Documentation for the LSDTopoToolBox

This documentation is for the Topographic Toolbox developed by the Land Surface Dynamics (LSD) Group at the University of Edinburgh’s School of GeoSciences.

Note this is a user guide and not documentation of the API. The detailed documentation of the software including objects, member functions and variables may be found at the Source code documentation site.

Authors

This software has been developed by:

• Simon M. Mudd; School of GeoSciences, University of Edinburgh
• Martin D. Hurst; British Geological Survey
• David T. Milodowski; School of GeoSciences, University of Edinburgh
• Stuart W.D. Grieve; School of GeoSciences, University of Edinburgh
• Fiona J. Clubb; School of GeoSciences, University of Edinburgh
• Declan A. Valters; School of Earth, Atmospheric and Environmental Sciences, University of Manchester

Contents

• 1. General Information
  • 1.1. What is this software?
  • 1.2. Why don’t we just use ArcMap? It has topographic analysis tools.
  • 1.3. How do I get the software?
• 2. Instructions specific to University of Edinburgh
  • 2.1. Getting onto our servers using NX
    • 2.1.1. Using NX from your home computer
  • 2.2. Using Subversion
    • 2.2.1. Examining past changes
    • 2.2.2. Looking at what is in the repository from the command line
    • 2.2.3. Accessing the repository and using subversion from a windows machine
    • 2.2.4. Checking out the code
    • 2.2.5. Updating your code at the start of an editing session
    • 2.2.6. Making changes to the code
    • 2.2.7. Tags and branches
    • 2.2.8. Importing a new directory tree into the repository
    • 2.2.9. Changing permissions
  • 2.3. Using the Edinburgh DataStore
    • 2.3.1. Donating storage to the DataStore (this gives you access to it)
    • 2.3.2. Creating a shortcut to the datastore from your home directory in Linux
  • 2.4. Using the supercomputer Eddie
    • 2.4.1. The work space
    • 2.4.2. Transfering data to and from Eddie
    • 2.4.3. Running jobs on Eddie
    • 2.4.4. Summary
  • 2.5. Installing Packages on Your Local Python Install
• 3. Instructions for external users: Libraries and Dependencies
  • 3.1. Basic Requirements
    • 3.1.1. Essentials
    • 3.1.2. TNT
  • 3.2. Requirements for LSDRasterSpectral
    • 3.2.1. Fast Fourier Transform Library
  • 3.3. Requirements for LSDRasterModel
    • 3.3.1. Boost
    • 3.3.2. MTL
  • 3.4. Requirements for LSDSwath (and LSDCloudBase)
    • 3.4.1. PCL
    • 3.4.2. libLAS
• 4. Version control with git
  • 4.1. Getting started with Git
  • 4.2. Adding files and directories to the repository
  • 4.3. Committing to the repository
  • 4.4. Pushing your repository to Github
  • 4.5. Problems with Setting up repos on github
    • 4.5.1. Creating local repo and then Github repository
• 5. Data preparation
  • 5.1. What data does LSDTopoToolbox take?
  • 5.2. Data Sources
  • 5.3. Important note on spatial reference systems
  • 5.4. Converting data from ArcMap
    • 5.4.1. Checking the spatial reference
    • 5.4.2. Projecting data in ArcMap
    • 5.4.3. Exporting to .flt format from Arc
    • 5.4.4. Exporting to ENVI .bil format from Arc THIS IS THE PREFERRED FORMAT
  • 5.5. Conversion of formats using QGIS
  • 5.6. Conversion of float files to other formats using GDAL
  • 5.7. Data Visualisation options
• 6. Data preparation 2: using GDAL
  • 6.1. Finding out what sort of data you’ve got
  • 6.2. Translating your raster into something that can be used by LSDTopoToolbox
    • 6.2.1. Changing raster projections with gdalwarp
    • 6.2.2. Changing raster format with gdal_translate
    • 6.2.3. Potential filename errors
  • 6.3. Clipping rasters with gdal
• 7. Extracting typical metrics
  • 7.1. Getting your raster into the correct format
  • 7.2. Compiling the driver function
  • 7.3. Running the driver function
• 8. Chi analysis: part 1: getting channel profiles
  • 8.1. Quick guide
  • 8.2. Overview
  • 8.3. Warning
  • 8.4. Getting the raw DEM into the toolkit
    • 8.4.1. Data Sources
    • 8.4.2. Getting the data into the chi profile tool
  • 8.5. Compiling the two driver functions
  • 8.6. Running the channel network extraction
    • 8.6.1. Writing junctions
    • 8.6.2. Extracting the .chan file
    • 8.6.3. Format of the .chan file
• 9. Chi analysis: part 2: extracting the m/n ratio and performing the chi transformation
