Impossible to import h5 elipse data from DLC

[DorianBattivelli]

Hello,

Sorry for reporting this small bug but I can't import my el.h5 file, the terminal reports:

What could be the error? FYI, I'm using 0.95.9 simba version on windows. Thank you, Best,

[DorianBattivelli]

I precise that it's a second importation of h5 file for the same video, since the first h5 contained some mistakes. I erased the coresponding csv file (from the first h5 file) in the csv folder.

[sronilsson]

Hi @DorianBattivelli thanks for reporting! Is it possible that you have some hidden files located within the directory you are importing the files from, or hidden files within your SimBA project_folder/videos directory? https://support.microsoft.com/en-us/windows/show-hidden-files-0320fe58-0117-fd59-6851-9b7f9840fdb2#:~:text=Select%20the%20Start%20button%2C%20then,drives%2C%20and%20then%20select%20OK.

[DorianBattivelli]

Thank you for the answer. I checked and I don't have any hidden in these directories

[sronilsson]

I bumped into this error myself a few times when I was troubleshooting something different. It happened when I have a file in the videos folder that does not have a file extension (or only an extension, no file-name) and I was about to insert a fix. Here, in the image, for example, there is a file called .DS_store in my videos directory that is hidden which is causing the code to fail (it can't find the video's name, only extension). I will insert a fix for this now, and let's see if it fixes the issue on your end, if not we can dig more.

[sronilsson]

@DorianBattivelli - if you update to 0.97.4 - do you still see the error?

[DorianBattivelli]

Thank you, unfortunatly the update did not fix the bug. Here the files and corresponding paths I use to import the h5 file:

[sronilsson]

Thanks @DorianBattivelli - I cant see the entire file explorer window. To troubleshoot, could you also tick the File name extensions box next to the Hidden items box and send me the screengrab?

If you move the Bh5 folder to a different location, does the error persist?

[DorianBattivelli]

I also tried by moving the folder on the desktop, and the problem persists.

I precise that I do not import the video since it is already present in the video folder. Could that create the error?

[sronilsson]

Yes, that should not cause an issue. In version 0.97.4, I inserted a print statement, that shows all the files SimBA finds in the video folder, before it starts to scan which one belongs to your el.h5 file.

Did you see that print statement?

[DorianBattivelli]

I also tried by moving the folder on the desktop, and the problem persists.

I precise that I do not import the video since it is already present in the video folder. Could that create the error?

Yes, that should not cause an issue. In version 0.97.4, I inserted a print statement, that shows all the files SimBA finds in the video folder, before it starts to scan which one belongs to your el.h5 file.

Did you see that print statement?

Not sure to understand, I should find the statement in the error that returns the terminal?

[sronilsson]

Hi - sorry I should have been clearer (I also put the print statement in the wrong place). First, update to simba 0.97.5 with pip install simba-uw-tf-dev --upgrade.

Then, when you import your data, SimBA prints out all of the files that are found inside your project_folder/videos directory, as is marked in the red box in the screengrab below. In your case, one of these files listed, does not have a file ending, or a filename. SimBA tries to identify the video file format, and the file-name, and it fails. This would happen for example if one if the files inside your project_folder/videos directory begins with the character .

[DorianBattivelli]

After updating, here what I get:

[sronilsson]

@DorianBattivelli - I've inserted some code that should filter out all subdirectories and hidden files, and show you the name of the offending file if you still hit an error. Can you update SimBA to 0.97.5 and let me know how it goes?

[DorianBattivelli]

Amazing, it solved the issue, thank you very much!

[DorianBattivelli]

Well actually I am stuck at the next tab, when trying to set the video parameters:

[sronilsson]

Alright - hang on, I will insert a more solid fix. There is likely to be some hidden file in that folder.

[sronilsson]

I'm sorry I don't have a fix. But hopefully I have an update that can help us figure out what is going on. If you update to version 0.97.7, and repeat the same process, what is the error message you see in the main SimBA terminal?

What you should see something like this - SIMBA ERROR: ThisFilename is not a valid filepath

[DorianBattivelli]

Thank you for the update, Indeed the error message is as you said

Loading F:/Territorial_Arena/Paper/Protocol_1/CD1/Simba/B1-MS_US/project_folder/project_config.ini... SIMBA ERROR: F:/Territorial_Arena/Paper/Protocol_1/CD1/Simba\B1-MS_US\project_folder\videos\Bh5 is not a valid filepath

[DorianBattivelli]

Okm annd removing the h5 folder fixed the problem ,) thank you!