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Normalize spectral data

Source: R/spct.normalize.r
normalize.Rd

This method returns a spectral object of the same class as the one supplied as argument but with the spectral data normalized to 1.0 at a specific wavelength. When the object contains multiple spectra, the normalisation is applied to each spectrum individually.

Usage

normalize(x, ...)

normalise(x, ...)

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

# S3 method for class 'source_spct'
normalize(
  x,
  ...,
  range = NULL,
  norm = "max",
  unit.out = NA,
  keep.scaling = FALSE,
  na.rm = FALSE
)

# S3 method for class 'response_spct'
normalize(
  x,
  ...,
  range = NULL,
  norm = "max",
  unit.out = NA,
  keep.scaling = FALSE,
  na.rm = FALSE
)

# S3 method for class 'filter_spct'
normalize(
  x,
  ...,
  range = NULL,
  norm = "max",
  qty.out = NA,
  keep.scaling = FALSE,
  na.rm = FALSE
)

# S3 method for class 'reflector_spct'
normalize(
  x,
  ...,
  range = NULL,
  norm = "max",
  qty.out = NA,
  keep.scaling = FALSE,
  na.rm = FALSE
)

# S3 method for class 'solute_spct'
normalize(
  x,
  ...,
  range = NULL,
  norm = "max",
  qty.out = NA,
  keep.scaling = FALSE,
  na.rm = FALSE
)

# S3 method for class 'raw_spct'
normalize(
  x,
  ...,
  range = NULL,
  norm = "max",
  keep.scaling = FALSE,
  na.rm = FALSE
)

# S3 method for class 'cps_spct'
normalize(
  x,
  ...,
  range = NULL,
  norm = "max",
  keep.scaling = FALSE,
  na.rm = FALSE
)

# S3 method for class 'generic_spct'
normalize(
  x,
  ...,
  range = NULL,
  norm = "max",
  col.names,
  keep.scaling = FALSE,
  na.rm = FALSE
)

# S3 method for class 'source_mspct'
normalize(
  x,
  ...,
  range = NULL,
  norm = "max",
  unit.out = NA,
  keep.scaling = FALSE,
  na.rm = FALSE,
  .parallel = FALSE,
  .paropts = NULL
)

# S3 method for class 'response_mspct'
normalize(
  x,
  ...,
  range = NULL,
  norm = "max",
  unit.out = NA,
  keep.scaling = FALSE,
  na.rm = FALSE,
  .parallel = FALSE,
  .paropts = NULL
)

# S3 method for class 'filter_mspct'
normalize(
  x,
  ...,
  range = NULL,
  norm = "max",
  qty.out = NA,
  keep.scaling = FALSE,
  na.rm = FALSE,
  .parallel = FALSE,
  .paropts = NULL
)

# S3 method for class 'reflector_mspct'
normalize(
  x,
  ...,
  range = x,
  norm = "max",
  qty.out = NA,
  keep.scaling = FALSE,
  na.rm = FALSE,
  .parallel = FALSE,
  .paropts = NULL
)

# S3 method for class 'raw_mspct'
normalize(
  x,
  ...,
  range = x,
  norm = "max",
  keep.scaling = FALSE,
  na.rm = FALSE,
  .parallel = FALSE,
  .paropts = NULL
)

# S3 method for class 'cps_mspct'
normalize(
  x,
  ...,
  range = x,
  norm = "max",
  keep.scaling = FALSE,
  na.rm = FALSE,
  .parallel = FALSE,
  .paropts = NULL
)

# S3 method for class 'solute_mspct'
normalize(
  x,
  ...,
  range = x,
  norm = "max",
  qty.out = NA,
  keep.scaling = FALSE,
  na.rm = FALSE,
  .parallel = FALSE,
  .paropts = NULL
)

# S3 method for class 'generic_mspct'
normalize(
  x,
  ...,
  range = NULL,
  norm = "max",
  col.names,
  keep.scaling = FALSE,
  na.rm = FALSE,
  .parallel = FALSE,
  .paropts = NULL
)

Arguments

x

An R object

...

not used in current version

range

An R object on which range() returns a numeric vector of length 2 with the limits of a range of wavelengths in nm, with min and max wavelengths (nm) used to set boundaries for search for normalization.

norm

numeric Normalization wavelength (nm) or character string "max", or "min" for normalization at the corresponding wavelength, "update" to update the normalization after modifying units of expression, quantity or range but respecting the previously used criterion, "undo" to revert an existing normalization or "skip" to force return of x unchanged.

unit.out

No longer supported and is ignored with a warning.

keep.scaling

logical or numeric Flag to indicate if any existing scaling should be preserved or not. The default, FALSE, preserves the behaviour of versions (<= 0.10.9). If numeric, the spectrum is scaled to this value before normalization and marked as not scaled.

na.rm

logical indicating whether NA values should be stripped before calculating the summary (e.g. "max") used for normalization.

qty.out

No longer supported and is ignored with a warning..

col.names

character vector containing the names of columns or variables. Columns in x matching the names in col.names are normalized, other columns are returned unchanged.

