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trc_gaitevents.py
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trc_gaitevents.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
##################################################
## GAIT EVENTS DETECTION ##
##################################################
Determine gait on and off from a TRC file of point coordinates.
N.B.: Could implement the methods listed there in the future.
Please feel free to make a pull-request or keep me informed if you do so!
Three available methods, each of them with their own pros and cons:
- "forward_coordinates":
on = max(XHeel - Xsacrum)
off = min(XToe - XSacrum)
++: Works well for walking (Zeni et al., 2008)
++: No argument nor tuning necessary
--: Not suitable for running
--: does not work if the person is not going on a straight line
- "height_coordinates":
on = YToe < height_threshold
off = YToe > height_threshold
++: Best results for running and walking
++: Works if the person is not going on a straight line
--: Does not work is the person is grazing the ground
--: Does not work if the field is not flat
--: height_threshold might need to be tuned
--: Heel point might be more accurate than toe point for walking
- "forward_velocity":
on = VToe < forward_velocity_threshold
off = VToe > forward_velocity_threshold
++: Works for running
--: More sensitive to noise
--: Tends to anticipate off if the marker is not at the tip of the toe
--: forward_velocity_threshold might need to be tuned
--: Does not work if the person is not going on a straight line
Usage:
List of available arguments:
python -m trc_gaitevents -h
import trc_gaitevents; trc_gaitevents.trc_gaitevents_func(trc_path=r'<input_trc_file>')
OR import trc_gaitevents; trc_gaitevents.trc_gaitevents_func(trc_path=r'<input_trc_file>', method='forward_coordinates', gait_direction='-X', plot=True, save_output=True, output_file='gaitevents.txt')
OR import trc_gaitevents; trc_gaitevents.trc_gaitevents_func(trc_path=r'<input_trc_file>', method='height_coordinates', up_direction='Y', height_threshold=6, right_toe_marker='RBigToe', left_toe_marker='LBigToe')
OR import trc_gaitevents; trc_gaitevents.trc_gaitevents_func(trc_path=r'<input_trc_file>', method='forward_velocity', gait_direction='-Z', forward_velocity_threshold=1, right_toe_marker='RBigToe', left_toe_marker='LBigToe')
python -m trc_gaitevents -i input_trc_file
OR python -m trc_gaitevents -i input_trc_file --method forward_coordinates --gait_direction=-X --plot True --save_output True --output_file gaitevents.txt
OR python -m trc_gaitevents -i input_trc_file --method height_coordinates --up_direction=Y --height_threshold 6 --right_toe_marker RBigToe --left_toe_marker LBigToe
OR python -m trc_gaitevents -i input_trc_file --method forward_velocity --gait_direction=-Z --forward_velocity_threshold 1 --right_toe_marker RBigToe --left_toe_marker LBigToe
'''
## INIT
import os
import argparse
import pandas as pd
import numpy as np
from scipy import signal
from scipy.ndimage import gaussian_filter1d
import matplotlib.pyplot as plt
## AUTHORSHIP INFORMATION
__author__ = "David Pagnon"
__copyright__ = "Copyright 2021, Pose2Sim"
__credits__ = ["David Pagnon"]
__license__ = "BSD 3-Clause License"
__version__ = "0.9.4"
__maintainer__ = "David Pagnon"
__email__ = "contact@david-pagnon.com"
__status__ = "Development"
## FUNCTIONS
def start_end_true_seq(series):
