[chronojump] graph.R code clean
- From: Xavier de Blas <xaviblas src gnome org>
- To: commits-list gnome org
- Cc:
- Subject: [chronojump] graph.R code clean
- Date: Tue, 28 Jan 2014 13:52:03 +0000 (UTC)
commit 5483bd77fe02ff3af657f9ad5f282dd87b6d4f3d
Author: Xavier de Blas <xaviblas gmail com>
Date: Tue Jan 28 14:51:34 2014 +0100
graph.R code clean
encoder/graph.R | 382 ++++++++++++++++++++++++++++---------------------------
1 files changed, 192 insertions(+), 190 deletions(-)
---
diff --git a/encoder/graph.R b/encoder/graph.R
index f6dea21..60ad5a2 100644
--- a/encoder/graph.R
+++ b/encoder/graph.R
@@ -128,43 +128,43 @@ OperatingSystem=options[22]
write("(1/5) Starting R", OutputData2)
-findCurves <- function(rawdata, eccon, min_height, draw, title) {
- a=cumsum(rawdata)
- b=extrema(a)
+findCurves <- function(displacement, eccon, min_height, draw, title) {
+ position=cumsum(displacement)
+ position.ext=extrema(position)
print("at findCurves")
- print(b)
+ print(position.ext)
start=0; end=0; startH=0
tempStart=0; tempEnd=0;
#TODO: fer algo per si no es detecta el minindex previ al salt
if(eccon=="c") {
- if(length(b$minindex)==0) { b$minindex=cbind(1,1) }
- if(length(b$maxindex)==0) { b$maxindex=cbind(length(a),length(a)) }
+ if(length(position.ext$minindex)==0) { position.ext$minindex=cbind(1,1) }
+ if(length(position.ext$maxindex)==0) {
position.ext$maxindex=cbind(length(position),length(position)) }
#fixes if 1st minindex is after 1st maxindex
- if(b$maxindex[1] < b$minindex[1]) { b$minindex = rbind(c(1,1),b$minindex) }
+ if(position.ext$maxindex[1] < position.ext$minindex[1]) { position.ext$minindex =
rbind(c(1,1),position.ext$minindex) }
row=1; i=1; j=1
- while(max(c(i,j)) <= min(c(length(b$minindex[,1]),length(b$maxindex[,1])))) {
+ while(max(c(i,j)) <=
min(c(length(position.ext$minindex[,1]),length(position.ext$maxindex[,1])))) {
#tempStart at the end of minindexs
- #tempStart = b$minindex[i,2]
+ #tempStart = position.ext$minindex[i,2]
#tempStart at the mean of minindexs
#this is better because has more data in order to reduceCurveBySpeed
#then we get similar results than pyserial_pyper.py
- tempStart = mean(c(b$minindex[i,1],b$minindex[i,2]))
+ tempStart = mean(c(position.ext$minindex[i,1],position.ext$minindex[i,2]))
#end at the mean of maximum values then reduceCurveBySpeed will end it when first
speed==0 at right of maxspeed
- tempEnd = mean(c(b$maxindex[j,1],b$maxindex[j,2]))
+ tempEnd = mean(c(position.ext$maxindex[j,1],position.ext$maxindex[j,2]))
#end at the first maximum value
- #tempEnd = b$maxindex[j,1]
+ #tempEnd = position.ext$maxindex[j,1]
- height=a[tempEnd]-a[tempStart]
+ height=position[tempEnd]-position[tempStart]
if(height >= min_height) {
start[row] = tempStart
end[row] = tempEnd
- startH[row]= a[b$minindex[i,1]] #height at start
+ startH[row]= position[position.ext$minindex[i,1]] #height at
start
row=row+1;
# if(eccon=="c") { break } #c only needs one result
}
@@ -175,24 +175,24 @@ findCurves <- function(rawdata, eccon, min_height, draw, title) {
referenceindex=0
if(eccon=="ec" || eccon=="ecS") {
- referenceindex=b$maxindex
+ referenceindex=position.ext$maxindex
} else {
- referenceindex=b$minindex
+ referenceindex=position.ext$minindex
}
#when saved a row with ec-con, and there's only this curve, extrema doesn't find maxindex
if(length(referenceindex) == 0) {
- start[1] =1
+ start[1] = 1
if(eccon=="ec" || eccon=="ecS")
- end[1] = mean(which(a == min(a)))
+ end[1] = mean(which(position == min(position)))
else
- end[1] = mean(which(a == max(a)))
+ end[1] = mean(which(position == max(position)))
- startH[1]=a[1]
+ startH[1]=position[1]
start[2] =end[1]+1
- end[2] =length(a)
- startH[2]=a[start[2]]
+ end[2] =length(position)
+ startH[2]=position[start[2]]
}
#if a person starts stand up and goes down, extrema maxindex don't find the initial position
@@ -205,39 +205,39 @@ findCurves <- function(rawdata, eccon, min_height, draw, title) {
tempEnd = mean(c(referenceindex[j,1],referenceindex[j,2]))
if(eccon=="ec" || eccon=="ecS") {
- opposite=min(a[tempStart:tempEnd]) #find min value between the two tops
- mintop=min(c(a[tempStart],a[tempEnd])) #find wich top is lower
+ opposite=min(position[tempStart:tempEnd]) #find min value between the two tops
+ mintop=min(c(position[tempStart],position[tempEnd])) #find wich top is lower
height=mintop-opposite
} else {
- opposite=max(a[tempStart:tempEnd]) #find max value between the two bottoms
- maxbottom=max(c(a[tempStart],a[tempEnd])) #find wich bottom is higher
+ opposite=max(position[tempStart:tempEnd]) #find max value between the two
bottoms
