Cannot import .h5 or .slp from SLEAP into SimBA

[srami0619]

Describe the bug
I am very new to using SimBA, so I'm sorry if this is frequently asked.
I'm trying to import a .h5 analysis file that I generated through SLEAP, but I am getting this error: OSError: Unable to synchronously open file (bad object header version number)

When I try it with a .slp file (the original project folder), it starts going through the frames (yay!), but it gets stuck once it finished and throws this:

Restructuring SLEAP frame: 353284/353285, Video: 20251208_TS1_Gr3_T1
SIMBA DATA HEADER ERROR: SIMBA ERROR: SimBA expects 48 columns of data inside the files within project_folder/csv/input_csv directory. However, within file 20251208_TS1_Gr3_T1 file, SimBA found 420 columns. Thus, there is 372 more data columns in the imported data than anticipated, which may represent 124 bodyparts if each body-part has an x, y and p value. Either revise the SimBA project pose-configuration with 124 more body-part, or include 124 less body-part in the imported data

So a similar issue I imagine?

I've been trying to open a .csv output, however, my videos are very large with a lot of labeled parts (353000 frames, 10 parts), so the file is 2.6 GB and takes a long time to open (I had it running for an hour and it still hadn't opened :/) . I have a lot of trials to go through, so this isn't very efficient.

To Reproduce
Steps to reproduce the behavior:

1. Create a project config as normal
2. Import a CSV (SLEAP) file in the project settings window

Expected behavior
I expect the program to open with my predictions from sleap and I can start classifying behaviors.

Screenshots

Unable to open .h5 file:

Unable to open .slp file

Desktop (please complete the following information):
Windows 11
Python 3.8
SimBA installed in a Anaconda environment in version 4.5.5
I am using SLEAP 1.4.1

Additional context
Add any other context about the problem here.

[sronilsson]

Hey @srami0619 - thanks for reaching out. If you bump into errors and can't readily find solution, then there is a good chance it's my fault 🙃

I want to first concentrate and fix the OSError: Unable to synchronously open file (bad object header version number) issue, because most people are importing .h5 files over slp's, I can't remember seeing this one before and want to make sure others don't hit this.

Is there any chance you can share this file with me?

Also, I see you are using python 3.8. SimBA is not tested in python 3.8 at all, and I am not sure if that could be related. Whilst sharing the file, could you also create a SimBA environment in python 3.6 or python 3.10 and see if you hit the same error?

[srami0619]

Yes, I can. It's not letting me upload to onto this thread so, I sent the .h5 file and video file to the email in your GitHub bio

I will try the different python versions right now and let you know

[sronilsson]

Got it thanks 👍🏻 , give me a little time to check it out later. I will let you know if I need any more info.

[srami0619]

Hello, I installed 3.10 python. I get this error from it.

For some reason, I just can't get simba to work on 3.6 on my system. It installed just fine in the conda environment, but when I try to open the GUI, it says it doesn't recognize the command:

only ran these commands in a fresh conda environment with python 3.6.15
pip install simba-uw-tf-dev
pip uninstall shapely
conda install -c conda-forge shapely
simba

[sronilsson]

Alright. You get the same error on 3.10 which suggest there is something unanticipated with the h5 format that I have to look into.

Regardless, on python 3.6, after running pip install simba-uw-tf-dev and it has installed, what do you see when running pip show simba-uw-tf-dev ?

You shouldn't have to re-install shapely. That used to be the instructions some time ago but that was removed. If using conda, there are up-to-date instructions here or here. there should be a short video there too going through it step by step.

[srami0619]

Hello, I tried it again in a new conda environment with the new instructions and getting the same thing :/

here is the output of pip show simba-uw-tf-dev

[sronilsson]

Thanks @srami0619 - about the python 3.6, its kind of odd as you don't seem to get the latest version of SimBA either, you seem to get version 4.5.1, if you do pip install simba-uw-tf-dev --upgrade do you get version 4.5.5?

