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Read a Bruker OPUS spectrum binary raw string

Source: R/read_opus_raw.R
read_opus_raw.Rd

Read single binary acquired with an Bruker Vertex FTIR Instrument

Usage

read_opus_raw(rw, type = "spec", atm_comp_minus4offset = FALSE)

Arguments

rw

a raw vector

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).

atm_comp_minus4offset

logical; whether spectra after atmospheric compensation are read with an offset of -4 bytes from Bruker OPUS files. Default is FALSE.

Value

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 atmospheric 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).

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

See also

read_opus()

Author

Philipp Baumann and Pierre Roudier