def test_without_region_pass(self):
"""Append centroids without region id."""
centr1 = Centroids()
centr1.tag = Tag('file_1.mat', 'description 1')
centr1.coord = np.array([[1, 2], [3, 4], [5, 6]])
centr1.id = np.array([5, 7, 9])
centr2 = Centroids()
centr2.tag = Tag('file_2.mat', 'description 2')
centr2.coord = np.array([[1, 2], [3, 4], [5, 6]])
centr2.id = np.array([5, 7, 9])
centr2.region_id = np.array([1, 1, 1])
centr1.append(centr2)
self.assertTrue(np.array_equal(centr1.region_id, np.array([], int)))
centr1 = Centroids()
centr1.tag = Tag('file_1.mat', 'description 1')
centr1.coord = np.array([[1, 2], [3, 4], [5, 6]])
centr1.id = np.array([5, 7, 9])
centr1.region_id = np.array([1, 1, 1])
centr2 = Centroids()
centr2.tag = Tag('file_2.mat', 'description 2')
centr2.coord = np.array([[1, 2], [3, 4], [5, 6]])
centr2.id = np.array([5, 7, 9])
centr1.append(centr2)
self.assertTrue(np.array_equal(centr1.region_id, np.array([1, 1, 1])))
def test_all_new_elem_pass(self):
"""Append a centroids with a new element."""
centr1 = Centroids()
centr1.tag = Tag('file_1.mat', 'description 1')
centr1.coord = np.array([[1, 2], [3, 4], [5, 6]])
centr1.id = np.array([5, 7, 9])
centr2 = Centroids()
centr2.tag = Tag('file_2.mat', 'description 2')
centr2.coord = np.array([[7, 8], [1, 5]])
centr2.id = np.array([5, 7])
centr1.append(centr2)
self.assertEqual(len(centr1.tag.file_name), 2)
self.assertEqual(len(centr1.tag.description), 2)
self.assertEqual(centr1.coord.shape, (5, 2))
self.assertTrue(np.array_equal(centr1.coord[0, :], [1, 2]))
self.assertTrue(np.array_equal(centr1.coord[1, :], [3, 4]))
self.assertTrue(np.array_equal(centr1.coord[2, :], [5, 6]))
self.assertTrue(np.array_equal(centr1.coord[3, :], [7, 8]))
self.assertTrue(np.array_equal(centr1.coord[4, :], [1, 5]))
self.assertEqual(centr1.id.shape, (5, ))
self.assertTrue(np.array_equal(centr1.id, \
np.array([5, 7, 9, 10, 11])))
self.assertTrue(np.array_equal(centr1.region_id, np.array([], int)))
def test_new_elem_pass(self):
"""Append a centroids with a new element."""
centr1 = Centroids()
centr1.tag = Tag('file_1.mat', 'description 1')
centr1.coord = np.array([[1, 2], [3, 4], [5, 6]])
centr1.id = np.array([5, 7, 9])
centr1.region_id = np.array([1, 2, 3])
centr1.dist_coast = np.array([1.5, 2.6, 3.5])
centr2 = Centroids()
centr2.tag = Tag('file_2.mat', 'description 2')
centr2.coord = np.array([[1, 2], [3, 4], [5, 6], [7, 8]])
centr2.id = np.array([6, 7, 9, 1])
centr2.region_id = np.array([3, 4, 5, 6])
centr2.dist_coast = np.array([4.5, 5.6, 6.5, 7.8])
centr1.append(centr2)
self.assertEqual(len(centr1.tag.file_name), 2)
self.assertEqual(len(centr1.tag.description), 2)
self.assertEqual(centr1.coord.shape, (4, 2))
self.assertTrue(np.array_equal(centr1.coord[0, :], [1, 2]))
self.assertTrue(np.array_equal(centr1.coord[1, :], [3, 4]))
self.assertTrue(np.array_equal(centr1.coord[2, :], [5, 6]))
self.assertTrue(np.array_equal(centr1.coord[3, :], [7, 8]))
self.assertEqual(centr1.id.shape, (4, ))
self.assertTrue(np.array_equal(centr1.id, np.array([5, 7, 9, 1])))
self.assertTrue(
np.array_equal(centr1.region_id, np.array([1, 2, 3, 6])))
self.assertTrue(
np.array_equal(centr1.dist_coast, np.array([1.5, 2.6, 3.5, 7.8])))
def good_centroids():
"""Define well a Centroids"""
cen = Centroids()
cen.coord = np.array([[1, 2], [3, 4], [5, 6]])
cen.id = np.array([1, 2, 3])
cen.region_id = np.array([1, 2, 3])
return cen
def _centroids_creation(firms, centr_res_factor):
""" Compute centroids for the firms dataset.
The number of centroids is defined according to the data resolution.
Parameters:
firms (dataframe): dataset obtained from FIRMS data
centr_res_factor (float): the factor applied to voluntarly decrease/increase
the centroids resolution
Returns:
centroids (Centroids)
res_data (float): data resolution (km)
"""
LOGGER.info('Defining the resolution of the centroids.')