+ maxbottom=max(c(position[tempStart],position[tempEnd])) #find wich bottom is
higher
height=abs(maxbottom-opposite)
}
if(height >= min_height) {
if(eccon == "ecS" || eccon == "ceS") {
start[row] = tempStart
- end[row] = mean(which(a[tempStart:tempEnd] == opposite) + tempStart)
- startH[row] = a[referenceindex[i,1]] #height at start
+ end[row] = mean(which(position[tempStart:tempEnd] == opposite) +
tempStart)
+ startH[row] = position[referenceindex[i,1]] #height at
start
row=row+1
start[row] = end[(row-1)] + 1
end[row] = tempEnd
- startH[row] = a[start[row]] #height at start
+ startH[row] = position[start[row]] #height at start
row=row+1
i=j
} else { #("ec" || "ce")
start[row] = tempStart
end[row] = tempEnd
- startH[row] = a[referenceindex[i,1]] #height at start
+ startH[row] = position[referenceindex[i,1]] #height at
start
row=row+1
i=j
}
} else {
if(eccon=="ec" || eccon=="ecS") {
- if(a[tempEnd] >= a[tempStart]) {
+ if(position[tempEnd] >= position[tempStart]) {
i=j
}
} else {
- if(a[tempEnd] <= a[tempStart]) {
+ if(position[tempEnd] <= position[tempStart]) {
i=j
}
}
@@ -248,10 +248,10 @@ findCurves <- function(rawdata, eccon, min_height, draw, title) {
if(draw) {
lty=1
col="black"
- plot((1:length(a))/1000 #ms -> s
- ,a/10, #mm -> cm
+ plot((1:length(position))/1000 #ms -> s
+ ,position/10, #mm -> cm
type="l",
- xlim=c(1,length(a))/1000, #ms -> s
+ xlim=c(1,length(position))/1000, #ms -> s
xlab="",ylab="",axes=T,
lty=lty,col=col)
@@ -262,38 +262,39 @@ findCurves <- function(rawdata, eccon, min_height, draw, title) {
return(as.data.frame(cbind(start,end,startH)))
}
-#all rawdata will be negative because we start on the top
-fixRawdataInertial <- function(rawdata) {
+#all displacement will be negative because we start on the top
+fixRawdataInertial <- function(displacement) {
#do not do this:
- #rawdata[which(rawdata.c >= 0)] = rawdata[which(rawdata.c >= 0)]*-1
+ #position=cumsum(displacement)
+ #displacement[which(position >= 0)] = displacement[which(position >= 0)]*-1
#do this: work with cumsum, do ABS on cumsum, then *-1
- #then to obtain rawdata again just do diff (and add first number)
+ #then to obtain displacement again just do diff (and add first number)
- rawdata.c = abs(cumsum(rawdata))*-1
+ position = abs(cumsum(displacement))*-1
#this is to make "inverted cumsum"
- rawdata = c(0,diff(rawdata.c))
+ displacement = c(0,diff(position))
- return(rawdata)
+ return(displacement)
}
#don't do this, because on inertial machines string will be rolled to machine and not connected to the body
-#fixRawdataLI <- function(rawdata) {
-# rawdata.c = cumsum(rawdata)
-# meanMax=mean(which(rawdata.c == max(rawdata.c)))
+#fixRawdataLI <- function(displacement) {
+# position = cumsum(displacement)
+# meanMax=mean(which(position == max(position)))
#
# #this is to make "inverted cumsum"
-# rawdata = c(0,diff(rawdata.c))
+# displacement = c(0,diff(position))
#
-# rawdata[meanMax:length(rawdata)] = rawdata[meanMax:length(rawdata)] * -1
+# displacement[meanMax:length(displacement)] = displacement[meanMax:length(displacement)] * -1
#
-# return(rawdata)
+# return(displacement)
#}
#called on "ec" and "ce" to have a smoothingOneEC for every curve
#this smoothingOneEC has produce same speeds than smoothing "c"
-findSmoothingsEC <- function(rawdata, curves, eccon, smoothingOneC) {
+findSmoothingsEC <- function(displacement, curves, eccon, smoothingOneC) {
smoothings = NULL
n=length(curves[,1])
@@ -307,10 +308,10 @@ findSmoothingsEC <- function(rawdata, curves, eccon, smoothingOneC) {
} else {
#on every curve...
for(i in 1:n) {
- eccentric.concentric = rawdata[curves[i,1]:curves[i,2]]
+ eccentric.concentric = displacement[curves[i,1]:curves[i,2]]
- #get the cumsum rawdata: rawdata.c
- rawdata.c=cumsum(rawdata[curves[i,1]:curves[i,2]])
+ #get the position
+ position=cumsum(displacement[curves[i,1]:curves[i,2]])
#analyze the "c" phase
#Note dividing phases can be done using the speed,
@@ -318,16 +319,16 @@ findSmoothingsEC <- function(rawdata, curves, eccon, smoothingOneC) {
start = 0
end = 0
if(eccon=="ec") {
- start = mean(which(rawdata.c == min(rawdata.c)))
- end = length(rawdata.c) -1
+ start = mean(which(position == min(position)))
+ end = length(position) -1
#the -1 is because the line below: "concentric=" will fail in curves[i,1]+end
#and will add an NA
} else { #(eccon=="ce")
start = 0
- end = mean(which(rawdata.c == max(rawdata.c)))
+ end = mean(which(position == max(position)))
}
- concentric=rawdata[(curves[i,1]+start):(curves[i,1]+end)]
+ concentric=displacement[(curves[i,1]+start):(curves[i,1]+end)]
#get max speed at "c"
speed <- smooth.spline( 1:length(concentric), concentric, spar=smoothingOneC)
@@ -356,18 +357,17 @@ findSmoothingsEC <- function(rawdata, curves, eccon, smoothingOneC) {
#used in alls eccons
#TODO: remember to change thi in python capture file because there it's only used in "c"
-reduceCurveBySpeed <- function(eccon, row, startT, rawdata, smoothingOneEC, smoothingOneC) {
- a=rawdata
-
+reduceCurveBySpeed <- function(eccon, row, startT, displacement, smoothingOneEC, smoothingOneC)
+{
print("at reduceCurveBySpeed")
smoothing = smoothingOneEC
if(eccon == "c" || eccon == "ecS" || eccon == "ceS")
smoothing = smoothingOneC
- speed <- smooth.spline( 1:length(a), a, spar=smoothing)
+ speed <- smooth.spline( 1:length(displacement), displacement, spar=smoothing)
- b=extrema(speed$y)
+ speed.ext=extrema(speed$y)
#in order to reduce curve by speed, we search the cross of speed (in 0m/s)
#before and after the peak value, but in "ec" and "ce" there are two peak values:
@@ -408,69 +408,72 @@ reduceCurveBySpeed <- function(eccon, row, startT, rawdata, smoothingOneEC, smoo
speed$y=abs(speed$y)
#left adjust
- #find the b$cross at left of max speed
+ #find the speed.ext$cross at left of max speed
x.ini = 0 #good to declare here
- bcrossLen = length(b$cross[,2])
- if(bcrossLen == 0)
+ ext.cross.len = length(speed.ext$cross[,2])
+ if(ext.cross.len == 0)
x.ini = 0
- else if(bcrossLen == 1) {
- if(b$cross[,2] < time1)
- x.ini = b$cross[,2]
+ else if(ext.cross.len == 1) {
+ if(speed.ext$cross[,2] < time1)
+ x.ini = speed.ext$cross[,2]
} else {
- for(i in b$cross[,2])
+ for(i in speed.ext$cross[,2])
if(i < time1)
x.ini = i
}
#right adjust
- #find the b$cross at right of max speed
- x.end = length(rawdata) #good to declare here
- #bcrossLen = length(b$cross[,2])
- if(bcrossLen == 0)
- x.end = length(rawdata)
- else if(bcrossLen == 1) {
- if(b$cross[,2] > time2)
- x.end = b$cross[,2]
+ #find the speed.ext$cross at right of max speed
+ x.end = length(displacement) #good to declare here
+ #ext.cross.len = length(speed.ext$cross[,2])
+ if(ext.cross.len == 0)
+ x.end = length(displacement)
+ else if(ext.cross.len == 1) {
+ if(speed.ext$cross[,2] > time2)
+ x.end = speed.ext$cross[,2]
} else {
- for(i in rev(b$cross[,2]))
+ for(i in rev(speed.ext$cross[,2]))
if(i > time2)
x.end = i
}
#debug
- print(b$cross[,2])
- #print(bcrossLen)
+ print(speed.ext$cross[,2])
+ #print(ext.cross.len)
print(c("time1,time2",time1,time2))
print(c("x.ini x.end",x.ini,x.end))
return(c(startT + x.ini, startT + x.end))
}
-findECPhases <- function(a,speed) {
- b=extrema(speed)
- #print(b)
+findECPhases <- function(displacement,speed) {
+ speed.ext=extrema(speed)
+ #print(speed.ext)
#print(speed)
+
#In all the extrema minindex values, search which range (row) has the min values,
#and in this range search last value
print("searchMinSpeedEnd")
searchMinSpeedEnd = max(which(speed == min(speed)))
print(searchMinSpeedEnd)
+
#In all the extrema maxindex values, search which range (row) has the max values,
#and in this range search first value
print("searchMaxSpeedIni")
searchMaxSpeedIni = min(which(speed == max(speed)))
print(searchMaxSpeedIni)
+
#find the cross between both
- print("b-Cross")
- print(b$cross[,1])
+ print("speed.ext-Cross")
+ print(speed.ext$cross[,1])
print("search min cross: crossMinRow")
- crossMinRow=which(b$cross[,1] > searchMinSpeedEnd & b$cross[,1] < searchMaxSpeedIni)
+ crossMinRow=which(speed.ext$cross[,1] > searchMinSpeedEnd & speed.ext$cross[,1] < searchMaxSpeedIni)
print(crossMinRow)
#if (length(crossMinRow) > 0) {
# print(crossMinRow)
#} else {
- # propulsiveEnd = length(a)
+ # propulsiveEnd = length(displacement)
# errorSearching = TRUE
#}
@@ -480,13 +483,13 @@ findECPhases <- function(a,speed) {
isometricUse = TRUE
if(isometricUse) {
- eccentric=1:min(b$cross[crossMinRow,1])
- isometric=c(min(b$cross[crossMinRow,1]), max(b$cross[crossMinRow,2]))
- concentric=max(b$cross[crossMinRow,2]):length(a)
+ eccentric=1:min(speed.ext$cross[crossMinRow,1])
+ isometric=c(min(speed.ext$cross[crossMinRow,1]), max(speed.ext$cross[crossMinRow,2]))
+ concentric=max(speed.ext$cross[crossMinRow,2]):length(displacement)
} else {
- eccentric=1:mean(b$cross[crossMinRow,1])
- isometric=c(mean(b$cross[crossMinRow,1]), mean(b$cross[crossMinRow,2]))
- concentric=mean(b$cross[crossMinRow,2]):length(a)
+ eccentric=1:mean(speed.ext$cross[crossMinRow,1])
+ isometric=c(mean(speed.ext$cross[crossMinRow,1]), mean(speed.ext$cross[crossMinRow,2]))
+ concentric=mean(speed.ext$cross[crossMinRow,2]):length(displacement)
}
return(list(
eccentric=eccentric,
