Scaling tool fails at "placing markers on model"

[Dominik Hoelbling]

Hello

I'm a new user of opensim, so maybe the answer to my question could be very easy to you.
I have some Vicon PlugInGate data, which I converted using the LeeSon Toolbox.
When I now display the experimental Data it looks fine.

I use the PlugInGait model from Tim Dorn, added his marker model after opening and also corrected a few marker position (FIN; Toe) and added the RBAK marker, which was not included. Afterwards I adapted the posture of the model (which was completely dislocated in the default) to the T-Pose.

The display of my experimental data looks from the static trial (and from the dynamic trial) looks good.

Then I tried to scale the model.
I added all information shown in https://www.youtube.com/watch?v=V5f7OMkfRBs
If I run the procedure and look in the messages it doesn't continue after:
Step 3: Placing markers on model

Does anyone know what the problem is?

Best regards,

Dominik

[Renee Degutis]

Hello

I'm a new user of opensim, so maybe the answer to my question could be very easy to you.
I have some Vicon PlugInGate data, which I converted using the LeeSon Toolbox.
When I now display the experimental Data it looks fine.

I use the PlugInGait model from Tim Dorn, added his marker model after opening and also corrected a few marker position (FIN; Toe) and added the RBAK marker, which was not included. Afterwards I adapted the posture of the model (which was completely dislocated in the default) to the T-Pose.

The display of my experimental data looks from the static trial (and from the dynamic trial) looks good.

Then I tried to scale the model.
I added all information shown in https://www.youtube.com/watch?v=V5f7OMkfRBs
If I run the procedure and look in the messages it doesn't continue after:
Step 3: Placing markers on model

Does anyone know what the problem is?

Best regards,

Dominik

Hello,

I have the issue with the step 3 - shows executing scaling, however it is stuck and the process is not completed (OpenSim 4.0). It is ok with OpenSim 3.3 though. Should I check the GUI panels perhaps? Can the issue be with the vtp files?

Regards,
Renee Degutis

[jimmy d]

Are you seeing a red circle in the bottom right-hand corner of the OpenSim GUI? We have seen this issue once or twice and there has been an error message (red circle) shown. If you click the red circle you should be able to let us know what the error is?

It is not likely that it is the VTP files. More likely is that there is an issue with the TRC File and the MarkerPlacer() function in the ScaleTool can't deal with it. OpenSim 4.0 is stricter with some of the file formating.

[jimmy d]

Attached is a script that attempts to extract the data and marker names out of a TRC and rewrites it to file using the OpenSim 4.0 API, thereby ensuring that it will be readable by 4.0.

The script will generate a new file in the same directory as the input trc, with a '_fixed.trc' appended. If you can run try and run it on the trc file you are using for scaling, then reattempt to scale using the trc output file and let me know how it goes?

-J

[Dominik Hoelbling]

Are you seeing a red circle in the bottom right-hand corner of the OpenSim GUI?

Yes, there is an error message:

Code: Select all

java.lang.RuntimeException: Error reading MetaData in file 'C:\Daten\Dissertation\A Dissertation\Visual 3D Article\Muskoloskeletal model\Trials\Static\Static.trc'. Unexpected key. Expected = OrigDataStartFrame. Received = OrigDataStarFrame.
	Thrown at trcfileadapter.cpp:90 in extendRead().
	at org.opensim.modeling.opensimActuatorsAnalysesToolsJNI.OpenSimContext_processModelMarkerPlacer__SWIG_0(Native Method)
	at org.opensim.modeling.OpenSimContext.processModelMarkerPlacer(OpenSimContext.java:305)
	at org.opensim.tracking.ScaleToolModel$ScaleToolWorker.construct(ScaleToolModel.java:349)
	at org.opensim.swingui.SwingWorker$2.run(SwingWorker.java:130)
[catch] at java.lang.Thread.run(Thread.java:748)

So the file fixer should work, I guess?

[jimmy d]

OrigDataStartFrame. Received = OrigDataStarFrame.

You can try and fix the TRC File by addressing the error above. You would do this by;
(i) Opening the TRC file in a text editor (like Notepad++, TextEdit, Sublime, or Atom)
(ii) Edit OrigDataStarFrame to OrigDataStartFrame
(iii) Resave the TRC file.

There may be other small mistakes in the TRC file that will no longer pass since 4.0 is a lot stricter on the format.

If you are comfortable with Matlab, then you should try the script. If it works and prints a file, the new TRC file is guaranteed to work since the TRCFileAdapter() writes the file.

[Dominik Hoelbling]

Thank you very much.

Unfortunatly, now I have a different problem.
I attached the TRC file, maybe you can find a solution?

java.lang.RuntimeException: Invalid time range: initial time 17.066700 >= final time = 1.408330
Thrown at timeseriestable.h:377 in averageRow().
at org.opensim.modeling.opensimActuatorsAnalysesToolsJNI.OpenSimContext_processModelMarkerPlacer__SWIG_0(Native Method)
at org.opensim.modeling.OpenSimContext.processModelMarkerPlacer(OpenSimContext.java:305)
at org.opensim.tracking.ScaleToolModel$ScaleToolWorker.construct(ScaleToolModel.java:349)
at org.opensim.swingui.SwingWorker$2.run(SwingWorker.java:130)
[catch] at java.lang.Thread.run(Thread.java:748)

[Thomas Uchida]

I attached the TRC file, maybe you can find a solution?

The file does not appear to be in the correct format (e.g., there is no Time column and a second table begins on row 111). Please see the "Marker (.trc) Files" page in the Confluence documentation: https://simtk-confluence.stanford.edu/d ... c%29+Files.

[Sandra Shefelbine]

I have been using the arm26_elbow_flex.trc for a class homework assignment for the past 14 years. Suddenly with OpenSim 4.0 it does not work anymore. It seems that the .trc file is not the correct format for OpenSim 4.0? I was unable to run the TRCFileFixer.m. Can you please fix this .trc for me?

Many thanks

[jimmy d]

Sandra- The arm26_elbow_flex.trc file distributed with 4.0 seems to open fine on our test machines. Are you using an older version of the file or the one distributed with 4.0?

-j