thunderfish

This repository is a collection of algorithms and programs for analysing electric field recordings of weakly electric fish.

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.

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.

EOD simulations

• fakefish.py: Generate artificial EOD waveforms and fields.
• fishshapes.py: Plot fish silhouettes.