Data Sources

DAYMET

The program starts with kilometer (km) resolution data from the DAYMET weather service

DAYMET hosts web-based tools and services that include both API and scripting downloads.

We have two options for gathering the DAYMET data:

Grab the entire continuous North American dataset (~50-80 mb per file) for every day of the entire record (~32 years), or
Grab sub-sets of the data around the relevant area where we want to do our analyses.

Data parameters:

tmax = Temperature Maximum
tmin = Temperature Minimum
srad = Solar Radiation
vp = Vapor Pressure
swe = Snow Water Equivalent
prcp = Precipitation
dayl = Day Length
na_dem = national digital elevation model (DEM)

Digital Elevation Model

The second required input is a digital elevation model (DEM). Any DEM with a coordinate reference system can be used.

OpenTopography

The second component of the project requires:

(1) Ground classified points only TIN digital elevation model (DEM) at 10m resolution
- We will start out trying 10m elevation models, but if these prove too intensive we can back out to 30m
- If the 10m models work well, and there is more resource availability we can increase their resolution up to 1m
(2) Ground classified point density
- We want to calculate the total number of points classified as bare earth so we can estimate the Leaf Area Index of the surface area
  - We will also need to calculate point density from the unclassified point cloud
(3) Unclassified points only Zmean DEM
- We want to calculate the average elevation of the unclassified points to estimate the mean vegetation height model
  - In order to calculate mean vegetation height we will need to subtract Zmean from the Bare Earth DEM
(4) Unclassified points only point density
- To complete the estimate of Leaf Area Index we will also need the point density of the unclassified points.
(5) Hydrologically Correct DEM
- The Hydrologiccally Correct DEM is calculated by OpenTopography with a TauDEM module
- This is the DEM we will use to calculate slope and aspect later on
(6) D-Infinity Flow direction
- TauDEM will also calculate the D-infinity flow direction
- We want the D-Infinity option rather than the D-8 option
(7) Catchment Area
- TauDEM calculated
(8) Topographic Wetness Index
- TWI is calculated from the TauDEM products and the slope calculated from the DEM

The OpenTopography website: http://www.opentopography.org/index.php allows registered users to select sub-sets of larger data sets and will generate surface models with defined characteristics.

To register as a user on OpenTopography click the myOpenTopo button in the upper right hand side of the website and register your email address. It should only take a few minutes to get an email confirmation.

From OpenTopography we will generate multiple surface models with defined grid parameters.

Click on the 'Data' tab
Select subheading 'LiDAR Point Cloud & Processing'
1. Select any one of the CZO LiDAR flights:
  1. Boulder Creek (snow-off)
  2. Christina River Basin (April)
  3. Eel River
  4. Jemez River Basin (snow-off)
  5. Southern Sierra (snow-off)
  6. Susquehanna Shale Hills (leaf-off)

Create the Bare Earth Digital Elevation Model (DEM, units in elevation), Zmean vegetation height model, and the point density models

1a. Select area of data to download or process
- Select a sub-set area within one of the Critical Zone Observatory sites
  - OpenTopography only allows you to select <200,000,000 points at a time - if the area is too large you will get an Warning message and be asked to re-select a new area.
  - Check to make sure only one type of Return Classification is turned on (e.g. Ground or Unclasssified) at a time - this will reduce the total point load.
1b. Choose Return Classification
- Select only the 'Ground' classified points for the Bare Earth model
  - First we are going to generate the Bare Earth DEM (using the TIN option in #3b)
  - At the same time we can calculate the point count density of the point cloud (using the Local Gridding Option in #3a)
  - Both of these outputs can be generated in the same submission request.
- For the second step, select only 'Unclassified' points for the Zmean (biomass height) model - you will do this AFTER you've submitted a request for the Bare Earth DEM
  - There is an option after you've submitted your request to 'Modify and Resubmit Job'
    - Clicking on that hyperlink takes you back to your same job with the previous parameters selected
    - You can reset the parameters to use the unclassified points rather than the Ground points for the second request.
2. Point Cloud Data Download
- We don't need any of the point cloud, so you can unselect all files
  - It appears that OpenTopography still generates the LAS file for you regardless of whether you selected it
3a.DEM Generation (Local Gridding)
- We will only use the Local Grid option for the Bare Earth model to calculate the point count grid density. In the second job request we will also select the Zmean option.
  - Gridding Method
    - For both the Bare Earth model and the Zmean models we want to calculate the point cloud density - the density layers will be used to calculate the 'Leaf Area Index' later on.
    - Select 'Calculate point count grid'
      - This will produce a point density layer for the resolution of the pixel
    - In the second job request, Select 'Calculate Zmean grid'
      - We don't want the Zmean of the Bare Earth Layer, only calculate this for the Unclassified points
      - Zmean - average elevation of non-ground unclassified points
        