'''
Find starts and ends of sequences of True values in a pandas Series
INPUTS:
- series: pandas Series of boolean values
OUTPUTS:
- start_indices: list of start indices
- end_indices: list of end indices
'''
diff = series.ne(series.shift())
start_indices = series.index[diff & series].tolist()
end_indices = (series.index[diff & ~series]-1).tolist()
if end_indices[0] == -1: end_indices.pop(0)
return start_indices, end_indices
def read_trc(trc_path):
'''
Read trc file
INPUTS:
- trc_path: path to the trc file
OUTPUTS:
- Q_coords: dataframe of coordinates
- frames_col: series of frames
- time_col: series of time
- markers: list of marker names
- header: list of header lines
'''
with open(trc_path, 'r') as trc_file:
header = [next(trc_file) for line in range(5)]
markers = header[3].split('\t')[2::3]
trc_df = pd.read_csv(trc_path, sep="\t", skiprows=4)
frames_col, time_col = pd.Series(trc_df.iloc[:,0], name='frames'), pd.Series(trc_df.iloc[:,1], name='time')
Q_coords = trc_df.drop(trc_df.columns[[0, 1]], axis=1)
return Q_coords, frames_col, time_col, markers, header
def first_step_side(Ron, Lon):
'''
Get first step side
INPUTS:
- Ron: list of right on times or frames
- Lon: list of left on times or frames
OUTPUTS:
- first_side: 'R' if right first, 'L' if left first
'''
if Ron[0]<Lon[0]:
first_side = 'R'
else:
first_side = 'L'
return first_side
def clean_gait_events(gait_events):
'''
Clean gait events to only keep right-left alternating and full contact pairs
INPUTS:
- gait_events: tuple of lists (Ron, Lon, Roff, Loff)
OUTPUTS:
- Ron, Lon, Roff, Loff = cleaned gait events
'''
Ron, Lon, Roff, Loff = gait_events
# Remove incomplete pairs at the start and end
if Ron[0]>Roff[0]: Roff.pop(0)
if Lon[0]>Loff[0]: Loff.pop(0)
if Ron[-1]>Roff[-1]: Ron.pop(-1)
if Lon[-1]>Loff[-1]: Lon.pop(-1)
# Remove lonely pairs that are not alternating with the other side at the beginning or the end
if Ron[0]<Lon[0]: # Right first
while Ron[1]<Lon[0]: Ron.pop(0)
while Lon[-2]>Ron[-1]: Lon.pop(-1)
while Roff[1]<Loff[0]: Roff.pop(0)
while Loff[-2]>Roff[-1]: Loff.pop(-1)
else: # Left first
while Lon[1]<Ron[0]: Lon.pop(0)
while Ron[-2]>Lon[-1]: Ron.pop(-1)
while Loff[1]<Roff[0]: Loff.pop(0)
while Roff[-2]>Loff[-1]: Roff.pop(-1)
return Ron, Lon, Roff, Loff
def gait_events_fwd_coords(trc_path, gait_direction, markers=['RHeel', 'RBigToe', 'LHeel', 'LBigToe', 'Hip'], plot=True):
'''
Determine gait on and off with "forward_coordinates" method
on = max(XHeel - Xsacrum)
off = min(XToe - XSacrum)
++: Works well for walking (Zeni et al., 2008)
++: No argument nor tuning necessary
--: Not suitable for running
--: does not work if the person is not going on a straight line
INPUTS:
- trc_path: path to the trc file
- gait_direction: tuple (sign, direction) with sign in {-1, 1} and direction in {'X', 'Y', 'Z'}
- markers: list of marker names in the following order: [right_heel_marker, right_toe_marker, left_heel_marker, left_toe_marker, sacrum_marker]
- plot: plot results or not (boolean)
OUTPUTS:
- t_Ron: list of right on times
- t_Lon: list of left on times
- t_Roff: list of right off times
- t_Loff: list of left off times
'''
# Retrieve gait direction
sign, direction = gait_direction
axis = ['X', 'Y', 'Z'].index(direction)
