Running Joint Reaction Analysis using Python

[Ali Tlisov]

Hi!

I'm trying to script JRA with Python.

First I noticed there are 2 different pythons used. OpenSim uses Jython that comes with it. Also one can use system's python (CPython) but I had to compile GitHub version of opensim-core in order to make my (anaconda) python able to import opensim.

Then I noticed difference in API for 2 versions of python.

In python a have to do

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import opensim

while in python I have to use already imported

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modelling

instance.

Than I adapted JRA script from this GitHub issue. My script is as follows. I tried to make it work both with Opensim's Jython and Python.

Also I used this model from OpenSim downloads.

Now running the script in python I get following error

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Updating Model file from 20302 to latest format...
Loaded model subject01 from file /Users/ali/Documents/OpenSim/JRA/subject01_simbody_adjusted.osim
Storage: read data file =/Users/ali/Documents/OpenSim/JRA/subject01_walk1_Kinematics.sto (nr=1500 nc=24)
IO.OpenInputFile(const string&,openmode mode): failed to open 
Traceback (most recent call last):
  File "jra.py", line 76, in <module>
    perform_jra(JRA_MODEL, JRA_KINEMATICS, JRA_JRF, JRA_JRF_XML, JRA_RESERVE_ACTUATORS, JRA_MUSCLE, JRA_RESULTS_DIR)
  File "jra.py", line 74, in perform_jra
    analysis.run()
  File "/Users/ali/miniconda3/envs/opensim/lib/python2.7/site-packages/opensim-4.0-py2.7.egg/opensim/tools.py", line 8730, in run
    return _tools.AnalyzeTool_run(self, *args)
RuntimeError: std::exception in 'bool OpenSim::AnalyzeTool::run()': Storage: Failed to open file ''. Verify that the file exists at the specified location.
	Thrown at Storage.cpp:181 in Storage().

While I'm pretty sure all paths are correct and I'm explicitly checking them for correctness.

Running the same in Juthon it fails earlier:

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Traceback (most recent call last):
  File "/Users/ali/Documents/OpenSim/jra.py", line 76, in <module>
    perform_jra(JRA_MODEL, JRA_KINEMATICS, JRA_JRF, JRA_JRF_XML, JRA_RESERVE_ACTUATORS, JRA_MUSCLE, JRA_RESULTS_DIR)
  File "/Users/ali/Documents/OpenSim/jra.py", line 40, in perform_jra
    external_loads = modeling.ExternalLoads(model, grf_xml)
	at org.opensim.modeling.opensimSimulationJNI.new_ExternalLoads__SWIG_3(Native Method)
	at org.opensim.modeling.ExternalLoads.<init>(ExternalLoads.java:73)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
	at org.python.core.PyReflectedConstructor.constructProxy(PyReflectedConstructor.java:210)

java.lang.NullPointerException: java.lang.NullPointerException: OpenSim::Model & reference is null