MATLAB Scripting: Inverse Kinematics Marker Error & RMS

[Justin Wager]

Hi,

I have MATLAB calling the IK tool successfully, but was wondering if there is a command to return the marker error and RMS values that are normally returned in the "Messages" window. I don't see anything that looks to be of use in the methods list.

Thanks,
Justin

[Luca Modenese]

Hi Justin,

calling the dos command in Matlab with '-echo' option should work:

Code: Select all

[status, log_mes]=dos('IK -S IK_Setup_file.xml','-echo');

I hope this helps,

Luca

[Justin Wager]

Thanks Luca, that did the trick. For anyone else using this command for the first time, make sure that your setup file (.xml) and model file (.osim) are in your working directory or specified with the full path.

Also, "IK" in the command is case sensitive, so if it is in your [InstallDir]/bin as "ik", you must use "ik" in the command.
The "-echo" turned out to be unnecessary as the dos command returns the error values in the log_mes variable.

Code: Select all

[status, log_mes]=dos('ik -S IK_Setup_file.xml');

Thanks again, Luca.

Justin

[ANDREW LAPRE]

Hi,

I'm currently running batch ik processing as given in the examples and it runs great. I'm having a problem getting the marker error and rms to show up to the command window. Using the dos command as described, leaves me with this error:

InverseKinematicsTool Failed: Object: ERR- Could not open file Unassigned. It may not exist or you don't have permission to read it.
Exception in IK: InverseKinematicsTool Failed, please see messages window for details...

Any ideas? I've tried to change the directories I have it in, with no luck. Ideally I need to save the error and rms to a file, but this is the first step.

Any help would be appreciated.
Thanks
-Andy

[Justin Wager]

Hey Andy,

It's been some time since I worked with the batch IK, but I remember getting this error a number of times. If you want to send the code you're using to setup the IK Tool, I am happy to take a quick look to see if I can spot the error. Feel free to email/PM me if you want.

Justin

[Matteo Arquilla]

Hi everybody,

I am trying and run the IK tool from cmd in windows and/or from Matlab and extract the OpenSim output message with marker errors.
I have exactly the same problem as Andrew, i.e. the following error:

InverseKinematicsTool Failed: Object: ERR- Could not open file Unassigned. It may not exist or you don't have permission to read it.
Exception in IK: InverseKinematicsTool Failed, please see messages window for details...

Could you finally manage to solve the issue?

Thanks in advance for your support.

Best,
Matteo

[Dimitar Stanev]

The model path is not correct. You can check the log file and see the path that IK uses and correct it accordingly in your xml.

[Samuel Hybois]

Hello everyone,

I am also trying to compute errors between experimental/IK-positioned markers, but I would like to get more than the "total squared error / RMS and max marker errors" that the 'echo' option computes at each frame.
That is why I would like to know if some of you managed to store (as IK output) the calculated position of markers from IK (that must be computed in the IK algorithm since the GUI allows to visualize IK results with markers..).
This topic was addressed here (viewtopicPhpbb.php?f=91&t=2094) but I did not manage to make it work because I do not know how to specify the output storage file of the <IKTrial> option.

Did anyone already face this issue ?

Thanks for your help,

Samuel

[Dimitar Stanev]

You can try the attached code. If you are not using c++ API, then you should port the code as an analysis plugin.

[Samuel Hybois]

Thanks a lot for your quick answer !

Actually I am not using C++ API, only running the OS tools from Matlab. I have to admit that I am not familiar with C++.. Do I have to build a .dll library from the files you sent, in order to use it as plug-in ? Is there a particular procedure to do so ?