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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.

Value

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

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.

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()

Author

Zacharias Steinmetz, Win Cowger

Examples

read_extdata("raman_hdpe.csv") |> read_text()
#>      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: 4ccaf521fcd9a972e0edd22d7e9615fe/571220198f6c0ce656d43e885947b621
#>                             file_id
#>                              <char>
#> 1: cb06ce2846b119d932fb6696479a445b
read_extdata("raman_atacamit.spc") |> read_spc()
#>      wavenumber intensity
#>           <num>     <num>
#>   1:   117.7800  218.7200
#>   2:   119.4506  236.4000
#>   3:   121.1213  242.0400
#>   4:   122.7919  233.0500
#>   5:   124.4626  219.4200
#>  ---                     
#> 555:  1043.3174   13.0066
#> 556:  1044.9881   12.4402
#> 557:  1046.6587   11.9187
#> 558:  1048.3294   11.3986
#> 559:  1050.0000   10.8148
#> 
#> $metadata
#>        x     y          file_name  license    col_id
#>    <int> <int>             <char>   <char>    <char>
#> 1:     1     1 raman_atacamit.spc CC BY-NC intensity
#>                                                           session_id
#>                                                               <char>
#> 1: 4ccaf521fcd9a972e0edd22d7e9615fe/571220198f6c0ce656d43e885947b621
#>                             file_id
#>                              <char>
#> 1: 2693c0b0295ce36c16b10e1e660241f2
read_extdata("ftir_ldpe_soil.asp") |> read_asp()
#>       wavenumber   intensity
#>            <num>       <num>
#>    1:   650.4205 0.027056019
#>    2:   652.2841 0.029133933
#>    3:   654.1478 0.032566057
#>    4:   656.0115 0.032249778
#>    5:   657.8751 0.028957002
#>   ---                       
#> 1794:  3991.9788 0.005803670
#> 1795:  3993.8425 0.005495489
#> 1796:  3995.7062 0.005133253
#> 1797:  3997.5698 0.005595756
#> 1798:  3999.4335 0.005694630
#> 
#> $metadata
#>        x     y          file_name  license    col_id
#>    <int> <int>             <char>   <char>    <char>
#> 1:     1     1 ftir_ldpe_soil.asp CC BY-NC intensity
#>                                                           session_id
#>                                                               <char>
#> 1: 4ccaf521fcd9a972e0edd22d7e9615fe/571220198f6c0ce656d43e885947b621
#>                             file_id
#>                              <char>
#> 1: a33700bad0376ddab156980f473bac92
read_extdata("testdata_zipped.zip") |> read_zip()
#> [[1]]
#>      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 testdata2 - Copy (2).csv CC BY-NC intensity
#>                                                           session_id
#>                                                               <char>
#> 1: 4ccaf521fcd9a972e0edd22d7e9615fe/571220198f6c0ce656d43e885947b621
#>                             file_id
#>                              <char>
#> 1: cb06ce2846b119d932fb6696479a445b
#> 
#> [[2]]
#>      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 testdata2 - Copy.csv CC BY-NC intensity
#>                                                           session_id
#>                                                               <char>
#> 1: 4ccaf521fcd9a972e0edd22d7e9615fe/571220198f6c0ce656d43e885947b621
#>                             file_id
#>                              <char>
#> 1: cb06ce2846b119d932fb6696479a445b
#> 
#> [[3]]
#>      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 testdata2.csv CC BY-NC intensity
#>                                                           session_id
#>                                                               <char>
#> 1: 4ccaf521fcd9a972e0edd22d7e9615fe/571220198f6c0ce656d43e885947b621
#>                             file_id
#>                              <char>
#> 1: cb06ce2846b119d932fb6696479a445b
#>