opus_read: Read Bruker OPUS Spectrum Binary Files

In pierreroudier/opusreader: Reading OPUS Binary Files in R

Read Bruker OPUS Spectrum Binary Files

Description

Read file(s) acquired with a Bruker Vertex FTIR Instrument.

Usage

opus_read(
  file,
  type = "spec",
  simplify = FALSE,
  wns_digits = 1L,
  progress = TRUE,
  atm_comp_minus4offset = FALSE
)

Arguments

file	Character vector with path to file(s).
type	Character vector of spectra types to extract from OPUS binary file. Default is "spec", which will extract the final spectra, e.g. expressed in absorbance (named AB in Bruker OPUS programs). Possible additional values for the character vector supplied to type are "spec_no_atm_comp" (spectrum of the sample without compensation for atmospheric gases, water vapor and/or carbon dioxide), "sc_sample" (single channel spectrum of the sample measurement), "sc_ref" (single channel spectrum of the reference measurement), "ig_sample" (interferogram of the sample measurement) and "ig_ref" (interferogram of the reference measurement).
simplify	Logical (defaults to FALSE): if set to TRUE, returns a flattened list. The first element of that list (wavenumbers) is the wavenumbers of the first file read. The second element (spectra) is a matrix of the corresponding spectra. Especially useful when passing more than one file to the file option, for example to read a suite of spectral file. directly into a matrix. If the files do not have the same number of wavebands, the wavebands of the very first file passed to file is used as a reference for linear interpolation.
wns_digits	Integer that specifies the number of decimal places used to round the wavenumbers (values of x-variables) if simplify = TRUE.
progress	Logical (defaults to TRUE) whether a message is printed when an OPUS binary file is parsed into an R list entry.
atm_comp_minus4offset	Logical whether spectra after atmospheric compensation are read with an offset of -4 bytes from Bruker OPUS files. Default is FALSE.

Details

The type of spectra returned by the function when using type = "spec" depends on the setting of the Bruker instrument: typically, it can be either absorbance or reflectance.

The type of spectra to extract from the file can also use Bruker's OPUS software naming conventions, as follows:

• ScSm corresponds to sc_sample

• ScRf corresponds to sc_ref

• IgSm corresponds to ig_sample

• IgRf corresponds to ig_ref

Value

The output of opus_read() depends on the value of the simplify option used in the function call.

• If simplify = FALSE (default), opus_read() returns a list of 10 elements:

  • metadata: a data.frame containing metadata from the OPUS file

  • spec If "spec" was requested in the type option, a matrix of the spectrum of the sample (otherwise set to NULL).

  • spec_no_atm_comp If "spec_no_atm_comp" was requested in the type option, a matrix of the spectrum of the sample without background compensation (otherwise set to NULL).

  • sc_sample If "sc_sample" was requested in the type option, a matrix of the single channel spectrum of the sample (otherwise set to NULL).

  • sc_ref If "sc_ref" was requested in the type option, a matrix of the single channel spectrum of the reference (otherwise set to NULL).

  • ig_sample If "ig_sample" was requested in the type option, a matrix of the interferogram of the sample (otherwise set to NULL).

  • ig_ref If "ig_ref" was requested in the type option, a matrix of the interferogram of the reference (otherwise set to NULL).

  • wavenumbers If "spec" or "spec_no_atm_comp" was requested in the type option, a numeric vector of the wavenumbers of the spectrum of the sample (otherwise set to NULL).

  • wavenumbers_sc_sample If "sc_sample" was requested in the type option, a numeric vector of the wavenumbers of the single channel spectrum of the sample (otherwise set to NULL).

  • wavenumbers_sc_ref If "sc_ref" was requested in the type option, a numeric vector of the wavenumbers of the single channel spectrum of the reference (otherwise set to NULL).

• If simplify = TRUE, a list of two elements is returned:

  • wavenumbers: Numeric vector with wavenumbers of the requested spectra.

  • spectra: Matrix with spectra of requested type (see argument type).

Author(s)

Philipp Baumann

pierreroudier/opusreader documentation built on Sept. 15, 2022, 12:32 p.m.