Title:	Read Spectroscopic Data from Bruker OPUS Binary Files
Version:	0.6.8
Description:	Reads data from Bruker OPUS binary files of Fourier-Transform infrared spectrometers of the company Bruker Optics GmbH & Co. This package is released independently from Bruker, and Bruker and OPUS are registered trademarks of Bruker Optics GmbH & Co. KG. https://www.bruker.com/en/products-and-solutions/infrared-and-raman/opus-spectroscopy-software/latest-release.html. It lets you import both measurement data and parameters from OPUS files. The main method is 'read_opus()', which reads one or multiple OPUS files into a standardized list class. Behind the scenes, the reader parses the file header for assigning spectral blocks and reading binary data from the respective byte positions, using a reverse engineering approach. Infrared spectroscopy combined with chemometrics and machine learning is an established method to scale up chemical diagnostics in various industries and scientific fields.
License:	MIT + file LICENSE
URL:	https://opusreader2.spectral-cockpit.codefloe.page/, https://codefloe.com/spectral-cockpit/opusreader2/
BugReports:	https://codefloe.com/spectral-cockpit/opusreader2/issues/
Encoding:	UTF-8
RoxygenNote:	7.3.3
Suggests:	knitr, rmarkdown, testthat (≥ 3.0.0), progressr, mirai (≥ 2.5.0)
Config/testthat/edition:	3
VignetteBuilder:	knitr
NeedsCompilation:	no
Language:	en-US
Packaged:	2026-01-29 05:14:13 UTC; philipp
Author:	Philipp Baumann [aut, cre], Thomas Knecht [aut], Pierre Roudier [aut], spectral-cockpit.com [cph, fnd]
Maintainer:	Philipp Baumann <baumann-philipp@protonmail.ch>
Repository:	CRAN
Date/Publication:	2026-02-03 10:30:08 UTC

calculate the full chunk size

Description

calculate the full chunk size

Usage

calc_chunk_size(ds)

Arguments

Calculate the parameter chunk size in bytes

Description

Calculate the parameter chunk size in bytes

Usage

calc_parameter_chunk_size(ds)

Arguments

Value

Number of bytes as length 1 numeric vector

assign the classes to the dataset list

Description

assign the classes to the dataset list

Usage

create_dataset(header_data)

Arguments

Construct new class list_opusreader2

Description

Construct new class list_opusreader2

Usage

new_list_opusreader2(dataset_list)

Arguments

List wrapper that reads a list of files (dsn) via read_opus_single() and returns spectra in a list

Description

List wrapper that reads a list of files (dsn) via read_opus_single() and returns spectra in a list

Usage

opus_lapply(dsn, data_only)

Arguments

Value

nested list where first-level elements are individual spectral measurements parsed from individual OPUS binary files; the output is identical to its user exposed reading interface, see ?read_opus

spectra list containing the elements described in ?read_opus

See Also

read_opus() read_opus_single()

Get File Paths of Sample OPUS Files Included in the Package

Description

Utility function that retrieves the location of the sample OPUS binary file on disk.

Usage

opus_test_dsn()

Value

a character vector with the paths OPUS files included in the package

Examples

(dsn <- opus_test_dsn())

Get path of a Selected Sample OPUS File Included in the Package

Description

Utility function that retrieves the location of the sample OPUS binary file on disk.

Usage

opus_test_file()

Value

a character vector with the path to a selected single sample OPUS file

Examples

(fn <- opus_test_file())

read chunk method

Description

read chunk method

Usage

parse_chunk(ds, raw)

Arguments

See Also

Parsing helper parse_header()

read chunk method for data

Description

read chunk method for data

Usage

## S3 method for class 'data'
parse_chunk(ds, raw)

Arguments

read chunk method for default

Description

read chunk method for default

Usage

## Default S3 method:
parse_chunk(ds, raw)

Arguments

read chunk method for parameter

Description

read chunk method for parameter

Usage

## S3 method for class 'parameter'
parse_chunk(ds, raw)

Arguments

read chunk method for text

Description

read chunk method for text

Usage

## S3 method for class 'text'
parse_chunk(ds, raw)

Arguments

parse the header of the opus file

Description

parse the header of the opus file

Usage

parse_header(raw)

Arguments

See Also

Parsing helper parse_chunk()

Parse data, parameters and text from raw vector of OPUS file saved after one spectral measurement of a Bruker FT-IR device.

Description

This function is internally used to parse the raw vector of the OPUS file after reading it with read_opus_raw().

