[chronojump] MIF. RFDs specified at Roptions.
- From: Xavier Padullés <xpadulles src gnome org>
- To: commits-list gnome org
- Cc:
- Subject: [chronojump] MIF. RFDs specified at Roptions.
- Date: Tue, 11 Apr 2017 14:34:58 +0000 (UTC)
commit 0950c3393e7e5324cafaf652bc2edd2cbe177c6f
Author: Xavier Padullés <x padulles gmail com>
Date: Tue Apr 11 16:33:16 2017 +0200
MIF. RFDs specified at Roptions.
r-scripts/maximumIsometricForce.R | 297 +++++++++++++++++++++---------------
1 files changed, 173 insertions(+), 124 deletions(-)
---
diff --git a/r-scripts/maximumIsometricForce.R b/r-scripts/maximumIsometricForce.R
index bb1d8c9..befd189 100644
--- a/r-scripts/maximumIsometricForce.R
+++ b/r-scripts/maximumIsometricForce.R
@@ -35,28 +35,26 @@ endGraph <- function()
dev.off()
}
-assignOptions <- function(options) {
- return(list(
- os = options[1],
- graphWidth = as.numeric(options[2]),
- graphHeight = as.numeric(options[3]),
- averageLength = as.numeric(options[4]),
- percentChange = as.numeric(options[5]),
- vlineT0 = as.numeric(options[6]),
- vline50fmax.raw = as.numeric(options[7]),
- vline50fmax.fitted = as.numeric(options[8]),
- hline50fmax.raw = as.numeric(options[9]),
- hline50fmax.fitted = as.numeric(options[10]),
- rfd0.fitted = as.numeric(options[11]),
- rfd100.raw = as.numeric(options[12]),
- rfd0_100.raw = as.numeric(options[13]),
- rfd0_100.fitted = as.numeric(options[14]),
- rfd200.raw = as.numeric(options[15]),
- rfd0_200.raw = as.numeric(options[16]),
- rfd0_200.fitted = as.numeric(options[17]),
- rfd50pfmax.raw = as.numeric(options[18]),
- rfd50pfmax.fitted = as.numeric(options[19])
- ))
+assignOptions <- function(options)
+{
+ drawRfdOptions = rep(NA, length(options) - 10)
+ for(n in 11:length(options))
+ {
+ drawRfdOptions[n-10] = options[n]
+ }
+ return(list(
+ os = options[1],
+ graphWidth = as.numeric(options[2]),
+ graphHeight = as.numeric(options[3]),
+ averageLength = as.numeric(options[4]),
+ percentChange = as.numeric(options[5]),
+ vlineT0 = as.numeric(options[6]),
+ vline50fmax.raw = as.numeric(options[7]),
+ vline50fmax.fitted = as.numeric(options[8]),
+ hline50fmax.raw = as.numeric(options[9]),
+ hline50fmax.fitted = as.numeric(options[10]),
+ drawRfdOptions = drawRfdOptions
+ ))
}
#-------------- get params -------------
@@ -144,6 +142,7 @@ getDynamicsFromLoadCellFile <- function(inputFile, averageLength = 0.1, percentC
rfd0_200.fitted = (f200.fitted - initf) / 0.2
rfd100_200.raw = ((f200.raw - f100.raw) * 10)
+ tfmax.raw = test$time[which.min(abs(test$force - fmax.raw))]
t50fmax.raw = test$time[which.min(abs(test$force - fmax.raw/2))]
t50fmax.fitted = originalTest$time[which.min(abs(f.fitted - (model$fmax + initf)/ 2))]
rfd50pfmax.raw = (test$force[which.min(abs(test$force - fmax.raw/2)) + 1] -
test$force[which.min(abs(test$force - fmax.raw/2)) - 1]) * 100 / 2 #RFD at the moment that the force is 50%
of the fmax
@@ -156,6 +155,7 @@ getDynamicsFromLoadCellFile <- function(inputFile, averageLength = 0.1, percentC
initf = initf,
f0.raw = f0.raw,
