pypismtools is a collection of python classes and functions to evaluate studies made with the Parallel Ice Sheet Model (PISM, http://www.pism-docs.org). pypismtools provides tools for binning and histogram plotting. It also includes helper functions and wrappers for things like unit conversion, defining figure sizes and parameters, and more. Additionally, some scripts are included, to plot netCDF variables over GeoTIFF files using basemap, to generate colorramps for QGIS, and to extract contour lines.
The following python modules have to be installed previously:
- netCDF4
- gdal (with python bindings)
- pyproj
- py_udunits2 (from https://github.com/ckhroulev/py_udunits2)
- matplotlib (http://matplotlib.org/)
- basemap (http://matplotlib.org/basemap/)
- python imaging library (PIL), optional, needed for some backgrounds)
To install for all users, run
$ sudo python setup.py install
To install for the current user, run
$ python setup.py install --user
basemap-plot.py is a script to plot a variety of ice sheet model relevant variables from a netCDF file from Greenland and Antarctica data sets. Projection information is retrieved from the first input file, and all subsequent plots are on-the-fly re-projected, which makes the script slow but flexible.
- Download a test data set, e.g. the SeaRISE master data set from
$ wget -nc http://websrv.cs.umt.edu/isis/images/a/a5/Greenland_5km_v1.1.nc
- First, plot the magnitude of horizontal surface velocities 'surfvelmag' and save as 'surfvelmag.png'.
$ basemap-plot.py --singlerow -v surfvelmag --colorbar_label -o surfvelmag.png Greenland_5km_v1.1.nc
Example 1: Magnitude of surface velocities.
- Now, add coastlines (intermediate resolution 'i') and plot ice thickness 'thk' over an etopo background
$ basemap-plot.py --background etopo --coastlines --map_resolution i --singlerow -v thk -o etopothk.png Greenland_5km_v1.1.nc
Example 2: Ice thickness with ETOPO background.
- Use a GeoTIFF file as background, plot the colorbar horizontally. In this case, projection information is taken from the GeoTIFF:
$ basemap-plot.py --geotiff mygeotiff.tif --singlecolumn -v
surfvelmag --colorbar_label -o geotiff.png Greenland_5km_v1.1.nc
Example 3: Magnitude of surface velocities over a MODIS mosaic of Greenland.
The script extract_profiles.py extracts variables stored in a NetCDF_ input.nc file along profiles given in a shape file myprofiles.shp and saves the extracted profiles in profile.nc.
extract_profiles.py myprofiles.shp input.nc profile.py
qgis-colorramp-plot.py creates linear and log-scaled colorramps for QGIS from GMT colormaps. Many great colormap can be downloaded from http://soliton.vm.bytemark.co.uk/pub/cpt-city/.
To show the bathymetry around Greenland, you can use the IBCAO colormap. By running the following command
qgis-colorramp.py --vmin -5000 --vmax 1400 --extend -10000 4000 ibcao.cpt
and you get a linear colorramp from -5000m to 1400m, where the first and last color
will be extended to -10000 and 4000m, respectively (in ibcao.txt). The result should like like
For a nice log-scaled colormap to show speeds, try:
qgis-colorramp.py --a 3 --log --extend 0 30000 Full_saturation_spectrum_CCW.cpt
To use the colorramp in QGIS, click on 'Layer Properties / Colormap' and then click on 'Load color map from file'. Choose the txt file. Also the colorbar is saved as a png file, and can be added in the 'Print Composer'.
contour2shp.py lets you extract a contour line from a variable in a netCDF file, and saves it as a polygon in a shapefile. Useful to create a polygon of a drainage basin from the mask. Or you can extract the 2000m elevation contour:
contour2shp.py -v usrf -c 2000 -s -o poly.shp Greenland_5km_v1.1.nc
create_greenland_grid.py creates a netCDF file with the SeaRISE Greenland grid with a given grid spacing. Run nc2cdo.py from pism/utils and you got a grid definition file that can be used for conservative remapping with CDO (https://code.zmaw.de/projects/cdo).
create_greenland_grid.py -g 2 searise_2km_grid.nc
Similar to create_greenland_grid.py but for the EPSG:3413 projection. Expects grid spacing in meters.
create_greenland_epsg3413_grid.py -g 1800 grid_1800m_grid.nc