Skip to content
RHESSysWorkflows provides Python scripts for building RHESSys models
Python
Find file
Latest commit aee5c9d Apr 19, 2016 @selimnairb Add link to grass64
Failed to load latest commit information.
bin Verbose more, only try to print stdout if data exists to print Jul 6, 2015
docs
etc
rhessysworkflows
.gitignore
Doxyfile 1.33 release Jul 6, 2015
MANIFEST.in
README.md
setup.py

README.md

RHESSysWorkflows {#index}

Introduction

RHESSysWorkflows provides a series of Python tools for performing RHESSys data preparation workflows. These tools build on the workflow system defined by EcohydroLib.

Before reading ahead, you might want to check out this screencast, which provides a conceptual overview RHESSysWorkflows.

Table of Contents

Authors

Brian Miles - brian_miles@unc.edu

Lawrence E. Band - lband@email.unc.edu

For questions or support contact Brian Miles

Funding

This work was supported by the following NSF grants

  • Award no. 1239678 EAGER: Collaborative Research: Interoperability Testbed-Assessing a Layered Architecture for Integration of Existing Capabilities

  • Award no. 0940841 DataNet Federation Consortium.

  • Award no. 1148090 Collaborative Research: SI2-SSI: An Interactive Software Infrastructure for Sustaining Collaborative Innovation in the Hydrologic Sciences

Source code

Source code can be found at: https://github.com/selimnairb/RHESSysWorkflows

Documentation can be found at: http://pythonhosted.org/rhessysworkflows

Installation instructions

These instructions will lead you through installing RHESSysWorkflows (and EcohydroLib) as well as GRASS 6.4 and QGIS open source GIS applications; GRASS is required by RHESSysWorkflows, and QGIS is convenient to have for visualizing GIS data acquired and produced as you make RHESSys models.

These instructions are tailored to OS X and Linux users (specifically Ubuntu 14.04, or 15.04; 15.10 is not compatible as it ships with GRASS 7 rather than GRASS 6.4), however installation under other Linux distributions is also possible. RHESSysWorkflows may in theory work under Windows, but this has never been tested. Windows users are encouraged to run an Ubuntu under a virtual machine.

RHESSysWorkflows is compatible with OS X 10.6 through 10.11, but only versions 10.9 through 10.11 are officially supported. For installation instructions for OS X 10.6 through 10.8, see Deprecated installation instructions toward the end of this document.

To find out what version of OS X you are currently running, click on the apple in the upper left corner of the screen and select About this Mac. To find out the latest version of OS X you computer can run, visit this helpful page.

If you encounter problems during installation, please check the installation notes before contacting the developers for support.

Installing on OS X using Homebrew

Previous methods for installing RHESSysWorkflows under OS X relied on the official GRASS 6.4 GIS packages. Unfortunately, the official GRASS 6.4 (and the new GRASS 7 for that matter) are not compatible with new security enhancements in OS X 10.11 (El Capitan). Rather than disable this new security measure (called System Integrity Protection), we recommend that RHESSysWorkflows users use a new Homebrew-based installation method, which will install GRASS without requiring that the security features of your operating system be disabled.

Homebrew is a third-party package management system that makes it easy to install open-source software under OS X. Each software package one can install through Homebrew is called a formula. To search for available software formula, visit Braumeister.

  • Install Homebrew by following the instructions here.

During installation you may be prompted to install OS X command line developer tools. Choose "Install".

If you already have Homebrew installed, make sure to do the following before proceeding:

brew update
brew upgrade
  • Next, install the OSGeo4Mac tap for Homebrew by following the instructions here.

A tap allows software developers to maintain a collection of software formulae; OSGeo4Mac curates a number of formula related to open source GIS software.

Now Homebrew is installed and we just need to install a few software dependencies before installing RHESSysWorkflows.

Install dependencies for GRASS, QGIS, and RHESSysWorkflows

First, install XQuartz, which is needed by GRASS, by running the following command from the Terminal application:

brew install Caskroom/cask/xquartz

Next, install Python 2.7:

brew install python

Note, this will install a separate copy of Python 2.7 so it will not interfere with the copy of Python 2 that ships with OS X.

Install RHESSysWorkflows and Python packages

To install RHESSysWorkflows and its dependencies (including EcohydroLib), enter the following from the terminal Terminal:

pip install rhessysworkflows
Upgrading to a new version of RHESSysWorkflows

To upgrade to a newer version of RHESSysWorkflows, enter the following into the Terminal:

pip install rhessysworkflows --upgrade --force-reinstall

If pip does not install the version you expect, it may be necessary to first remove RHESSysWorkflows and Ecohydrolib before installing the new version (especially under Linux where some Python packages fail to build when installed via pip):

pip uninstall rhessysworkflows
pip uninstall ecohydrolib

Then install as above:

pip install rhessysworkflows

Install GRASS and QGIS

Install GRASS and QGIS using Homebrew as follows from the Terminal:

brew install grass-64 gdal-20 qgis-214 --without-server ffmpeg
brew link grass-64 --force
brew linkapps qgis-214

You will also need to install a Python library for accessing PostGIS geospatial databases; This is required by QGIS:

pip install psycopg2 # Do after installing QGIS, which will install PostqreSQL

This concludes the OS X Homebrew-specific portion of the installation instructions.

Installing on Ubuntu Linux 14.04 or 15.04

Install RHESSysWorkflows/EcohydroLib dependencies using apt-get:

sudo apt-get install build-essential git subversion p7zip-full \
python python-dev python-pip python-scipy \
libxml2-dev libxslt-dev \
gdal gdal-bin python-gdal \
grass grass-dev \
libbsd-dev ffmpeg vlc

Note: the above works for Ubuntu 14.04. For 15.04 the packaging of GDAL has changed use the following to install dependencies under Ubuntu 15.04:

sudo apt-get install build-essential git subversion p7zip-full \
python python-dev python-pip python-scipy \
libxml2-dev libxslt-dev \
libgdal-dev libgdal-doc gdal-bin python-gdal \
grass grass-dev \
libbsd-dev ffmpeg vlc

Ubuntu 15.10 is not compatible with RHESSys or RHESSysWorkflows as this version of Ubuntu uses GRASS 7, which is not yet supported by RHESSys or RHESSysWorkflows. If you want to use another Linux distribution, make sure that it provides similar versions of the above dependencies.

Install RHESSysWorkflows and Python packages under Linux

To install RHESSysWorkflows and its dependencies (including EcohydroLib), enter the following from your Terminal:

sudo pip install rhessysworkflows
Upgrading to a new version of RHESSysWorkflows

To upgrade to a newer version of RHESSysWorkflows, enter the following into the Terminal:

sudo pip install rhessysworkflows --upgrade --force-reinstall

If pip does not install the version you expect, it may be necessary to first remove RHESSysWorkflows and Ecohydrolib before installing the new version (especially under Linux where some Python packages fail to build when installed via pip):

sudo pip uninstall rhessysworkflows
sudo pip uninstall ecohydrolib

Then install as above:

sudo pip install rhessysworkflows

This concludes the Linux-specific portion of the installation instructions.

A note on RHESSysWorkflows version numbers

Each project can only be used with compatible versions of RHESSysWorkflows/Ecohydrolib. Compatible versions are those that write the same version number to the metadata store for a given project. This compatibility check is necessary to ensure both scientific reproducibility and to make sure your workflows do not become corrupted by incompatible versions. We strive to maintain compatibility between releases of RHESSysWorkflows/Ecohydrolib, however sometimes enabling new workflow scenarios requires incompatible changes. The release notes for each release will note when a new version breaks backward compatibility. The good news is that you can have multiple copies of RHESSysWorkflows/Ecohydrolib installed on your computer at the same time. To do so, you must do the following:

  1. Install virtualenv

  2. Create a new virtual environment for each version of RHESSysWorkflows you would like to run

  3. Activate a virtual environment you would like to install a specific version of RHESSysWorkflows into

  4. Install RHESSysWorkflows in the virtual environment, for example to install version 1.0:

    pip install rhessysworkflows==1.0

Not that you do not need to use 'sudo' when running in a virtual environment as the files are installed in a directory owned by your user account.

Install GRASS Addons for RHESSysWorkflows

Follow these steps to install the GRASS addons under OS X and Linux:

  1. Start GRASS:

    • OS X: In the Terminal, type:
brew link gettext --force   # Make sure GRASS's g.extension program can find gettext, which is used in internationalization.
grass64
  • Linux: on a command line type: grass64
  1. Create a new location (it doesn't matter where, we'll only use it to run the g.extension command to install the extensions).

  2. Install r.soils.texture

    g.extension extension=r.soils.texture

  3. Install r.findtheriver

    g.extension extension=r.findtheriver

  4. Exit GRASS (close all GUI windows, then type exit in the GRASS command line window).

  5. On OS X only, once you have exited GRASS do the following:

brew unlink gettext     # Re-hide the version of gettext installed by Homebrew, which may conflict of that of OS X.

For more information on these addons (r.soils.texture and r.findtheriver), see:

Setup EcohydroLib and RHESSysWorkflows configuration file

  • Choose the appropriate prototype configuration file:

  • Save into a file named '.ecohydro.cfg' stored in your home directory and replace all occurances of <myusername> with your user name (To find out your OS X or Linux user name, use the whoami command in Terminal).

