 changes: 2 additions & 0 deletions tests/datasets/datasets_test.py
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Expand Up @@ -32,6 +32,7 @@
pytest.param(pm.datasets.GazeBase, 'GazeBase', id='GazeBase'),
pytest.param(pm.datasets.GazeBaseVR, 'GazeBaseVR', id='GazeBaseVR'),
pytest.param(pm.datasets.GazeOnFaces, 'GazeOnFaces', id='GazeOnFaces'),
pytest.param(pm.datasets.HBN, 'HBN', id='HBN'),
pytest.param(pm.datasets.JuDo1000, 'JuDo1000', id='JuDo1000'),
pytest.param(pm.datasets.SBSAT, 'SBSAT', id='SBSAT'),
],
Expand All @@ -49,6 +50,7 @@ def test_public_dataset_registered(definition_class, dataset_name):
pytest.param(pm.datasets.GazeBase, id='GazeBase'),
pytest.param(pm.datasets.GazeBaseVR, id='GazeBaseVR'),
pytest.param(pm.datasets.GazeOnFaces, id='GazeOnFaces'),
pytest.param(pm.datasets.HBN, id='HBN'),
pytest.param(pm.datasets.JuDo1000, id='JuDo1000'),
pytest.param(pm.datasets.SBSAT, id='SBSAT'),
],
Expand Down
79 changes: 79 additions & 0 deletions tests/datasets/hbn_test.py
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@@ -0,0 +1,79 @@
# Copyright (c) 2023 The pymovements Project Authors
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
"""Test all functionality in pymovements.dataset.hbn."""
from pathlib import Path

import pytest

import pymovements as pm


@pytest.mark.parametrize(
'init_path, expected_paths',
[
pytest.param(
'/data/set/path',
{
'root': Path('/data/set/path/'),
'dataset': Path('/data/set/path/'),
'download': Path('/data/set/path/downloads'),
},
),
pytest.param(
pm.DatasetPaths(root='/data/set/path'),
{
'root': Path('/data/set/path/'),
'dataset': Path('/data/set/path/HBN'),
'download': Path('/data/set/path/HBN/downloads'),
},
),
pytest.param(
pm.DatasetPaths(root='/data/set/path', dataset='.'),
{
'root': Path('/data/set/path/'),
'dataset': Path('/data/set/path/'),
'download': Path('/data/set/path/downloads'),
},
),
pytest.param(
pm.DatasetPaths(root='/data/set/path', dataset='dataset'),
{
'root': Path('/data/set/path/'),
'dataset': Path('/data/set/path/dataset'),
'download': Path('/data/set/path/dataset/downloads'),
},
),
pytest.param(
pm.DatasetPaths(root='/data/set/path', downloads='custom_downloads'),
{
'root': Path('/data/set/path/'),
'dataset': Path('/data/set/path/HBN'),
'download': Path('/data/set/path/HBN/custom_downloads'),
},
),
],
)
def test_paths(init_path, expected_paths):
dataset = pm.Dataset(pm.datasets.HBN, path=init_path)

assert dataset.paths.root == expected_paths['root']
assert dataset.path == expected_paths['dataset']
assert dataset.paths.dataset == expected_paths['dataset']
assert dataset.paths.downloads == expected_paths['download']

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