fmax.raw = fmax.raw, fmax.smoothed = fmax.smoothed,
+ tfmax.raw = tfmax.raw,
f100.raw = f100.raw,
f100.fitted = f100.fitted,
f200.raw = f200.raw,
@@ -180,9 +180,7 @@ getDynamicsFromLoadCellFile <- function(inputFile, averageLength = 0.1, percentC
drawDynamicsFromLoadCell <- function(
dynamics, vlineT0=T, vline50fmax.raw=F, vline50fmax.fitted=F,
hline50fmax.raw=F, hline50fmax.fitted=F,
- rfd0.fitted=F, rfd100.raw=F, rfd0_100.raw=F, rfd0_100.fitted = F,
rfd200.raw=F, rfd0_200.raw=F,
- rfd0_200.fitted = F, rfd50pfmax.raw=F, rfd50pfmax.fitted=F,
- xlimits=NA)
+ rfdDrawingOptions, xlimits = NA)
{
par(mar = c(5, 4, 6, 4))
@@ -253,108 +251,146 @@ drawDynamicsFromLoadCell <- function(
plotWidth = dev.size()[1]*72 - (par()$mar[2] + par()$mar[4])*pixelsPerLine
plotHeight = dev.size()[2]*72 - (par()$mar[1] + par()$mar[3])*pixelsPerLine
- #Plotting RFD0
- if(rfd0.fitted)
- {
- windowSlope = dynamics$rfd0.fitted*(plotHeight/yHeight)/(plotWidth/xWidth)
- intercepstartTime.fitted = dynamics$f.fitted[which.min(abs(dynamics$time -
dynamics$startTime))] - dynamics$rfd0.fitted*(dynamics$startTime)
- abline(a = intercepstartTime.fitted, b = dynamics$rfd0.fitted, col="blue", lty = 2)
- text(x = (yHeight - 5 - intercepstartTime.fitted)/dynamics$rfd0.fitted, y = yHeight - 5,
- label=paste("RFD0 =", round(dynamics$rfd0.fitted, digits=0), "N/s"),
- srt=atan(windowSlope)*180/pi, pos = 2, col = "blue")
- points(x = dynamics$startTime, y = dynamics$initf, col = "blue")
- }
-
- if(rfd100.raw)
- {
- windowSlope = dynamics$rfd100.raw*(plotHeight/yHeight)/(plotWidth/xWidth)
- intercept100.raw = dynamics$f100.raw - dynamics$rfd100.raw * (dynamics$startTime + 0.1)
- abline(a = intercept100.raw, b = dynamics$rfd100.raw, lty = 2)
- text(x = (yHeight - 5 - intercept100.raw)/dynamics$rfd100.raw, y = yHeight - 5,
- label=paste("RFD100 =", round(dynamics$rfd100, digits=0), "N/s"),
- srt=atan(windowSlope)*180/pi, pos = 2)
- points(x = dynamics$startTime + 0.1, y = dynamics$f100.raw)
- }
-
- if(rfd0_100.raw)
- {
- windowSlope = dynamics$rfd0_100.raw*(plotHeight/yHeight)/(plotWidth/xWidth)
- intercepstartTime_100.raw = dynamics$f0.raw - dynamics$rfd0_100.raw * dynamics$startTime
- abline(a = intercepstartTime_100.raw, b = dynamics$rfd0_100.raw, lty = 2)
- text(x = (yHeight - 5 - intercepstartTime_100.raw)/dynamics$rfd0_100.raw, y = yHeight - 5,
- label=paste("RFD0_100 =", round(dynamics$rfd0_100.raw, digits=0), "N/s"),
- srt=atan(windowSlope)*180/pi, pos = 2)
- points(x = c(dynamics$startTime, dynamics$startTime + 0.1), y = c(dynamics$f0.raw,
dynamics$f100.raw))
- }
-
- if(rfd0_100.fitted)
- {
- windowSlope = dynamics$rfd0_100.fitted*(plotHeight/yHeight)/(plotWidth/xWidth)
- intercepstartTime_100.fitted = dynamics$initf - dynamics$rfd0_100.fitted * dynamics$startTime
- abline(a = intercepstartTime_100.fitted, b = dynamics$rfd0_100.fitted, lty = 2, col = "blue")
- text(x = (yHeight - 5 - intercepstartTime_100.fitted)/dynamics$rfd0_100.fitted, y = yHeight
- 5,
- label=paste("RFD0_100 =", round(dynamics$rfd0_100.fitted, digits=0), "N/s"),
