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. The thunderfish package provides algorithms and tools for analysing both wavefish and pulsefish EODs.
ThunderFish is available from PyPi. Simply run:
pip install thunderfish
This should also install:
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 bythunderfish.eodexplorer: View and explore properties of EOD waveforms.thunderbrowse: Browse multi-channel EOD recordings.thunderlogger: Extract EOD waveforms from logger recordings.
The following modules provide the algorithms for analyzing EOD recordings. Look into the modules for more information.
hopkinsloader: Load EODs from Hopkins files.
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.
fakefish: Simulate EOD waveforms.efield: Simulations of spatial electric fields.fishshapes: Manipulate and plot fish outlines.