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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

Simply run (as superuser):

pip install thunderfish

If you have problems loading specific audio files with thunderfish, then you need to install further packages. Follow the installation instructions of the AudioIO package.

Software

The thunderfish package provides the following software:

  • fishfinder: Browse EOD recordings and detect EOD frequencyies on the fly.
  • thunderfish: Automatically detect and analyze all EOD waveforms in a short recording and generate a summary plot and data tables. Read documentation.
  • collectfish: Collect data generated by thunderfish. Read documentation.
  • eodexplorer: View and explore properties of EOD waveforms. Read documentation.

Algorithms

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

Input/output

  • configfile.py: Configuration file with help texts for analysis parameter.
  • consoleinput.py: User input from console.
  • dataloader.py: Load time-series data from files.
  • tabledata.py: Read and write tables with a rich hierarchical header including units and formats.

Basic data analysis

  • eventdetection.py: Detect and hande peaks and troughs as well as threshold crossings in data arrays.
  • powerspectrum.py: Compute and plot powerspectra and spectrograms for a given minimum frequency resolution.
  • voronoi.py: Analyse Voronoi diagrams based on scipy.spatial.
  • multivariateexplorer.py: Simple GUI for viewing and exploring multivariate data.

EOD analysis

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

EOD simulations

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