def test_grid_hdf_container():
f,fname = tempfile.mkstemp()
os.close(f)
try:
#test grid container
container = GridHDFContainer.create(fname)
# before we put anything in here, let's make sure we get empty lists from
# all of the methods that are supposed to return lists of stuff.
assert container.getGrids() == []
#test grid2d
geodict = GeoDict.createDictFromBox(-118.5,-114.5,32.1,36.7,0.01,0.02)
nrows,ncols = geodict.ny,geodict.nx
data = np.random.rand(nrows,ncols)
metadata = {'name':'Gandalf',
'color':'white',
'powers':'magic'}
grid = Grid2D(data,geodict)
container.setGrid('testgrid',grid,metadata=metadata)
outgrid,outmetadata = container.getGrid('testgrid')
np.testing.assert_array_equal(outgrid.getData(),data)
assert outgrid.getGeoDict() == geodict
assert outmetadata == metadata
#set another grid without compression
geodict = GeoDict.createDictFromBox(-119.5,-115.5,32.3,37.7,0.01,0.02)
nrows,ncols = geodict.ny,geodict.nx
data = np.random.rand(nrows,ncols)
metadata = {'name':'Legolas',
'color':'green',
'powers':'stealth'}
grid2 = Grid2D(data,geodict)
container.setGrid('testgrid2',grid2,metadata=metadata,compression=False)
outgrid2,outmetadata2 = container.getGrid('testgrid2')
np.testing.assert_array_equal(outgrid2.getData(),data)
assert outgrid2.getGeoDict() == geodict
assert outmetadata2 == metadata
#test getGridNames()
names = container.getGrids()
assert sorted(names) == ['testgrid','testgrid2']
#test looking for a grid that does not exist
try:
container.getGrid('foo')
except LookupError as le:
pass
#test dropping a grid
container.dropGrid('testgrid2')
container.close()
container2 = GridHDFContainer.load(fname)
names = container2.getGrids()
assert sorted(names) == ['testgrid']
except:
assert 1==2
finally:
os.remove(fname)
def getIMTGrids(self, imt_name, component):
"""
Retrieve a Grid2D object and any associated metadata from the
container.
Args:
imt_name (str):
The name of the IMT stored in the container.
Returns:
dict: Dictionary containing 4 items:
- mean Grid2D object for IMT mean values.
- mean_metadata Dictionary containing any metadata
describing mean layer.
- std Grid2D object for IMT standard deviation values.
- std_metadata Dictionary containing any metadata describing
standard deviation layer.
"""
if self.getDataType() != 'grid':
raise TypeError('Requesting grid data from file containing points')
group_name = '%s_%s' % (imt_name, component)
if GROUPS['imt'] not in self._hdfobj:
raise LookupError('No IMTs stored in HDF file %s'
% (self.getFileName()))
if group_name not in self._hdfobj[GROUPS['imt']]:
raise LookupError('No group called %s in HDF file %s'
% (imt_name, self.getFileName()))
imt_group = self._hdfobj[GROUPS['imt']][group_name]
# get the mean data and metadata
mean_dset = imt_group['mean']
mean_data = mean_dset[()]
array_metadata, mean_metadata = _split_dset_attrs(mean_dset)
mean_geodict = GeoDict(array_metadata)
mean_grid = Grid2D(mean_data, mean_geodict)
# get the std data and metadata
std_dset = imt_group['std']
std_data = std_dset[()]
array_metadata, std_metadata = _split_dset_attrs(std_dset)
std_geodict = GeoDict(array_metadata)
std_grid = Grid2D(std_data, std_geodict)
# create an output dictionary
imt_dict = {
'mean': mean_grid,
'mean_metadata': mean_metadata,
'std': std_grid,
'std_metadata': std_metadata
}
return imt_dict
def test_interpolate():
geodict = GeoDict({
'xmin': 0.5,
'xmax': 6.5,
'ymin': 1.5,
'ymax': 6.5,
'dx': 1.0,
'dy': 1.0,
'ny': 6,
'nx': 7
})
data = np.arange(14, 56).reshape(6, 7)
for method in ['nearest', 'linear', 'cubic']:
print('Testing interpolate with method "%s"...' % method)
grid = Grid2D(data, geodict)
sampledict = GeoDict({
'xmin': 3.0,
'xmax': 4.0,
'ymin': 3.0,
'ymax': 4.0,
'dx': 1.0,
'dy': 1.0,
'ny': 2,
'nx': 2
})
grid = grid.interpolateToGrid(sampledict, method=method)
tgrid = grid.interpolate2(sampledict, method=method)
if method == 'nearest':
output = np.array([[30.0, 31.0], [37.0, 38.0]])
elif method == 'linear':
output = np.array([[34., 35.], [41., 42.]])
elif method == 'cubic':
output = np.array([[34., 35.], [41., 42.]])
