Automated_Rotating_Beam_Analysis/R_scripts/stride_angle_calculation.R

Folder="/home/user/owncloud/DLC_Analyse_RotatingBeam/PB_T3_Sham/PB_T3_"
Middle="_P3_RotatingBeam_"
csv="croppedDLC_resnet50_RotatingBeam3.0Jul12shuffle1_200000_filtered.csv"

Number_of_videos=31

T3_12_3_1=paste0(Folder, "12_3", Middle, "1", csv)
T3_12_3_2=paste0(Folder, "12_3", Middle, "2", csv)
T3_12_3_3=paste0(Folder, "12_3", Middle, "3", csv)
T3_12_3_4=paste0(Folder, "12_3", Middle, "4", csv)
T3_13_2_1=paste0(Folder, "13_2", Middle, "1", csv)
T3_13_2_2=paste0(Folder, "13_2", Middle, "2", csv)
T3_13_2_3=paste0(Folder, "13_2", Middle, "3", csv)
T3_13_2_4=paste0(Folder, "13_2", Middle, "4", csv)
T3_13_3_1=paste0(Folder, "13_3", Middle, "1", csv)
T3_13_3_2=paste0(Folder, "13_3", Middle, "2", csv)
T3_13_3_3=paste0(Folder, "13_3", Middle, "3", csv)
T3_13_3_4=paste0(Folder, "13_3", Middle, "4", csv)
T3_14_2_2=paste0(Folder, "14_2", Middle, "2", csv)
T3_14_2_3=paste0(Folder, "14_2", Middle, "3", csv)
T3_14_2_4=paste0(Folder, "14_2", Middle, "4", csv)
T3_14_4_1=paste0(Folder, "14_4", Middle, "1", csv)
T3_14_4_2=paste0(Folder, "14_4", Middle, "2", csv)
T3_14_4_3=paste0(Folder, "14_4", Middle, "3", csv)
T3_14_4_4=paste0(Folder, "14_4", Middle, "4", csv)
T3_15_2_1=paste0(Folder, "15_2", Middle, "1", csv)
T3_15_2_2=paste0(Folder, "15_2", Middle, "2", csv)
T3_15_2_3=paste0(Folder, "15_2", Middle, "3", csv)
T3_15_2_4=paste0(Folder, "15_2", Middle, "4", csv)
T3_16_1_1=paste0(Folder, "16_1", Middle, "1", csv)
T3_16_1_2=paste0(Folder, "16_1", Middle, "2", csv)
T3_16_1_3=paste0(Folder, "16_1", Middle, "3", csv)
T3_16_1_4=paste0(Folder, "16_1", Middle, "4", csv)
T3_17_2_1=paste0(Folder, "17_2", Middle, "1", csv)
T3_17_2_2=paste0(Folder, "17_2", Middle, "2", csv)
T3_17_2_3=paste0(Folder, "17_2", Middle, "3", csv)
T3_17_2_4=paste0(Folder, "17_2", Middle, "4", csv)

ResolutionHeight=1080
ResolutionWidth=1920

Shamnames2<-c("1231", "1232", "1233", "1234", "1321", "1322", "1323", "1324", "1331", "1332", "1333", "1334", "1422", "1423", "1424", "1441", "1442", "1443", "1444", "1521", "1522", "1523", "1524", "1611", "1612", "1613", "1614", "1721", "1722", "1723", "1724")
Shamnames3<-c("PB_T3_12_3_P3_RotatingBeam_1", "PB_T3_12_3_P3_RotatingBeam_2", "PB_T3_12_3_P3_RotatingBeam_3", "PB_T3_12_3_P3_RotatingBeam_4", "PB_T3_13_2_P3_RotatingBeam_1", "PB_T3_13_2_P3_RotatingBeam_2", "PB_T3_13_2_P3_RotatingBeam_3", "PB_T3_13_2_P3_RotatingBeam_4", "PB_T3_13_3_P3_RotatingBeam_1", "PB_T3_13_3_P3_RotatingBeam_2", "PB_T3_13_3_P3_RotatingBeam_3", "PB_T3_13_3_P3_RotatingBeam_4", "PB_T3_14_2_P3_RotatingBeam_2", "PB_T3_14_2_P3_RotatingBeam_3", "PB_T3_14_2_P3_RotatingBeam_4", "PB_T3_14_4_P3_RotatingBeam_1", "PB_T3_14_4_P3_RotatingBeam_2", "PB_T3_14_4_P3_RotatingBeam_3", "PB_T3_14_4_P3_RotatingBeam_4", "PB_T3_15_2_P3_RotatingBeam_1", "PB_T3_15_2_P3_RotatingBeam_2", "PB_T3_15_2_P3_RotatingBeam_3", "PB_T3_15_2_P3_RotatingBeam_4", "PB_T3_16_1_P3_RotatingBeam_1", "PB_T3_16_1_P3_RotatingBeam_2", "PB_T3_16_1_P3_RotatingBeam_3", "PB_T3_16_1_P3_RotatingBeam_4", "PB_T3_17_2_P3_RotatingBeam_1", "PB_T3_17_2_P3_RotatingBeam_2", "PB_T3_17_2_P3_RotatingBeam_3", "PB_T3_17_2_P3_RotatingBeam_4")
Shamnames4<-c(T3_12_3_1, T3_12_3_2, T3_12_3_3, T3_12_3_4, T3_13_2_1, T3_13_2_2, T3_13_2_3, T3_13_2_4, T3_13_3_1, T3_13_3_2, T3_13_3_3, T3_13_3_4, T3_14_2_2, T3_14_2_3, T3_14_2_4, T3_14_4_1, T3_14_4_2, T3_14_4_3, T3_14_4_4, T3_15_2_1, T3_15_2_2, T3_15_2_3, T3_15_2_4, T3_16_1_1, T3_16_1_2, T3_16_1_3, T3_16_1_4, T3_17_2_1, T3_17_2_2, T3_17_2_3, T3_17_2_4)
ShamFPS<-c(30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30)

