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,
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).
- 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 (namedABin Bruker OPUS programs). Possible additional values for the character vector supplied totypeare"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.
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:
ScSmcorresponds tosc_sampleScRfcorresponds tosc_refIgSmcorresponds toig_sampleIgRfcorresponds toig_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();
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: 21962655aad2b41b81a70dcc102093d5/ce677c69f675c083f7694e66af69ba31
#> file_id
#> <char>
#> 1: 0e9318d04fdb3beb4cd61145b080ccb6