Data Processing Software
Python
SpecDAL
For the processing of data acquired using the facility’s full range field spectroradiometer suite, we suggest the use of the Python package SpecDAL. SpecDAL was created by the Environmental Spectroscopy Lab at the University of Wisconsin, and an updated fork is maintained by the facility at our GitHub. A full description for the installation of SpecDAL is provided in our Online Training package. In brief, in your active Python environment, which must have installed the Git, GitDB, and GitPython packages, type the following into a command prompt or powershell in which the environment is active:
pip install --upgrade git+https://github.com/NERC-FSF/SpecDAL.git
FieldSpecUtils
The FieldSpecUtils package contains functions for the calculation of various spectral indices when provided, as an argument, a pandas dataframe where the index column is a wavelength range extending from 350 nm to 2500 nm, and columns are reflectance values from 0 to 1. The package also contains functions to resample, using “convolution” routines, hyperspectral data at 1 nm increments to various in-orbit sensors e.g. Sentinel-2, WorldView-2, Planet etc. Convolution functions require two arguments; a pandas dataframe where the index column is a wavelength range extending from 350 nm to 2500 nm, and columns are reflectance values from 0 to 1; and the spectral response feature file (provided by the facility on request) for the sensor of interest. A full description for the installation of SpecDAL is provided in our Online Training package. In brief, in your active Python environment, which must have installed the Git,type the following into a command prompt or powershell in which the environment is active: GitDB, and GitPython packages,
pip install --upgrade git+https://github.com/NERC-FSF/FieldSpecUtils.git
PyMicrotops3
The PyMicrotops3 package, originally developed as PyMicrotops by Robin Wilson, is a Python package designed to communicate with SolarLight Microtops handheld sunphotometers and extract data from their flash drives. To install PyMicrotops3, in your active Python environment, which must have installed the Git, GitDB, and GitPython packages, type the following into a command prompt or powershell in which the environment is active:
pip install --upgrade git+https://github.com/NERC-FieldSpectroscopyFacility/PyMicrotops3.git
MATLAB
Field Spectroscopy Facility Post Processing Toolbox
Notice Please note that the Field Spectroscopy Facility Post Processing Toolbox is no longer actively maintained by the facility, and that functionality may be impaired.
The Field Spectroscopy Facility Post Processing Toolbox provides a selection of useful utilities designed to facilitate the handling and processing of data recorded by field-portable spectroradiometers. The utilities include a set of MATLAB scripts for importing and processing spectral data. The toolbox was created by Dr Alasdair Mac Arthur and Dr Iain Robinson, formerly of the Field Spectroscopy Facility. To install, download the file, unzip, and copy the FSFPostProcessing1.3.0 folder into a location accessible from MATLAB (e.g. onto the server on which MATLAB runs). Start MATLAB, and add the folder to the MATLAB path using the search path tool.
Atmospheric Correction using Atmospheric Radiative Transfer Simulations
Py6S
Py6S is a interface to the Second Simulation of the Satellite Signal in the Solar Spectrum (6S) atmospheric Radiative Transfer Model through the Python programming language. It allows you to run many 6S simulations using a simple Python syntax.
ACOLITE
ACOLITE allows for the simple and fast atmospheric correction of imagery from various satellites, including Landsat (5/7/8/9) and Sentinel-2/MSI (A/B), PlanetScope (Dove and SuperDove) and RapidEye, Venµs, SPOT and Pléiades, QuickBird2, WorldView-2 and -3, Sentinel-3/OLCI (A/B) and ENVISAT/MERIS, as well as several hyperspectral sensors (CHRIS, HYPERION, HICO, PRISMA, DESIS). ACOLITE is specifically designed for coastal and inland water applications.
ARCSI
The Atmospheric and Radiometric Correction of Satellite Imagery (ARCSI) software provides a command line tool for the atmospheric correction of Earth Observation imagery. ARCSI can be used for the processing of inland data.
Leaf Reflectance Modelling
PyProSAIL
PyProSAIL is a Python interface to the ProSAIL combined leaf and canopy optical model. PyProSAIL was developed by Robin Wilson and is now maintained by the Earth Observation of Agroecosystems Team at the Swiss Center For Excellence in Agricultural Research, Agroscope. To install PyProSAIL, in your active environment:
pip install pyprosail
To test your installation, in your active environment, open a Python session, and type the following:
import pyprosail
result[:,0] # These are the wavelengths (in micrometres)
result[:,1] # These are the reflectances (as a fraction)
Atmospheric Retrieval
plumeIR
plumeIR is a program designed to retrieve gas and particulate column densities from IR spectra measured in emission geometry by Open-Path Fourier Transform (OP-FTIR) spectrometers (such as the Midac Model M4401-SP, with the specific purpose of monitoring volcanic emissions. plumeIR is maintained by Dr Jean-Francois Smekens.