Version 125 (modified by jjr8, 5 years ago)

--

Marine Geospatial Ecology Tools

Marine Geospatial Ecology Tools (MGET), also known as the GeoEco Python package, is an open source geoprocessing toolbox designed for coastal and marine researchers and GIS analysts who work with spatially-explicit ecological and oceanographic data in scientific or management workflows. MGET includes over 150 tools useful for a variety of tasks, such as converting oceanographic data to ArcGIS formats, identifying fronts in sea surface temperature images, fitting and evaluating statistical models such as GAMs and GLMs by automatically interfacing ArcGIS with the R statistics program, analyzing coral reef connectivity by simulating hydrodynamic larval dispersal, and building grids that summarize fishing effort, CPUE and other statistics. Currently under development are tools for identifying rings and eddy cores in sea surface height images, for analyzing connectivity networks, for estimating fishing effort when no effort data are available, for predicting hard bottom habitat from coarse grain bathymetry, and much more.

MGET may be accessed from ArcGIS as a toolbox in the ArcToolbox window and from programming languages as a set of Python modules and COM components.

Key Features

  • Free, open-source software written mainly in Python, R and MATLAB
  • Distributed as a self-installing setup program, for easy installation
  • Each "tool" is a software subroutine designed to be invoked programmatically
  • For easy execution from many environments, each tool is exposed from:
    • A Python class
    • A dual-interface Microsoft COM class (on Windows)
    • An ArcGIS geoprocessing toolbox
  • Many tools have both single-input and multi-input (batch processing) implementations
  • All tools include full documentation, one version tailored to  Python programmers and another to  ArcGIS users
  • A verbose logging system eases troubleshooting of difficult failures
  • All tools are written to maximize reliability, interoperability and performance
  • Many tools do not require Windows or ArcGIS; we hope to issue non-Windows releases in the future

A Simple Example

Many oceanography products are published in HDF format but ArcGIS still has difficulty reading this format. The HDF SDS to ArcGIS Raster tool efficiently converts a Scientific Data Set in an HDF file to ArcGIS raster format and performs common post-processing steps.

Project Status

23-Sep-08 - MGET 0.6a5 is released. This release includes the second batch of work needed to make MGET compatible with ArcGIS 9.3. Many tools will now work properly on 9.3, but more work is needed. This release also includes Eric Treml's coral reef connectivity tools and tools for downloading SSH, geostrophic currents, and other data from  Aviso using the OPeNDAP protocol. Also, the Microsoft .NET Framework dependency has been removed from the MGET setup program. Now you no longer need to have the .NET Framework or ArcGIS .NET Support installed in order to install MGET.

14-Jun-08 - MGET 0.5 is released. MGET 0.5 integrates many of Ben Best's  ArcRStats/HabMod tools for exploring and modeling statistical data using GLMs and GAMs. Also included: tools for converting 2-dimensional netCDF variables, with no requirement that the netCDF file adhere to a particular netCDF metadata convention (ArcGIS 9.2's built-in tools have that requirement); improvement of the MGET tools that invoke R, including the ability to easily load ArcGIS tables into R (all data types are supported, including dates!); additional simplification of MGET setup, including automatic installation of all R packages used by MGET; and many bug fixes. The final release of MGET 0.5 will be issued within a week.

14-Jan-08 - MGET 0.4 is released. This release adds tools for creating fishnets (useful for summarizing fishing effort points using a grid), for downloading and sampling climate indices from  NOAA ERSL, and for converting the  GSHHS high-resolution shoreline database to ArcGIS vector formats. Many bug fixes and smaller enhancements are also included.

20-Sep-07 - MGET 0.3 is released. This is the first release to include tools for a specific oceanographic data product, NOAA CoastWatch AVHRR SST, available from  NOAA CLASS. Many  CoastWatch tools were developed, including those for converting CoastWatch data to ArcGIS, binary and HDF formats, for masking clouds, and for  identifying SST fronts using the Cayula-Cornillon (1992) edge detection algorithm. Rather than porting the Cayula-Cornillon code from the prior unreleased package of tools, I reimplemented it from scratch in platform-independent, thread-safe C++ code, with many optimizations. The new implementation can also operate on arbitrary SST data stored in  binary rasters or  numpy arrays. In future releases, I will implement customized versions for other common SST products, such as  MODIS Terra and Aqua, and  NODC 4 km AVHRR Pathfinder.

