POSE ESTIMATION PLOTTING (GPU)

Overlaying pose-estimation data on videos is useful for visually validating the performance of the tracking model.

However, with many long videos at high resolution and sample rates, creating these visualizations can be time-consuming using standard CPU methods and we may want to dump this work on to a GPU device to speed things up.

How fast things can be plotted depends on your hardware, but on standard lab computers and video resolutions you should be able read, plot and save about-ish 20k images a minute. This below is me running it on a rtx 4080 GPU and 32GB RAM.

NOTE: Before running these methods, make sure: * you have simba version >= 3.2.8. * I’d run this in python 3.10.

[1]:

import os
from simba.data_processors.cuda.image import pose_plotter
from simba.utils.read_write import find_files_of_filetypes_in_directory, find_video_of_file

[2]:

### DEFINITIONS
DATA_DIRECTORY = "/mnt/c/troubleshooting/mitra/project_folder/csv/outlier_corrected_movement_location/"
INPUT_VIDEO_DIRECTORY = "/mnt/c/troubleshooting/mitra/project_folder/videos/"
OUTPUT_VIDEO_DIRECTORY = "/mnt/c/troubleshooting/mitra/project_folder/videos/pose"
CIRCLE_SIZE = None # SET THIS VALUE TO AN INTEGER (E.G., 3) IF YOU DON'T WANT SIMBA TO ESTIMATE  FITTING BODY-PART CIRCLE SIZE FROM YOU VIDEO RESOLUTION
COLORS = 'Set1' # NAME OF COLOR PALLETE TO USE FOR THE BODY-PARTS. OTHER EXAMPLES INCLUDE EG :"Pastel1", "Pastel2","Paired", "Accent", "Dark2", "Set2", "Set3", "tab10", "tab20"
VERBOSE = True #If True, prints progress. If too much is being printed and you find it's spamming your console, set this to False.
BATCH_SIZE = 1500 #The number of frames to process concurrently on the GPU. Default: 750. Increase this value if host and device RAM allows it to improve runtime. Decrease if you hit memory errors.

[3]:

## FIND ALL DATA FILES IN THE DATA_DIRECTORY
data_files = find_files_of_filetypes_in_directory(directory=DATA_DIRECTORY, extensions=['.csv'], as_dict=True, raise_error=True)
data_files

[3]:

{'501_MA142_Gi_CNO_0521': '/mnt/c/troubleshooting/mitra/project_folder/csv/outlier_corrected_movement_location/501_MA142_Gi_CNO_0521.csv',
 '501_MA142_Gi_DCZ_0603': '/mnt/c/troubleshooting/mitra/project_folder/csv/outlier_corrected_movement_location/501_MA142_Gi_DCZ_0603.csv',
 '501_MA142_Gi_Saline_0513': '/mnt/c/troubleshooting/mitra/project_folder/csv/outlier_corrected_movement_location/501_MA142_Gi_Saline_0513.csv',
 '501_MA142_Gi_Saline_0515': '/mnt/c/troubleshooting/mitra/project_folder/csv/outlier_corrected_movement_location/501_MA142_Gi_Saline_0515.csv',
 '501_MA142_Gi_Saline_0517': '/mnt/c/troubleshooting/mitra/project_folder/csv/outlier_corrected_movement_location/501_MA142_Gi_Saline_0517.csv',
 '502_MA141_Gi_CNO_0514': '/mnt/c/troubleshooting/mitra/project_folder/csv/outlier_corrected_movement_location/502_MA141_Gi_CNO_0514.csv'}

[4]:

