| 13 | | |
| 14 | | = Marine Geospatial Ecology Tools = |
| 15 | | |
| 16 | | 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 300 tools useful for a variety of tasks, such as downloading popular oceanographic datasets in GIS-compatible formats, identifying fronts and eddies in satellite images, building statistical habitat models from species observations and creating habitat maps, modeling biological connectivity by simulating hydrodynamic larval dispersal, and building grids that summarize fishing effort, CPUE and other statistics. Currently under development are tools 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. |
| 17 | | |
| 18 | | == MGET in ArcGIS == |
| 19 | | |
| 20 | | In ArcGIS, MGET appears in the !ArcToolbox window. You can browse the available tools below. Click the [[Image(source:/WikiFiles/MgetTree/img/icon_expander.png, title="Expander", link="")]] icons to drill into the toolbox. Each [[Image(source:/WikiFiles/MgetTree/img/icon_script.png, title="Tool", link="")]] icon represents a tool. Click on it to view its documentation. |
| 21 | | |
| 22 | | {{{ |
| 23 | | #!html |
| 24 | | <div id="MgetTree" style="max-width:800px">MGET ArcGIS Toolbox</div> |
| 25 | | |
| 26 | | <script type="text/javascript" src="/projects/mget/chrome/site/jquery_plugins/jquery.jstree.js"></script> |
| 27 | | <script type="text/javascript"> |
| 28 | | $(function () { |
| 29 | | $("#MgetTree").jstree({ |
| 30 | | "xml_data" : { |
| 31 | | "ajax" : { |
| 32 | | "url" : "/projects/mget/export/HEAD/MGET/Trunk/PythonPackage/dist/MGETArcGISToolbox_jsTree.xml" |
| 33 | | }, |
| 34 | | "xsl" : "nest" |
| 35 | | }, |
| 36 | | "plugins" : [ "themes", "xml_data" ] |
| 37 | | }); |
| 38 | | }); |
| 39 | | |
| 40 | | /* |
| 41 | | Extra function to enable jstree expansion on items without explicit href links, based on: |
| 42 | | http://www.deanoj.co.uk/programming/javascript/jstree-with-support-for-label-toggle_node-action-and-leaf-href-click-actions/ |
| 43 | | */ |
| 44 | | $("#MgetTree").delegate("a","click", function (e) { |
| 45 | | if (this.attributes.href.value=='#') { |
| 46 | | $("#MgetTree").jstree("toggle_node", this); |
| 47 | | e.preventDefault(); |
| 48 | | return false; |
| 49 | | } |
| 50 | | }); |
| 51 | | |
| 52 | | </script> |
| 53 | | }}} |
| 54 | | |
| 55 | | MGET can also be easily invoked from Python and [wiki:"Invoking MGET tools programmatically" many other programming languages]. |
| 56 | | |
| 57 | | == Example Scenarios == |
| 58 | | |
| 59 | | Here are a few examples of how you can use MGET: |
| 60 | | |
| 61 | | * ["Converting HDFs to ArcGIS rasters"] |
| 62 | | * [wiki:"SinusoidalMODIS" "Converting MODIS HDFs with sinusoidal projections to ArcGIS raster format"] |
| 63 | | * ["Sampling time series rasters"] |
| 64 | | * [wiki:"HabitatModeling" "Modeling species habitat with environmental predictor variables"] - includes downloadable example and video-recorded presentation (UPDATED 30 April 2012) |
| 65 | | * [wiki:"DiGIR" "Downloading species observations from the Ocean Biogeographic Information System (OBIS) with the DiGIR protocol"] |
| 66 | | * [wiki:"SpeciesDiversity" "Calculating species diversity index grids from species presence points"] |
| 67 | | |
| 68 | | This list does not come close to illustrating all of MGET's capabilities. We are currently overhauling the examples and hope to provide more complete list soon. If you have any questions about whether MGET can help with your scenario, please email us (see instructions below). |
| 69 | | |
| 70 | | == Download and Installation == |
| 71 | | |
| 72 | | If you have never installed MGET before, we '''highly recommend''' you review the installation instructions before installing it. |