  • Set ECOHYDROLIB_CFG environment variable so that RHESSysWorkflows can find your configuration file

    • Under OS X, from Terminal, do the following:

      echo "export ECOHYDROLIB_CFG=${HOME}/.ecohydro.cfg" >> ~/.bash_profile

    • If you're running Linux, do the following:

      echo "export ECOHYDROLIB_CFG=${HOME}/.ecohydro.cfg" >> ~/.profile

      echo "export LD_LIBRARY_PATH=/usr/lib/grass64/lib:${LD_LIBRARY_PATH}" >> ~/.profile

    • Re-load bash profile (or close and open a new Terminal window):

      source ~/.bash_profile (~/.profile under Linux)

This concludes the configuration portion of the installation and configuration instructions.

Using RHESSysWorkflows - Introduction

All EcohydroLib and RHESSysWorkflows tools are executed from the command line. Each tool stores the data and metadata associated with a single workflow in a directory, called a project directory. Metadata are stored in a file in the project directory called metadata.txt. There can only be one metadata.txt in a project directory, so it is essential that each workflow have its own project directory.

In addition to automatically recording provenance information for data and the processing steps of a workflow, the metadata store allows for loose coupling between the tools that are used to carry out a particular workflow. By design, each workflow tool performs roughly one discrete function. This allows for flexible workflows. Each workflow tool writes a series of entries to the metadata to reflect the work done by the tool. Most workflow tools require certain entries to be present in the metadata store to perform the work they will do. For example, before DEM data for the study are can be downloaded from DEMExplorer, the bounding box for the study area must be known. The tool that queries DEMExplorer need not know how the bounding box was generated, it only cares that the bounding box is present in the metadata store. Lastly, the metadata store helps users to orchestrate workflows by requiring that only new information required at each step be entered to run a particular command, other information required can be queried from the metadata.

Each workflow tool will print usage information when run on its own for example running:

GetNHDStreamflowGageIdentifiersAndLocation.py 

Will yield:

usage: GetNHDStreamflowGageIdentifiersAndLocation.py [-h] [-i CONFIGFILE] -p
PROJECTDIR -g GAGEID
GetNHDStreamflowGageIdentifiersAndLocation.py: error: argument -p/--projectDir is required

This indicates that the -p (a.k.a. --projectDir) argument is required; that is, you must specify the project directory associated with workflow for which you are running the tool. For many EcohydroLib/RHESSyWorkflows tools, this is the only required command line parameter.

It's good practice when running a command to first execute the command with no command line arguments. This will show you the required and optional parameters. To get detailed help for a given command, run the command with the -h (a.k.a. --help) argument, for example:

GetNHDStreamflowGageIdentifiersAndLocation.py -h

Note that while this particular tool, and RHESSysWorkflows tools in general, have long names, they are long to be descriptive so as to be easier to use. To avoid having to type these long names out, you are encouraged to make use of tab completion in Terminal. To use tab completion, simply type the first few characters of a command and then hit the 'tab' key on your keyboard; the entire command name will be 'completed' for you on the command line. If the entire name is not 'completed' for you, hit tab again to see that list of commands that match what you've typed so far. Once you type enough characters to uniquely identify the command, hitting tab once more will complete the command name.

Using RHESSysWorkflows - Typical workflows

A typical workflow will consist of running data processing/registration tools from EcohydroLib. Once the required datasets are in place (e.g. DEM, soils, landcover, etc.) RHESSysWorkflows tools can be run to create the world file and flow table associated with a RHESSys model.

In the following sections two example workflows are described: (1) using data from national spatial data infrastructure (USGS, NHD, NLCD, SSURGO, SRTM); and (2) using custom local data. The combinations of tools executed in these workflows represent two of the many unique workflows possible.

National spatial data workflow

Start by creating a directory called 'standard'. This will be your project directory for this example workflow. You can create this directory anywhere on your computer where you have write access (e.g. in your home directory).

Specify a USGS streamflow data to locate on the NHD network

First, choose the USGS streamflow gage, identified by the USGS site number, you wish to build a RHESSys model for. Note that while you can select gages that drain large basins, if you are planning to use SSRUGO soils data acquired using the RHESSysWorkflows tool GetSSURGOFeaturesForBoundingbox the study area must be less than 10,000 sq. km.

To locate the USGS gage of interest on the NHD flow line network run the following tool:

GetNHDStreamflowGageIdentifiersAndLocation.py -p standard -g 01589312

This will create the metadata store for your project in a file named metadata.txt in the project directory 'standard'. The metadata store will be populated with the gage ID (the site number you specified on the command line), and the NHD reachcode and reach measure associated with this gage. By default, RHESSysWorkflows will use a web service to perform this query. (If you are using a local copy of the NHDPlusV2 data add the -s local command line argument to the above command; Most users should ignore this.)

Note that USGS NWIS gage identifiers can begin with '0'. You must enter this leading 0 when specifying a streamflow gage.

Extract NHD catchments that drain through the streamflow gage

The NHD database relates stream flowlines to the catchments that drain into them. RHESSysWorkflows can use these catchments, stored in a shapefile in your project directory, to determine the geographic bounding box for your study area (see below). This bounding box can then beused extract spatial data for your study area from datasets stored locally as well as those available via web services interfaces.

To extract a shapefile of the NHD catchments that drain through your streamflow gage, run the following tool:

GetCatchmentShapefileForNHDStreamflowGage.py -p standard

(If you are using a local copy of the NHDPlusV2 data add the -s local command line argument to the above command; Most users should ignore this.)

You should now see the study area shapefile in your project directory. You can visualize the study area, along with the streamflow gage, in QGIS. Note that the study area shapefile does not represent the delineation of your watershed, but should instead be a superset of the watershed. We will delineate your watershed using GRASS GIS.

Get bounding box for study area

Now that RHESSysWorkflows has a GIS representation of your study area, it can determine the extent or bounding box (also sometimes called the 'minimum bounding rectangle') of the study area. Do so by running the following tool:

GetBoundingboxFromStudyareaShapefile.py -p standard

As with many EcohydroLib/RHESSysWorkflows commands, you won't see much in the way of output printed to the screen; don't fear. The commands are writing what's needed for future workflow steps to the metadata store associated with your project directory. If you open the metadata store, the file called metadata.txt in the project directory standard, you can see the bounding box coordinates stored in the study_area section; look for the attribute named bbox_wgs84.

Acquire terrain data from U.S. Geological Survey

U.S. Geological Survey (USGS) has developed a prototype web service for downloading terrain data based on the National Elevation Dataset (NED). Now that we've defined the bounding box for our study area, it's very easy to download DEM data from this web service, as follows:

GetUSGSDEMForBoundingbox.py -p standard

By default, this tool will download an extract terrain data for your study area from the National Elevation Dataset (NED) 30-meter (1/3 arcsecond) USA DEM. The DEM will be stored in a UTM project (WGS84 datum) with the appropriate UTM zone chosen for you. You can override both the DEM coverage type and target spatial reference system by specifying the appropriate command line parameters; spatial reference systems must be refered to by their EPSG code (see http://www.spatialreference.org/ref/epsg/ for more information). Additionally, you can choose to resample the DEM extract to another spatial resolution. To learn how to specify these options, issue the help command line argument as follows:

GetUSGSDEMForBoundingbox.py -h

Note that EcohydroLib/RHESSysWorkflows uses the DEM resolution, extent, and sptial reference the reference for all other rasters imported into or generated by subsequent workflow tools.

Lastly, you are not required to use a DEM from the USGS web service. See the Custom local data workflow example below, as well as the Working in watersheds outside the United States section for more information.

Extract landcover data from local NLCD 2006 or 2011 data

EcohydroLib makes it easy to import custom NLCD 2006 or 2011 tiles for your study area into your project from web services hosted by U.S. Geological Survey. For example, to acquire NLCD 2011 data:

GetUSGSNLCDForDEMExtent.py -p standard

This command will download an NLCD 2011 data matching the extent, resolution, and spatial reference of your DEM and store the tile in your project directory. (If you wish to give your NLCD tile a particular name, use the outfile command line option. To instead download NLCD 2006 data, do the following:

GetUSGSNLCDForDEMExtent.py -p standard -t NLCD2006

Download soils data from SSURGO

The USDA NRCS provides the Soil Data Mart, a sophisticated web services-based interface for querying and downloading high-resolution SSURGO soils data. SSURGO data are structured as a complex database consisting of both spatial and tabular data. For more information on this database format and the soil survey data exposed through the SSRUGO database please see the SSURGO metadata.

EcohydroLib provides two tools that make it easy to generate soil hydraulic properties commonly needed for ecohydrology modeling (namely the numeric properties Ksat, porosity, percent sand, percent silt, and percent clay). The first tool downloads spatial mapunit features for your study area as well as tabular soil hydraulic property data. These spatial and tabular data are joined, and written to your project directory as an ESRI Shapefile. For more information on what attributes are queried and how non-spatial mapunit commponents are aggregated by the code, please see the EcohydroLib source code here and here.

