Closed AnnabelPerry closed 2 years ago
Hi @AnnabelPerry - thanks for sharing the files on the gdrive. I will take a look what might be going on but can't get to it straighaway. It seems the error is caused by the outlier correction functions of SimBA thinking you have fewer body-parts than the 9 that you actually have. I would suggest skipping the outlier correction and proceed without it to see if the rest of the pipeline works OK.
Hi, I'm still having a problem with this. I skipped outlier correction and moved straight to extracting features. When extracting, I get the following message:
Pose-estimation body part setting for feature extraction: 9
0
Extracting features from 0 files...
Extracting features from 0 file(s)...
All feature extraction complete.
I'm not entirely clear on what feature extraction is supposed to do, but it doesn't seem right that SimBA is registering 0 files.
When I proceed to behavior labeling and click Select video (create new video annotation)
, I get the following error:
Number of Frames: 38981
/home/blackmonlab/Documents/Annabel/NeuralNetworkProject/SimBATestProject/project_folder/csv/features_extracted/Surface 1 41486_cropped.csv @@@@@@@@@@@@@
The CSV file could not be located at the following path: /home/blackmonlab/Documents/Annabel/NeuralNetworkProject/SimBATestProject/project_folder/csv/features_extracted/Surface 1 41486_cropped.csv . It may be that you missed a step in the analysis. Please generate the file before proceeding.
None
Applying settings for classical tracking...
There seems to be an issue with extracting features - could this be related to the issue with outlier correction, or should I open a second issue?
Hi @AnnabelPerry - yes you are right it is related to the outlier extraction, let's try to get passed it.
(i) SimBA takes the files inside of the the project_folder/csv/outlier_corrected_movement_location
folder and extracts features from these files. A feature
in your case, could be the angular rotation of the fish, the velocity of the fish body-parts etc. The message Extracting features from 0 files..
suggests that there are 0 files inside of this folder in your project, so we need to get this folder populated so we have files to extract features from.
(ii) The Pose-estimation body part setting for feature extraction: 9
message suggests that you are sing one of SimBAs built in pose-estimation configurations. I don't think this is accurate, as you are classifying behaviors of fish, and there is no built in configuration for fish as the moment. That message should be reading user-defined
rather than 9
.
(iii) The core issue probably comes from point ii, where SimBA thinks you have 9 in-built body-parts but you don't. When you click skip outlier correction
SimBA tries to apply the in-built body-part names to your CSV files but fails as your pose-estimation files contains more/less body-parts. Could you try to use a user-defined body-part configuration and see if that fixes it?
Hi, thanks for your rapid response! I generated a new project and manually-defined body parts using a screenshot from one of the videos. I went through the steps I described in the original post and ended up with this message after clicking "extract features". It still says Extracting features from 0 files...
Pose-estimation body part setting for feature extraction: user_defined
0
Applying settings for classical tracking...
Extracting features from 0 files...
All feature extraction complete.
When I attempt to label behaviors, I still get this message:
The CSV file could not be located at the following path: /home/blackmonlab/Documents/Annabel/NeuralNetworkProject/SimBATestProject/SurfaceProject/project_folder/csv/features_extracted/Surface 1 41486_cropped.csv . It may be that you missed a step in the analysis. Please generate the file before proceeding.
Hi @AnnabelPerry - just to confirm: when yo skipped outlier correctio, this you indicate this by pressing this button?
Yes, I did skip outlier correction
My bad, I had not pressed the button on this most recent outlier correction. I did this and the issue appears to have been fixed. Thank you!
Describe the bug I am new to SimBA and am trying to use it to classify behaviors in a fish species. Before running on my full dataset, I am troubleshooting SimBA on a single video. I have been following the ReadTheDocs instructions (https://simba-docs.readthedocs.io/en/latest/docs/getting_started/simba_tutorial.html#part-1-create-a-new-project) and am on Part 2, Step 4. I am trying to correct for outliers. However, it has been 6 hours since I started the outlier correction process and the main SimBA window is still displaying the following message:
Pressing "Run outlier correction" generated the following error in the terminal:
To Reproduce The video and DeepLabCut data are attached as Google Drive files at the bottom of this post. To prep the video, I just cropped it a bit. To get this error, I followed the steps from the SimBA ReadTheDocs, SimBA Pipeline section. Below are the specific parameters I used for each step which required user input:
In Part 1, Steps 1.4-1.5, I specified 9 behaviors:
In Part 1, Step 1.6, I specified classic tracking
For Part 1, Step 1.7, I specified 1 animal, 9 body parts
In Part 2, Step 3.1, I set Distance_in_mm to 225 mm (the length of the top of my fish's tank)
In Part 2, Step 3.6, I drew a line across top of tank
In Part 2, Step 4.2, I used nose and tail as reference body parts
In Part 2, Step 4.3, I listed 120mm for both Movement criterion and Location criterion. I know these are both probably bad parameters. I used them because the maximum size of the fish is 120mm (though mine are probably closer to 50mm). I will probably adjust them once I can see the results of outlier correction.
Expected behavior ReadTheDocs indicates I should expect to find 2 log files in the
/project_folder/logs/
directory upon successful completion, and presumably a message stating that the program is looking for location outliers, followed by some sort of "done" messageDesktop Ubuntu 18.04 Python 3.6.10 I am using Anaconda
Additional context Here is a Google Drive Folder with the video and DeepLabCut tracking data I am using in this process. Please don't hesitate to message me if there are sharing issues: https://drive.google.com/drive/folders/1JB3nE14e3-8AcZE0DsZ0F1wXpwmMqM_J?usp=sharing