Usage

parse_opus(raw, data_only)

Arguments

Value

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:

See Also

read_opus_raw()

Print method for collection of OPUS spectra with class list_opusreader2

Description

Print method for collection of OPUS spectra with class list_opusreader2

Usage

## S3 method for class 'list_opusreader2'
print(x, ...)

Arguments

Value

Returns x invisibly.

read character from binary

Description

read character from binary

Usage

read_character(raw, cursor, n = 1L, n_char, encoding = "latin1")

Arguments

read double from binary (double-precision, 64 bits)

Description

read double from binary (double-precision, 64 bits)

Usage

read_double(raw, cursor, n = 1L)

Arguments

read float from binary (single-precision, 32 bits)

Description

read float from binary (single-precision, 32 bits)

Usage

read_float(raw, cursor, n = 1L)

Arguments

Read OPUS binary files from Bruker spectrometers

Description

Read and parse OPUS files with spectral data from individual measurements

Usage

read_opus(dsn, data_only = FALSE, parallel = FALSE, progress_bar = FALSE)

Arguments

Value

List with OPUS spectra collection of class list_opusreader2. The individual elements are individual sample measurement data extracted from the corresponding OPUS binary files, as parsed from the encoded data blocks.

Each element in list_opusreader2 contains metadata and measurement data equivalent to their names displayed in the Bruker OPUS viewer software. However, we used snake_case and standardized the naming for better output handling.

Each parsed block element is a sublist that contains

1. 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)).

2. 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 (⁠:= log10(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: class parameter (metadata; viewer: "FT - Parameters Rf"). Fourier transform parameters of the reference sample like Apodization function ("APF"), end frequency limit ("HFQ"), start frequency limit ("LFQ"), nonlinearity correction ("NLI"), phase resolution ("PHR"), phase correction mode ("PHZ"), zero filling factor ("ZFF").

• fourier_transformation: class parameter (metadata; viewer: "FT - Parameters"). Fourier transform parameters of the sample measurement. See fourier_transformation_ref for possible elements contained.

• sample: class parameter (metadata; viewer: "Sample Parameters"). Extra information such as the "Operator Name", "Experiment", or "Location".

• acquisition: class parameter (metadata; viewer. "Acquisition Parameters"). Settings of sample measurement, such as "Additional Data Treatment", (number) of "Background Scans" or "Result Spectrum" (e.g. value "Absorbance").

• instrument_ref: class parameter (metadata; viewer: "Instrument Parameters Rf"). Detailed instrument properties for the reference measurement, such as "High Folding Limit", "Number of Sample Scans", or "Actual Signal Gain 2nd Channel".

• instrument: class parameter (metadata; viewer: "Instrument Parameters"). Detailed instrument properties for the sample measurement. See instrument_ref.

• lab_and_process_param_raw: class parameter (metadata). Laboratory sample annotations such as "Product Group", "Product", "Label Product Info 1" (e.g., for sample_id), "Value Product Info 1" (e.g., the sample_id value), or the "Measurement Position Microplate" (e.g., for HTS-XT extension)

• lab_and_process_param_processed: class parameter (metadata). Laboratory sample annotations for measurements done with additional OPUS data processing methods. See lab_and_process_param_raw

• info_block: class parameter (metadata). Infos such as "Operator", measurement "Group", "Sample ID". These can e.g. be set though the OPUS/LAB sofware interface.

• history: class parameter (metadata). Character vector with OPUS command history.

• unknown: if a block-type can not be matched, no parsing is done and an empty list entry is returned. This gives you a hint that there is a block that can not yet be parsed. You can take further steps by opening an issue.

Details

read_opus() is the high-level interface to read multiple OPUS files at once from a data source name (dsn).

It optionally supports parallel reads via the {mirai} backend. {mirai} provides a highly efficient asynchronous parallel evaluation framework via the Nanomsg Next Gen (NNG), high-performance, lightweight messaging library for distributed and concurrent applications.

When reading in parallel, a progress bar can be enabled.

Read chunks of OPUS files in parallel using {mirai} backend via mirai::mirai_map()

Description

Relies on background processes (daemons) set up via mirai::daemon()

Usage

read_opus_parallel_mirai(dsn, data_only, progress_bar)

Arguments

Read the raw vector of an opus data source

Description

Read the raw vector of an opus data source

Usage

read_opus_raw(dsn)

Arguments

Value

list of raw vectors

Read a single OPUS file

Description

Read a single OPUS file

Usage

read_opus_single(dsn, data_only = FALSE)

Arguments

Value

list with parsed OPUS measurement and data blocks of the spectrum measurement contained in the OPUS file. See read_opus() for details on the list elements returned (first-level block names and information provided).

Dispatch method for the open_connection

Description

Dispatch method for the open_connection

Usage

read_raw(dsn)

Arguments

method to open the connection for an opus file

Description

method to open the connection for an opus file

Usage

## S3 method for class 'file'
read_raw(dsn)

Arguments

read signed integer from binary

Description

read signed integer from binary

Usage

read_signed_int(raw, cursor, n = 1L)

Arguments

read unsigned integer from binary

Description

read unsigned integer from binary

Usage

read_unsigned_int(raw, cursor, n = 1L)

Arguments

define class of dsn

Description

define class of dsn

Usage

set_connection_class(dsn)

Arguments