else:
pass
np.testing.assert_almost_equal(grid.getData(), output)
print('Passed interpolate with method "%s".' % method)
np.testing.assert_almost_equal(tgrid.getData(), output)
print('Passed interpolate2 with method "%s".' % method)
# speed test of interpolateToGrid and interpolate2
geodict = GeoDict.createDictFromBox(0, 10, 0, 10, 0.01, 0.01)
data = np.random.rand(geodict.ny, geodict.nx)
grid = Grid2D(data, geodict)
sampledict = GeoDict.createDictFromBox(2, 8, 2, 8, 0.098, 0.098)
t1 = time.time()
grid2 = grid.interpolateToGrid(sampledict, method='linear')
t2 = time.time()
grid3 = grid.interpolate2(sampledict, method='linear')
t3 = time.time()
#np.testing.assert_almost_equal(grid2._data.sum(),grid3._data.sum())
print('scipy method: %.3f seconds' % (t2 - t1))
print('gdal method: %.3f seconds' % (t3 - t2))
def test():
print('Testing MultiGrid interpolate...')
data = np.arange(14,56).reshape(6,7)
geodict = GeoDict({'xmin':0.5,'xmax':6.5,'ymin':1.5,'ymax':6.5,'dx':1.0,'dy':1.0,'ny':6,'nx':7})
layers = OrderedDict()
layers['layer1'] = Grid2D(data,geodict)
mgrid = MultiGrid(layers)
sampledict = GeoDict({'xmin':3.0,'xmax':4.0,
'ymin':3.0,'ymax':4.0,
'dx':1.0,'dy':1.0,
'ny':2,'nx':2})
for method in ['nearest','linear','cubic']:
mgrid2 = mgrid.interpolateToGrid(sampledict,method=method)
if method == 'nearest':
output = np.array([[30.0,31.0],[37.0,38.0]])
elif method == 'linear':
output = np.array([[34.,35.],[41.,42.]])
elif method == 'cubic':
output = np.array([[34.,35.],[41.,42.]])
else:
pass
np.testing.assert_almost_equal(mgrid2.getLayer('layer1').getData(),output)
print('Passed MultiGrid interpolate test.')
print('Testing bounds retrieval...')
b1 = np.array(mgrid.getBounds())
b2 = np.array((geodict.xmin,geodict.xmax,geodict.ymin,geodict.ymax))
np.testing.assert_almost_equal(b1,b2)
print('Passed bounds retrieval...')
print('Testing MultiGrid subdivide test...')
data = np.arange(0,9).reshape((3,3))
geodict = GeoDict({'xmin':0.0,'xmax':10.0,
'ymin':0.0,'ymax':10.0,
'dx':5.0,'dy':5.0,
'ny':3,'nx':3})
layers = OrderedDict()
layers['layer1'] = Grid2D(data,geodict)
hostgrid = MultiGrid(layers)
finedict = GeoDict({'xmin':-2.5,'xmax':11.5,
'ymin':-1.5,'ymax':10.5,
'dx':2.0,'dy':2.0,
'nx':8,'ny':7})
N = np.nan
finegrid = hostgrid.subdivide(finedict,cellFill='min')
output = np.array([[ N, 0., 0., 1., 1., 1., 2., 2.],
[ N, 0., 0., 1., 1., 1., 2., 2.],
[ N, 3., 3., 4., 4., 4., 5., 5.],
[ N, 3., 3., 4., 4., 4., 5., 5.],
[ N, 3., 3., 4., 4., 4., 5., 5.],
[ N, 6., 6., 7., 7., 7., 8., 8.],
[ N, 6., 6., 7., 7., 7., 8., 8.]])
np.testing.assert_almost_equal(finegrid.getLayer('layer1').getData(),output)
print('Passed MultiGrid subdivide test.')
def getIMT(self, imt_name, component):
"""
Retrieve a Grid2D object and any associated metadata from the container.
Args:
imt_name (str):
The name of the Grid2D object stored in the container.
Returns:
dict: Dictionary containing 4 items:
- mean Grid2D object for IMT mean values.
- mean_metadata Dictionary containing any metadata
describing mean layer.
- std Grid2D object for IMT standard deviation values.
- std_metadata Dictionary containing any metadata describing
standard deviation layer.
"""
logger = logging.getLogger()
logger.info('Inside OutputContainer')
group_name = '__imt_%s_%s__' % (imt_name, component)
if group_name not in self._hdfobj:
raise LookupError('No group called %s in HDF file %s'
% (imt_name, self.getFileName()))
imt_group = self._hdfobj[group_name]
# get the mean data and metadata
mean_name = '__mean_%s_%s__' % (imt_name, component)
mean_dset = imt_group[mean_name]
mean_data = mean_dset[()]
array_metadata, mean_metadata = _split_dset_attrs(mean_dset)
mean_geodict = GeoDict(array_metadata)
mean_grid = Grid2D(mean_data, mean_geodict)
# get the std data and metadata
std_name = '__std_%s_%s__' % (imt_name, component)
std_dset = imt_group[std_name]
std_data = std_dset[()]
array_metadata, std_metadata = _split_dset_attrs(std_dset)
std_geodict = GeoDict(array_metadata)
std_grid = Grid2D(std_data, std_geodict)
# create an output dictionary
imt_dict = {
'mean': mean_grid,
'mean_metadata': mean_metadata,
'std': std_grid,
'std_metadata': std_metadata
}
return imt_dict
def test_cut():
geodict = GeoDict({'xmin': 0.5, 'xmax': 4.5, 'ymin': 0.5,
'ymax': 4.5, 'dx': 1.0, 'dy': 1.0, 'ny': 5, 'nx': 5})
data = np.arange(0, 25).reshape(5, 5)
print('Testing data extraction...')