# Resolution of the centroids depends on the data origin.
# Resolution in km.
if 'instrument' in firms.columns:
if firms['instrument'].any() == 'MODIS':
res_data = 1.0
else:
res_data = 0.375 # For VIIRS data
else:
res_data = RES_DATA # For undefined data origin, defined by user
LOGGER.info('Computing centroids.')
centroids = Centroids()
dlat_km = abs(firms['latitude'].min() - firms['latitude'].max()) * ONE_LAT_KM
dlon_km = abs(firms['longitude'].min() - firms['longitude'].max()) * ONE_LAT_KM* \
np.cos(np.radians((abs(firms['latitude'].min() - firms['latitude'].max()))/2))
nb_centr_lat = int(dlat_km/res_data * centr_res_factor)
nb_centr_lon = int(dlon_km/res_data * centr_res_factor)
centroids.coord = (np.mgrid[firms['latitude'].min() : firms['latitude'].max() : \
complex(0, nb_centr_lat),
firms['longitude'].min() : firms['longitude'].max() : \
complex(0, nb_centr_lon)]).\
reshape(2, nb_centr_lat*nb_centr_lon).transpose()
centroids._resolution = (\
(abs(firms['latitude'].min() - firms['latitude'].max())/nb_centr_lat),
(abs(firms['longitude'].min() - firms['longitude'].max())/nb_centr_lon))
centroids.id = np.arange(len(centroids.coord))
# Calculate the area attributed to each centroid
centroids.set_area_per_centroid()
# Calculate if the centroids is on land or not
centroids.set_on_land()
# Calculate to distance to coast
centroids.set_dist_coast()
# Create on land grid
centroids.land = np.zeros((nb_centr_lat, nb_centr_lon))
for _, centr in enumerate(centroids.id):
if centroids.on_land[centr]:
centr_ix = int(centr/nb_centr_lon)
centr_iy = centr%nb_centr_lon
centroids.land[centr_ix, centr_iy] = 1
centroids.nb_centr_lat = nb_centr_lat
centroids.nb_centr_lon = nb_centr_lon
return centroids, res_data
def test_appended_type(self):
"""Append the same centroids."""
centr1 = Centroids()
centr1.tag = Tag('file_1.mat', 'description 1')
centr1.coord = np.array([[1, 2], [3, 4], [5, 6]])
centr1.id = np.array([5, 7, 9])
centr2 = centr1
centr1.append(centr2)
self.assertEqual(type(centr1.tag.file_name), str)
self.assertEqual(type(centr1.tag.description), str)
self.assertEqual(type(centr1.coord), np.ndarray)
self.assertEqual(type(centr1.id), np.ndarray)
self.assertTrue(type(centr1.region_id), np.ndarray)
def test_append_to_empty_fill(self):
"""Append to empty centroids."""
centr1 = Centroids()
centr2 = Centroids()
centr2.tag = Tag('file_1.mat', 'description 1')
centr2.coord = np.array([[1, 2], [3, 4], [5, 6]])
centr2.id = np.array([5, 7, 9])
centr1.append(centr2)
self.assertEqual(centr1.tag.file_name, 'file_1.mat')
self.assertEqual(centr1.tag.description, 'description 1')
self.assertEqual(centr1.coord.shape, (3, 2))
self.assertTrue(np.array_equal(centr1.coord[0, :], [1, 2]))
self.assertTrue(np.array_equal(centr1.coord[1, :], [3, 4]))
self.assertTrue(np.array_equal(centr1.coord[2, :], [5, 6]))
self.assertEqual(centr1.id.shape, (3, ))
self.assertTrue(np.array_equal(centr1.id, np.array([5, 7, 9])))
self.assertTrue(np.array_equal(centr1.region_id, np.array([], int)))
def _centroids_from_nc(file_name):
""" Construct Centroids from the grid described by 'latitude' and
'longitude' variables in a netCDF file.
"""
LOGGER.info('Constructing centroids from %s', file_name)
ncdf = xr.open_dataset(file_name)
if hasattr(ncdf, 'latitude'):
lats = ncdf.latitude.data
lons = ncdf.longitude.data
new_coord = np.array([
np.repeat(lats, len(lons)),
np.tile(lons, len(lats)),
]).T
elif hasattr(ncdf, 'lat'):
lats = ncdf.lat.data
lons = ncdf.lon.data
new_coord = np.array([
np.repeat(lats, len(lons)),
np.tile(lons, len(lats)),
]).T
elif hasattr(ncdf, 'lat_1'):
lats = ncdf.lat_1.data
lons = ncdf.lon_1.data
new_coord = np.array([
lats.reshape(-1),
lons.reshape(-1),
]).T
else:
raise AttributeError('netcdf file has no field named latitude or '
'other know abrivation for coordinates.')
cent = Centroids()
cent.coord = new_coord
cent.id = np.arange(0, len(cent.coord))
cent.tag.description = 'Centroids constructed from: ' + file_name
ncdf.close()
cent.set_area_per_centroid()
cent.set_on_land()
return cent
