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sollan / alma

Fully automated (rodent) limb motion analysis toolbox for behavioral analysis with bodypart coordinate data, building upon markerless pose estimation.
GNU General Public License v3.0
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Errors and example dataset #28

Closed mdbudde closed 1 year ago

mdbudde commented 1 year ago

Hello,

I've resolved the installation issues, but continue to have issue trying to use ALMA to do kinematic analysis. A recent error is below, and it is not clear if this is a version issue or something else.

I'm wondering if it is possible to see the 'pip freeze' output you used so I can just replicate my environment/version exactly. requirements.txt is a start, but there have still been some compatibility issues and deprecated functions as I try to use it.

Also, is it possible to include an example DLC file to import into the program to ensure my own DLC output is appropriate?

This looks like a great program and very useful, but I can't get it to work at all.

thanks!

The most recent error is: Traceback (most recent call last): File "./ALMAToolbox/alma/Panels/AnalyzeStride.py", line 697, in ExtractParameters parameters, pd_dataframe_coords, is_stance, bodyparts = KinematicsFunctions.extract_parameters(self.frame_rate, self.df, self.cutoff_f, 'toe', File "./ALMAToolbox/alma/Functions/KinematicsFunctions.py", line 803, in extract_parameters return pd.DataFrame(data=np.array([ File "~/opt/anaconda3/envs/alma/lib/python3.8/site-packages/pandas/core/frame.py", line 694, in init mgr = ndarray_to_mgr( File "~/opt/anaconda3/envs/alma/lib/python3.8/site-packages/pandas/core/internals/construction.py", line 351, in ndarray_to_mgr _check_values_indices_shape_match(values, index, columns) File "~/opt/anaconda3/envs/alma/lib/python3.8/site-packages/pandas/core/internals/construction.py", line 422, in _check_values_indices_shape_match raise ValueError(f"Shape of passed values is {passed}, indices imply {implied}") ValueError: Shape of passed values is (46, 1), indices imply (46, 46)

sollan commented 1 year ago

Hi there! Looks like there's a problem with your DLC file, but it's unclear based solely on this error message.

It would help us in debugging the issue if you could provide an example of your data (DLC output) to see if it works in the correct environment, and if there's any format issue with your file. Please get in touch via the correspondence info in our publication (https://www.nature.com/articles/s42003-022-03077-6) and mention this Github issue.