Difference between revisions of "How to convert data for Geogrid"

Latest revision as of 01:59, 17 February 2021

Back to the WRF-SFIRE user guide.

This wiki page explains how to transform geotiff files to geogrid using convert_geotiff script in wrfxpy.

Get Anaconda3 distribution

Download and install the Python 3 Anaconda Python distribution for your platform. We recommend an installation into the user's home directory.

Install environment

Create the python environment:

 conda update -n base -c defaults conda
 conda create -n wrfx python=3 gdal netcdf4 pyproj paramiko dill h5py psutil proj4 pytz flask pandas
 conda activate wrfx
 conda install -c conda-forge simplekml pygrib f90nml pyhdf xmltodict basemap rasterio scipy
 pip install MesoPy python-cmr

Note that conda and pip are package managers available in the Anaconda Python distribution.

Get wrfxpy repository

Get repository wrfxpy and checkout to convert_geotiff branch. Shortly, it is going to be available in the master branch.

git clone https://github.com/openwfm/wrfxpy
cd wrfxpy
git checkout convert_geotiff

Run convert_geotiff.sh

Run the code to generate geogrid from geotiff files. Run the following line for each variable to process.

./convert_geotiff.sh geotiff_file geo_data_path wrf_variable_name [bbox]

where:

geotiff_file - path to a geotiff file to be converted to geogrid
geo_data_path - any path where to save all the variables
wrf_variable - WRF variable created on src/geo/var_wisdom.py
bbox - optional, bounding box to sample the original geotiff file from, using WGS84 coordinates. Format: min_lon,max_lon,min_lat,max_lat

If you want to know more information and the existing options for wrf_variable, run ./convert_geotiff.sh without inputs

./convert_geotiff.sh

Some examples:

./convert_geotiff.sh elevation.tif geo_data ZSF
./convert_geotiff.sh fuel.tif geo_data NFUEL_CAT
./convert_geotiff.sh fuel.tif geo_data NFUEL_CAT -112.8115,-112.1661,39.4820,39.9750

Results from convert_geotiff.sh

The convert_geotiff.sh script will generate a folder specified by the user by geo_data_path with

Variable folders: A folder for each variable previously run (ZSF and NFUEL_CAT folders) containing:
- a geogrid file of the variable.
- an index file of the variable.
geogrid_tbl.json: A JSON file with all the geogrid information for each variable.
GEOGRID.TBL: A text file with the information to add to GEOGRID.TBL (depends on src/geo/var_wisdom.py, so only copy what you need).
index.json: A JSON file with index information for each variable.

@@ Line 5: / Line 5: @@
 == Get Anaconda3 distribution ==
-Download and install the Python 3 [https://www.continuum.io/downloads Anaconda Python] distribution for your platform. We recommend an installation into the user's home directory.
+Download and install the Python 3 [https://www.anaconda.com/products/individual Anaconda Python] distribution for your platform. We recommend an installation into the user's home directory.
- wget https://repo.continuum.io/archive/Anaconda3-2019.10-Linux-x86_64.sh
- chmod +x Anaconda3-2019.10-Linux-x86_64.sh
- ./Anaconda3-2019.10-Linux-x86_64.sh
-Add your environment (~/.custom.csh) the following line
+== Install environment ==
- setenv PROJ_LIB "$HOME/anaconda3/share/proj"
-or if you are using bash to ~/.profile or ~/.bashrc
- export PROJ_LIB="$HOME/anaconda3/share/proj"
-== Install environment ==
+Create the python environment:
-Create a python environment for gdal compatibility. Shortly this is going to be the environment for wrfxpy installation.
+<pre>
-  conda create -n wrfxpy python=3 gdal netcdf4 pyproj paramiko dill scikit-learn h5py pandas psutil proj4
+ conda update -n base -c defaults conda
-  conda activate wrfxpy
+  conda create -n wrfx python=3 gdal netcdf4 pyproj paramiko dill h5py psutil proj4 pytz flask pandas
-  conda install -c conda-forge simplekml pygrib f90nml pyhdf xmltodict basemap
+  conda activate wrfx
+  conda install -c conda-forge simplekml pygrib f90nml pyhdf xmltodict basemap rasterio scipy
   pip install MesoPy python-cmr
+</pre>
 Note that <tt>conda</tt> and <tt>pip</tt> are package managers available in the Anaconda Python distribution.
@@ Line 29: / Line 25: @@
 Get repository wrfxpy and checkout to convert_geotiff branch. Shortly, it is going to be available in the master branch.
   git clone https://github.com/openwfm/wrfxpy
+ cd wrfxpy
   git checkout convert_geotiff
@@ Line 38: / Line 35: @@
 where:
-<tt>geotiff_file</tt> - path to a GeoTIFF file to be converted to geogrid
+* <tt>geotiff_file</tt> - path to a geotiff file to be converted to geogrid
-<tt>geo_data_path</tt> - any path where to save all the variables
+* <tt>geo_data_path</tt> - any path where to save all the variables
-<tt>wrf_variable</tt> - variable created on src/geo/var_wisdom.py
+* <tt>wrf_variable</tt> - WRF variable created on src/geo/var_wisdom.py
-<tt>bbox</tt> - optional, bounding box to sample the original geotiff file from using WGS84 coordinates. Format: min_lon,max_lon,min_lat,max_lat
+* <tt>bbox</tt> - optional, bounding box to sample the original geotiff file from, using WGS84 coordinates. Format: min_lon,max_lon,min_lat,max_lat
 If you want to know more information and the existing options for wrf_variable, run ./convert_geotiff.sh without inputs
@@ Line 49: / Line 46: @@
   ./convert_geotiff.sh elevation.tif geo_data ZSF
   ./convert_geotiff.sh fuel.tif geo_data NFUEL_CAT
-  ./convert_geotiff.sh ./fuel.tif ./geo_data NFUEL_CAT -112.8115,-112.1661,39.4820,39.9750
+  ./convert_geotiff.sh fuel.tif geo_data NFUEL_CAT -112.8115,-112.1661,39.4820,39.9750
-----
+== Results from convert_geotiff.sh ==
+The convert_geotiff.sh script will generate a folder specified by the user by <tt>geo_data_path</tt> with
-See the github repository for [https://github.com/jbeezley/convert_geotiff.git convert_geotiff] for the latest documentation and source code.
+* '''Variable folders:''' A folder for each variable previously run (ZSF and NFUEL_CAT folders) containing:
+** a geogrid file of the variable.
+** an index file of the variable.
+* '''geogrid_tbl.json:''' A JSON file with all the geogrid information for each variable.
+* '''GEOGRID.TBL:''' A text file with the information to add to GEOGRID.TBL (depends on src/geo/var_wisdom.py, so only copy what you need).
+* '''index.json:''' A JSON file with index information for each variable.
 [[Category:WRF-Fire]]
 [[Category:Howtos|Convert data for Geogrid]]
 [[Category:Data]]