for(i in 1:Number_of_videos){
  x<-prep.dlc(Shamnames4[i], Height=ResolutionHeight, Width=ResolutionWidth, FPS=ShamFPS[i])
  assign(paste("T", as.character(Shamnames2[i]), sep=""), x)
}

Shamnames<-list(T1231, T1232, T1233, T1234, T1321, T1322, T1323, T1324, T1331, T1332, T1333, T1334, T1422, T1423, T1424, T1441, T1442, T1443, T1444, T1521, T1522, T1523, T1524, T1611, T1612, T1613, T1614, T1721, T1722, T1723, T1724)

Difs<-data.frame()
for(i in 1:length(DLCnames)){
  for(j in 1:nrow(DLCnames[[i]])){
    if(is.na(DLCnames[[i]]$forepaw_right_x[j])==F && is.na(DLCnames[[i]]$hindpaw_right_x[j])==F){
      Difs[j,i]=(as.numeric(DLCnames[[i]]$forepaw_right_x[j])-as.numeric(DLCnames[[i]]$hindpaw_right_x[j]))
    }
  }
}

SDifs<-data.frame()
for(i in 1:length(Shamnames)){
  for(j in 1:nrow(Shamnames[[i]])){
    if(is.na(Shamnames[[i]]$forepaw_right_x[j])==F && is.na(Shamnames[[i]]$hindpaw_right_x[j])==F){
      SDifs[j,i]=(as.numeric(Shamnames[[i]]$forepaw_right_x[j])-as.numeric(Shamnames[[i]]$hindpaw_right_x[j]))
    }
  }
}

Steps<-data.frame()
for(i in 1:length(DLCnames)){
  stepcount=0
  stepblock=0
  for(j in 1:nrow(Difs)){
    if(stepblock==0 && is.na(Difs[j,i])==F && is.na(Difs[j+1,i])==F && Difs[j,i]<(Difs[j+1,i])+1){
      stepcount=stepcount+1
      stepblock=1
      Steps[stepcount, i]=DLCnames[[i]]$seq[j]
    }
    if(is.na(Difs[j,i])==F && is.na(Difs[j+1,i])==F && Difs[j,i]>(Difs[j+1,i]+1)){
      stepblock=0
    }
  }
}

SSteps<-data.frame()
for(i in 1:length(Shamnames)){
  stepcount=0
  stepblock=0
  for(j in 1:nrow(SDifs)){
    if(stepblock==0 && is.na(SDifs[j,i])==F && is.na(SDifs[j+1,i])==F && SDifs[j,i]<(SDifs[j+1,i])+1){
      stepcount=stepcount+1
      stepblock=1
      SSteps[stepcount, i]=Shamnames[[i]]$seq[j]
    }
    if(is.na(SDifs[j,i])==F && is.na(SDifs[j+1,i])==F && SDifs[j,i]>(SDifs[j+1,i]+1)){
      stepblock=0
    }
  }
}

