TIMESAT CLI

TIMESAT CLI is a command line interface and workflow manager for the TIMESAT package. It provides a convenient way to configure and execute TIMESAT processing pipelines directly from the command line or automated scripts.

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Requirements

Before you begin, make sure you have:

• Miniconda or Anaconda (for environment management)
  Download: https://docs.conda.io/en/latest/miniconda.html
• Python 3.10+

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Installation

timesat-cli is available on PyPI and can be installed using pip.
Although it is not published on Conda, you can safely install it inside a Conda environment.

Option 1 — Install inside a Conda environment

conda create -n timesat-cli python=3.12
conda activate timesat-cli
pip install timesat-cli

This approach uses Conda only for environment isolation.
The installation itself is handled by pip, which will automatically install timesat and all required dependencies.

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Option 2 — Direct installation with pip

If you already have Python 3.10+ installed:

pip install timesat-cli

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Running the Application

After installation, start the CLI with:

timesat-cli path/to/settings.json

or equivalently:

python -m timesat_cli path/to/settings.json

To migrate a legacy config (settings + class1/class2/...) to the new grouped schema:

timesat-cli migrate-config old_settings.json new_settings.json

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Advanced Usage

If you wish to customize or extend the workflow, you can also run or modify the main script directly:

python timesat_run.py

The file 'timesat_run.py' contains the full example pipeline that invokes core modules from the 'timesat_cli' package, including configuration loading, file management, TIMESAT processing, and output writing.

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Configuration Format

timesat-cli only supports grouped JSON:

For a complete parameter reference, see docs/parameters.md.

• input: s3env, tv_list, image_file_list, quality_file_list, lc_file
• output: outputfolder, outputvariables, time_sampling, time_step_days, monthly_days, drop_first_year, drop_last_year, p_nodata, p_hrvppformat, vpp_dtype, yfit_prefix, vpp_prefix, vpp_variables
• general: imwindow, p_band_id, p_ignoreday, p_ylu, p_a, p_davailwin, p_outlier, p_printflag, max_memory_gb, scale, offset, classes (and optional p_nclasses)

vpp_variables controls which VPP layers are written and how they are named. Each entry supports:

• source (required): source TIMESAT variable name, e.g. SOSD, TPROD
• name (optional): output layer name; defaults to source
• enabled (optional): defaults to true

yfit_prefix and vpp_prefix control the filename prefix independently:

• yfit: <yfit_prefix>_<YYYYMMDD>.tif and <yfit_prefix>_<YYYYMMDD>_QA.tif
• VPP: <vpp_prefix>_<Output Name>_<year>_season_<n>.tif
• VPP QA: <vpp_prefix>_QA_<year>_season_<n>.tif

vpp_dtype controls the raster data type used for VPP outputs. It is optional and defaults to float32. Supported values: uint8, uint16, int16, uint32, int32, float32, float64.

Output time series dates are controlled by:

• time_sampling: regular or monthly
• time_step_days: day interval used when time_sampling is regular; 1 means daily synthetic 365-day output
• monthly_days: month days used when time_sampling is monthly, for example [1, 11, 21]
• drop_first_year / drop_last_year: independently remove buffer years from the output date range

The legacy p_st_timestep key is still accepted. p_st_timestep = -1 is interpreted as:

{
  "time_sampling": "monthly",
  "time_step_days": 1,
  "monthly_days": [1, 11, 21],
  "drop_first_year": true,
  "drop_last_year": true
}

general.classes is required and must be a non-empty list. general.p_nclasses is optional; when provided, it must equal len(general.classes).

