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, 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",
  share = NULL,
  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,
  share = NULL,
  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,
  share = NULL,
  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,
  share = NULL,
  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,
  share = NULL,
  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)

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.
share	defaults to NULL; needed to share spectra with the Open Specy community; see share_spec() for details.
metadata	a named list of the metadata; see as_OpenSpecy() for details.
...	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

All read_*() functions return data frames containing two columns named "wavenumber" and "intensity".

Author(s)

Zacharias Steinmetz, Win Cowger

See Also

read_spec() for reading .y(a)ml, .json, or .rds (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 Nov. 26, 2023, 1:09 a.m.