adj_range: Range restriction and flattening for spectra

In OpenSpecy: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra

Range restriction and flattening for spectra

Description

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 = 2,
  tail_n = 5L,
  co2_region = c(2200, 2420),
  max_crop = 0.2,
  saturation = NULL,
  saturation_min_run = NULL,
  saturation_tolerance = sqrt(.Machine$double.eps),
  saturation_guard = 1L,
  max_saturation_loss = 0.7,
  min_remaining = 3L,
  ...
)

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 = 2,
  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. The default 2 triggers at twice the control-region maximum; higher values make automatic correction less sensitive.
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.
saturation	NULL, "auto", or one finite numeric detector ceiling. Non-NULL values trigger shared saturation restriction.
saturation_min_run	integer or NULL; minimum adjacent saturated values. The conservative automatic default accepts a two-sample hard plateau; supply an explicit value to calibrate longer plateaus. A known numeric detector ceiling defaults to one sample.
saturation_tolerance	numeric; relative tolerance used to recognize an effectively constant automatic detector plateau.
saturation_guard	integer; sampled points added to both sides of each detected saturated interval before the shared union is removed.
max_saturation_loss	numeric; largest fraction of wavenumber coverage that saturation restriction may remove. The default is 0.70.
min_remaining	integer; minimum retained wavenumber count after saturation restriction.
...	additional arguments passed to subfunctions; currently not in use.

Value

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

Author(s)

Win Cowger, Zacharias Steinmetz

See Also

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

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)
restrict_range(test_noise, automate = TRUE, make_rel = FALSE)

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

OpenSpecy documentation built on Oct. 6, 2026, 1:07 a.m.