[chronojump] Cleaned R code and delete lots of slow prints
- From: Xavier de Blas <xaviblas src gnome org>
- To: commits-list gnome org
- Cc:
- Subject: [chronojump] Cleaned R code and delete lots of slow prints
- Date: Thu, 3 Mar 2016 14:40:18 +0000 (UTC)
commit c7a3c1344bdb1c4eede8e596478a867f9b31a1ea
Author: Xavier de Blas <xaviblas gmail com>
Date: Thu Mar 3 15:37:07 2016 +0100
Cleaned R code and delete lots of slow prints
encoder/graph.R | 39 +++-------------------
encoder/graphSmoothingEC.R | 50 +++--------------------------
encoder/util.R | 74 +------------------------------------------
3 files changed, 14 insertions(+), 149 deletions(-)
---
diff --git a/encoder/graph.R b/encoder/graph.R
index 78b7b23..742861e 100644
--- a/encoder/graph.R
+++ b/encoder/graph.R
@@ -1170,8 +1170,8 @@ paintPowerPeakPowerBars <- function(singleFile, title, paf, Eccon, height, n, sh
peakPowerName = translateToPrint("Peak Power")
}
- print("powerData")
- print(powerData)
+ #print("powerData")
+ #print(powerData)
#put lowerY on power, but definetively, leave it at 0
#lowerY=min(powerData)-100
@@ -1252,8 +1252,6 @@ paintPowerPeakPowerBars <- function(singleFile, title, paf, Eccon, height, n, sh
mean(height[which(load == i)]),
myLabel, "darkgreen", "white", ypad=1)
- #print(paste("mean",i,mean(height[which(load == i)])))
-
segments(
bp[2,min(which(load == i))],mean(height[which(load == i)]),
bp[2,max(which(load == i))],mean(height[which(load == i)]),
@@ -1407,7 +1405,6 @@ getModelPValue <- function(model) {
#> round(-0.0002,4)
#[1] -2e-04
round.scientific <- function(x) {
- print(c("at round.scientic",x))
if(x == 0)
return(0)
@@ -1435,7 +1432,6 @@ round.scientific <- function(x) {
#http://stackoverflow.com/a/6234664
#see if two labels overlap
stroverlap <- function(x1,y1,s1, x2,y2,s2) {
- #print(c(x1,y1,s1, x2,y2,s2))
sh1 <- strheight(s1)
sw1 <- strwidth(s1)
sh2 <- strheight(s2)
@@ -1458,7 +1454,6 @@ stroverlap <- function(x1,y1,s1, x2,y2,s2) {
stroverlapArray <- function(newPoint, points) {
overlap = FALSE
- #print(c("at Array newPoint, points",newPoint, points))
if(length(points$x) == 1) #if there's only one row
return (stroverlap(
as.numeric(newPoint[1]), as.numeric(newPoint[2]), newPoint[3],
@@ -1513,9 +1508,6 @@ paintCrossVariables <- function (paf, varX, varY, option, isAlone, title, single
if(varX == "Inertia")
x = x * 10000
- #print("seriesName")
- #print(seriesName)
-
colBalls = NULL
bgBalls = NULL
@@ -1526,7 +1518,6 @@ paintCrossVariables <- function (paf, varX, varY, option, isAlone, title, single
varXut = addUnitsAndTranslate(varX)
varYut = addUnitsAndTranslate(varY)
- #nums.print.df = NULL
nums.print = NULL
#if only one series
@@ -1584,9 +1575,6 @@ paintCrossVariables <- function (paf, varX, varY, option, isAlone, title, single
if(do1RM != FALSE & do1RM != "0") {