StepangleKnee=data.frame()
for(i in 1:ncol(Steps)){
  for(j in 1:nrow(Steps)){
    if(is.na(Steps[j,i])==F && is.na(Steps[j+1,i])==F){
      steprow=nrow(StepangleKnee)+1
      for(k in 1:(as.numeric(Steps[j+1,i]-as.numeric(Steps[j,i])))){
        StepangleKnee[steprow,k]=singleangle(DLCnames[[i]], (Steps[j,i]+k), "hip_right", "knee_right", "ankle_right")
      }
    }
  }
}

SStepangleKnee=data.frame()
for(i in 1:ncol(SSteps)){
  for(j in 1:nrow(SSteps)){
    if(is.na(SSteps[j,i])==F && is.na(SSteps[j+1,i])==F){
      steprow=nrow(SStepangleKnee)+1
      for(k in 1:(as.numeric(SSteps[j+1,i]-as.numeric(SSteps[j,i])))){
        SStepangleKnee[steprow,k]=singleangle(Shamnames[[i]], (SSteps[j,i]+k), "hip_right", "knee_right", "ankle_right")
      }
    }
  }
}

colSums(!is.na(StepangleKnee))#mindestens 20 values -> bis column 23
cmax=23
StepangleKnee2<-data.frame()
for(i in 1:cmax){
  StepangleKnee2[i,1]=(i*(100/cmax))
  StepangleKnee2[i,2]=mean(StepangleKnee[,i], na.rm=T)
  StepangleKnee2[i,3]=sd(StepangleKnee[,i], na.rm=T)  
}

colSums(!is.na(SStepangleKnee))#mindestens 20 values -> bis column 23
SStepangleKnee2<-data.frame()
for(i in 1:cmax){
  SStepangleKnee2[i,1]=(i*(100/cmax))
  SStepangleKnee2[i,2]=mean(SStepangleKnee[,i], na.rm=T)
  SStepangleKnee2[i,3]=sd(SStepangleKnee[,i], na.rm=T)  
}

ggplot()+
  geom_ribbon(aes(ymin=StepangleKnee2$V2-StepangleKnee2$V3, ymax=StepangleKnee2$V2+StepangleKnee2$V3, x=StepangleKnee2$V1), fill="blue", alpha=0.5)+
  geom_ribbon(aes(ymin=SStepangleKnee2$V2-SStepangleKnee2$V3, ymax=SStepangleKnee2$V2+SStepangleKnee2$V3, x=SStepangleKnee2$V1), fill="red", alpha=0.5)+
  geom_line(aes(y=StepangleKnee2$V2, x=StepangleKnee2$V1), color="darkblue")+
  geom_line(aes(y=SStepangleKnee2$V2, x=SStepangleKnee2$V1), color="darkred")+
  scale_y_continuous(limits = c(0,180))+
  theme_classic()+
  xlab("% stride")+
  ylab("Knee angle (degree)")

StepangleHip=data.frame()
for(i in 1:ncol(Steps)){
  for(j in 1:nrow(Steps)){
    if(is.na(Steps[j,i])==F && is.na(Steps[j+1,i])==F){
      steprow=nrow(StepangleHip)+1
      for(k in 1:(as.numeric(Steps[j+1,i]-as.numeric(Steps[j,i])))){
        StepangleHip[steprow,k]=singleangle(DLCnames[[i]], (Steps[j,i]+k), "middle_back", "hip_right", "knee_right")
      }
    }
  }
}

SStepangleHip=data.frame()
for(i in 1:ncol(SSteps)){
  for(j in 1:nrow(SSteps)){
    if(is.na(SSteps[j,i])==F && is.na(SSteps[j+1,i])==F){
      steprow=nrow(SStepangleHip)+1
      for(k in 1:(as.numeric(SSteps[j+1,i]-as.numeric(SSteps[j,i])))){
        SStepangleHip[steprow,k]=singleangle(Shamnames[[i]], (SSteps[j,i]+k), "middle_back", "hip_right", "knee_right")
      }
    }
  }
}

colSums(!is.na(StepangleHip))#mindestens 20 values -> bis column 19
cmax=19
StepangleHip2<-data.frame()
for(i in 1:cmax){
  StepangleHip2[i,1]=(i*(100/cmax))
  StepangleHip2[i,2]=mean(StepangleHip[,i], na.rm=T)
  StepangleHip2[i,3]=sd(StepangleHip[,i], na.rm=T)  
}

colSums(!is.na(SStepangleHip))#mindestens 20 values -> bis column 19
SStepangleHip2<-data.frame()
for(i in 1:cmax){
  SStepangleHip2[i,1]=(i*(100/cmax))
  SStepangleHip2[i,2]=mean(SStepangleHip[,i], na.rm=T)
  SStepangleHip2[i,3]=sd(SStepangleHip[,i], na.rm=T)  
}

