Version 63 (modified by jjr8, 6 years ago)

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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 will focus on tools useful in habitat studies, including tools for processing and sampling remotely-sensed oceanographic data and mapping and filtering ARGOS satellite telemetry. Subsequent releases will include more advanced tools presently under development at Duke's Marine Geospatial Ecology Laboratory and elsewhere.

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

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.

20-Jun-07 - MGET 0.2 is released. The major feature of this release is the batch processing infrastructure, which automatically generates the code, metadata and documentation for batch processing versions of non-batched tools. We introduced very few new non-batched tools in this release, but all existing tools now have two batched versions, in addition to the existing non-batched version.

Please contact us if you would like a tool that is currently available only in the prior unreleased package. We will provide you with a private copy.

Download and Installation

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

MGET Version Release Date Python Version Installation Package Installation Instructions Change List
0.3 2007-09-20 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 2007-06-20 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.)

Reporting Bugs and Getting Help

Please email Jason Roberts ( jason.roberts@duke.edu). Previously we allowed anonymous users to open new tickets but had to close this due to ticket spam.

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. 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

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