def test_resample_bilinear(self):
"""Test whole bilinear resampling."""
from pyresample.bilinear import resample_bilinear
# Single array
res = resample_bilinear(self.data1,
self.swath_def,
self.target_def,
50e5,
neighbours=32,
nprocs=1)
self.assertEqual(res.shape, self.target_def.shape)
# There are 12 pixels with value 1, all others are zero
self.assertEqual(res.sum(), 12)
self.assertEqual((res == 0).sum(), 4)
# Single array with masked output
res = resample_bilinear(self.data1,
self.swath_def,
self.target_def,
50e5,
neighbours=32,
nprocs=1,
fill_value=None)
self.assertTrue(hasattr(res, 'mask'))
# There should be 12 valid pixels
self.assertEqual(self.target_def.size - res.mask.sum(), 12)
# Two stacked arrays
data = np.dstack((self.data1, self.data2))
res = resample_bilinear(data, self.swath_def, self.target_def)
shp = res.shape
self.assertEqual(shp[0:2], self.target_def.shape)
self.assertEqual(shp[-1], 2)
def test_resample_bilinear(self):
# Single array
res = bil.resample_bilinear(self.data1,
self.swath_def,
self.target_def,
50e5, neighbours=32,
nprocs=1)
self.assertEqual(res.shape, self.target_def.shape)
# There are 12 pixels with value 1, all others are zero
self.assertEqual(res.sum(), 12)
self.assertEqual((res == 0).sum(), 4)
# Single array with masked output
res = bil.resample_bilinear(self.data1,
self.swath_def,
self.target_def,
50e5, neighbours=32,
nprocs=1, fill_value=None)
self.assertTrue(hasattr(res, 'mask'))
# There should be 12 valid pixels
self.assertEqual(self.target_def.size - res.mask.sum(), 12)
# Two stacked arrays
data = np.dstack((self.data1, self.data2))
res = bil.resample_bilinear(data,
self.swath_def,
self.target_def)
shp = res.shape
self.assertEqual(shp[0:2], self.target_def.shape)
self.assertEqual(shp[-1], 2)
def test_resample_bilinear(self):
# Single array
res = bil.resample_bilinear(self.data1,
self.swath_def,
self.target_def)
self.assertEqual(res.size, self.target_def.size)
# There should be only one pixel with value 1, all others are 0
self.assertEqual(res.sum(), 1)
# Single array with masked output
res = bil.resample_bilinear(self.data1,
self.swath_def,
self.target_def, fill_value=None)
self.assertTrue(hasattr(res, 'mask'))
# There should be only one valid pixel
self.assertEqual(self.target_def.size - res.mask.sum(), 1)
# Two stacked arrays
data = np.dstack((self.data1, self.data2))
res = bil.resample_bilinear(data,
self.swath_def,
self.target_def)
shp = res.shape
self.assertEqual(shp[0], self.target_def.size)
self.assertEqual(shp[1], 2)
def resample(self, target_geo_def):
"""Resamples image to area definition using bilinear approach
Parameters
----------
target_geo_def : object
Target geometry definition
Returns
-------
image_container : object
ImageContainerBilinear object of resampled geometry
"""
if self.image_data.ndim > 2 and self.ndim > 1:
image_data = self.image_data.reshape(
self.image_data.shape[0] * self.image_data.shape[1],
self.image_data.shape[2])
else:
image_data = self.image_data.ravel()
try:
mask = image_data.mask.copy()
image_data = image_data.data.copy()
image_data[mask] = np.nan
except AttributeError:
pass
resampled_image = \
bilinear.resample_bilinear(image_data,
self.geo_def,
target_geo_def,
radius=self.radius_of_influence,
neighbours=self.neighbours,
epsilon=self.epsilon,
fill_value=self.fill_value,
nprocs=self.nprocs,
reduce_data=self.reduce_data,
segments=self.segments)
try:
resampled_image = resampled_image.reshape(target_geo_def.shape)
except ValueError:
# The input data was 3D
shp = target_geo_def.shape
new_shp = [shp[0], shp[1], image_data.shape[-1]]
resampled_image = resampled_image.reshape(new_shp)
return ImageContainerBilinear(resampled_image,
target_geo_def,
self.radius_of_influence,
epsilon=self.epsilon,
fill_value=self.fill_value,
reduce_data=self.reduce_data,
nprocs=self.nprocs,
segments=self.segments)
def resample(self, target_geo_def):
"""Resamples image to area definition using bilinear approach
Parameters
----------
target_geo_def : object
Target geometry definition
Returns
-------
image_container : object
ImageContainerBilinear object of resampled geometry
"""
if self.image_data.ndim > 2 and self.ndim > 1:
image_data = self.image_data.reshape(self.image_data.shape[0] *
self.image_data.shape[1],
self.image_data.shape[2])
else:
image_data = self.image_data.ravel()
try:
mask = image_data.mask.copy()
image_data = image_data.data.copy()
image_data[mask] = np.nan
except AttributeError:
pass
resampled_image = \
bilinear.resample_bilinear(image_data,
self.geo_def,
target_geo_def,
radius=self.radius_of_influence,
neighbours=self.neighbours,
epsilon=self.epsilon,
fill_value=self.fill_value,
nprocs=self.nprocs,
reduce_data=self.reduce_data,
segments=self.segments)
try:
resampled_image = resampled_image.reshape(target_geo_def.shape)
except ValueError:
# The input data was 3D
shp = target_geo_def.shape
new_shp = [shp[0], shp[1], image_data.shape[-1]]
resampled_image = resampled_image.reshape(new_shp)
return ImageContainerBilinear(resampled_image, target_geo_def,
self.radius_of_influence,
epsilon=self.epsilon,
fill_value=self.fill_value,
reduce_data=self.reduce_data,
nprocs=self.nprocs,
segments=self.segments)
def resample(self, target_geo_def):
"""Resamples image to area definition using bilinear approach.
