teruyuki-yamasaki / helloopensim

helloOpenSim

hello OpenColab

package installation

#@title Step 1: Install OpenSim package from link above & other dependency packages
import time
start_time = time.time()
!pip uninstall -y -q plotly; pip install -q plotly
!pip uninstall -y -q pandas; pip install -q pandas
import pandas as pd 
import plotly
pd.set_option('plotting.backend','plotly')
def enable_plotly_in_cell():
    import IPython
    from plotly.offline import init_notebook_mode
    display(IPython.core.display.HTML('''<script src="/static/components/requirejs/require.js"></script>'''))
    init_notebook_mode(connected=False)
get_ipython().events.register('pre_run_cell', enable_plotly_in_cell)
!wget -c https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.3-Linux-x86_64.sh
!chmod +x Miniconda3-py37_4.8.3-Linux-x86_64.sh
!bash ./Miniconda3-py37_4.8.3-Linux-x86_64.sh -b -f -p /usr/local
import sys
sys.path.append('/usr/local/lib/python3.7/site-packages')
!conda install -y --prefix /usr/local -c ember123 opencolab
!apt-get update -y
!apt-get install -y x11-apps
!apt install mesa-utils 
!apt-get install xvfb x11-utils
!pip install pyvirtualdisplay
from pyvirtualdisplay import Display
Display(visible=0, size=(1400, 900)).start()
!pip install c3d
!pip install numpy --upgrade
!pip install -q --upgrade ipython
!pip install -q --upgrade ipykernel
!pip install tensorflow==2.0.0.alpha0
!conda install -c plotly -y plotly-orca
!pip install svgutils
!apt install libadolc2
!apt-get install coinor-libipopt-dev 
import opensim as osim
print('OpenSim Version Installed is version:',osim.__version__)
print(f'The execution time of OpenSim Package Installation is {(time.time() - start_time)} sec')

#@title Step 2: Let's import dataset from 5 GitHub URLs
# OpenSim models etc from github
 
!git clone https://github.com/opensim-org/opensim-models.git # models needed
!git clone https://github.com/HernandezVincent/OpenSim.git  # models needed
!cp /content/opensim-models/Models/Gait2354_Simbody/* /content/opensim-models/Pipelines/Gait2354_Simbody
!git clone https://github.com/ESJiang/2354_xml.git
!cp -rf /content/2354_xml/* /content/opensim-models/Pipelines/Gait2354_Simbody
!git clone https://github.com/ESJiang/2354_result.git
!git clone https://github.com/ESJiang/testc3d.git

#@title **`7 useful functions for plotting `** (Mandatory)
#- by Fangwei: feel free to reuse my functions for other opensim model analysis` (mandatory for generating all the data and do plotting in this notebook)**
#this is right foot off timing!
from linecache import getline
import plotly.graph_objects as go
from plotly.subplots import make_subplots
from matplotlib import pyplot
import numpy as np 
import cv2

#dash='dashdot'
#mode="lines"

def find_nearest_element(time, start, end):
    print(min(time, key=lambda x: abs(x-Decimal(start))))
    print(time.index(min(time, key=lambda x: abs(x-Decimal(start)))))
    print(min(time, key=lambda x: abs(x-Decimal(end))))
    print(time.index(min(time, key=lambda x: abs(x-Decimal(end)))))
    print((min(time, key=lambda x: abs(x-Decimal(1.840)))+min(time, key=lambda x: abs(x-Decimal(0.600))))/2)
    print(time.index(min(time, key=lambda x: abs(x-(min(time, key=lambda x: abs(x-Decimal(end)))+min(time, key=lambda x: abs(x-Decimal(start))))/2))))
 
def judge_line_number(path):
    count = 1
    f = open(path,"r")
    line = f.readline()
    while line!="":
        s=line[:4]
        if s.upper()=="time".upper():
          return count
        else:
          count = count + 1
          line = f.readline()
 
def generate_dict(path):
    def sto_Getline(path):
      return getline(path, judge_line_number(path)).strip('\n').split()
    for each in dict(zip(sto_Getline(path), range(0,len(sto_Getline(path))))):
      print(each, ':', dict(zip(sto_Getline(path), range(0,len(sto_Getline(path)))))[each])

