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version 1.11 on Jan 9th, 2014

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RHESSysWorkflows                        {#index}
=======================

This software is provided free of charge under the New BSD License. Please see the following license information:

Copyright (c) 2013, University of North Carolina at Chapel Hill All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

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  • Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
  • Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
  • Neither the name of the University of North Carolina at Chapel Hill nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Authors

Brian Miles - brian_miles@unc.edu

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

For questions or support contact [Brian Miles](brian_miles@unc.edu)

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

Introduction

RHESSysWorkflows provides a series of Python tools for performing [RHESSys](http://fiesta.bren.ucsb.edu/~rhessys/) data preparation workflows. These tools build on the workflow system defined by [EcohydroLib](https://github.com/selimnairb/EcohydroLib).

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 are tailored to OS X and Linux users (specifically Ubuntu 13.04 a.k.a. Raring Ringtail), however installation under Linux is also possible. RHESSysWorkflows may in theory work under Windows, but this has never been tested. Windows users are encouraged to run a Ubuntu under a virtual machine.

RHESSysWorkflows is compatible with OS X 10.6, 10.7, and 10.8. 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 http://www.everymac.com/systems/by_capability/maximum-macos-supported.html.

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 10.7 or 10.8 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](http://support.apple.com/kb/HT4103?viewlocale=en_US&locale=en_US) > for more information.

### OS X 10.6 only: Install Python 2.7

#### Download and install Python 2.7 (for Mac OS 10.6 and later) 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 non-Python dependencies

#### OS X 10.6: Install Xcode (OS X developer tools)

1. Download and install Xcode 3.2.6 and iOS SDK 4.3 for Snow Leopard [here](https://developer.apple.com/downloads/index.action) (This requires you to register for a free developer account)

  1. 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.

#### OS X 10.7 and 10.8: Install Xcode (OS X developer tools): 1. Install Xcode via the App Store 2. Launch Xcode 3. Install 'Command Line Tools' from menu Xcode > Preferences... > Downloads

#### Install GIS tools: GRASS QGIS Note, GRASS version 6.4.2 is required for RHESSysWorkflows. 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 1.9 framework
  2. FreeType framework
  3. cairo framework
  4. GRASS.app

While you are there, I recommend you also install QGIS (Quantum GIS) from http://www.kyngchaos.com/software/qgis

In addition to GRASS and components installed above, install:

  1. GSL framework
  2. QGIS

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

#### Installing dependencies under Ubuntu Linux First install aptitude:

apt-get install aptitude

The install RHESSysWorkflows/EcohydroLib dependencies using aptitude:

aptitude install build-essential git subversion p7zip-full aptitude install python python-dev python-pip libxml2-dev libxslt-dev gdal gdal-bin python-gdal grass grass-dev libbsd-dev

#### Install GRASS Addons for RHESSysWorkflows Download and install GRASS addons from: http://ecohydrology.web.unc.edu/files/2013/07/GRASSAddons-RHESSysworkflows.dmg_.zip

For non-OS X users, these addons (r.soils.texture and r.findtheriver) are also available for installation from the GRASS addons repository via g.extension. You can download r.findtheriver [here](http://grasswiki.osgeo.org/wiki/AddOns/GRASS_6#r.findtheriver) and r.soils.texture [here](http://grasswiki.osgeo.org/wiki/AddOns/GRASS_6#r.soils.texture).

Follow these steps to install the GRASS addons under Linux:

  1. First start GRASS by typing grass64 from the command line

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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
  1. Install r.findtheriver

    g.extension extension=r.findtheriver

### Install Python modules The steps in this section is the same for OS X and Linux (except where noted for OS X 10.6).

#### 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

#### OS X 10.6: 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) To install RHESSysWorkflows and its dependencies (including EcohydroLib), enter the following from your Terminal:

sudo pip install rhessysworkflows

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').

### 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

If pip does not install the version you expect, it may be necessary to first remove RHESSysWorkflows and Ecohydrolib before installing the new version:

sudo pip uninstall rhessysworkflows sudo pip uninstall ecohydrolib

The install as above:

sudo pip install rhessysworkflows

### A note on 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 (https://pypi.python.org/pypi/virtualenv)

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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.

### Setup EcohydroLib and RHESSysWorkflows configuration file - Choose the appropriate 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 or Linux user name, use the whoami command in Terminal).

  • 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

    • If you're running Linux also add the following to your bash profile:

      export LD_LIBRARY_PATH=/usr/lib/grass64/lib:${LD_LIBRARY_PATH}

    • Save the file

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

      source ~/.bash_profile

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.)

#### 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 DEM Explorer

[DEM Explorer](http://geobrain.laits.gmu.edu), developed and maintained by the Center for Spatial Information Science and Systems at George Mason University in partnership with NASA EOS, provides web-based access to USA and global DEM data from a number of data sources (currently SRTM, GLS, ASTER, and GTOPO). In addition to a browser-based interface, DEM Explorer provides an HTTP query service to allow applications such as EcohydroLib to programmatically query and download DEM data. Now that we've defined the bounding box for our study area, its very easy to download DEM data from DEM Explorer, as follows:

GetDEMExplorerDEMForBoundingbox.py -p standard

By default, this tool will download an extract for your study area from the SRTM 30-meter (27.58-meter actual) 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:

GetDEMExplorerDEMForBoundingbox.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 DEM Explorer. See the Custom local data workflow example below for more information.

