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 = 2indicating the column names for the wavenumber and intensity; ifNULLcolumns are guessed.- method
submethod to be used for reading text files; defaults to
fread()butread.csv()works as well.- share
defaults to
NULL; needed to share spectra with the Open Specy community; seeshare_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.
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: e6e6e53e53b006a13f1789e95d67f8f2/12ddfcc39eec20b94a64a2ba6539aaa1
#> 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: e6e6e53e53b006a13f1789e95d67f8f2/12ddfcc39eec20b94a64a2ba6539aaa1
#> 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: e6e6e53e53b006a13f1789e95d67f8f2/12ddfcc39eec20b94a64a2ba6539aaa1
#> 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: e6e6e53e53b006a13f1789e95d67f8f2/12ddfcc39eec20b94a64a2ba6539aaa1
#> 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: e6e6e53e53b006a13f1789e95d67f8f2/12ddfcc39eec20b94a64a2ba6539aaa1
#> 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: e6e6e53e53b006a13f1789e95d67f8f2/12ddfcc39eec20b94a64a2ba6539aaa1
#> file_id
#> <char>
#> 1: cb06ce2846b119d932fb6696479a445b
#>