.parallel

if TRUE, apply function in parallel, using parallel backend provided by foreach

.paropts

a list of additional options passed into the foreach function when parallel computation is enabled. This is important if (for example) your code relies on external data or packages: use the .export and .packages arguments to supply them so that all cluster nodes have the correct environment set up for computing.

Value

A copy of the object passed as argument to x with the values of the spectral quantity rescaled to 1 at the normalization wavelength. If the normalization wavelength is not already present in x, it is added by interpolation—i.e. the returned value may be one row longer than x. Attributes normalized and normalization are set to keep a log of the computations applied.

Details

By default normalization is done based on the maximum of the spectral data. It is possible to also do the normalization based on a user-supplied wavelength expressed in nanometres or the minimum. An existing normalization can be updated for a different unit of expression or after a conversion to a related spectral quantity.

By default the function is applied to the whole spectrum, but by passing a range of wavelengths as input, the search, e.g., for the maximum, can be limited to a range of wavelengths of interest instead of the whole spectrum.

In 'photobiology' (>= 0.10.8) detailed information about the normalization is stored in an attribute. In 'photobiology' (>= 0.10.10) applying a new normalization to an already normalized spectrum recomputes the multiplier factors stored in the attributes whenever possible. This ensures that the returned object is identical, except for possible accumulated loss of precision due to floating-point arithmetic, independently of the previous application of a different normalization.

Methods (by class)

  • normalize(default): Default for generic function

  • normalize(source_spct): Normalize a source_spct object.

  • normalize(response_spct): Normalize a response spectrum.

  • normalize(filter_spct): Normalize a filter spectrum.

  • normalize(reflector_spct): Normalize a reflector spectrum.

  • normalize(solute_spct): Normalize a solute spectrum.

  • normalize(raw_spct): Normalize a raw spectrum.

  • normalize(cps_spct): Normalize a cps spectrum.

  • normalize(generic_spct): Normalize a raw spectrum.

  • normalize(source_mspct): Normalize the members of a source_mspct object.

  • normalize(response_mspct): Normalize the members of a response_mspct object.

  • normalize(filter_mspct): Normalize the members of a filter_mspct object.

  • normalize(reflector_mspct): Normalize the members of a reflector_mspct object.

  • normalize(raw_mspct): Normalize the members of a raw_mspct object.

  • normalize(cps_mspct): Normalize the members of a cps_mspct object.

  • normalize(solute_mspct): Normalize the members of a solute_mspct object.

  • normalize(generic_mspct): Normalize the members of a solute_mspct object.

Note

When the spectrum passed as argument to x had been previously scaled, in 'photobiology' (<= 0.10.9) the scaling attribute was always removed and no normalization factors returned. In 'photobiology' (>= 0.10.10) scaling information can be preserved by passing keep.scaling = TRUE.

By default if x contains one or more NA values and the normalization is based on a summary quantity, the returned spectrum will contain only NA values. If na.rm == TRUE then the summary quantity will be calculated after striping NA values, and only the values that were NA in x will be NA values in the returned spectrum.

When a numeric value is passed as argument to keep.scaling, the scaling uses f = "total" or f = "mean" depending on the class of x. Prescaling is only occasionally needed.

Method normalize is implemented for solute_spct objects but as the spectral data stored in them are a description of an intensive property of a substance, normalization is unlikely to useful. To represent solutions of specific concentrations of solutes, filter_spct objects should be used instead.

normalise() is a synonym for this normalize() method.

