labda 0.0.13.dev0__tar.gz → 0.1.0__tar.gz

{labda-0.0.13.dev0 → labda-0.1.0}/.gitignore

@@ -1,6 +1,6 @@
 # Byte-compiled / optimized / DLL files
 __pycache__/
-*.py[cod]
+*.py[codz]
 *$py.class
 
 # C extensions
@@ -46,7 +46,7 @@ htmlcov/
 nosetests.xml
 coverage.xml
 *.cover
-*.py,cover
+*.py.cover
 .hypothesis/
 .pytest_cache/
 cover/
@@ -94,20 +94,35 @@ ipython_config.py
 #   install all needed dependencies.
 #Pipfile.lock
 
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
 # poetry
 #   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
 #   This is especially recommended for binary packages to ensure reproducibility, and is more
 #   commonly ignored for libraries.
 #   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
 #poetry.lock
+#poetry.toml
 
 # pdm
 #   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
 #pdm.lock
-#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
-#   in version control.
-#   https://pdm.fming.dev/#use-with-ide
-.pdm.toml
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
 
 # PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
 __pypackages__/
@@ -121,6 +136,7 @@ celerybeat.pid
 
 # Environments
 .env
+.envrc
 .venv
 env/
 venv/
@@ -159,14 +175,37 @@ cython_debug/
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
 
-# Poetry
-poetry.lock
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
 
 # Custom
 temp
-examples/cache
-.ruff_cache
-*.parquet
-cache
-prepared
-diaries
+*.zip

labda-0.1.0/LICENSE

@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2025, Josef Heidler
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

labda-0.1.0/PKG-INFO

@@ -0,0 +1,50 @@
+Metadata-Version: 2.4
+Name: labda
+Version: 0.1.0
+Summary: A Python package built for health researchers, transforms raw movement data into compelling stories about human behaviour.
+Project-URL: Homepage, https://labda.josefheidler.cz
+Project-URL: Documentation, https://labda.josefheidler.cz
+Project-URL: Source, https://github.com/josefheidler/labda
+Project-URL: Changelog, https://github.com/josefheidler/labda/blob/main/CHANGELOG.md
+Author-email: Josef Heidler <jheidler@health.sdu.dk>
+License-Expression: BSD-3-Clause
+License-File: LICENSE
+Keywords: accelerometers,gnss,gps,movement-behavior,physical-activity,sedentary-behaviour,transportation,wearables
+Classifier: Intended Audience :: Education
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.11
+Requires-Dist: agcounts>=0.2.6
+Requires-Dist: altair>=5.5.0
+Requires-Dist: colorcet>=3.1.0
+Requires-Dist: geopandas>=1.1.1
+Requires-Dist: httpx>=0.28.1
+Requires-Dist: numba>=0.61.2
+Requires-Dist: osmnx>=2.0.5
+Requires-Dist: pandas>=2.3.1
+Requires-Dist: pingouin>=0.5.5
+Requires-Dist: pyarrow>=20.0.0
+Requires-Dist: pydeck>=0.9.1
+Requires-Dist: pygt3x>=0.7.1
+Requires-Dist: resampy>=0.4.3
+Requires-Dist: rich>=14.2.0
+Requires-Dist: scikit-digital-health>=0.17.9
+Requires-Dist: timezonefinder>=7.0.2
+Requires-Dist: vegafusion[embed]>=2.0.2
+Requires-Dist: vl-convert-python>=1.8.0
+Description-Content-Type: text/markdown
+
+[![pypi](https://img.shields.io/pypi/v/labda.svg)](https://pypi.python.org/pypi/labda)
+[![versions](https://img.shields.io/pypi/pyversions/labda.svg)](https://github.com/josefheidler/labda)
+[![downloads](https://static.pepy.tech/badge/labda/month)](https://pepy.tech/project/labda)
+[![discord](https://img.shields.io/discord/1165947556807848016)](https://discord.gg/qu6ax5Q64j)
+
+# LABDA: Library for Advanced Behavioural Data Analysis
+
+LABDA, a Python package built for health researchers, transforms raw movement data into compelling stories about human behaviour.

