How to convert .c3d to .mot and .trc in python

[corrine bao]

Hello,

I checked this link https://simtk-confluence.stanford.edu:8 ... d%29+Files, in which .c3d can be written into two .sto files using python.

I know that MATLAB can convert .c3d to .mot and .trc files, is it possible to do so in python? If so, does anyone have any examples?

Many thanks,

[Dimitar Stanev]

Hi,

I am attaching a script and some utility functions that I use in Python. Please note that some settings (rotation, mirror) should be changed to correspond to your lab's coordinate system.

scripts.zip

(7.21 KiB) Downloaded 62 times

[Mohammadreza Rezaie]

scripts.zip

Hi Dimitar,

Many thanks for sharing these scripts.
Do you have any solution for python 3.7 (OpenSim 4.1)?
It seems that the BTK package has been only developed for python 2.7.

Cheers

[Dimitar Stanev]

These should work with Python 3.7. Actually btk and any related functions can be removed from utils.py. I do some additional processing of c3d that is currently not supported in OpenSim. By the way I had a PR on btk so that it can be build with Python 3:

https://github.com/Biomechanical-ToolKi ... re/pull/29

[Kenneth Smale]

Hi,

I am attaching a script and some utility functions that I use in Python. Please note that some settings (rotation, mirror) should be changed to correspond to your lab's coordinate system.

scripts.zip

Hi @Dimitar,

I've set up python 3.7 and OpenSim 4.1 in my Anaconda-Spyder environment. When I try to read my c3d file through the adapter, I get the following error:

Code: Select all

static = adapter.read(os.path.join(c3d_dir, static_file), 1)
Traceback (most recent call last):

  File "<ipython-input-73-526983ac6a6d>", line 1, in <module>
    static = adapter.read(os.path.join(c3d_dir, static_file), 1)

TypeError: read() takes 2 positional arguments but 3 were given

This error is confusing because I believe I'm only passing two arguments (full file name, and 1) so I'm not sure what the issue is. If I simply pass the file path and name to adapter.read, it passes without error but my datatype is "common.StdMapStringAbstractDataTable", which I believe causes problems later on when trying rotate_data_table.

Any idea where I'm going awry here?

[Ayman Habib]

Hello,

Here's an example from our code base (version 4.2 (beta))
https://github.com/opensim-org/opensim- ... ter.py#L33

Hope this helps,
Ayman

[Mohammadreza Rezaie]

Hi Kenneth,

First, I would like to thank Dr. Dimitar Stanev for sharing the scripts.

BTK can be installed in python 3.x via this conda distribution:

Code: Select all

conda install -c conda-forge btk

Regarding the error, please add this line before "static":

Code: Select all

adapter.setLocationForForceExpression(opensim.C3DFileAdapter.ForceLocation_CenterOfPressure)

and modify the "static" to:

Code: Select all

static = adapter.read(os.path.join(c3d_dir, static_file))

You can find more info here:
https://simtk.org/api_docs/opensim/api_ ... apter.html

Hope this helps.

Regards,
Mohammadreza