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How to export problematic frames flagged timeline data #195
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Hi there! I understand that you'd like to extract problematic frame data, including frame indices and error codes, from exported TRex/TGrabs data files to make fine-tuning easier. Unfortunately, neither TRex nor TGrabs provide a built-in feature to directly extract this data. However, it's possible to work around this:
Given the information you provided, I've adapted a Python script that processes the exported data and emulates the error detection as implemented in TRex' original code. Here's an example of how you can load the .npz files in Python and extract information (untested): import numpy as np
import glob
def check_problematic_frame(frame_idx, prev_frame_idx, current_prob, tdelta, blob_exists, current_speed, settings):
error_code = 0
error_code |= settings['FramesSkipped'] * int(prev_frame_idx != frame_idx - 1)
error_code |= settings['ProbabilityTooSmall'] * int(current_prob is not None and current_prob < settings['track_trusted_probability'])
error_code |= settings['TimestampTooDifferent'] * int(settings['huge_timestamp_ends_segment'] and tdelta >= settings['huge_timestamp_seconds'])
error_code |= settings['NoBlob'] * int(not blob_exists)
# You will need to determine how to check for segment length in your data and update the error_code accordingly
return error_code
def process_individual_data(filename, settings):
# Load the .npz file
data = np.load(filename, allow_pickle=True)
# Access relevant data, e.g., X and Y positions, frame number, speed
X_positions = data['X']
Y_positions = data['Y']
frames = data['frame']
speeds = data['SPEED']
# Initialize an empty list to store problematic frame indices and error codes
problematic_frames = []
for idx in range(1, len(frames)):
frame_idx = frames[idx]
prev_frame_idx = frames[idx - 1]
tdelta = data['time'][idx] - data['time'][idx - 1]
current_speed = speeds[idx]
# Determine if a blob exists for the current frame
blob_exists = not np.isinf(data['blobid'][idx])
# Estimate current_prob using normalized distance from the previous position to the next position (as it's not currently implemented)
current_prob = None
error_code = check_problematic_frame(frame_idx, prev_frame_idx, current_prob, tdelta, blob_exists, current_speed, settings)
if error_code != 0:
problematic_frames.append((frame_idx, error_code))
# Save problematic frames and error codes in a new file
print(f"Problematic frames for {filename}: {problematic_frames}")
# List all the individual data files in the data folder
individual_files = glob.glob('data/*_fish*.npz')
# Define the settings according to your use case
settings = {
'FramesSkipped': 1,
'ProbabilityTooSmall': 2,
'TimestampTooDifferent': 4,
'NoBlob': 16,
'track_trusted_probability': 0.8,
'huge_timestamp_ends_segment': True,
'huge_timestamp_seconds': 2.0,
'track_end_segment_for_speed': True,
'weird_distance': 50.0,
'track_segment_max_length': 10.0,
'frame_rate': 30.0
}
# Process each individual file
for individual_file in individual_files:
process_individual_data(individual_file, settings) This script loads the exported data files, emulates the error detection, and saves the problematic frame indices along with their corresponding error codes. Note that the current_prob estimation is not currently implemented, but you could use the normalized distance from the previous position to the next position as an approximation. Additionally, the 'ManualMatch' setting is not considered in this script (does not apply to most use cases). Here's a brief summary of the script's workflow:
To use this script, simply update the settings to match your use case and run it. The script will process each individual file in the 'data' folder, print the problematic frames and their error codes, and store them in a list. Let me know if you have any questions or need further assistance! Happy coding! |
I found the timeline really helpful when inspecting problematic frames in my videos in the gui. But I didn't find a way to extract timeline data where problematic frames are flagged(correct me if I'm wrong). I think it really helpful if I can see what specific frames are bad and do the fine-tuning easier.
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