# Read trc file
Q_coords, _, time_col, trc_markers, header = read_trc(trc_path)
unit = header[2].split('\t')[4]
peak_prominence = .1 if unit=='m' else 1 if unit=='dm' else 10 if unit=='cm' else 100 if unit=='mm' else np.inf
RHeel_idx, RBigToe_idx, LHeel_idx, LBigToe_idx, Hip_idx = [trc_markers.index(m) for m in markers]
RHeel_df, RBigToe_df, LHeel_df, LBigToe_df, Hip_df = (Q_coords.iloc[:,axis+idx*3] for idx in [RHeel_idx, RBigToe_idx, LHeel_idx, LBigToe_idx, Hip_idx])
# Find gait events
max_r_heel_hip_proj = sign*(RHeel_df-Hip_df)
frame_Ron = signal.find_peaks(max_r_heel_hip_proj, prominence=peak_prominence)[0].tolist()
t_Ron = time_col[frame_Ron].tolist()
max_l_heel_hip_proj = sign*(LHeel_df-Hip_df)
frame_Lon = signal.find_peaks(max_l_heel_hip_proj, prominence=peak_prominence)[0].tolist()
t_Lon = time_col[frame_Lon].tolist()
max_r_hip_toe_proj = sign*(Hip_df-RBigToe_df)
frame_Roff = signal.find_peaks(max_r_hip_toe_proj, prominence=peak_prominence)[0].tolist()
t_Roff = time_col[frame_Roff].tolist()
max_l_hip_toe_proj = sign*(Hip_df-LBigToe_df)
frame_Loff = signal.find_peaks(max_l_hip_toe_proj, prominence=peak_prominence)[0].tolist()
t_Loff = time_col[frame_Loff].tolist()
# Clean gait events
frame_Ron, frame_Lon, frame_Roff, frame_Loff = clean_gait_events((frame_Ron, frame_Lon, frame_Roff, frame_Loff))
t_Ron, t_Lon, t_Roff, t_Loff = clean_gait_events((t_Ron, t_Lon, t_Roff, t_Loff))
# Plot
if plot:
plt.plot(time_col, max_r_heel_hip_proj, 'C0', label='Right on')
plt.plot(time_col[frame_Ron], max_r_heel_hip_proj[frame_Ron], 'g+')
plt.plot(time_col, max_l_heel_hip_proj, 'C1', label='Left on')
plt.plot(time_col[frame_Lon], max_l_heel_hip_proj[frame_Lon], 'g+')
plt.plot(time_col, max_r_hip_toe_proj, 'C0', label='Right off')
plt.plot(time_col[frame_Roff], max_r_hip_toe_proj[frame_Roff], 'r+')
plt.plot(time_col, max_l_hip_toe_proj, 'C1', label='Left off')
plt.plot(time_col[frame_Loff], max_l_hip_toe_proj[frame_Loff], 'r+')
plt.title('Gait events')
plt.xlabel('Time (s)')
plt.ylabel('Distance (cm)')
plt.legend()
plt.show()
print('Times:')
print('Right on:', t_Ron)
print('Right off:', t_Roff)
print('Left on:', t_Lon)
print('Left off:', t_Loff)
print('\nFrames:')
print('Right on:', frame_Ron)
print('Right off:', frame_Roff)
print('Left on:', frame_Lon)
print('Left off:', frame_Loff)
return (t_Ron, t_Lon, t_Roff, t_Loff), (frame_Ron, frame_Lon, frame_Roff, frame_Loff)
def gait_events_height_coords(trc_path, up_direction, height_threshold=6, filter_fs=10, markers=['RBigToe', 'LBigToe'], plot=True):
'''
Determine gait on and off with "height_coordinates" method
on = YToe < height_threshold
off = YToe > height_threshold
++: Best results for running and walking
++: Works if the person is not going on a straight line
--: Does not work is the person is grazing the ground
--: Does not work if the field is not flat
--: height_threshold might need to be tuned
--: Heel point might be more accurate than toe point for walking
INPUTS:
- trc_path: path to the trc file
- up_direction: tuple (sign, direction) with sign in {-1, 1} and direction in {'X', 'Y', 'Z'}
- height_threshold: height below which the foot is considered to have touched the ground (cm)
- filter_fs: butterworth filter cutoff frequency (Hz)
- markers: list of marker names in the following order: [right_toe_marker, left_toe_marker]
- plot: plot results or not (boolean)
OUTPUTS:
- t_Ron: list of right on times
- t_Lon: list of left on times
- t_Roff: list of right off times
- t_Loff: list of left off times
'''
# Retrieve gait direction
sign, direction = up_direction
axis = ['X', 'Y', 'Z'].index(direction)
# Read trc file
Q_coords, _, time_col, trc_markers, header = read_trc(trc_path)
unit = header[2].split('\t')[4]
unit_factor = 100 if unit=='m' else 10 if unit=='dm' else 1 if unit=='cm' else .1 if unit=='mm' else np.inf
Q_coords *= unit_factor
# Calculate height
Y_height = Q_coords.iloc[:,axis::3]
Y_height.columns = trc_markers
Rfoot_height, Lfoot_height = (Y_height[m] for m in markers)
dt = time_col.diff().mean()
b, a = signal.butter(4/2, filter_fs*dt*2, 'low', analog=False)
Rfoot_height_filtered = pd.Series(signal.filtfilt(b, a, Rfoot_height[1:]), name=Rfoot_height.name)
Lfoot_height_filtered = pd.Series(signal.filtfilt(b, a, Lfoot_height[1:]), name=Lfoot_height.name)
# Find gait events
low_Rfoot_height = Rfoot_height_filtered<height_threshold
frame_Ron, frame_Roff = start_end_true_seq(low_Rfoot_height)
if 0 in frame_Ron: frame_Ron.remove(0)
t_Ron, t_Roff = time_col[frame_Ron].tolist(), time_col[frame_Roff].tolist()
low_Lfoot_height = Lfoot_height_filtered<height_threshold
frame_Lon, frame_Loff = start_end_true_seq(low_Lfoot_height)
if 0 in frame_Lon: frame_Lon.remove(0)
t_Lon, t_Loff = time_col[frame_Lon].tolist(), time_col[frame_Loff].tolist()
# Clean gait events
frame_Ron, frame_Lon, frame_Roff, frame_Loff = clean_gait_events((frame_Ron, frame_Lon, frame_Roff, frame_Loff))
t_Ron, t_Lon, t_Roff, t_Loff = clean_gait_events((t_Ron, t_Lon, t_Roff, t_Loff))
# Plot
if plot:
plt.plot(time_col[1:], Rfoot_height_filtered, 'C0', label='Right foot height filtered')
plt.plot(time_col[1:][frame_Ron], Rfoot_height_filtered[frame_Ron], 'g+')
plt.plot(time_col[1:][frame_Roff], Rfoot_height_filtered[frame_Roff], 'r+')
plt.plot(time_col[1:], Lfoot_height_filtered, 'C1', label='Left foot height filtered')
plt.plot(time_col[1:][frame_Lon], Lfoot_height_filtered[frame_Lon], 'g+')
plt.plot(time_col[1:][frame_Loff], Lfoot_height_filtered[frame_Loff], 'r+')
plt.title('Gait events')
plt.xlabel('Time (s)')
plt.ylabel('Height (cm)')
plt.legend()
plt.show()
print('Times:')
print('Right on:', t_Ron)
print('Right off:', t_Roff)
print('Left on:', t_Lon)
print('Left off:', t_Loff)
print('\nFrames:')
print('Right on:', frame_Ron)
print('Right off:', frame_Roff)
print('Left on:', frame_Lon)
print('Left off:', frame_Loff)
return (t_Ron, t_Lon, t_Roff, t_Loff), (frame_Ron, frame_Lon, frame_Roff, frame_Loff)
def gait_events_fwd_vel(trc_path, gait_direction, forward_velocity_threshold=1, filter_fs=10, markers=['RBigToe', 'LBigToe'], plot=True):
'''
Determine gait on and off with "forward_velocity" method
on = VToe < forward_velocity_threshold
off = VToe > forward_velocity_threshold
++: Works for running and walking
--: Tends to anticipate off if marker is not at the tip of the toe
--: forward_velocity_threshold might need to be tuned
--: does not work if the person is not going on a straight line
INPUTS:
- trc_path: path to the trc file
- gait_direction: tuple (sign, direction) with sign in {-1, 1} and direction in {'X', 'Y', 'Z'}
- forward_velocity_threshold: forward velocity below which the foot is considered to have touched the ground (m/s)
- filter_fs: butterworth filter cutoff frequency (Hz)
