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my_plotLib.py
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# -*- coding: utf-8 -*-
"""
Created on Thu Nov 12 17:12:21 2015
@author: b.ellinger
"""
import numpy as np
import matplotlib.pyplot as plt
from scipy.integrate import simps
import re
import csv
from datetime import datetime as dt
# ----------------------------------------------------------------------------------------
# LOAD DATA
# ----------------------------------------------------------------------------------------
def load_data(text_data):
# here we load the data out of the desired file and search for the specific column-entries of the Vars we wanna use
forces = {"fx":[],"fy":[],"fz":[]}
angles = {"hip":[], "knee":[]}
# open file for searching
content = open(text_data, 'r')
fObj = csv.reader(content, delimiter=';')
for a in range(15):
header = fObj.__next__()
for b in range(len(header)):
if re.search(r"[Ff]x\d", header[b]):
stopper = a
forces["fx"].append(b)
elif re.search(r"[Ff]y\d", header[b]):
#forces["fy"].append(b)
forces["fz"].append(b)
elif re.search(r"[Ff]z[3-4]", header[b]):
forces["fz"].append(b)
elif re.search(r"H*fte\sFlexion", header[b]):
angles["hip"].append(b)
elif re.search(r"Knie\sFlexion", header[b]):
angles["knee"].append(b)
content.close()
data_osp = np.genfromtxt(text_data, skip_header=stopper+1, delimiter=";")
#data_osp = np.matrix(data_osp)
return [data_osp,forces,angles]
# ----------------------------------------------------------------------------------------
# CALCULATE KISTLER
# ----------------------------------------------------------------------------------------
def calc_kistler(data_matrix, angle_dict, joint_choice, angle_step, forces_dict):
# -------------------------------------------------------------------------
# Calculaing the difference between every single data-point
# this wil be used for defining the alteration of the joint angles
# -------------------------------------------------------------------------
if joint_choice == 1:
# hip difference calculation; I'm taking the absolute values and calculate a mean value of the flexion between right
# and left side
difference_angle = np.zeros([len(data_matrix)-1, 2])
difference_angle[:,0] = np.abs(data_matrix[0:-1,angle_dict["hip"][0]]) - np.abs(data_matrix[1::,angle_dict["hip"][0]])
difference_angle[:,1] = np.abs(data_matrix[0:-1,angle_dict["hip"][1]]) - np.abs(data_matrix[1::,angle_dict["hip"][1]])
mean_diff = np.mean(np.abs(difference_angle), axis=1)
elif joint_choice == 2:
# knee difference calculation; I'm taking the absolute values and calculate a mean value of the flexion between right
# and left side
difference_angle = np.zeros([len(data_matrix)-1, 2])
difference_angle[:,0] = np.abs(data_matrix[0:-1,angle_dict["knee"][0]]) - np.abs(data_matrix[1::,angle_dict["knee"][0]])
difference_angle[:,1] = np.abs(data_matrix[0:-1,angle_dict["knee"][1]]) - np.abs(data_matrix[1::,angle_dict["knee"][1]])
mean_diff = np.mean(np.abs(difference_angle), axis=1)
# -------------------------------------------------------------------------
# -------------------------------------------------------------------------
# I -- FORCE
# this is Fz for all data points; 1500Hz
# -------------------------------------------------------------------------
Fz_tot = np.sum(data_matrix[:, forces_dict["fz"]],axis=1)
