despike: Remove spikes from spectrum

Description

Function that returns an R object with observations corresponding to spikes replaced by values computed from neighboring pixels. Spikes are values in spectra that are unusually high compared to neighbors. They are usually individual values or very short runs of similar "unusual" values. Spikes caused by cosmic radiation are a frequent problem in Raman spectra. Another source of spikes are "hot pixels" in CCD and diode array detectors.

Usage

despike(x, z.threshold, max.spike.width, window.width, method, na.rm, ...)
# S3 method for default
despike(
  x,
  z.threshold = NA,
  max.spike.width = NA,
  window.width = NA,
  method = "run.mean",
  na.rm = FALSE,
  ...
)
# S3 method for numeric
despike(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  window.width = 11,
  method = "run.mean",
  na.rm = FALSE,
  ...
)
# S3 method for data.frame
despike(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  window.width = 11,
  method = "run.mean",
  na.rm = FALSE,
  ...,
  y.var.name = NULL,
  var.name = y.var.name
)
# S3 method for generic_spct
despike(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  window.width = 11,
  method = "run.mean",
  na.rm = FALSE,
  ...,
  y.var.name = NULL,
  var.name = y.var.name
)
# S3 method for source_spct
despike(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  window.width = 11,
  method = "run.mean",
  na.rm = FALSE,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  ...
)
# S3 method for response_spct
despike(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  window.width = 11,
  method = "run.mean",
  na.rm = FALSE,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  ...
)
# S3 method for filter_spct
despike(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  window.width = 11,
  method = "run.mean",
  na.rm = FALSE,
  filter.qty = getOption("photobiology.filter.qty", default = "transmittance"),
  ...
)
# S3 method for reflector_spct
despike(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  window.width = 11,
  method = "run.mean",
  na.rm = FALSE,
  ...
)
# S3 method for cps_spct
despike(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  window.width = 11,
  method = "run.mean",
  na.rm = FALSE,
  ...
)
# S3 method for raw_spct
despike(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  window.width = 11,
  method = "run.mean",
  na.rm = FALSE,
  ...
)
# S3 method for generic_mspct
despike(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  window.width = 11,
  method = "run.mean",
  na.rm = FALSE,
  ...,
  y.var.name = NULL,
  var.name = y.var.name,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for source_mspct
despike(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  window.width = 11,
  method = "run.mean",
  na.rm = FALSE,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  ...,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for response_mspct
despike(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  window.width = 11,
  method = "run.mean",
  na.rm = FALSE,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  ...,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for filter_mspct
despike(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  window.width = 11,
  method = "run.mean",
  na.rm = FALSE,
  filter.qty = getOption("photobiology.filter.qty", default = "transmittance"),
  ...,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for reflector_mspct
despike(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  window.width = 11,
  method = "run.mean",
  na.rm = FALSE,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for cps_mspct
despike(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  window.width = 11,
  method = "run.mean",
  na.rm = FALSE,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for raw_mspct
despike(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  window.width = 11,
  method = "run.mean",
  na.rm = FALSE,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

Arguments

an R object

z.threshold

numeric Modified Z values larger than z.threshold are considered to correspond to spikes.

max.spike.width

integer Wider regions with high Z values are not detected as spikes.

window.width

integer. The full width of the window used for the running mean used as replacement.

method

character The name of the method: "run.mean" is running mean as described in Whitaker and Hayes (2018); "adj.mean" is mean of adjacent neighbors (isolated bad pixels only).

na.rm

logical indicating whether NA values should be treated as spikes and replaced.

...

Arguments passed by name to find_spikes().

var.name, y.var.name

character Names of columns where to look for spikes to remove.

unit.out

character One of "energy" or "photon"

filter.qty

character One of "transmittance" or "absorbance"

.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

x with rows corresponding to spikes replaced by a local average of adjacent neighbors outside the spike.

Methods (by class)

default: Default returning always NA.
numeric: Default function usable on numeric vectors.
data.frame: Method for "data.frame" objects.
generic_spct: Method for "generic_spct" objects.
source_spct: Method for "source_spct" objects.
response_spct: Method for "response_spct" objects.
filter_spct: Method for "filter_spct" objects.
reflector_spct: Method for "reflector_spct" objects.
cps_spct: Method for "cps_spct" objects.
raw_spct: Method for "raw_spct" objects.
generic_mspct: Method for "generic_mspct" objects.
source_mspct: Method for "source_mspct" objects.
response_mspct: Method for "cps_mspct" objects.
filter_mspct: Method for "filter_mspct" objects.
reflector_mspct: Method for "reflector_mspct" objects.
cps_mspct: Method for "cps_mspct" objects.
raw_mspct: Method for "raw_mspct" objects.

Examples

Run this code

# NOT RUN {
white_led.raw_spct[120:125, ]

# find and replace spike at 245.93 nm
despike(white_led.raw_spct,
        z.threshold = 10,
        window.width = 25)[120:125, ]

# }