@@ -512,7 +515,7 @@ return (propulsiveEnd)
#eccon="c" one time each curve
#eccon="ec" one time each curve
#eccon="ecS" means ecSeparated. two times each curve: one for "e", one for "c"
-kinematicsF <- function(a, mass, smoothingOneEC, smoothingOneC, g, eccon, isPropulsive) {
+kinematicsF <- function(displacement, mass, smoothingOneEC, smoothingOneC, g, eccon, isPropulsive) {
smoothing = 0
if(eccon == "c" || eccon == "e")
@@ -523,15 +526,15 @@ kinematicsF <- function(a, mass, smoothingOneEC, smoothingOneC, g, eccon, isProp
print(c("at kinematicsF smoothing:",smoothing))
#x vector should contain at least 4 different values
- if(length(a) >= 4)
- speed <- smooth.spline( 1:length(a), a, spar=smoothing)
+ if(length(displacement) >= 4)
+ speed <- smooth.spline( 1:length(displacement), displacement, spar=smoothing)
else
- speed=list(y=rep(0,length(a)))
+ speed=list(y=rep(0,length(displacement)))
- if(length(a) >= 4)
+ if(length(displacement) >= 4)
accel <- predict( speed, deriv=1 )
else
- accel=list(y=rep(0,length(a)))
+ accel=list(y=rep(0,length(displacement)))
#speed comes in mm/ms when derivate to accel its mm/ms^2 to convert it to m/s^2 need to *1000 because
it's quadratic
accel$y <- accel$y * 1000
@@ -546,10 +549,10 @@ kinematicsF <- function(a, mass, smoothingOneEC, smoothingOneC, g, eccon, isProp
#search propulsiveEnd
if(isPropulsive) {
if(eccon=="c") {
- concentric=1:length(a)
+ concentric=1:length(displacement)
propulsiveEnd = findPropulsiveEnd(accel$y,concentric)
} else if(eccon=="ec") {
- phases=findECPhases(a,speed$y)
+ phases=findECPhases(displacement,speed$y)
eccentric = phases$eccentric
isometric = phases$isometric
concentric = phases$concentric
@@ -618,7 +621,7 @@ powerBars <- function(eccon, kinematics) {
kinematics$mass,meanForce,maxForce))
}
-kinematicRanges <- function(singleFile,rawdata,curves,mass,smoothingsEC,smoothingOneC,g,eccon,isPropulsive) {
+kinematicRanges <-
function(singleFile,displacement,curves,mass,smoothingsEC,smoothingOneC,g,eccon,isPropulsive) {
n=length(curves[,1])
maxSpeedy=0; maxAccely=0; maxForce=0; maxPower=0
myEccon = eccon
@@ -629,7 +632,7 @@ kinematicRanges <- function(singleFile,rawdata,curves,mass,smoothingsEC,smoothin
myMass = curves[i,5]
myEccon = curves[i,7]
}
-
kn=kinematicsF(rawdata[curves[i,1]:curves[i,2]],myMass,smoothingsEC[i],smoothingOneC,g,myEccon,isPropulsive)
+
kn=kinematicsF(displacement[curves[i,1]:curves[i,2]],myMass,smoothingsEC[i],smoothingOneC,g,myEccon,isPropulsive)
if(max(abs(kn$speedy)) > maxSpeedy)
maxSpeedy = max(abs(kn$speedy))
if(max(abs(kn$accely)) > maxAccely)
@@ -647,7 +650,7 @@ kinematicRanges <- function(singleFile,rawdata,curves,mass,smoothingsEC,smoothin
}
-paint <- function(rawdata, eccon, xmin, xmax, yrange, knRanges, superpose, highlight,
+paint <- function(displacement, eccon, xmin, xmax, yrange, knRanges, superpose, highlight,
startX, startH, smoothingOneEC, smoothingOneC, mass, title, subtitle, draw, showLabels, marShrink,
showAxes, legend,
Analysis, isPropulsive, inertialType, exercisePercentBodyWeight,
showSpeed, showAccel, showForce, showPower
@@ -670,9 +673,9 @@ paint <- function(rawdata, eccon, xmin, xmax, yrange, knRanges, superpose, highl
print(c("xmin,xmax",xmin,xmax))
- rawdata=rawdata[xmin:xmax]
- a=cumsum(rawdata)
- a=a+startH
+ displacement=displacement[xmin:xmax]
+ position=cumsum(displacement)
+ position=position+startH
#to control the placement of the diferent axis on the right
axisLineRight = 0
@@ -687,7 +690,7 @@ paint <- function(rawdata, eccon, xmin, xmax, yrange, knRanges, superpose, highl
marginRight = marginRight -2
#all in meters
- #a=a/1000
+ #position=position/1000
if(draw) {
#three vertical axis inspired on http://www.r-bloggers.com/multiple-y-axis-in-a-r-plot/
@@ -704,7 +707,7 @@ paint <- function(rawdata, eccon, xmin, xmax, yrange, knRanges, superpose, highl
#}
ylim=yrange
if(ylim[1]=="undefined") { ylim=NULL }
- plot(a-min(a),type="n",xlim=c(1,length(a)),ylim=ylim,xlab=xlab, ylab=ylab, col="gray", axes=F)
+ plot(position-min(position),type="n",xlim=c(1,length(position)),ylim=ylim,xlab=xlab,
ylab=ylab, col="gray", axes=F)
title(main=title,line=-2,outer=T)
mtext(subtitle,side=1,adj=0,cex=.8)
@@ -719,19 +722,19 @@ paint <- function(rawdata, eccon, xmin, xmax, yrange, knRanges, superpose, highl
colNormal="black"
if(superpose)
colNormal="gray30"
- yValues = a[startX:length(a)]-min(a[startX:length(a)])
+ yValues = position[startX:length(position)]-min(position[startX:length(position)])
if(highlight==FALSE) {
- plot(startX:length(a),yValues,type="l",xlim=c(1,length(a)),ylim=ylim,
+ plot(startX:length(position),yValues,type="l",xlim=c(1,length(position)),ylim=ylim,
