In [1]:
from pylab import *
import iris
import iris.plot as iplt
import cartopy.crs as ccrs
import netCDF4
import datetime as dt
from time import time
In [2]:
year = 2007
start = dt.datetime(year,1,1,0,0,0)
stop = dt.datetime(year,12,31,18,0,0)
bbox = [-77., -63., 34., 46.] # [lon_min lon_max lat_min lat_max]
In [3]:
# CFSR NOMADS OPeNDAP URL
url='http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cmd_ocnh/%4.4d/%4.4d01/%4.4d0101/ocnh01.gdas.%4.4d010100.grb2' % (year,year,year,year)
print url
In [4]:
# specify name of output file that will be created
ofile = '/usgs/data2/rsignell/models/ncep/CFSR/cfsr_%4.4d.nc' % year
print ofile
In [5]:
cubes = iris.load(url)
In [6]:
print cubes
In [7]:
long_name = 'Potential_temperature @ depth_below_sea'
cube = iris.load_cube(url,long_name)
slice = cube.extract(iris.Constraint(longitude=lambda cell: bbox[0]+360. < cell < bbox[1]+360.,
latitude=lambda cell: bbox[2] < cell < bbox[3]))
shape(slice)
In [8]:
# convert to degC
slice.convert_units('degC')
In [9]:
print slice
In [10]:
# select surface layer at 1st time step for a test plot
slice2d=slice[0,-1,:,:]
shape(slice2d)
In [11]:
figure(figsize=(12,8))
# set the projection
ax1 = plt.axes(projection=ccrs.Mercator())
# color filled contour plot
h = iplt.contourf(slice2d,64)
# add coastlines, colorbar and title
plt.gca().coastlines(resolution='10m')
colorbar(h,orientation='vertical');
title('Ocean Temperature');
In [12]:
iris.save(slice,ofile)
In [13]:
origin = dt.datetime(1900,1,1,0,0,0)
nsteps = int((stop - start).total_seconds()/3600/6) # 6 hour time steps
print nsteps
nc = netCDF4.Dataset(ofile,'r+')
nc.variables['time'].units = 'hours since 1900-01-01T00:00:00Z'
# start from penultimate time step (or 0)
istart=max(len(nc.dimensions['time'])-1,0)
#istart = 439
nc.close()
for i in range(istart,nsteps):
time0=time()
nc = netCDF4.Dataset(ofile,'r+')
dtime = start + dt.timedelta(hours=(6*i))
dhours=(dtime - origin).total_seconds()/3600.
url='http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/\
cmd_ocnh/%4.4d/%4.4d%2.2d/%4.4d%2.2d%2.2d/ocnh01.gdas.%4.4d%2.2d%2.2d%2.2d.grb2' \
% (dtime.year,
dtime.year,dtime.month,
dtime.year,dtime.month,dtime.day,
dtime.year,dtime.month,dtime.day,dtime.hour)
cube = iris.load_cube(url,long_name)
slice = cube.extract(iris.Constraint(longitude=lambda cell: bbox[0]+360. < cell < bbox[1]+360.,
latitude=lambda cell: bbox[2] < cell < bbox[3]))
slice.convert_units('degC')
nc.variables['Potential_temperature'][i,:,:,:]=slice.data
nc.variables['time'][i] = int(dhours)
nc.close()
print '%d, Step %d, %5.2f percent, elapsed time %5.3f seconds' % (i-istart, i,i*100./nsteps, (time()-time0))
127, Step 127, 8.70 percent, elapsed time 7.450 seconds
128, Step 128, 8.77 percent, elapsed time 7.600 seconds
129, Step 129, 8.84 percent, elapsed time 5.476 seconds
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---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
<ipython-input-13-5a2fc7e77361> in <module>()
23
24
---> 25 cube = iris.load_cube(url,long_name)
26 slice = cube.extract(iris.Constraint(longitude=lambda cell: bbox[0]+360. < cell < bbox[1]+360.,
27 latitude=lambda cell: bbox[2] < cell < bbox[3]))
/home/local/python27_epd/lib/python2.7/site-packages/Iris-1.5.0_dev-py2.7.egg/iris/__init__.pyc in load_cube(uris, constraint, callback)
226 raise ValueError('only a single constraint is allowed')
227
--> 228 cubes = _load_collection(uris, constraints, callback).merged().cubes()
229
230 if len(cubes) != 1:
/home/local/python27_epd/lib/python2.7/site-packages/Iris-1.5.0_dev-py2.7.egg/iris/__init__.pyc in _load_collection(uris, constraints, callback)
166 try:
167 cubes = _generate_cubes(uris, callback)
--> 168 result = iris.cube._CubeFilterCollection.from_cubes(cubes, constraints)
169 except EOFError as e:
170 raise iris.exceptions.TranslationError(
/home/local/python27_epd/lib/python2.7/site-packages/Iris-1.5.0_dev-py2.7.egg/iris/cube.pyc in from_cubes(cubes, constraints)
133 pairs = [_CubeFilter(constraint) for constraint in constraints]
134 collection = _CubeFilterCollection(pairs)
--> 135 for cube in cubes:
136 collection.add_cube(cube)
137 return collection
/home/local/python27_epd/lib/python2.7/site-packages/Iris-1.5.0_dev-py2.7.egg/iris/__init__.pyc in _generate_cubes(uris, callback)
157 elif scheme in ['http', 'https']:
158 urls = [':'.join(x) for x in groups]
--> 159 for cube in iris.io.load_http(urls, callback):
160 yield cube
161 else:
/home/local/python27_epd/lib/python2.7/site-packages/Iris-1.5.0_dev-py2.7.egg/iris/io/__init__.pyc in load_http(urls, callback)
198 # Call each iris format handler with the appropriate filenames
199 for handling_format_spec, fnames in handler_map.iteritems():
--> 200 for cube in handling_format_spec.handler(fnames, callback):
201 yield cube
202
/home/local/python27_epd/lib/python2.7/site-packages/Iris-1.5.0_dev-py2.7.egg/iris/fileformats/netcdf.pyc in load_cubes(filenames, callback)
454 for filename in filenames:
455 # Ingest the netCDF file.
--> 456 cf = iris.fileformats.cf.CFReader(filename)
457
458 # Process each CF data variable.
/home/local/python27_epd/lib/python2.7/site-packages/Iris-1.5.0_dev-py2.7.egg/iris/fileformats/cf.pyc in __init__(self, filename, warn, monotonic)
792 '''Collection of CF-netCDF variables associated with this netCDF file'''
793
--> 794 self._dataset = netCDF4.Dataset(self._filename, mode='r')
795
796 # Issue load optimisation warning.
/home/local/python27_epd/lib/python2.7/site-packages/netCDF4.so in netCDF4.Dataset.__init__ (netCDF4.c:15904)()
RuntimeError: NetCDF: Malformed or inaccessible DAP DDS
In [ ]:
In [ ]:
# check file we created
cubes = iris.load(ofile)
print cubes[0]
In [ ]:
Content source: rsignell-usgs/ipython-notebooks
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