SecHaz is a program that calculates liquefaction and landslide probabilities given ground motions and a number of global data sets.
- Add zoom capability
- Add ability to turn off scenario watermark
- Fix input panel plots - titles (I think) are reversed top-to-bottom.
This package depends on:
- numpy, the fundamental package for scientific computing with Python. http://www.numpy.org/
- matplotlib, a Python 2D plotting library which produces publication quality figures. <a href="http://matplotlib.org/index.html
- basemap, a mapping package built on top of matplotlib. http://matplotlib.org/basemap/
- fiona, a package for reading vector data file formats (in this case, road shapefiles).
- neicio, a Python library for reading/writing various spatial data formats (including ShakeMap grid.xml).
- neicmap, a Python library for doing various spatial calculations (distance, angle, etc.)
- neicutil, a Python library which is a grab bag of interpolation routines, text manipulation functions, and time functions.
- shapely, a Python library for manipulation and analysis of geometric objects in the cartesian plane.
The best way to install numpy,matplotlib,scipy and fiona is to use one of the Python distributions described here:
http://www.scipy.org/install.html
The Anaconda distributions have been successfully tested with sechaz.
You may need to open a new terminal window to ensure that the newly installed versions of python and pip are in your path.
To install basemap:
If you are using anaconda (see above):
conda install basemap
Otherwise, see the installation instructions here:
http://matplotlib.org/basemap/users/installing.html
To install fiona:
If you are using anaconda (see above):
conda install fiona
Otherwise, see the installation instructions here:
http://toblerity.org/fiona/README.html#installation
To install neicio:
pip install git+git://github.com/usgs/neicio.git
To install neicmap:
pip install git+git://github.com/usgs/neicmap.git
To install neicutil:
pip install git+git://github.com/usgs/neicutil.git
To install this package:
pip install git+git://github.com/mhearne-usgs/secondary.git
To upgrade this package:
pip install -U git+git://github.com/mhearne-usgs/secondary.git
To uninstall this package:
pip uninstall secondary
To install shapely:
If you are using anaconda (see above):
conda install shapely
Otherwise, see the installation instructions here:
https://pypi.python.org/pypi/Shapely
The base data used for this software comes from open sources, and is processed using open source tools:
- gdal - http://trac.osgeo.org/gdal/wiki/DownloadingGdalBinaries
- GMT 5 - http://gmt.soest.hawaii.edu/projects/gmt/wiki/Installing
Topography: USGS Global Multi-resolution Terrain Elevation Data 2010 (GMTED2010) http://topotools.cr.usgs.gov/gmted_viewer/data/Grid_ZipFiles/md30_grd.zip
To convert this data to a GMT-style NetCDF 3 file, you can do the following on a Unix-like system:
- unzip md30_grd.zip
- gdal_translate -of AAIGrid md30_grd md30_grd.ascii
- gmt grdreformat md30_grd.ascii=ei md30_grid_gmt5.grd=cs
Roads: Global Roads Open Access Data Set (gROADS) http://sedac.ciesin.columbia.edu/data/set/groads-global-roads-open-access-v1/data-download (requires registration)
Download all of the regional shapefile road data sets into a common data directory, and unzip them in place. The roadfolder configuration option should point to that common data directory.
An automation program is included with this distribution - autosec.py.
This program, when run (manually or at intervals by something like cron), will search the NEIC one hour earthquake data feed (http://earthquake.usgs.gov/earthquakes/feed/v1.0/summary/4.5_hour.geojson) for new ShakeMaps for events matching magnitude, mmi, or PAGER impact level criteria in a config file (see below).
When an event matching one or more of those thresholds is found, autosec.py will run sechaz.py and then email the PNG and PDF probability map to a configured list of email recipients.
The liquefaction and landslide models are defined in a configuration file, which must be located in the user's home folder in a sub-folder called ".secondary". The file must be named "config.ini". As an example, for a user called "frogers" would need to have a file called:
Mac: /Users/frogers/.secondary/config.ini
Linux: /home/frogers/.secondary/config.ini
Windows (untested!): c:\Documents and Settings\frogers.secondary\config.ini
Below is a sample configuration file:
[LIQUEFACTION_MODEL] #layers must be in GMT NetCDF format cti_layer = /Users/frogers/secondary/data/globalcti.grd vs30_layer = /Users/frogers/secondary/data/global_vs30.grd #coefficients for the model b0 = 24.1 b1 = 2.067 b2 = 0.355 b3 = -4.784 #certain variables are available from the ShakeMap: #MW = magnitude #PGV = pgv layer from the grid #PGA = pga layer from the grid #MMI = mmi layer from the grid #terms to be multiplied by corresponding coefficients #certain operators are allowed: +,-,*,/,log,power,log10 b1_term = log((PGA/100)*(power(MW,2.56)/power(10,2.24))) b2_term = cti/100 b3_term = log(vs30) #what is the grid to which all other grids will be resampled? baselayer = vs30 #custom settings for rendering of individual layers - value must be a valid matplotlib colormap name. vs30_colormap = jet_r [LANDSLIDE_MODEL] #layers must be in GMT NetCDF format cohesion_layer = /Users/frogers/secondary/data/cohesion_10i.grd slope_layer = /Users/frogers/secondary/data/slope_50.grd #coefficients for the model b0 = -7.15 b1 = 0.0604 b2 = 0.000825 b3 = 0.0201 b4 = 1.45e-05 #certain variables are available from the ShakeMap: #MW = magnitude #PGV = pgv layer from the grid #PGA = pga layer from the grid #MMI = mmi layer from the grid #terms to be multiplied by corresponding coefficients #certain operators are allowed: +,-,*,/,log,power,log10 b1_term = PGA b2_term = slope b3_term = cohesion/10.0 b4_term = PGA*slope #what is the grid wo which all other grids will be resampled? baselayer = cohesion [SHAKEMAP] variables = PGV,PGA,MW [OUTPUT] folder = /Users/frogers/secondary/output [MAPDATA] #required layers topo = /Users/frogers/secondary/data/etopo1_bed_g_f4.grd slope = /Users/frogers/secondary/data/slope_50.grd #required slope parameters - pixels with slope > slopemax will not be liquefied slopemin = 5.0 slopemax = 5.0 #optional layers roadfolder = /Users/mhearne/secondary/data/roads roadcolor = 00FF00 countrycolor = 177F10
autosec.py looks for a file in the ~/.secondary folder called mailconfig.ini. That file should look something like this:
[THRESHOLDS] eis = yellow mag = 7.5 mmi = 7 [MAIL] server = yourmailserver.yourorganization.org sender = genericaddress@yourorganization.org recipients = user1@yourorganization.org,user2@yourorganization.org,
usage: sechaz.py [-h] [-c CONFIGFILE] [-r] [-n] [GRIDFILE]
Run the landslide and liquefaction models defined by coefficients found in a
config.ini file. Output is a pdf map with liquefaction/landslide results
layered on topography.
positional arguments:
GRIDFILE ShakeMap grid.xml file (default: None)
optional arguments:
-h, --help show this help message and exit
-c CONFIGFILE, --config CONFIGFILE
Use a custom config file (default:
/Users/mhearne/.secondary/config.ini)
-r, --roads Draw roads (default: False)
-n, --noscenario Turn off scenario watermark (use with caution)
(default: False)