- srt=atan(windowSlope)*180/pi, pos = 2, col = "blue")
- points(x = c(dynamics$startTime, dynamics$startTime + 0.1), y = c(dynamics$initf,
dynamics$f100.fitted), col = "blue")
- }
-
- if(rfd200.raw)
- {
- windowSlope = dynamics$rfd200.raw*(plotHeight/yHeight)/(plotWidth/xWidth)
- intercept200.raw = dynamics$f200.raw - dynamics$rfd200.raw * (dynamics$startTime + 0.2)
- abline(a = intercept200.raw, b = dynamics$rfd200.raw, lty = 2)
- text(x = (yHeight - 5 - intercept200.raw)/dynamics$rfd200.raw, y = yHeight - 5,
- label=paste("RFD200 =", round(dynamics$rfd200.raw, digits=0), "N/s"),
- srt=atan(windowSlope)*180/pi, pos = 2)
- points(x = dynamics$startTime + 0.2, y = dynamics$f200.raw)
- }
- if(rfd0_200.raw)
+ #Drawing the RFD data
+ print(paste("op$drawRfdOptions =", op$drawRfdOptions))
+ for (n in 1:length(rfdDrawingOptions))
{
- windowSlope = dynamics$rfd0_200.raw*(plotHeight/yHeight)/(plotWidth/xWidth)
- intercepstartTime_200.raw = dynamics$f0.raw - dynamics$rfd0_200.raw * dynamics$startTime
- abline(a = intercepstartTime_200.raw, b = dynamics$rfd0_200.raw, lty = 2)
- text(x = (yHeight - 5 - intercepstartTime_200.raw)/dynamics$rfd0_200.raw, y = yHeight - 5,
- label=paste("RFD0_200 =", round(dynamics$rfd0_200.raw, digits=0), "N/s"),
- srt=atan(windowSlope)*180/pi, pos = 2)
- points(x = c(dynamics$startTime, dynamics$startTime + 0.2), y =
c(dynamics$f0.raw,dynamics$f200.raw))
- }
-
- if(rfd0_200.fitted)
- {
- windowSlope = dynamics$rfd0_200.fitted*(plotHeight/yHeight)/(plotWidth/xWidth)
- intercepstartTime_200.fitted = dynamics$initf - dynamics$rfd0_200.fitted * dynamics$startTime
- abline(a = intercepstartTime_200.fitted, b = dynamics$rfd0_200.fitted, lty = 2, col = "blue")
- text(x = (yHeight - 5 - intercepstartTime_200.fitted)/dynamics$rfd0_200.fitted, y = yHeight
- 5,
- label=paste("RFD0_200 =", round(dynamics$rfd0_200.fitted, digits=0), "N/s"),
- srt=atan(windowSlope)*180/pi, pos = 2, col = "blue")
- points(x = c(dynamics$startTime, dynamics$startTime + 0.2), y =
c(dynamics$initf,dynamics$f200.fitted), col = "blue")
- }
-
- if(rfd50pfmax.raw){
- windowSlope = dynamics$rfd50pfmax.raw*(plotHeight/yHeight)/(plotWidth/xWidth)
- intercept50fmax.raw = dynamics$f50fmax.raw - dynamics$rfd50pfmax.raw * dynamics$t50fmax.raw
- abline(a = intercept50fmax.raw, b = dynamics$rfd50pfmax.raw, lty = 2)
- text(x = (yHeight - 5 - intercept50fmax.raw)/dynamics$rfd50pfmax.raw, y = yHeight - 5,
- label=paste("rfd50%fmax =", round(dynamics$rfd50pfmax.raw, digits=0), "N/s"),
- srt=atan(windowSlope)*180/pi, pos = 2)
- points(x =dynamics$t50fmax.raw, y = dynamics$f50fmax.raw)
- }
-
- if(rfd50pfmax.fitted){
- windowSlope = dynamics$rfd50pfmax.fitted*(plotHeight/yHeight)/(plotWidth/xWidth)
- intercept50fmax.fitted = dynamics$f50fmax.fitted - dynamics$rfd50pfmax.fitted *
dynamics$t50fmax.fitted
- abline(a = intercept50fmax.fitted, b = dynamics$rfd50pfmax.fitted, col ="blue", lty = 2)
- text(x = (yHeight - 5 - intercept50fmax.fitted)/dynamics$rfd50pfmax.fitted, y = yHeight - 5,
col = "blue",