speed1RM = as.numeric(do1RM)
- print("speed1RM")
- print(speed1RM)
-
#lineal stuff
fit = lm(y ~ x) #declare
if(do1RMMethod == "NONWEIGHTED") {
@@ -1595,15 +1583,12 @@ paintCrossVariables <- function (paf, varX, varY, option, isAlone, title, single
} else if(do1RMMethod == "WEIGHTED") {
#weights x
fit = lm(y ~ x, weights=x/max(x))
- print(x/max(x))
} else if(do1RMMethod == "WEIGHTED2") {
#weights x^2
fit = lm(y ~ x, weights=x^2/max(x^2))
- print(x^2/max(x^2))
} else if(do1RMMethod == "WEIGHTED3") {
#weights x^3 (as higher then more important are the right values)
fit = lm(y ~ x, weights=x^3/max(x^3))
- print(x^3/max(x^3))
}
c.intercept = coef(fit)[[1]]
@@ -2368,9 +2353,6 @@ doProcess <- function(options)
position=cumsum(displacement)
- #print(c("position",position))
- #print(c("displacement",displacement))
-
curves=findCurvesNew(displacement, op$Eccon, isInertial(op$EncoderConfigurationName),
op$MinHeight, curvesPlot, op$Title)
@@ -2380,8 +2362,8 @@ doProcess <- function(options)
n=length(curves[,1])
quitIfNoData(n, curves, op$OutputData1)
- print("curves before reduceCurveBySpeed")
- print(curves)
+ #print("curves before reduceCurveBySpeed")
+ #print(curves)
#reduceCurveBySpeed, don't do in inertial because it doesn't do a good right adjust on
changing phase
#what reduceCurveBySpeed is doing in inertial is adding a value at right, and this value is a
descending value
@@ -2399,8 +2381,8 @@ doProcess <- function(options)
}
}
- print("curves after reduceCurveBySpeed")
- print(curves)
+ #print("curves after reduceCurveBySpeed")
+ #print(curves)
#find SmoothingsEC
SmoothingsEC = findSmoothingsEC(
@@ -2471,7 +2453,6 @@ doProcess <- function(options)
#write(paste("(4/5)",translateToPrint("Repetitions processed")), op$FeedbackFileBase)
print("Creating (op$FeedbackFileBase)4.txt with touch method...")
file.create(paste(op$FeedbackFileBase,"4.txt",sep=""))
- print("Created")
#print(curves)
if(op$Analysis=="single") {
@@ -2701,8 +2682,6 @@ doProcess <- function(options)
else
repOpSeparated$eccon = "e"
}
- print("start integer before kinematicsF __________")
- print(c(curves[i,1], displacement[curves[i,1]]))
paf = rbind(paf,(pafGenerate(
repOp$eccon,
@@ -2749,11 +2728,6 @@ doProcess <- function(options)
ecconVector = createEcconVector(singleFile, op$Eccon, length(curves[,1]), curves[,8])
- #print("AnalysisVariables:")
- #print(op$AnalysisVariables[1])
- #print(op$AnalysisVariables[2])
- #print(op$AnalysisVariables[3])
-
if(op$AnalysisVariables[1] == "Speed,Power") {
par(mar=c(5,4,5,5))
analysisVertVars = unlist(strsplit(op$AnalysisVariables[1], "\\,"))
@@ -3090,7 +3064,6 @@ doProcess <- function(options)
#write(paste("(5/5)",translateToPrint("R tasks done")), op$FeedbackFileBase)
print("Creating (op$FeedbackFileBase)5.txt with touch method...")