Example:

{
  "input": {
    "s3env": "",
    "tv_list": "filelists/time_list.txt",
    "image_file_list": "filelists/image_files.txt",
    "quality_file_list": "filelists/qa_files.txt",
    "lc_file": "landcover.tif"
  },
  "output": {
    "outputfolder": "outputs/",
    "outputvariables": 1,
    "time_sampling": "regular",
    "time_step_days": 1,
    "monthly_days": [1, 11, 21],
    "drop_first_year": false,
    "drop_last_year": false,
    "p_nodata": -9999,
    "p_hrvppformat": 1,
    "vpp_dtype": "float32",
    "yfit_prefix": "TIMESAT",
    "vpp_prefix": "TIMESAT",
    "vpp_variables": [
      { "source": "SOSD" },
      { "source": "TPROD", "name": "TI_PPI" }
    ]
  },
  "general": {
    "imwindow": [0, 0, 0, 0],
    "p_band_id": 1,
    "p_ignoreday": 366,
    "p_ylu": [0.00001, 2],
    "p_a": [],
    "p_davailwin": 45,
    "p_outlier": 0,
    "p_printflag": 0,
    "max_memory_gb": 10,
    "scale": 1,
    "offset": 0,
    "p_nclasses": 1,
    "classes": [
      {
        "landuse": 1,
        "p_fitmethod": 2,
        "p_smooth": 1000,
        "p_nenvi": 1,
        "p_wfactnum": 1,
        "p_startmethod": 1,
        "p_startcutoff": [0.25, 0.15],
        "p_low_percentile": 0.0,
        "p_fillbase": 0,
        "p_seasonmethod": 1,
        "p_seapar": 1,
        "lowrangemode": 1,
        "highrangemode": 0,
        "rangedownweight": 0.5
      }
    ]
  }
}

Range handling modes are class-specific. lowrangemode and highrangemode use: 0 invalid (w = 0, keep y), 1 clip to the boundary and keep w, and 2 clip to the boundary and multiply w by rangedownweight. If omitted, vegetation-index products use lowrangemode = 0, highrangemode = 0, and rangedownweight = 0.5.

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HRVPP Notes — QFLAG2 weights

If you work with HRVPP quality flags (QFLAG2), the following weights w are commonly applied:

QFLAG2 value	Weight w
1	1.0
4097	1.0
8193	1.0
12289	1.0
1025	0.5
9217	0.5
2049	0.5
6145	0.5
3073	0.5

Grouped-schema example:

"general": {
  "p_a": [
    [1, 1.0],
    [4097, 1.0],
    [8193, 1.0],
    [12289, 1.0],
    [1025, 0.5],
    [9217, 0.5],
    [2049, 0.5],
    [6145, 0.5],
    [3073, 0.5]
  ],
  "classes": [ ... ]
}

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License

TIMESAT-CLI is released under the MIT License.

You are free to use, modify, and distribute this software under the terms of the MIT License.

The MIT License applies only to the source code and assets provided in this repository.

📦 Dependency and Usage Notice

TIMESAT-CLI is an open-source command-line interface that depends on the TIMESAT core, which is proprietary software and licensed separately.

Use of TIMESAT-CLI does not grant any rights to use the TIMESAT core beyond the terms of the TIMESAT license.

• The TIMESAT core is freely available for non-commercial scientific research, academic teaching, and personal use.
• Commercial use of the TIMESAT core requires a separate written agreement with the authors.

Each dependency installed with this software retains its own license (MIT, BSD, Apache, etc.). Users are responsible for complying with the license terms of all installed components.

⚖️ License Summary

Component	License Type	Notes
TIMESAT-CLI	MIT License	Open-source CLI and workflow manager.
TIMESAT core	Proprietary	Licensed separately; commercial use requires agreement.
Other dependencies	Various (MIT/BSD/Apache)	See individual package licenses.

For full license texts, see the LICENSE and NOTICE files included with this repository and installed packages.

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Citation

If you use TIMESAT, TIMESAT-CLI or TIMESAT-GUI in your research, please cite the corresponding release on Zenodo:

Cai, Z., Eklundh, L., & Jönsson, P. (2025). TIMESAT4: is a software package for analysing time-series of satellite sensor data (Version 4.1.x) [Computer software]. Zenodo.
https://doi.org/10.5281/zenodo.17369757

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Acknowledgments

• This project acknowledges the Swedish National Space Agency (SNSA), the European Environment Agency (EEA), and the European Space Agency (ESA) for their support and for providing access to satellite data and related resources that made this software possible.

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