Functions for reading and writing spectral data to and from OpenSpecy format.
OpenSpecy objects are lists with components wavenumber, spectra,
and metadata. Currently supported formats are .y(a)ml, .json, .csv, or .rds.
Usage
write_spec(x, ...)
# S3 method for default
write_spec(x, ...)
# S3 method for OpenSpecy
write_spec(x, file, method = NULL, digits = getOption("digits"), ...)
read_spec(file, share = NULL, method = NULL, ...)
as_hyperSpec(x)Arguments
- x
an object of class
OpenSpecy.- file
file path to be read from or written to.
- method
optional; function to be used as a custom reader or writer. Defaults to the appropriate function based on the file extension.
- digits
number of significant digits to use when formatting numeric values; defaults to
getOption("digits").- share
defaults to
NULL; needed to share spectra with the Open Specy community; seeshare_spec()for details.- ...
further arguments passed to the submethods.
Value
read_spec() reads data formatted as an OpenSpecy object and
returns a list object of class OpenSpecy containing spectral
data.
write_spec() writes a file for an object of class
OpenSpecy containing spectral data.
as_hyperspec() converts an OpenSpecy object to a
hyperSpec-class object.
Details
Due to floating point number errors there may be some differences in the
precision of the numbers returned if using multiple devices for .json and
.yaml files but the numbers should be nearly identical.
readRDS() should return the exact same object every time.
Examples
read_extdata("raman_hdpe.yml") |> read_spec()
#> wavenumber intensity
#> <num> <int>
#> 1: 301.040 26
#> 2: 304.632 50
#> 3: 308.221 48
#> 4: 311.810 45
#> 5: 315.398 46
#> ---
#> 960: 3187.990 71
#> 961: 3190.520 71
#> 962: 3193.060 75
#> 963: 3195.590 75
#> 964: 3198.120 67
#>
#> $metadata
#> x y user_name spectrum_type spectrum_identity organization
#> <int> <int> <char> <char> <char> <char>
#> 1: 1 1 Win Cowger Raman HDPE Horiba Scientific
#> license session_id
#> <char> <char>
#> 1: CC BY-NC 5728ddde4f649fd71f6f487fc5ad8d80/dc85257201307a131e71d9ec24aaccbf
#> file_id file_name col_id
#> <char> <char> <char>
#> 1: cb06ce2846b119d932fb6696479a445b raman_hdpe.yml intensity
read_extdata("raman_hdpe.json") |> read_spec()
#> wavenumber intensity
#> <num> <int>
#> 1: 301.040 26
#> 2: 304.632 50
#> 3: 308.221 48
#> 4: 311.810 45
#> 5: 315.398 46
#> ---
#> 960: 3187.990 71
#> 961: 3190.520 71
#> 962: 3193.060 75
#> 963: 3195.590 75
#> 964: 3198.120 67
#>
#> $metadata
#> x y user_name spectrum_type spectrum_identity organization
#> <int> <int> <char> <char> <char> <char>
#> 1: 1 1 Win Cowger Raman HDPE Horiba Scientific
#> license session_id
#> <char> <char>
#> 1: CC BY-NC 5728ddde4f649fd71f6f487fc5ad8d80/dc85257201307a131e71d9ec24aaccbf
#> file_id file_name col_id
#> <char> <char> <char>
#> 1: cb06ce2846b119d932fb6696479a445b raman_hdpe.json intensity
read_extdata("raman_hdpe.rds") |> read_spec()
#> wavenumber intensity
#> <num> <int>
#> 1: 301.040 26
#> 2: 304.632 50
#> 3: 308.221 48
#> 4: 311.810 45
#> 5: 315.398 46
#> ---
#> 960: 3187.990 71
#> 961: 3190.520 71
#> 962: 3193.060 75
#> 963: 3195.590 75
#> 964: 3198.120 67
#>
#> $metadata
#> x y user_name spectrum_type spectrum_identity organization
#> <int> <int> <char> <char> <char> <char>
#> 1: 1 1 Win Cowger Raman HDPE Horiba Scientific
#> license session_id
#> <char> <char>
#> 1: CC BY-NC 5728ddde4f649fd71f6f487fc5ad8d80/dc85257201307a131e71d9ec24aaccbf
#> file_id file_name
#> <char> <char>
#> 1: cb06ce2846b119d932fb6696479a445b raman_hdpe.rds
read_extdata("raman_hdpe.csv") |> read_spec()
#> wavenumber intensity
#> <num> <int>
#> 1: 301.040 26
#> 2: 304.632 50
#> 3: 308.221 48
#> 4: 311.810 45
#> 5: 315.398 46
#> ---
#> 960: 3187.990 71
#> 961: 3190.520 71
#> 962: 3193.060 75
#> 963: 3195.590 75
#> 964: 3198.120 67
#>
#> $metadata
#> x y file_name license col_id
#> <int> <int> <char> <char> <char>
#> 1: 1 1 raman_hdpe.csv CC BY-NC intensity
#> session_id
#> <char>
#> 1: 919e3e54e4c2f1b1e4db64651b451179/7b524d8ec8dc80c61977c331bd1e6f3d
#> file_id
#> <char>
#> 1: cb06ce2846b119d932fb6696479a445b
if (FALSE) {
data(raman_hdpe)
write_spec(raman_hdpe, "raman_hdpe.yml")
write_spec(raman_hdpe, "raman_hdpe.json")
write_spec(raman_hdpe, "raman_hdpe.rds")
write_spec(raman_hdpe, "raman_hdpe.csv")
# Convert an OpenSpecy object to a hyperSpec object
hyper <- as_hyperSpec(raman_hdpe)
}