read_ext: Read spectral data

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

Read spectral data

Description

Functions for reading spectral data from external file types. Currently supported reading formats are .csv and other text files, .asp, .spa, .spc, .xyz, and .jdx. Additionally, .0 (OPUS) and .dat (ENVI) files are supported via read_opus() and read_envi(), respectively. read_zip() takes any of the files listed above. Note that proprietary file formats like .0, .asp, and .spa are poorly supported but will likely still work in most cases.

Usage

read_text(
  file,
  colnames = NULL,
  method = "fread",
  comma_decimal = TRUE,
  metadata = list(file_name = basename(file), 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, 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"),
  ...
)

read_asp(
  file,
  metadata = list(file_name = basename(file), 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, 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"),
  ...
)

read_spa(
  file,
  metadata = list(file_name = basename(file), 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, 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"),
  ...
)

read_spc(
  file,
  metadata = list(file_name = basename(file), 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, 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"),
  ...
)

read_jdx(
  file,
  metadata = list(file_name = basename(file), 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, 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"),
  ...
)

read_extdata(file = NULL)

read_h5(
  file,
  collapse = FALSE,
  spectral_smooth = FALSE,
  sigma = c(1, 1, 1),
  read_visual = TRUE,
  representation = c("OpenSpecy", "Specs"),
  background_filter = NULL,
  ...
)

Arguments

file	file to be read from or written to.
colnames	character vector of length = 2 indicating the column names for the wavenumber and intensity; if NULL columns are guessed.
method	submethod to be used for reading text files; defaults to fread() but read.csv() works as well.
comma_decimal	logical(1) whether commas may represent decimals.
metadata	a named list of the metadata; see
collapse	whether or not to use collapse_spec() by particle_id. For read_h5(), the default is FALSE so region pixels are returned in raw form.
spectral_smooth	logical; whether H5 cubes should be smoothed before matrix conversion.
sigma	numeric vector passed to gaussianSmooth().
read_visual	logical; whether H5 mosaic images should be attached as visual-image attributes when present. H5 region stage coordinates are kept in nanometres and all mosaic tiles intersecting each region are registered for overlays and feature color extraction. as_OpenSpecy() for details.
representation	for H5 maps, return an ordinary dense "OpenSpecy" (the default) or a compact in-memory "Specs".
background_filter	optional H5 map policy returned by specs_background_filter(); rejected/non-finite source pixels receive mapping 0 and foreground spectra retain their read values.
...	further arguments passed to the submethods.

Details

read_spc() and read_jdx() are wrappers around the functions provided by the hyperSpec. Other functions have been adapted various online sources. Metadata is harvested if possible. There are many unique iterations of spectral file formats so there may be bugs in the file conversion. Please contact us if you identify any.

Value

Text and single-spectrum readers return their established objects. read_h5() returns an OpenSpecy object by default or a compact Specs object when requested.

Author(s)

Zacharias Steinmetz, Win Cowger

See Also

read_spec() for reading .json, .rds, or .csv (OpenSpecy) files; read_opus() for reading .0 (OPUS) files; read_envi() for reading .dat (ENVI) files; read_zip() and read_any() for wrapper functions; read.jdx(); read.spc()

Examples

read_extdata("raman_hdpe.csv") |> read_text()
read_extdata("raman_atacamit.spc") |> read_spc()
read_extdata("ftir_ldpe_soil.asp") |> read_asp()
read_extdata("testdata_zipped.zip") |> read_zip()

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