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Smooth spectral intensities

Source: R/smooth_intens.R
smooth_intens.Rd

This smoother can enhance the signal to noise ratio of the data useing a Savitzky-Golay or Whittaker-Henderson filter.

Usage

smooth_intens(x, ...)

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

# S3 method for class 'OpenSpecy'
smooth_intens(
  x,
  polynomial = 3,
  window = 11,
  derivative = 1,
  abs = TRUE,
  lambda = 1600,
  d = 2,
  type = "sg",
  lag = 2,
  make_rel = TRUE,
  ...
)

calc_window_points(x, ...)

# Default S3 method
calc_window_points(x, wavenum_width = 70, ...)

# S3 method for class 'OpenSpecy'
calc_window_points(x, wavenum_width = 70, ...)

Arguments

x

an object of class OpenSpecy or vector for calc_window_points().

polynomial

polynomial order for the filter

window

number of data points in the window, filter length (must be odd).

derivative

the derivative order if you want to calculate the derivative. Zero (default) is no derivative.

abs

logical; whether you want to calculate the absolute value of the resulting output.

lambda

smoothing parameter for Whittaker-Henderson smoothing, 50 results in rough smoothing and 10^4 results in a high level of smoothing.

d

order of differences to use for Whittaker-Henderson smoothing, typically set to 2.

type

the type of smoothing to use "wh" for Whittaker-Henerson or "sg" for Savitzky-Golay.

lag

the lag to use for the numeric derivative calculation if using Whittaker-Henderson. Greater values lead to smoother derivatives, 1 or 2 is common.

make_rel

logical; if TRUE spectra are automatically normalized with make_rel().

wavenum_width

the width of the window you want in wavenumbers.

...

further arguments passed to sgolay().

Value

smooth_intens() returns an OpenSpecy object.

calc_window_points() returns a single numberic vector object of the number of points needed to fill the window and can be passed to smooth_intens(). For many applications, this is more reusable than specifying a static number of points.

Details

For Savitzky-Golay this is a wrapper around the filter function in the signal package to improve integration with other Open Specy functions. A typical good smooth can be achieved with 11 data point window and a 3rd or 4th order polynomial. For Whittaker-Henderson, the code is largely based off of the whittaker() function in the pracma package. In general Whittaker-Henderson is expected to be slower but more robust than Savitzky-Golay.

References

Savitzky A, Golay MJ (1964). “Smoothing and Differentiation of Data by Simplified Least Squares Procedures.” Analytical Chemistry, 36(8), 1627–1639.

See also

sgolay()

Author

Win Cowger, Zacharias Steinmetz

Examples

data("raman_hdpe")

smooth_intens(raman_hdpe)
#>      wavenumber   intensity
#>           <num>       <num>
#>   1:    301.040 0.102500885
#>   2:    304.632 0.063171177
#>   3:    308.221 0.031695428
#>   4:    311.810 0.008073638
#>   5:    315.398 0.007614310
#>  ---                       
#> 960:   3187.990 0.002890315
#> 961:   3190.520 0.005482884
#> 962:   3193.060 0.009382631
#> 963:   3195.590 0.014589555
#> 964:   3198.120 0.021103657
#> 
#> $metadata
#>        x     y  user_name spectrum_type spectrum_identity      organization
#>    <int> <int>     <char>        <char>            <char>            <char>
#> 1:     1     1 Win Cowger         Raman              HDPE Horiba Scientific
#>     license                                                        session_id
#>      <char>                                                            <char>
#> 1: CC BY-NC 5728ddde4f649fd71f6f487fc5ad8d80/dc85257201307a131e71d9ec24aaccbf
#>                             file_id
#>                              <char>
#> 1: cb06ce2846b119d932fb6696479a445b

smooth_intens(raman_hdpe, window = calc_window_points(x = raman_hdpe, wavenum_width = 70))
#>      wavenumber  intensity
#>           <num>      <num>
#>   1:    301.040 0.06819092
#>   2:    304.632 0.05691608
#>   3:    308.221 0.04668103
#>   4:    311.810 0.03748578
#>   5:    315.398 0.02933032
#>  ---                      
#> 960:   3187.990 0.01418184
#> 961:   3190.520 0.01677777
#> 962:   3193.060 0.01949510
#> 963:   3195.590 0.02233386
#> 964:   3198.120 0.02529402
#> 
#> $metadata
#>        x     y  user_name spectrum_type spectrum_identity      organization
#>    <int> <int>     <char>        <char>            <char>            <char>
#> 1:     1     1 Win Cowger         Raman              HDPE Horiba Scientific
#>     license                                                        session_id
#>      <char>                                                            <char>
#> 1: CC BY-NC 5728ddde4f649fd71f6f487fc5ad8d80/dc85257201307a131e71d9ec24aaccbf
#>                             file_id
#>                              <char>
#> 1: cb06ce2846b119d932fb6696479a445b

smooth_intens(raman_hdpe, lambda = 1600, d = 2, lag = 2, type = "wh")
#>      wavenumber  intensity
#>           <num>      <num>
#>   1:    301.040 0.09445155
#>   2:    304.632 0.08547362
#>   3:    308.221 0.07684707
#>   4:    311.810 0.06877658
#>   5:    315.398 0.06138149
#>  ---                      
#> 960:   3187.990 0.07254546
#> 961:   3190.520 0.08301247
#> 962:   3193.060 0.09396644
#> 963:   3195.590 0.10515688
#> 964:   3198.120 0.11642380
#> 
#> $metadata
#>        x     y  user_name spectrum_type spectrum_identity      organization
#>    <int> <int>     <char>        <char>            <char>            <char>
#> 1:     1     1 Win Cowger         Raman              HDPE Horiba Scientific
#>     license                                                        session_id
#>      <char>                                                            <char>
#> 1: CC BY-NC 5728ddde4f649fd71f6f487fc5ad8d80/dc85257201307a131e71d9ec24aaccbf
#>                             file_id
#>                              <char>
#> 1: cb06ce2846b119d932fb6696479a445b