def three(fig, y1, y1_name, y2, y2_name, y3, y3_name, title):
    fig.add_trace(go.Scatter(x=time_5, y=y1, name=y1_name, mode="lines",
                         line=dict(color='red', width=0.5, dash='solid')))
    fig.add_trace(go.Scatter(x=time_10, y=y2, name=y2_name, mode="lines",
                         line=dict(color='blue', width=0.5, dash='solid')))
    fig.add_trace(go.Scatter(x=time_20, y=y3, name=y3_name, mode="lines",
                         line=dict(color='green', width=0.5, dash='solid')))
    fig.update_layout(title='<b>'+title+'<b>', xaxis_title='time', yaxis_title='value',font=dict(
        family="Courier New, monospace",
        size=24,
        #color="RebeccaPurple"
    ))
    fig.show()

def four(fig, x, y1, y1_name, y2, y2_name, y3, y3_name, y4, y4_name, title, fig_name):
    fig.add_trace(go.Scatter(x=x, y=y1, name=y1_name, mode="lines",
                         line=dict(color='black', width=2, dash='solid')))
    fig.add_trace(go.Scatter(x=x, y=y2, name=y2_name, mode="lines",
                         line=dict(color='grey', width=2, dash='solid')))
    fig.add_trace(go.Scatter(x=x, y=y3, name=y3_name, mode="lines",
                         line=dict(color='black', width=2, dash='dash')))
    fig.add_trace(go.Scatter(x=x, y=y4, name=y4_name, mode="lines",
                         line = dict(color='grey', width=2, dash='dash')))
    fig.update_layout(title={
    'text': '<b>'+title+'<b>',
    'y': 0.9,
    'x': 0.5,
    'xanchor': 'center',
    'yanchor': 'top'}, xaxis_title='time', yaxis_title='value',font=dict(
        family="Courier New, monospace",
        size=24), template="simple_white"
        )
    
r_FO = 1.43 #@param {type:"number"}

def four_IDTool(fig, x, y1, y1_name, y2, y2_name, y3, y3_name, y4, y4_name, title, fig_name):
    fig.add_trace(go.Scatter(x=x, y=y1, name=y1_name, mode="lines",
                         line=dict(color='black', width=2, dash='solid')))
    fig.add_trace(go.Scatter(x=x, y=y2, name=y2_name, mode="lines",
                         line=dict(color='grey', width=2, dash='solid')))
    fig.add_trace(go.Scatter(x=x, y=y3, name=y3_name, mode="lines",
                         line=dict(color='black', width=2, dash='dash')))
    fig.add_trace(go.Scatter(x=x, y=y4, name=y4_name, mode="lines",
                         line = dict(color='grey', width=2, dash='dash')))
    fig.add_vline(x=r_FO, annotation_position="top",annotation_text="r_FO", line_width=2, line_dash="dash", line_color="red")
    #fig.add_vline(x=0.308, annotation_position="bottom",annotation_text="l_FO", line_width=1, line_dash="dash", line_color="blue")
    #fig.add_vline(x=0.888, annotation_position="top",annotation_text="l-FS", line_width=1, line_dash="dash", line_color="red")
    #fig.add_vline(x=0.918, annotation_position="bottom",annotation_text="r_FO", line_width=1, line_dash="dash", line_color="blue")
    fig.update_layout(title={
    'text': '<b>'+title+'<b>',
    'y': 0.95,
    'x': 0.5,
    'xanchor': 'center',
    'yanchor': 'top'}, yaxis_title='value',font=dict(
        family="Courier New, monospace",
        size=24), template="simple_white"
        )

def six(fig, x, y1, y1_name, y2, y2_name, y3, y3_name, y4, y4_name, y5, y5_name, y6, y6_name, title, fig_name):
    fig.add_trace(go.Scatter(x=x, y=y1, name=y1_name, mode="lines",
                            line=dict(color='black', width=2, dash='solid')))
    fig.add_trace(go.Scatter(x=x, y=y2, name=y2_name, mode="lines",
                            line=dict(color='grey', width=2, dash='solid')))
    fig.add_trace(go.Scatter(x=x, y=y3, name=y3_name, mode="lines",
                            line=dict(color='black', width=2, dash='solid')))
    fig.add_trace(go.Scatter(x=x, y=y4, name=y4_name, mode="lines",
                            line = dict(color='grey', width=2, dash='solid')))
    fig.add_trace(go.Scatter(x=x, y=y5, name=y5_name, mode="lines",
                            line=dict(color='black', width=2, dash='solid')))
    fig.add_trace(go.Scatter(x=x, y=y6, name=y6_name, mode="lines",
                            line = dict(color='grey', width=2, dash='solid')))
    fig.update_layout(title='<b>'+title+'<b>', xaxis_title='time', yaxis_title='value',font=dict(
        family="Courier New, monospace",
        size=24,
        #color="RebeccaPurple"
    ))
    fig.show()
    fig.write_image(fig_name)

logs

• 20220410 osim_walk_jnp.py