Dealing with nan in ..._filt_<filter>.trc causing condition 'convertOk' not met during kinematics

[jtoerber]

Hi,
I have 2 Cameras. One of the camera could see my right small toe all of the time, the other not.
So after FIltering I have nan in the trc-File for the corresponding Landmark/Keypoint.
When I do Inverse Kinematics to get the angles, I get an error message:

Pose2Sim.kinematics()
  File "C:\Users\toerberj\.conda\envs\Pose2Sim\lib\site-packages\Pose2Sim\Pose2Sim.py", line 505, in kinematics
    kinematics(config_dict)
  File "C:\Users\toerberj\.conda\envs\Pose2Sim\lib\site-packages\Pose2Sim\kinematics.py", line 627, in kinematics
    perform_scaling(trc_file, kinematics_dir, osim_setup_dir, model_name, right_left_symmetry=right_left_symmetry, subject_height=subject_height[p], subject_mass=subject_mass[p], remove_scaling_setup=remove_scaling_setup)
  File "C:\Users\toerberj\.conda\envs\Pose2Sim\lib\site-packages\Pose2Sim\kinematics.py", line 476, in perform_scaling
    opensim.ScaleTool(scaling_path_temp).run()
  File "C:\Users\toerberj\.conda\envs\Pose2Sim\lib\opensim\tools.py", line 2220, in __init__
    _tools.ScaleTool_swiginit(self, _tools.new_ScaleTool(*args))
RuntimeError: std::exception in 'OpenSim::ScaleTool::ScaleTool(std::string const &)': SimTK Exception thrown at String.h:466:
  Error detected by Simbody method String::convertTo(): Couldn't interpret string 'inf inf inf' as type T=SimTK::Array_.
  (Required condition 'convertOK' was not met.)

Lowering the thresholds did not work.
I am not able to work with more than two Cameras as they need high FPS (>=100) in my case.
In this specific case I am able to adjust the positions of the cameras.
But, in another case I want to track arm and fingers and it will happen that there are gaps, which are even larger than (large) interp_if_gap_smaller_than-Parameter, especially for landmarks/keypoints, which are in a specific case not interesting.
How am I able to get InverseKinematics running?
I could replace nan with 0.0?
I could (at least try to) remove the non interesting landmark(s)?
Any recommendations?
Interestingly the filtering has a problem with that not the triangulation, which may decide to take the Landmark/Keypoint from the Camera, that is able to see it.

[jtoerber]

Issue: #114: fill_large_gaps_with = 'last_value' # 'last_value', 'nan', or 'zeros'
Could the (only) value of the other Camera be taken? Or is then in the Case of 2 cameras the 3D information missing?

[davidpagnon]

Hi,

You need at least 2 cameras to triangulate the coordinates. When there is a hole for a few frames you can interpolate it, but if a point is not seen for the whole sequence, it is not going to work.

Here are a few ideas, by order of hackiness:

• Capture the sequence again and make sure the foot is seen by both cameras
• Capture with more cameras
• Edit Pose2Sim/OpenSim_Setup/Scaling_Setup_Pose2Sim*.xml, and set to false
  Do it for your IK_Setup file as well
  Then set fill_large_gaps_with = 'zeros' (if it does not work, replace the columns with zeros in pandas or a spreadsheet editor)

Please tell me how it goes!

[jtoerber]

Hi,
I guess you mean:

<IKMarkerTask name="RSmallToe">
    <!--Whether or not this task will be used during inverse kinematics solve, default is true.-->
    <!-- <apply>true</apply> -->
    <apply>false</apply>
    <!--Weight given to the task when solving inverse kinematics problems, default is 0.-->
    <weight>1</weight>
</IKMarkerTask>

in
IK_Setup_Pose2Sim_.xml
Scaling_Setup_Pose2Sim_.xml

With
fill_large_gaps_with = 'zeros' # 'last_value', 'nan', or 'zeros'
I get a lot of 0.0, not only for the nan.
With
fill_large_gaps_with = 'last_value' # 'last_value', 'nan', or 'zeros'
and manually replacing the nan with 0.0 makes "kinematics" possible.

In Opensim there are some issues with it as maybe the number of Cameras may not be enough or the alignment of the two used Cameras is not properly. The person is not really standing nor doing what it did in the Video. In OpenCap there were no problems with two cameras.
(if interested the last_values, zeros and manually are in attached zip-file)
Demo_SinglePerson.zip

[davidpagnon]

There are definitely issues in your triangulated trc files. How did you calibrate?

