def average_timeseries(self, source, region, variable=None):
"""
Calculates mean of all time series in a region.
Parameters
----------
source : str
Data source from which time series should be read.
region : str, optional
Region of interest, set to first defined region if None.
variable : str, optional
Variable to display, set to first variable of source if None.
Returns
-------
ts : pd.DataFrame
Timeseries for the selected data.
"""
grid = ShapeGrid(region, self.spatial_resolution, self.shapefile)
points = grid.get_gridpoints()
df = pd.DataFrame()
locations = []
if region in self.regions:
region = region
locations = list(points.index)
else:
for i, sr in enumerate(self.sub_regions):
if region in sr:
idx = i
break
region = self.regions[idx]
lat = points['lat'].tolist()
lon = points['lon'].tolist()
for i in range(0, points.shape[0]):
locations.append((lon[i], lat[i]))
if len(points) < 1:
return 'ERROR: No points available in the selected region.'
df, gpis = self.bulkread_timeseries(source,
locations,
region,
variable=variable)
df_mean = pd.DataFrame()
for var in df.keys():
df_mean[var + '_mean'] = df[var].mean(axis=1)
return df_mean, len(gpis)
def average_timeseries(self, source, region, variable=None):
"""
Calculates mean of all time series in a region.
Parameters
----------
source : str
Data source from which time series should be read.
region : str, optional
Region of interest, set to first defined region if None.
variable : str, optional
Variable to display, set to first variable of source if None.
Returns
-------
ts : pd.DataFrame
Timeseries for the selected data.
"""
grid = ShapeGrid(region, self.spatial_resolution, self.shapefile)
points = grid.get_gridpoints()
df = pd.DataFrame()
locations = []
if region in self.regions:
region = region
locations = list(points.index)
else:
for i, sr in enumerate(self.sub_regions):
if region in sr:
idx = i
break
region = self.regions[idx]
lat = points['lat'].tolist()
lon = points['lon'].tolist()
for i in range(0, points.shape[0]):
locations.append((lon[i], lat[i]))
if len(points) < 1:
return 'ERROR: No points available in the selected region.'
df, gpis = self.bulkread_timeseries(source, locations, region,
variable=variable)
df_mean = pd.DataFrame()
for var in df.keys():
df_mean[var + '_mean'] = df[var].mean(axis=1)
return df_mean, len(gpis)
def test_ShapeGrid(self):
# general case
cgrid = ShapeGrid(self.region, sp_res=self.sp_res)
bbox = (cgrid.arrlat.min(), cgrid.arrlat.max(),
cgrid.arrlon.min(), cgrid.arrlon.max())
assert cgrid.get_grid_points()[0].size == 290
assert bbox == (46.625, 48.875, 9.875, 16.875)
assert cgrid.get_gridpoints().shape == (158, 2)
# test special case NZ
cgrid = ShapeGrid('NZ', sp_res=self.sp_res1)
bbox = (cgrid.arrlat[0], cgrid.arrlat[-1],
cgrid.arrlon[0], cgrid.arrlon[-1])
assert cgrid.shape == (34, 24)
assert cgrid.get_gridpoints().shape == (116, 2)
assert bbox == (-46.75, -35.25, 167.37, -176.5)
def get_gridpoints(self):
"""Returns gridpoints from NetCDF file.
Parameters
----------
region : str
Identifier of the region in the NetCDF file.
Returns
-------
gridpoints : dict of pandas.DataFrame
Dict containing Dataframes with gridpoint index as index,
longitutes and latitudes as columns for each region.
"""
gridpoints = {}
if self.regions == ['global']:
filename = (self.regions[0] + '_' + str(self.spatial_resolution) +
'_' + str(self.temporal_resolution) + '.nc')
ncfile = os.path.join(self.data_path, filename)
with Dataset(ncfile, 'r+', format='NETCDF4') as nc:
gpis = nc.variables['gpi'][:]
lons = nc.variables['lon'][:]
lats = nc.variables['lat'][:]
gpis = gpis.flatten()
lons, lats = np.meshgrid(lons, lats)
lons = lons.flatten()
lats = lats.flatten()
points = pd.DataFrame(index=gpis)
points['lon'] = lons
points['lat'] = lats
gridpoints['global'] = points
else:
for region in self.regions:
grid = ShapeGrid(region, self.spatial_resolution,
self.shapefile)
points = grid.get_gridpoints()
gridpoints[region] = points
return gridpoints
def get_gridpoints(self):
"""Returns gridpoints from NetCDF file.