  • 9.1. Steps involved to perform channel analysis
  • 9.2. Performing a statistical analysis to constrain the best fit m/n ratio
    • 9.2.1. Compiling the code
    • 9.2.2. Running the code
    • 9.2.3. The ‘movern’ file
    • 9.2.4. Performing a sensitivity analysis on the best fit ratio
  • 9.3. Extracting the transformed chi-elevation profiles
    • 9.3.1. The .tree file
  • 9.4. Visualising the analysis
    • 9.4.1. AICc_plotting.py
    • 9.4.2. Plotting sensitivity: AICc_plotting_multiple.py
    • 9.4.3. Plotting chi profiles and values chi_visualisation.py
    • 9.4.4. Plotting the sensitivity of best fit values to parameters: bf_movern_sensitivity.py
    • 9.4.5. Plotting the spatial distribution of values: raster_plotter_2d_only.py
  • 9.5. A Sample Chi Analysis Workflow
• 10. Scripting and Supercomputing for Topographic Analysis
  • 10.1. Creating multiple driver files for a list of basins
  • 10.2. Embarassingly Parallel Topographic Analysis
    • 10.2.1. The Simple Case - A single cpu, multi-core laptop
  • 10.3. Topographic Analysis on a Supercomputer
    • 10.3.1. PBS Example
    • 10.3.2. SGE Script Example
    • 10.3.3. Checking your jobs
    • 10.3.4. Module issues
    • 10.3.5. Compilation and library issues
• 11. Selecting a window size for surface fitting
  • 11.1. Quick guide
  • 11.2. Overview
  • 11.3. Warning
  • 11.4. Before You Start
  • 11.5. Input Data
    • 11.5.1. Raw DEM
  • 11.6. Compile The Driver
  • 11.7. Run The Code
  • 11.8. The Output Data
  • 11.9. Using Python To Select A Window Size
• 12. Extraction of Hillslope Lengths and Basin Metrics
  • 12.1. Quick guide
  • 12.2. Overview
  • 12.3. Warning
  • 12.4. Before You Start
  • 12.5. Input Data
    • 12.5.1. Raw DEM
    • 12.5.2. Floodplain Mask (Optional)
    • 12.5.3. Generating Channel Heads
    • 12.5.4. Getting The Window Size
  • 12.6. Compile The Driver
  • 12.7. Run The Code
  • 12.8. Analysing The Results
• 13. Generating E* R* data
  • 13.1. Quick guide
  • 13.2. Overview
  • 13.3. Warning
  • 13.4. Before You Start
  • 13.5. Input Data
    • 13.5.1. Input Topographic Data
  • 13.6. Compile The Driver
  • 13.7. Run The Code
  • 13.8. The Output Data
  • 13.9. Using Python To Analyse The Data
    • 13.9.1. Plotting The Segments
    • 13.9.2. Plotting The Raw Data
    • 13.9.3. Binning the Raw Data
    • 13.9.4. Getting A Best Fit Critical Slope
• 14. Extraction of channel networks
  • 14.1. Quick guide
  • 14.2. Overview
  • 14.3. Warning
  • 14.4. Before You Start
  • 14.5. Getting the correct m/n value
  • 14.6. Downloading the DrEICH algorithm
  • 14.7. Creating a parameter file
  • 14.8. Run the channel head driver
• 15. Junction Extraction
  • 15.1. Quick guide
  • 15.2. Overview
  • 15.3. Warning
  • 15.4. Before You Start
  • 15.5. Compile The Driver
  • 15.6. Run The Code
  • 15.7. The Results
    • 15.7.1. Junction File
• 16. Swath profiles
  • 16.1. Preprocessing step 1: Getting your raster into the correct format
  • 16.2. Preprocessing step 2: Creating the baseline
  • 16.3. Compiling the driver function
  • 16.4. Running the driver function
  • 16.5. Program outputs
  • 16.6. Channel Long Profiles using the Swath Tools
    • 16.6.1. Example Applications
    • 16.6.2. Example Usage
• 17. Computing length scales using the spectral method
  • 17.1. Compiling the driver function
  • 17.2. Running the driver function
  • 17.3. Program outputs
• 18. Landscape Evolution Model
  • 18.1. Parameter File
  • 18.2. Model Domain
  • 18.3. Fluvial Component
  • 18.4. Hillslope Component
  • 18.5. Running the Model
  • 18.6. Model Output
• 19. Catchment/Basin Evolution Model
  • 19.1. What does this model do?
  • 19.2. How does LSDCatchmentModel fit in with LSDRasterModel?
  • 19.3. Brief Usage Guide
  • 19.4. DEM preparation
  • 19.5. Model Parameters
• 20. Basinwide cosmogenics
  • 20.1. Getting your raster into the correct format
  • 20.2. Compiling the comsogenic program
  • 20.3. Setting up your data directories
    • 20.3.1. The parameter file
    • 20.3.2. The cosmogenic data file
    • 20.3.3. The raster names file
  • 20.4. Calculating topographic shielding rasters
    • 20.4.1. Steps for preparing the rasters for shielding calculations
    • 20.4.2. Shielding computation
  • 20.5. Running the driver function
  • 20.6. The output files

Search

• Search Page