grid = Grid2D(data, geodict)
xmin, xmax, ymin, ymax = (2.5, 3.5, 2.5, 3.5)
newgrid = grid.cut(xmin, xmax, ymin, ymax)
output = np.array([[7, 8], [12, 13]])
np.testing.assert_almost_equal(newgrid.getData(), output)
print('Passed data extraction...')
print('Testing data trimming with resampling...')
# make a more complicated test using getboundswithin
data = np.arange(0, 84).reshape(7, 12)
geodict = GeoDict({'xmin': -180, 'xmax': 150,
'ymin': -90, 'ymax': 90,
'dx': 30, 'dy': 30,
'nx': 12, 'ny': 7})
grid = Grid2D(data, geodict)
sampledict = GeoDict.createDictFromBox(-75,
45, -45, 75, geodict.dx, geodict.dy)
cutdict = geodict.getBoundsWithin(sampledict)
newgrid = grid.cut(cutdict.xmin, cutdict.xmax, cutdict.ymin, cutdict.ymax)
output = np.array([[16, 17, 18, 19],
[28, 29, 30, 31],
[40, 41, 42, 43],
[52, 53, 54, 55]])
np.testing.assert_almost_equal(newgrid.getData(), output)
print('Passed data trimming with resampling...')
print('Test cut with self-alignment...')
geodict = GeoDict({'xmin': 0.5, 'xmax': 4.5,
'ymin': 0.5, 'ymax': 6.5,
'dx': 1.0, 'dy': 1.0,
'nx': 5, 'ny': 7})
data = np.arange(0, 35).astype(np.float32).reshape(7, 5)
grid = Grid2D(data, geodict)
cutxmin = 1.7
cutxmax = 3.7
cutymin = 1.7
cutymax = 5.7
cutgrid = grid.cut(cutxmin, cutxmax, cutymin, cutymax, align=True)
output = np.array([[7, 8],
[12, 13],
[17, 18],
[22, 23]])
np.testing.assert_almost_equal(cutgrid.getData(), output)
print('Passed cut with self-alignment.')
def _trim_grid(ingrid):
outgrid = Grid2D.copyFromGrid(ingrid)
while np.isnan(outgrid._data).any():
nrows, ncols = outgrid._data.shape
top = outgrid._data[0, :]
bottom = outgrid._data[-1, :]
left = outgrid._data[:, 0]
right = outgrid._data[:, -1]
ftop = np.isnan(top).sum() / ncols
fbottom = np.isnan(bottom).sum() / ncols
fleft = np.isnan(left).sum() / nrows
fright = np.isnan(right).sum() / nrows
side = np.argmax([ftop, fbottom, fleft, fright])
gdict = outgrid.getGeoDict().asDict()
if side == 0: # removing top row
outgrid._data = outgrid._data[1:, :]
gdict['ymax'] -= gdict['dy']
gdict['ny'] -= 1
elif side == 1: # removing bottom row
outgrid._data = outgrid._data[0:-1, :]
gdict['ymin'] += gdict['dy']
gdict['ny'] -= 1
elif side == 2: # removing left column
outgrid._data = outgrid._data[:, 1:]
gdict['xmin'] += gdict['dx']
gdict['nx'] -= 1
elif side == 3: # removing right column
outgrid._data = outgrid._data[:, 0:-1]
gdict['xmax'] -= gdict['dx']
gdict['nx'] -= 1
geodict = GeoDict(gdict)
outgrid = Grid2D(data=outgrid._data, geodict=geodict)
return outgrid
def test_write():
data = np.arange(0, 25).reshape(5, 5).astype(np.float32)
gdict = {
'xmin': 5.0,
'xmax': 9.0,
'ymin': 4.0,
'ymax': 8.0,
'dx': 1.0,
'dy': 1.0,
'nx': 5,
'ny': 5
}
gd = GeoDict(gdict)
grid = Grid2D(data, gd)
for format_type in ['netcdf', 'esri', 'hdf']:
tdir = tempfile.mkdtemp()
fname = os.path.join(tdir, 'tempfile.grd')
try:
write(grid, fname, format_type)
src = rasterio.open(fname, 'r')
tdata = src.read(1)
np.testing.assert_almost_equal(tdata, data)
except Exception as e:
raise e
finally:
shutil.rmtree(tdir)
def test_setData():
data = np.arange(0, 16).astype(np.float32).reshape(4, 4)
geodict = GeoDict({
'xmin': 0.5,
'xmax': 3.5,
'ymin': 0.5,
'ymax': 3.5,
'dx': 1.0,
'dy': 1.0,
'ny': 4,
'nx': 4
})
grid1 = Grid2D(data, geodict)
x = np.ones((4, 4))
try:
grid1.setData(x) #this should pass
print('setData test passed.')