xlab="",ylab="",col="black",lty=lty[1],lwd=2,axes=F)
par(new=T)
- plot(startX:length(a),yValues,type="h",xlim=c(1,length(a)),ylim=ylim,
+ plot(startX:length(position),yValues,type="h",xlim=c(1,length(position)),ylim=ylim,
xlab="",ylab="",col="grey90",lty=lty[1],lwd=1,axes=F)
}
else
-
plot(startX:length(a),yValues,type="l",xlim=c(1,length(a)),ylim=ylim,xlab="",ylab="",col=colNormal,lty=2,lwd=3,axes=F)
+
plot(startX:length(position),yValues,type="l",xlim=c(1,length(position)),ylim=ylim,xlab="",ylab="",col=colNormal,lty=2,lwd=3,axes=F)
abline(h=0,lty=3,col="black")
- #abline(v=seq(from=0,to=length(a),by=500),lty=3,col="gray")
+ #abline(v=seq(from=0,to=length(position),by=500),lty=3,col="gray")
#print("ROTARY")
@@ -744,12 +747,10 @@ paint <- function(rawdata, eccon, xmin, xmax, yrange, knRanges, superpose, highl
}
#speed
- #scan file again (raw data: mm displaced every ms, no cumulative sum)
- a=rawdata
- speed <- smooth.spline( 1:length(a), a, spar=smoothing)
+ speed <- smooth.spline( 1:length(displacement), displacement, spar=smoothing)
if(draw & showSpeed) {
- ylim=c(-max(abs(range(a))),max(abs(range(a)))) #put 0 in the middle
+ ylim=c(-max(abs(range(displacement))),max(abs(range(displacement)))) #put 0 in the middle
if(knRanges[1] != "undefined")
ylim = knRanges$speedy
par(new=T)
@@ -761,10 +762,10 @@ paint <- function(rawdata, eccon, xmin, xmax, yrange, knRanges, superpose, highl
if(highlight==FALSE)
plot(startX:length(speedPlot),speedPlot[startX:length(speedPlot)],type="l",
-
xlim=c(1,length(a)),ylim=ylim,xlab="",ylab="",col=cols[1],lty=lty[1],lwd=1,axes=F)
+
xlim=c(1,length(displacement)),ylim=ylim,xlab="",ylab="",col=cols[1],lty=lty[1],lwd=1,axes=F)
else
plot(startX:length(speedPlot),speedPlot[startX:length(speedPlot)],type="l",
- xlim=c(1,length(a)),ylim=ylim,xlab="",ylab="",col="darkgreen",lty=2,lwd=3,axes=F)
+
xlim=c(1,length(displacement)),ylim=ylim,xlab="",ylab="",col="darkgreen",lty=2,lwd=3,axes=F)
}
#time to arrive to max speed
@@ -779,23 +780,23 @@ paint <- function(rawdata, eccon, xmin, xmax, yrange, knRanges, superpose, highl
#show extrema values in speed
- b=extrema(speed$y)
+ speed.ext=extrema(speed$y)
#if(draw & !superpose)
- # segments(x0=b$maxindex,y0=0,x1=b$maxindex,y1=speed$y[b$maxindex],col=cols[1])
+ #
segments(x0=speed.ext$maxindex,y0=0,x1=speed.ext$maxindex,y1=speed$y[speed.ext$maxindex],col=cols[1])
#declare variables:
eccentric=0
isometric=0
concentric=0
if(eccon=="c") {
- concentric=1:length(a)
+ concentric=1:length(displacement)
} else { #"ec", "ce". Eccons "ecS" and "ceS" are not painted
print("EXTREMA")
- #abline(v=b$maxindex,lty=3,col="yellow");
- #abline(v=b$minindex,lty=3,col="magenta")
- print(b)
+ #abline(v=speed.ext$maxindex,lty=3,col="yellow");
+ #abline(v=speed.ext$minindex,lty=3,col="magenta")
+ print(speed.ext)
time1 = 0
time2 = 0
@@ -808,18 +809,18 @@ paint <- function(rawdata, eccon, xmin, xmax, yrange, knRanges, superpose, highl
time2 = min(which(speed$y == min(speed$y)))
labelsXeXc = c("Xc","Xe")
}
- crossMinRow=which(b$cross[,1] > time1 & b$cross[,1] < time2)
+ crossMinRow=which(speed.ext$cross[,1] > time1 & speed.ext$cross[,1] < time2)
isometricUse = TRUE
#TODO: con-ecc is opposite
if(isometricUse) {
- eccentric=1:min(b$cross[crossMinRow,1])
- isometric=c(min(b$cross[crossMinRow,1]), max(b$cross[crossMinRow,2]))
- concentric=max(b$cross[crossMinRow,2]):length(a)
+ eccentric=1:min(speed.ext$cross[crossMinRow,1])
+ isometric=c(min(speed.ext$cross[crossMinRow,1]), max(speed.ext$cross[crossMinRow,2]))
+ concentric=max(speed.ext$cross[crossMinRow,2]):length(displacement)
} else {
- eccentric=1:mean(b$cross[crossMinRow,1])
- isometric=c(mean(b$cross[crossMinRow,1]), mean(b$cross[crossMinRow,2]))
- concentric=mean(b$cross[crossMinRow,2]):length(a)
+ eccentric=1:mean(speed.ext$cross[crossMinRow,1])
+ isometric=c(mean(speed.ext$cross[crossMinRow,1]),
mean(speed.ext$cross[crossMinRow,2]))
+ concentric=mean(speed.ext$cross[crossMinRow,2]):length(displacement)
}
if(draw) {
@@ -910,10 +911,10 @@ paint <- function(rawdata, eccon, xmin, xmax, yrange, knRanges, superpose, highl
par(new=T)
if(highlight==FALSE)
plot(startX:length(accel$y),accel$y[startX:length(accel$y)],type="l",
-
xlim=c(1,length(a)),ylim=ylim,xlab="",ylab="",col="magenta",lty=lty[2],lwd=1,axes=F)
+
xlim=c(1,length(displacement)),ylim=ylim,xlab="",ylab="",col="magenta",lty=lty[2],lwd=1,axes=F)
else
plot(startX:length(accel$y),accel$y[startX:length(accel$y)],type="l",
-
xlim=c(1,length(a)),ylim=ylim,xlab="",ylab="",col="darkblue",lty=2,lwd=3,axes=F)
+
