Issue when importing DLC .H5 file

[sgoldenlab]

Issue when importing DLC .H5 file

[sgoldenlab]

Hi @franciscamachado - first, the file you have in your \training-datasets\iteration-0\UnaugmentedDataSet folder is likely not the DLC output file we need to import into SimBA. The \training-datasets\iteration-0\UnaugmentedDataSet folder typically does not store pose estimation tracking data (unless you moved a video in there and then analyzed it, which is a little unusual), but rather it stores your annotations which is used to train DLC models. In order words, the file you may be trying to import into SimBA may look a little like this (if opening the .csv version of the file), and contain the coordinates of your own mouse clicks during annotations in DLC (you are likely to have less empty cells than this, but I just want to make the point):

What we need to import into SimBA from maDLC it the H5 file generated when analyzing a video in DLC. This file will be located in the same folder as the video file you analyzed. For example, in this screenshot below, I have analyzed a video in maDLC called "Together1.mp4" using the "skeleton" option in DLC:

In the SimBA interface you tell which option you used to analyze the file in DLC (skeleton or box). If you used "skeleton" in DLC, then you h5 files will be tagged with a file ending "_sk.h5", as in my example screenshoot above. If you used box, then the files will be tagged with a file ending "_bx.h5". If you tell SimBA you used a skeleton setting, then SimBA is looking for files in your selected folder ending with "_sk.h5". I think that part of the issue you are having is that you are pointing SimBA to a folder that does not contain any "_sk.h5" files. Let me know if this makes sense! Thanks

[franciscamachado]

Thank you for the reply and help. I was using maDLC and I had to go through the refine tracklets stage to get the h5. As you described, after that stage, the h5 does appear on the same folder of the original video.

Related to this issue, when I import the h5 into SIMBA I get an error if I used an .avi video file to create the h5 file, as SIMBA always ends up looking for a .mp4 file. If I convert the video to .mp4 it works fine. How can i solve this problem?

Thank you.

[sgoldenlab]

Hi @franciscamachado - yes I noticed this the other day - it was reported by another user #46 (comment)

Can you update SimBA to the latest version via pip - pip install simba-uw-no-tf==1.2.6 or pip install simba-uw-tf==1.2.6 and let me know if that fixes the issue?