# LOOP OVER EACH DATA FILE, FIND THE CORRESPONDING VIDEO IN THE INPUT VIDEO_DIRECTORY, AND CREATE VIDEO AND SAVE IT IN THE OUTPUT_VIDEO_DIRECTORY
for data_file_name, data_file_path in data_files.items():
    video_input_path = find_video_of_file(video_dir=INPUT_VIDEO_DIRECTORY, filename=data_file_name, raise_error=False)
    video_output_path = os.path.join(OUTPUT_VIDEO_DIRECTORY, f'{data_file_name}.mp4')
    _ = pose_plotter(data=data_file_path, video_path=video_input_path, save_path=video_output_path, circle_size=CIRCLE_SIZE, colors=COLORS, verbose=VERBOSE, batch_size=BATCH_SIZE)

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SIMBA COMPLETE: Pose-estimation video saved at /mnt/c/troubleshooting/mitra/project_folder/videos/pose/501_MA142_Gi_CNO_0521.mp4. (elapsed time: 129.6568s)     complete
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SIMBA COMPLETE: Pose-estimation video saved at /mnt/c/troubleshooting/mitra/project_folder/videos/pose/501_MA142_Gi_DCZ_0603.mp4. (elapsed time: 98.4894s)      complete
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SIMBA COMPLETE: Pose-estimation video saved at /mnt/c/troubleshooting/mitra/project_folder/videos/pose/501_MA142_Gi_Saline_0513.mp4. (elapsed time: 140.5787s)  complete
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SIMBA COMPLETE: Pose-estimation video saved at /mnt/c/troubleshooting/mitra/project_folder/videos/pose/501_MA142_Gi_Saline_0515.mp4. (elapsed time: 123.0275s)  complete
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Processing images 3000 - 4500 (of 36118; batch count: 3/25)...
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Processing images 4500 - 6000 (of 36118; batch count: 4/25)...
Moving frames 4500-6000 to device...
Creating frames 4500-6000 ...
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Processing images 6000 - 7500 (of 36118; batch count: 5/25)...
Moving frames 6000-7500 to device...
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Processing images 7500 - 9000 (of 36118; batch count: 6/25)...
Moving frames 7500-9000 to device...
Creating frames 7500-9000 ...
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Processing images 9000 - 10500 (of 36118; batch count: 7/25)...
Moving frames 9000-10500 to device...
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Processing images 10500 - 12000 (of 36118; batch count: 8/25)...
Moving frames 10500-12000 to device...
Creating frames 10500-12000 ...
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Processing images 12000 - 13500 (of 36118; batch count: 9/25)...
Moving frames 12000-13500 to device...
Creating frames 12000-13500 ...
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Processing images 13500 - 15000 (of 36118; batch count: 10/25)...
Moving frames 13500-15000 to device...
Creating frames 13500-15000 ...
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Processing images 15000 - 16500 (of 36118; batch count: 11/25)...
Moving frames 15000-16500 to device...
Creating frames 15000-16500 ...
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Processing images 16500 - 18000 (of 36118; batch count: 12/25)...
Moving frames 16500-18000 to device...
Creating frames 16500-18000 ...
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Processing images 18000 - 19500 (of 36118; batch count: 13/25)...
Moving frames 18000-19500 to device...
Creating frames 18000-19500 ...
Moving frames to host 18000-19500 ...
Writing frames to host 18000-19500 ...
Processing images 19500 - 21000 (of 36118; batch count: 14/25)...
Moving frames 19500-21000 to device...
Creating frames 19500-21000 ...
Moving frames to host 19500-21000 ...
Writing frames to host 19500-21000 ...
Processing images 21000 - 22500 (of 36118; batch count: 15/25)...
Moving frames 21000-22500 to device...
Creating frames 21000-22500 ...
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Writing frames to host 21000-22500 ...
