-
Notifications
You must be signed in to change notification settings - Fork 1
/
ESR-class.R
261 lines (254 loc) · 10.8 KB
/
ESR-class.R
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
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
#' ESR class objects
#'
#' Objects of class \code{ESR}, \code{ESR.Spectrum} are \link{R6} objects and hence are
#' usable in a more typical object-oriented language than R. For the user the main difference
#' to R's internal \code{S3} and \code{S4} object implementation is that methods for \link{R6}
#' objects belong to the object itself. See details.
#'
#' @docType class
#'
#' @slot originator \code{\link{character}} Name of the function call that
#' created this object
#' @slot data \code{\link{data.frame}} XY data of the ESR spectrum
#'
#' @param originator \code{\link{character}} name of the function call that
#' created this object
#' @param data \code{\link{data.frame}} the ESR spectrum to be stored in the
#'
#' @section Methods:
#' \describe{
#' \item{\code{new(originator, data)}}{ Initialize a new object of class \code{ESR}}
#' \item{\code{set_data(data)}}{ Sets the data of the object }
#' \item{\code{set_origin(originator)}}{ Sets the originator of the object }
#' }
#'
#' @usage
#' # ESR$new(originator, data)
#' # ESR$set_data(data)
#' # ESR$set_origin(originator)
#'
#' @format \link{R6Class} generator objects
#' @keywords classes methods
#' @author Christoph Burow, University of Cologne (Germany)
#' @examples
#'
#' ## create an empty ESR base class object
#' x <- ESR$new()
#'
#' @export
ESR <- R6Class("ESR",
public = list(
originator = NA,
data = NA,
initialize = function(originator, data) {
if (!missing(originator))
self$originator <- originator
else
self$originator <- "ESR$new()"
if (!missing(data))
self$data <- data
else
self$data <- setnames(data.frame(matrix(ncol = 2, nrow = 1024)), c("x","y"))
},
set_origin = function(originator) {
self$originator <- originator
},
set_data = function(data) {
if (!is.null(data) && ncol(data) == 2) {
self$data <- setnames(data, c("x", "y"))
attr(self$data, "spectrum") <- "spectrum"
}
else
message("Invalid data format! Data was not saved.")
}
)
)
#' ESR.Spectrum class objects
#'
#' Objects of class \code{ESR}, \code{ESR.Spectrum} are \link{R6} objects and hence are
#' usable in a more typical object-oriented language than R. For the user the main difference
#' to R's internal \code{S3} and \code{S4} object implementation is that methods for \link{R6}
#' objects belong to the object itself. See details.
#'
#' @docType class
#'
#' @slot originator \code{\link{character}} Name of the function call that
#' created this object
#' @slot data \code{\link{data.frame}} XY data of the ESR spectrum
#' @slot parameter \code{\link{data.frame}} experimental parameters
#' @slot type \code{\link{character}} currently unused
#'
#' @param x \code{\link{data.frame}} XY data of the ESR spectrum
#' @param originator \code{\link{character}} name of the function call that
#' created this object
#' @param data \code{\link{data.frame}} XY values of the ESR spectrum
#' @param par \code{\link{data.frame}} experimental parameters
#' @param order \code{\link{integer}} order of the differential
#' @param v \code{\link{numeric}} The microwave frequency in GHz
#' @param H \code{\link{numeric}} A vector of magnetic field values in Gauss
#' @param interval \code{\link{numeric}} a vector of length two specifying
#' the range of x-values where peaks are searched
#' @param th \code{\link{numeric}}: an integer specifying the number of neighbouring values
#' to compare each x-value to
#' @param ... Further arguments passed to method specific functions.
#'
#'
#' @section Methods:
#' \describe{
#' \item{\code{new(originator, data)}}{ Initialize a new object of class \code{ESR.Spectrum}}
#' \item{\code{set_data(data)}}{ Sets the data of the object }
#' \item{\code{set_origin(originator)}}{ Sets the originator of the object }
#' \item{\code{set_par(par)}}{ Sets the experimental settings of the object }
#' \item{\code{get_diff(x, order = 1, ...)}}{ Returns the differential of the spectrum }
#' \item{\code{get_integral(x)}}{ Returns the integrant of the spectrum }
#' \item{\code{get_spline(x, ...)}}{ Returns a smoothed spectrum using the \code{\link{smooth.spline}} function }
#' \item{\code{get_gvalues(v, H, x)}}{ Calculates and returns the g-values of the spectrum }
#' \item{\code{get_peaks(x, interval, th = 10)}}{ Returns a \code{\link{vector}} of local minima and maxima in the spectrum. For details see \code{\link{find_Peaks}}. }
#' }
#'
#' @usage
#' # ESR.Spectrum$new(originator, data)
#' # ESR.Spectrum$set_origin(originator)
#' # ESR.Spectrum$set_data(data)
#' # ESR.Spectrum$set_par(par)
#' # ESR.Spectrum$get_diff(x, order, ...)