ggplot()+
  geom_ribbon(aes(ymin=StepangleHip2$V2-StepangleHip2$V3, ymax=StepangleHip2$V2+StepangleHip2$V3, x=StepangleHip2$V1), fill="blue", alpha=0.5)+
  geom_ribbon(aes(ymin=SStepangleHip2$V2-SStepangleHip2$V3, ymax=SStepangleHip2$V2+SStepangleHip2$V3, x=SStepangleHip2$V1), fill="red", alpha=0.5)+
  geom_line(aes(y=StepangleHip2$V2, x=StepangleHip2$V1), color="darkblue")+
  geom_line(aes(y=SStepangleHip2$V2, x=SStepangleHip2$V1), color="darkred")+
  scale_y_continuous(limits = c(0,180))+
  theme_classic()+
  xlab("% stride")+
  ylab("Hip angle (degree)")


anovaANGHip<-aov(SStepangleHip2$V2~StepangleHip2$V2)
summary(anovaANGHip)

StepangleAnkle=data.frame()
for(i in 1:ncol(Steps)){
  for(j in 1:nrow(Steps)){
    if(is.na(Steps[j,i])==F && is.na(Steps[j+1,i])==F){
      steprow=nrow(StepangleAnkle)+1
      for(k in 1:(as.numeric(Steps[j+1,i]-as.numeric(Steps[j,i])))){
        StepangleAnkle[steprow,k]=singleangle(DLCnames[[i]], (Steps[j,i]+k), "forepaw_right", "ankle_right", "knee_right")
      }
    }
  }
}

SStepangleAnkle=data.frame()
for(i in 1:ncol(SSteps)){
  for(j in 1:nrow(SSteps)){
    if(is.na(SSteps[j,i])==F && is.na(SSteps[j+1,i])==F){
      steprow=nrow(SStepangleAnkle)+1
      for(k in 1:(as.numeric(SSteps[j+1,i]-as.numeric(SSteps[j,i])))){
        SStepangleAnkle[steprow,k]=singleangle(Shamnames[[i]], (SSteps[j,i]+k), "forepaw_right", "ankle_right", "knee_right")
      }
    }
  }
}

colSums(!is.na(StepangleAnkle))#mindestens 20 values -> bis column 22
cmax=22
StepangleAnkle2<-data.frame()
for(i in 1:cmax){
  StepangleAnkle2[i,1]=(i*(100/cmax))
  StepangleAnkle2[i,2]=mean(StepangleAnkle[,i], na.rm=T)
  StepangleAnkle2[i,3]=sd(StepangleAnkle[,i], na.rm=T)  
}

colSums(!is.na(SStepangleAnkle))#mindestens 20 values -> bis column 22
SStepangleAnkle2<-data.frame()
for(i in 1:cmax){
  SStepangleAnkle2[i,1]=(i*(100/cmax))
  SStepangleAnkle2[i,2]=mean(SStepangleAnkle[,i], na.rm=T)
  SStepangleAnkle2[i,3]=sd(SStepangleAnkle[,i], na.rm=T)  
}

ggplot()+
  geom_ribbon(aes(ymin=StepangleAnkle2$V2-StepangleAnkle2$V3, ymax=StepangleAnkle2$V2+StepangleAnkle2$V3, x=StepangleAnkle2$V1), fill="darkblue", alpha=0.5)+
  geom_ribbon(aes(ymin=SStepangleAnkle2$V2-SStepangleAnkle2$V3, ymax=SStepangleAnkle2$V2+SStepangleAnkle2$V3, x=SStepangleAnkle2$V1), fill="red", alpha=0.5)+
  geom_line(aes(y=StepangleAnkle2$V2, x=StepangleAnkle2$V1), color="darkblue")+
  geom_line(aes(y=SStepangleAnkle2$V2, x=SStepangleAnkle2$V1), color="darkred")+
  scale_y_continuous(limits = c(0,180))+
  theme_classic()+
  xlab("% stride")+
  ylab("Ankle angle (degree)")

ggplot()+
  geom_bar(stat="identity", aes(y=Difs$V2, x=seq(1, nrow(Difs))), na.rm=T)+
  scale_x_continuous(limits = c(0,300))

ggplot()+
  geom_line(aes(y=Difs$V1, x=seq(1, nrow(Difs))), na.rm=T)+
  scale_x_continuous(limits = c(0,300))+
  theme_classic()+
  xlab("Frame Indices")+
  ylab("Distance Forepaw/Hindpaw (px)")