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Read spectral data from Bruker OPUS binary files

Source: R/read_opus.R
read_opus.Rd

Read file(s) acquired with a Bruker Vertex FTIR Instrument. This function is basically a fork of opus_read() from https://github.com/pierreroudier/opusreader.

Usage

read_opus(
  file,
  share = NULL,
  metadata = list(file_name = basename(file), user_name = NULL, contact_info = NULL,
    organization = NULL, citation = NULL, spectrum_type = NULL, spectrum_identity = NULL,
    material_form = NULL, material_phase = NULL, material_producer = NULL,
    material_purity = NULL, material_quality = NULL, material_color = NULL,
    material_other = NULL, cas_number = NULL, instrument_used = NULL,
    instrument_accessories = NULL, instrument_mode = NULL, spectral_resolution = NULL,
    laser_light_used = NULL, number_of_accumulations = NULL, 
    
    total_acquisition_time_s = NULL, data_processing_procedure = NULL,
    level_of_confidence_in_identification = NULL, other_info = NULL, license =
    "CC BY-NC"),
  type = "spec",
  digits = 1L,
  atm_comp_minus4offset = FALSE
)

Arguments

file

character vector with path to file(s).

share

defaults to NULL; needed to share spectra with the Open Specy community; see share_spec() for details.

metadata

a named list of the metadata; see as_OpenSpecy() for details.

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).

digits

Integer that specifies the number of decimal places used to round the wavenumbers (values of x-variables).

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

An OpenSpecy object.

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_spec() for reading .y(a)ml, .json, or .rds (OpenSpecy) files; read_text(), read_asp(), read_spa(), read_spc(), and read_jdx() for text files, .asp, .spa, .spa, .spc, and .jdx formats, respectively; read_text() for reading .dat (ENVI) files; read_zip() and read_any() for wrapper functions; read_opus_raw();

Author

Philipp Baumann, Zacharias Steinmetz, Win Cowger

Examples

read_extdata("ftir_ps.0") |> read_opus()
#>       wavenumber         V1
#>            <num>      <num>
#>    1:   399.2239 0.01660202
#>    2:   401.1525 0.01790014
#>    3:   403.0811 0.01831616
#>    4:   405.0097 0.01894823
#>    5:   406.9384 0.02070733
#>   ---                      
#> 2122:  4489.8223 0.02349887
#> 2123:  4491.7509 0.02352615
#> 2124:  4493.6796 0.02357077
#> 2125:  4495.6082 0.02362563
#> 2126:  4497.5368 0.02361715
#> 
#> $metadata
#>        x     y file_name  license                         unique_id
#>    <int> <int>    <char>   <char>                            <char>
#> 1:     1     1 ftir_ps.0 CC BY-NC sample1_PSnew_2020-10-28 14:33:02
#>        sample_id        date_time_sm        date_time_rf   sample_name
#>           <char>              <POSc>              <POSc>        <char>
#> 1: sample1_PSnew 2020-10-28 14:33:02 2020-10-28 14:23:20 sample1_PSnew
#>    instr_name_range resolution_wn result_spc beamspl laser_wn
#>              <char>         <int>     <char>  <char>    <num>
#> 1:    VERTEX 70-MIR             4         AB     KBr 15799.24
#>                               spc_in_file zero_filling temp_scanner_sm
#>                                    <char>        <int>           <num>
#> 1: ig_sample;ig_ref;sc_sample;sc_ref;spec            2            27.9
#>    temp_scanner_rf hum_rel_sm hum_rel_rf hum_abs_sm hum_abs_rf col_id
#>              <num>      <int>     <lgcl>     <lgcl>     <lgcl> <char>
#> 1:            27.9          2         NA         NA         NA     V1
#>                                                           session_id
#>                                                               <char>
#> 1: 919e3e54e4c2f1b1e4db64651b451179/7b524d8ec8dc80c61977c331bd1e6f3d
#>                             file_id
#>                              <char>
#> 1: 0e9318d04fdb3beb4cd61145b080ccb6