How to use deeplabcut.analyzeskeleton

I have gotten my analyze video working now, but how do I use deeplabcut.analyzeskeleton to find the angle between the hind limb of the rabbit and the ground using the data from analyze video? I have been using the GUI, is it somehow accessible through there? Or do I have to use the terminal on my mac to use analyzeskeleton? Any help would be greatly appreciated!

@jpierce, you’ll have to use the terminal. In IPython, you could type deeplabcut.analyzeskeleton? to print the documentation. See here too. But essentially (and like most DLC functions), it will require your config.yaml, a list of videos, and certainly of interest the flag save_as_csv=True.


Thank you . I was also looking into this . Slowly getting a hang of DLC

@jeylau, I have been working with deeplabcut in the terminal but it says that my config file cannot be found, even when I go to the file and right-click and press “Get Info” in order to get the full file path. This is the code that I have been putting in:

deeplabcut.analyzeskeleton(’/Macintosh HD/Users/jessicapierce/trialGO1Left-Jessica Pierce -2020-09-23/G01left2-Jessica Pierce -2020-10-23/G01left2-Jessica Pierce -2020-10-23/config.yaml’, ‘Macintosh HD/Users/jessicapierce/trialG01left-Jessica Pierce -2020-09-23/G01left2-JessicaPierce -2020-10-23/G01left2-Jessica Pierce -2020-10-23/videos/G01(left)’, videotype=“mp4”, shuffle=1, trainingsetindex=0, filtered=True, save_as_csv=True, destfolder=None)

Please let me know if you can see anything wrong.

or @MWMathis, or anyone that is willing to help, I got rid of the slash at the beginning and I found that I had put an O instead of a 0 but I am still getting the error:

“Config file is not found. Please make sure that the file exists and/or that you passed the path of the config file correctly!”
FileNotFoundError: Config file is not found. Please make sure that the file exists and/or that you passed the path of the config file correctly!

Any help is appreciated!

@jpierce, the paths look wrong to me (your video path does not include its extension for example). The safest way is to right click on your file and press the Option key (the one between Control and Command), you should now see that the ‘Copy’ menu has turned into ‘Copy as path’. Try that for both the config and the video (which should be passed into the function as a list by the way) and you should be fine :slight_smile:

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Ok, so I got past the config.yaml error, but now the message that I get is

Processing /Users/jessicapierce/trialG01Left-Jessica Pierce -2020-09-23/G01left2-Jessica Pierce -2020-10-23/G01left2-Jessica Pierce -2020-10-23/videos/G01(left).mp4

No unfiltered data file found in /Users/jessicapierce/trialG01Left-Jessica Pierce -2020-09-23/G01left2-Jessica Pierce -2020-10-23/G01left2-Jessica Pierce -2020-10-23/videos for video G01(left) and scorer DLC_mobnet_100_G01left2Oct23shuffle1_21000.

Not sure what to do here, do I need to go back into the gui and do something to the video file? Any pointers help, thank you for all your help so far!

Actually I got it to work! The skeleton csv printed and everything. Thanks!!

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