- label=paste("rfd50%fmax =", round(dynamics$rfd50pfmax.fitted, digits=0), "N/s"),
- srt=atan(windowSlope)*180/pi, pos=2)
- points(x = dynamics$t50fmax.fitted, y = dynamics$f50fmax.fitted, col = "blue")
+ print("----------------------------------------")
+ print(paste("n =", n))
+ options = readRFDOptions(op$drawRfdOptions[n])
+ print(options)
+
+ RFD = NULL
+ sample2 = NA
+ pointForce2 = NA
+
+ if(options$rfdFunction == "fitted")
+ {
+ color = "blue"
+ } else if(options$rfdFunction == "raw")
+ {
+ color = "black"
+ }
+
+ if(options$type == "instant") # TODO: || percent ...(all except AVG)
+ {
+ if (options$rfdFunction == "fitted")
+ {
+ #Slope of the line
+ RFD = dynamics$fmax.fitted * dynamics$k.fitted * exp(-dynamics$k.fitted *
options$start)
+ #Y coordinate of a point of the line
+ pointForce1 = dynamics$fmax.fitted*(1 - exp(-dynamics$k.fitted *
options$start)) + dynamics$initf
+
+ } else if(options$rfdFunction == "raw")
+ {
+ color = "black"
+ sample1 = which.min(abs(dynamics$time - dynamics$startTime - options$start))
+
+ #Slope of the line
+ RFD = dynamics$rfd[sample1]
+
+ #Y coordinate of a point of the line
+ pointForce1 = dynamics$f.raw[sample1]
+ }
+ } else if(options$type == "avg")
+ {
+ if (options$rfdFunction == "fitted")
+ {
+ #Slope of the line
+ RFD = dynamics$fmax.fitted*(exp( -dynamics$k.fitted * options$start) - exp(
-dynamics$k.fitted * options$end)) / (options$end - options$start)
+ #Y coordinate of a point of the line
+ pointForce1 = dynamics$fmax.fitted*(1 - exp( -dynamics$k.fitted *
options$start)) + dynamics$initf
+
+ } else if(options$rfdFunction == "raw")
+ {
+ sample1 = which.min(abs(dynamics$time - dynamics$startTime - options$start))
+ sample2 = which.min(abs(dynamics$time - dynamics$startTime - options$end))
+
+ #Slope of the line
+ RFD = (dynamics$f.raw[sample2] - dynamics$f.raw[sample1]) /
(dynamics$time[sample2] - dynamics$time[sample1])
+
+ #Y coordinate of a point of the line
+ pointForce1 = dynamics$f.raw[sample1]
+ }
+
+ } else if(options$type == "%fmax")
+ {
+
+ if (options$rfdFunction == "fitted")
+ {
+ #Force that is the % of the raw fmax
+ fpfmax = dynamics$fmax.raw*options$start/100
+ print(paste("fpfmax =", fpfmax))
+
+ #Translating options$start to time in seconds
+ options$start = dynamics$time[which.min(abs(dynamics$f.fitted - fpfmax))] -
dynamics$startTime
+
+ #dynamics$tfmax.raw * options$start / 100 - dynamics$startTime
+ RFD = dynamics$fmax.fitted * dynamics$k.fitted * exp(-dynamics$k.fitted *
options$start)
+
+ #Y coordinate of a point of the line
+ pointForce1 = dynamics$fmax.fitted*(1 - exp(-dynamics$k.fitted *
options$start)) + dynamics$initf
+
+ } else if(options$rfdFunction == "raw")
+ {
+ #Calculing at which sample force is equal to the percent of fmax specified
in options$start
+ sample1 = which.min(abs(dynamics$f.raw -
dynamics$fmax.raw*options$start/100))
+
+ #Translating options$start to time in seconds
+ options$start = dynamics$time[sample1] - dynamics$startTime
+
+ #Slope of the line
+ RFD = dynamics$rfd[sample1]
+
+ #Y coordinate of a point of the line