See also

Other rescaling functions: fscale(), fshift(), getNormalized(), getScaled(), is_normalized(), is_scaled(), setNormalized(), setScaled()

Examples


normalize(sun.spct)
#> Object: source_spct [522 x 3]
#> Wavelength range 280-800 nm, step 0.9230769-1 nm 
#> Label: sunlight, simulated 
#> Measured on 2010-06-22 09:51:00 UTC 
#> Measured at 60.20911 N, 24.96474 E; Kumpula, Helsinki, FI 
#> Spectral data in s.e.irrad, s.q.irrad normalized to 1 at 451 nm, 531 nm (max in 280-800 nm)
#> Variables:
#>  w.length: Wavelength [nm]
#>  s.e.irrad: Spectral energy irradiance [normalized]
#>  s.q.irrad: Spectral photon irradiance [normalized] 
#> --
#> # A tibble: 522 × 3
#>    w.length s.e.irrad s.q.irrad
#>       <dbl>     <dbl>     <dbl>
#>  1     280          0         0
#>  2     281.         0         0
#>  3     282.         0         0
#>  4     283.         0         0
#>  5     284.         0         0
#>  6     285.         0         0
#>  7     286.         0         0
#>  8     286.         0         0
#>  9     287.         0         0
#> 10     288.         0         0
#> # ℹ 512 more rows
normalise(sun.spct) # equivalent
#> Object: source_spct [522 x 3]
#> Wavelength range 280-800 nm, step 0.9230769-1 nm 
#> Label: sunlight, simulated 
#> Measured on 2010-06-22 09:51:00 UTC 
#> Measured at 60.20911 N, 24.96474 E; Kumpula, Helsinki, FI 
#> Spectral data in s.e.irrad, s.q.irrad normalized to 1 at 451 nm, 531 nm (max in 280-800 nm)
#> Variables:
#>  w.length: Wavelength [nm]
#>  s.e.irrad: Spectral energy irradiance [normalized]
#>  s.q.irrad: Spectral photon irradiance [normalized] 
#> --
#> # A tibble: 522 × 3
#>    w.length s.e.irrad s.q.irrad
#>       <dbl>     <dbl>     <dbl>
#>  1     280          0         0
#>  2     281.         0         0
#>  3     282.         0         0
#>  4     283.         0         0
#>  5     284.         0         0
#>  6     285.         0         0
#>  7     286.         0         0
#>  8     286.         0         0
#>  9     287.         0         0
#> 10     288.         0         0
#> # ℹ 512 more rows

normalize(sun.spct, norm = "max")
#> Object: source_spct [522 x 3]
#> Wavelength range 280-800 nm, step 0.9230769-1 nm 
#> Label: sunlight, simulated 
#> Measured on 2010-06-22 09:51:00 UTC 
#> Measured at 60.20911 N, 24.96474 E; Kumpula, Helsinki, FI 
#> Spectral data in s.e.irrad, s.q.irrad normalized to 1 at 451 nm, 531 nm (max in 280-800 nm)
#> Variables:
#>  w.length: Wavelength [nm]
#>  s.e.irrad: Spectral energy irradiance [normalized]
#>  s.q.irrad: Spectral photon irradiance [normalized] 
#> --
#> # A tibble: 522 × 3
#>    w.length s.e.irrad s.q.irrad
#>       <dbl>     <dbl>     <dbl>
#>  1     280          0         0
#>  2     281.         0         0
#>  3     282.         0         0
#>  4     283.         0         0
#>  5     284.         0         0
#>  6     285.         0         0
#>  7     286.         0         0
#>  8     286.         0         0
#>  9     287.         0         0
#> 10     288.         0         0
#> # ℹ 512 more rows
normalize(sun.spct, norm = 400)
#> Object: source_spct [522 x 3]
#> Wavelength range 280-800 nm, step 0.9230769-1 nm 
#> Label: sunlight, simulated 
#> Measured on 2010-06-22 09:51:00 UTC 
#> Measured at 60.20911 N, 24.96474 E; Kumpula, Helsinki, FI 
#> Spectral data in s.e.irrad, s.q.irrad normalized to 1 at 400 nm, 400 nm (wavelength)
#> Variables:
#>  w.length: Wavelength [nm]
#>  s.e.irrad: Spectral energy irradiance [normalized]
#>  s.q.irrad: Spectral photon irradiance [normalized] 
#> --
#> # A tibble: 522 × 3
#>    w.length s.e.irrad s.q.irrad
#>       <dbl>     <dbl>     <dbl>
#>  1     280          0         0
#>  2     281.         0         0
#>  3     282.         0         0
#>  4     283.         0         0
#>  5     284.         0         0
#>  6     285.         0         0
#>  7     286.         0         0
#>  8     286.         0         0
#>  9     287.         0         0
#> 10     288.         0         0
#> # ℹ 512 more rows