Description Usage Arguments Value Methods (by class) Note See Also Examples
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 | despike(x, z.threshold, max.spike.width, window.width, method, na.rm, ...)
## Default S3 method:
despike(
x,
z.threshold = NA,
max.spike.width = NA,
window.width = NA,
method = "run.mean",
na.rm = FALSE,
...
)
## S3 method for class 'numeric'
despike(
x,
z.threshold = 9,
max.spike.width = 8,
window.width = 11,
method = "run.mean",
na.rm = FALSE,
...
)
## S3 method for class '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 class '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 class '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 class '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 class '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 class 'reflector_spct'
despike(
x,
z.threshold = 9,
max.spike.width = 8,
window.width = 11,
method = "run.mean",
na.rm = FALSE,
...
)
## S3 method for class 'cps_spct'
despike(
x,
z.threshold = 9,
max.spike.width = 8,
window.width = 11,
method = "run.mean",
na.rm = FALSE,
...
)
## S3 method for class 'raw_spct'
despike(
x,
z.threshold = 9,
max.spike.width = 8,
window.width = 11,
method = "run.mean",
na.rm = FALSE,
...
)
## S3 method for class '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 class '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 class '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 class '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 class '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 class '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 class 'raw_mspct'
despike(
x,
z.threshold = 9,
max.spike.width = 8,
window.width = 11,
method = "run.mean",
na.rm = FALSE,
...,
.parallel = FALSE,
.paropts = NULL
)
|
x |
an R object |
z.threshold |
numeric Modified Z values larger than |
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: |
na.rm |
logical indicating whether |
... |
Arguments passed by name to |
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. |
x
with rows corresponding to spikes replaced by a local
average of adjacent neighbors outside the spike.
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.
Current algorithm misidentifies steep smooth slopes as spikes, so
manual inspection is needed together with adjustment by trial and error
of a suitable argument value for z.threshold
.
See the documentation for find_spikes
and
replace_bad_pixs
for details of the algorithm and
implementation.
1 2 3 4 5 6 | 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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