Fz_tot = Fz_tot / 0.94
interval = 5
for f in range(len(Fz_tot)):
difference = np.mean(Fz_tot[f:f+interval]) - np.mean(Fz_tot[f+interval:f+2*interval])
if difference > 3:
print(f)
# mass = np.mean(Fz_tot[f/2:(f/2)+200]) / 9.81
mass = np.mean(Fz_tot[f:f+200]) / 9.81
print("Mass ="+str(mass)+" in interval: "+str(f/2)+" : "+str((f/2)+200))
break
# -------------------------------------------------------------------------
# -------------------------------------------------------------------------
# II -- SPEED and speed-dependent parameters
# calculating the velocity throughout integration of discrete values
# -------------------------------------------------------------------------
accel_tot = 1/1500 * ((Fz_tot/mass) - 9.81) # 1/1500 is measure frequdncy
speed_tot=[]
for c in range(len(accel_tot)):
speed_tot.append(simps(accel_tot[0:c+1]))
speed_tot = np.array(speed_tot)
impulse_tot = speed_tot * mass
power_tot = Fz_tot * speed_tot
power_rel = power_tot / mass
# -------------------------------------------------------------------------
# -------------------------------------------------------------------------
# III -- ALTERATION of joint angles
# here we detect the time points having the desired steps in degree-terms
# --- IMPROVE IT ---
# -------------------------------------------------------------------------
step_sum = mean_diff[0]
time_point = []
for row in range(len(mean_diff)):
step_sum = step_sum + mean_diff[row]
if step_sum >= angle_step:
time_point.append(row)
step_sum = mean_diff[row]
Fz,Fy,Fx = np.zeros([len(time_point), 1]),np.zeros([len(time_point), 1]),np.zeros([len(time_point), 1])
F_tot = np.zeros([len(time_point), 3])
curr_angle = np.zeros([len(time_point), 1])
if joint_choice == 1:
curr_angle = np.mean([data_matrix[time_point, angle_dict["knee"][0]], data_matrix[time_point, angle_dict["knee"][1]]], axis=0)
elif joint_choice == 2:
curr_angle = np.mean([data_matrix[time_point, angle_dict["hip"][0]], data_matrix[time_point, angle_dict["hip"][1]]], axis=0)
# -------------------------------------------------------------------------
# -------------------------------------------------------------------------
# IV -- CUTTED PARAMETERS
# defining the parameters which are cutted throughout myoMOTION data
# -------------------------------------------------------------------------
Fz = Fz_tot[time_point]
impulse = impulse_tot[time_point]
power = power_tot[time_point]
speed = speed_tot[time_point]
power_rel_myo = power_rel[time_point]
# reshaping variables in form "data x 1"
curr_angle, Fz, speed, impulse, power = curr_angle.reshape(len(curr_angle),1), Fz.reshape(len(curr_angle),1), speed.reshape(len(curr_angle),1), impulse.reshape(len(curr_angle),1), power.reshape(len(curr_angle),1)
Fz_tot, speed_tot, impulse_tot, power_tot = Fz_tot.reshape(len(Fz_tot),1), speed_tot.reshape(len(Fz_tot),1), impulse_tot.reshape(len(Fz_tot),1), power_tot.reshape(len(Fz_tot),1)
power_rel, power_rel_myo = power_rel.reshape(len(Fz_tot),1), power_rel_myo.reshape(len(curr_angle),1)
return [curr_angle,Fz,Fz_tot,speed,speed_tot,impulse,impulse_tot,power,power_tot,power_rel,power_rel_myo]
