as_OpenSpecy: Create 'OpenSpecy' objects

In OpenSpecy: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra

Create OpenSpecy objects

Description

Functions to check if an object is an OpenSpecy, or coerce it if possible.

Usage

as_OpenSpecy(x, ...)

## S3 method for class 'OpenSpecy'
as_OpenSpecy(x, session_id = FALSE, ...)

## S3 method for class 'list'
as_OpenSpecy(x, ...)

## S3 method for class 'hyperSpec'
as_OpenSpecy(x, ...)

## S3 method for class 'data.frame'
as_OpenSpecy(x, colnames = list(wavenumber = NULL, spectra = NULL), ...)

## Default S3 method:
as_OpenSpecy(
  x,
  spectra,
  metadata = list(file_name = NULL, 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,
    intensity_units = 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"),
  attributes = list(intensity_unit = NULL, derivative_order = NULL, baseline = NULL,
    spectra_type = NULL),
  coords = "gen_grid",
  session_id = FALSE,
  ...
)

is_OpenSpecy(x)

check_OpenSpecy(x)

OpenSpecy(x, ...)

gen_grid(n)

Arguments

x	depending on the method, a list with all OpenSpecy parameters, a vector with the wavenumbers for all spectra, or a data.frame with a full spectrum in the classic Open Specy format.
session_id	logical. Whether to add a session ID to the metadata. The session ID is based on current session info so metadata of the same spectra will not return equal if session info changes. Sometimes that is desirable.
colnames	names of the wavenumber column and spectra column, makes assumptions based on column names or placement if NULL.
spectra	spectral intensities formatted as a data.table with one column per spectrum.
metadata	metadata for each spectrum with one row per spectrum, see details.
attributes	a list of attributes describing critical aspects for interpreting the spectra. see details.
coords	spatial coordinates for the spectra.
n	number of spectra to generate the spatial coordinate grid with.
...	additional arguments passed to submethods.

Details

as_OpenSpecy() converts spectral datasets to a three part list; the first with a vector of the wavenumbers of the spectra, the second with a data.table of all spectral intensities ordered as columns, the third item is another data.table with any metadata the user provides or is harvested from the files themselves.

The metadata argument may contain a named list with the following details (* = minimum recommended).

⁠file_name*⁠

The file name, defaults to basename() if not specified

⁠user_name*⁠

User name, e.g. "Win Cowger"

contact_info

Contact information, e.g. "1-513-673-8956, [e-mail]"

organization

Affiliation, e.g. "University of California, Riverside"

citation

Data citation, e.g. "Primpke, S., Wirth, M., Lorenz, C., & Gerdts, G. (2018). Reference database design for the automated analysis of microplastic samples based on Fourier transform infrared (FTIR) spectroscopy. Analytical and Bioanalytical Chemistry. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1007/s00216-018-1156-x")}"

⁠spectrum_type*⁠

Raman or FTIR

⁠spectrum_identity*⁠

Material/polymer analyzed, e.g. "Polystyrene"

material_form

Form of the material analyzed, e.g. textile fiber, rubber band, sphere, granule

material_phase

Phase of the material analyzed (liquid, gas, solid)

material_producer

Producer of the material analyzed, e.g. Dow

material_purity

Purity of the material analyzed, e.g. 99.98%

material_quality

Quality of the material analyzed, e.g. consumer product, manufacturer material, analytical standard, environmental sample

material_color

Color of the material analyzed, e.g. blue, #0000ff, (0, 0, 255)

material_other

Other material description, e.g. 5 µm diameter fibers, 1 mm spherical particles

cas_number

CAS number, e.g. 9003-53-6

instrument_used

Instrument used, e.g. Horiba LabRam

instrument_accessories

Instrument accessories, e.g. Focal Plane Array, CCD

instrument_mode

Instrument modes/settings, e.g. transmission, reflectance

⁠intensity_units*⁠

Units of the intensity values for the spectrum, options transmittance, reflectance, absorbance

spectral_resolution

Spectral resolution, e.g. 4/cm

laser_light_used

Wavelength of the laser/light used, e.g. 785 nm

number_of_accumulations

Number of accumulations, e.g 5

total_acquisition_time_s

Total acquisition time (s), e.g. 10 s

data_processing_procedure

Data processing procedure, e.g. spikefilter, baseline correction, none

level_of_confidence_in_identification

Level of confidence in identification, e.g. 99%

other_info

Other information

license

The license of the shared spectrum; defaults to "CC BY-NC" (see https://creativecommons.org/licenses/by-nc/4.0/ for details). Any other creative commons license is allowed, for example, CC0 or CC BY

session_id

A unique user and session identifier; populated automatically with paste(digest(Sys.info()), digest(sessionInfo()), sep = "/")

file_id

A unique file identifier; populated automatically with digest(object[c("wavenumber", "spectra")])

The attributes argument may contain a named list with the following details, when set, they will be used to automate transformations and warning messages:

intensity_units

supported options include "absorbance", "transmittance", or "reflectance"

derivative_order

supported options include "0", "1", or "2"

baseline

supported options include "raw" or "nobaseline"

spectra_type

supported options include "ftir" or "raman"

Value

as_OpenSpecy() and OpenSpecy() returns three part lists described in details. is_OpenSpecy() returns TRUE if the object is an OpenSpecy and FALSE if not. gen_grid() returns a data.table with x and y coordinates to use for generating a spatial grid for the spectra if one is not specified in the data.

Author(s)

Zacharias Steinmetz, Win Cowger

See Also

read_spec() for reading OpenSpecy objects.

Examples

data("raman_hdpe")

# Inspect the spectra
raman_hdpe # see how OpenSpecy objects print.
raman_hdpe$wavenumber # look at just the wavenumbers of the spectra.
raman_hdpe$spectra # look at just the spectral intensities data.table.
raman_hdpe$metadata # look at just the metadata of the spectra.

# Creating a list and transforming to OpenSpecy
as_OpenSpecy(list(wavenumber = raman_hdpe$wavenumber,
                  spectra = raman_hdpe$spectra,
                  metadata = raman_hdpe$metadata[,-c("x", "y")]))

# If you try to produce an OpenSpecy using an OpenSpecy it will just return
# the same object.
as_OpenSpecy(raman_hdpe)

# Creating an OpenSpecy from a data.frame
as_OpenSpecy(x = data.frame(wavenumber = raman_hdpe$wavenumber,
                            spectra = raman_hdpe$spectra$intensity))

# Test that the spectrum is formatted as an OpenSpecy object.
is_OpenSpecy(raman_hdpe)
is_OpenSpecy(raman_hdpe$spectra)

OpenSpecy documentation built on Nov. 26, 2023, 1:09 a.m.