About the h5 file, I tried to open it in a bunch of different ways, in python using 'tables', 'pytables', 'h5netcdf', 'netCDF4', 'pandas', and outside in the HDFViewer GUI app. All failed.

Do you have any more h5's from sleap to test? If you recreate the h5 in sleap, how does it look?

If you try to open the h5's, on your own in python or outside, can you read it or is it corrupted?

[srami0619]

Okay, I upgraded Simba, but I get an import error when trying to open the GUI:

(simba36) C:\Users\aylas>simba
Traceback (most recent call last):
File "c:\users\aylas\anaconda3\envs\simba36\lib\runpy.py", line 193, in run_module_as_main
"main", mod_spec)
File "c:\users\aylas\anaconda3\envs\simba36\lib\runpy.py", line 85, in run_code
exec(code, run_globals)
File "C:\Users\aylas\anaconda3\envs\simba36\Scripts\simba.exe_main.py", line 4, in
File "c:\users\aylas\anaconda3\envs\simba36\lib\site-packages\simba\SimBA.py", line 131, in
from simba.ui.pop_ups.pose_bp_drop_pop_up import DropTrackingDataPopUp
File "c:\users\aylas\anaconda3\envs\simba36\lib\site-packages\simba\ui\pop_ups\pose_bp_drop_pop_up.py", line 6, in
from simba.pose_processors.remove_keypoints import KeypointRemover
File "c:\users\aylas\anaconda3\envs\simba36\lib\site-packages\simba\pose_processors\remove_keypoints.py", line 9, in
from tables import NaturalNameWarning
File "C:\Users\aylas\AppData\Roaming\Python\Python36\site-packages\tables_init.py", line 99, in
from .utilsextension import (
ImportError: DLL load failed: The specified module could not be found.

However, I was able to open the .h5 file in my python (see below). I was able to replicate this in 3.10 as well

[sronilsson]

ah interesting!, which version of h5py? @srami0619

[sronilsson]

What do you see when running:

import h5py
print("HDF5 library version:", h5py.version.hdf5_version) 
print("h5py version:", h5py.__version__) 

[srami0619]

Hi sorry I was in a meeting. here is the output

[sronilsson]

I have the same versions as you....

I noticed in your screenshot earlier, when you read the content of two h5 files.

The first file did not work, but the second file worked.

The two file paths had the same file name, but placed in different sub-directories.

Which of those two files did you share with me, the one that you could read or the one you could not read?

[sronilsson]

EDIT: sorry I read it wrong.. it was a mistake in the path the first time around.

[sronilsson]

... what about running this to give me a little more info:

import h5py
import sys
import platform

print("Python:", sys.version)
print("Platform:", platform.platform())
print("h5py version:", h5py.version)
print("HDF5 version:", h5py.version.hdf5_version)
print("\nFull h5py info:")
print(h5py.version.info)

[srami0619]

print("Python:", sys.version)
Python: 3.6.10 |Anaconda, Inc.| (default, May 7 2020, 19:46:08) [MSC v.1916 64 bit (AMD64)]
print("Platform:", platform.platform())
Platform: Windows-10-10.0.26100-SP0
print("h5py version:", h5py.version)
h5py version: <module 'h5py.version' from 'C:\Users\aylas\AppData\Roaming\Python\Python36\site-packages\h5py\ve
rsion.py'>
print("HDF5 version:", h5py.version.hdf5_version)
HDF5 version: 1.10.4
print("\nFull h5py info:")
Full h5py info:
print(h5py.version.info)
Summary of the h5py configuration

h5py 2.9.0
HDF5 1.10.4
Python 3.6.10 |Anaconda, Inc.| (default, May 7 2020, 19:46:08) [MSC v.1916 64 bit (AMD64)]
sys.platform win32
sys.maxsize 9223372036854775807
numpy 1.19.1