file.create(paste(op$FeedbackFileBase,"5.txt",sep=""))
- print("Created")
write("created ...5.txt", stderr())
warnings()
diff --git a/encoder/graphSmoothingEC.R b/encoder/graphSmoothingEC.R
index b2919ad..e0b48af 100644
--- a/encoder/graphSmoothingEC.R
+++ b/encoder/graphSmoothingEC.R
@@ -83,32 +83,10 @@ findSmoothingsECYPoints <- function(eccentric.concentric, conStart, conEnd, x, m
findSmoothingsEC <- function(singleFile, displacement, curves, eccon, smoothingOneC,
singleFileEncoderConfigurationName, singleFileDiameter,
singleFileInertiaMomentum, singleFileGearedDown)
{
-print("singleFile")
-print(singleFile)
-print("displacement")
-print(displacement)
-print("curves")
-print(curves)
-print("eccon")
-print(eccon)
-print("smoothingOneC")
-print(smoothingOneC)
-print("singleFileEncoderConfigurationName")
-print(singleFileEncoderConfigurationName)
-print("singleFileDiameter")
-print(singleFileDiameter)
-print("singleFileInertiaMomentum")
-print(singleFileInertiaMomentum)
-print("singleFileGearedDown")
-print(singleFileGearedDown)
-
-
ptm <- as.vector(proc.time()[3])
write("time start", stderr())
write(ptm, stderr())
- #print(c("findSmoothingsEC: eccon smoothingOneC", eccon, smoothingOneC))
-
smoothings = NULL
n=length(curves[,1])
@@ -147,24 +125,8 @@ print(singleFileGearedDown)
conEnd = mean(which(position == max(position)))
}
-print("position")
-print(position)
-print("which(position == min(position))")
-print(which(position == min(position)))
-print("i conStart, conEnd, curves[i,1] curves[i,2] 1st part, 2nd part")
-print(i)
-print(conStart)
-print(conEnd)
-print(curves[i,1])
-print(curves[i,2])
-print((curves[i,1]+conStart))
-print((curves[i,1]+conStart))
-print((curves[i,1]+conEnd))
-print("displacement[(curves[i,1]+conStart):(curves[i,1]+conEnd)]")
-print(displacement[(curves[i,1]+conStart):(curves[i,1]+conEnd)])
- concentric=displacement[(curves[i,1]+conStart):(curves[i,1]+conEnd)]
-#1 get max power concentric at concentric phase with current smoothing
+ #1 get max power concentric at concentric phase with current smoothing
speed <- getSpeed(concentric, smoothingOneC)
@@ -189,7 +151,7 @@ print(displacement[(curves[i,1]+conStart):(curves[i,1]+conEnd)])
maxPowerConAtCon <- max(powerTemp)
-#2 get max power concentric (y) at eccentric-concentric phase with current smoothing of an interval of
possible smoothings (x)
+ #2 get max power concentric (y) at eccentric-concentric phase with current
smoothing of an interval of possible smoothings (x)
x <- seq(from = as.numeric(smoothingOneC),
to = as.numeric(smoothingOneC)/2,
@@ -216,7 +178,7 @@ print(displacement[(curves[i,1]+conStart):(curves[i,1]+conEnd)])
#find the max power in concentric phase of this ecc-con movement
maxPowerConAtFullrep <- max(powerTemp[conStart:conEnd])
-#3 check if first aproximation is OK
+ #3 check if first aproximation is OK
#write(paste("MID i, smoothingOneEC, maxPowerConAtFullrep, maxPowerConAtCon,
diff",
# i, smoothingOneEC,
@@ -225,7 +187,7 @@ print(displacement[(curves[i,1]+conStart):(curves[i,1]+conEnd)])
# round( (maxPowerConAtFullrep - maxPowerConAtCon),2 ))
#, stderr())
-#4 create new x values closer
+ #4 create new x values closer
#eg
#x: .7, .6125, .525, .4375, .35
@@ -254,7 +216,7 @@ print(displacement[(curves[i,1]+conStart):(curves[i,1]+conEnd)])
}
-#5 get max power concentric (y) at eccentric-concentric phase with current smoothing of an interval of
possible smoothings (x)
+ #5 get max power concentric (y) at eccentric-concentric phase with current
smoothing of an interval of possible smoothings (x)
x <- seq(
from = xUpperValue,
@@ -267,7 +229,7 @@ print(displacement[(curves[i,1]+conStart):(curves[i,1]+conEnd)])
