Package: echofilter
Latest ReleaseLicenseDocumentationBuild StatusCode styleCitationEchofilter is an application for segmenting an echogram. It takes as its
input anEchoview.EV file, and produces as its output several lines and
regions:entrained air (turbulence) lineseafloor linesurface linenearfield linepassive data regions(unreliable) bad data regions for entirely removed periods of time, in the form
of boxes covering the entire vertical depth(unreliable) bad data regions for localised anomalies, in the form of polygonal
contour patchesEchofilter uses a machine learning model to complete this task.
The machine learning model was trained on upfacing stationary and downfacing
mobile data provided by Fundy Ocean Research Centre for Energy (FORCE).
The training and evaluation data isavailable for download.
Queries regarding dataset access should be directed to FORCE,info@fundyforce.ca.The experimental methodology and results can be found in ourcompanion paper, published in Frontiers in Marine Science.Full documentation of how to use echofilter can be viewed atreadthedocs.If you encounter a specific problem pleaseopen a new issue.UsageAfter installing, the model can be applied at the command prompt with:echofilterPATHPATH2...Any number of paths can be specified. Each path can either be a path to
a single csv file to process (exported using theEchoviewapplication),
or a directory containing csv files. If a directory is given, all csv files
within nested subfolders of the directory will be processed.All optional parameters can be seen by runningechofilterwith the help
argument.echofilter--helpFor more details, see theUsage Guide,
and thecommand line interface (CLI) referencedocumentation.InstallationInstalling as a stand-alone executableFor your convenience, we provide a copy of Echofilter compiled as
a stand-alone executable for Windows.
To install this, download and unzip the echofilter-executable-M.N.P.zip file
from the latest release in thereleases tab.
For example:echofilter-executable-1.2.0.zipFor more details, see the step-by-step instructions in theUsage Guide.Note: The precompiled executable has only CPU support, and does not support
running on GPU.Installing in PythonAlternatively, the echofilter package can be installed for Python 3.6 or 3.7
using pip as follows.First, install torch.Either with CPU-only capabilities:pipinstalltorch==1.4.0+cputorchvision==0.5.0+cpu-fhttps://download.pytorch.org/whl/torch_stable.htmlOr with CUDA GPU support as well:pipinstalltorch==1.4.0torchvision==0.5.0-fhttps://download.pytorch.org/whl/torch_stable.htmlThen install the rest of the requirements.pipinstall-rfrozen_requirements.txtpipinstallechofilterCiting EchofilterFor technical details about how the Echofilter model was trained, and our
findings about its empirical results, please consult our companion paper:SC Lowe, LP McGarry, J Douglas, J Newport, S Oore, C Whidden, DJ Hasselman (2022). Echofilter: A Deep Learning Segmention Model Improves the Automation, Standardization, and Timeliness for Post-Processing Echosounder Data in Tidal Energy Streams.Front. Mar. Sci.,9, 1â€“21.
doi:10.3389/fmars.2022.867857.If you use Echofilter for your research, we would be grateful if you could cite
this paper in any resulting publications.For your convenience, we provide a copy of this citation inbibtexformat.You can browse papers which utilise Echofilterhere.LicenseCopyright (C) 2020-2022  Scott C. Lowe and Offshore Energy Research Association (OERA)This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, version 3.This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU Affero General Public License for more details.You should have received a copy of the GNU Affero General Public License
along with this program.  If not, see <https://www.gnu.org/licenses/>.