[chronojump] inertial capture not fully extended correction DONE. Need tests.

[Xavier de Blas <xaviblas src gnome org>]

commit 7983609ae26f71e1cf68931d6c98e16f9c1fafa7
Author: Xavier de Blas <xaviblas gmail com>
Date:   Thu Jul 21 14:44:56 2016 +0200

    inertial capture not fully extended correction DONE. Need tests.

 encoder/graph.R    |   36 ++++++++++++++++++++++--------------
 encoder/util.R     |   24 ++++++++++++++++++------
 src/gui/encoder.cs |   14 ++++++++++----
 3 files changed, 50 insertions(+), 24 deletions(-)
---
diff --git a/encoder/graph.R b/encoder/graph.R
index 3b87e03..d79f6da 100644
--- a/encoder/graph.R
+++ b/encoder/graph.R
@@ -2228,7 +2228,7 @@ doProcess <- function(options)
        #       titleType="jump"
 
        curvesPlot = FALSE
-       if(op$Analysis == "curves") {
+       if(op$Analysis == "curves" || op$Analysis == "curvesAC") {
                curvesPlot = TRUE
                par(mar=c(2,2.5,2,1))
        }
@@ -2431,26 +2431,33 @@ doProcess <- function(options)
                                                        NULL, NULL, NULL, NULL) #this row is only needed for 
singleFile (signal)
                print(c("SmoothingsEC:",SmoothingsEC))
        } else {        #singleFile == True. reads a signal file
-               displacement=scan(file=op$File,sep=",")
+               displacement <- scan(file=op$File,sep=",")
                #if data file ends with comma. Last character will be an NA. remove it
                #this removes all NAs
-               displacement  = displacement[!is.na(displacement)]
+               displacement <- displacement[!is.na(displacement)]
                displacementInertialNotBody <- NULL
 
                if(isInertial(op$EncoderConfigurationName)) 
                {
-                       diametersPerMs = getInertialDiametersPerMs(displacement, op$diameter)
-                       displacement = getDisplacementInertial(displacement, op$EncoderConfigurationName, 
+                       #This process is only done on the curves after capture (not on recalculate or load)
+                       if(op$Analysis == "curvesAC")
+                               displacement <- fixInertialSignalIfNotFullyExtended(displacement, 
+                                                                                   paste(op$EncoderTempPath,
+                                                                                         
"/chronojump-last-encoder-data.txt",
+                                                                                         sep=""), 
+                                                                                   FALSE)
+
+                       diametersPerMs <- getInertialDiametersPerMs(displacement, op$diameter)
+                       displacement <- getDisplacementInertial(displacement, op$EncoderConfigurationName, 
                                                               diametersPerMs, op$diameterExt, op$gearedDown)
 
-               
                        displacementInertialNotBody <- displacement #store a copy to be used on "single" (all 
set) to have a better set smooth
-                       displacement = getDisplacementInertialBody(0, displacement, curvesPlot, op$Title)
+                       displacement <- getDisplacementInertialBody(0, displacement, curvesPlot, op$Title)
                        #positionStart is 0 in graph.R. It is different on capture.R because depends on the 
start of every repetition
 
-                       curvesPlot = FALSE
+                       curvesPlot <- FALSE
                } else {
-                       displacement = getDisplacement(op$EncoderConfigurationName, displacement, 
op$diameter, op$diameterExt)
+                       displacement <- getDisplacement(op$EncoderConfigurationName, displacement, 
op$diameter, op$diameterExt)
                }
 
                #TODO: is this needed at all?
@@ -2467,7 +2474,7 @@ doProcess <- function(options)
                curves=findCurvesNew(displacement, op$Eccon, isInertial(op$EncoderConfigurationName), 
                                     op$MinHeight, curvesPlot, op$Title)
                
-               if(op$Analysis == "curves")
+               if(op$Analysis == "curves" || op$Analysis == "curvesAC")
                        curvesPlot = TRUE
 
                n=length(curves[,1])
@@ -2917,7 +2924,8 @@ doProcess <- function(options)
        if(
           op$Analysis == "powerBars" || op$Analysis == "cross" || 
           op$Analysis == "1RMBadillo2010" || op$Analysis == "1RMAnyExercise" || 
-          op$Analysis == "curves" || op$Analysis == "neuromuscularProfile" ||
+          op$Analysis == "curves" || op$Analysis == "curvesAC" ||
+          op$Analysis == "neuromuscularProfile" ||
           writeCurves) 
        {
                paf = data.frame()
@@ -3125,7 +3133,7 @@ doProcess <- function(options)
                        neuromuscularProfileWriteData(npj, op$OutputData1)
                }
                
-               if(op$Analysis == "curves" || writeCurves) {
+               if(op$Analysis == "curves" || op$Analysis == "curvesAC" || writeCurves) {
                        #create pafCurves to be printed on CSV. This columns are going to be removed:
 
                        #print("---- 1 ----")
@@ -3171,8 +3179,8 @@ doProcess <- function(options)
                                        )
                
