R/_const_data_02_.R

In ymatts/emgR: surface electromyography (sEMG) analyzer with R

home = "~/Dropbox/matsui/gitR/EMG/data/Example/"
setwd(home)
library(data.table)

load("inst/data/CYCLE_TIMES.RData")
load("inst/data/RAW_EMG.RData")
cycs = 10
#npoints = 200
emg = vector("list",length(RAW_EMG))
id = gsub("RAW_EMG_","",names(RAW_EMG))
pid = sapply(strsplit(id,"_"),function(x)x[1])
tid = sapply(strsplit(id,"_"),function(x)x[2])
names(emg) = id
for(id in seq_along(RAW_EMG)){
emg_data = RAW_EMG[[id]]
emg_data$t = 0:(nrow(emg_data)-1)
c_time = CYCLE_TIMES[[id]]
freq <- round(nrow(emg_data)/(tail(emg_data$Time, 1)+emg_data$Time[2]), 0)
cyc_stance <- cyc_swing <-
matrix(NA,nrow=cycs,ncol=4,
dimnames = list(NULL,c("st","ed","cycle","phase")))
cyc_stance = as.data.frame(cyc_stance)
for(jj in  1:cycs){
# Stance
t1   <- round(c_time[jj,1]*freq+1, 0)
t2   <- round((c_time[jj,1]+c_time[jj,2])*freq+1, 0)
if (t1>nrow(emg_data) || t2>nrow(emg_data)) {
cycs <- jj-1
break
} else {
#temp  <- emg_data[t1:t2,]
cyc_stance[jj,]  <- c(t1,t2,jj,"stance")
}
# Swing
t1   <- (c_time[jj,1]+c_time[jj,2])*freq+1
t2   <- c_time[jj+1,1]*freq+1
cyc_swing[jj,] = c(t1,t2,jj,"swing")
# Check if there is data
if (sum(t1:t2, na.rm=T)==0) next
}
cycle_anno = rbind(cyc_stance,cyc_swing)
cycle_emg = vector("list",cycs)
names(cycle_emg) = 1:cycs
for(i in seq_along(cycle_emg)){
anno = cycle_anno[cycle_anno$cycle==i,]
idx1 = anno[anno$phase=="stance",1:2]
idx2 = anno[anno$phase=="swing",1:2]
stance = emg_data[idx1$st:idx1$ed,]
swing = emg_data[idx2$st:idx2$ed,]
#x1 = apply(stance,2,function(x)approx(x,method="linear",n = npoints/2))
#x2 = apply(swing,2,function(x)approx(x,method="linear",n = npoints/2))
x1 = data.frame(pid=pid[id],tid=tid[id],seqid=id,cycle=i,phase="swing",Time = swing$Time,swing[,!colnames(swing)%in%c("Time","t")])
x2 = data.frame(pid = pid[id],tid=tid[id],seqid=id,cycle=i,phase="stance",Time = stance$Time,stance[,!colnames(stance)%in%c("Time","t")])
cycle_emg[[i]] = rbind(x1,x2)
}
emg[[id]] = do.call(rbind,cycle_emg)
cat(id,"\n")
}
emg = do.call(rbind,emg)
rownames(emg) = NULL
select_tid = "01"
emg = emg[emg$tid==select_tid,]
#select_pid = unique(emg$pid)[1:10]
#emg = emg[emg$pid%in%select_pid,]
save(emg,file="inst/data/emg.rda")