Reading OPUS Binary Files in R
This package implements a driver for FTIR spectroscopy data collected in the OPUS binary format.
This package is a fork from the read_opus_bin_univ
from the simplerspec
package authored by Philipp Baumann, who deserves all of the credit for this contribution. Here the simplerspec
functions are modified so they can read raw
streams directly, and to keep the functionality in a lighter package.
You can use the remotes
package to install opusreader
:
remotes::install_github("pierreroudier/opusreader")
The package includes a sample OPUS spectra for demonstration purposes. Its location can be determined using the function opus_file()
:
> opus_file()
[1] "/path/to/opusreader/inst/extdata/test_spectra.0"
Two functions are available to actually read the data:
opus_read
is the workhorse of the package, and allows to read binary files:# File name of the OPUS file to read
fn <- opus_file()
# Read OPUS file
s <- opus_read(fn)
# Plot the spectra
plot(s$wavenumbers, s$spec, type = 'l')
opus_read_raw
function is lower level, and allows to read a raw
representation of the OPUS file. It is useful if the OPUS file is "streamed" over eg a web service:# Store OPUS file content as raw binary data
fn <- opus_file()
rw <- readBin(fn, "raw", 1e5)
# Read raw binary data directly
s <- opus_read_raw(rw)
# Plot the spectra
plot(s$wavenumbers, s$spc, type = 'l')