 
-                       #Add "Max", "AVG" and "SD" when analyzing, not on "curves"
-                       if(op$Analysis != "curves") {
+                       #Add "Max", "AVG" and "SD" when analyzing, not on "curves", not on "curvesAC"
+                       if(op$Analysis != "curves" && op$Analysis != "curvesAC") {
                                addSD = FALSE
                                if(length(pafCurves[,1]) > 1)
                                        addSD = TRUE
diff --git a/encoder/util.R b/encoder/util.R
index 683722c..a229c2b 100644
--- a/encoder/util.R
+++ b/encoder/util.R
@@ -1102,7 +1102,8 @@ getDisplacementInertialBody <- function(positionStart, displacement, draw, title
 
 #used when user captures without string fully extended
 #d is displacement, graph is to debug
-fixInertialSignalNotFullyExtendedString <- function(d, graph)
+#see codeExplained/image detect-and-fix-inertial-string-not-fully-extended.png
+fixInertialSignalIfNotFullyExtended <- function(d, saveFile, graph)
 {
        pos <- cumsum(d)
 
@@ -1129,7 +1130,7 @@ fixInertialSignalNotFullyExtendedString <- function(d, graph)
 
        #return if no data
        if(length(maximums) < 1 | length(minimums) < 1)
-               return()
+               return(d)
 
        #ensure both maximums and minimums have same length
        while(length(maximums) != length(minimums))
@@ -1143,10 +1144,13 @@ fixInertialSignalNotFullyExtendedString <- function(d, graph)
        meanByExtrema <- mean(c(pos[maximums], pos[minimums]))
        posCorrected <- pos - meanByExtrema
 
+       #remove the initial part of the signal. Remove from ms 1 to when posCorrected crosses 0
+       posCorrectedCrossZero = extrema(posCorrected)$cross[1,1]
+
        if(graph) {
                par(mfrow=c(1,2))
 
-               #1st graph
+               #1st graph (left)
                plot(pos, type="l", lty=2, xlab="time", ylab="position", main="String NOT fully extended")
                lines(abs(pos)*-1, lwd=2)
                points(maximumsCopy, pos[maximumsCopy], col="black", cex=1)
@@ -1155,14 +1159,22 @@ fixInertialSignalNotFullyExtendedString <- function(d, graph)
                points(minimums, pos[minimums], col="green", cex=3)
                abline(h = meanByExtrema, col="red")
 
-               #2nd graph
-               plot(posCorrected, type="l", lty=2, xlab="time", ylab="position", main="Set corrected")
+               #2nd graph (right)
+               plot(posCorrected, type="l", lty=2, xlab="time", ylab="position", main="Corrected set")
                lines(abs(posCorrected)*-1, lwd=2)
+               abline(v=c(posCorrectedCrossZero, length(posCorrected)), col="green")
+               mtext("Start", at=posCorrectedCrossZero, side=3, col="green")
+               mtext("End", at=length(posCorrected), side=3, col="green")
 
                par(mfrow=c(1,1))
        }
 
-       return()
+       #define new displacement
+       d <- d[posCorrectedCrossZero:length(d)]
+       
+       #write to file and return displacement to be used
+       write(d, file=saveFile, ncolumns=length(d), sep=", ")
+       return(d)
 }
 
 
diff --git a/src/gui/encoder.cs b/src/gui/encoder.cs
index 79bca07..6fc151e 100644
--- a/src/gui/encoder.cs
+++ b/src/gui/encoder.cs
@@ -932,13 +932,19 @@ public partial class ChronoJumpWindow
        }
 
 
+       private void encoderDoCurvesGraphR_curves() {
+               encoderDoCurvesGraphR("curves");
+       }
+       private void encoderDoCurvesGraphR_curvesAC() {
+               encoderDoCurvesGraphR("curvesAC");
+       }
        //this is called by non gtk thread. Don't do gtk stuff here
        //I suppose reading gtk is ok, changing will be the problem
        //called on calculatecurves, recalculate and load
-       private void encoderDoCurvesGraphR() 
+       private void encoderDoCurvesGraphR(string analysisSent)
        {
                LogB.Debug("encoderDoCurvesGraphR() start");
-               string analysis = "curves";
+               string analysis = analysisSent;
 
                string analysisOptions = getEncoderAnalysisOptions();
 
@@ -4570,7 +4576,7 @@ public partial class ChronoJumpWindow
                                //don't need because ItemToggled is deactivated during capture
                                //treeview_encoder_capture_curves.Sensitive = false;
                                
-                               encoderThread = new Thread(new ThreadStart(encoderDoCurvesGraphR));
+                               encoderThread = new Thread(new ThreadStart(encoderDoCurvesGraphR_curves));
                                if(action == encoderActions.CURVES)
                                        GLib.Idle.Add (new GLib.IdleHandler (pulseGTKEncoderCurves));
                                else // action == encoderActions.LOAD
@@ -4591,7 +4597,7 @@ public partial class ChronoJumpWindow
                                
                                //_______ 2) run stuff
                                //this does not run a pulseGTK
-                               encoderDoCurvesGraphR();
+                               encoderDoCurvesGraphR_curvesAC();
                                encoderButtonsSensitive(encoderSensEnum.PROCESSINGR);
                        }
                } else { //encoderActions.ANALYZE