raab/competition_experiments
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Updated and structured scripts to evaluate electric and video data of two competing fish in staged competition experiments.
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Till Raab e3a5cadc0c works nice... adapt loop and clean up the code.
2023-05-30 15:03:48 +02:00
complete_analysis.py event time ananlysis started. tried to implement bootstrap with cupy ... memory issues ... resolve on monday 2023-05-25 15:39:04 +02:00
eval_LED.py files to analyse competition experiments 2022-07-11 16:29:58 +02:00
event_time_analysis.py works nice... adapt loop and clean up the code. 2023-05-30 15:03:48 +02:00
event_videos.py idk 2023-04-26 09:21:09 +02:00
id_meta.csv added meta files for convinience 2023-05-30 07:07:29 +02:00
LED_detect.py LED_detect.py needs to be done for all recordings. next we need to check if trial_analysis.py does everything we need. 2023-04-27 15:40:44 +02:00
order_meta.csv added meta files for convinience 2023-05-30 07:07:29 +02:00
README.md all files for init commit added 2022-06-02 13:51:21 +02:00
trail_analysis.py bf 2023-05-19 08:17:31 +02:00
trial_summary_eval.py event time ananlysis started. tried to implement bootstrap with cupy ... memory issues ... resolve on monday 2023-05-25 15:39:04 +02:00
trial_summary.csv event time ananlysis started. tried to implement bootstrap with cupy ... memory issues ... resolve on monday 2023-05-25 15:39:04 +02:00

README.md

How to competition experiment

Workflow (Python-scripts/applications):

  1. wavetracker.trackingGUI
  2. wavetracker.EODsorter
  3. LED_detect.py
  4. eval_LED.py
  5. trial_analysis.py
  6. event_videos.py (optional)

Raw data analysis using the wavetracker-modul

trackingGUI.py

Frequency extraction and tracking

  • open Raw-file (traces-grid1.raw)
  • 'Spectrogram'-settings:
    • overlap fraction: 0.8
    • frequency resolution: 1
  • check 'Auto-save'; press 'Run'

Fine spectrogram

  • repeat steps above but press 'Calc. fine spec' instead of Run
    • fine spec data saved in /home/"user"/analysis/"filename"

EODsorter.py

  • load dataset/folder
  • correct tracked EOD traces
  • fill EOD traces
    • fine spec data needs to be manually added to the dataset-folder

Competition trial analysis

trail_analysis.py

  • Detection of winners, their EODf traces, rises, etc. Results stored in "data-path"/analysis.
  • (optional) Meta.csv file in base-path of analyzed data. Creates entries for each analyzed recording (index = file names) and stores Meta-data. Manual competation suggested.

Video analysis

LED_detect.py

  • Detect blinking LED (emitted by electric recording setup). Used for synchronization.
  • "-c" argument to identify correct detection area for LED
  • '-x' (tuple) borders of LED detection window on X-axis (in pixels)
  • '-y' (tuple) borders of LED detection window on Y-axis (in pixels)

eval_LED.py

  • creates time vector to synchronize electric and video recording
  • for each frame contains a time-point (in s) that corresponds to the electric recordings.

Rise videos (optional)

  • generates for each detected rise a short video showing the fish's behavior around the rise event.
  • sorted in 'base-path'/rise_video.