[jtoerber]

Hi,
I did
Pose2Sim.calibration()
with a 3x5 (45mm) checkerboard.

You did not specify which issues there are in the trc files.
And btw.: The synchronization seems to be not deterministic as I usually get 3 frames difference in this case, but once 166 frames, which are about 10 seconds here. I guess setting a frame-range may help here.

[davidpagnon]

Check this thread starting from the linked comment maybe. It seems like if you download synchronized videos from OpenCap, they are exported at half the resolution, which leads to a faulty calibration
#142 (comment)

EDIT: Sorry I had not seen your last message, let me read it

[davidpagnon]

The issues are that the trc files look don't look like a human being doing anything 😅

Synchronization is likely to be another issue indeed. Check the appropriate doc section to make sure it is correct: https://github.com/perfanalytics/pose2sim/blob/main/README.md#synchronization

If results are not satisfying, edit your Config.toml file:
All keypoints can be taken into account, or a subset of them.
The whole capture can be used for synchronization, or you can choose a time range when the participant is roughly horizontally static but with a clear vertical motion (set approx_time_maxspeed and time_range_around_maxspeed accordingly).

N.B.: Works best when:

• the participant does not move towards or away from the cameras
• they perform a clear vertical movement
• the capture lasts at least 5 seconds long, so that there is enough data to synchronize on
• the capture lasts a few minutes maximum, so that cameras are less likely to drift with time

[jtoerber]

I think in calibration.py you should check the resolution of all the videos and their frames per second.
Your advantage/disadvantage opposite to OpenCap is that you allow all kind of cameras.
This may even lead to inhomogenous cameras or camera settings during one recording.

Got new camera. I'll try my final setting tomorrow.

Synchronization:
I did calibration and poseEstimation.
Then I did all but calibration and poseEstimation.
Hence same videos and Pose-Estimations and then I got once 166 frames difference instead of 3 frames with a clear right wrist raise in the first seconds and Videos captured in one Thread to be (relatively) safe/close.

[davidpagnon]

Calibration does check the resolution of videos, I just tried to make a guess based on the information your provided but I went in the wrong direction. To be clearer, if you capture with OpenCap and convert its calibration files, and the export the wrong videos, you will have a discrepancy between the resolutions of the calibration file and the videos. But that's not what you did.

The framerate is also detected automatically, see Config.toml:
frame_rate = 'auto' # fps # int or 'auto'. If 'auto', finds from video (or defaults to 60 fps if you work with images)

Synchronization should be deterministic if you run on the same videos with the same parameters. If the right wrist clearly raises only at one time, it should not give you such different results, unless there is a problem in the parameters of your Config.toml file.

If you want to send some of your data to [email protected], I can look at it and search for the bug.

[jtoerber]

What does Pose2Sim.personAssociation() do?
I get:

\personAssociation.py:588: RuntimeWarning: Mean of empty slice
  mean_error_px = np.around(np.nanmean(error), decimals=1)

--> Mean reprojection error for Neck point on all frames is nan px, which roughly corresponds to nan mm.
--> In average, 0.01 cameras had to be excluded to reach the demanded 20 px error threshold after excluding points with likelihood below 0.3.

Tracked json files are stored in ...

Associating persons took 00h00m02s.

Then when running triangulation I get:

...
  raise Exception('No persons have been triangulated. Please check your calibration and your synchronization, or the triangulation parameters in Config.toml.')
Exception: No persons have been triangulated. Please check your calibration and your synchronization, or the triangulation parameters in Config.toml.

[davidpagnon]

personAssociation sorts out people to ensure that you triangulate the same person across cameras rather than trying to triangulate two different persons together (in single-person mode, it removes people in the background). If you only have one person in the scene, you do not need to run it.

This error still means that either your calibration or your synchronization is not good. Did you try trimming the video by hand to make sure the problem was not about synchronization?

[jtoerber]

Before I had one Webcam vertical and one Smartphone horizontal because of DroidCam-Setting.
Perhaps this was the reason for the synchronization problem.

Now:
Got new Camera. Now complete new setting with two different cameras. New video recording.
Played a little bit with approx_time_maxspeed.