except DataSetException as dse:
print('setData test failed.')
try:
x = np.ones((5, 5))
grid1.setData(x)
print('setData test did not fail when it should have.')
except DataSetException as dse:
print('setData test failed as expected.')
try:
x = 'fred'
grid1.setData(x)
print('setData test did not fail when it should have.')
except DataSetException as dse:
print('setData test failed as expected.')
def test_copy():
data = np.arange(0,16).astype(np.float32).reshape(4,4)
geodict = GeoDict({'xmin':0.5,'xmax':3.5,'ymin':0.5,'ymax':3.5,'dx':1.0,'dy':1.0,'ny':4,'nx':4})
grid1 = Grid2D(data,geodict)
grid2 = grid1.copyFromGrid(grid1)
grid1._data[0,0] = np.nan
print(grid2._data)
print(grid2._geodict)
def createFromCenter(cls,
cx,
cy,
xspan,
yspan,
dx,
dy,
defaultVs30=686.0,
vs30File=None,
vs30measured_grid=None,
backarc=False,
padding=False,
resample=False):
"""
Create a Sites object by defining a center point, resolution, extent,
and Vs30 values.
:param cx:
X coordinate of desired center point.
:param cy:
Y coordinate of desired center point.
:param xspan:
Width of desired grid.
:param yspan:
Height of desired grid.
:param dx:
Resolution of desired grid in X direction.
:param dy:
Resolution of desired grid in Y direction.
:param defaultVs30:
Default Vs30 value to use if vs30File not specified.
:param vs30File:
Name of GMT or GDAL format grid file containing Vs30 values.
:param vs30measured_grid:
Boolean grid indicating whether Vs30 values were measured or derived
(i.e., from slope)
:param backarc:
Boolean indicating whether event is on the backarc as defined
`here <http://earthquake.usgs.gov/learn/glossary/?term=backarc>`__.
:param padding:
Boolean indicating whether or not to pad resulting Vs30 grid out to
edges of input bounds. If False, grid will be clipped to the extent
of the input file.
:param resample:
Boolean indicating whether or not the grid should be resampled.
"""
geodict = GeoDict.createDictFromCenter(cx, cy, dx, dy, xspan, yspan)
if vs30File is not None:
vs30grid = cls._create(geodict, defaultVs30, vs30File, padding,
resample)
else:
griddata = np.ones(
(geodict.ny, geodict.nx), dtype=np.float64) * defaultVs30
vs30grid = Grid2D(griddata, geodict)
return cls(vs30grid,
vs30measured_grid=vs30measured_grid,
backarc=backarc,
defaultVs30=defaultVs30)
def test_basics():
geodict = GeoDict({
'xmin': 0.5,
'xmax': 3.5,
'ymin': 0.5,
'ymax': 3.5,
'dx': 1.0,
'dy': 1.0,
'ny': 4,
'nx': 4
})
data = np.arange(0, 16).reshape(4, 4).astype(np.float32)
grid = Grid2D(data, geodict)
print(
'Testing basic Grid2D functionality (retrieving data, lat/lon to pixel coordinates, etc...'
)
np.testing.assert_almost_equal(grid.getData(), data)
assert grid.getGeoDict() == geodict
assert grid.getBounds() == (geodict.xmin, geodict.xmax, geodict.ymin,
geodict.ymax)
lat, lon = grid.getLatLon(0, 0)
assert lat == 3.5 and lon == 0.5
row, col = grid.getRowCol(lat, lon)
assert row == 0 and col == 0
value = grid.getValue(lat, lon)
assert value == 0
frow, fcol = grid.getRowCol(1.0, 3.0, returnFloat=True)
assert frow == 2.5 and fcol == 2.5
irow, icol = grid.getRowCol(1.0, 3.0, returnFloat=False)
assert irow == 2 and icol == 2
#test getting values in and outside of the grid bounds
lat = np.array([0.0, 0.5, 2.5, 4.0])
lon = np.array([0.0, 0.5, 2.5, 4.0])
default = np.nan
output = np.array([np.nan, 12, 6, np.nan])
value = grid.getValue(lat, lon, default=default)
np.testing.assert_almost_equal(value, output)
print(
'Passed basic Grid2D functionality (retrieving data, lat/lon to pixel coordinates, etc...'
)
def _get_average_grid(gc, contents, myimt):
"""
Given an SA(X) IMT, attempt to find the grids that bracket its
period and return an interpolated grid that is weighted average
(weighted by the (log) differeences in period). If the period
is less than the lowest, or greater than the highest, available
period, then the closest endpoint grid is returned.
