No Behaviors Marked as None? #382
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Hi @kjmartin44! This suggest that when SimBA reads in your project_config.ini, to check out what the expected classifier names are, there are some missing values that SimBA doesn't know what to do with, for example. There could be something looking like this:
If you drag-and-drop the project_config.ini (you may have to zip it) into this thread I can have a look at it to see where the error could come from? |
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project_config - Copy.zip Thank you |
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Got it - thanks. Check on line 73 in that file:
It says None. That value is typically set when you set your hyperparameters in this menu:
You can change it manually in the project_congig, or do it through the GUI and click "SAVE SETTINGS (GLOBAL ENVIRONMENT)" at the bottom of the Let me know if that makes sense. |
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SIMBA INVALID ML TRAINING SET ERROR: 28 feature columns exist in some files, but missing in others. The feature files are found in the project_folder/csv/targets_inserted directory. SimBA expects all files within the project_folder/csv/targets_inserted directory to have the same number of features: the first 10 column names with mismatches are: ['Movement_Nose', 'Movement_Right Hand', 'Movement_R1', 'Movement_R2', 'Movement_R3', 'Movement_R4', 'Movement_RElbow', 'Movement_RShoulder', 'Movement_Left Hand'] I am now getting this error, I only have one file that has been labelled though so it should not vary. |
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Hi @kjmartin44 - how many files exist within the I can't soenload the CSV. I think you may have to zip it before uploading it here as previously. |
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Here is both the screengrab and the file |
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There are a lot of infs in there for the first 28 features. That probably has something to do with it, but I am not sure yet why they are there instead of real values. How big is your entire project_folder? If you can share that, maybe through a gdrive link or similar, I can figure out how this has happaned? |
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PS. what is the FPS of your video? |
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The project folder is 42 gb. I am uploading it to Drive and can email it to you when it is finished. My videos are 499 fps |
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that's probably where the issues lie, with the FPS... Speculating but... For a human recognize the behaviors you are interested in the videos by eye, is 499 FPS a requirement, if not - do you know what the lower limit is? |
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I was testing out simba to see if I could identify sub-movements within a task as I can with deepethogram. My animals move so fast that some of the movements are complete within 3 frames at 499 fps so I cannot lower this number. However, I have some body parts that do not move much while others are incredibly active. Would removing those mostly still tracked body parts from the project possibly help? |
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Or would you recommend editing the videos so that the video is the same but the frame rate is 40 fps, so that the videos are analyzed in slow motion? |
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Ah OK, if a behavior is completed within 3 frames at 499 fps, there is no room to resample the videos., thats less than a millisecond i think very short. I'm curios about this, let me troubleshoot with the project and fix infs once I got it and get back to you. |
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I removed all of the body parts that have little to no motion from the csvs and I still have the issue of the inability to read the movement columns because it marks them as 0 or inf. Have you found any solutions so that I am able to use my data? |
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Sorry @kjmartin44 - fell between the chairs thanks for reminding me I'm going to try to replicate your error after setting the FPS to 499 |
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Hi @kjmartin44 - I gave it a go trying to replicate this error on some 499 FPS projects and I couldn't do it... Which version of SimBA are you running and can see with |
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Here is the info on that Name: Simba-UW-tf-dev and if it helps here is what comes up with conda list on my env |
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It is unlikely to be the 7k frames, it's also unlikely the SimBA version. I haven't updated these functions for a while. It may have something to do with the missing values. But only if there are tons would it explain the infs. Can you share with me your |
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I had not used outlier correction before but I can try now. I had opted to skip because its only one animal. |
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No that file looks fine, I don't see any overwhelming amounts of missing values. I one last thing, could you share your |
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project_bp_names.zip |
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OK, one more thing :) What is the pixels per millimeter conversion factor for the video in the |
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I had autopopulated the video parameters with 120 mm but i hadnt set a pixel conversion factor. Do i need to redo everything with the pixel conversion facor in place? |
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Ah maybe that could be it, let me see if I get an error like that on my data if the pixels per millimeter conversion factor is missing.. |
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See how it runs after you make sure this column has a value on your end:
I will insert an error msg in the code if its not a valid integer or float value. |
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Do I need to re-run other steps? After fixing that it still is giving me the same error. |
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If you click |
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Yes the infs are still there |
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So odd - what is the pixels per millimeter? |
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1.15302. I chose based on what I assumed was a mm in the video but I could be wrong there. |
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would it be best for me to share my whole project folder with you over google drive? |
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Thank @kjmartin44 - yes I am having troubles reproducing the infs. I have used a dummy project with what I believe is your project settings (single animal, user-defined pose configuration, 499 FPS, 1.15302 pixels per millimeter) without luck. There maybe something in the data that I overlook. |
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What email would work best to send? I do not have enough space on my google drive but I can share it over box. |
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I think that works, you can share it with [email protected] |
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Hi @kjmartin44 thanks for the data looks like a super interesting project. Two things: i) The project is so big because the frames are extracted for every video. There is no need to do that for any process in SimBA so you could skip that. ii) I look at the files inside the |
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Thank you. |
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Yeah, just to check: If you try to annotate a second video, just a couple of frames here and there, and save those annotations, do you see the infs for the second video too targets inserted directory? |
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... would just be halpful to know, if there is something in the code related to the annotations parts that somehow introduced those infs. |
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Im not sure what introduced the infs but reopening and closing labelling seems to have fixed everything. However my machine learning will not run because of an attribute error. |
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Do you have a full copy paste of the error msg? |
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Exception in Tkinter callback |
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What do you see in the SimBA main terminal window GUI before this happens? What version of simba do you have installed |
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Reading in 2 annotated files... |
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What did you choose in this dropdown? |
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If not |
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It is on RF |
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Can you send me the project config again and I will take a look? |
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project_config.zip |
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I see nothing odd.. but I'm on my phone and I don't have a computer to test it with. I was caught by hurricane on Friday and no electricity. I will try as soon as I can. |
Describe the bug
After normal frame labelling in the GUI I attempt to use machine learning but I get an error for apparently having no behaviors marked as None. However, I do indeed have frames that contain no behavior labels.
To Reproduce
Steps to reproduce the behavior:
SIMBA MISSING COLUMN ERROR: Data for video 20240401SPT35_1-04012024154559 does not contain any annotations for behavior None. Delete classifier None from the SimBA project, or add annotations for behavior None to the video 20240401SPT35_1-04012024154559
Expected behavior
The Machine Model Successfully begins training
Desktop (please complete the following information):
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