{labda-0.0.13.dev0 → labda-0.1.0}/README.md

@@ -1,9 +1,8 @@
 [![pypi](https://img.shields.io/pypi/v/labda.svg)](https://pypi.python.org/pypi/labda)
-[![downloads](https://static.pepy.tech/badge/labda/month)](https://pepy.tech/project/labda)
 [![versions](https://img.shields.io/pypi/pyversions/labda.svg)](https://github.com/josefheidler/labda)
+[![downloads](https://static.pepy.tech/badge/labda/month)](https://pepy.tech/project/labda)
 [![discord](https://img.shields.io/discord/1165947556807848016)](https://discord.gg/qu6ax5Q64j)
 
 # LABDA: Library for Advanced Behavioural Data Analysis
 
-LABDA, a Python package built for health researchers, transforms raw movement data into compelling stories about human behaviour.
-
+LABDA, a Python package built for health researchers, transforms raw movement data into compelling stories about human behaviour.

labda-0.1.0/pyproject.toml

@@ -0,0 +1,119 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+include = [
+  "src/labda/surveys/indicators/who_bmi_z_score.parquet"
+]
+
+[project]
+name = "labda"
+version = "0.1.0"
+description = "A Python package built for health researchers, transforms raw movement data into compelling stories about human behaviour."
+readme = "README.md"
+authors = [
+    { name = "Josef Heidler", email = "jheidler@health.sdu.dk" }
+]
+license = "BSD-3-Clause"
+license-files = ["LICENSE"]
+keywords = ["wearables", "accelerometers", "gps", "gnss", "movement-behavior", "physical-activity", "sedentary-behaviour", "transportation"]
+classifiers = [
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    'Operating System :: OS Independent',
+    "Intended Audience :: Education",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering",
+]
+requires-python = ">=3.11"
+dependencies = [
+    "agcounts>=0.2.6",
+    "altair>=5.5.0",
+    "colorcet>=3.1.0",
+    "geopandas>=1.1.1",
+    "httpx>=0.28.1",
+    "numba>=0.61.2",
+    "osmnx>=2.0.5",
+    "pandas>=2.3.1",
+    "pingouin>=0.5.5",
+    "pyarrow>=20.0.0",
+    "pydeck>=0.9.1",
+    "pygt3x>=0.7.1",
+    "resampy>=0.4.3",
+    "rich>=14.2.0",
+    "scikit-digital-health>=0.17.9",
+    "timezonefinder>=7.0.2",
+    "vegafusion[embed]>=2.0.2",
+    "vl-convert-python>=1.8.0",
+]
+
+[project.urls]
+Homepage = 'https://labda.josefheidler.cz'
+Documentation = 'https://labda.josefheidler.cz'
+Source = 'https://github.com/josefheidler/labda'
+Changelog = 'https://github.com/josefheidler/labda/blob/main/CHANGELOG.md'
+
+[dependency-groups]
+dev = [
+    "acti-motus",
+    "black>=25.12.0",
+    "fiona>=1.10.1",
+    "keplergl>=0.3.7",
+    "pre-commit>=4.2.0",
+    "pytest>=8.4.1",
+]
+jupyter = [
+    "ipykernel>=6.29.5",
+    "ipywidgets>=8.1.7",
+    "openpyxl>=3.1.5",
+]
+docs = [
+    "mkdocs>=1.6.1",
+    "mkdocs-material>=9.7.1",
+    "mkdocs-glightbox>=0.5.2",
+    "mkdocstrings[python]>=1.0.0",
+]
+
+[tool.hatch.build.targets.sdist]
+# Limit which files are included in the sdist (.tar.gz) asset,
+include = [
+    '/README.md',
+    '/src',
+]
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/labda"]
+
+[tool.ruff.lint]
+pydocstyle = { convention = 'google' }
+
+[tool.ruff]
+line-length = 120
+target-version = 'py311'
+
+[tool.ruff.format]
+quote-style = 'double'
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]
+addopts = [
+    "-v",
+    "--tb=short",
+    "--strict-markers",
+    "--disable-warnings",
+]
+markers = [
+    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
+    "integration: marks tests as integration tests",
+]
+
+[tool.uv]
+default-groups = ["jupyter"]
+
+[tool.uv.sources]
+acti-motus = { path = "../acti-motus", editable = true}

labda-0.1.0/src/labda/accelerometers/__init__.py

@@ -0,0 +1,3 @@
+from .intensity import *
+from .metrics import *
+from .preprocessing import *

labda-0.1.0/src/labda/accelerometers/intensity/__init__.py

@@ -0,0 +1,5 @@
+from .acceleration import MAD_CUT_POINTS
+from .counts import COUNTS_CUT_POINTS
+from .intensity import ActivityIntensity
+
+__all__ = ["COUNTS_CUT_POINTS", "ActivityIntensity", "MAD_CUT_POINTS"]

