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.
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 solute_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 solute_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
)
A copy of the object passed as argument to x with values
detected as spikes replaced by a local average of adjacent neighbors
outside the spike.
an R object
numeric Modified Z values larger than z.threshold
are considered to correspond to spikes.
integer Wider regions with high Z values are not detected as spikes.
integer. The full width of the window used for the running mean used as replacement.
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).
logical indicating whether NA values should be treated
as spikes and replaced.
Arguments passed by name to find_spikes().
character Names of columns where to look for spikes to remove.
character One of "energy" or "photon"
character One of "transmittance" or "absorbance"
if TRUE, apply function in parallel, using parallel backend provided by foreach
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.
despike(default): Default returning always NA.
despike(numeric): Default function usable on numeric vectors.
despike(data.frame): Method for "data.frame" objects.
despike(generic_spct): Method for "generic_spct" objects.
despike(source_spct): Method for "source_spct" objects.
despike(response_spct): Method for "response_spct" objects.
despike(filter_spct): Method for "filter_spct" objects.
despike(reflector_spct): Method for "reflector_spct" objects.
despike(solute_spct): Method for "solute_spct" objects.
despike(cps_spct): Method for "cps_spct" objects.
despike(raw_spct): Method for "raw_spct" objects.
despike(generic_mspct): Method for "generic_mspct" objects.
despike(source_mspct): Method for "source_mspct" objects.
despike(response_mspct): Method for "cps_mspct" objects.
despike(filter_mspct): Method for "filter_mspct" objects.
despike(reflector_mspct): Method for "reflector_mspct" objects.
despike(solute_mspct): Method for "solute_mspct" objects.
despike(cps_mspct): Method for "cps_mspct" objects.
despike(raw_mspct): Method for "raw_mspct" objects.
Spikes are detected based on a modified Z score calculated from the
differenced spectrum. The Z threshold used should be adjusted to the
characteristics of the input and desired sensitivity. The lower the
threshold the more stringent the test becomes, resulting in most cases in
more spikes being detected. A modified version of the algorithm is used if
a value different from NULL is passed as argument to
max.spike.width. In such a case, an additional step filters out
broader spikes (or falsely detected steep slopes) from the returned values.
Simple interpolation replaces values of isolated bad pixels by the mean of their two closest neighbors. The running mean approach allows the replacement of short runs of bad pixels by the running mean of neighboring pixels within a window of user-specified width. The first approach works well for spectra from array spectrometers to correct for hot and dead pixels in an instrument. The second approach is most suitable for Raman spectra in which spikes triggered by radiation are wider than a single pixel but usually not more than five pixels wide.
When the argument passed to x contains multiple spectra, the spikes
are searched for and replaced in each spectrum independently of other
spectra.
See the documentation for find_spikes and
replace_bad_pixs for details of the algorithm and
implementation.
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, ]
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