R/parse_opus.R
parse_opus.RdThis function is internally used to parse the raw vector of the OPUS file
after reading it with read_opus_raw().
parse_opus(raw, data_only)Nested list (S3 object) containing the parsed contents of the binary
encoded blocks of an OPUS file. The first level names of the list correspond
to the display names as shown in the Bruker OPUS viewer software. However, in
snake_case and more standardized naming to allow for better output handling.
Each parsed block element is a sublist containing a) the binary read
instructions decoded/derived from the header ($block_type, $channel_type,
$text_type and $additional_type, $offset (bytes), $next_offset
(bytes), $chunk_size (bytes)); b) if parameter block, nested list of
specific parameters under $parameters, which has elements named according
to capitalized Bruker-internal "three-letter-string" definitions (e.g.,
"DPF := Data Point Format"). Possible first-level block names and
information provided include:
refl_no_atm_comp_data_param : class "parameter"
(viewer: "Data Parameters Refl". Parameter list with metadata for refl
data block (refl).
refl_no_atm_comp: class "data" (spectrum; viewer: "Refl").
Unprocessed (raw; i.e, not atmospherically compensated) reflectance spectra
(:= sc_sample / sc_ref). Note that this element is the
untreated spectra before an eventual "atmospheric compensation"
routine is applied.
refl_data_param : class "parameter" (viewer: "Data Parameters Refl").
Parameter list with metadata for refl data block (metadata of
reflectance spectrum; see refl output).
Note that this element only results if "atmospheric compensation" was
activated in the OPUS measurement settings.
refl: class "data" (spectrum; viewer: "Refl"). Atmospherically
compensated reflectance spectra (:= sc_sample_corr / sc_ref_corr). This
result spectrum only exists if either correction of CO2 and/or water vapour
bands is set in OPUS setting (proprietary algorithm; could possibly be
reverse engineered). If refl exists, it has always a corresponding
untreated refl_no_atm_comp spectrum (the latter present in file but not
shown in the OPUS viewer, where only (final) ab is displayed)
quant_report_refl: class "parameter" (viewer: "Quant Report Refl").
Quantification report for tools of multivariate calibration on refl data
(i.e., PLS regression) offered in the QUANT2 OPUS package. Nested list with
Bruker-internal "three-letter-string" definitions. "TIT" is the title of
a nested quantification table, "E<digit>[2]" stands probably for entry,
"F<digit>[2]" for field, and "Z<digit>[2]" we do not yet know what it
maps to. There seems more information needed, which we can get by expanding
the header parsing algorithm.
ab_no_atm_comp_data_param : class "parameter"
(viewer: "Data Parameters AB"). Parameter list with metadata for ab
data block (spectrum; see ab output).
ab_no_atm_comp: class "data" (spectrum; viewer: "Refl").
Unprocessed (raw; i.e, not atmospherically compensated) reflectance spectra
(:= sc_sample/ sc_ref).
ab_data_param : class "parameter" (viewer: "Data Parameters Refl").
Parameter list with metadata for ab data block (spectrum; see ab).
Note that this element only results if "atmospheric compensation" was
activated in the OPUS measurement settings.
ab: class "data" (spectrum; viewer: "AB"). Atmospherically
compensated (apparent) absorbance spectra
(:= log(1 / (sc_sample_corr / sc_ref_corr)). Only
exists if either correction of CO2 and/or water vapour bands is set in OPUS
setting (proprietary algorithm; could possibly be reverse engineered).
If AB exists, it has always a corresponding untreated
ab_no_atm_comp spectrum (the latter present in file but not shown in
the OPUS viewer, where only final ab is displayed).
quant_report_ab: class "parameter" (viewer: "Quant Report AB").
Quantification report for tools of multivariate calibration on ab data
(i.e., PLS regression) offered in the QUANT2 OPUS package. Nested list with
Bruker-internal "three-letter-string" definitions. "TIT" is the title of
a nested quantification table, "E<digit>[2]" stands probably for entry,
"F<digit>[2]" for field, and "Z<digit>[2]" we do not yet know what it
maps to. There seems more information needed, which we can get by expanding
the header parsing algorithm.
sc_sample_data_param: class "parameter" (metadata; viewer:
"Data Parameters ScSm").
Describes the sc_sample data block (see sc_sample).
sc_sample: class "data" (spectrum). Single channel (sc) spectrum of
the sample (y-axis: intensity).
ig_sample_data_param: class "parameter" (metadata; viewer:
"Data Parameters IgSm").
ig_sample: class "data" (signal, viewer: "IgSm").
Interferogram of the sample measurement. Oscillatory signal
(x-axis: optical path difference (OPD); y-axis: amplitude of the signal).
sc_ref_data_param: class "parameter" (metadata; viewer:
"Data Parameters ScRf").
Describes the sc_sample data block (see sc_ref).
sc_ref: class "data" (spectrum; viewer: "Data Parameters IgSm").
Single channel (sc) spectrum of the reference (background material: e.g.,
gold; y-axis: intensity).
ig_ref_data_param: class "parameter" (metadata; viewer:
"Data Parameters IgRf").
ig_ref: class "data" (spectrum; viewer: "IgRf").
Interferogram of the reference measurement. (background material: e.g.,
gold). Oscillatory signal (x-axis: optical path difference (OPD);
y-axis: amplitude of the signal)
optics: class "parameter (metadata; viewer: "Optic Parameters").
Optic setup and settings such as "Accessory", "Detector Setting" or
"Source Setting".
optics_ref: class "parameter (metadata; viewer: "Optic Parameters
Rf"). Optic setup and settings specific to reference measurement such as
"Accessory", "Detector Setting" or "Source Setting".
acquisition_ref: class "parameter" (metadata; viewer: "Acquisition
parameters Rf". Settings such as ""Additional Data Treatment", (number) of
"Background Scans" or "Result Spectrum" (e.g. value "Absorbance").
fourier_transformation_ref:
fourier_transformation: class "parameter"
sample:
acquisition:
instrument_ref:
instrument:
lab_and_process_param_1:
lab_and_process_param_2:
info_block:
history: