palmwtc 0.2.2

Automated whole-tree chamber workflow for oil-palm ecophysiology — QC, flux calculation, science validation.

palmwtc

Automated whole-tree chamber workflow for oil-palm ecophysiology.

palmwtc is the data-processing and analysis pipeline for the first automated whole-tree chamber (WTC) sized to enclose individual oil palm trees, deployed at the LIBZ field site (Riau, Indonesia) and instrumented with LI-COR LI-850 gas analyzers. It transforms raw sensor cycles into validated CO₂ and H₂O fluxes, applies multi-stage quality control, and produces inputs for the XPalm digital-twin calibration pipeline.

What it does

raw chamber cycles  ──►  QC (rules + ML + breakpoints)  ──►  flux calculation  ──►  science validation
        │                                                                                  │
        └── 30-min weather + soil + tree biophysics ──┬───────────────────────────────────►┘
                                                       └── high-confidence calibration windows

End-to-end run on the bundled synthetic sample:

pip install palmwtc
palmwtc run            # uses bundled sample if no PALMWTC_DATA_DIR set

For your own data:

export PALMWTC_DATA_DIR=/path/to/your/chamber/data
palmwtc run --skip 022 025          # mirrors the original notebook-runner CLI
palmwtc run --notebooks             # papermill mode, produces HTML reports

Install

pip install palmwtc                 # core only
pip install 'palmwtc[ml]'           # + scikit-learn IsolationForest QC
pip install 'palmwtc[interactive]'  # + ipywidgets / anywidget for Jupyter dashboards
pip install 'palmwtc[gpu]'          # + torch (Apple-Silicon MPS / CUDA)
pip install 'palmwtc[all]'          # everything

Requires Python 3.11–3.13.

Library use

from palmwtc.config import DataPaths
from palmwtc.qc import QCProcessor
from palmwtc.flux import calculate_flux_cycles

paths = DataPaths.resolve()                     # layered: CLI → env → yaml → sample
qc_result = QCProcessor(paths).run("CO2_C1")
flux = calculate_flux_cycles(qc_result.data)

Full API reference: adisapoetro.github.io/palmwtc/api/

Citation

If you use palmwtc in scientific work, please cite the Zenodo DOI. The concept DOI 10.5281/zenodo.19680893 always resolves to the latest version; to cite a specific release, use its own version DOI (visible on the Zenodo record → Versions panel).

@software{adisaputro_palmwtc_2026,
  author  = {Adisaputro, Didi},
  title   = {palmwtc: Automated whole-tree chamber workflow for oil-palm ecophysiology},
  year    = {2026},
  version = {0.2.0},
  doi     = {10.5281/zenodo.19680893},
  url     = {https://github.com/adisapoetro/palmwtc},
}

See CITATION.cff for machine-readable metadata.

Background

Most ecosystem-scale flux measurements over oil-palm plantations use eddy covariance, which integrates over hectares of canopy and cannot resolve single-tree behaviour. palmwtc is built around a different instrument: an automated whole-tree chamber, sized and ventilated to enclose an individual mature oil palm, with an LI-COR LI-850 gas analyzer cycling open and closed on a programmed schedule. This is, to our knowledge, the first WTC deployment for oil palm — the WTC method was previously applied to temperate broadleaf species (Medlyn et al. 2016).

Contributing

See CONTRIBUTING.md. Bug reports and feature requests: github.com/adisapoetro/palmwtc/issues.

License

MIT — see LICENSE.