# -------------------------------------------------------------------------
# ----------------------------------------------------------------------------------------
# PLOT DATA
# ----------------------------------------------------------------------------------------
def plot_data(force_myo, impulse_myo, speed_myo, power_myo, curr_angle, force_tot, impulse_tot, speed_tot, power_tot,
plotselection, plotcut, plotall_myo, plotall_tot):
# setting time points for cutting data
t_unload_tot, t_unload_myo = np.where(force_tot < 10)[0][0], np.where(force_myo < 10)[0][0]
minus_myo = round(len(force_myo)*0.17)
cut_tot, cut_myo = np.argmax(force_tot[(t_unload_tot - 400):t_unload_tot]), np.argmax(force_myo[t_unload_myo-minus_myo:t_unload_myo])
cut_tot, cut_myo = t_unload_tot - (400 - cut_tot), t_unload_myo - (minus_myo - cut_myo)
# defining time ranges for x-Axis
time_tot, time_myo = np.arange(0,len(force_tot)), np.arange(0,len(force_myo))
if plotcut == 1: # cutted plots - till first force maximum
if plotall_tot == 1:
fig1 = plt.figure("Alle Plots - geschnitten (Kistler-basiert)")
f_tot_plot = fig1.add_subplot(221)
f_tot_plot = plt.ylabel("N"),plt.xlabel("t [Hz]"),plt.title("Kraft")
f_tot_plot = plt.plot(time_tot[0:cut_tot],force_tot[0:cut_tot])
p_tot_plot = fig1.add_subplot(222)
p_tot_plot = plt.ylabel("Ns"),plt.xlabel("t [Hz]"),plt.title("Impuls")
p_tot_plot = plt.plot(time_tot[0:cut_tot],impulse_tot[0:cut_tot])
v_tot_plot = fig1.add_subplot(223)
v_tot_plot = plt.ylabel("m/s"),plt.xlabel("t [Hz]"),plt.title("Geschwindigkeit")
v_tot_plot = plt.plot(time_tot[0:cut_tot],speed_tot[0:cut_tot])
w_Tot_plot = fig1.add_subplot(224)
w_Tot_plot = plt.ylabel("W"),plt.xlabel("t [Hz]"),plt.title("Leistung")
w_Tot_plot = plt.plot(time_tot[0:cut_tot],power_tot[0:cut_tot])
elif plotall_myo == 1:
fig2 = plt.figure("Alle Plots - geschnitten (myoMOTION-basiert)")
f_tot_plot = fig2.add_subplot(221)
f_tot_plot = plt.ylabel("N"),plt.xlabel("t [Hz]"),plt.title("Kraft")
f_tot_plot = plt.plot(time_myo[0:cut_myo],force_myo[0:cut_myo])
p_tot_plot = fig2.add_subplot(222)
p_tot_plot = plt.ylabel("Ns"),plt.xlabel("t [Hz]"),plt.title("Impuls")
p_tot_plot = plt.plot(time_myo[0:cut_myo],impulse_myo[0:cut_myo])
v_tot_plot = fig2.add_subplot(223)
v_tot_plot = plt.ylabel("m/s"),plt.xlabel("t [Hz]"),plt.title("Geschwindigkeit")
v_tot_plot = plt.plot(time_myo[0:cut_myo],speed_myo[0:cut_myo])
w_Tot_plot = fig2.add_subplot(224)
w_Tot_plot = plt.ylabel("W"),plt.xlabel("t [Hz]"),plt.title("Leistung")
w_Tot_plot = plt.plot(time_myo[0:cut_myo],power_myo[0:cut_myo])
elif plotselection == 1:
plt.figure("Kraft - geschnitten (myoMOTION-basiert)")
plt.ylabel("N"), plt.xlabel("t [deg]"), plt.title("Kraft")
plt.plot(time_myo[0:cut_myo], force_myo[0:cut_myo])
elif plotselection == 2:
plt.figure("Impuls - geschnitten (myoMOTION-basiert)")
plt.ylabel("Ns"), plt.xlabel("t [deg]"), plt.title("Impuls")
plt.plot(time_myo[0:cut_myo], impulse_myo[0:cut_myo])
elif plotselection == 3:
plt.figure("Geschwindigkeit - geschnitten (myoMOTION-basiert)")
plt.ylabel("m/s"), plt.xlabel("t [deg]"), plt.title("Geschwindigkeit")
plt.plot(time_myo[0:cut_myo], speed_myo[0:cut_myo])
elif plotselection == 4:
plt.figure("Leistung - geschnitten (myoMOTION-basiert)")
plt.ylabel("W"), plt.xlabel("t [deg]"), plt.title("Leistung")
plt.plot(time_myo[0:cut_myo], power_myo[0:cut_myo])
elif plotselection == 5:
plt.figure("Kraft - geschnitten (Kistler-basiert)")
