=========== EchoMetrics

This python package implements a set of metrics intended to concisely describe the vertical distribution of acoustic backscatter in the water column. Given an echogram (a 2-D array of acoustic backscatter values indexed by depth on the vertical axis and time and/or location on the horizontal), these metrics will measure various characteristics of the vertical distribution of backscatter (i.e., animal density) ping-by-ping.

The original version of this code was written to help analyze a large set of acoustic data collected from an ocean observing system in Monterey Bay, CA. A more detailed description of the algorithms can be found in:

Urmy, S.S., Horne, J.K., and Barbee, D.H., 2012. Measuring the vertical distributional variability of pelagic fauna in Monterey Bay. ICES Journal of Marine Science 69 (2): 184-196. http://icesjms.oxfordjournals.org/cgi/content/full/fsr205?ijkey=tSU0noNUWz4bj57&keytype=ref

Installation

Depends

This package depends on a few other Python packages, which can all be found on PyPi:

• NumPy and SciPy, for array operations

• Pandas, for data-reshaping purposes

• Matplotlib for plotting. This is not strictly necessary, but the "show" method of the Echogram class won't work without it.

Installing

Download the package, then extract it and cd into the directory:

tar -xf EchoMetrics-x.x.x.tar.gz
cd EchoMetrics-x.x.x

then install it manually using distutils:

python setup.py install

Metrics

Eight metric functions are included in the package at this time. They are:

• sv_avg: The (linear) average value of volumetric backscatter in the water column.

• depth_integral: Summation of backscatter over the whole water column or a specified depth range.

• center_of_mass: The mean location of backscatter in the water column (the centroid)

• inertia: A measure of spatial dispersion around the center of mass.

• aggregation_index: Measures the degree of aggregation. Higher when high densities are concentrated in small areas.

• equivalent_area: Measure of evenness (it is the reciprocal of the aggregation index). Represents the area of the water column that would be occupied if all cells had the mean density.

• proportion_occupied: The proportion of the water column with density above the echogram's threshold value.

• nlayers: Number of distinct scattering layers detected by an image-analysis algorithm.

Usage

An example of usage is as follows::

import echometrics
import matplotlib.pyplot as plt

filename = "path/to/data/My_EchoView_export.csv"
index = ["Lon_M", "Lat_M"]
depth = "Depth_M"
value = "Sv_mean"
echo = echometrics.read_flat(fileame, index, depth, value)
echo.show()
cm = echometrics.center_of_mass(echo)
plt.figure()
plt.plot(cm)
plt.show()