xlim=c(1,length(displacement)),ylim=ylim,xlab="",ylab="",col="darkblue",lty=2,lwd=3,axes=F)
}
if(isPropulsive) {
@@ -946,10 +947,10 @@ paint <- function(rawdata, eccon, xmin, xmax, yrange, knRanges, superpose, highl
par(new=T)
if(highlight==FALSE)
plot(startX:length(force),force[startX:length(force)],type="l",
-
xlim=c(1,length(a)),ylim=ylim,xlab="",ylab="",col=cols[2],lty=lty[2],lwd=1,axes=F)
+
xlim=c(1,length(displacement)),ylim=ylim,xlab="",ylab="",col=cols[2],lty=lty[2],lwd=1,axes=F)
else
plot(startX:length(force),force[startX:length(force)],type="l",
- xlim=c(1,length(a)),ylim=ylim,xlab="",ylab="",col="darkblue",lty=2,lwd=3,axes=F)
+
xlim=c(1,length(displacement)),ylim=ylim,xlab="",ylab="",col="darkblue",lty=2,lwd=3,axes=F)
if(showAxes) {
axis(4, col=cols[2], lty=lty[2], line=axisLineRight, lwd=1, padj=-.5)
axisLineRight = axisLineRight +2
@@ -960,7 +961,7 @@ paint <- function(rawdata, eccon, xmin, xmax, yrange, knRanges, superpose, highl
#mark when it's air and land
#if it was a eccon concentric-eccentric, will be useful to calculate flight time
#but this eccon will be not done
- #if(draw & (!superpose || (superpose & highlight)) & isJump) {
+ #if(draw & (!superpose || (superpose & highlight)) & isJump)
if(draw & (!superpose || (superpose & highlight)) & exercisePercentBodyWeight == 100) {
weight=mass*9.81
abline(h=weight,lty=1,col=cols[2]) #body force, lower than this, person in the air (in a jump)
@@ -977,10 +978,11 @@ paint <- function(rawdata, eccon, xmin, xmax, yrange, knRanges, superpose, highl
}
}
#forceToBodyMass <- force - weight
- #b=extrema(forceToBodyMass)
- #abline(v=b$cross[,1],lty=3,col=cols[2]) #body force, lower than this, person in the air (in a jump)
- #text(x=(mean(b$cross[1,1],b$cross[1,2])+mean(b$cross[2,1],b$cross[2,2]))/2, y=weight,
- # labels=paste("flight time:",
mean(b$cross[2,1],b$cross[2,2])-mean(b$cross[1,1],b$cross[1,2]),"ms"),
+ #force.ext=extrema(forceToBodyMass)
+ #abline(v=force.ext$cross[,1],lty=3,col=cols[2]) #body force, lower than this, person in the air (in
a jump)
+
#text(x=(mean(force.ext$cross[1,1],force.ext$cross[1,2])+mean(force.ext$cross[2,1],force.ext$cross[2,2]))/2,
y=weight,
+ # labels=paste("flight time:",
+ #
mean(force.ext$cross[2,1],force.ext$cross[2,2])-mean(force.ext$cross[1,1],force.ext$cross[1,2]),"ms"),
# col=cols[2], cex=.8, adj=c(0.5,0))
#power #normalment m=massa barra + peses: F=m*a #com es va contra gravetat:
F=m*a+m*g F=m*(a+g) #g sempre es positiva. a es negativa en la baixada de manera que en caiguda lliure
F=0 #cal afegir la resistencia del encoder a la força #Potència P=F*V #si es treballa amb el pes corporal,
cal afegir-lo
@@ -1026,10 +1028,10 @@ paint <- function(rawdata, eccon, xmin, xmax, yrange, knRanges, superpose, highl
par(new=T);
if(highlight==FALSE)
plot(startX:length(power),power[startX:length(power)],type="l",
-
xlim=c(1,length(a)),ylim=ylim,xlab="",ylab="",col=cols[3],lty=lty[3],lwd=2,axes=F)
+
xlim=c(1,length(displacement)),ylim=ylim,xlab="",ylab="",col=cols[3],lty=lty[3],lwd=2,axes=F)
else
plot(startX:length(power),power[startX:length(power)],type="l",
- xlim=c(1,length(a)),ylim=ylim,xlab="",ylab="",col="darkred",lty=2,lwd=3,axes=F)
+
xlim=c(1,length(displacement)),ylim=ylim,xlab="",ylab="",col="darkred",lty=2,lwd=3,axes=F)
meanPowerC = mean(power[min(concentric):max(concentric)])
@@ -1581,12 +1583,12 @@ find.mfrow <- function(n) {
else return(c(3, ceiling(n/3)))
}
-find.yrange <- function(singleFile, rawdata, curves) {
+find.yrange <- function(singleFile, displacement, curves) {
n=length(curves[,1])
y.max = 0
y.min = 10000
for(i in 1:n) {
- y.current = cumsum(rawdata[curves[i,1]:curves[i,2]])
+ y.current = cumsum(displacement[curves[i,1]:curves[i,2]])
if(max(y.current) > y.max)
y.max = max(y.current)
if(min(y.current) < y.min)
@@ -1599,21 +1601,23 @@ find.yrange <- function(singleFile, rawdata, curves) {
return (c(y.min,y.max))
}
-#encoderConfiguration conversions
+#-------------------- encoderConfiguration conversions --------------------------
+
#in signals and curves, need to do conversions (invert, inertiaMomentum, diameter)
-encoderConfigurationConversions <- function(rawdata, encoderConfiguration, diameter) {
- #write(rawdata, "debug-file.txt")
+#we use 'data' variable because can be position or displacement
+getDisplacement <- function(data, encoderConfiguration, diameter) {
if(encoderConfiguration == "LINEARINVERTED") {
- rawdata = -rawdata
+ data = -data
} else if(encoderConfiguration == "ROTARYAXIS") {
ticksRotaryEncoder = 200 #our rotary axis encoder send 200 ticks by turn
#diameter m -> mm