#' # ESR.Spectrum$get_integral(x)
#' # ESR.Spectrum$get_spline(x, ...)
#' # ESR.Spectrum$get_gvalues(v, H, x)
#' # ESR.Spectrum$get_peaks(x, interval, th = 10)
#'
#' @format \link{R6Class} generator objects
#' @keywords classes methods
#' @author Christoph Burow, University of Cologne (Germany)
#' @examples
#'
#' ## create an object of class ESR.Spectrum
#' ## and fill random data
#' x <- ESR.Spectrum$new()
#' x$set_data(data.frame(seq(3350, 3450, length.out = 1024),
#' runif(1024, -1000, 1000)))
#'
#' # plot the random data
#' plot(x)
#'
#' \dontrun{
#' ## public set methods
#' x$set_par()
#' x$set_data()
#' x$set_origin()
#' }
#'
#' ## public get methods
#' x$get_diff()
#' x$get_integral()
#' x$get_spline()
#' \dontrun{
#' x$get_gvalues()
#' }
#' @include methods.R
#' @export
ESR.Spectrum <- R6Class("ESR.Spectrum",
inherit = ESR,
public = list(
parameter = NA,
type = "Spectrum",
initialize = function() {
super$initialize(originator = "ESR.Spectrum$new()")
},
set_par = function(par) {
self$parameter <- par
},
get_gvalues = function(v, H, x = self$data) {
if (missing(v)) {
if(typeof(self$parameter) != "list")
return(message("Missing microwave frequency (GHz)!"))
if ("MF" %in% self$parameter[ ,1])
v <- as.numeric(self$parameter[which(self$parameter[,1]=="MF"), 2])
if ("MWFQ" %in% self$parameter[,1])
v <- as.numeric(self$parameter[which(self$parameter[,1]=="MWFQ"), 2])
}
if (missing(H)) {
H <- self$data$x
if (any(H<=2048))
return(message("Invalid or no magnetic field data!"))
}
return(get_gvalues(v, H, x))
},
get_diff = function(data = self$data, order = 1, ...) {
return(get_diff(data, order, ...))
},
get_integral = function(data = self$data) {
return(get_integral(data))
},
get_spline = function(data = self$data, ...) {
return(get_spline(data, ...))
},
get_peaks = function(data = self$data, interval, th = 10) {
return(get_peaks(data, interval, th))
},
align_spectrum = function(x = self$data, reference) {
return(align_spectrum(x, reference))
}
)
)
#' ESR.Spectrum.2D class objects
#'
#' Objects of class \code{ESR}, \code{ESR.Spectrum} are \link{R6} objects and hence are
#' usable in a more typical object-oriented language than R. For the user the main difference
#' to R's internal \code{S3} and \code{S4} object implementation is that methods for \link{R6}
#' objects belong to the object itself. See details.
#'
#' @docType class
#'
#'
#'
#' @section Methods:
#'
#' See \code{ESR.Spectrum}-class
#'
#' @usage
#' # ESR.Spectrum.2D$new()
#'
#' @format \link{R6Class} generator objects
#' @keywords classes methods
#' @author Christoph Burow, University of Cologne (Germany)
#' @examples
#'
#' # none
#'
#' @include methods.R
#' @export
ESR.Spectrum.2D <- R6Class("ESR.Spectrum.2D",
inherit = ESR,
public = list(
initialize = function(...) {
self$originator = super$set_origin("ESR.Spectrum.2D$new()")
self$data = setnames(data.frame(matrix(ncol = 3, nrow = 1024)), c("x","y", "z"))
},
secondary_dimension = NA_character_,
parameter = NA,
set_data = function(data) {
if (!is.null(data) && ncol(data) == 3) {
self$data <- setnames(data, c("x", "y", "z"))
attr(self$data, "spectrum") <- "spectrum"
}
},
set_par = function(par) {
self$parameter <- par
},
split = function() {
lktable <- c("Microwave Power" = "Power (mW)",
"Modulation Amplitude" = "ModAmp (G)",
"Gain" = "Gain (dB)")
spectra <- Map(function(x, sec) {
s <- ESR.Spectrum$new()
s$set_origin(paste0(self$originator, " (", self$secondary_dimension, " = ", round(sec, 2), ")"))
s$set_data(x[ ,1:2])
s$set_par(self$parameter)
s$parameter[which(s$parameter[ ,1] == lktable[self$secondary_dimension]), 2] <- sec
return(s)
}, split(self$data, self$data$z), unique(self$data$z))
},
type = "2D Spectrum"
)
)