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:

• fishfinder: Browse EOD recordings and detect EOD frequencyies on the fly.
• thunderfish: Detect, analyze, and plot all EOD waveforms in short recordings.
• collectfish: Collect data generated by thunderfish.
• eodexplorer: View and explore properties of EOD waveforms.
• thunderbrowse: Browse multi-channel EOD recordings.
• thunderlogger: Extract EOD waveforms from logger recordings.

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.