- rawdata = ( rawdata / ticksRotaryEncoder ) * 2 * pi * ( diameter * 1000 / 2 )
+ data = ( data / ticksRotaryEncoder ) * 2 * pi * ( diameter * 1000 / 2 )
}
- #write(rawdata, "debug-file2.txt")
- return(rawdata)
+ return(data)
}
+#-------------- end of encoderConfiguration conversions -------------------------
+
quitIfNoData <- function(n, curves, outputData1) {
#if not found curves with this data, plot a "sorry" message and exit
if(n == 1 & curves[1,1] == 0 & curves[1,2] == 0) {
@@ -1742,7 +1746,7 @@ doProcess <- function(options) {
if(! singleFile) { #reads CSV with curves to analyze
- #this produces a rawdata, but note that a cumsum(rawdata) cannot be done because:
+ #this produces a displacement, but note that a position = cumsum(displacement) cannot be done
because:
#this are separated movements
#maybe all are concentric (there's no returning to 0 phase)
@@ -1751,7 +1755,7 @@ doProcess <- function(options) {
inputMultiData=read.csv(file=File,sep=",",stringsAsFactors=F)
- rawdata = NULL
+ displacement = NULL
count = 1
start = NULL; end = NULL; startH = NULL
status = NULL; id = NULL; exerciseName = NULL; mass = NULL; smooth = NULL
@@ -1775,7 +1779,7 @@ doProcess <- function(options) {
#this removes all NAs on a curve
dataTempFile = dataTempFile[!is.na(dataTempFile)]
- dataTempFile = encoderConfigurationConversions(dataTempFile, encoderConfiguration,
diameter)
+ dataTempFile = getDisplacement(dataTempFile, encoderConfiguration, diameter)
dataTempPhase=dataTempFile
processTimes = 1
@@ -1798,7 +1802,7 @@ doProcess <- function(options) {
newLines=newLines+1
}
}
- rawdata = c(rawdata, dataTempPhase)
+ displacement = c(displacement, dataTempPhase)
id[(i+newLines)] = countLines
start[(i+newLines)] = count
end[(i+newLines)] = length(dataTempPhase) + count -1
@@ -1834,7 +1838,7 @@ doProcess <- function(options) {
}
}
- #rawdata.cumsum=cumsum(rawdata)
+ #position=cumsum(displacement)
#curves =
data.frame(id,start,end,startH,exerciseName,mass,smooth,dateTime,myEccon,stringsAsFactors=F,row.names=1)
#this is a problem when there's only one row as seen by the R code of data.frame. ?data.frame:
@@ -1860,17 +1864,17 @@ doProcess <- function(options) {
print(curves)
#find SmoothingsEC
- SmoothingsEC = findSmoothingsEC(rawdata, curves, Eccon, SmoothingOneC)
+ SmoothingsEC = findSmoothingsEC(displacement, curves, Eccon, SmoothingOneC)
} else { #singleFile == True. reads a signal file
- rawdata=scan(file=File,sep=",")
+ displacement=scan(file=File,sep=",")
#if data file ends with comma. Last character will be an NA. remove it
#this removes all NAs
- rawdata = rawdata[!is.na(rawdata)]
+ displacement = displacement[!is.na(displacement)]
- rawdata = encoderConfigurationConversions(rawdata, encoderConfiguration, diameter)
+ displacement = getDisplacement(displacement, encoderConfiguration, diameter)
- if(length(rawdata)==0) {
+ if(length(displacement)==0) {
plot(0,0,type="n",axes=F,xlab="",ylab="")
text(x=0,y=0,"Encoder is not connected.",cex=1.5)
dev.off()
@@ -1879,24 +1883,24 @@ doProcess <- function(options) {
}
if(inertialType == "ri")
- rawdata = fixRawdataInertial(rawdata)
+ displacement = fixRawdataInertial(displacement)
- curves=findCurves(rawdata, Eccon, MinHeight, curvesPlot, Title)
+ curves=findCurves(displacement, Eccon, MinHeight, curvesPlot, Title)
- rawdata.cumsum=cumsum(rawdata)
+ position=cumsum(displacement)
n=length(curves[,1])
quitIfNoData(n, curves, OutputData1)
#find SmoothingsEC
- SmoothingsEC = findSmoothingsEC(rawdata, curves, Eccon, SmoothingOneC)
+ SmoothingsEC = findSmoothingsEC(displacement, curves, Eccon, SmoothingOneC)
print("curves before reduceCurveBySpeed")
print(curves)
#reduceCurveBySpeed
for(i in 1:n) {
- reduceTemp=reduceCurveBySpeed(Eccon, i, curves[i,1],
rawdata[curves[i,1]:curves[i,2]],
+ reduceTemp=reduceCurveBySpeed(Eccon, i, curves[i,1],
displacement[curves[i,1]:curves[i,2]],
SmoothingsEC[i], SmoothingOneC)
curves[i,1] = reduceTemp[1]
curves[i,2] = reduceTemp[2]
@@ -1906,7 +1910,7 @@ doProcess <- function(options) {
#/10 mm -> cm
for(i in 1:length(curves[,1])) {
myLabel = i
- myY = min(rawdata.cumsum)/10
+ myY = min(position)/10
adjVert = 0
if(Eccon=="ceS")
adjVert = 1
@@ -1917,7 +1921,7 @@ doProcess <- function(options) {
myEc=c("e","c")
myLabel = paste(trunc((i+1)/2),myEc[((i%%2)+1)],sep="")
- myY = rawdata.cumsum[curves[i,1]]/10
+ myY = position[curves[i,1]]/10
if(i%%2 == 1) {
adjVert = 1
if(Eccon=="ceS")
@@ -1936,10 +1940,10 @@ doProcess <- function(options) {
#plot speed
par(new=T)
- speed <- smooth.spline( 1:length(rawdata), rawdata, spar=smoothingAll)
- plot((1:length(rawdata))/1000, speed$y, col="green2",