To download SSURGO features and attributes into your project, run the following command:

GetSSURGOFeaturesForBoundingbox.py -p standard

Note that for server performance and network bandwidth issues, Soil Data Mart limits SSURGO spatial queries to areas of less than roughly 10,000 sq. km. For performance reasons, EcohydroLib (and therefore RHESSysWorkflows) limits the size of SSURGO queries to ~2,500 sq. km. If your study area is larger than this, you must instruct GetSSURGOFeaturesForBoundingbox to tile the query into multiple sub queries. SSURGO query tiling is enabled using the --tile option:

GetSSURGOFeaturesForBoundingbox.py -p MYPROJECT_DIRECTORY --tile

What this does is to split the larger query to the Soil Data Mart into many smaller queries (possibly hundreds or thousands). The results of these sub-queries are then automatically assembled into a single vector feature layer by EcohydroLib. To reduce download times, tiled queries are by default performed in parallel. The number queries to run in parallel is determined automatically by the number of simultaneous threads your computer supports (see here for more information). Use the --nprocesses option to change the number of SSURGO queries to perform in parallel. For example, to perform 16 queries in parallel (which should be fine on an 8-thread machine):

GetSSURGOFeaturesForBoundingbox.py -p MYPROJECT_DIRECTORY --tile --nprocesses 16

To disable parallel queries:

GetSSURGOFeaturesForBoundingbox.py -p MYPROJECT_DIRECTORY --tile --nprocesses 1

You can visualize the downloaded SSURGO features and joined tabular data by opening the shapfile in QGIS. The SSURGO shapefile has a long, though descriptive, name that includes the bounding box coordinates for your study area. If you are unsure what shapefile in your project directory to open, the soil_features attribute of the manifest section of your metadata store lists the filename.

While you're looking at the metadata store, scroll down to the provenance section. While the attribute names are a bit messy, you can see that for each manifest entry, there EcohydroLib has recorded detailed provenance information. For the SSURGO soil features, the Soil Data Mart web services URL is listed as the datasource; for the DEM data downloaded from DEM Explorer, EcohydroLib records the exact URL used to download your DEM. Lastly, if you scroll down a bit farther, you can see that the history section of the metadata store records the order of every EcohydroLib/RHESSysWorkflow command you've run in this workflow, including all of the command line parameters.

EcohydroLib also provides a second tool for dealing with SSURGO soils data. This tool allows you to create raster maps of SSURGO mapunit polygons using the following numeric soil properties as raster values: Ksat, porosity, percent clay, percent silt, and percent sand). Use the following command to generate all of these rasters in your project directory:

GenerateSoilPropertyRastersFromSSURGO.py -p standard

Later on in this example workflow, we'll use the percent sand and percent clay rasters to generate a USDA soil texture map, which we'll use to define RHESSys soil parameters for our study watershed.

Registering custom local data: LAI data

EcohydroLib does not current provide direct access to vegetation leaf area index data from remote sensing sources. LAI data are needed by RHESSys to initialize vegetation carbon and nitrogen stores. RHESSysWorkflows relies can use a user-supplied LAI rasters to supply these initial LAI data to RHESSys. For this example workflow, you can download an LAI image here. Use the following command to register this user-supplied raster into your project:

RegisterRaster.py -p standard -t lai -r /path/to/static_lai-01589312.tif -b "Brian Miles <brian_miles@unc.edu>"

To make this command work, you'll have to change the path to the file name passed to the -r argument to reflect the location on your computer to which you downloaded the example LAI image.

Note that EcohydroLib/RHESSysWorkflows do not work with files or directories whose names contain spaces. This will be addressed in a future release.

Also, the extent of the LAI image doesn't quite match that of our DEM. By default, RegisterRaster will not import a raster that does not match the extent of the DEM. Use the --force option to force RegisterRaster to import the raster:

RegisterRaster.py -p standard -t lai -r /path/to/static_lai-01589312.tif -b "Brian Miles <brian_miles@unc.edu>" --force

When using the force option, it is even more important that you check the results of the command to ensure the data registered with the workflow are appropriate for the modeling you plan to perform. Go ahead and browse to your project directory, find the DEM and LAI rasters and open them in QGIS (you will likely have to set a color map for each, otherwise all values will render in grey).

Note the -b (a.k.a. --publisher) argument given to the above command. When specified, this optional parameter will be stored in the provenance matadata store entry of the raster.

RegisterRaster is a generic EcohydroLib tool that knows how to import several types of raster into your workflow; the -t lai argument indicates that we are importing an LAI raster (see the Custom local data workflow for to learn how to import other raster types). RegisterRaster will copy the raster being imported into your project directory; the raster will be resampled and reprojected to match the resolution and spatial reference of the DEM already present in the workflow. You can choose the resampling method to use, or turn off resampling, though the raster will be resampled if the spatial reference system does not match that of the DEM; see the help message for more information.

At this point, we have enough spatial data in a generic format (e.g. GeoTIFF) to build RHESSys-specific datasets using RHESSysWorkflows.

Create a new GRASS location

RHESSys requires that all spatial data used to create a world file and flow table for a RHESSys model be stored in a GRASS GIS mapset. We'll start building these data in RHESSysWorkflows by creating a new GRASS location and mapset within our project directory, and importing our DEM into this mapset:

CreateGRASSLocationFromDEM.py -p standard -d "RHESSys model for Dead Run 5 watershed near Catonsville, MD"

The -d (a.k.a. *--description") parameter is a textual description of this GRASS location; always wrap this parameter in quotes. If you choose, you can specify custome names of the following GRASS parameters:

  1. dbase, the directory within the project directory where your GRASS location will be stored (defaults to 'GRASSData')
  2. location (defaults to 'default')
  3. mapset (defaults to 'PERMANENT')

Use the --overwrite option to CreateGRASSLocationfromDEM to overwrite the GRASS location created by a previous invocation of CreateGRASSLocationFromDEM. Note that most RHESSysWorkflows commands provide the same option. The ability to overwrite GRASS datasets accomodates the often exploratory nature of ecohydrology data preparation workflows. While the data will be overwritten, the command history stored in the metadata store will retain a listing of the order in which you ran all workflow steps. This can help you to retrace the steps you took to arrive at the current workflow state.

Go ahead and open GRASS, pointing it to the dbase named GRASSData in your project directory, and then opening the mapset PERMANENT in the location default. You should be able to load the DEM raster into the map view. We'll use GRASS to visualize the results of the next few workflow steps, so keep GRASS open in the background.

Import RHESSys source code into your project

To create worldfiles and flow tables RHESSysWorkflows needs a copy of RHESSys source code. RHESSysWorkflows also uses the new RHESSys ParamDB database and Python libraries to generate vegetation, soil, land use and other parameters needed by RHESSys. RHESSysWorkflows is only compatible with the pre-release version of RHESSys 5.16 and later versions of the code. At present, and for first-time users, the most reliable way to import ParamDB and RHESSys source code into your project is to download the code from GitHub using the ImportRHESSysSource tool. However, this tool is also capable of importing RHESSys source code stored on your computer. This allows you to import the code from a previous RHESSysWorkflows project; ParamDB is always downloaded from GitHub, even when RHESSys source code is imported from a local source.

To download ParamDB and the RHESSys source code and store them in your project directory issue the following command:

ImportRHESSysSource.py -p standard

If you want to checkout an alternate branch, use the -b option to specify the Git branch of RHESSys to use (e.g. 'develop'). By default, ImportRHESSysSource will use the master branch, which is the appropriate branch to use with RHESSys 5.18.

Once ImportRHESSysSource finishes importing RHESSys source code into the project directory, it will compile all the tools necessary to create world files and flow tables, while also compiling the RHESSys binary. Once the command finishes, open the rhessys directory in your project directory. Here you can see the familiar RHESSys directory structure for storing model parameters, templates, worldfiles, flow tables, temporal event files, and model output; the RHESSys tools compiled by ImportRHESSysSource will be copied into the bin directory of the rhessys directory. Also note that all the source code for RHESSys is stored in the src directory.

Import RHESSys climate data

Because of the greater variability of climate data formats, and the complexity of time-series workflows, we have chosen to focus development effort on RHESSysWorkflows toward making it easier to acquire and manipulate geospatial data required for building RHESSys work files and flow tables. This means that the modeler is responsible for building the climate data necessary for building RHESSys world files and performing model runs.

RHESSysWorkflows provides the ImportClimateData tool to import RHESSys climate data into your project. To run this example workflow, download example climate data here. Unzip the file to a location on your computer (e.g. in your home directory), this will result in a directory named clim in the location. Issue the following command to import these data:

ImportClimateData.py -p standard -s /path/to/clim

You will have to replace /path/to/clim with the path of the clim folder unpacked from the zip file downloaded above.

For your own climate data to work with ImportClimateData the data must be stored in their own directory, with each base station having file name that ends in .base. See the help for ImportClimateData for more information.

Create climate stations map

If your study watershed has multiple climate stations that you would like to use, you must use a climate stations map to associate each zone in your world file with a particular climate station. RHESSysWorkflows provides the GenerateBaseStationMap tool to create a raster map of your climate stations using Thiessen polygons derived from climate station points, these points must be specified in a text file in a format supported by GRASS's v.in.acsii tool. For this tutorial, we'll use a dummy point to associated with the bwi climate station imported above. You can download this point here. Once downloaded, unzip the file to reveal the text file containing the point, which should look like this:

1|349093.638022|4350309.809951|bwi

In a real-world case, there would be additional lines in this file, one for each climate station. The first column is the base station ID and must match the base_station_ID field of the ${STATION}.base file associated with each climate station.

When we create the world file template later on in this tutorial, the tool that we use to do so, GenerateWorldTemplate, will make sure that there is a climate base station file for each unique raster value in your base station map; the world file template will not be generated if this is not the case.

The second and third columns represent the X and Y coordinates (or easting and northing) of the point feature we will use to represent the location of the climate station. The final column is the name of the climate station and should match ${STATION} in ${STATION}.base (i.e. if your base station file name is 'bwi.base', the final field should be 'bwi').

