Where communities thrive

• Join over 1.5M+ people
• Join over 100K+ communities
• Free without limits
Activity
Nirjal444
@Nirjal444
I see three different videos which I have used for pose estimation in sleap.
Simon Nilsson
@sronilsson
@Nirjal444 yes, you would see this error, as SimBA doesn't know which video represents aggression.slp. SimBA expects there to be en Aggression.mp4 or similar (eg Avi) in the project, and can't locate it.
Nirjal444
@Nirjal444
@sronilsson This aggression.slp is the sleap main project file. As per your answer does each videos has their own .slp file? Or am i uploading the wrong slp file? Will renaming the videos fix the error?
Simon Nilsson
@sronilsson
@Nirjal444 - that's right, use your sleap project to generate predictions (run inference) on videos, to create a slp file for each video, then import those slp files
17 replies
Nuno Beltrao
@nunobeltrao_gitlab
Hello! I'm new to SimBA and I'm having some trouble getting it started. I've done the installation as described in the documentation page, but when I try to start SimBA there's an import error. Could you help me solve this? Thanks!
Nuno Beltrao
@nunobeltrao_gitlab
Yes, it did fix it @sronilsson ! Thanks for your help!
Simon Nilsson
@sronilsson
:thumbsup:
Nuno Beltrao
@nunobeltrao_gitlab

@sronilsson I'm having another issue. I'm trying to use DLC through SimBA, but I get an error when I try to create the DLC project. What should I do?

Exception in Tkinter callback
Traceback (most recent call last):
File "C:\Users\nunob\miniconda3\envs\simbaenv\lib\tkinter__init.py", line 1705, in call__
return self.func(*args)
File "C:\Users\nunob\miniconda3\envs\simbaenv\lib\site-packages\simba\SimBA.py", line 1497, in createprojectcommand
config_path = deeplabcut.create_new_project(str(projectname), str(experimentalname), videolist,working_directory=str(self.folderpath1selected.folder_path), copy_videos=copyvid)
NameError: name 'deeplabcut' is not defined

Simon Nilsson
@sronilsson
Hi @nunobeltrao_gitlab. Got it. We have removed support for DLC within SimBA - it is possible to use it through earlier versions of simba-uw-tf. However, I haven't been maintaining it for some years. Those menus where built before DLC had their GUI. I highly recommend using DLC (or SLEAP), which both are great GUIs now, instead of accessing the DLC package through the SimBA menus.
vchiang001
@vchiang001
5 replies
Nirjal444
@Nirjal444
marinasoong
@marinasoong
Hello Simon @sronilsson , I got some data from DLC and am planning to use SimBA, but I get errors when I install it. Could you have a look at it, please?
Simon Nilsson
@sronilsson
Hi @marinasoong! I think platform.linux_distribution is removed in python 3.8 and above. If you use python 3.6, does it work?
3 replies
ayah26
@ayah26

Hello! I am on step 10 (sklearn visualization) and I attempted to generate videos to visualize classification results for all of my videos -- but in the simBA window it stopped after almost finishing the first video and gave this error in command--

Exception in Tkinter callback
Traceback (most recent call last):
File "c:\users\owner\anaconda3\envs\simbaenv-2\lib\tkinter__init.py", line 1705, in call
return self.func(*args)
File "c:\users\owner\anaconda3\envs\simbaenv-2\lib\site-packages\simba\SimBA.py", line 5852, in plotsklearn_result
plotsklearnresult(self.projectconfigini,self.videovar.get(),self.genframevar.get())
File "c:\users\owner\anaconda3\envs\simbaenv-2\lib\site-packages\simba\sklearn_plot_scripts\plot_sklearn_results_2.py", line 141, in plotsklearnresult
File "c:\users\owner\anaconda3\envs\simbaenv-2\lib\site-packages\pandas\core\indexes\base.py", line 4280, in
getitem__
return getitem(key)
IndexError: index 9203 is out of bounds for axis 0 with size 9203

Simon Nilsson
@sronilsson
Hi @ayah26! Got it, can you try to update simba pip install simba-uw-tf --dev and let me know if error persists?
29 replies
Marcelobot
@Marcelobot

Hello im struggling oftentimes with importing new H5 Files and recieve the following term in the terminal:
"All multi-animal DLC .h5 tracking files ordered and imported into SimBA project in the chosen workflow file format"

