diive 0.75.0

Time series processing

Time series data processing

diive is a Python library for time series processing, in particular ecosystem data. Originally developed by the ETH Grassland Sciences group for Swiss FluxNet.

Recent updates: CHANGELOG
Recent releases: Releases

Example notebooks can be found in the folder notebooks. More notebooks are added constantly.

Current Features

Analyses

• Calculate z-aggregates in quantiles (classes) of x and y (notebook example)
• Daily correlation (notebook example)
• Decoupling: Sorting bins method (notebook example)
• Find data gaps (notebook example)
• Histogram (notebook example)
• Optimum range
• Percentiles (notebook example)

Corrections

• Offset correction
• Set to threshold
• Wind direction offset detection and correction (notebook example)

Create variable

• Calculate time since last occurrence, e.g. since last precipitation (notebook example)
• Calculate daytime flag, nighttime flag and potential radiation from latitude and longitude (notebook example)
• Day/night flag from sun angle
• VPD from air temperature and RH (notebook example)

Eddy covariance high-resolution

• Flux detection limit from high-resolution data
• Find maximum covariance between turbulent wind and scalar
• Wind rotation to calculate turbulent departures of wind components and scalar (e.g. CO2)

Files

• Detect expected and unexpected (irregular) files in a list of files
• Split multiple files into smaller parts and export them as (compressed) CSV files
• Read single data file with parameters (notebook example)
• Read single data file with pre-defined filetype (notebook example)
• Read multiple data files with pre-defined filetype (notebook example)

Fits

• Bin fitter

Flux

• Critical heat days for NEP, based on air temperature and VPD
• CO2 penalty
• USTAR threshold scenarios

Flux processing chain

For info about the Swiss FluxNet flux levels, see here.

• Flux processing chain (notebook example)
  • The notebook example shows the application of:
    • Level-2 quality flags
    • Level-3.1 storage correction
    • Level-3.2 outlier removal
• Quick flux processing chain (notebook example)

Formats

Format data to specific formats

• Convert EddyPro fluxnet output files for upload to FLUXNET database (notebook example)
• Load and save parquet files (notebook example)

Gap-filling

Fill gaps in time series with various methods

• XGBoostTS (notebook example (minimal), notebook example (more extensive))
• RandomForestTS (notebook example)
• Linear interpolation (notebook example)
• Quick random forest gap-filling (notebook example)

Outlier Detection

Single outlier tests create a flag where 0=OK and 2=outlier.

Multiple tests combined

• Step-wise outlier detection

Single tests

• Absolute limits (notebook example)
• Absolute limits, separately defined for daytime and nighttime data (notebook example)
• Incremental z-score: Identify outliers based on the z-score of increments
• Local standard deviation: Identify outliers based on the local standard deviation from a running median
• Local outlier factor: Identify outliers based on local outlier factor, across all data
• Local outlier factor: Identify outliers based on local outlier factor, daytime nighttime separately
• Manual removal: Remove time periods (from-to) or single records from time series
• Missing values: Simply creates a flag that indicated available and missing data in a time series
• z-score: Identify outliers based on the z-score across all time series data
• z-score: Identify outliers based on the z-score, separately for daytime and nighttime
• z-score: Identify outliers based on max z-scores in the interquartile range data

Plotting

• Heatmap showing values (z) of time series as date (y) vs time ( x) (notebook example)
• Heatmap showing values (z) of time series as year (y) vs month ( x) (notebook example)
• Long-term anomalies per year (notebook example)
• Simple (interactive) time series plot (notebook example)
• ScatterXY plot (notebook example)
• Various classes to generate heatmaps, bar plots, time series plots and scatter plots, among others

Quality control

• Stepwise MeteoScreening from database (notebook example)

Stats

• Time series stats (notebook example)

Timestamps

• Create continuous timestamp based on number of records in the file and the file duration
• Detect time resolution from data (notebook example)
• Insert additional timestamps in various formats

Installation

diive can be installed from source code, e.g. using poetry for dependencies.

diive is currently developed under Python 3.9.7, but newer (and many older) versions should also work.

diive can be installed using conda with conda intall -c conda-forge diive

One way to install and use diive with a specific Python version on a local machine:

• Install miniconda
• Start miniconda prompt
• Create a environment named diive-env that contains Python 3.9.7: conda create --name diive-env python=3.9.7
• Activate the new environment: conda activate diive-env
• Install diive version directly from source code: pip install https://github.com/holukas/diive/archive/refs/tags/v0.63.1.tar.gz (select .tar.gz file of the desired version)
• If you want to use diive in Jupyter notebooks, you can install Jupyterlab. In this example Jupyterlab is installed from the conda distribution channel conda-forge: conda install -c conda-forge jupyterlab
• If used in Jupyter notebooks, diive can generate dynamic plots. This requires the installation of: conda install -c bokeh jupyter_bokeh