Now we're ready to use GenerateBaseStationMap to: import the climate station points; make Thiessen polygons based on the points, and rasterize the polygons:

GenerateBaseStationMap.py -p standard -b /path/to/dummy_stations1.txt

The GRASS tool v.voronoi is used to generate the Thiessen polygons. Note that some versions of this tool can fail if you have only two points. Hopefully this will be fixed when GRASS 6.4.3 is released later in 2013.

Delineate watershed and generate derived data products

RHESSysWorkflows automates the process of delineating your study watershed based on the location of the streamflow gage registered in the workflow. As part of this process, many datasets needed by RHESSys will be derived from the DEM. To delineate the watershed:

DelineateWatershed.py -p standard -t 500 -a 1.5

Here the -t (a.k.a. --threshold) parameter specifies the minimum size (in DEM cells) for subwatersheds generated by the GRASS command r.watershed.

The -a (a.k.a. --areaEstimate) parameter allows you to provide a guess of the area (in sq. km) of the delineated watershed. DelineateWatershed will report whether the watershed is within 20% of the area. You can view the delineated watershed in GRASS by displaying the raster map named basin. If the area or the shape of the delineated watershed differs greatly from what you expect, you may need to vary how DelineateWatershed snaps your streamflow gage onto the stream network. This is accomplished by either changing the -s (a.k.a. --streamThreshold) or stream threshold parameter and/or the -w (a.k.a. --streamWindow) parameter passed to r.findtheriver.

To debug watershed delineation problems, it is also helpful to view the original streamflow gage and the snapped streamflow gage overlaid on the upslope accumulated area map (UAA). DelineateWatershed will create vector layers for each of the streamflow gage coordinants (named gage and gage_snapped) as well as a UAA raster map (named uaa).

Though we do not recommend that you make changes to the metadata store by hand, as a last resort, you can snap the gage location by hand using GRASS and update the gage_easting_raw and gage_northing_raw attributes in the rhessys section of the metadata store. Then re-run DelineateWatershed as before with the addition of the --overwrite option.

For a listing of the derived datasets generated by DelineateWatershed, use the GRASS command g.list rast or check the DelineateWatershed source code.

Generating a patch map

RHESSysWorkflows provides GeneratePatchMap, an automated tool for creating gridded and clumped patch maps. Gridded patch maps consist of a regular grid of the same resolution and extent as the DEM; clumped maps can be created using elevation or topographic wetness index rasters. Modelers can also use custom patch maps registered via EcohydroLib's RegisterRaster tool and imported into GRASS using ImportRasterMapIntoGRASS (see below for a general description of this command).

To create a gridded patch map, enter the following into your Terminal:

GeneratePatchMap.py -p standard -t grid

To create an elevation clumped patch map:

GeneratePatchMap.py -p standard -t clump -c elevation

... and a topographic wetness index clumped map:

GeneratePatchMap.py -p standard -t clump -c wetness_index

Clumped patch maps are generated by calling GRASS's r.clump command with the appropriate source raster as import.

By default GeneratePatchMap will set the zone map to be that of the patch map, but only if a custom zone map has not been registered with the workflow (e.g. via a combination of RegisterRaster and ImportRasterMapIntoGRASS; see custom data tutorial below). If you wish to overwrite your custom zone map with the patch map, use the --forceZone option to GeneratePatchMap.

Generating soil texture map

Since we used EcohydroLib's SSURGO tools to generate percent sand and percent clay raster maps for our watershed, we can use the GRASS add-on r.soils.texture to generate USDA soil texture classes, for which RHESSys's ParamDB contains parameters. It is also possible to use custom soil maps, which we'll explore in the custom local data workflow section below.

To generate our soil texture map in GRASS, as well as the corresponding RHESSys soil definition files, use the GenerateSoilTextureMap tool as follows:

GenerateSoilTextureMap.py -p standard

This command will print information about what soil texture classes were encountered in the soil texture map, and what RHESSys soil default IDs these classes map onto. You can view the resulting soil texture map (named soil_texture) in GRASS. The soil definition files will be stored in the defs directory of the rhessys directory stored in your project directory.

Import LAI map into GRASS

We'll use the general command ImportRasterMapIntoGRASS to import our LAI map from the project directory into GRASS, where RHESSys will be able to make use of it (you can also derive an LAI map from your landcover map; see below):

ImportRasterMapIntoGRASS.py -p standard -t lai -m nearest

The -m (a.k.a. --method) paramer specifies how GRASS should resample the raster being imported. Value resampling methods are those supported by GRASS's r.resamp.interp command, as well as none, which will cause ImportRasterMapIntoGRASS to skip the resampling step.

Generate landcover maps in GRASS

RHESSysWorkflows uses a single landcover map to generate the following maps used by RHESSys:

  • Vegetation type (stratum)
  • Land use
  • Roads
  • Impervious surfaces
  • Leaf area index (LAI; optional)

The first step in generating these maps is to import the landcover raster from your project directory into GRASS using ImportRasterMapIntoGRASS:

ImportRasterMapIntoGRASS.py -p standard -t landcover -m nearest

In our case, the landcover map in our project directory came the NLCD 2011 data hosted by USGS. However, RHESSysWorkflows supports the use of custom landcover maps regsitered via RegisterRaster. In either case, we need to provide raster reclassification rules so that RHESSysWorkflows will know how to generate vegetation, land use, roads, impervious, and optionally LAI maps from the landcover map.
To do this, we use the RegisterLandcoverReclassRules tool:

RegisterLandcoverReclassRules.py -p standard -k

NLCD2011 is a known landcover type in RHESysWorkflows (in addition to NLCD2006), so all we need do is use the -k (a.k.a. --generateKnownRules) option. For a custom landcover map, we could instead use the -b (a.k.a. --buildPrototypeRules) option to generate prototype rules that we can edit as needed. It is also possible to specify that existing reclass rules should be imported from another directory on your computer using the -r (a.k.a. --ruleDir) parameter. To include LAI reclass rules when registering prototype or existing rules, you must use the -l (a.k.a. --includeLaiRules) parameter

The known rules for NLCD2006 and NLCD2011 that ship with RHESSysWorkflows include an LAI reclass rules file with values for grassland, and evergreen needle leaf and deciduous broadleaf forests (both temperate) drawn from the International Satellite Land Surface Climatology Project II (ISLSCP II) project. These data can be downloaded here.

Whether using known rules, building prototype rules, or importing existing rules, RegisterLandcoverReclassRules will result in the following four rules files being created in the rules directory of your project directory:

  • stratum.rule
  • landuse.rule
  • impervious.rule
  • road.rule
  • lai-recode.rule (if the --includeLaiRules option was selected)

There is no need to edit these rules for this NLCD2011 example, but you should take a moment to look at how these rules work. RHESSysWorkflows uses GRASS's r.reclass command (r.recode for creating LAI maps), and so the rules files follow this format.
It's important to note that the landcover reclass rules for stratum and landuse must result in raster maps whose values labels match class names present in the RHESSys ParamDB database. Thus, be very careful in editing the righthand side of the expressions in your stratum and landuse reclass rules.

Note that to keep track of edits you make to your project's reclass rules in your project metadata, you should use the RunCmd workflow command (see the section on custom workflows to learn how to use this tool).

You can find information on NLCD classes here

Once the landcover reclass rules are in place, it is very easy to generate the raster maps derived from the landcover data as well as the vegetation and land use definition files needed by RHESSys; this is done using the following command:

GenerateLandcoverMaps.py -p standard

If you would like an LAI map to be generate, you must use the -l (a.k.a. --makeLaiMap) parameter on the above command line. This will only work if you are using known landcover reclass rules, or if you requested that RegisterLandcoverReclassRules include LAI reclass rules when creating prototype rules or using existing rules.

Like with the soil texture map and definition generation step, GenerateLandcoverMaps will provide descriptive output of the vegetation and land use definition types encountered in the raster data.

Creating the worldfile for a watershed

Now we are almost ready to create the worldfile for our watershed. First we must create the template from which the world file will be created. To do this, we'll use the GenerateWorldTemplate tool. Fortunately this is very easy because the metadata store contains nearly all the information needed to create the template. If you are using multiple climate stations, and therefore have a base station map that you created using GenerateBaseStationMap, all you need do is:

GenerateWorldTemplate.py -p standard

If you are using a single climate station and did not create a climate station map, you must specify the climate station as follows:

GenerateWorldTemplate.py -p standard -c bwi

Here we're using the climate station named bwi.

In either case, if your workflow is missing any information necessary for making the world template, GenerateWorldTemplate will exit with a corresponding error.

If you want to see the template file generate, as well as other information, use the -v (a.k.a. --verbose) option

Now use the CreateWorldfile tool to create a world file using this template:

CreateWorldfile.py -p standard -v

We've specified the the -v (a.k.a. --verbose) command line option. This will print details about what CreateWorldfile, and the programs it runs on your behalf, is doing. This is recommended as these programs can fail in complex ways that CreateWorldfile may not be able to detect, so you'll likely want to know what's going on under the hood.

When CreateWorldfile finishes, it will create an initial worldfile named worldfile_init in the worldfiles directory in the rhessys directory in your project directory.

Creating the flow table

As with worldfile creation, at this point in the workflow, RHESSysWorkflows's metadata store contains nearly all the information needed to create a flow table using the createflowpaths (CF) RHESSys program. The two choices you have are whether CF should create a flow table that includes roads and/or includes a surface flow table to modeling non-topographic routing of rooftops. We'll route roads in this example, leaving rooftops for the custom local data workflow discussed below.

Run CreateFlowtable as follows:

CreateFlowtable.py -p standard --routeRoads

This will result in the creation of a flow table called world.flow in the flow directory of your rhessys directory. Now we have almost everything we need to run RHESSys simulations.

Initializing vegetation carbon stores

RHESSys provides a program called LAIread to initialize vegetation carbon stores in your worldfile.

Note, LAIread should only be used for RHESSys simulations with static vegetation (i.e. not dynamic vegetation mode enable via the -g command line option to RHESSys).

Initializing carbon stores is a multi-step process that involves running LAI read to generate a redefine worldfile, running a 3-day RHESSys simulation to incorporate the redefine worldfile, writing out a new worldfile with initialized vegetation carbon stores.
RHESSysWorkflows automates all of these processes for you, it can even figure out what date to start the 3-day RHESSys simulation on based on your climate data.

In the current version of RHESSysWorkflows, RunLAIRead is only able to read simulation start dates from point time-series climate data. Users of ASCII or NetCDF gridded climate data must run LAI read by hand. The next release of RHESSysWorkflows will add support for gridded climate data to RunLAIRead.

You can run RunLAIRead as follows:

RunLAIRead.py -p standard -v

Note that we use the verbose command line option here as well. The new GRASS-based version of LAIread is relatively new and not as well tested, so we advise you to keep a close watch on what it is doing.

LAIread relies on allometric relationships to initialize vegetation carbon stores. These allometric parameters have not yet been added to RHESSys ParamDB. A default version of the parameters for RHESSys base vegetation classes is stored in the RHESSys ParamDB source code repository. RHESSysWorkflows stores this file under the name allometric.txt in the allometry folder of the ParamDB of your rhessys/db folder.
You can edit this file to suit your needs before running RunLAIRead.
Consult the RHESSys wiki for more information on allometric relationships used by LAIread.

When finished, a final worldfile named world will be created in the worldfiles directory of your rhessys directory. With this worldfile, you are ready to perform subsequent model workflow steps including: spin-up, calibration, scenario runs, and analysis and visualization.

This concludes this tutorial using RHESSysWorkflows to create a RHESSys world file and flow table using standard spatial data infrastructure.

Running RHESSys models

We need one more thing before we can run our model, a TEC file. TEC stands for "temporal event controller". We use a TEC file to tell RHESSys to do things on at certain times during a simulation.
For example, to redefine the worldfile to simulate timber harvest or forest fire. We also use tec files to tell RHESSys what model outputs should be produced when. To create a TEC file that tells RHESSys to print daily model outputs starting on 10/1/2008, do the following:

RunCmd.py -p standard echo "2008 10 1 1 print_daily_on" > standard/rhessys/tecfiles/tec_daily.txt

For more information on tec file format, see the RHESSys wiki.

Once you have built a RHESSys model using RHESSysWorkflows, you can run your model manually. However this will not capture information about model runs in your project metadata. If you would like to record your runs in your project metadata, use the RunModel command:

RunModel.py -v -p standard -d "Test model run" --basin -pre test -st 2008 1 1 1 -ed 2010 10 1 1 -w world -t tec_daily.txt -r world.flow -- -s 0.07041256017 133.552915269 1.81282283058 -sv 4.12459677088 78.3440566535 -gw 0.00736592779294 0.340346799457

Notice the '--' in the command line. All of the command line options before the '--' are options required by RunModel.py; some of these are also common RHESSys options. All of the options after the '--' will be passed to RHESSys. Because the project metadata knows where RHESSys is installed in your project directory, you don't have to specify the full path of any of the RHESSys input files (e.g. world files, flow tables, tec files, etc), just specify the filenames. RunModel will echo RHESSys console outlet to the screen (if the -v or verbose option is specified as above), and will always save the same output into a file named 'rhessys.out' stored in the output folder for each model run. The output folder will be named based on the value you provide for the '-pre' or output prefix option.

Working in watersheds outside the United States

The above standard U.S. spatial data acquisition workflow steps do not provide access to data outside the U.S. (by definition). However, it is still possible to use RHESSysWorkflows to develop RHESSys models for watersheds outside the U.S. One option is to use custom local data, which is described here. If you are working in Australia, EcohydroLib (and by extension RHESSysWorkflows) provides access to 1-second (~30-meter) resolution DEM data (derived from SRTM data) using web services interfaces provided by Geoscience Australia. These data can be accessed using the GetGADEMForBoundingBox command. A typical workflow would begin as follows. First, define your study area using the RegisterStudyAreaShapefile command:

RegisterStudyAreaShapefile.py -p PROJECT_DIR -s /path/to/my/study/area/shapfile.shp

(Replace PROJECT_DIR with the name of your EcohydroLib project).

next, extract the bounding box coordinates for your study area:

GetBoundingboxFromStudyareaShapefile.py -p PROJECT_DIR

then, download Geoscience Australia DEM data:

GetGADEMForBoundingBox.py -p PROJECT_DIR

Currently, there are three types of DEM data available:

  • 1 second SRTM Digital Elevation Model of Australia
  • 1 second SRTM Digital Elevation Model - Hydrologically Enforced
  • 1 second SRTM Digital Elevation Model - Smoothed

To acquire the 1 second SRTM Digital Elevation Model of Australia data, run GetGADEMForBoundingBox as follows:

GetGADEMForBoundingBox.py -p PROJECT_DIR -d dem_1s

to acquire the 1 second SRTM Digital Elevation Model - Hydrologically Enforced data:

GetGADEMForBoundingBox.py -p PROJECT_DIR -d dem_h_1s

and to acquire the 1 second SRTM Digital Elevation Model - Smoothed data:

GetGADEMForBoundingBox.py -p PROJECT_DIR -d dem_s_1s

Consult the Geoscience Australia metadata catalog for more information about these data sets.

The remainder of your workflow would proceed with importing streamflow gage coordinates and subsequent steps described here.

In addition to Australia DEM, EcohydroLib provides access to gridded soils data provided by CSIRO and availble as part of the Soil and Landscape Grid of Australia dataset. To download these data into your project use the GetSoilGridAustralia command:

GetSoilGridAustralia.py -p PROJECT_DIR

This will download a subset of the available gridded Australia Soils Data from the Australia-wide 3D Soil Attributes dataset; currently GetSoilGridAustralia will download the percent sand, percent silt, and percent clay layers. Data for the first 1-m of the soil profile is downloaded, and a depth-weighted average value for each pixel is generated using these layers. Once these data have been downloaded, you can use the GenerateSoilTextureMap command to generate RHESSys soil texture map and parameters for USDA soil classes:

GenerateSoilTextureMap.py -p PROJECT_DIR

See above for more details.

Custom local data workflow

The following sections outline how one might use RHESSysWorkflows to build RHESSys input files using custom data already available on your computer. Unlike the above standard spatial data tutorial, we won't provide data for the workflow steps below. Instead, we'll describe how your data should be formatted to work with each workflow tool. To avoid duplication, only those concepts specific to using local data in RHESSysWorkflows will be discussed. You are encouraged to read the standard spatial data tutorial above as well. The workflow sequence covered below is not the only possible workflow involving local data. Also, it is possible to combine steps from this example workflow with steps from the standard spatial data tutorial.

Import a DEM into your project

When working in watersheds outside the coverage of the NHD (such as when working outside of the U.S.) the first workflow step is to import a digital elevation model data using the RegisterDEM tool. The DEM to be imported must be in a format readable by GDAL.

Run RegisterDEM as follows:

RegisterDEM.py -p PROJECT_DIR -d /path/to/my/DEM.tif -b "City of Springfield, Custom LIDAR"

To run this command, replace PROJECT_DIR with the absolute or relative path of an empty directory where you would like the data and metadata for your project to be stored (i.e. your project directory). It is also possible to reproject or resample the DEM on import. See RegisterDEM's help for more information (i.e. run with the -h option).

RegisterDEM will result in the DEM being copied to your project directory, also the DEM extent will be used to determine the bounding box for the study area; a polygon of the DEM extent will be generated and saved as a shapefile in your project directory.

Use a DEM with streams and storm drains burned into it

If you are working with an urbanized catchment, it is often necessary to "burn" streams or storm drains into your DEM so that you can properly delineate the "sewershed." RHESSysWorkflows allows you do use both a "stream burned" and a standard "non-burned" DEM in the same workflow.
The burned DEM will only be used for operations that require it (e.g. watershed delineation, flow table creations); the standard DEM will be used for determining elevation, slope, aspect, etc. To use a stream burned DEM, do the following:

RegisterRaster.py -p PROJECT_DIR -t stream_burned_dem -r /path/to/my/burnedDEM.tif -b "City of Springfield, Custom LIDAR, storm drain burned with Whitebox GAT 3.1.2"

Once the stream burned raster has been registered with the workflow the DelineateWatershed and CreateFlowtable tools will know to use this raster instead of the standard DEM; all other tools that use the DEM will continue to use the standard DEM. If you want to override this behavior (e.g. to test the effect that the burned DEM has on watershed delineation), you can pass the --ignoreBurnedDEM option to DelineateWatershed or CreateFlowtable, which will cause them to use the standard DEM instead.

We recommend the excellent open-source Whitebox GAT for burning streams into DEM datasets.

Import streamflow gage coordinates

The coordinates of the streamflow gage associated with your watershed are registered with the workflow using the RegisterGage tool. The tool takes as input a point shapefile containing one or more points; the WGS84 lat-lon coordinates for the desired gage will be extracted from the shapefile. These coordinates will be written to the metadata store, and a new point shapefile containing a point only for the selected gage will be created in the project directory.

A typical way to run RegisterGage is:

RegisterGage.py -p PROJECT_DIR -g /path/to/gage/shapefile.shp -l DATASET_NAME -a GAGE_ID_ATTRIBUTE -d GAGE_ID

To run this comment, replace PROJECT_DIR as above, specify the input shapefile you'd like to use, the name of the dataset within the shapefile, the name of the ID gage attribute in the dataset, and the ID of the desired gage. The name of the dataset is usually the same as the filename of the shapefile (minus the .shp). If you are unsure, you can use the command line tool ogrinfo, which ships with GDAL.

Importing data into GRASS for use with RHESSys

The following workflow steps are identical whether using standard spatial data or custom local data and will not be covered here:

  • Create a new GRASS location
  • Import RHESSys source code into your project
  • Import RHESSys climate data
  • Delineate watershed and generate derived data products
  • Generate landcover maps in GRASS

See the above standard spatial data tutorial for detailed information on these steps.

Importing other raster layers

For a list of all of the current raster map types supported by EcohydroLib, run the RegisterRaster tool as follows:

RegisterRaster.py -h

This will also show all of the resampling and other import options available.

What follows is a series of examples showing how to input some of these raster types. All rasters must be stored in a file format readable by GDAL (see above).

Landcover data
RegisterRaster.py -p PROJECT_DIR -t landcover -r /path/to/my/landcover_map.tif --noresample -b "Baltimore Ecosystem Study LTER" --force

Here we are importing a landcover raster map obtained from the Baltimore Ecosystem Study LTER where we've asked RegisterRaster not to resample the raster (unless its spatial reference system differs from the DEM; i.e. the resolution of the raster cells won't be changed). We're also telling RegisterRaster to ignore the fact that the extent of the landcover raster does not exactly match the extent of the DEM/study area. After import, you are strongly encouraged to visualize the landcover map overlaid on the DEM using QGIS to ensure that the landcover will cover an adequate portion of your study area.

For landcover maps, we recommend that you do not resample when registering the raster using RegisterRaster, but instead let GRASS handle the resampling.

To make the landcover map in the project directory available to RHESSys, it must be imported into GRASS as follows:

ImportRasterMapIntoGRASS.py -p PROJECT_DIR -t landcover -m nearest

This will import the landcover raster into GRASS, and then resample the raster using the nearest neighbor method. For a list of valid resampling methods, run ImportRasterMapIntoGRASS with the -h option; you may also specify none as the resampling method and the raster will not be resampled.

Rooftop connectivity

Starting with RHESSys 5.16, the createflowpaths (CF) utility is able to create surface flow tables that can incorporate non-topographic routing of flow from rooftops to nearby impervious and pervious areas. RHESSys 5.16 can use separate surface and subsurface flow tables to simulate the effect of such non-topographic routing on the landscape. You can find more information on using surface flowtable routing in RHESSys here.

To import a rooftop connectivity raster, use RegisterRaster as follows:

RegisterRaster.py -p PROJECT_DIR -t roof_connectivity -r /path/to/my/roof_map.tif --noresample --force

As with landcover maps, we recommend do not let RegisterRaster resample roof connectivity rasters, instead letting GRASS handle the resampling. RegisterRaster uses GDAL to resample rasters. GDAL ignore null/nodata pixels when resampling, whereas GRASS's r.resamp.interp does not. Thus, when a landcover and a roof top connectivity raster, which contains nodata values for all non-roof pixels, are resampled in RegisterRaster, they can become mis-registered, which will result in an invalid surface routing table.

Then make your rooftop connectivity raster available for RHESSys by importing it into GRASS:

ImportRasterMapIntoGRASS.py -p PROJECT_DIR -t roof_connectivity -m nearest
Vegetation LAI

As described in the standard spatial data tutorial above, EcohydroLib/RHESSysWorkflows requires that the user provide their own LAI data, which can be imported into a project using RegisterRaster:

 RegisterRaster.py -p PROJECT_DIR -t lai -r /path/to/my/lai_map.tif --force

Now make your LAI raster available for RHESSys by importing it into GRASS:

ImportRasterMapIntoGRASS.py -p PROJECT_DIR -t lai -m none
Custom patch map

A custom patch map can be imported into a project as follows:

RegisterRaster.py -p PROJECT_DIR -t patch -r /path/to/my/patch_map.tif --noresample

Then make your patch raster available for RHESSys by importing it into GRASS:

ImportRasterMapIntoGRASS.py -p PROJECT_DIR -t patch -m none
Custom soils data

A custom soils map can be imported into a project as follows:

RegisterRaster.py -p PROJECT_DIR -t soil -r /path/to/my/soils_map.tif -b "Brian Miles <brian_miles@unc.edu>, based on field observations"

Then make your soil raster available for RHESSys by importing it into GRASS:

ImportRasterMapIntoGRASS.py -p PROJECT_DIR -t soils -m none
Climate station zone map

The GeneratePatchMap tool will use the patch map as the zone map. If you wish to use another map for the zone map, do the following after running DelineateWatershed:

RegisterRaster.py -p PROJECT_DIR -t zone -r /path/to/my/zone_map.tif -b "Brian Miles <brian_miles@unc.edu>, climate station zones based on lapse rate"

Then make your zone raster available for RHESSys by importing it into GRASS:

ImportRasterMapIntoGRASS.py -p PROJECT_DIR -t zone -m none
Isohyet map

By default no isohyet map will be used when creating the world file for a watershed. If you wish to use an isohyet map, do the following before running GenerateWorldTemplate:

RegisterRaster.py -p PROJECT_DIR -t isohyet -r /path/to/my/isohyet_map.tif -b "Brian Miles <brian_miles@unc.edu>, isohyet map"

Then make your isohyet raster available for RHESSys by importing it into GRASS:

ImportRasterMapIntoGRASS.py -p PROJECT_DIR -t isohyet -m none --integer

Note that we tell ImportRasterMapIntoGRASS to transform the isohyet raster values to integers on import. This is necessary due to limitations in the current version of the RHESSys tool grass2world. When doing the, integer conversion, ImportRasterMapIntoGRASS wil multiply the raster values by 1000, giving three significant digits. To use another value, specify the --multiplier option.

Generating RHESSys definitions for custom soil data

When using custom soil data with RHESSysWorkflows you need to create soil definition files before you can create a worldfile. To create soil definitions, you must first create raster reclass rules that map between your soil type and a soil type known to RHESSys ParamDB. At present, ParamDB contains definitions drawn from the literature for USDA soil textures. However you may load custom soil parameters into your own local copy of ParamDB. For more information, see the ParamDB README.

To create prototype soil reclass rules for a project, do the following:

RegisterCustomSoilReclassRules.py -p PROJECT_DIR -b

Here we're using the -b (a.k.a. --buildPrototypeRules) command line option. This will result in the creation of a file called soils.rule in the rules directory of your project directory. You will need to edit this file as necessary to map your custom soil types to ParamDB soil types.

Make sure that the soil class names on the righthand side of each reclass rule correspond to soil class names in ParamDB

You can also import existing soil reclass rules as follows:

RegisterCustomSoilReclassRules.py -p PROJECT_DIR -r /path/to/my/existing/reclass_rules/

The -r (a.k.a. --ruleDir) parameter must point to a directory that contains a file named soils.rule. This will will be copied into the rules directory of your project directory.

Once you have valid soil reclass rules in place, you can generate RHESSys soil parameter definition files for your custom soils using the following command:

GenerateCustomSoilDefinitions.py -p PROJECT_DIR 

This tool will print information to the screen about each soil type encountered and the RHESSys ParamDB soil parameter classes they map to. If you see no such print out, check your soil reclass rule file to make sure it is correct. The resulting soil definition files will be written to the defs directory in the rhessys directory of your project directory.

Remember most RHESSysWorkflows commands support the --overwrite command line option for overwriting existing data stored in the project directory or in GRASS.

Creating a world file template in areas with low slope

Due to limitations in the current version of RHESSys's grass2world tool, slope values less than 1.0 will be truncated to 0.0. This causes values of NaN (i.e. not a number) to result for the spherical average of aspect calculation. To work around this, you can use the --aspectMinSlopeOne command line option to instruct GenerateWorldTemplate to use a slope map whose minimum value is 1.0 when calculating the spherical average of aspect:

GenerateWorldTemplate.py -p PROJECT_DIR --aspectMinSlopeOne -c MY_CLIMATE_STATION1

Creating a surface flow table using a roof connectivity map

If you are using a roof connectivity map in your workflow, you need to explicitly tell CreateFlowtable to use the roof connectivity map to generate a surface flow table. Do so as follows:

CreateFlowtable.py -p PROJECT_DIR --routeRoofs --routeRoads

Here we're using both the --routeRoofs and --routeRoads options. You are not required to use both together, but usually when modeling rooftop connectivity you will be working in a watershed that also has roads whose effects on routing you will also want to consider.

Creating the worldfile and initializing vegetation carbon stores

The following workflow steps are identical whether using standard spatial data or custom local data and will not be covered here:

  • Creating the worldfile for a watershed
  • Initializing vegetation carbon stores

See the above standard spatial data tutorial for detailed information on these steps.

Running custom commands

RHESSysWorkflows provides many tools for preparing RHESSys models, however there are many possible other tools and workflow steps that can be used to build a model. To allow arbitrary commands to be carried out on data stored in a project directory, RHESSysWorkflows provides the RunCmd command, for example you may which to edit your worldfile template and then re-run grass2world by hand:

RunCmd.py -p PROJECT_DIR cp PROJECT_DIR/rhessys/templates/template PROJECT_DIR/rhessys/templates/template.orig
RunCmd.py -p PROJECT_DIR emacs PROJECT_DIR/rhessys/templates/template
export PATH=PROJECT_DIR/rhessys/bin:${PATH}
RunCmd.py -p PROJECT_DIR PROJECT_DIR/rhessys/bin/g2w ...

(it is necessary to manually add your project directory's copy of the RHESSys binaries to your path because grass2world runs a helper program called rat that must be in your path)

Although RHESSysWorkflows will not be able to capture full metadata about the input and output files used and produced by commands run through RunCmd, it will write an entry to the processing history of your project metadata. This way, you at least have a record of the custom workflow steps you applied to the data in your project directory.

Creating multiple worldfiles based on subbasins

For large model domains, it may be desirable to break up your watershed into multiple worldfiles. RHESSysWorkflows allows you to do this using the CreateWorldfileMultiple command:

CreateWorldfileMultiple.py -p PROJECT_DIR

This will create one worldfile for each subbasin delineated for your watershed.

Once you've created multiple worldfiles, you can create corresponding flow tables using the CreateFlowtableMultiple command:

CreateFlowtableMultiple.py -p PROJECT_DIR

CreateFlowtableMultiple supports the same command line options as its counterpart CreateFlowtable.

Finally, you can initialize vegetation carbon and nitrogen stores for multiple worldfiles using RunLAIReadMultiple:

RunLAIReadMultiple.py -p PROJECT_DIR

Appendix

Visualizing RHESSys output

RHESSysWorkflows includes tools to visualize RHESSys model output.

Note that these tools are still in development, but beta versions are provided for your convenience; functionality and options may change without notice.

The first tool, RHESSysPlot, will produce plots for basin-scale variables such as streamflow. This tool is very flexible, and includes the ability to plot observed data vs. modeled data, and to plot data for multiple simulations. A prototypical usage to plot observed and simulated hydrographs with rainfall plotted on a second y-axis is as follows:

RHESSysPlot.py --plottype standard -o PATH_TO_OBSERVED -d PATH_TO_SIMULATION/rhessys_basin.daily -c streamflow --secondaryData PATH_TO_SIMULATION/rhessys_basin.daily --secondaryColumn precip --secondaryLabel "Rainfall (mm/day)" -t "DR5 streamflow" -l "Test simulation" -f test_plot --figureX 8 --figureY 3 -y "Streamflow (mm/day)" --color magenta

Go here to download example observed streamflow for the DR5 study catchment used in the first part of this tutorial

The --figureX and --figureY options control the size of the plot (in inches). RHESSysPlot also allows you to make standard time series, semi-log scale timeseries, and cumulative distribution function plots. For a full description of options, use the --help option:

RHESSysPlot.py --help

In addition to making static plots of basin-scale output variables, RHESSysWorkflows provides a tool, PatchToMovie, for making animations of patch-scale output variables. To use this tool, you first need to have RHESSys simulations for which patch-scale output was created (e.g. using the -p output option). The following example will create a 30-frames-per-second animation for infiltration:

PatchToMovie.py -p PROJECT_DIR -d PATH_TO_SIMULATION_WITH_PATCH_OUTPUT/rhessys_patch.daily -o OUTPUT_DIRECTORY -f OUTPUT_FILENAME -v "recharge * 1000.0" --mask GRASS_RASTER_LAYER --overlay GRASS_RASTER_LAYER_1 [GRASS_RASTER_LAYER_N] --fps 30 -t "infiltration"

Note that the variable can be an aribitrary mathematical expression (using '+', '-', '', and '/') combining patch-level RHESSys variable names as well as numerical constants (as in the example). When using such expressions, you'll want to specify a title for each frame in your animation using the *-t (a.k.a. --mapTitle) option (otherwise the expression will be used as the title, which likely won't fit on the frame).

When specifying simulation output (e.g. -r) and the GRASS mapset (e.g. -g), it is important to use the same GRASS mapset that was used to create the worldfile used to run the simulation.

For a full description of options, use the --help option:

PatchToMovie.py --help  

PatchToMovie uses a command line program called ffmpeg to encode individual maps into a movie file. To install ffmpeg do the following:

OS X

  • Install Homebrew
  • Install ffmpeg:

    brew install ffmpeg

Linux (Debian/Ubuntu-based systems)

  • Install ffmpeg (and vlc for viewing animations):

    sudo apt-get install ffmpeg vlc

Lastly, you must add an entry to your EcohydroLib configuration file. For OS X:

[RHESSYS]
PATH_OF_FFMPEG = /usr/local/bin/ffmpeg

For Linux:

[RHESSYS]
PATH_OF_FFMPEG = /usr/bin/ffmpeg

See Setup EcohydroLib and RHESSysWorkflows configuration file for more details on setting up your configuration file.

Deprecated installation instructions

OS X 10.7 through 10.10 using Kyngchaos GIS packages

Install Xcode (OS X developer tools):
  • Install Xcode via the App Store

  • Launch Xcode

  • Make sure that Xcode command line tools are installed by running the following from the command line (e.g. using the Terminal app):

xcode-select --install
  • Agree to the Xcode license by running the following command (we only run this command to force Xcode show us the license): sudo cc
Install GIS tools: GRASS & QGIS

Note, GRASS version 6.4 is required for RHESSysWorkflows (GRASS 7.0 is not supported at this time). GRASS is used internally to carry out workflow steps (leading to the creation of RHESSys world files and flow tables).
You will also find it useful to use GRASS to visualize the results from some workflow steps.

Before installing GRASS, etc. under OS X 10.8, 10.9 or 10.10, you will need to enable applications from any source to be installed. To do so open System Preferences > Security & Privacy > General and choose "Allow apps downloaded from: Anywhere". Doing so exposes your computer to more security risks from downloaded software. We recommend that you revert this setting once you are finished with installation.

To install GRASS on OS X, visit http://www.kyngchaos.com/software/grass

Here you will need to download and install the following:

  1. GDAL Complete framework
  2. FreeType framework
  3. cairo framework
  4. PIL (Python imaging library)
  5. GRASS.app

While you are there, we recommend you also install QGIS (Quantum GIS)

In addition to GRASS and components installed above, install:

  1. NumPy from http://www.kyngchaos.com/software/python
  2. SciPy from http://www.kyngchaos.com/software/python
  3. Matplotlib Python module from http://www.kyngchaos.com/software/python
  4. QGIS from from http://www.kyngchaos.com/software/qgis

QGIS is useful for visualizing output for earlier workflow steps that precede the importing data into GRASS.

Install RHESSysWorkflows Python modules (including EcohydroLib)

Before installing RHESSysWorkflows, we need to install some dependencies by hand (this is annoying, but unavoidable):

sudo pip install pandas patsy

This is necessary because another depdendency (statsmodels) requires that we install its dependencies first. If you are running XCode 5.1 or later, you may encounter this error:

clang: warning: unknown argument: '-mno-fused-madd' [-Wunused-command-line-argument-hard-error-in-future]
clang: note: this will be a hard error (cannot be downgraded to a warning) in the future
clang: warning: argument unused during compilation: '-mno-fused-madd'

If you don't see the above error, skip the next step. To work around the error, install statsmodels' dependencies this way (you'll probably want to copy and paste this rather than typing it):

sudo ARCHFLAGS=-Wno-error=unused-command-line-argument-hard-error-in-future pip install pandas patsy

This too is annoying, but is unaviodable (for now).

To install RHESSysWorkflows and its dependencies (including EcohydroLib), enter the following from your Terminal if you are running XCode 5.0 or earlier:

sudo pip install rhessysworkflows

If you are running Xcode 5.1 (but not Xcode 6.1 or later), we need to set the ARCHFLAGS variable as above:

sudo ARCHFLAGS=-Wno-error=unused-command-line-argument-hard-error-in-future pip install rhessysworkflows

Again, only do the above step if youa re running Xcode 5.1, not Xcode 6.1.

This may take a while as several of the modules rely on non-Python code that has to be compiled.

Why are GDAL Python libraries not included as a dependency of RHESSysWorkflows? This is to make life easier for users of OS X 10.7 and 10.8. For these OSes, the GDAL complete installer that accompanies GRASS will install GDAL Python modules in the copy of Python 2.7 that ships with the OS, and the GDAL Python module does not successfully build by itself under OS X, which would make the rhessysworkflows install fail. Linux users will have to make sure they install GDAL Python modules in addition to GDAL itself (e.g. via a companion package, or by 'sudo pip install GDAL').

Install GRASS Addons for RHESSysWorkflows

Follow these steps to install the GRASS addons needed by RHESSysWorkflows:

  1. First start GRASS

    • Double-click on the GRASS-6.4 icon in your Applications folder
  2. Create a new location (it doesn't matter where, we'll only use it to run the g.extension command to install the extensions)

  3. Install r.soils.texture

    g.extension extension=r.soils.texture

  4. Install r.findtheriver

    g.extension extension=r.findtheriver

  5. Exit GRASS

For more information on these addons (r.soils.texture and r.findtheriver), see:

Setup EcohydroLib and RHESSysWorkflows configuration file
  • Download a prototype configuration file.

  • Save into a file named '.ecohydro.cfg' stored in your home directory and replace all occurances of <myusername> with your user name (To find out your OS X user name, use the whoami command in Terminal).