+ pointForce1 = dynamics$f.raw[sample1]
+ }
+ } else if(options$type == "rfdmax")
+ {
+ if (options$rfdFunction == "fitted")
+ {
+
+ } else if(options$rfdFunction == "raw")
+ {
+ #Calculing the sample at which the rfd is max
+ sample1 = which.max(dynamics$rfd)
+
+ #Translating options$start to time in seconds
+ options$start = dynamics$time[sample1] - dynamics$startTime
+
+ #Slope of the line
+ RFD = dynamics$rfd[sample1]
+ RFD = dynamics$rfd[sample1]
+
+ #Y coordinate of a point of the line
+ pointForce1 = dynamics$f.raw[sample1]
+
+ }
+
+ }
+
+ #The Y coordinate of the line at t=0
+ intercept = pointForce1 - RFD * (dynamics$startTime + options$start)
+ print(paste("Intercept =", intercept))
+
+ #The slope of the line seen in the screen(pixels units), NOT in the time-force units
+ windowSlope = RFD*(plotHeight/yHeight)/(plotWidth/xWidth)
+
+ #Drawing the line
+ abline(a = intercept, b = RFD, lty = 2, col = color)
+ text(x = (yHeight - 5 - intercept)/RFD, y = yHeight - 5,
+ label=paste("RFD =", round(RFD, digits=0), "N/s"),
+ srt=atan(windowSlope)*180/pi, pos = 2, col = color)
+ #Drawing the points where the line touch the function
+ points(x = c(options$start + dynamics$startTime, options$end), y = c(pointForce1,
pointForce2), col = color)
+ print(paste("startTime =", dynamics$startTime))
+ print(paste("options$start =", options$start))
+ print(paste("RFD :", RFD))
+ print(paste("PointForce1 =", pointForce1))
}
#Plotting instantaneous RFD
par(new = T)
- print(dynamics$time)
- print(dynamics$f.raw)
- print(dynamics$rfd)
plot(dynamics$time[(dynamics$startSample):dynamics$endSample],
dynamics$rfd[(dynamics$startSample):dynamics$endSample],
type = "l", col = "red", axes = F,
xlim = c(xmin, xmax), xlab = "", ylab = "", yaxs= "i", xaxs = "i")
@@ -448,11 +484,24 @@ getMovingAverageForce <- function(test, averageLength = 0.1)
return(movingAverageForce)
}
+#Converts the drawRfdOptions string to a list of parameters
+readRFDOptions <- function(optionsStr)
+{
+ options = unlist(strsplit(optionsStr, "\\;"))
+
+ return(list(
+ rfdFunction = options[1], # raw or fitted
+ type = options[2], # instantaeous, average, %fmax, rfdmax
+ start = as.numeric(options[3]), # second at which the analysis starts
+ end = as.numeric(options[4]) # second at which the analysis ends
+))
+}
+
prepareGraph(op$os, pngFile, op$graphWidth, op$graphHeight)
dynamics = getDynamicsFromLoadCellFile(dataFile, op$averageLength, op$percentChange)
drawDynamicsFromLoadCell(dynamics, op$vlineT0, op$vline50fmax.raw, op$vline50fmax.fitted,
op$hline50fmax.raw, op$hline50fmax.fitted,
- op$rfd0.fitted, op$rfd100.raw, op$rfd0_100.raw, op$rfd0_100.fitted, op$rfd200.raw,
op$rfd0_200.raw, op$rfd0_200.fitted,
- op$rfd50pfmax.raw, op$rfd50pfmax.fitted)
+ op$drawRfdOptions)
+# op$drawRfdOptions, xlimits = c(0.5, 1.5))
endGraph()
#dynamics = getDynamicsFromLoadCellFile("~/ownCloud/Xavier/Recerca/Yoyo-Tests/Galga/RowData/APl1",
averageLength = 0.1, percentChange = 5, sep = ";", dec = ",")
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