Processing images 22500 - 24000 (of 36118; batch count: 16/25)...
Moving frames 22500-24000 to device...
Creating frames 22500-24000 ...
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Writing frames to host 22500-24000 ...
Processing images 24000 - 25500 (of 36118; batch count: 17/25)...
Moving frames 24000-25500 to device...
Creating frames 24000-25500 ...
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Processing images 25500 - 27000 (of 36118; batch count: 18/25)...
Moving frames 25500-27000 to device...
Creating frames 25500-27000 ...
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Processing images 27000 - 28500 (of 36118; batch count: 19/25)...
Moving frames 27000-28500 to device...
Creating frames 27000-28500 ...
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Writing frames to host 27000-28500 ...
Processing images 28500 - 30000 (of 36118; batch count: 20/25)...
Moving frames 28500-30000 to device...
Creating frames 28500-30000 ...
Moving frames to host 28500-30000 ...
Writing frames to host 28500-30000 ...
Processing images 30000 - 31500 (of 36118; batch count: 21/25)...
Moving frames 30000-31500 to device...
Creating frames 30000-31500 ...
Moving frames to host 30000-31500 ...
Writing frames to host 30000-31500 ...
Processing images 31500 - 33000 (of 36118; batch count: 22/25)...
Moving frames 31500-33000 to device...
Creating frames 31500-33000 ...
Moving frames to host 31500-33000 ...
Writing frames to host 31500-33000 ...
Processing images 33000 - 34500 (of 36118; batch count: 23/25)...
Moving frames 33000-34500 to device...
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Processing images 34500 - 36000 (of 36118; batch count: 24/25)...
Moving frames 34500-36000 to device...
Creating frames 34500-36000 ...
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Processing images 36000 - 36118 (of 36118; batch count: 25/25)...
Moving frames 36000-36118 to device...
Creating frames 36000-36118 ...
Moving frames to host 36000-36118 ...
Writing frames to host 36000-36118 ...
SIMBA COMPLETE: Pose-estimation video saved at /mnt/c/troubleshooting/mitra/project_folder/videos/pose/501_MA142_Gi_Saline_0517.mp4. (elapsed time: 116.8925s)  complete
Processing images 0 - 1500 (of 36210; batch count: 1/25)...
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Creating frames 0-1500 ...
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Writing frames to host 0-1500 ...
Processing images 1500 - 3000 (of 36210; batch count: 2/25)...
Moving frames 1500-3000 to device...
Creating frames 1500-3000 ...
Moving frames to host 1500-3000 ...
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Processing images 3000 - 4500 (of 36210; batch count: 3/25)...
Moving frames 3000-4500 to device...
Creating frames 3000-4500 ...
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Processing images 4500 - 6000 (of 36210; batch count: 4/25)...
Moving frames 4500-6000 to device...
Creating frames 4500-6000 ...
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Writing frames to host 4500-6000 ...
Processing images 6000 - 7500 (of 36210; batch count: 5/25)...
Moving frames 6000-7500 to device...
Creating frames 6000-7500 ...
Moving frames to host 6000-7500 ...
Writing frames to host 6000-7500 ...
Processing images 7500 - 9000 (of 36210; batch count: 6/25)...
Moving frames 7500-9000 to device...
Creating frames 7500-9000 ...
Moving frames to host 7500-9000 ...
Writing frames to host 7500-9000 ...
Processing images 9000 - 10500 (of 36210; batch count: 7/25)...
Moving frames 9000-10500 to device...
Creating frames 9000-10500 ...
Moving frames to host 9000-10500 ...
Writing frames to host 9000-10500 ...
Processing images 10500 - 12000 (of 36210; batch count: 8/25)...
Moving frames 10500-12000 to device...
Creating frames 10500-12000 ...
Moving frames to host 10500-12000 ...
