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Calculate signal and noise metrics for OpenSpecy objects

Source: R/sig_noise.R
sig_noise.Rd

This function calculates common signal and noise metrics for OpenSpecy objects.

Usage

sig_noise(x, ...)

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

# S3 method for class 'OpenSpecy'
sig_noise(
  x,
  metric = "run_sig_over_noise",
  na.rm = TRUE,
  prob = 0.5,
  step = 20,
  breaks = seq(min(unlist(x$spectra)), max(unlist(x$spectra)), length =
    ((nrow(x$spectra)^(1/3)) * (max(unlist(x$spectra)) - min(unlist(x$spectra))))/(2 *
    IQR(unlist(x$spectra)))),
  sig_min = NULL,
  sig_max = NULL,
  noise_min = NULL,
  noise_max = NULL,
  abs = T,
  spatial_smooth = F,
  sigma = c(1, 1),
  threshold = NULL,
  ...
)

Arguments

x

an OpenSpecy object.

metric

character; specifying the desired metric to calculate. Options include "sig" (mean intensity), "noise" (standard deviation of intensity), "sig_times_noise" (absolute value of signal times noise), "sig_over_noise" (absolute value of signal / noise), "run_sig_over_noise" (absolute value of signal / noise where signal is estimated as the max intensity and noise is estimated as the height of a low intensity region.), "log_tot_sig" (sum of the inverse log intensities, useful for spectra in log units), "tot_sig" (sum of intensities), or "entropy" (Shannon entropy of intensities)..

na.rm

logical; indicating whether missing values should be removed when calculating signal and noise. Default is TRUE.

prob

numeric single value; the probability to retrieve for the quantile where the noise will be interpreted with the run_sig_over_noise option.

step

numeric; the step size of the region to look for the run_sig_over_noise option.

breaks

numeric; the number or positions of the breaks for entropy calculation. Defaults to infer a decent value from the data.

sig_min

numeric; the minimum wavenumber value for the signal region.

sig_max

numeric; the maximum wavenumber value for the signal region.

noise_min

numeric; the minimum wavenumber value for the noise region.

noise_max

numeric; the maximum wavenumber value for the noise region.

abs

logical; whether to return the absolute value of the result

spatial_smooth

logical; whether to spatially smooth the sig/noise using the xy coordinates and a gaussian smoother.

sigma

numeric; two value vector describing standard deviation for smoother in each dimension, y is specified first followed by x, should be the same for each in most cases.

threshold

numeric; if NULL, no threshold is set, otherwise use a numeric value to set the target threshold which true signal or noise should be above. The function will return a logical value instead of numeric if a threshold is set.

...

further arguments passed to subfunctions; currently not used.

Value

A numeric vector containing the calculated metric for each spectrum in the OpenSpecy object or logical value if threshold is set describing if the numbers where above or equal to (TRUE) the threshold.

See also

restrict_range()

Examples

data("raman_hdpe")

sig_noise(raman_hdpe, metric = "sig")
#> intensity 
#>  101.1691 
sig_noise(raman_hdpe, metric = "noise")
#> intensity 
#>  61.00777 
sig_noise(raman_hdpe, metric = "sig_times_noise")
#> intensity 
#>    6172.1