error during calibration about anipose HOT 11 CLOSED

Thank you for the reply, attached is the two videos, toml file and the generated pickle.
califilesgutanipo.zip

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I just realized i log in with a different account. same person.

from anipose.

Hi @cgutierrez-Ibanez ,

Thank you for filing this issue.
It seems to not be finding any detected checkerboards pairs, which is odd since it seems that checkerboards are detected in all frames.

I need to reproduce this bug to diagnose it further.

Could you share:

• your config.toml file
• the pickle file that is generated
• the calibration videos used

Thank you!

from anipose.

Hi @cgutierrez-Ibanez ,

I was able to reproduce the issue.

It turns out that you had misspecified your camera regex pattern, so that it was not matching your files appropriately. In particular, your cam_regex variable was set to:
cam_regex = 'cam([1-9])$'
which translates to 'cam' followed by a digit 1-9 (which is the name of the camera), followed by the end of the filename.

However, your calibration video files are named cam1cut.avi and cam2cut.avi , so the "cam1" and "cam2" parts are not at the end of the name. To fix this, simply update the cam_regex to:
cam_regex = 'cam([1-9])'

You will need to delete your detections.pickle file to reprocess properly.
After changing cam_regex and deleting the pickle file, I was able to obtain a good calibration.

Let me know if that works.

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To mitigate this issue for future users, I will update Anipose to throw an error/warning when the camera regex name does not match the files to highlight this issue better.

from anipose.

Hi @cgutierrez-Ibanez ,

Did you end up trying out the fix? Did it work for you?

Let me know

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Hi,

Sorry, it has been a busy week. Yes, it works! thank you. It now creates a full calibration, but then when trying to analyze videos, it seems to start deeplabcut, but then nothing happens. I believe the naming is correct. I named the cameras cam1 and cam 2 and the video files are named xxxcam1.avi and xxxcam2.avi, I tried cam_regex = 'cam([1-9])$' and cam_regex = 'cam([1-9])' but in both cases is the same. I have a main anipose3d folder in which there is a session1folder, and in there two subfolders, one called calibration and the other videos-raw. Is probably some naming problem or something I am missing on the tom file. or maybe the path to the deeplabcut folder?

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Ah, I think for your folder structure, you should set nesting = 1 in your config.toml.

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sorry about that. Now is (mostly) working. I can get 3d poses, which look very similar to what I got using the deeplabcut triangulation. The one problem is that using filter-3d gives me almost completely blank .csv files.

also, while I have your attention, in the 3d pose files, is the data in mm? Thank you for all the help, patience and great work.

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Yes, if you've got missing data, the 3D median filter probably will not work that well. In any case, there is now a better filter available, which smooths the data and can constrain the length of certain joint pairs. It will also interpolate the missing data.

Here's an example configuration for constrained optimization:

[triangulation]
optim = true
constraints = [
    ['right_middle_knuckle', 'right_wrist'], ['left_middle_knuckle', 'left_wrist'] # set of constant limb length constraints written out as pairs
]
scale_smooth = 2 # strength of smoothness constraint, higher gives smoother trajectory
scale_length = 2 # strength of length constraint, higher enforces less variability in limb lengths
reproj_error_threshold = 5 # in pixels, for robust triangulation
score_threshold = 0.3 # score threshold for triangulation
n_deriv_smooth = 2 # derivative to minimize for smoothness

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I think the original issue is resolved, so I am closing this issue.

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