hyperSpec.utils

This R package is a collection of utility functions to work with objects of the class hyperSpec as defined by the package {hyperSpec}. While it is independent from the popular {hyperSpec} package (written by Claudia Beleites), {hyperSpec.utils} intends to add some convenient shortcuts for data analysis, some more conversion, import and export functions, tools for interactive data exploration, as well as some extended functionality (such as cosmic ray removal). The package can be considered as work in progress and substantial (also backwards incompatible) changes are to be expected.

Installation

You can install hyperSpec.utils from GitHub with:

# install.packages("remotes")
remotes::install_github("konradmayer/hyperSpec.utils")

Use the argument dependencies = TRUE to also install suggested dependencies, mainly needed for the function spcmap_explorer(), as well as individual plotting, import/export and conversion functions.

What is yet to come?

Multiple additional functions are currently planned and ideas are added to the issues section with an label attached.

If you have more ideas for useful functions, please open an issue with appropriate tag, or, even better, open a pull request to propose your ideas on a possible implementation.

What is included?

The package will get continuously extended and currently holds functions

• for extended import and export (export to Witec ASCII graph format with write.txt.Witec.Graph() or to JCAMP-DX with write_jdx(), experimental import of OPUS binary files with read_opus())
• for spectral unmixing (wrappers als() for MCR-ALS, nmf() for NMF, vca() for VCA and ica() for ICA)
• for doing mixture analysis (omp() for the orthogonal matching pursuit, and linear_combination() for fitting linear combinations of reference spectra)
• for interactive visualization (e.g. spcmap_explorer(), which is demonstrated below, and cubeview())
• introducing additional functionality (crr() for cosmic ray removal as defined in and provided with this publication by Whitaker and Hayes 2018, a S4 method for diff() or extending the test functions of {hyperSpec} by the simple is.hyperSpec() and is.hyperSpecMap() for consistency with the respective {base} functions, returning a logical value in all cases)
• with focus on spatially resolved spectral data (spectral maps; such as spcmap2array() to get an array of the spectral hypercube, spcmap_dim(), is_hyperSpecMap() as well as most visualization functions)
• being convenient shortcuts for already existing functionality (e.g. for normalization minmax_normalization(), snv_normalization(), vector_normalization(), area_normalization() and band_normalization(), for band aggregation aggregate_wl() resp. integration integrate_wl() plotting with the viridis color scale plotmap_viridis())

Acknowledgments

This package was developed at the BIONAMI (biological materials at the nano and micro scale) group at the University of Natural Resources and Life Sciences, Vienna, Institute for Biophysics, with funding from the European community (ERC-consolidator grant SCATAPNUT 681885).