io_spec: Read and write spectral data

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

Read and write spectral data

Description

Functions for reading and writing spectral data to and from OpenSpecy format. OpenSpecy objects are lists with components wavenumber, spectra, and metadata; their supported formats are .json, .csv, and .rds. A file-backed FileSpecs method writes a new ENVI pair.

Usage

## S3 method for class 'FileSpecs'
write_spec(x, file, method = NULL, ...)

write_spec(x, ...)

## Default S3 method:
write_spec(x, ...)

## S3 method for class 'OpenSpecy'
write_spec(x, file, method = NULL, digits = getOption("digits"), ...)

read_spec(file, method = NULL, ...)

as_hyperSpec(x)

Arguments

x	an object of class OpenSpecy or a file-backed FileSpecs descriptor. File-backed objects are exported as a new ENVI header/binary pair and never overwrite source members.
file	file path to be read from or written to.
method	optional custom reader or OpenSpecy writer. FileSpecs rejects custom writers so its source-protection guarantee cannot be bypassed. Otherwise defaults to the file extension's method.
digits	number of significant digits to use when formatting numeric values; defaults to getOption("digits").
...	further arguments passed to the submethods.

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 .csv files but the numbers should be nearly identical. readRDS() should return the exact same object every time. write_spec.FileSpecs() streams one complete rectangular region to a new ENVI BIP pair using float64 spectra and a round-trip-safe wavelength axis. It refuses custom writers, source-member targets, existing outputs, and multi-region or incomplete views.

Value

read_spec() reads data formatted as an OpenSpecy object and returns a list object of class OpenSpecy containing spectral data. write_spec() writes spectral data. For FileSpecs, it invisibly returns the new ENVI header and binary paths; other methods are called for their file-writing side effect. as_hyperspec() converts an OpenSpecy object to a hyperSpec-class object.

Author(s)

Zacharias Steinmetz, Win Cowger

See Also

OpenSpecy(); read_text(), read_asp(), read_spa(), read_spc(), and read_jdx() for text files, .asp, .spa, .spa, .spc, and .jdx formats, respectively; read_zip() and read_any() for wrapper functions; saveRDS(); readRDS(); write_json(); read_json();

Examples

read_extdata("raman_hdpe.json") |> read_spec()
read_extdata("raman_hdpe.rds") |> read_spec()
read_extdata("raman_hdpe.csv") |> read_spec()

## Not run: 
data(raman_hdpe)
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)

## End(Not run)

OpenSpecy documentation built on Oct. 6, 2026, 1:07 a.m.