# Simple script to inject bathymetry onto a mesh
# Phillip Wolfram, 01/19/2018
from __future__ import absolute_import, division, print_function, \
unicode_literals
from mpas_tools.mesh.creation.open_msh import readmsh
from mpas_tools.mesh.interpolation import interp_bilin
import numpy as np
from scipy import interpolate
import netCDF4 as nc4
import timeit
import os
import sys
[docs]
def inject_bathymetry(mesh_file):
# Open NetCDF mesh file and read mesh points
nc_mesh = nc4.Dataset(mesh_file, 'r+')
lon_mesh = np.mod(
nc_mesh.variables['lonCell'][:] + np.pi,
2 * np.pi) - np.pi
lat_mesh = nc_mesh.variables['latCell'][:]
# Interpolate bathymetry on to mesh points
if os.path.isfile("earth_relief_15s.nc"):
bathymetry = interpolate_SRTM(lon_mesh, lat_mesh)
elif os.path.isfile("topo.msh"):
bathymetry = interpolate_topomsh(lon_mesh, lat_mesh)
else:
print("Bathymetry data file not found")
raise SystemExit(0)
# Create new NetCDF variables in mesh file, if necessary
nc_vars = nc_mesh.variables.keys()
if 'bottomDepthObserved' not in nc_vars:
nc_mesh.createVariable('bottomDepthObserved', 'f8', ('nCells'))
# Write to mesh file
nc_mesh.variables['bottomDepthObserved'][:] = bathymetry
nc_mesh.close()
def interpolate_SRTM(lon_pts, lat_pts):
# Open NetCDF data file and read cooordintes
nc_data = nc4.Dataset("earth_relief_15s.nc", "r")
lon_data = np.deg2rad(nc_data.variables['lon'][:])
lat_data = np.deg2rad(nc_data.variables['lat'][:])
# Setup interpolation boxes (for large bathymetry datasets)
n = 15
xbox = np.deg2rad(np.linspace(-180, 180, n))
ybox = np.deg2rad(np.linspace(-90, 90, n))
dx = xbox[1] - xbox[0]
dy = ybox[1] - ybox[0]
boxes = []
for i in range(n - 1):
for j in range(n - 1):
boxes.append(np.asarray(
[xbox[i], xbox[i + 1], ybox[j], ybox[j + 1]]))
# Initialize bathymetry
bathymetry = np.zeros(np.shape(lon_pts))
bathymetry.fill(np.nan)
# Interpolate inside each box
start = timeit.default_timer()
for i, box in enumerate(boxes):
print(i + 1, "/", len(boxes))
# Get data inside box (plus a small overlap region)
overlap = 0.1
lon_idx, = np.where(
(lon_data >= box[0] - overlap * dx) & (lon_data <= box[1] + overlap * dx))
lat_idx, = np.where(
(lat_data >= box[2] - overlap * dy) & (lat_data <= box[3] + overlap * dy))
xdata = lon_data[lon_idx]
ydata = lat_data[lat_idx]
zdata = nc_data.variables['z'][lat_idx, lon_idx]
# Get points inside box
lon_idx, = np.where((lon_pts >= box[0]) & (lon_pts <= box[1]))
lat_idx, = np.where((lat_pts >= box[2]) & (lat_pts <= box[3]))
idx = np.intersect1d(lon_idx, lat_idx)
xpts = lon_pts[idx]
ypts = lat_pts[idx]
bathymetry[idx] = interp_bilin(xdata, ydata, zdata, xpts, ypts)
end = timeit.default_timer()
print(end - start, " seconds")
return bathymetry
def interpolate_topomsh(lon_pts, lat_pts):
topo = readmsh('topo.msh')
xpos = np.deg2rad(topo['COORD1'])
ypos = np.deg2rad(topo['COORD2'])
zlev = np.reshape(topo['VALUE'], (len(ypos), len(xpos)))
Y, X = np.meshgrid(ypos, xpos)
bathy = interpolate.LinearNDInterpolator(
np.vstack((X.ravel(), Y.ravel())).T, zlev.ravel())
bathymetry = bathy(np.vstack((lon_pts, lat_pts)).T)
return bathymetry
def main():
# Open NetCDF mesh file and read mesh points
mesh_file = sys.argv[1]
inject_bathymetry(mesh_file)