Issue to generate path plot

[DorianBattivelli]

Hello,

I'm using SimBA v4.2.5 on Windows 11, with Python 3.10
I imported DLC 3 CSV from single animal project.

I'm getting the following error when using CREATE PATH PLOTS function (Visualizations tab):

Exception in Tkinter callback
Traceback (most recent call last):
File "C:\Users\battivel\AppData\Local\Programs\Python\Python310\lib\tkinter_init_.py", line 1921, in call
return self.func(*args)
File "C:\Users\battivel\simba-env\lib\site-packages\simba\ui\tkinter_functions.py", line 424, in execute_command
cmd(**evaluated_kwargs)
File "C:\Users\battivel\simba-env\lib\site-packages\simba\ui\pop_ups\path_plot_pop_up.py", line 362, in _run
threading.Thread(target=path_plotter.run()).start()
File "C:\Users\battivel\simba-env\lib\site-packages\simba\plotting\path_plotter_mp.py", line 307, in run
last_frm = PlottingMixin.make_path_plot(data=line_data,
File "C:\Users\battivel\simba-env\lib\site-packages\simba\mixins\plotting_mixin.py", line 1471, in make_path_plot
cv2.line(
cv2.error: OpenCV(4.8.1) 👎 error: (-5:Bad argument) in function 'line'

Overload resolution failed:

• Can't parse 'pt1'. Sequence item with index 0 has a wrong type
• Can't parse 'pt1'. Sequence item with index 0 has a wrong type

I precise that my true DLC bodyparts does not respect the expected ones from DLC 4 body parts. Rather I labeled:

• Nose
• Minisco
• Back
• Tail_base

Since SimBA does not show me these true labels but the pre defined ones (ear_left etc.), I select the nose as BP to plot, that should correspond to my "Back" label (3rd body part in both lists)... right?

How can I fix this error?
Thank you
Best

[sronilsson]

Thanks @DorianBattivelli - much appreciated for the report! My guess is that SimBA tries to plot a line but gets None, inf, nan, a negative value for the coordinates (or something similar), and I haven't inserted an appropriate control for this (or, have mistakenly removed this control)..

Could you send me the CSV data file for this file you are trying to plot, so I can reproduce the error? It would be from the relevant video inside the project_folder/csv/outlier_corrected_movement_location.

EDIT:
I just read the bottom of your message properly :)

The body-parts in the project is defined inside project_folder\logs\measures\pose_configs\bp_names\project_bp_names.csv. If you update that file to have the correct body-parts named, save the file, then click to correct (or skip outliers) again, so you see the right body-parts listed?

[DorianBattivelli]

Here the corresponding csv

Hyb_P2_VMHvl-Syn_B11_C2_B.csv

I'll try soon to change the name of the body parts and keep you updated,
Thank you for the support

[DorianBattivelli]

Yes, I managed to update the BPs thank you for this

[sronilsson]

Thanks @DorianBattivelli as always, I will insert a better error message. Please let me know if you bump into any other errors.

[DorianBattivelli]

Thanks to you for the fix. Instead regarding the issue to generate the plot, do you see what goes wrong with my csv?

[DorianBattivelli]

The problem is that when I try to plot the path with the true bp I get
Exception in Tkinter callback
Traceback (most recent call last):
File "C:\Users\battivel\AppData\Local\Programs\Python\Python310\lib\tkinter_init_.py", line 1921, in call
return self.func(*args)
File "C:\Users\battivel\simba-env\lib\site-packages\simba\ui\tkinter_functions.py", line 424, in execute_command
cmd(**evaluated_kwargs)
File "C:\Users\battivel\simba-env\lib\site-packages\simba\ui\pop_ups\path_plot_pop_up.py", line 362, in _run
threading.Thread(target=path_plotter.run()).start()
File "C:\Users\battivel\simba-env\lib\site-packages\simba\plotting\path_plotter_mp.py", line 263, in run
check_valid_dataframe(df=self.in_df, source=file_path, valid_dtypes=Formats.NUMERIC_DTYPES.value, required_fields=self.data_cols)
File "C:\Users\battivel\simba-env\lib\site-packages\simba\utils\checks.py", line 1499, in check_valid_dataframe
raise InvalidInputError(
simba.utils.errors.InvalidInputError: SIMBA VALUE ERROR: The dataframe E:/Paper2/SimBA\GCaMP6f\project_folder\csv\outlier_corrected_movement_location\Hyb_P2_VMHvl-Syn_B11_C2_B.csv are missing required columns ['Back_x', 'Back_y'].

So maybe at this point it is better to continue with the false labels?

[sronilsson]

I am checking your file now, it does appear to run fun but will do more checks.

After you have inserted the correct body-parts in the CSV file at project_folder\logs\measures\pose_configs\bp_names\project_bp_names.csv, did you click to skip (or perform) outlier correction again? This should insert the correct body-parts in the CSV files in the project_folder/csv/outlier_corrected_movement_location directory. Before you correct (or skip) outlier correction, the older files may remain in that folder with the older body-part column names.

[DorianBattivelli]

I just rerun outlier correction with updated bpm and tried again the path plot function, but i got the same error than in my first post

[sronilsson]

Thanks for testing: Are you plotting with or without classification locations?

Second, if you open E:/Paper2/SimBA\GCaMP6f\project_folder\csv\outlier_corrected_movement_location\Hyb_P2_VMHvl-Syn_B11_C2_B.csv does it still have the "old" column headers?

EDIT:
Does all of the files in the outlier_corrected_movement_location have the old headers, or are there some in there that has the correct headers?

[sronilsson]

The data you sent plots... think we just need to figure out these body-parts names...

[DorianBattivelli]

I sampled 3 files randomly out of 44, that showed the correct headers.
I see that all the csv have been created at the same time so I guess they are all correct

[sronilsson]

Did the E:/Paper2/SimBA\GCaMP6f\project_folder\csv\outlier_corrected_movement_location\Hyb_P2_VMHvl-Syn_B11_C2_B.csv show the correct headers too?

If you share it with me I could take a look also why SimBA cant find the body-part...

[DorianBattivelli]

Hyb_P2_VMHvl-Syn_B11_C2_B.csv
Yes

Btw, I plot without classification location

[DorianBattivelli]

I also copied the csv from outlier_corrected_movement_location to machine results folder, because long time ago it was required to plot the path, is that still true?

[sronilsson]

No, I fixed that, so SImBA would only look in that directory IF classification locations are being plotted, otherwise it's looking in outlier_corrected_movement_location.

Yeah I can clearly see that you have Back_x and Back_y in that file, I am a little confused, if SimBA project path might be pointing to a different SimBA project... where you have another Hyb_P2_VMHvl-Syn_B11_C2_B.csv maybe but its a long shot. Can you share your project_config.ini?