- markers: list of marker names in the following order: [right_toe_marker, left_toe_marker]
- plot: plot results or not (boolean)
OUTPUTS:
- t_Ron: list of right on times
- t_Lon: list of left on times
- t_Roff: list of right off times
- t_Loff: list of left off times
'''
# Retrieve gait direction
sign, direction = gait_direction
axis = ['X', 'Y', 'Z'].index(direction)
# Read trc file
Q_coords, _, time_col, trc_markers, header = read_trc(trc_path)
unit = header[2].split('\t')[4]
unit_factor = 1 if unit=='m' else 10 if unit=='dm' else 100 if unit=='cm' else 1000 if unit=='mm' else np.inf
forward_velocity_threshold *= unit_factor
Q_coords *= unit_factor
# Calculate speed
dt = time_col.diff().mean()
b, a = signal.butter(4/2, filter_fs*dt*2, 'low', analog=False)
X_speed = Q_coords.iloc[:,axis::3].diff()/dt
X_speed.columns = trc_markers
Rfoot_speed, Lfoot_speed = (X_speed[m] for m in markers)
Rfoot_speed = Rfoot_speed.where(Rfoot_speed<0, other=0) if sign==-1 else Rfoot_speed.where(Rfoot_speed>0, other=0)
Rfoot_speed = Rfoot_speed.abs()
# Rfoot_speed_filtered = pd.Series(signal.filtfilt(b, a, Rfoot_speed[1:]), name=Rfoot_speed.name)
Rfoot_speed_filtered = pd.Series(gaussian_filter1d(Rfoot_speed[1:], 5), name=Rfoot_speed.name)
Lfoot_speed = Lfoot_speed.where(Lfoot_speed<0, other=0) if sign==-1 else Lfoot_speed.where(Lfoot_speed>0, other=0)
Lfoot_speed = Lfoot_speed.abs()
# Lfoot_speed_filtered = pd.Series(signal.filtfilt(b, a, Lfoot_speed[1:]), name=Lfoot_speed.name)
Lfoot_speed_filtered = pd.Series(gaussian_filter1d(Lfoot_speed[1:], 5), name=Lfoot_speed.name)
# Find gait events
low_Rfoot_speed = Rfoot_speed_filtered<forward_velocity_threshold
frame_Ron, frame_Roff = start_end_true_seq(low_Rfoot_speed)
if 0 in frame_Ron: frame_Ron.remove(0)
t_Ron, t_Roff = time_col[frame_Ron].tolist(), time_col[frame_Roff].tolist()
low_Lfoot_speed = Lfoot_speed_filtered<forward_velocity_threshold
frame_Lon, frame_Loff = start_end_true_seq(low_Lfoot_speed)
if 0 in frame_Lon: frame_Lon.remove(0)
t_Lon, t_Loff = time_col[frame_Lon].tolist(), time_col[frame_Loff].tolist()
# Clean gait events
frame_Ron, frame_Lon, frame_Roff, frame_Loff = clean_gait_events((frame_Ron, frame_Lon, frame_Roff, frame_Loff))
t_Ron, t_Lon, t_Roff, t_Loff = clean_gait_events((t_Ron, t_Lon, t_Roff, t_Loff))
# Plot
if plot:
plt.plot(time_col[1:], Rfoot_speed_filtered, 'C0', label='Right foot speed filtered')
plt.plot(time_col[1:][frame_Ron], Rfoot_speed_filtered[frame_Ron], 'g+')
plt.plot(time_col[1:][frame_Roff], Rfoot_speed_filtered[frame_Roff], 'r+')
plt.plot(time_col[1:], Lfoot_speed_filtered, 'C1', label='Left foot speed filtered')
plt.plot(time_col[1:][frame_Lon], Lfoot_speed_filtered[frame_Lon], 'g+')
plt.plot(time_col[1:][frame_Loff], Lfoot_speed_filtered[frame_Loff], 'r+')
plt.title('Gait events')
plt.xlabel('Time (s)')
plt.ylabel('Speed (m/s)')
plt.legend()
plt.show()
print('Times:')
print('Right on:', t_Ron)
print('Right off:', t_Roff)
print('Left on:', t_Lon)
print('Left off:', t_Loff)
print('\nFrames:')
print('Right on:', frame_Ron)
print('Right off:', frame_Roff)
print('Left on:', frame_Lon)
print('Left off:', frame_Loff)
return (t_Ron, t_Lon, t_Roff, t_Loff), (frame_Ron, frame_Lon, frame_Roff, frame_Loff)
def trc_gaitevents_func(**args):
'''
Determine gait on and off from a TRC file of point coordinates.