smodel <- smooth.spline(y,x)
smoothingOneEC <- predict(smodel, maxPowerConAtCon)$y
-#6 check if aproximation is OK
+ #6 check if aproximation is OK
if(! isInertial(myEncoderConfigurationName) )
powerTemp <- findSmoothingsECGetPowerNI(speed)
diff --git a/encoder/util.R b/encoder/util.R
index 8b69f54..d86d4ca 100644
--- a/encoder/util.R
+++ b/encoder/util.R
@@ -229,15 +229,10 @@ findTakeOff <- function(forceConcentric, maxSpeedTInConcentric)
#2 create df2 with only the rows where force is below or equal zero
df2 = subset(df,subset=df$belowZero)
- #print("df2")
- #print(df2)
-
#3 find takeoff as the df2 row with less distance to maxSpeedT
df2row = min(which(df2$dist == min(df2$dist)))
takeoff = as.integer(rownames(df2)[df2row])
- #print(c("takeoff",takeoff))
-
return(takeoff)
}
@@ -404,16 +399,10 @@ reduceCurveBySpeed <- function(eccon, row, startT, startH, displacement, smoothi
x.end = i
}
- #print(speed.ext$cross[,2])
- #print(ext.cross.len)
- #print(c("time1,time2",time1,time2))
- #print(c("x.ini x.end",x.ini,x.end))
-
#to know the new startH
#calculate displacement from original start to the new: x.ini
startH.old = startH
startH = startH + sum(displacement[1:x.ini])
- #print(c("old startH:", startH.old, "; new startH:", startH))
return(c(startT + x.ini, startT + x.end, startH))
}
@@ -493,11 +482,6 @@ kinematicsF <- function(displacement, repOp, smoothingOneEC, smoothingOneC, g, i
accel <- getAccelerationSafe(speed)
- #print(c(" ms",round(mean(speed$y),5)," ma",round(mean(accel$y),5)))
- #print(c(" Ms",round(max(speed$y),5)," Ma",round(max(accel$y),5)))
- #print(c(" |ms|",round(mean(abs(speed$y)),5)," |ma|:",round(mean(abs(accel$y)),5)))
- #print(c(" |Ms|",round(max(abs(speed$y)),5)," |Ma|",round(max(abs(accel$y)),5)))
-
#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
@@ -505,8 +489,6 @@ kinematicsF <- function(displacement, repOp, smoothingOneEC, smoothingOneC, g, i
concentric = 0
propulsiveEnd = 0
- #print(c("at kinematicsF eccon: ", repOp$eccon, " length(displacement): ",length(displacement)))
-
#search propulsiveEnd
if(isPropulsive) {
if(repOp$eccon=="c") {
@@ -535,7 +517,6 @@ kinematicsF <- function(displacement, repOp, smoothingOneEC, smoothingOneC, g, i
findPropulsiveEnd(accel$y, concentric, maxSpeedTInConcentric,
repOp$econfName, repOp$anglePush,
repOp$angleWeight,
repOp$massBody, repOp$massExtra,
repOp$exPercentBodyWeight)
- #print(c("lengths: ", length(eccentric), length(isometric),
findPropulsiveEnd(accel$y,concentric), propulsiveEnd))
}
} else if(repOp$eccon=="e") {
#not repOp$eccon="e" because not propulsive calculations on eccentric
@@ -580,7 +561,6 @@ kinematicsF <- function(displacement, repOp, smoothingOneEC, smoothingOneC, g, i
end <- propulsiveEnd
#as acceleration can oscillate, start at the eccentric part where there are not negative values
- #print(c(inertiaMomentum, repOp$eccon, length(eccentric), min(accel$y[eccentric])))
if(repOp$inertiaM > 0 && (repOp$eccon == "e" || repOp$eccon == "ec"))
{
if(repOp$eccon=="e") {
@@ -590,16 +570,6 @@ kinematicsF <- function(displacement, repOp, smoothingOneEC, smoothingOneC, g, i
#if there is eccentric data and there are negative values
if(length(eccentric) > 0 && min(accel$y[eccentric]) < 0)
{
- #print(c("length(eccentric)",length(eccentric)))
- #print("min accel y eccentric ++++++++++++")
- #print(c("min(accel$y[eccentric])",min(accel$y[eccentric])))
-
- #print(c("accel$y[eccentric]", accel$y[eccentric]))
- #print("displacement eccentric")
- #print(displacement[eccentric])
-
-
-
#deactivated:
#start = max(which(accel$y[eccentric] < 0)) +1