labda-0.1.0/src/labda/accelerometers/intensity/acceleration.py

@@ -0,0 +1,123 @@
+import logging
+from datetime import timedelta
+from typing import Any
+
+import pandas as pd
+
+from ...core.utils import check_for_required_data
+
+logger = logging.getLogger(__name__)
+
+ENMO_CUT_POINTS: dict[str, Any] = {
+    "hildebrand_2014-2017": {
+        "name": "Hildebrand (2014-2017, Actigraph)",
+        "reference": [
+            "https://doi.org/10.1249/MSS.0000000000000289",
+            "https://doi.org/10.1111/sms.12795",
+        ],
+        "epoch": "5s",
+        "category": "adults",
+        "placement": "hip",
+        "required_data": ["enmo"],
+        "thresholds": [
+            {"name": "sedentary", "max": 47.4},
+            {"name": "light", "max": 69.1},
+            {"name": "moderate", "max": 258.7},
+            {"name": "vigorous", "max": float("inf")},
+        ],
+    },
+}
+
+
+MAD_CUT_POINTS: dict[str, Any] = {
+    "aittasalo_children_2015": {
+        "name": "Aittasalo (2015, Actigraph)",
+        "reference": "https://doi.org/10.1186/s13102-015-0010-0",
+        "epoch": "5s",
+        "category": "children",
+        "placement": "hip",
+        "required_data": ["mad"],
+        "thresholds": [
+            {"name": "sedentary", "max": 26.9},
+            {"name": "light", "max": 332.0},
+            {"name": "moderate", "max": 558.3},
+            {"name": "vigorous", "max": float("inf")},
+        ],
+    },
+    "beck_children_thigh_2023": {
+        "name": "Beck Children (2023, Thigh, Move4)",
+        "reference": "https://doi.org/10.1186/s13102-023-00775-4",
+        "epoch": "5s",
+        "category": "children",
+        "placement": "thigh",
+        "required_data": ["mad"],
+        "thresholds": [
+            {"name": "sedentary", "max": 62.4},
+            {"name": "light", "max": 260.7},
+            {"name": "moderate", "max": 674.5},
+            {"name": "vigorous", "max": float("inf")},
+        ],
+    },
+    "beck_children_hip_2023": {
+        "name": "Beck Children (2023, Hip, Move4)",
+        "reference": "https://doi.org/10.1186/s13102-023-00775-4",
+        "epoch": "5s",
+        "category": "children",
+        "placement": "hip",
+        "required_data": ["mad"],
+        "thresholds": [
+            {"name": "sedentary", "max": 52.9},
+            {"name": "light", "max": 173.3},
+            {"name": "moderate", "max": 543.6},
+            {"name": "vigorous", "max": float("inf")},
+        ],
+    },
+    "vaha-ypya_hip_2015-2017": {
+        "name": "Vaha-Ypya Adults (2015-2017, Hip, Hookie AM20)",
+        "reference": [
+            "https://doi.org/10.1371/journal.pone.0134813",
+            "https://doi.org/10.1111/sms.13017",
+        ],
+        "epoch": "5s",  # Originally 6s, but opted for 5s here for consistency, and should have minimal impact
+        "category": "adults",
+        "placement": "hip",
+        "required_data": ["mad"],
+        "thresholds": [
+            {"name": "sedentary", "max": 22.5},
+            {"name": "light", "max": 91},
+            {"name": "moderate", "max": 414},
+            {"name": "vigorous", "max": float("inf")},
+        ],
+    },
+}
+
+
+def get_activity_intensities_from_acceleration_metric(
+    df: pd.DataFrame,
+    thresholds: dict[str, Any],
+    epoch: timedelta,
+):
+    # TODO: Reformat this function and function from counts.py to reduce redundancy
+    epoch_cut_points = pd.to_timedelta(thresholds["epoch"])
+    required_data = thresholds["required_data"]
+
+    cut_points = thresholds["thresholds"]
+    bins = [-float("inf")] + [cp["max"] for cp in cut_points]
+    labels = [cp["name"] for cp in cut_points]
+
+    check_for_required_data(required_data, df.columns)
+
+    if epoch_cut_points != epoch:
+        raise ValueError(
+            "Resampling is not supported for acceleration metric based intensity classification. Please provide data with the same epoch as the cut points."
+        )
+
+    if not len(required_data) == 1:
+        raise ValueError("For acceleration metric data, only one axis (variable) is supported.")
+
+    required_data = required_data[0]
+
+    intensities = pd.cut(df[required_data], bins=bins, labels=labels)
+    intensities.name = "activity_intensity"
+
+    return intensities