Args:
gc (GridHDFContainer): The container holding the amplification
grids, labeled by IMT string.
contents (list): A list of the IMTs available in gc.
myimt (str): The target IMT; must be of type "SA(X)".
Returns:
tuple: A grid and its associated metadata.
"""
#
# Make a list of the SA IMTs, add the target IMT to the list
# and then sort by period.
#
imt_list = [thisimt for thisimt in contents if thisimt.startswith('SA(')]
if len(imt_list) == 0:
logging.warning('Generic Amp Factors: No SA grids in file')
return None, None
imt_list.append(myimt)
imt_list_sorted = sorted(imt_list, key=get_period_from_imt)
nimt = len(imt_list_sorted)
ix = imt_list_sorted.index(myimt)
if ix == 0:
logging.warning("Generic Amp Factors:IMT %s less than min available "
"imt, using %s" % (myimt, imt_list_sorted[1]))
return gc.getGrid(imt_list_sorted[1])
elif ix == (nimt - 1):
logging.warning("Generic Amp Factors:IMT %s greater than max "
"available imt, using %s" %
(myimt, imt_list_sorted[-2]))
return gc.getGrid(imt_list_sorted[-2])
else:
# Interpolate using (log) period: p1 is the shorter period,
# p2 is the longer period, and p0 is the target period.
g1, md1 = gc.getGrid(imt_list_sorted[ix - 1])
g2, md1 = gc.getGrid(imt_list_sorted[ix + 1])
p1 = np.log(get_period_from_imt(imt_list_sorted[ix - 1]))
p2 = np.log(get_period_from_imt(imt_list_sorted[ix + 1]))
p0 = np.log(get_period_from_imt(myimt))
w1 = (p2 - p0) / (p2 - p1)
w2 = 1.0 - w1
gmean = g1.getData() * w1 + g2.getData() * w2
return Grid2D(gmean, g1.getGeoDict()), md1
def make_generic_amps():
imts = ['PGA', 'SA(0.3)', 'SA(1.0)', 'SA(3.0)']
install_path, _ = get_config_paths()
geodict = {
'dx': 0.016666666666666666,
'dy': 0.016666666666666666,
'nx': 301,
'ny': 151,
'xmax': -116.0,
'xmin': -121.0,
'ymax': 35.5,
'ymin': 33.0
}
gd = GeoDict(geodict)
# make east-west file (1s on the left, 0s on the right)
data = np.ones((gd.ny, gd.nx))
data[:, 151:] = 0
outfolder = os.path.join(install_path, 'data', 'GenericAmpFactors')
east_west_file = os.path.join(outfolder, 'Test_basin_east_west.hdf')
east_west = GridHDFContainer.create(east_west_file)
for imt in imts:
grid = Grid2D(data, gd)
east_west.setGrid(imt, grid)
east_west.close()
# make east-west file (1s on the left, 0s on the right)
data = np.ones((gd.ny, gd.nx))
data[76:151, :] = 0
outfolder = os.path.join(install_path, 'data', 'GenericAmpFactors')
north_south_file = os.path.join(outfolder, 'Test_basin_north_south.hdf')
north_south = GridHDFContainer.create(north_south_file)
for imt in imts:
grid = Grid2D(data, gd)
north_south.setGrid(imt, grid)
north_south.close()
return (east_west_file, north_south_file)
def big_test():
xmin = -180
xmax = -170
ymin = 30
ymax = 40
dx = 0.0083
dy = 0.0083
gd = GeoDict.createDictFromBox(xmin, xmax, ymin, ymax, dx, dy)
data = np.random.rand(gd.ny, gd.nx)
grid = Grid2D(data, gd)
fname = os.path.join(os.path.expanduser('~'), 'tempfile.grd')
write(grid, fname, 'hdf')
print(fname)
src = rasterio.open(fname, 'r')
def fromBounds(cls,
xmin,
xmax,
ymin,
ymax,
dx,
dy,
defaultVs30=686.0,
vs30File=None,
vs30measured_grid=None,
backarc=None,
padding=False,
resample=False):
"""
Create a Sites object by defining a center point, resolution, extent,
and Vs30 values.
Args:
xmin: X coordinate of left edge of bounds.
xmax: X coordinate of right edge of bounds.
ymin: Y coordinate of bottom edge of bounds.
ymax: Y coordinate of top edge of bounds.
dx: Resolution of desired grid in X direction.
dy: Resolution of desired grid in Y direction.
defaultVs30: Default Vs30 value to use if vs30File not specified.
vs30File: Name of GMT or GDAL format grid file containing Vs30
values.
vs30measured_grid: Boolean grid indicating whether Vs30 values were
measured or derived (i.e., from slope).
backarc: Boolean array indicating whether site is in the subduction
`backarc <http://earthquake.usgs.gov/learn/glossary/?term=backarc>`__.
padding: Boolean indicating whether or not to pad resulting Vs30
grid out to edges of input bounds. If False, grid will be
clipped to the extent of the input file.
resample: Boolean indicating whether or not the grid should be
resampled.
""" # noqa
geodict = GeoDict.createDictFromBox(xmin, xmax, ymin, ymax, dx, dy)
if vs30File is not None:
vs30grid = cls._create(geodict, defaultVs30, vs30File, padding,
resample)
else:
griddata = np.ones(
(geodict.ny, geodict.nx), dtype=np.float64) * defaultVs30
vs30grid = Grid2D(griddata, geodict)
return cls(vs30grid,
vs30measured_grid=vs30measured_grid,
backarc=backarc,
defaultVs30=defaultVs30)
def getGrid(self, name):
"""
Retrieve a Grid2D object and any associated metadata from the container.
Args:
name (str):
The name of the Grid2D object stored in the container.
Returns:
(tuple) Grid2D object, and a dictionary of metadata.
"""
array_name = '__grid_%s__' % name
if array_name not in self._hdfobj:
raise LookupError('Array %s not in %s' %
(name, self.getFileName()))
dset = self._hdfobj[array_name]
data = dset[()]
array_metadata, meta_metadata = _split_dset_attrs(dset)
geodict = GeoDict(array_metadata)
grid = Grid2D(data, geodict)
return grid, meta_metadata
def test_getvalue():
array = np.arange(1, 26).reshape(5, 5)
gdict = GeoDict({'xmin': 1.0,
'xmax': 5.0,
'ymin': 1.0,
'ymax': 5.0,
'dx': 1.0,
'dy': 1.0,
'nx': 5,
'ny': 5})
grid = Grid2D(array, gdict)
assert grid.getValue(3.0, 3.0) == 13
lat = np.array([3.0, 4.0])
lon = np.array([3.0, 3.0])
test = grid.getValue(lat, lon)
np.testing.assert_almost_equal(test, np.array([13, 8]))
lat = np.array([[3.0, 4.0],
[4.0, 5.0]])
lon = np.array([[3.0, 3.0],
[4.0, 4.0]])
test = grid.getValue(lat, lon)
np.testing.assert_almost_equal(test, np.array([[13, 8], [9, 4]]))
def test_interpolate():
geodict = GeoDict({'xmin':0.5,'xmax':6.5,'ymin':1.5,'ymax':6.5,'dx':1.0,'dy':1.0,'ny':6,'nx':7})
data = np.arange(14,56).reshape(6,7)
for method in ['nearest','linear','cubic']:
print('Testing interpolate with method "%s"...' % method)
grid = Grid2D(data,geodict)
sampledict = GeoDict({'xmin':3.0,'xmax':4.0,
'ymin':3.0,'ymax':4.0,
'dx':1.0,'dy':1.0,
'ny':2,'nx':2})
grid = grid.interpolateToGrid(sampledict,method=method)
if method == 'nearest':
output = np.array([[30.0,31.0],[37.0,38.0]])
elif method == 'linear':
output = np.array([[34.,35.],[41.,42.]])
elif method == 'cubic':
output = np.array([[34.,35.],[41.,42.]])
else:
pass
np.testing.assert_almost_equal(grid.getData(),output)
print('Passed interpolate with method "%s".' % method)
def updateSequences(self, stime):
etime = stime + timedelta(days=1)
events = search(starttime=stime,
endtime=etime,
minlatitude=-90,
maxlatitude=90,
minlongitude=-180,
maxlongitude=180,
minmagnitude=0.0,
maxmagnitude=9.9)
todayframe = get_summary_data_frame(events)
todaydata = get_day_counts(GDICT, todayframe)
todaygrid = Grid2D(data=todaydata, geodict=GDICT)
for row in range(0, GDICT.ny):
for col in range(0, GDICT.nx):
if row == 19 and col == 29:
foo = 1
clat, clon = GDICT.getLatLon(row, col)
tvalue = todaygrid._data[row, col]
mvalue = self._meangrid._data[row, col]
svalue = self._stdgrid._data[row, col]
# thresh = tvalue > mvalue + svalue * 3
thresh = tvalue > MINEQ
xmin = clon - GDICT.dx / 2
xmax = clon + GDICT.dx / 2
ymin = clat - GDICT.dy / 2
ymax = clat + GDICT.dy / 2
if thresh:
c1 = todayframe['latitude'] > ymin
c2 = todayframe['latitude'] <= ymax
c3 = todayframe['longitude'] > xmin
c4 = todayframe['longitude'] <= xmax
cluster = todayframe[c1 & c2 & c3 & c4].copy()
class_frame, pproj = self.get_clusters(cluster, clon, clat)
self.insertSequences(class_frame, pproj)
# call a method that filters out clusters that don't match the definition
# of an earthquake sequence.
self.cleanSequences()
def getSitesContext(self, lldict=None, rock_vs30=None):
"""
Create a SitesContext object by sampling the current Sites object.