Parameters
----------
target_geo_def : object
Target geometry definition
Returns
-------
image_container : object
ImageContainerBilinear object of resampled geometry
"""
# import here, instead of the top of the script, to avoid xarray/zarr warning msg
# while import the top level pyresample module
from pyresample import bilinear
image_data = self.image_data
try:
mask = image_data.mask.copy()
image_data = image_data.data.copy()
image_data[mask] = np.nan
except AttributeError:
pass
resampled_image = \
bilinear.resample_bilinear(image_data,
self.geo_def,
target_geo_def,
radius=self.radius_of_influence,
neighbours=self.neighbours,
epsilon=self.epsilon,
fill_value=self.fill_value,
nprocs=self.nprocs,
reduce_data=self.reduce_data,
segments=self.segments)
return ImageContainerBilinear(resampled_image,
target_geo_def,
self.radius_of_influence,
epsilon=self.epsilon,
fill_value=self.fill_value,
reduce_data=self.reduce_data,
nprocs=self.nprocs,
segments=self.segments)
def resample(self, target_geo_def):
"""Resamples image to area definition using bilinear approach
Parameters
----------
target_geo_def : object
Target geometry definition
Returns
-------
image_container : object
ImageContainerBilinear object of resampled geometry
"""
image_data = self.image_data
try:
mask = image_data.mask.copy()
image_data = image_data.data.copy()
image_data[mask] = np.nan
except AttributeError:
pass
resampled_image = \
bilinear.resample_bilinear(image_data,
self.geo_def,
target_geo_def,
radius=self.radius_of_influence,
neighbours=self.neighbours,
epsilon=self.epsilon,
fill_value=self.fill_value,
nprocs=self.nprocs,
reduce_data=self.reduce_data,
segments=self.segments)
return ImageContainerBilinear(resampled_image, target_geo_def,
self.radius_of_influence,
epsilon=self.epsilon,
fill_value=self.fill_value,
reduce_data=self.reduce_data,
nprocs=self.nprocs,
segments=self.segments)
def resample_WRF(self, st, et, delta):
'''
Create Times variable and resample emission species DataArray.
'''
# generate date every hour
datetime_list = list(self.perdelta(st, et, timedelta(hours=1)))
t_format = '%Y-%m-%d_%H:%M:%S'
# convert datetime to date string
Times = []
for timstep in datetime_list:
times_str = strftime(t_format, timstep.timetuple())
Times.append(times_str)
# the method of creating "Times" with unlimited dimension
# ref: htttps://github.com/pydata/xarray/issues/3407
Times = xr.DataArray(np.array(Times,
dtype=np.dtype(('S', 19))
),
dims=['Time'])
self.chemi = xr.Dataset({'Times': Times})
# resample
orig_def = SwathDefinition(lons=self.emi['longitude'],
lats=self.emi['latitude'])
for vname in self.emi.data_vars:
if 'E_' in vname:
logging.info(f'Resample {vname} ...')
resampled_list = []
for t in range(self.emi[vname].shape[0]):
# different resample methods
# see: http://earthpy.org/interpolation_between_grids_with_pyresample.html
if resample_method == 'nearest':
resampled_list.append(resample_nearest(
orig_def,
self.emi[vname][t, :, :].values,
self.area_def,
radius_of_influence=self.radius_of_influence,
fill_value=0.)
)
elif resample_method == 'idw':
resampled_list.append(resample_custom(
orig_def,
self.emi[vname][t, :, :].values,
self.area_def,
radius_of_influence=self.radius_of_influence,
neighbours=10,
weight_funcs=lambda r: 1/r**2,
fill_value=0.)
)
elif resample_method == 'bilinear':
resampled_list.append(resample_bilinear(
self.emi[vname][t, :, :].values,
orig_def,
self.area_def,
radius=self.radius_of_influence,
neighbours=10,
nprocs=4,
reduce_data=True,
segments=None,
fill_value=0.,
epsilon=0)
)
# combine 2d array list to one 3d
# ref: https://stackoverflow.com/questions/4341359/
# convert-a-list-of-2d-numpy-arrays-to-one-3d-numpy-array
# we also need to flip the 3d array,
# because of the "strange" order of 1d array in MEIC nc file
# then add another dimension for zdim.
resampled_data = np.flip(np.rollaxis(np.dstack(resampled_list), -1), 1)[:, np.newaxis, ...]
# assign to self.chemi with dims
self.chemi[vname] = xr.DataArray(resampled_data,
dims=['Time',
'emissions_zdim',
'south_north',
'west_east'
]
)
# add attrs needed by WRF-Chem
v_attrs = {'FieldType': 104,
'MemoryOrder': 'XYZ',
'description': vname,
'stagger': '',
'coordinates': 'XLONG XLAT',
'units': self.emi[vname].attrs['units']
}
self.chemi[vname] = self.chemi[vname].assign_attrs(v_attrs)
logging.debug(' '*8 +
' min: ' + str(self.chemi[vname].min().values) +
' max: ' + str(self.chemi[vname].max().values) +
' mean ' + str(self.chemi[vname].mean().values)
)
def atms(
infile,
gridding_radius=25000,
):
ds = xr.open_dataset(infile)
outEpsg = 3857
nd = -999
outProj = Proj(init='epsg:{0}'.format(outEpsg))
inProj = Proj(init='epsg:4326')
lons, lats = ds.lon.values, ds.lat.values
xx, yy = transform(inProj, outProj, lons, lats)
minx, miny = transform(inProj, outProj, -180, -86)
maxx, maxy = transform(inProj, outProj, 180, 86)
res = 16000
eastings = np.arange(round(minx), round(maxx), res)
northings = np.arange(round(miny), round(maxy), res)
ee = eastings[np.where((eastings > xx.min()) & (eastings < xx.max()))]
nn = northings[np.where((northings > yy.min()) & (northings < yy.max()))]
swath_def = geometry.SwathDefinition(lons=lons, lats=lats)
area_def = geometry.AreaDefinition(
'mercator', 'WGS 84 / Pseudo-Mercator - Projected', 'mercator', {
'x_0': '0.0',
'y_0': '0.0',
'lat_ts': '0.00',
'lon_0': '0.00',
'proj': 'merc',
'k': '1.0',
'datum': 'WGS84',
'ellps': 'WGS84',
'a': '6378137',
'b': '6378137'
}, ee.size, nn.size,
[ee.min(), nn.min(), ee.max(), nn.max()])
data = None
# TODO: dynamically estimate sigama based on beam footprints
eps = 0.1
result = bilinear.resample_bilinear(
ds.land_frac.where(ds['sat_zen'] < 50).values,
swath_def,
area_def,
radius=gridding_radius,
neighbours=32,
nprocs=1,
fill_value=nd,
reduce_data=True,
segments=None,
epsilon=eps)
result[np.where(
result >= 0)] = np.abs(result[np.where(result >= 0)] - 1) * 10000
name, _ = os.path.splitext(infile)
outName = name + '_waterfrac.TIF'
gt = (ee.min(), res, 0, nn.max(), 0, -res)
writeGeotiff(outName, result, gt, outEpsg, noData=nd)
return outName
def atms(
infile,
gridding_radius=25000,
):
ds = xr.open_dataset(infile)
outEpsg = 3857
nd = -999
outProj = Proj(init="epsg:{0}".format(outEpsg))
inProj = Proj(init="epsg:4326")
lons, lats = ds.lon.values, ds.lat.values
xx, yy = transform(inProj, outProj, lons, lats)
minx, miny = transform(inProj, outProj, -180, -86)
maxx, maxy = transform(inProj, outProj, 180, 86)
res = 16000
eastings = np.arange(round(minx), round(maxx), res)
northings = np.arange(round(miny), round(maxy), res)
ee = eastings[np.where((eastings > xx.min()) & (eastings < xx.max()))]
nn = northings[np.where((northings > yy.min()) & (northings < yy.max()))]
swath_def = geometry.SwathDefinition(lons=lons, lats=lats)
area_def = geometry.AreaDefinition(
"mercator",
"WGS 84 / Pseudo-Mercator - Projected",
"mercator",
{
"x_0": "0.0",
"y_0": "0.0",
"lat_ts": "0.00",
"lon_0": "0.00",
"proj": "merc",
"k": "1.0",
"datum": "WGS84",
"ellps": "WGS84",
"a": "6378137",
"b": "6378137",
},
ee.size,
nn.size,
[ee.min(), nn.min(), ee.max(), nn.max()],
)
data = None
# TODO: dynamically estimate sigama based on beam footprints
eps = 0.1
result = bilinear.resample_bilinear(
ds.land_frac.where(ds["sat_zen"] < 50).values,
swath_def,
area_def,
radius=gridding_radius,
neighbours=32,
nprocs=1,
fill_value=nd,
reduce_data=True,
segments=None,
epsilon=eps,
)
result[np.where(
result >= 0)] = np.abs(result[np.where(result >= 0)] - 1) * 10000
name, _ = os.path.splitext(infile)
out_name = name + "_waterfrac.TIF"
gt = (ee.min(), res, 0, nn.max(), 0, -res)
write_geotiff(out_name, result, gt, outEpsg, no_data=nd)
return out_name