        where Z = z-axis or elevation, mean = average elevation
  - Gridding Parameters
    - Grid Resolution: 10m
      - For right now let's try 10 meters - but, we may need to back out to a larger resolution, e.g. 30 meters, for computational limitations
      - Remember the default is 1 meter! These layers are really cool to look at - but may be computationally too expensive even for our HPC!
    - Radius value: leave set as the default value
  - Grid Format
    - Set to 'GeoTiff'
  - Null Filling
    - Set to '3'
- We also want to calculate the density of the points (so we can come up with Leaf Area Index estimates later on)
  - Gridding Method
    - Select 'Calculate Point count grid'
      - We are going to run this twice - first with the Ground Classified points and then with the Unclassified points
  - Gridding Parametres
    - Grid Resolution: 10m
      - Same option as above - we will start with 10m resolution
    - Radius value: default
  - Grid Format
- Set to 'GeoTiff'
  - Null Filling
- Set to '3'
3b. DEM Generation (TIN) Option
- Grid Method
  - Check on 'Calculate TIN'
- Gridding Parameters
  - Grid Resolution: 10 meters
  - Max Triangle Size: leave as Default (50)
- Grid Format: GeoTiff
4. Derivative Products
- You can unselect these for right now - unless you want to look at the hillshade in a GUI
- The derivatives that are created are (1) a Hillshade and (2) a Slope model
  - The Hillshade is used for visualziation purposes
  - The Slope Model is used for calculating the Hydrological Terrain products (#6)
    - Because OpenTopo breaks up this slope model separately from the DEM we will not use this option and instead create our own slope in GRASS later on.
5. Visualization
- Same as above -unselect this option unless you plan on looking at your outputs in a GUI
- FYI this produces a 'hillshade' or 'relief' model that is easy on the eyes to look at topography, e.g. the Google Maps Terrain Surface in the viewer is a type of relief model.
6. Hydrologic Terrain Analysis Products (TauDEM)
- Select 'Hydrologically Correct DEM'
  - We want to generate a hydrologically correct DEM - this will be the actual layer we use in the later modelling exercises
- Select 'D-Infinity Flow Direction'
- Select 'D-Infinity Specific Catchment Area'
- Do not select 'D-8 Flow Direction'
  - This uses a simpler 8 directional calculation - whereas the D-Infinity option gives proportional flow path weights
- Do not select 'D-8 Contributing Area'
- Select 'Topographic Wetness Index'
  - This is a model derived from the Catchment area divided by the slope.

Additional Detail on Projections and Raster File Types

The models we are going to create are spatial and are defined by 'geo-referencing', i.e. coordinates of latitude and longitude or units of Universal Transverse Mercator (UTM) projection. There are multiple coordinate reference systems out there - but all of the data should come tagged with the appropriate meta-data. The software tools we will be using will *ideally* recognize these projections from the metadata and bring the layers together for us. However - as Nirav always says 'design for failure' - so keep an eye out for this problem.

There is a command line script called 'GeoConvert' by Charles Karney available online that should help with this problem: http://geographiclib.sourceforge.net/1.33/GeoConvert.1.html

DAYMET data are in netCDF format but can be converted using GDAL to the GeoTiff format we are using from OpenTopography.

From DAYMET a document describing how to convert and merge Daymet netCDF files using the Geospatial Data Abstraction Library (GDAL). GDAL is one of the packages that is included in the QGIS download.

OpenTopography Projections and Datum = MANY DIFFERENT KINDS OF PROJECTION AND UNITS
- Critical Zone Observatory Projections and DATUM = UTM (Different Zones across USA) vertical reference = NAVD88, UTM Coordinate Reference = WGS_84

DAYMET Projection and Datum = Lambert Conformal Conic, Coordinate Reference = WGS_1984
- Supplemental info on DAYMET data derivations and spatial projections: http://daac.ornl.gov/Daymet/guides/Daymet_mosaics.html
In QGIS the Coordinate Reference System Selector should set a Generated CRS value that looks like:
- Generated CRS (+proj=lcc +lat_1=25 +lat_2=60 +lat_0=42.5 +lon_0=-100 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs)
- The DAYMET website has projection information at the bottom of this page: http://daymet.ornl.gov/datasupport.html