But the truth is, that everything was well stored and ready for import:

What could be the reason behind? Ive tried all different types of interpolation

The related Code in Terminal:

Simon Nilsson
@sronilsson
hello @Marcelobot - does it only happen when you use interpolation? if you open the project_config.ini, what does it say under [General settings][animal_no], and under [Multi animal IDs][id_list] ?
hzsugar
@hzsugar

Hi! When trying to create a project (multi-animal DLC, 8bp) in the dev version (which I checked for updates today) I get this error:

Exception in Tkinter callback
Traceback (most recent call last):
File "C:\Users\hczakhar\Anaconda3\envs\hzsimba\lib\tkinter__init.py", line 1705, in call__
return self.func(*args)
File "C:\Users\hczakhar\Anaconda3\envs\hzsimba\lib\site-packages\simba\SimBA.py", line 3754, in make_projectini
self.configinifile = write_inifile(msconfig,project_path,project_name,no_targets,target_list,bp, listindex, animalNo, self.csvORparquet.getChoices())
File "C:\Users\hczakhar\Anaconda3\envs\hzsimba\lib\site-packages\simba\create_project_ini.py", line 91, in write_inifile
f.write('modelpath' + str(i+1) + ' = ' + os.path.join(str(models_folder), str(target_list[i])) + '.sav' +'\n')
IndexError: list index out of range

Simon Nilsson
@sronilsson
Thanks @hzsugar! very helpful, I was just cleaning this function yesterday, and create_project_ini.py and self.configinifile = write_inifile ... shouldn't be used or exist anymore, surprised to see this. Can you update SimBA, version 0.94.1, and let me know if the error still persist?
hzsugar
@hzsugar
Thanks, that worked, and fixed an issue I was having earlier! (Wasn't able to import videos or tracking data.)
Simon Nilsson
@sronilsson
Thanks for letting me know!
Marcelobot
@Marcelobot
Is there a parameter to improve the quality of the videos?
Actually its not about the size of letters but more the quality so that the video is less flattering while watching
2 replies
marinasoong
@marinasoong
Hi @sronilsson , my colleagues and I tried to install SimBA in python 3.6, but ran into issues with wxpython. Could you help me with that?
Nastacia Goodwin
@goodwinnastacia
@sssm12 please look here for files
kkw11
@kkw11
Trying to analyze more data with trained models. When I try to extract features on the corrected DLC csv it gives an error. Any suggestions on what to change? Exception in thread Thread-3:
Traceback (most recent call last):
File "C:\Users\kkw11.conda\envs\SimBA\lib\threading.py", line 916, in _bootstrap_inner
self.run()
File "C:\Users\kkw11.conda\envs\SimBA\lib\threading.py", line 864, in run
self._target(self._args, *self._kwargs)
File "C:\Users\kkw11.conda\envs\SimBA\lib\site-packages\simba\SimBA.py", line 5933, in extractfeatures
extract_features_wotarget_user_defined(self.projectconfigini)
File "C:\Users\kkw11.conda\envs\SimBA\lib\site-packages\simba\features_scripts\extract_features_user_defined.py", line 80, in extract_features_wotarget_user_defined
roll_windows.append(int(fps / roll_windows_values[i]))
OverflowError: cannot convert float infinity to integer
5 replies
AlbaLM94
@AlbaLM94

Hi! I am using the latest version and I am in the outlier correction step. I could choose the settings for outlier correction without any issues bit when I click Correct outlier I get this error: Exception in Tkinter callback
Traceback (most recent call last):
File "C:\Users\BePhysLab\anaconda3\envs\simBA\lib\tkinter__init.py", line 1705, in call__
return self.func(*args)
File "C:\Users\BePhysLab\anaconda3\envs\simBA\lib\site-packages\simba\SimBA.py", line 5543, in correct_outlier
dev_move_user_defined(configini)
File "C:\Users\BePhysLab\anaconda3\envs\simBA\lib\site-packages\simba\outlier_scripts\movement\correct_devs_mov_user_defined.py", line 52, in dev_move_user_defined
x_cols, y_cols, p_cols = getBpNames(configFile)
File "C:\Users\BePhysLab\anaconda3\envs\simBA\lib\site-packages\simba\drop_bp_cords.py", line 132, in getBpNames
TypeError: unsupported operand type(s) for +: 'float' and 'str'