Three available methods, each of them with their own pros and cons:
- "forward_coordinates":
on = max(XHeel - Xsacrum)
off = min(XToe - XSacrum)
++: Works well for walking (Zeni et al., 2008)
++: No argument nor tuning necessary
--: Not suitable for running
--: does not work if the person is not going on a straight line
- "height_coordinates":
on = YToe < height_threshold
off = YToe > height_threshold
++: Best results for running and walking
++: Works if the person is not going on a straight line
--: Does not work is the person is grazing the ground
--: Does not work if the field is not flat
--: height_threshold might need to be tuned
--: Heel point might be more accurate than toe point for walking
- "forward_velocity":
on = VToe < forward_velocity_threshold
off = VToe > forward_velocity_threshold
++: Works for running
--: More sensitive to noise
--: Tends to anticipate off if the marker is not at the tip of the toe
--: forward_velocity_threshold might need to be tuned
--: Does not work if the person is not going on a straight line
Usage:
List of available arguments:
python -m trc_gaitevents -h
import trc_gaitevents; trc_gaitevents.trc_gaitevents_func(trc_path=r'<input_trc_file>')
OR import trc_gaitevents; trc_gaitevents.trc_gaitevents_func(trc_path=r'<input_trc_file>', method='forward_coordinates', gait_direction='-X', plot=True, save_output=True, output_file='gaitevents.txt')
OR import trc_gaitevents; trc_gaitevents.trc_gaitevents_func(trc_path=r'<input_trc_file>', method='height_coordinates', up_direction='Y', height_threshold=6, right_toe_marker='RBigToe', left_toe_marker='LBigToe')
OR import trc_gaitevents; trc_gaitevents.trc_gaitevents_func(trc_path=r'<input_trc_file>', method='forward_velocity', gait_direction='-Z', forward_velocity_threshold=1, right_toe_marker='RBigToe', left_toe_marker='LBigToe')
python -m trc_gaitevents -i input_trc_file
OR python -m trc_gaitevents -i input_trc_file --method forward_coordinates --gait_direction=-X --plot True --save_output True --output_file gaitevents.txt
OR python -m trc_gaitevents -i input_trc_file --method height_coordinates --up_direction=Y --height_threshold 6 --right_toe_marker RBigToe --left_toe_marker LBigToe
OR python -m trc_gaitevents -i input_trc_file --method forward_velocity --gait_direction=-Z --forward_velocity_threshold 1 --right_toe_marker RBigToe --left_toe_marker LBigToe
'''
# Retrieve arguments
trc_path = args.get('trc_path')
gait_direction = args.get('gait_direction')
up_direction = args.get('up_direction')
method = args.get('method')
forward_velocity_threshold = args.get('forward_velocity_threshold')
height_threshold = args.get('height_threshold')
sacrum_marker = args.get('sacrum_marker')
right_heel_marker = args.get('right_heel_marker')
right_toe_marker = args.get('right_toe_marker')
left_heel_marker = args.get('left_heel_marker')
left_toe_marker = args.get('left_toe_marker')
plot = args.get('plot')
save_output = args.get('save_output')
output_file = args.get('output_file')
filter_fs = 6
# If invoked via a function
if gait_direction == None: gait_direction = '+X'
if up_direction == None: up_direction = '+Y'
if method == None: method = 'height_coordinates'
if forward_velocity_threshold == None: forward_velocity_threshold = 1
if height_threshold == None: height_threshold = 6
if sacrum_marker == None: sacrum_marker = 'Hip'
if right_heel_marker == None: right_heel_marker = 'RHeel'
if right_toe_marker == None: right_toe_marker = 'RBigToe'
if left_heel_marker == None: left_heel_marker = 'LHeel'
if left_toe_marker == None: left_toe_marker = 'LBigToe'
if plot == None: plot = True
if save_output == None: save_output = True
if output_file == None: output_file = 'gaitevents.txt'
# In case of a sign in direction (eg -X)
if len(gait_direction)==1:
gait_direction = +1, gait_direction
elif len(gait_direction)==2:
gait_direction = int(gait_direction[0]+'1'), gait_direction[1]
if len(up_direction)==1:
up_direction = +1, up_direction
elif len(up_direction)==2:
up_direction = int(up_direction[0]+'1'), up_direction
if method not in ['forward_coordinates', 'height_coordinates', 'forward_velocity']:
raise ValueError('Method must be "forward_coordinates", "height_coordinates", or "forward_velocity"')
# Retrieve gait events
if method == 'forward_coordinates':
print('Method: forward_coordinates')
