Transcript Geog 375 final project

William Perry
U.S. Geological Survey
Western Ecological Research Center
Geography 375 Final Project
May 22, 2013
Background
• Rapidly growing field of landscape genetics in ecological research
• Promising approach using GIS visualization and analysis of genetic landscapes
• Allows users to map patterns of genetic divergence and diversity
• Need to automate a series of steps to create these genetic landscapes
• Python tool speeds up work and reduces error in complex, repetitive workflows
Python Script
Script Output
Script Overview
Three Main Sections -
1. Read in species point data, create TIN edges with midpoints,
join back to points to create composite key
2. Read in file with genetic distance data, create composite key,
join back to the species midpoints file
3. Create single species genetic surfaces
Input data
Species collection points
Table with genetic distance values
Python Script
• Read in species point feature class.
• Create TIN
• Edit TIN to add in the species point information.
• Create TIN triangle polygons and TIN edges.
• Convert feature vertices to points from TIN edges.
• Add XY coordinates to the Mid points of TIN edge.
• Make Table view to do a spatial join between input points and TIN edge lines
• Add field to store genetic distance data
• Add fields to store unique composite key to start and end population names.
• Read in dbf file containing genetic data.
• Create composite key for start and end populations.
• Create genetic landscape surface using IDW interpolation.
• Clip genetic landscape surface to study area grid.
• Create Minimum, Maximum, AllNegative, Allpositive grids using Map Algebra.
• Divide the species grid by the Maximum grid to get standardized grid.
Python Script
Script Info
Python Script
Create variables
for tool dialog
Set the workspace
Python Script
Create scratch
geodatabase
Python Script
Create TIN, edit TIN,
create TIN edges, start,
end and mid points
Add XY coordinates
to TIN midpoint file
Python Script
Spatial join from TIN edge
start points back to point
features
Spatial join from TIN edge
end points back to point
features
Python Script
Add fields, create
composite key
Read in file with genetic
distance values
Add fields, create
composite key
Python Script
Write genetic values
to species midpoints
Create the genetic surface
using IDW, clip to study
area grid, then clip to TIN
polygon tag file
Python Script
Create grids needed
for final output grid
Create final standardized
grid and grid with raw
values
Files Created
Tool Dialog in ArcMap
Tool runs successfully!
Tool Output
Obstacles Encountered
• Exported python from ModelBuilder for code outline
• Numerous changes required to get tools to function in python
• Changes in tool syntax between ArcGIS versions (Map Algebra)
• Excel files not supported in x64 version of python!
• Additional troubleshooting required to run as tool in ArcGIS
Test script for 64 vs 32 bit python to read in Excel files
Batch file to run 32 bit version of python
Future Enhancements
• Add support for additional input formats (csv)
• Finish polishing script and include with toolbox for distribution
• Customize script tool behavior using python validation