Download and Installation

If you have never installed MGET before, we highly recommend you review the installation instructions before installing it.

ArcGIS 9.3 users: We are currently working on making MGET compatible with ArcGIS 9.3. Many tools in 0.6 alpha 4 release will work properly with 9.3, but more work is still needed to make all of them compatible. This work is underway and we hope to release a version of MGET that is fully compatible with 9.3 sometime in September, 2008.

MGET Version Release Date Python Version Recommended For Installation Package Installation Instructions Change List
0.6 alpha 5 23-Sep-08 2.4 ArcGIS 9.2 users GeoEco-0.6a5.win32-py2.4.exe GeoEco 0.6 Installation Instructions GeoEco 0.6 Change List
2.5 ArcGIS 9.1 and 9.3 users GeoEco-0.6a5.win32-py2.5.exe
0.5 14-Jun-08 2.4 ArcGIS 9.2 users GeoEco-0.5.win32-py2.4.exe GeoEco 0.5 Installation Instructions GeoEco 0.5 Change List
2.5 ArcGIS 9.1 users GeoEco-0.5.win32-py2.5.exe
0.4 14-Jan-08 2.4 ArcGIS 9.2 users GeoEco-0.4.win32-py2.4.exe GeoEco 0.4 Installation Instructions GeoEco 0.4 Change List
2.5 ArcGIS 9.1 users GeoEco-0.4.win32-py2.5.exe
0.3 20-Sep-07 2.4 ArcGIS 9.2 users GeoEco-0.3.win32-py2.4.exe GeoEco 0.3 Installation Instructions GeoEco 0.3 Change List
2.5 ArcGIS 9.1 users GeoEco-0.3.win32-py2.5.exe
0.2 20-Jun-07 2.4 ArcGIS 9.2 users GeoEco-0.2.win32-py2.4.exe GeoEco 0.2 Installation Instructions Not available
2.5 ArcGIS 9.1 users GeoEco-0.2.win32-py2.5.exe

Note: The proper file names end in .exe. Internet Explorer may mangle the file name to end with [1] instead. For example, it may turn "GeoEco?-0.3.win32-py2.4.exe" into "GeoEco?-0.3.win32-py2.4[1]". If this happens, save the file to your desktop, using the correct name, and run it from there. (This is a bug in the Trac Wiki system we use. It has been fixed but the new version of Trac has not been released yet.)

Citation Instructions

If you use Marine Geospatial Ecology Tools for a project that results in a peer-reviewed paper or other scientific report, please cite it as follows:

Roberts, J. J., B. D. Best, and P. N. Halpin. 2007. Marine Geospatial Ecology Tools. Available online:  http://mgel.env.duke.edu/tools.

Your citations help us obtain funding for additional development and allow us to continue to offer MGET as free software. Thank you for your support. We are preparing a manuscript for publication in a peer-reviewed journal later this year. Please check back to see if the citation instructions have changed.

More Information

Contact Us

Please email Jason Roberts ( jason.roberts@duke.edu) with any questions or feedback. Thanks for your interest in Marine Geospatial Ecology Tools!

To receive notification of new releases of MGET and upcoming presentations related to MGET, please  subscribe to our mailing list. Privacy policy: To subscribe to this list, you must provide us with an email address. Your address will only be used for this list. We will not intentionally share it with anyone else for any reason.

Software License

Marine Geospatial Ecology Tools is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Marine Geospatial Ecology Tools 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 General Public License (available in the file  LICENSE.TXT) for more details.

Acknowledgements

Marine Geospatial Ecology Tools is built atop a lot of other software, much of it free. We would particularly like to thank these developers? for making their excellent work freely reusable. Without your work, MGET would never have gotten off the ground. Cheers to all of you!

Development of Marine Geospatial Ecology Tools is funded by:

source:/WikiFiles/Images/nasa-logo.gif source:/WikiFiles/Images/Packard_Logo_Big.jpg