Parameters
----------
region : str
Identifier of the region in the NetCDF file.
Returns
-------
gridpoints : dict of pandas.DataFrame
Dict containing Dataframes with gridpoint index as index,
longitutes and latitudes as columns for each region.
"""
gridpoints = {}
if self.regions == ['global']:
filename = (self.regions[0] + '_' + str(self.spatial_resolution)
+ '_' + str(self.temporal_resolution) + '.nc')
ncfile = os.path.join(self.data_path, filename)
with Dataset(ncfile, 'r+', format='NETCDF4') as nc:
gpis = nc.variables['gpi'][:]
lons = nc.variables['lon'][:]
lats = nc.variables['lat'][:]
gpis = gpis.flatten()
lons, lats = np.meshgrid(lons, lats)
lons = lons.flatten()
lats = lats.flatten()
points = pd.DataFrame(index=gpis)
points['lon'] = lons
points['lat'] = lats
gridpoints['global'] = points
else:
for region in self.regions:
grid = ShapeGrid(region, self.spatial_resolution,
self.shapefile)
points = grid.get_gridpoints()
gridpoints[region] = points
return gridpoints
def image_bounds(country, sp_res, shapefile=None):
"""
Calculates bounding box, center coordinates and zoom level of an image
for web overlay purposes.
Parameters
----------
country : str
FIPS country code (https://en.wikipedia.org/wiki/FIPS_country_code)
sp_res : numeric
Spatial resolution of the image
shapefile : str, optional
Paht to a custom shapefile.
Returns
-------
lon_min : int
Minimum longitude.
lon_max : int
Maximum longitude.
lat_min : int
Minimum latitude.
lat_max : int
Maximum latitude.
c_lat : int
Center latidute of image.
c_lon : int
Center longitude of image.
zoom : int
Zoom level for openlayers.
"""
shp = ShapeGrid(country, sp_res, shapefile=shapefile)
lon_min = shp.arrlon.min() - (sp_res / 2)
lon_max = shp.arrlon.max() + (sp_res / 2)
lat_min = shp.arrlat.min() - (sp_res / 2)
lat_max = shp.arrlat.max() + (sp_res / 2)
e_lon = lon_max - lon_min
e_lat = lat_max - lat_min
c_lon = lon_min + e_lon / 2
c_lat = lat_min + e_lat / 2
zoom = 0
i = 1024 # To be replaced with the width of the map container!
while i / 2 > e_lon:
zoom += 1
i = i / 2
return lon_min, lon_max, lat_min, lat_max, c_lat, c_lon, zoom
def test_ShapeGrid(self):
# general case
cgrid = ShapeGrid(self.region, sp_res=self.sp_res)
bbox = (cgrid.arrlat.min(), cgrid.arrlat.max(), cgrid.arrlon.min(),
cgrid.arrlon.max())
assert cgrid.get_grid_points()[0].size == 290
assert bbox == (46.625, 48.875, 9.875, 16.875)
assert cgrid.get_gridpoints().shape == (158, 2)
# test special case NZ
cgrid = ShapeGrid('NZ', sp_res=self.sp_res1)
bbox = (cgrid.arrlat[0], cgrid.arrlat[-1], cgrid.arrlon[0],
cgrid.arrlon[-1])
assert cgrid.shape == (34, 24)
assert cgrid.get_gridpoints().shape == (116, 2)
assert bbox == (-46.75, -35.25, 167.37, -176.5)
def bulkread_ts(self,
locations,
region=None,
variable=None,
shapefile=None,
scaled=True,
grid=None):
"""Gets timeseries from netCDF file for a number of gridpoints.
Parameters
----------
location : list of int or list of tuples
Either a list of Grid point indices given as integer value [0,1,2]
or a list of Longitude/Latitude tuples [(0.0, 0.0),(45.0, 45.0)].
region : str, optional
Region of interest, set to first defined region if not set.
variable : str, optional
Variable to display, selects all available variables if None.
shapefile : str, optional
Path to custom shapefile.
scaled : bool, optional
If true, data will be scaled to a predefined range; if false, data
will be shown as given in rawdata file; defaults to True
grid : poets.grid.grids RegularGrid or ShapeGrid, optional
Grid with point and lon/lat information; defaults to None.
Returns
-------
df_list : list of pd.DataFrames
List with timeseries for selected variables.
gpis : list of int
List of gpi values.
