Marine Geospatial Ecology Tools
Marine Geospatial Ecology Tools (MGET), also known as the GeoEco Python package, is an open source programming library designed for coastal and marine researchers and GIS analysts who work with spatially-explicit ecological and oceanographic data in scientific or managerial workflows. The initial MGET releases focus on tools useful in habitat modeling, including tools for processing and sampling remotely-sensed oceanographic data and for creating and evaluating statistical models. Subsequent releases will include more advanced tools presently under development, such as tools for hydrodynamic modeling, connectivity modeling, and spatially-explicit fishery modeling.
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
30-Jul-08 - MGET 0.6a2 is released. Very little new functionality has been added so far, but 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 users: We have not tested MGET with ArcGIS 9.3 yet but will do so as soon as we obtain a copy of 9.3. Based on our experience with the transition from 9.1 to 9.2, we expect that MGET will not work with 9.3 without some code changes. If you try it, please let us know how it goes.
| MGET Version | Release Date | Python Version | Installation Package | Installation Instructions | Change List |
|---|---|---|---|---|---|
| 0.6 alpha 2 | 30-Jul-08 | 2.4 | GeoEco-0.6a2.win32-py2.4.exe | GeoEco 0.6 Installation Instructions | GeoEco 0.6 Change List |
| 2.5 | GeoEco-0.6a2.win32-py2.5.exe | ||||
| 0.5 | 14-Jun-08 | 2.4 | GeoEco-0.5.win32-py2.4.exe | GeoEco 0.5 Installation Instructions | GeoEco 0.5 Change List |
| 2.5 | GeoEco-0.5.win32-py2.5.exe | ||||
| 0.4 | 14-Jan-08 | 2.4 | GeoEco-0.4.win32-py2.4.exe | GeoEco 0.4 Installation Instructions | GeoEco 0.4 Change List |
| 2.5 | GeoEco-0.4.win32-py2.5.exe | ||||
| 0.3 | 20-Sep-07 | 2.4 | GeoEco-0.3.win32-py2.4.exe | GeoEco 0.3 Installation Instructions | GeoEco 0.3 Change List |
| 2.5 | GeoEco-0.3.win32-py2.5.exe | ||||
| 0.2 | 20-Jun-07 | 2.4 | GeoEco-0.2.win32-py2.4.exe | GeoEco 0.2 Installation Instructions | Not available |
| 2.5 | 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
- MGET examples
- Projects that used MGET
- Online documentation
- MGET Overview for 2007 ESRI User Conference (Microsoft PowerPoint format)
- MGET NOAA Coastal GeoTools Conference poster (Microsoft PowerPoint format)
Contact Us
Please email Jason Roberts (jason.roberts@duke.edu) with any questions or feedback. Thanks for your interest in Marine Geospatial Ecology Tools!
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:
