def test_cube_with_multiple(fname=os.path.join(data_path, 'OCOS.nc')):
cube = iris.load_cube(fname, 'potential temperature')
with pytest.raises(iris.exceptions.CoordinateNotFoundError):
cube.coord(axis='X')
cube.coord(axis='Y')
grid = gridgeo.GridGeo(cube)
assert isinstance(grid, gridgeo.GridGeo)
def get_models(self):
self.dap_urls = []
self.grids = {}
self.model_urls = []
for i, df_row in self.df.iterrows():
row = df_row.to_dict()
# Handle the presenece of "opendap" in the NOAA NOS-COOPS obs domain
url = row['url']
if row['scheme'] == 'OPeNDAP:OPeNDAP' or 'dodsC' in url:
if not '.html' in url:
self.dap_urls.append(url)
for url in self.dap_urls:
try:
nc = Dataset(url)
except:
continue
try:
temp = nc.get_variables_by_attributes(standard_name=lambda x: x in self.target)[0]
standard_name = temp.standard_name
except:
continue
try:
grid = gridgeo.GridGeo(nc, standard_name=standard_name)
title = getattr(nc, 'title', url)
self.model_urls.append(url)
except Exception:
continue
self.grids.update({title: grid})
print(self.grids)
def get_models(self):
'''
Function for pulling models from the url queries.
'''
self.dap_urls = []
self.grids = {}
self.model_urls = []
# Query each url in the database
for i, df_row in self.df.iterrows():
row = df_row.to_dict()
# Handle the presenece of "opendap" in the NOAA NOS-COOPS obs domain
url = row['url']
if row['scheme'] == 'OPeNDAP:OPeNDAP' or 'dodsC' in url:
if not '.html' in url:
self.dap_urls.append(url)
# for the valid URLs, try to pull the data
for url in self.dap_urls:
# Some files may not be in the proper format. Ignore them.
try:
nc = Dataset(url)
except:
continue
# Some files may not contain relevant information, even after filtering. Ignore them.
try:
temp = nc.get_variables_by_attributes(
standard_name=lambda x: x in self.target)[0]
standard_name = temp.standard_name
except:
continue
# Some files may not properly convert to a geo-object. Ignore them.
try:
grid = gridgeo.GridGeo(nc, standard_name=standard_name)
title = getattr(nc, 'title', url)
self.model_urls.append(url)
except Exception:
continue
self.grids.update({title: grid})
print(self.grids)
from pathlib import Path
import numpy as np
from shapely.geometry import MultiPolygon, Polygon
import gridgeo
p = Path(__file__).parent.absolute()
fname = p.joinpath("data", "unknown_2d.nc")
grid = gridgeo.GridGeo(fname, standard_name="sea_water_temperature")
npoly = 12706
_iterables = (tuple, list, np.ndarray)
def test_mesh():
assert grid.mesh == "unknown_2d"
def test__str__():
assert grid.__str__() == grid.mesh
def test_outline():
assert isinstance(grid.outline, (MultiPolygon, Polygon))
def test_polygons():
assert isinstance(grid.polygons, _iterables)
import gridgeo
import numpy as np
from shapely.geometry import MultiPolygon, Polygon
url = 'http://geoport.whoi.edu/thredds/dodsC/clay/usgs/users/jcwarner/Sandy/triple_nest/00_dir_NYB07.ncml' # noqa
grid = gridgeo.GridGeo(
url,
standard_name='sea_water_potential_temperature'
)
npoly = 43688
_iterables = (tuple, list, np.ndarray)
def test_mesh():
assert grid.mesh == 'sgrid'
def test__str__():
assert grid.__str__() == grid.mesh
def test_outline():
assert isinstance(grid.outline, (MultiPolygon, Polygon))
def test_no_grid():
with pytest.raises(ValueError):
gridgeo.GridGeo(point_time_series_string)
def test_more_than_one_grid():
with pytest.raises(ValueError):
gridgeo.GridGeo(espresso_string)
def test_nc_from_object():
nc = Dataset(coawst_string)
grid = gridgeo.GridGeo(nc)
assert isinstance(grid.nc, Dataset)
import os
import types
import pysgrid
import numpy as np
from netCDF4 import Dataset
from shapely.geometry import MultiPolygon, Polygon
import gridgeo
data_path = os.path.join(os.path.dirname(__file__), 'data')
coawst_string = os.path.join(data_path, '00_dir_NYB05.nc')
grid = gridgeo.GridGeo(coawst_string)
def test_nc_from_string():
assert isinstance(grid.nc, str)
def test_grid():
assert isinstance(grid.grid, pysgrid.SGrid)
def test_mesh():
assert grid.mesh == 'sgrid'
def test__str__():
def test_rgrid_from_cube(fname=os.path.join(data_path, 'CA_DAS.nc')):
cube = iris.load_cube(fname, 'sea_water_temperature')
grid = gridgeo.GridGeo(cube)
assert isinstance(grid, gridgeo.GridGeo)
def test_ugrid_from_cube(fname=os.path.join(data_path,
'FVCOM-Nowcast-Agg.nc')):
cube = iris.load_cube(fname, 'sea_water_potential_temperature')
with pytest.raises(NotImplementedError):
gridgeo.GridGeo(cube)
def test_sgrid_from_cube(fname=os.path.join(data_path, '00_dir_NYB05.nc')):
cube = iris.load_cube(fname, 'sea_water_potential_temperature')
grid = gridgeo.GridGeo(cube)
assert isinstance(grid, gridgeo.GridGeo)
import pytest
import numpy as np
import iris
from shapely.geometry import MultiPolygon, Polygon
import gridgeo
data_path = os.path.join(os.path.dirname(__file__), 'data')
espresso_string = os.path.join(data_path,
'ESPRESSO_Real-Time_v2_Averages_Best.nc')
cube = iris.load_cube(espresso_string, 'sea_water_potential_temperature')
grid = gridgeo.GridGeo(cube)
def test_from_cube():
assert isinstance(grid.nc, iris.cube.Cube)
def test_grid():
assert not grid.grid
def test_mesh():
assert grid.mesh == 'non-compliant'
def test__str__():
import os
import types
import numpy as np
from netCDF4 import Dataset
from shapely.geometry import MultiPolygon, Polygon
import gridgeo
data_path = os.path.join(os.path.dirname(__file__), 'data')
ca_das_string = os.path.join(data_path, 'CA_DAS.nc')
grid = gridgeo.GridGeo(ca_das_string)
def test_nc_from_string():
assert isinstance(grid.nc, str)
def test_grid():
assert not grid.grid
def test_mesh():
assert grid.mesh == 'non-compliant'
def test__str__():
import os
import types
import pyugrid
import numpy as np
from netCDF4 import Dataset
from shapely.geometry import MultiPolygon, Polygon
import gridgeo
data_path = os.path.join(os.path.dirname(__file__), 'data')
fvcom_string = os.path.join(data_path, 'FVCOM-Nowcast-Agg.nc')
grid = gridgeo.GridGeo(fvcom_string)
def test_nc_from_string():
assert isinstance(grid.nc, str)
def test_grid():
assert isinstance(grid.grid, pyugrid.UGrid)
def test_mesh():
assert grid.mesh == 'ugrid'
def test__str__():