Writing frames to host 10500-12000 ...
Processing images 12000 - 13500 (of 36210; batch count: 9/25)...
Moving frames 12000-13500 to device...
Creating frames 12000-13500 ...
Moving frames to host 12000-13500 ...
Writing frames to host 12000-13500 ...
Processing images 13500 - 15000 (of 36210; batch count: 10/25)...
Moving frames 13500-15000 to device...
Creating frames 13500-15000 ...
Moving frames to host 13500-15000 ...
Writing frames to host 13500-15000 ...
Processing images 15000 - 16500 (of 36210; batch count: 11/25)...
Moving frames 15000-16500 to device...
Creating frames 15000-16500 ...
Moving frames to host 15000-16500 ...
Writing frames to host 15000-16500 ...
Processing images 16500 - 18000 (of 36210; batch count: 12/25)...
Moving frames 16500-18000 to device...
Creating frames 16500-18000 ...
Moving frames to host 16500-18000 ...
Writing frames to host 16500-18000 ...
Processing images 18000 - 19500 (of 36210; batch count: 13/25)...
Moving frames 18000-19500 to device...
Creating frames 18000-19500 ...
Moving frames to host 18000-19500 ...
Writing frames to host 18000-19500 ...
Processing images 19500 - 21000 (of 36210; batch count: 14/25)...
Moving frames 19500-21000 to device...
Creating frames 19500-21000 ...
Moving frames to host 19500-21000 ...
Writing frames to host 19500-21000 ...
Processing images 21000 - 22500 (of 36210; batch count: 15/25)...
Moving frames 21000-22500 to device...
Creating frames 21000-22500 ...
Moving frames to host 21000-22500 ...
Writing frames to host 21000-22500 ...
Processing images 22500 - 24000 (of 36210; batch count: 16/25)...
Moving frames 22500-24000 to device...
Creating frames 22500-24000 ...
Moving frames to host 22500-24000 ...
Writing frames to host 22500-24000 ...
Processing images 24000 - 25500 (of 36210; batch count: 17/25)...
Moving frames 24000-25500 to device...
Creating frames 24000-25500 ...
Moving frames to host 24000-25500 ...
Writing frames to host 24000-25500 ...
Processing images 25500 - 27000 (of 36210; batch count: 18/25)...
Moving frames 25500-27000 to device...
Creating frames 25500-27000 ...
Moving frames to host 25500-27000 ...
Writing frames to host 25500-27000 ...
Processing images 27000 - 28500 (of 36210; batch count: 19/25)...
Moving frames 27000-28500 to device...
Creating frames 27000-28500 ...
Moving frames to host 27000-28500 ...
Writing frames to host 27000-28500 ...
Processing images 28500 - 30000 (of 36210; batch count: 20/25)...
Moving frames 28500-30000 to device...
Creating frames 28500-30000 ...
Moving frames to host 28500-30000 ...
Writing frames to host 28500-30000 ...
Processing images 30000 - 31500 (of 36210; batch count: 21/25)...
Moving frames 30000-31500 to device...
Creating frames 30000-31500 ...
Moving frames to host 30000-31500 ...
Writing frames to host 30000-31500 ...
Processing images 31500 - 33000 (of 36210; batch count: 22/25)...
Moving frames 31500-33000 to device...
Creating frames 31500-33000 ...
Moving frames to host 31500-33000 ...
Writing frames to host 31500-33000 ...
Processing images 33000 - 34500 (of 36210; batch count: 23/25)...
Moving frames 33000-34500 to device...
Creating frames 33000-34500 ...
Moving frames to host 33000-34500 ...
Writing frames to host 33000-34500 ...
Processing images 34500 - 36000 (of 36210; batch count: 24/25)...
Moving frames 34500-36000 to device...
Creating frames 34500-36000 ...
Moving frames to host 34500-36000 ...
Writing frames to host 34500-36000 ...
Processing images 36000 - 36210 (of 36210; batch count: 25/25)...
Moving frames 36000-36210 to device...
Creating frames 36000-36210 ...
Moving frames to host 36000-36210 ...
Writing frames to host 36000-36210 ...
SIMBA COMPLETE: Pose-estimation video saved at /mnt/c/troubleshooting/mitra/project_folder/videos/pose/502_MA141_Gi_CNO_0514.mp4. (elapsed time: 123.267s)      complete

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