+ speed <- smooth.spline( 1:length(displacement), displacement, spar=smoothingAll)
+ plot((1:length(displacement))/1000, speed$y, col="green2",
type="l",
- xlim=c(1,length(rawdata))/1000, #ms -> s
+ xlim=c(1,length(displacement))/1000, #ms -> s
#ylim=c(-.25,.25), #to test speed at small changes
xlab="",ylab="",axes=F)
mtext("speed ",side=4,adj=1,line=-1,col="green2")
@@ -1968,11 +1972,11 @@ doProcess <- function(options) {
#don't do this, because on inertial machines string will be rolled to machine and not
connected to the body
#if(inertialType == "li") {
- # rawdata[myStart:myEnd] = fixRawdataLI(rawdata[myStart:myEnd])
+ # displacement[myStart:myEnd] = fixRawdataLI(displacement[myStart:myEnd])
# myEccon="c"
#}
- paint(rawdata, myEccon, myStart, myEnd,"undefined","undefined",FALSE,FALSE,
+ paint(displacement, myEccon, myStart, myEnd,"undefined","undefined",FALSE,FALSE,
1,curves[Jump,3],SmoothingsEC[as.numeric(Jump)],SmoothingOneC,myMass,
paste(Title, " ", Analysis, " ", myEccon, " ", myCurveStr, sep=""),
"", #subtitle
@@ -1994,11 +1998,9 @@ doProcess <- function(options) {
#comparar 6 salts, falta que xlim i ylim sigui el mateix
par(mfrow=find.mfrow(n))
- #a=cumsum(rawdata)
- #yrange=c(min(a),max(a))
- yrange=find.yrange(singleFile, rawdata, curves)
+ yrange=find.yrange(singleFile, displacement, curves)
- knRanges=kinematicRanges(singleFile,rawdata,curves,Mass,SmoothingsEC,SmoothingOneC,
+ knRanges=kinematicRanges(singleFile,displacement,curves,Mass,SmoothingsEC,SmoothingOneC,
g,Eccon,isPropulsive)
for(i in 1:n) {
@@ -2019,7 +2021,7 @@ doProcess <- function(options) {
mySubtitle = paste("curve=", rownames(curves)[i], ", ", myMass, "Kg", sep="")
- paint(rawdata, myEccon, curves[i,1],curves[i,2],yrange,knRanges,FALSE,FALSE,
+ paint(displacement, myEccon, curves[i,1],curves[i,2],yrange,knRanges,FALSE,FALSE,
1,curves[i,3],SmoothingsEC[i],SmoothingOneC,myMass,myTitle,mySubtitle,
TRUE, #draw
FALSE, #showLabels
@@ -2043,11 +2045,11 @@ doProcess <- function(options) {
# #fer que es pugui enviar colors que es vol per cada curva, o linetypes
# wide=max(curves$end-curves$start)
#
-# #a=cumsum(rawdata)
-# #yrange=c(min(a),max(a))
-# yrange=find.yrange(singleFile, rawdata,curves)
+# #position=cumsum(displacement)
+# #yrange=c(min(position),max(position))
+# yrange=find.yrange(singleFile, displacement,curves)
#
-#
knRanges=kinematicRanges(singleFile,rawdata,curves,Mass,SmoothingOneEC,SmoothingOneC,g,Eccon,isPropulsive)
+#
knRanges=kinematicRanges(singleFile,displacement,curves,Mass,SmoothingOneEC,SmoothingOneC,g,Eccon,isPropulsive)
# for(i in 1:n) {
# #in superpose all jumps end at max height
# #start can change, some are longer than other
@@ -2059,7 +2061,7 @@ doProcess <- function(options) {
# if(i==1)
# myTitle = paste(titleType,Jump);
#
-# paint(rawdata, Eccon, curves[i,2]-wide,curves[i,2],yrange,knRanges,TRUE,(i==Jump),
+# paint(displacement, Eccon,
curves[i,2]-wide,curves[i,2],yrange,knRanges,TRUE,(i==Jump),
# startX,curves[i,3],SmoothingOneEC,SmoothingOneC,Mass,myTitle,"",
# TRUE, #draw
# TRUE, #showLabels
@@ -2131,7 +2133,7 @@ doProcess <- function(options) {
myEcconKn = "e"
}
paf=rbind(paf,(powerBars(myEccon,
- kinematicsF(rawdata[curves[i,1]:curves[i,2]],
+ kinematicsF(displacement[curves[i,1]:curves[i,2]],
myMass, SmoothingsEC[i],SmoothingOneC,
g, myEcconKn, isPropulsive))))
}
@@ -2159,7 +2161,7 @@ doProcess <- function(options) {
else
paintPowerPeakPowerBars(singleFile, Title, paf,
curves[,7], Eccon, #myEccon,
Eccon
- rawdata.cumsum[curves[,2]]-curves[,3], #height
+ position[curves[,2]]-curves[,3], #height
n,
(AnalysisVariables[1] == "TimeToPeakPower"), #show
time to pp
(AnalysisVariables[2] == "Range") #show
range
@@ -2215,7 +2217,7 @@ doProcess <- function(options) {
"exerciseName",
Mass,
curves[,1],
- curves[,2]-curves[,1],rawdata.cumsum[curves[,2]]-curves[,3],paf)
+ curves[,2]-curves[,1],position[curves[,2]]-curves[,3],paf)
else {
if(discardingCurves)
curvesHeight = curvesHeight[-discardedCurves]
@@ -2258,12 +2260,12 @@ doProcess <- function(options) {
namesNums=paste(namesNums, units)
for(i in 1:curvesNum) {
- kn = kinematicsF (rawdata[curves[i,1]:curves[i,2]], Mass,
+ kn = kinematicsF (displacement[curves[i,1]:curves[i,2]], Mass,
SmoothingsEC[i], SmoothingOneC, g, Eccon, isPropulsive)
#fill with NAs in order to have the same length
- col1 = rawdata[curves[i,1]:curves[i,2]]
- col2 = rawdata.cumsum[curves[i,1]:curves[i,2]]
+ col1 = displacement[curves[i,1]:curves[i,2]]
+ col2 = position[curves[i,1]:curves[i,2]]
#add mean, max, and time to max
col1=append(col1,
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