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Parse Avantes binary file

Source: R/parse_avantes_binary.R
lr_parse_trm.Rd

Parse Avantes binary file (TRM, ABS, ROH, DRK, REF, RAW8, RFL8 file extensions). https://www.avantes.com/products/spectrometers/

Usage

lr_parse_trm(filename)

lr_parse_abs(filename)

lr_parse_roh(filename)

lr_parse_rfl8(filename, specnum = 1L)

lr_parse_raw8(filename, specnum = 1L)

lr_parse_irr8(filename, specnum = 1L)

Arguments

filename

Path of the file to parse

specnum

Integer representing the position of the spectrum to read in the file. This option only makes sense for AvaSoft8 files and is ignored in the other cases.

Value

A named list of two elements:

  • data: a dataframe with columns "wl", "dark", "white", "scope" and "processed", in this order.

  • metadata: a character vector with metadata including:

    • user: Name of the spectrometer operator

    • datetime: Timestamp of the recording in format '%Y-%m-%d %H:%M:%S' and UTC timezone. If timezone is missing in source file, UTC time will be assumed (for reproducibility purposes across computers with different localtimes).

    • spec_model: Model of the spectrometer

    • spec_ID: Unique ID of the spectrometer

    • white_inttime: Integration time of the white reference (in ms)

    • dark_inttime: Integration time of the dark reference (in ms)

    • sample_inttime: Integration time of the sample (in ms)

    • white_avgs: Number of averaged measurements for the white reference

    • dark_avgs: Number of averaged measurements for the dark reference

    • sample_avgs: Number of averaged measurements for the sample

    • white_boxcar: Boxcar width for the white reference

    • dark_boxcar: Boxcar width for the dark reference

    • sample_boxcar: Boxcar width for the sample reference

Details

'processed' column computed by lightr with the function lr_compute_processed().

Examples

res_trm <- lr_parse_trm(
  system.file("testdata", "avantes_trans.TRM", package = "lightr")
)
head(res_trm$data)
#>         wl   dark  white  scope processed
#> 1 179.1006   2.40  72.50  23.65 30.313837
#> 2 179.6990  11.35 102.85  20.10  9.562842
#> 3 180.2974 -43.55  44.30 -26.75 19.123505
#> 4 180.8958 -22.15  62.55  -8.90 15.643448
#> 5 181.4942 -11.20  89.30   1.05 12.189054
#> 6 182.0925 -17.25  82.05  -6.20 11.127895
res_trm$metadata
#>  [1] NA          NA          NA          "0804016U1" "100"       "100"      
#>  [7] "100"       "20"        "20"        "20"        "0"         "0"        
#> [13] "0"        

res_roh <- lr_parse_roh(
  system.file("testdata", "avantes_reflect.ROH", package = "lightr")
)
head(res_roh$data)
#>         wl dark white    scope processed
#> 1 275.2718   NA    NA 805.0000        NA
#> 2 275.8698   NA    NA 816.3375        NA
#> 3 276.4678   NA    NA 817.1125        NA
#> 4 277.0657   NA    NA 812.4125        NA
#> 5 277.6637   NA    NA 814.3125        NA
#> 6 278.2616   NA    NA 817.6375        NA
res_roh$metadata
#>  [1] NA          NA          NA          "1305084U1" "95"        "95"       
#>  [7] "95"        "20"        "20"        "20"        "1"         "1"        
#> [13] "1"        

# This parser has a unique `specnum` argument
res_rfl8_1 <- lr_parse_rfl8(
  system.file("testdata", "compare", "Avantes", "feather.RFL8", package = "lightr"),
  specnum = 1
)
head(res_rfl8_1$data)
#>          wl      dark     white     scope processed
#> 1  995.6217 -730.5000 -155.8333 -575.1667  27.03016
#> 2 1002.5419 3427.8333 4034.8333 3589.1667  26.57883
#> 3 1009.4579 6536.5000 7168.1665 6763.1665  35.88389
#> 4 1016.3698  508.5000 1351.8334  767.8333  30.75098
#> 5 1023.2774 1193.1666 2192.5000 1529.8334  33.68913
#> 6 1030.1808  895.1667 1988.8334 1220.8334  29.77751
res_rfl8_1$metadata
#>  [1] NA                NA                NA                "1511108U1"      
#>  [5] "639.25732421875" "639.25732421875" "639.25732421875" "3"              
#>  [9] "3"               "3"               "0"               "0"              
#> [13] "0"              

res_rfl8_2 <- lr_parse_rfl8(
  system.file("testdata", "compare", "Avantes", "feather.RFL8", package = "lightr"),
  specnum = 2
)
head(res_rfl8_2$data)
#>         wl       dark    white      scope processed
#> 1 174.7803 -14.500000  2.40000 -15.000000  -2.95858
#> 2 175.3842   3.166667 14.33333  14.400000 100.59701
#> 3 175.9881   7.000000 19.76667  17.000000  78.32898
#> 4 176.5919  13.266666 21.40000  20.633333  90.57377
#> 5 177.1958  -2.666667 18.26667   3.233333  28.18471
#> 6 177.7995  19.200001 40.16667  40.933334 103.65660
res_rfl8_2$metadata
#>  [1] NA                 NA                 NA                 "1501154U1"       
#>  [5] "84.9001541137695" "84.9001541137695" "84.9001541137695" "10"              
#>  [9] "10"               "10"               "1"                "1"               
#> [13] "1"