Args:
lldict: Either
- None, in which case the SitesContext for the complete Sites
grid is returned, or
- A location dictionary (elements are 'lats' and 'lons' and
each is a numpy array). Each element must have the same
shape. In this case the SitesContext for these locaitons is
returned.
rock_vs30: Either
- None, in which case the SitesContext will reflect the Vs30
grid in the Sites instance, or
- A float for the rock Vs30 value, in which case the
SitesContext will be constructed for this constant Vs30
value.
Returns:
SitesContext object.
Raises:
ShakeLibException: When lat/lon input sequences do not share
dimensionality.
""" # noqa
sctx = SitesContext()
if lldict is not None:
lats = lldict['lats']
lons = lldict['lons']
latshape = lats.shape
lonshape = lons.shape
if latshape != lonshape:
msg = 'Input lat/lon arrays must have the same dimensions'
raise ShakeLibException(msg)
if rock_vs30 is not None:
tmp = self._Vs30.getValue(
lats, lons, default=self._defaultVs30)
sctx.vs30 = np.ones_like(tmp) * rock_vs30
else:
sctx.vs30 = self._Vs30.getValue(
lats, lons, default=self._defaultVs30)
sctx.lats = lats
sctx.lons = lons
else:
sctx.lats = self._lats.copy()
sctx.lons = self._lons.copy()
if rock_vs30 is not None:
sctx.vs30 = np.full_like(self._Vs30.getData(), rock_vs30)
else:
sctx.vs30 = self._Vs30.getData().copy()
sctx = Sites._addDepthParameters(sctx)
# For ShakeMap purposes, vs30 measured is always Fales
sctx.vs30measured = np.zeros_like(sctx.vs30, dtype=bool)
# Backarc should be a numpy array
if lldict is not None:
backarcgrid = Grid2D(self._backarc, self._Vs30.getGeoDict())
sctx.backarc = backarcgrid.getValue(lats, lons, default=False)
else:
sctx.backarc = self._backarc.copy()
return sctx
def test_output_container():
geodict = GeoDict.createDictFromBox(-118.5, -114.5, 32.1, 36.7, 0.01, 0.02)
nrows, ncols = geodict.ny, geodict.nx
# create MMI mean data for maximum component
mean_mmi_maximum_data = np.random.rand(nrows, ncols)
mean_mmi_maximum_metadata = {
'name': 'Gandalf',
'color': 'white',
'powers': 'magic'
}
mean_mmi_maximum_grid = Grid2D(mean_mmi_maximum_data, geodict)
# create MMI std data for maximum component
std_mmi_maximum_data = mean_mmi_maximum_data / 10
std_mmi_maximum_metadata = {
'name': 'Legolas',
'color': 'green',
'powers': 'good hair'
}
std_mmi_maximum_grid = Grid2D(std_mmi_maximum_data, geodict)
# create MMI mean data for rotd50 component
mean_mmi_rotd50_data = np.random.rand(nrows, ncols)
mean_mmi_rotd50_metadata = {
'name': 'Gimli',
'color': 'brown',
'powers': 'axing'
}
mean_mmi_rotd50_grid = Grid2D(mean_mmi_rotd50_data, geodict)
# create MMI std data for rotd50 component
std_mmi_rotd50_data = mean_mmi_rotd50_data / 10
std_mmi_rotd50_metadata = {
'name': 'Aragorn',
'color': 'white',
'powers': 'scruffiness'
}
std_mmi_rotd50_grid = Grid2D(std_mmi_rotd50_data, geodict)
# create PGA mean data for maximum component
mean_pga_maximum_data = np.random.rand(nrows, ncols)
mean_pga_maximum_metadata = {
'name': 'Pippin',
'color': 'purple',
'powers': 'rashness'
}
mean_pga_maximum_grid = Grid2D(mean_pga_maximum_data, geodict)
# create PGA std data for maximum component
std_pga_maximum_data = mean_pga_maximum_data / 10
std_pga_maximum_metadata = {
'name': 'Merry',
'color': 'grey',
'powers': 'hunger'
}
std_pga_maximum_grid = Grid2D(std_pga_maximum_data, geodict)
f, datafile = tempfile.mkstemp()
os.close(f)
try:
container = ShakeMapOutputContainer.create(datafile)
container.setIMTGrids('mmi',
mean_mmi_maximum_grid,
mean_mmi_maximum_metadata,
std_mmi_maximum_grid,
std_mmi_maximum_metadata,
component='maximum')
container.setIMTGrids('mmi',
mean_mmi_rotd50_grid,
mean_mmi_rotd50_metadata,
std_mmi_rotd50_grid,
std_mmi_rotd50_metadata,
component='rotd50')
container.setIMTGrids('pga',
mean_pga_maximum_grid,
mean_pga_maximum_metadata,
std_pga_maximum_grid,
std_pga_maximum_metadata,
component='maximum')
# get the maximum MMI imt data
mmi_max_dict = container.getIMTGrids('mmi', component='maximum')
np.testing.assert_array_equal(mmi_max_dict['mean'].getData(),
mean_mmi_maximum_data)
np.testing.assert_array_equal(mmi_max_dict['std'].getData(),