  • Set ECOHYDROLIB_CFG environment variable so that RHESSysWorkflows can find your configuration file

    • From Terminal, do the following:

      echo "export ECOHYDROLIB_CFG=${HOME}/.ecohydro.cfg" >> ~/.bash_profile

    • Re-load bash profile (or close and open a new Terminal window):

      source ~/.bash_profile

This concludes installation and configuration instructions for OS X 10.7 through 10.10 using Kyngchaos GIS packages.

OS X 10.6

Apple, and thus many third-party software developers, no longer supports OS X 10.6. If you are still running OS X 10.6, you may want to explore upgrade options as many older Macs can run newer operating systems, upto and including the latest version. If your Mac still has some life in it, it is important to upgrade from OS X 10.6 this version is no longer receiving security updates from Apple, and because newer versions have more security features by design.

If you wish to install RHESSysWorkflows on OS X 10.6, follow the instructions below (though we no longer have a OS X 10.6 machine to test on, so we won't be able to help if you run into problems).

Due to its age, there are a few more installation steps needed under OS X 10.6. Also, once Apple stops support this version of the OS, support for OS X 10.6 will also be dropped from subsequent releases of RHESSysWorkflows. If you were thinking of upgrading from OS X 10.6 to 10.9 for other reasons, this may add another.

You will need to use the sudo command line tool to install many of the components needed for EcohydroLib/RHESSysWorkflows. The sudo command allows you to run other commands as a super user. Under OS X, by default, only users who are 'admins' have permission to run sudo. To check if your user account is an administrator, or to make your user an administrator open System Preferences > Users & Groups. Note that to use sudo, your account will also have to have a non-blank password. See this Apple support article for more information.

Download and install Python 2.7 from: http://www.python.org/download/

Once installation has completed, make sure that Python 2.7 is the default Python version by doing the following from the Terminal:

python

This will load the Python interpreter. The first line of output will display the Python version number. Type exit() to exit the interpreter.

Download setuptools from: https://pypi.python.org/pypi/setuptools/0.8

Install setuptools as follows: 1. Unpack the archive by double-clicking on it in Finder 2. From Terminal:

cd setuptools-0.8
sudo python ez_setup.py
Install Xcode (OS X developer tools)
  1. Download and install Xcode 3.2.6 and iOS SDK 4.3 for Snow Leopard here (This requires you to register for a free developer account)

  2. Download and install Git from http://git-scm.com/download/mac

RHESSysWorkflows uses Git to download RHESSys source code so you don't have to.

Install PIP, a tool for installing Python modules

Pip is the recommended way to install Python modules (i.e. rather than using easy_install). For example, Pip allows you to easily uninstall modules. To install pip, enter the following in a Terminal window:

sudo easy_install pip
Install GIS tools: GRASS & QGIS

Note, GRASS version 6.4 is required for RHESSysWorkflows (GRASS 7.0 is not supported at this time). GRASS is used internally to carry out workflow steps (leading to the creation of RHESSys world files and flow tables).
You will also find it useful to use GRASS to visualize the results from some workflow steps.

To install GRASS on OS X, visit http://www.kyngchaos.com/software/grass

Here you will need to download and install the following:

  1. GDAL Complete framework
  2. FreeType framework
  3. cairo framework
  4. PIL (Python imaging library)
  5. GRASS.app

While you are there, we recommend you also install QGIS (Quantum GIS)

In addition to GRASS and components installed above, install:

  1. NumPy from http://www.kyngchaos.com/software/python
  2. SciPy from http://www.kyngchaos.com/software/python
  3. Matplotlib Python module from http://www.kyngchaos.com/software/python
  4. QGIS from from http://www.kyngchaos.com/software/qgis

QGIS is useful for visualizing output for earlier workflow steps that precede the importing data into GRASS.

Install GDAL Python modules

Even though we installed the GDAL complete framework above, we still need to install the GDAL Python modules for the copy of Python 2.7 we installed above; the GDAL framework only installs the Python modules for Python 2.6, which RHESSysWorkflows is not compatible with. These installation steps are a little ugly, but bear with me (or upgrade from OS X 10.6). From a Terminal window type the following:

export PATH=${PATH}:/Library/Frameworks/GDAL.framework/unix/bin
sudo pip install --no-install GDAL
cd /tmp/pip-build-root/GDAL
sudo python setup.py build_ext --include-dirs=/Library/Frameworks/GDAL.framework/Headers --library-dirs=/Library/Frameworks/GDAL.framework/Versions/Current/unix/lib
sudo pip install --no-download GDAL
Install RHESSysWorkflows Python modules (including EcohydroLib)

Before installing RHESSysWorkflows, we need to install some dependencies by hand (this is annoying, but unavoidable):

sudo pip install pandas patsy

This is necessary because another depdendency (statsmodels) requires that we install its dependencies first.

To install RHESSysWorkflows and its dependencies (including EcohydroLib), enter the following from your Terminal if you are running XCode 5.0 or earlier:

sudo pip install rhessysworkflows
Install GRASS Addons for RHESSysWorkflows

Follow these steps to install the GRASS addons needed by RHESSysWorkflows:

  1. First start GRASS

    • Double-click on the GRASS-6.4 icon in your Applications folder
  2. Create a new location (it doesn't matter where, we'll only use it to run the g.extension command to install the extensions)

  3. Install r.soils.texture

    g.extension extension=r.soils.texture

  4. Install r.findtheriver

    g.extension extension=r.findtheriver

  5. Exit GRASS

For more information on these addons (r.soils.texture and r.findtheriver), see:

Setup EcohydroLib and RHESSysWorkflows configuration file
  • Download a prototype configuration file.

  • Save into a file named '.ecohydro.cfg' stored in your home directory Replace all occurances of <myusername> with your user name (To find out your OS X user name, use the whoami command in Terminal).

  • Set ECOHYDROLIB_CFG environment variable so that RHESSysWorkflows can find your configuration file

    • From Terminal, do the following:

      echo "export ECOHYDROLIB_CFG=${HOME}/.ecohydro.cfg" >> ~/.bash_profile

    • Re-load bash profile (or close and open a new Terminal window):

      source ~/.bash_profile

This concludes installation and configuration instructions for OS X 10.6.

Install local data

RHESSysWorkflows allows you to use local copies of the National Hydrography Dataset Plus (NHD Plus) to locate USGS streamflow gages, and the National Landcover Dataset (NLCD 2006). If you will be building many models across the U.S. or are running RHESSysWorkflows in a server environment and would like to minimize calls to external web services, you may wish to install these datasets locally to improve performance. This is entirely optional. Most users can ignore this as querying webservices for these data is preferable to downloading and installing these relatively large datasets.

Setup NLCD2006 data

To setup a local copy of NLCD2006 land cover data, do the following:

  • Download NLCD2006 data here

    It is important that you download this version of the dataset, and not the official data from http://www.mrlc.gov/nlcd06_data.php. The offical data are packaged using a version of PkZip that is not compatible with OS X's GUI or commandline unzip utilities.

  • Copy NLCD2006 archive to the parent folder where you would like to store it

    For example, under OS X, create a folder called 'data' in your home directory

  • Unpack NLCD2006 data (this will take a while...time for a coffee break):

    • OS X 10.6: From the command line:

      tar xvjf nlcd2006_landcover_4-20-11_se5.tar.bz2

    • OS X 10.7/10.8: double-click on the archive in Finder

Setup pre-packaged NHDPlusV2 data

If you want to setup a local copy of NHDPlusV2 data you can obtain these data by downloading all or a subset of the NHDPlusV2 data and building the database as described in the EcohydroLib documentation. Alternatively, you can download a pre-built copy of the NHDPlusV2 database needed by RHESSysWorkflows here. To download and unpack the pre-built data, do the following:

  • Download pre-packaged NHDPlusV2 database here

    Note, the compressed data are nearly 7 GB, nearly 11 GB uncompressed, the download may take a while

  • Copy the pre-packaged NHDPlusV2 database archive to the parent folder where you would like to store it

    For example, under OS X, create a folder called 'data' in your home directory

  • Unpack NHDPlusV2 database archive (this will take a while...have a cup of tea)

    • OS X 10.6: From the command line:

      tar xvjf NHDPlusV2.tar.bz2

    • OS X 10.7/10.8: double-click on the archive in Finder

    Setup EcohydroLib and RHESSysWorkflows configuration file for local data

  • Choose the appropriate prototype configuration file:

  • Save into a file named '.ecohydro.cfg' stored in your home directory Replace all occurances of '' with your user name (To find out your OS X or Linux user name, use the whoami command in Terminal).

  • Modify the example configuration to point to your NHDPlusV2 and NLCD2006 local data [if you are using these data]:

    If you are using OS X, and if you placed the data in a directory called 'data' in your home directory, the only changes you need to make is to substitute '' with your user name.

    If you chose to store local NLCD or NHDPlusV2 somewhere else, simply use the absolute path of each file.

  • Set ECOHYDROLIB_CFG environment variable so that RHESSysWorkflows can find your configuration file

    For example, under OS X, from Terminal, do the following:

    • Open your bash profile in an editor:

      nano ~/.bash_profile

    • Add the following at the end of the file:

      export ECOHYDROLIB_CFG=${HOME}/.ecohydro.cfg

    • Save the file

    • Re-load bash profile (or close and open a new Terminal window):

      source ~/.bash_profile

Something went wrong with that request. Please try again.