ThunderFish

Algorithms and programs for analysing electric field recordings of weakly electric fish.

Documentation | API Reference

Weakly electric fish generate an electric organ discharge (EOD). In wave-type fish the EOD resembles a sinewave of a specific frequency and with higher harmonics. In pulse-type fish EODs have a distinct waveform and are separated in time. The thunderfish package provides algorithms and tools for analysing both wavefish and pulsefish EODs.

Installation

ThunderFish is available from PyPi. Simply run:

pip install thunderfish

This should also install:

• ThunderLab
• AudioIO

Software

The thunderfish package provides the following software:

• thunderfish: Detect, analyze, and plot all EOD waveforms in short recordings. Simply run

  > thunderfish data/Apteronotus-Fishfinder-Panama-RioCanita-2014-05-17-L13.wav

  To produce the image shown above. Read more
• collectfish: Collect data generated by thunderfish.
• eodexplorer: View and explore properties of EOD waveforms.
• thunderlogger: Extract EOD waveforms from logger recordings.

Various viewers

They will eventually be replaced by some plugins for audian.

• fishfinder: Browse EOD recordings and detect EOD frequencyies on the fly.
• thunderbrowse: Browse multi-channel EOD recordings.

Data

In data/you find a view recordings on which you can run thunderfish software.

You find more fishfinder recordings for rigorous testing in the pulseeods repository that has been assembled by Liz Weerdmeester.

Algorithms

The following modules provide the algorithms for analyzing EOD recordings. Look into the modules for more information.

Input/output

• hopkinsloader: Load EODs from Hopkins files.

EOD analysis

• bestwindow: Select the region within a recording with the most stable signal of largest amplitude that is not clipped.
• checkpulse: Check whether a pulse-type or a wave-type weakly electric fish is present in a recording.
• consistentfishes: Create a list of EOD frequencies with fishes present in all provided fish lists.
• eodanalysis: Analyse EOD waveforms.
• harmonics: Extract and analyze harmonic frequencies from power spectra.
• pulses: Extract and cluster EOD waverforms of pulse-type electric fish.

EOD simulations

• fakefish: Simulate EOD waveforms.
• efield: Simulations of spatial electric fields.
• fishshapes: Manipulate and plot fish outlines.