#### Extract landcover data from local NLCD 2006 data

EcohydroLib makes it easy to import custom NLCD 2006 tiles for your study area into your project from either locally stored data or via WCS hosted at the Distributed Active Archive Center for Biogeochemical Dynamics group at ORNL (see installation instructions above to download and configure local NLCD data). For example, to use local data:

GetNLCDForDEMExtent.py -p standard

This command will download an NLCD tile 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. (If you are using a local copy of the NLCD 2006 data add the -s local command line argument to the above command; Most users should ignore this.)

#### Download soils data from SSURGO

The USDA NRCS provides the [Soil Data Mart](http://soildatamart.nrcs.usda.gov), 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](http://soildatamart.nrcs.usda.gov/SSURGOMetadata.aspx).

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](https://github.com/selimnairb/EcohydroLib/blob/master/ecohydrolib/ssurgo/featurequery.py) and [here](https://github.com/selimnairb/EcohydroLib/blob/master/ecohydrolib/ssurgo/attributequery.py).

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. If your study area is larger than this, you may wish to obtain a copy of the SURRGO data and extract your own soils data. In the future we hope to address this limitation by hosting a copy of SSURGO at UNC, however this work is still underway.

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 provides a second tool for detailing 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, though we are working to make available Landsat LAI data generated from the Landsat archive on [NASA NEX](https://c3.nasa.gov/nex/). 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](https://docs.google.com/file/d/0B7aK-9pTSLS-eEJaZXctaEtkb2s/edit?usp=sharing). 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:

System Message: WARNING/2 (<string>, line 661); backlink

Inline emphasis start-string without end-string.

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 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](https://github.com/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 alows 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](https://docs.google.com/file/d/0B7aK-9pTSLS-Q1NQbUJzVXZKeUE/edit?usp=sharing). 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](http://grass.osgeo.org/grass64/manuals/v.in.ascii.html) 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](https://docs.google.com/file/d/0B7aK-9pTSLS-cmVWdmNxNThRc1U/edit?usp=sharing). 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](http://grass.osgeo.org/grass64/manuals/v.voronoi.html) > 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](http://grass.osgeo.org/grass64/manuals/r.watershed.html).

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 delinated 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 changing the -s (a.k.a. --streamThreshold) or stream threshold parameter passed to [r.findtheriver](https://svn.osgeo.org/grass/grass-addons/grass6/raster/r.findtheriver/description.html).

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](https://github.com/selimnairb/RHESSysWorkflows/blob/master/bin/DelineateWatershed.py).

#### 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 addon 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 th 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:

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](http://grass.osgeo.org/grass64/manuals/r.resamp.interp.html) 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

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 from our local copy of NLCD2006. 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, and impervious surface maps from the landcover map. To do this, we use the RegisterLandcoverReclassRules tool:

RegisterLandcoverReclassRules.py -p standard -k

NLCD2006 is a known landcover type in RHESysWorkflows (the only one), 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.

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

There is no need to edit these rules for this NLCD2006 example, but you should take a moment to look at how these rules work. RHESSysWorkflows uses GRASS's [r.reclass](http://grass.osgeo.org/grass64/manuals/r.reclass.html) command, and so the rules files follow this format. It's important to note that your landcover reclass rules must result in raster maps whose values labels match class names present in the RHESSys ParamDB database. Thus, be very carful in editing the righthand side of the expressions in your reclass rules.

> You can find information on NLCD2006 classes [here](http://www.mrlc.gov/nlcd06_leg.php)

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

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. Additionally, the template used to create the worldfile will be saved as template in the templates folder of the rhessys folder. Currently, this template will be regenerated each time CreateWorldfile is run. However the next release of RHESSysWorkflows will separate the creation of the template from the creation of the worldfile, allowing you to customize the generated template before grass2world is called. In the mean time, there is nothing to stop you from editing the template and re-running grass2world by hand.

#### 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 sufrace 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. 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](https://github.com/RHESSys/ParamDB/blob/develop/allometry/allometric.txt). 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](http://wiki.icess.ucsb.edu/rhessys/index.php/Main_Page) 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.

### 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](http://www.gdal.org/formats_list.html).

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.

#### 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](http://www.gdal.org/ogrinfo.html), 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](https://github.com/RHESSys/RHESSys/wiki/Surface-Flowtable-Routing).

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

#### 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](https://github.com/RHESSys/ParamDB).

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 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.

Appendix

### 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](https://docs.google.com/file/d/0B7aK-9pTSLS-MHRrRTVVRV9zdVk/edit?usp=sharing)

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](https://github.com/selimnairb/EcohydroLib). Alternatively, you can download a pre-built copy of the NHDPlusV2 database needed by RHESSysWorkflows [here](https://docs.google.com/file/d/0B7aK-9pTSLS-dGVzWGRCd1NwNzQ/edit?usp=sharing). To download and unpack the pre-built data, do the following:

  • Download pre-packaged NHDPlusV2 database [here](https://docs.google.com/file/d/0B7aK-9pTSLS-dGVzWGRCd1NwNzQ/edit?usp=sharing)

    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 '<myusername>' with your user name (To find

    System Message: WARNING/2 (<string>, line 1461)

    Block quote ends without a blank line; unexpected unindent.

    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 '<myusername>' 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

Docutils System Messages

System Message: ERROR/3 (<string>, line 181); backlink

Unknown target name: "grassaddons-rhessysworkflows.dmg".

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Last updated Jan 9th, 2014

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