| 73 | | |
| 74 | | {{{ |
| 75 | | #!rst |
| 76 | | |
| 77 | | +------------------+--------------+--------------------+----------------------------------+------------------------------+----------------------------------+--------------------+ |
| 78 | | | **MGET Version** | **Released** | **Python Version** | **Recommended For** | **Installation Package** | **Installation Instructions** | **Change List** | |
| 79 | | +==================+==============+====================+==================================+==============================+==================================+====================+ |
| 80 | | | 0.8 alpha 43 | 03-Aug-12 | 2.4 | ArcGIS 9.2 users | MGET-0.8a43.win32-py2.4.exe_ | `0.8 Installation Instructions`_ | `0.8 Change List`_ | |
| 81 | | | | +--------------------+----------------------------------+------------------------------+ | | |
| 82 | | | | | 2.5 | ArcGIS 9.1, 9.3, and 9.3.1 users | MGET-0.8a43.win32-py2.5.exe_ | | | |
| 83 | | | | +--------------------+----------------------------------+------------------------------+ | | |
| 84 | | | | | 2.6 | ArcGIS 10 users | MGET-0.8a43.win32-py2.6.exe_ | | | |
| 85 | | +------------------+--------------+--------------------+----------------------------------+------------------------------+----------------------------------+--------------------+ |
| 86 | | | 0.7 | 31-Jul-09 | 2.4 | ArcGIS 9.2 users | GeoEco-0.7.win32-py2.4.exe_ | `0.7 Installation Instructions`_ | `0.7 Change List`_ | |
| 87 | | | | +--------------------+----------------------------------+------------------------------+ | | |
| 88 | | | | | 2.5 | ArcGIS 9.1, 9.3, and 9.3.1 users | GeoEco-0.7.win32-py2.5.exe_ | | | |
| 89 | | +------------------+--------------+--------------------+----------------------------------+------------------------------+----------------------------------+--------------------+ |
| 90 | | |
| 91 | | .. _MGET-0.8a43.win32-py2.4.exe: http://code.nicholas.duke.edu/projects/mget/export/HEAD/MGET/Trunk/PythonPackage/dist/MGET-0.8a43.win32-py2.4.exe |
| 92 | | .. _MGET-0.8a43.win32-py2.5.exe: http://code.nicholas.duke.edu/projects/mget/export/HEAD/MGET/Trunk/PythonPackage/dist/MGET-0.8a43.win32-py2.5.exe |
| 93 | | .. _MGET-0.8a43.win32-py2.6.exe: http://code.nicholas.duke.edu/projects/mget/export/HEAD/MGET/Trunk/PythonPackage/dist/MGET-0.8a43.win32-py2.6.exe |
| 94 | | .. _0.8 Installation Instructions: http://code.nicholas.duke.edu/projects/mget/export/HEAD/MGET/Trunk/PythonPackage/dist/TracOnlineDocumentation/Documentation/GettingStarted.html#Installation |
| 95 | | .. _0.8 Change List: http://code.nicholas.duke.edu/projects/mget/report/9?MILESTONE=0.8 |
| 96 | | .. _GeoEco-0.7.win32-py2.4.exe: http://code.nicholas.duke.edu/projects/mget/export/HEAD/MGET/Tags/GeoEco-0.7/PythonPackage/dist/GeoEco-0.7.win32-py2.4.exe |
| 97 | | .. _GeoEco-0.7.win32-py2.5.exe: http://code.nicholas.duke.edu/projects/mget/export/HEAD/MGET/Tags/GeoEco-0.7/PythonPackage/dist/GeoEco-0.7.win32-py2.5.exe |
| 98 | | .. _0.7 Installation Instructions: http://code.nicholas.duke.edu/projects/mget/export/HEAD/MGET/Tags/GeoEco-0.7/PythonPackage/dist/TracOnlineDocumentation/Documentation/GettingStarted.html#Installation |
| 99 | | .. _0.7 Change List: http://code.nicholas.duke.edu/projects/mget/report/9?MILESTONE=0.7 |
| 100 | | }}} |
| 101 | | |
| 102 | | To help us continue to improve MGET and provide it as free software, the installation program automatically reports the result of the installation and several other pieces of data to the MGET development team. For more information about this, please review our ["Privacy Policy"]. |
| 103 | | |
| 104 | | You can also [wiki:"MGET releases" download old releases]. |
