normalize: Normalize spectral data

In photobiology: Photobiological Calculations

Normalize spectral data

Description

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.

Usage

normalize(x, ...)

normalise(x, ...)

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

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

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

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

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

## S3 method for class 'solute_spct'
normalize(
  x,
  ...,
  range = NULL,
  norm = "max",
  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 = getOption("photobiology.radiation.unit", default = "energy"),
  keep.scaling = FALSE,
  na.rm = FALSE,
  .parallel = FALSE,
  .paropts = NULL
)

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

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

## S3 method for class 'reflector_mspct'
normalize(
  x,
  ...,
  range = x,
  norm = "max",
  qty.out = NULL,
  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
)

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, or "skip" to force return of x unchanged.
unit.out	character Allowed values "energy", and "photon", or its alias "quantum"
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	character string Allowed values are "transmittance", and "absorbance" indicating on which quantity to apply the normalization.
col.names	character vector containing the names of columns or variables to which to apply the normalization.
.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.

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. It is also possible to update an existing normalization for different units 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 can be limited to a region of interest within the 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 independently of the previous application of a different normalization.

Value

A copy of x, with spectral data values normalized to one for the criterion specified by the argument passed to norm with information about the normalization applied saved in attributes "normalized" and "normalization".

A copy of 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.

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.

Note

If the spectrum passed as argument to x has 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 (experimental feature).

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

1) 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. 2) 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.

The argument passed to parameter keep.scaling affects only the metadata stored in the "normalization" and "scaling" attributes of the returned object.

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, care should be taken of when normalization is applied. To represent solutions of specific concentrations of solutes, filter_spct objects can be used instead.

See Also

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

Examples

normalize(sun.spct)
normalise(sun.spct) # equivalent

normalize(sun.spct, norm = "max")
normalize(sun.spct, norm = 400)

photobiology documentation built on Oct. 21, 2023, 1:06 a.m.