#print("------------ start -----------")
@@ -608,7 +578,6 @@ kinematicsF <- function(displacement, repOp, smoothingOneEC, smoothingOneC, g, i
}
#print(c("kinematicsF start end",start,end))
-
#write("kinematicsF speed length and mean,", stderr())
#write(length(speed$y[start:end]), stderr())
#write(mean(speed$y[start:end]), stderr())
@@ -624,28 +593,17 @@ kinematicsF <- function(displacement, repOp, smoothingOneEC, smoothingOneC, g, i
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("speed.ext-Cross")
- #print(speed.ext$cross[,1])
- #print("search min cross: crossMinRow")
-
crossMinRow=which(speed.ext$cross[,1] > searchMinSpeedEnd & speed.ext$cross[,1] < searchMaxSpeedIni)
- #print(crossMinRow)
eccentric = 0
@@ -662,8 +620,6 @@ findECPhases <- function(displacement,speed) {
isometricUse = TRUE
- #print("at findECPhases")
-
if(isometricUse) {
eccentric=1:min(speed.ext$cross[crossMinRow,1])
isometric=min(speed.ext$cross[crossMinRow,1]+1):max(speed.ext$cross[crossMinRow,2])
@@ -719,10 +675,8 @@ findPropulsiveEnd <- function(accel, concentric, maxSpeedTInConcentric,
return (propulsiveEnd)
}
-pafGenerate <- function(eccon, kinematics, massBody, massExtra, laterality, inertiaMomentum) {
- #print("speed$y")
- #print(kinematics$speedy)
-
+pafGenerate <- function(eccon, kinematics, massBody, massExtra, laterality, inertiaMomentum)
+{
meanSpeed <- mean(kinematics$speedy)
#max speed and max speed time can be at eccentric or concentric
@@ -736,15 +690,9 @@ pafGenerate <- function(eccon, kinematics, massBody, massExtra, laterality, iner
meanPower <- mean(abs(kinematics$power))
}
- #print(c("eccon meanPowerSigned meanPowerABS",eccon, mean(kinematics$power),
mean(abs(kinematics$power))))
- #print("kinematics$power")
- #print(abs(kinematics$power))
-
peakPower <- max(abs(kinematics$power))
peakPowerT <- min(which(abs(kinematics$power) == peakPower))
- #print(which(abs(kinematics$power) == peakPower))
-
pp_ppt <- peakPower / (peakPowerT/1000) # ms->s
meanForce <- mean(kinematics$force)
maxForce <- max(abs(kinematics$force))
@@ -996,26 +944,12 @@ getDisplacementInertial <- function(displacement, encoderConfigurationName, diam
{
write("at getDisplacementInertial", stderr())
- print("encoderConfigurationName")
- print(encoderConfigurationName)
-
- print("diameter")
- print(diameter)
- print("diameterExt")
- print(diameterExt)
- print("gearedDown")
- print(gearedDown)
-
- print("displacement at beginning of getDisplacementInertial")
- print(displacement)
-
#scanned displacement is ticks of rotary axis encoder
#now convert it to mm of body displacement
if(encoderConfigurationName == "ROTARYAXISINERTIAL" ||
encoderConfigurationName == "ROTARYAXISINERTIALLATERAL" ||
encoderConfigurationName == "ROTARYAXISINERTIALMOVPULLEY") {
ticksRotaryEncoder = 200 #our rotary axis encoder send 200 ticks per revolution
-# diameterMeters = diameter / 100 #cm -> m
#Number of revolutions that the flywheel rotates every millisecond
revolutionsPerMs = displacement / ticksRotaryEncoder # One revolution every
ticksRotaryEncoder ticks
@@ -1041,9 +975,6 @@ getDisplacementInertial <- function(displacement, encoderConfigurationName, diam
}
- print("displacement at end of getDisplacementInertial")
- print(displacement)
-
return (displacement)
}
@@ -1065,7 +996,6 @@ getDisplacementInertialBody <- function(positionStart, displacement, draw, title
position.ext=extrema(position)
#print("at findCurvesInertial")
- #print(position.ext)
#do if extrema(position)$nextreme == 0... then do not use extrema
#TODO: check if started backwards on realtime capture (extrema is null)
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