| 105 | | |
| 106 | | == Help, Feedback, and Mailing List == |
| 107 | | |
| 108 | | To get help, suggest an improvement, or send us feedback, please email [mailto:mget-help@nicholas.duke.edu]. You can provide extra debug information by [wiki:"Configuring MGET logging"].We will reply as soon as possible. You may also [https://lists.nicholas.duke.edu/sympa/arc/mget-help "browse the archive"] or [https://lists.nicholas.duke.edu/sympa/subscribe/mget-help "subscribe to the list"] to see what others are saying. |
| 109 | | |
| 110 | | To receive notification of new releases of MGET and upcoming presentations related to MGET, please [https://lists.nicholas.duke.edu/sympa/subscribe/mget-announce "subscribe to our announcements mailing list"]. |
| 111 | | |
| 112 | | If you have any privacy concerns, please review our ["Privacy Policy"] before emailing or subscribing. |
| 113 | | |
| 114 | | == Citation Instructions == |
| 115 | | |
| 116 | | 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: |
| 117 | | |
| 118 | | Roberts, J.J., B.D. Best, D.C. Dunn, E.A. Treml, and P.N. Halpin (2010). Marine Geospatial Ecology Tools: An integrated framework for ecological geoprocessing with ArcGIS, Python, R, MATLAB, and C++. ''Environmental Modelling & Software 25:'' 1197-1207 [http://dx.doi.org/10.1016/j.envsoft.2010.03.029 doi:10.1016/j.envsoft.2010.03.029]. |
| 119 | | |
| 120 | | If you do not have access to the journal and would like a private copy of the paper, please email us. 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. |
| 121 | | |
| 122 | | == More Information == |
| 123 | | |
| 124 | | * [export:/WikiFiles/PowerPoint/MGET_Overview_GeoTools_2009.ppt MGET Overview for NOAA Coastal GeoTools 2009 Conference] (Microsoft !PowerPoint format) |
| 125 | | * ["MGET examples"] |
| 126 | | * ["MGET installation statistics"] |
| 127 | | * [wiki:"Publications" Publications about MGET and projects that used it] |
| 128 | | * [export:/MGET/Trunk/PythonPackage/dist/TracOnlineDocumentation/Documentation/GettingStarted.html Online documentation] |
| 129 | | * [export:/MGET/Trunk/PythonPackage/dist/TracOnlineDocumentation/Documentation/ArcGISReference/ArcGISReference.html ArcGIS Geoprocessing Reference] |
| 130 | | * [export:/MGET/Trunk/PythonPackage/dist/TracOnlineDocumentation/Documentation/PythonReference/PythonReference.html Python Reference] |
| 131 | | |
| 132 | | == Software License == |
| 133 | | |
| 134 | | 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. |
| 135 | | |
| 136 | | 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 [export:/MGET/Trunk/LICENSE.txt LICENSE.TXT]) for more details. |
| 137 | | |
| 138 | | == Acknowledgments == |
| 139 | | |
| 140 | | Marine Geospatial Ecology Tools is built atop a lot of other software, much of it free. We would particularly like to thank [wiki:"Acknowledgments" 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! |
| 141 | | |
| 142 | | Development of Marine Geospatial Ecology Tools is funded by: |
| 143 | | |
| 144 | | [[Image(source:/WikiFiles/Images/noaa_logo.png, link=http://www.noaa.gov/, title="National Oceanic and Atmospheric Administration")]] [[Image(source:/WikiFiles/Images/nasa-logo.gif, link=http://www.nasa.gov/, title="National Aeronautics and Space Administration")]] [[Image(source:/WikiFiles/Images/CCCHFA_logo.jpg, link=http://www.ccchfa.org/, title="Cape Cod Commercial Hook Fishermen's Association")]] [[Image(source:/WikiFiles/Images/coml_logo.png, link=http://www.coml.org/, title="Census of Marine Life")]] [[Image(source:/WikiFiles/Images/Packard_Logo_Big.jpg, link=http://www.packard.org/, title="The David & Lucile Packard Foundation")]] |