markers = [right_heel_marker, right_toe_marker, left_heel_marker, left_toe_marker, sacrum_marker]
(t_Ron, t_Lon, t_Roff, t_Loff), (frame_Ron, frame_Lon, frame_Roff, frame_Loff) \
= gait_events_fwd_coords(trc_path, gait_direction, markers=markers, plot=plot)
elif method == 'height_coordinates':
print(f'Method: height_coordinates. Height threshold: {height_threshold} cm')
markers = [right_toe_marker, left_toe_marker]
(t_Ron, t_Lon, t_Roff, t_Loff), (frame_Ron, frame_Lon, frame_Roff, frame_Loff) \
= gait_events_height_coords(trc_path, up_direction, height_threshold=height_threshold, filter_fs=filter_fs, markers=markers, plot=plot)
elif method == 'forward_velocity':
print(f'Method: forward_velocity. Forward velocity threshold: {forward_velocity_threshold} m/s')
markers = [right_toe_marker, left_toe_marker]
(t_Ron, t_Lon, t_Roff, t_Loff), (frame_Ron, frame_Lon, frame_Roff, frame_Loff) \
= gait_events_fwd_vel(trc_path, gait_direction, forward_velocity_threshold=forward_velocity_threshold, filter_fs=filter_fs, markers=markers, plot=plot)
if save_output or save_output==None:
trc_dir = os.path.dirname(trc_path)
trc_name = os.path.basename(trc_path)
if output_file == None: output_file = 'gaitevents.txt'
with open(os.path.join(trc_dir, output_file), 'a') as gaitevents:
L = trc_name + '\n'
L += f'Method: {method}. '
L+= f'Height threshold: {height_threshold}\n' if method=='height_coordinates' else f'Forward velovity threshold: {forward_velocity_threshold}\n' if method == 'forward_velocity' else '\n'
L += 'Times:\n'
L += '\tRight on: ' + str(t_Ron) + '\n'
L += '\tLeft on: ' + str(t_Lon) + '\n'
L += '\tRight off: ' + str(t_Roff) + '\n'
L += '\tLeft off: ' + str(t_Loff) + '\n'
L += 'Frames:\n'
L += '\tRight on: ' + str(frame_Ron) + '\n'
L += '\tLeft on: ' + str(frame_Lon) + '\n'
L += '\tRight off: ' + str(frame_Roff) + '\n'
L += '\tLeft off: ' + str(frame_Loff) + '\n\n'
gaitevents.write(L)
return (t_Ron, t_Lon, t_Roff, t_Loff), (frame_Ron, frame_Lon, frame_Roff, frame_Loff)
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Determine gait on and off with "forward_coordinates", "height_coordinates", or "forward_velocity" method. More details in the file description.')
parser.add_argument('-i', '--trc_path', required = True, help='Trc input file')
parser.add_argument('-g', '--gait_direction', default = 'X', required = False, help='Direction of the gait. "X", "Y", "Z", "-X", "-Y", or "-Z". Default: "X". Requires an equal sign if negative, eg -g=-X')
parser.add_argument('-u', '--up_direction', default = 'Y', required = False, help='Up direction. "X", "Y", or "Z", "-X", "-Y", or "-Z". Default: "Y"')
parser.add_argument('-m', '--method', default = 'height_coordinates', required = False, help='Method to determine gait events. "forward_coordinates", "height_coordinates", or "forward_velocity". Default:"height_coordinates"')
parser.add_argument('-V', '--forward_velocity_threshold', default = 1, type=float, required = False, help='Forward velocity below which the foot is considered to have touched the ground (m/s). Used if method is forward_velocity. Default: 1.5')
parser.add_argument('-H', '--height_threshold', default = 6, type=float, required = False, help='Height below which the foot is considered to have touched the ground (cm). Used if method is height_coordinates. Default: 6')
parser.add_argument('--sacrum_marker', default = 'Hip', required = False, help='Hip marker name. Default: "Hip"')
parser.add_argument('--right_heel_marker', default = 'RHeel', required = False, help='Right heel marker name. Default: "RHeel"')
parser.add_argument('--right_toe_marker', default = 'RBigToe', required = False, help='Right toe marker name. Default: "RBigToe"')
parser.add_argument('--left_heel_marker', default = 'LHeel', required = False, help='Left heel marker name. Default: "LHeel"')
parser.add_argument('--left_toe_marker', default = 'LBigToe', required = False, help='Left toe marker name. Default: "LBigToe"')
parser.add_argument('-p', '--plot', default = True, required = False, help='Plot results. Default: True')
parser.add_argument('-s', '--save_output', default = True, required = False, help='Save output in csv file. Default: True')
parser.add_argument('-o', '--output_file', default = 'gaitevents.txt', required = False, help='Output file name. Default: "gaitevents.txt"')
args = vars(parser.parse_args())
trc_gaitevents_func(**args)