labda-0.1.0/src/labda/accelerometers/intensity/counts.py

@@ -0,0 +1,119 @@
+from datetime import timedelta
+from typing import Any
+
+import pandas as pd
+
+from ...core.expander import Expander
+from ...core.resampler import Resampler
+from ...core.utils import check_for_required_data
+
+COUNTS_CUT_POINTS: dict[str, Any] = {
+    "freedson_adults_1998": {
+        "name": "Freedson Adults (1998)",
+        "reference": "https://journals.lww.com/acsm-msse/fulltext/1998/05000/calibration_of_the_computer_science_and.21.aspx",
+        "epoch": "60s",
+        "category": "adults",
+        "placement": "hip",
+        "required_data": ["counts_y"],
+        "thresholds": [
+            {"name": "sedentary", "max": 99},
+            {"name": "light", "max": 1951},
+            {"name": "moderate", "max": 5724},
+            {"name": "vigorous", "max": 9498},
+            {"name": "very-vigorous", "max": float("inf")},
+        ],
+    },
+    "freedson_adults_vm3_2011": {
+        "name": "Freedson Adults VM3 (2011)",
+        "reference": "https://doi.org/10.1016/j.jsams.2011.04.003",
+        "epoch": "60s",
+        "category": "adults",
+        "placement": "hip",
+        "required_data": ["counts_x", "counts_y", "counts_z"],
+        "thresholds": [
+            {"name": "light", "max": 2689},
+            {"name": "moderate", "max": 6166},
+            {"name": "vigorous", "max": 9642},
+            {"name": "very-vigorous", "max": float("inf")},
+        ],
+    },
+    "freedson_children_2005": {
+        "name": "Freedson Children (2005)",
+        "reference": "https://doi.org/10.1249/01.mss.0000185658.28284.ba",
+        "epoch": "60s",
+        "category": "children",
+        "placement": "hip",
+        "required_data": ["counts_y"],
+        "thresholds": [
+            {"name": "sedentary", "max": 149},
+            {"name": "light", "max": 499},
+            {"name": "moderate", "max": 3999},
+            {"name": "vigorous", "max": 7599},
+            {"name": "very-vigorous", "max": float("inf")},
+        ],
+    },
+    "evenson_children_2018": {
+        "name": "Evenson Children (2008)",
+        "reference": "https://doi.org/10.1080/02640410802334196",
+        "epoch": "15s",
+        "category": "children",
+        "placement": "hip",
+        "required_data": ["counts_y"],
+        "thresholds": [
+            {"name": "sedentary", "max": 25},
+            {"name": "light", "max": 573},
+            {"name": "moderate", "max": 1002},
+            {"name": "vigorous", "max": float("inf")},
+        ],
+    },
+    "troiano_adults_2008": {
+        "name": "Troiano Adults (2008)",
+        "reference": "https://doi.org/10.1249/mss.0b013e31815a51b3",
+        "epoch": "60s",
+        "category": "adults",
+        "placement": "hip",
+        "required_data": ["counts_y"],
+        "thresholds": [
+            {"name": "sedentary", "max": 99},
+            {"name": "light", "max": 2019},
+            {"name": "moderate", "max": 5998},
+            {"name": "vigorous", "max": float("inf")},
+        ],
+    },
+}
+
+
+def get_activity_intensities_from_counts(
+    df: pd.DataFrame,
+    thresholds: dict[str, Any],
+    epoch: timedelta,
+) -> pd.Series:
+    epoch_cut_points = pd.to_timedelta(thresholds["epoch"])
+    required_data = thresholds["required_data"]
+
+    cut_points = thresholds["thresholds"]
+    bins = [-float("inf")] + [cp["max"] for cp in cut_points]
+    labels = [cp["name"] for cp in cut_points]
+
+    check_for_required_data(required_data, df.columns)
+
+    if epoch_cut_points > epoch:
+        df = Resampler(epoch_cut_points).resample(df[required_data], epoch)
+    elif epoch_cut_points < epoch:
+        raise ValueError(
+            f"Epoch for cut points ({epoch_cut_points}) is smaller than the epoch of the data ({epoch}). Upsampling is not supported."
+        )
+
+    if required_data == ["counts_x", "counts_y", "counts_z"]:
+        df = df[["counts_x", "counts_y", "counts_z"]].copy()
+        df["counts_vm"] = Expander().vector_magnitude(df[required_data])
+        required_data = "counts_vm"
+    elif len(required_data) == 1:
+        required_data = required_data[0]
+    else:
+        raise ValueError("For counts data, only uniaxial or vector magnitude data is supported.")
+
+    intensities = pd.cut(df[required_data], bins=bins, labels=labels)
+    intensities.name = "activity_intensity"
+
+    return intensities