3 replies
Simon Nilsson
@sronilsson
Thanks for reporting @AlbaLM94 - can you confirm which version of Simba you have with pip show simba-uw-tf-dev and I will check if I can replicate.
AlbaLM94
@AlbaLM94
Sure. I have Version: 0.94.3
8 replies
aloksneurobot1
@aloksneurobot1
Hi @sronilsson While training my model i end up getting error that shap_features_categories.csv file was not found. I checked my folders in anaconda and its present there. following is the error log from cmd window : Exception in Tkinter callback
Traceback (most recent call last):
File "C:\Users\user\anaconda3\envs\simbaenv\lib\tkinter__init.py", line 1705, in call
return self.func(args)
File "C:\Users\user\anaconda3\envs\simbaenv\lib\site-packages\simba\SimBA.py", line 4035, in <lambda>
File "C:\Users\user\anaconda3\envs\simbaenv\lib\site-packages\simba\train_model_2.py", line 389, in trainmodel2
generateShapLog(data_train, target_train, feature_list, classifierName, shap_target_present_no,shap_target_absent_no, inifile)
File "C:\Users\user\anaconda3\envs\simbaenv\lib\site-packages\simba\train_model_2.py", line 132, in generateShapLog
shap_summary_calculations(inifile, outputDfShap, classifierName, expected_value, tree_evaluations_out)
File "C:\Users\user\anaconda3\envs\simbaenv\lib\site-packages\simba\shap_calcs.py", line 50, in shap_summary_calculations
File "C:\Users\user\anaconda3\envs\simbaenv\lib\site-packages\pandas\io\parsers.py", line 685, in parser_f
File "C:\Users\user\anaconda3\envs\simbaenv\lib\site-packages\pandas\io\parsers.py", line 457, in _read
kwds)
File "C:\Users\user\anaconda3\envs\simbaenv\lib\site-packages\pandas\io\parsers.py", line 895, in
init
self._make_engine(self.engine)
File "C:\Users\user\anaconda3\envs\simbaenv\lib\site-packages\pandas\io\parsers.py", line 1135, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "C:\Users\user\anaconda3\envs\simbaenv\lib\site-packages\pandas\io\parsers.py", line 1917, in
init
File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.
cinit__
File "pandas/_libs/parsers.pyx", line 689, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] File b'C:\Users\user\simba\assets\shap\feature_categories\shap_feature_categories.csv' does not exist: b'C:\Users\user\simba\assets\shap\feature_categories\shap_feature_categories.csv'
5 replies
Could you kindly direct me to reasons for this error? How can I solve this ? thank you!!
Marcelobot
@Marcelobot
Marcelobot
@Marcelobot

Hello Could you explain how the F1_score is calculated to this classification report?

Ive actually understood how in general its calculated and it sounds clear, that it might will be the best parameter for objectively messure the performance of models BUT to be honest it seems a bit confusing how it developes better or getting worse.

Which data is exactly used to create those classification reports after every training?
And would you say i should go strictly after this f1_score to compare performaces of networks?

Here ive tried out different undersample Ratios for training, as you recommented to me. And compared them for all 11 different models. The marker used has been the f1_score ive recieved by this mentioned classification reports of trainings.

hzsugar
@hzsugar

Hi, I'm having some difficulty with videos and .csv files of tracking data from DLC not importing correctly: I receive the message "Copying videos..." in the terminal but even after some time no files appear in the directory. When I manually place videos and .csv files in the proper directories, and try to extract frames, I get this error: "('expected str, bytes or os.PathLike object, not ConfigParser',)
Please make sure videos are imported and located in /project_folder/videos"

Am I going about this the right way? At the moment I have a trained DLC model that I am trying to import into SimBA for behavior labeling. Is there an easier way to do this?

6 replies
VAmoroso13
@VAmoroso13

Simon, thank you again for the help!

I have one further question that builds on something hzsugar asked. I came across SimBA after using DLC extensively and have some pretrained networks and data that have been optimized well. I would like to use the SimBA pipeline for analysis, how does one go about importing this? I'm afraid I'm a bit lost.