plt.ylabel("N"), plt.xlabel("t [Hz]"), plt.title("Kraft")
plt.plot(time_tot[0:cut_tot], force_tot[0:cut_tot])
elif plotselection == 6:
plt.figure("Impuls - geschnitten (Kistler-basiert)")
plt.ylabel("Ns"), plt.xlabel("t [Hz]"), plt.title("Impuls")
plt.plot(time_tot[0:cut_tot], impulse_tot[0:cut_tot])
elif plotselection == 7:
plt.figure("Geschwindigkeit - geschnitten (Kistler-basiert)")
plt.ylabel("m/s"), plt.xlabel("t [Hz]"), plt.title("Geschwindigkeit")
plt.plot(time_tot[0:cut_tot], speed_tot[0:cut_tot])
elif plotselection == 8:
plt.figure("Leistung - geschnitten (Kistler-basiert)")
plt.ylabel("W"), plt.xlabel("t [Hz]"), plt.title("Leistung")
plt.plot(time_tot[0:cut_tot], power_tot[0:cut_tot])
elif plotcut == 2: # uncutted plots - whole Data stream either Kistler or myoMOTION based
if plotall_tot == 1:
fig3 = plt.figure("Alle Plots - ungeschnitten (Kistler-basiert)")
# fig3 = plt.figure("plots")
f_tot_plot = fig3.add_subplot(221)
f_tot_plot = plt.ylabel("N"),plt.xlabel("t [Hz]"),plt.title("Kraft")
f_tot_plot = plt.plot(time_tot,force_tot)
p_tot_plot = fig3.add_subplot(222)
p_tot_plot = plt.ylabel("Ns"),plt.xlabel("t [Hz]"),plt.title("Impuls")
p_tot_plot = plt.plot(time_tot,impulse_tot)
v_tot_plot = fig3.add_subplot(223)
v_tot_plot = plt.ylabel("m/s"),plt.xlabel("t [Hz]"),plt.title("Geschwindigkeit")
v_tot_plot = plt.plot(time_tot,speed_tot)
w_Tot_plot = fig3.add_subplot(224)
w_Tot_plot = plt.ylabel("W"),plt.xlabel("t [Hz]"),plt.title("Leistung")
w_Tot_plot = plt.plot(time_tot,power_tot)
elif plotall_myo == 1:
fig4 = plt.figure("Alle Plots - ungeschnitten (myoMOTION-basiert)")
f_tot_plot = fig4.add_subplot(221)
f_tot_plot = plt.ylabel("N"),plt.xlabel("t [deg]"),plt.title("Kraft")
f_tot_plot = plt.plot(time_myo,force_myo)
p_tot_plot = fig4.add_subplot(222)
p_tot_plot = plt.ylabel("Ns"),plt.xlabel("t [deg]"),plt.title("Impuls")
p_tot_plot = plt.plot(time_myo,impulse_myo)
v_tot_plot = fig4.add_subplot(223)
v_tot_plot = plt.ylabel("m/s"),plt.xlabel("t [deg]"),plt.title("Geschwindigkeit")
v_tot_plot = plt.plot(time_myo,speed_myo)
w_Tot_plot = fig4.add_subplot(224)
w_Tot_plot = plt.ylabel("W"),plt.xlabel("t [deg]"),plt.title("Leistung")
w_Tot_plot = plt.plot(time_myo,power_myo)
elif plotselection == 1:
plt.figure("Kraft - ungeschnitten (myoMOTION-basiert)")
plt.ylabel("N"), plt.xlabel("t [deg]"), plt.title("Kraft")
plt.plot(time_myo, force_myo)
elif plotselection == 2:
plt.figure("Impuls - ungeschnitten (myoMOTION-basiert)")
plt.ylabel("Ns"), plt.xlabel("t [deg]"), plt.title("Impuls")
plt.plot(time_myo, impulse_myo)
elif plotselection == 3:
plt.figure("Geschwindigkeit - ungeschnitten (myoMOTION-basiert)")
plt.ylabel("m/s"), plt.xlabel("t [deg]"), plt.title("Geschwindigkeit")
plt.plot(time_myo, speed_myo)
elif plotselection == 4:
plt.figure("Leistung - ungeschnitten (myoMOTION-basiert)")
plt.ylabel("W"), plt.xlabel("t [deg]"), plt.title("Leistung")
plt.plot(time_myo, power_myo)
elif plotselection == 5:
plt.figure("Kraft - ungeschnitten (Kistler-basiert)")
plt.ylabel("N"), plt.xlabel("t [Hz]"), plt.title("Kraft")
plt.plot(time_tot, force_tot)
elif plotselection == 6:
plt.figure("Impuls - ungeschnitten (Kistler-basiert)")
plt.ylabel("Ns"), plt.xlabel("t [Hz]"), plt.title("Impuls")
plt.plot(time_tot, impulse_tot)
elif plotselection == 7:
plt.figure("Geschwindigkeit - ungeschnitten (Kistler-basiert)")
plt.ylabel("m/s"), plt.xlabel("t [Hz]"), plt.title("Geschwindigkeit")
plt.plot(time_tot, speed_tot)
elif plotselection == 8:
plt.figure("Leistung - ungeschnitten (Kistler-basiert)")
plt.ylabel("W"), plt.xlabel("t [Hz]"), plt.title("Leistung")
plt.plot(time_tot, power_tot)
plt.legend()
plt.show()
# ----------------------------------------------------------------------------------------
# EXPORT DATA
# ----------------------------------------------------------------------------------------
def export_data(export_name, curr_angle, force_myo, impulse_myo, speed_myo, power_myo,
force_tot, impulse_tot, speed_tot, power_tot, power_rel_tot, power_rel_myo):
# setting time points for cutting data
cut_tot, cut_myo = np.argmax(force_tot[0:np.argmax(speed_tot)]), np.argmax(force_myo[0:np.argmax(speed_myo)])
Fz_tot_max, impulse_tot_max,speed_tot_max,power_tot_max = np.max(force_tot[0:np.argmax(speed_tot)]), np.max(impulse_tot), np.max(speed_tot), np.max(power_tot)
Fz_myo_max, impulse_myo_max,speed_myo_max,power_myo_max = np.max(force_myo[0:np.argmax(speed_myo)]), np.max(impulse_myo), np.max(speed_myo), np.max(power_myo)
power_rel_tot_max, power_rel_myo_max = np.max(power_rel_tot), np.max(power_rel_myo)
tot_max, tot_myo = [Fz_tot_max, impulse_tot_max,speed_tot_max,power_tot_max,power_rel_tot_max], [Fz_myo_max, impulse_myo_max,speed_myo_max,power_myo_max,power_rel_myo_max]
tot_max, tot_myo = np.array(tot_max), np.array(tot_myo)
tot_max, tot_myo = tot_max.round(decimals=3), tot_myo.round(decimals=3)
# calculation jump height using flight time method
t1, t2 = np.where(force_tot < 10)[0][0], np.where(force_tot < 10)[0][-1]
delta_t = (t2 - t1) / 1500
height = 9.81 * (0.5*delta_t)**2 * 0.5
height = round(height, 3)
# date and time values for file header specs
date = str(dt.now())
date = date.split(' ')
# combining the huge single arrays to one huge array
time_range = np.arange(len(force_tot))
time_range = time_range.reshape(len(time_range),1)
all_tot = np.concatenate((time_range, force_tot, impulse_tot, speed_tot, power_tot, power_rel_tot), axis=1)
all_myo = np.concatenate((curr_angle, force_myo, impulse_myo, speed_myo, power_myo, power_rel_myo), axis=1)
# all_tot, all_myo = all_tot.round(decimals=3), all_myo.round(decimals=3)
with open(export_name+'.csv', 'w+') as fileID:
fileID.write("Datum\t" + date[0] + "\nZeit\t" + date[1].split('.')[0] + "\n\n")
fileID.write("KSP-h(max)[m]\tZeile-Schnitt(alle_Daten)\tZeile_Schnitt(MM-Daten)\n" + str(height) +"\t" + str(cut_tot) + "\t" + str(cut_myo)+"\n\n\n" +
"Kistler-basierte Maximalwerte\n")
fileID.write("Fz_max[N]\tI_max[Ns]\tv_max[m/s]\tP_abs_max[W]\tP_rel_max[W]\n")
tot_max.tofile(fileID, sep="\t", format="%s")
fileID.write("\n" + "myoMOTION-basierte Maximalwerte\n")
fileID.write("Fz_max[N]\tI_max[Ns]\tv_max[m/s]\tP_abs_max[W]\tP_rel_max[W]\n")
tot_myo.tofile(fileID, sep="\t", format="%s")
fileID.write("\n\n\n")
all_tot, all_myo = np.round(all_tot, 3), np.round(all_myo, 3)
with open(export_name+'.csv', 'ab') as output:
np.savetxt(output, all_tot, delimiter="\t", header = "Zeit[Hz]\tKraft[N]\tImpuls[Ns]\tGeschw[m/s]\tP_abs[W]\tP_rel[W]", fmt="%f")
np.savetxt(output, all_myo, delimiter="\t", header = "\n\n\nWinkel[°]\tKraft[N]\tImpuls[Ns]\tGeschw[m/s]\tP_abs[W]\tP_rel[W]", fmt="%f")