It seems that also personAssociation (and perhaps triangulation) need some minimal video length to work properly (in addition to synchronization). Perhaps you should display a warning or even an error. Switched temporarily to lightweight for my local computer.
With 7 seconds video length it did not work. Now I have 11 seconds.
This worked except kinematics. Skeleton is standing at the beginning, then it is creeping on the ground.
Found: "The OpenSim uses relative coordinates in its formulation and a skeleton is
generally modeled as a set of rigid bodies interconnected by kinematic joints, which
define how a child body can move with respect to its parent body."
Perhaps the
fill_large_gaps_with = zeros
"nail" it at least at some point on the ground?
(https://repositorium.sdum.uminho.pt/bitstream/1822/24564/3/Part%20III.pdf)

What means 0.03 excluded cameras? 3% of something?

[davidpagnon]

Hi again,
It should work with 7 seconds videos, and in any case, kinematics should also work.
It's really hard to help you figure it out, could you maybe send me a project folder (with short videos, I'm running out of space on my laptop), so that I can see what's wrong?

[medpar]

I am getting the same error as you when trying to process the demo videos on the OpenCap page. I have downloaded the raw videos (.mov) and it does all the steps correctly, but when I try to calculate the inverse kinematics, it returns this error:

RuntimeError: std::exception in 'OpenSim::ScaleTool::ScaleTool(std::string const &)': SimTK Exception thrown at String.h:466:
  Error detected by Simbody method String::convertTo(): Couldn't interpret string 'inf inf inf' as type T=SimTK::Array_<double,unsigned>.
  (Required condition 'convertOK' was not met.)

The only video from which I have been able to calculate the inverse kinematics is the one for the activity '1legjumpdroplanding' . All the others have given me the same error.

[jtoerber]

Hi,

in my video cam01.mp4 with the script below I can see that if I use 9 times each 30th frame I get different rvecs values than if I do it only one, two or three times.

If you use

cv2.drawChessboardCorners(img, CHECKERBOARD, corners2, ret)

usually the chessboard is red to ... in colors. At some point you can see that the Chessboard is ... to red, so 180 degress rotated or something like that.

Perhaps this helps finding the problem.

Btw.: Could not execute "caliscope" after pip installing it.

How large must the Charuco board be for Freemocap?

my_calibration.zip

[davidpagnon]

Hi all, sorry my job is keeping me quite busy, but I'll try to answer by the end of the week!

[davidpagnon]

Hi Jens and Mario,

@medpar, It seems like there is something shady with OpenCap data that I can't figure out there. Would you mind sending me your full project folders, including the calibration files and/or videos?). I suppose there must be some Nan in the TRC file, which would be caused by a bad triangulation. Are results for "1legjumpdroplanding" good?

@jtoerber I just tried the data you are sent me.

• First thing, the toes are not well detected at all. The video is not of great quality but I've never seen anything like that.
  Be aware that COCO_133 models don't perform as well on body points as Halpe_26. So you could either ditch the hand keypoints, or use it in "performance" mode.
• Synchronization worked when I set approx_time_maxspeed = [1.0,1.0] # the left wrist motion roughly happens at 1 second on each camera
• Considering the poor results of pose estimation, I increased reproj_error_threshold_triangulation = 30 instead of 15, and interp_if_gap_smaller_than = 50 instead of 10. Of course, triangulation is not good on toes.
• It seems like the person is lying to the side, which is probably due to the different OpenCap calibration. You can reorient your TRC file prior kinematics with this script: https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Utilities/trc_Zup_to_Yup.py
• Since the feet are not well detected, I removed them from kinematics. You have to find your Pose2Sim\OpenSim_Setup\Scaling_Setup_Pose2Sim_Coco133.xml and D:\softs\github_david\pose2sim\Pose2Sim\OpenSim_Setup\IK_Setup_Pose2Sim_Coco133.xml files (type pip show pose2sim for fine Pose2Sim location). In scaling, set to false. In scaling and IK, you should set IKMarkerTask to false for all feet points. I would do the same for the hands, because since they are not well detected, the make the shoulder lock anddisturb the whole body kinematics.
  With so few cameras with poor quality, I would actually tinker with the parameters directly within the OpenSim API: https://github.com/perfanalytics/pose2sim?tab=readme-ov-file#within-opensim-gui

[jtoerber]

Hi,

there is a misunderstanding. I do not use Opencap. Hence Calibration is done by Pose2Sim.
I need COCO_133 because of fingers.
Currently not much time, so will Take a while to Test it.

And: Would you please so kind and remove the Image in your last Post. Thanks in advance.

[davidpagnon]

Sure, sorry for the image!

Okay, I may have misunderstood concerning OpenCap then. In this case, you just need to flip Y and Z coordinates and make Z=-Z in your configuration file and you should have the person upright!

So by order of impact, you should:

• have better lighting
• use more cameras
• use the performance mode