-
Notifications
You must be signed in to change notification settings - Fork 46
/
trc_plot.py
166 lines (129 loc) · 4.63 KB
/
trc_plot.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
##################################################
## Plot TRC files ##
##################################################
Display each point of a TRC file in a different matplotlib tab.
Usage:
from Pose2Sim.Utilities import trc_plot; trc_plot.trc_plot_func(r'<input_trc_file>')
OR python -m trc_plot -i input_trc_file
'''
## INIT
import pandas as pd
import sys
import matplotlib.pyplot as plt
import matplotlib as mpl
mpl.use('qt5agg')
mpl.rc('figure', max_open_warning=0)
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar
from PyQt5.QtWidgets import QMainWindow, QApplication, QWidget, QTabWidget, QVBoxLayout
from scipy import signal
from scipy.ndimage import gaussian_filter1d
from statsmodels.nonparametric.smoothers_lowess import lowess
import argparse
## 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"
## CLASSES
class plotWindow():
'''
Display several figures in tabs
Taken from https://github.com/superjax/plotWindow/blob/master/plotWindow.py
USAGE:
pw = plotWindow()
f = plt.figure()
plt.plot(x1, y1)
pw.addPlot("1", f)
f = plt.figure()
plt.plot(x2, y2)
pw.addPlot("2", f)
'''
def __init__(self, parent=None):
self.app = QApplication(sys.argv)
self.MainWindow = QMainWindow()
self.MainWindow.__init__()
self.MainWindow.setWindowTitle("Multitabs figure")
self.canvases = []
self.figure_handles = []
self.toolbar_handles = []
self.tab_handles = []
self.current_window = -1
self.tabs = QTabWidget()
self.MainWindow.setCentralWidget(self.tabs)
self.MainWindow.resize(1280, 720)
self.MainWindow.show()
def addPlot(self, title, figure):
new_tab = QWidget()
layout = QVBoxLayout()
new_tab.setLayout(layout)
figure.subplots_adjust(left=0.1, right=0.99, bottom=0.1, top=0.91, wspace=0.2, hspace=0.2)
new_canvas = FigureCanvas(figure)
new_toolbar = NavigationToolbar(new_canvas, new_tab)
layout.addWidget(new_canvas)
layout.addWidget(new_toolbar)
self.tabs.addTab(new_tab, title)
self.toolbar_handles.append(new_toolbar)
self.canvases.append(new_canvas)
self.figure_handles.append(figure)
self.tab_handles.append(new_tab)
def show(self):
self.app.exec_()
## FUNCTIONS
def display_figures_fun(Q, time_col, keypoints_names):
'''
Displays filtered and unfiltered data for comparison
INPUTS:
- Q: pandas dataframe of 3D coordinates
- time_col: pandas column
- keypoints_names: list of strings
OUTPUT:
- matplotlib window with tabbed figures for each keypoint
'''
pw = plotWindow()
for id, keypoint in enumerate(keypoints_names):
f = plt.figure()
axX = plt.subplot(311)
plt.plot(time_col, Q.iloc[:,id*3])
plt.setp(axX.get_xticklabels(), visible=False)
axX.set_ylabel(keypoint+' X')
axY = plt.subplot(312)
plt.plot(time_col, Q.iloc[:,id*3+1])
plt.setp(axY.get_xticklabels(), visible=False)
axY.set_ylabel(keypoint+' Y')
axZ = plt.subplot(313)
plt.plot(time_col, Q.iloc[:,id*3+2])
axZ.set_ylabel(keypoint+' Z')
axZ.set_xlabel('Time')
pw.addPlot(keypoint, f)
pw.show()
def trc_plot_func(*args):
'''
Plot trc files.
Usage:
import trc_plot; trc_plot.trc_plot_func(r'<input_trc_file>')
OR trc_plot -i input_trc_file
'''
try:
trc_path = args[0].get('input_file') # invoked with argparse
except:
trc_path = args[0] # invoked as a function
# Read trc coordinates values
trc_df = pd.read_csv(trc_path, sep="\t", skiprows=4)
time_col =trc_df.iloc[:,1]
Q_coord = trc_df.drop(trc_df.columns[[0, 1]], axis=1)
# Display figures
keypoints_names = pd.read_csv(trc_path, sep="\t", skiprows=3, nrows=0).columns[2::3].tolist()
display_figures_fun(Q_coord, time_col, keypoints_names)
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('-i', '--input_file', required = True, help='trc input file')
args = vars(parser.parse_args())
trc_plot_func(args)