"""
if region is None:
region = self.valid_regions[0]
if type(locations[0]) is tuple:
if grid is None:
if region == 'global':
grid = RegularGrid(self.dest_sp_res)
else:
grid = ShapeGrid(region, self.dest_sp_res, shapefile)
gpis = []
for loc in locations:
gp, _ = grid.find_nearest_gpi(loc[0], loc[1])
gpis.append(gp)
else:
gpis = locations
variable = self._set_variable(variable)
source_file = self.src_file[region]
var_dates = self._check_current_date()
df_list = {}
lat_pos = []
lon_pos = []
with Dataset(source_file, 'r', format='NETCDF4') as nc:
time = nc.variables['time']
dates = num2date(time[:], units=time.units, calendar=time.calendar)
for gp in gpis:
position = np.where(nc.variables['gpi'][:] == gp)
lat_pos = np.append(lat_pos, int(position[0][0]))
lon_pos = np.append(lon_pos, int(position[1][0]))
lat_pos = map(int, lat_pos)
lon_pos = map(int, lon_pos)
df = pd.DataFrame(index=pd.DatetimeIndex(dates))
for ncv in variable:
begin = np.where(dates == var_dates[region][ncv][0])[0][0]
end = np.where(dates == var_dates[region][ncv][1])[0][0]
ts = nc.variables[ncv][begin:end + 1, :, :]
ts = ts[:, lat_pos, lon_pos]
ts = np.swapaxes(ts, 1, 0)
for idx, gp in enumerate(gpis):
df['gpi_' + str(gp)] = np.NAN
df['gpi_' + str(gp)][begin:end + 1] = ts[idx, :]
if nc.variables[ncv]._FillValue is not None:
df = df.replace(nc.variables[ncv]._FillValue, np.NAN)
if 'scaling_factor' in nc.variables[ncv].ncattrs():
nv = nc.variables[ncv]
if nv.getncattr('scaling_factor') < 0:
df[ncv] = (df[ncv] *
float(nv.getncattr('scaling_factor')))
else:
df[ncv] = (df[ncv] /
float(nv.getncattr('scaling_factor')))
if scaled:
if self.valid_range is not None:
if self.data_range is not None:
df[ncv] = self._scale_values(df[ncv])
df_list[ncv] = df
return df_list, gpis
def read_ts(self,
location,
region=None,
variable=None,
shapefile=None,
scaled=True):
"""Gets timeseries from netCDF file for one gridpoint.
Parameters
----------
location : int or tuple of floats
Either Grid point index as integer value or Longitude/Latitude
given as tuple.
region : str, optional
Region of interest, set to first defined region if not set.
variable : str, optional
Variable to display, selects all available variables if None.
shapefile : str, optional
Path to custom shapefile.
scaled : bool, optional
If true, data will be scaled to a predefined range; if false, data
will be shown as given in rawdata file; defaults to True
Returns
-------
df : pd.DataFrame
Timeseries for selected variables.
"""
if region is None:
region = self.valid_regions[0]
if type(location) is tuple:
if region == 'global':
grid = RegularGrid(self.dest_sp_res)
else:
grid = ShapeGrid(region, self.dest_sp_res, shapefile)
gp, _ = grid.find_nearest_gpi(location[0], location[1])
else:
gp = location
variable = self._set_variable(variable)
source_file = self.src_file[region]
var_dates = self._check_current_date()
with Dataset(source_file, 'r', format='NETCDF4') as nc:
time = nc.variables['time']
dates = num2date(time[:], units=time.units, calendar=time.calendar)
position = np.where(nc.variables['gpi'][:] == gp)
lat_pos = position[0][0]
lon_pos = position[1][0]
df = pd.DataFrame(index=pd.DatetimeIndex(dates))
for ncvar in variable:
begin = np.where(dates == var_dates[region][ncvar][0])[0][0]
end = np.where(dates == var_dates[region][ncvar][1])[0][0]
df[ncvar] = np.NAN
ts = nc.variables[ncvar][begin:end + 1, lat_pos, lon_pos]
df[ncvar][begin:end + 1] = ts
if nc.variables[ncvar]._FillValue is not None:
df = df.replace(nc.variables[ncvar]._FillValue, np.NAN)
if 'scaling_factor' in nc.variables[ncvar].ncattrs():
vvar = nc.variables[ncvar]
if vvar.getncattr('scaling_factor') < 0:
df[ncvar] = (df[ncvar] *
float(vvar.getncattr('scaling_factor')))
else:
df[ncvar] = (df[ncvar] /
float(vvar.getncattr('scaling_factor')))
if scaled:
if self.valid_range is not None:
if self.data_range is not None:
df[ncvar] = self._scale_values(df[ncvar])
return df