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Range restriction and flattening for spectra

Source: R/adj_range.R
adj_range.Rd

restrict_range() restricts wavenumber ranges to user specified values. Multiple ranges can be specified by inputting a series of max and min values in order. flatten_range() will flatten ranges of the spectra that should have no peaks. Multiple ranges can be specified by inputting the series of max and min values in order.

Usage

restrict_range(x, ...)

# Default S3 method
restrict_range(x, ...)

# S3 method for class 'OpenSpecy'
restrict_range(
  x,
  min = NULL,
  max = NULL,
  make_rel = TRUE,
  automate = FALSE,
  artifact_ratio = 3,
  tail_n = 5L,
  co2_region = c(2200, 2420),
  max_crop = 0.2,
  ...
)

flatten_range(x, ...)

# Default S3 method
flatten_range(x, ...)

# S3 method for class 'OpenSpecy'
flatten_range(
  x,
  min = 2200,
  max = 2400,
  make_rel = TRUE,
  automate = FALSE,
  artifact_ratio = 3,
  tail_n = 5L,
  ...
)

Arguments

x

an OpenSpecy object.

min

a vector of minimum values for the range to be flattened.

max

a vector of maximum values for the range to be flattened.

make_rel

logical; should the output intensities be normalized to the range [0, 1] using make_rel() function?

automate

logical; if TRUE, first assess the relevant artifact and only restrict a high tail or flatten a high CO2 region when detected.

artifact_ratio

numeric; minimum artifact-to-control maximum ratio.

tail_n

integer; number of points defining each spectral tail.

co2_region

numeric length two; carbon dioxide exclusion region used by automatic tail assessment.

max_crop

numeric; maximum fraction of the full wavenumber span that automatic tail restriction may remove across both ends.

...

additional arguments passed to subfunctions; currently not in use.

Value

An OpenSpecy object with the spectral intensities within specified ranges restricted or flattened.

See also

conform_spec() for conforming wavenumbers to be matched with a reference library; adj_intens() for log transformation functions; min() and round()

Author

Win Cowger, Zacharias Steinmetz

Examples

test_noise <- as_OpenSpecy(x = seq(400,4000, by = 10),
                           spectra = data.frame(intensity = rnorm(361)))
plot(test_noise)


restrict_range(test_noise, min = 1000, max = 2000)
#>      wavenumber intensity
#>           <num>     <num>
#>   1:       1000 0.7779144
#>   2:       1010 0.4108821
#>   3:       1020 0.7862717
#>   4:       1030 0.4993344
#>   5:       1040 0.3027464
#>  ---                     
#>  97:       1960 0.5593439
#>  98:       1970 0.4760214
#>  99:       1980 0.7164056
#> 100:       1990 0.7209565
#> 101:       2000 0.1502945
#> 
#> $metadata
#>        x     y  license    col_id                          file_id
#>    <int> <int>   <char>    <char>                           <char>
#> 1:     1     1 CC BY-NC intensity 7f0c522b3f5dd2daf7a24cdd3ead3366
restrict_range(test_noise, automate = TRUE, make_rel = FALSE)
#>      wavenumber    intensity
#>           <num>        <num>
#>   1:        400 -1.400043517
#>   2:        410  0.255317055
#>   3:        420 -2.437263611
#>   4:        430 -0.005571287
#>   5:        440  0.621552721
#>  ---                        
#> 357:       3960 -0.384007254
#> 358:       3970  1.827125177
#> 359:       3980 -0.551491750
#> 360:       3990 -0.865753541
#> 361:       4000 -0.343831481
#> 
#> $metadata
#>        x     y  license    col_id                          file_id
#>    <int> <int>   <char>    <char>                           <char>
#> 1:     1     1 CC BY-NC intensity 7f0c522b3f5dd2daf7a24cdd3ead3366

flattened_intensities <- flatten_range(test_noise, min = c(1000, 2000),
                                       max = c(1500, 2500))
plot(flattened_intensities)