std_mmi_maximum_data)
assert mmi_max_dict['mean_metadata'] == mean_mmi_maximum_metadata
assert mmi_max_dict['std_metadata'] == std_mmi_maximum_metadata
# get the rotd50 MMI imt data
mmi_rot_dict = container.getIMTGrids('mmi', component='rotd50')
np.testing.assert_array_equal(mmi_rot_dict['mean'].getData(),
mean_mmi_rotd50_data)
np.testing.assert_array_equal(mmi_rot_dict['std'].getData(),
std_mmi_rotd50_data)
assert mmi_rot_dict['mean_metadata'] == mean_mmi_rotd50_metadata
assert mmi_rot_dict['std_metadata'] == std_mmi_rotd50_metadata
# Check repr method
assert repr(container) == '''Data type: grid
use "getIMTGrids" method to access interpolated IMTs
Rupture: None
Config: None
Stations: None
Metadata: None
Available IMTs (components):
mmi (maximum, rotd50)
pga (maximum)
'''
# get list of all imts
imts = container.getIMTs()
# get list of maximum imts
max_imts = container.getIMTs(component='maximum')
assert sorted(max_imts) == ['mmi', 'pga']
# get list of components for mmi
mmi_comps = container.getComponents('mmi')
assert sorted(mmi_comps) == ['maximum', 'rotd50']
# Test dropIMT
imts = container.getIMTs('maximum')
assert imts == ['mmi', 'pga']
container.dropIMT('mmi')
imts = container.getIMTs('maximum')
assert imts == ['pga']
container.close()
except Exception as e:
raise (e)
finally:
os.remove(datafile)
def draw_contour(shakegrid,
popgrid,
oceanfile,
oceangridfile,
cityfile,
basename,
borderfile=None,
is_scenario=False):
"""Create a contour map showing MMI contours over greyscale population.
:param shakegrid:
ShakeGrid object.
:param popgrid:
Grid2D object containing population data.
:param oceanfile:
String path to file containing ocean vector data in a format compatible
with fiona.
:param oceangridfile:
String path to file containing ocean grid data .
:param cityfile:
String path to file containing GeoNames cities data.
:param basename:
String path containing desired output PDF base name, i.e.,
/home/pager/exposure. ".pdf" and ".png" files will
be made.
:param make_png:
Boolean indicating whether a PNG version of the file should also be
created in the same output folder as the PDF.
:returns:
Tuple containing:
- Name of PNG file created, or None if PNG output not specified.
- Cities object containing the cities that were rendered on the
contour map.
"""
gd = shakegrid.getGeoDict()
# Retrieve the epicenter - this will get used on the map
center_lat = shakegrid.getEventDict()['lat']
center_lon = shakegrid.getEventDict()['lon']
# load the ocean grid file (has 1s in ocean, 0s over land)
# having this file saves us almost 30 seconds!
oceangrid = read(oceangridfile,
samplegeodict=gd,
resample=True,
doPadding=True)
# load the cities data, limit to cities within shakemap bounds
allcities = Cities.fromDefault()
cities = allcities.limitByBounds((gd.xmin, gd.xmax, gd.ymin, gd.ymax))
# define the map
# first cope with stupid 180 meridian
height = (gd.ymax - gd.ymin) * DEG2KM
if gd.xmin < gd.xmax:
width = (gd.xmax - gd.xmin) * np.cos(np.radians(center_lat)) * DEG2KM
xmin, xmax, ymin, ymax = (gd.xmin, gd.xmax, gd.ymin, gd.ymax)
else:
xmin, xmax, ymin, ymax = (gd.xmin, gd.xmax, gd.ymin, gd.ymax)
xmax += 360
width = ((gd.xmax + 360) - gd.xmin) * \
np.cos(np.radians(center_lat)) * DEG2KM
aspect = width / height
# if the aspect is not 1, then trim bounds in x or y direction
# as appropriate
if width > height:
dw = (width - height) / 2.0 # this is width in km
xmin = xmin + dw / (np.cos(np.radians(center_lat)) * DEG2KM)
xmax = xmax - dw / (np.cos(np.radians(center_lat)) * DEG2KM)
width = (xmax - xmin) * np.cos(np.radians(center_lat)) * DEG2KM
if height > width:
dh = (height - width) / 2.0 # this is width in km
ymin = ymin + dh / DEG2KM
ymax = ymax - dh / DEG2KM
height = (ymax - ymin) * DEG2KM
aspect = width / height
figheight = FIGWIDTH / aspect
bbox = (xmin, ymin, xmax, ymax)
bounds = (xmin, xmax, ymin, ymax)
figsize = (FIGWIDTH, figheight)
# Create the MercatorMap object, which holds a separate but identical
# axes object used to determine collisions between city labels.
mmap = MercatorMap(bounds, figsize, cities, padding=0.5)
fig = mmap.figure
ax = mmap.axes
# this needs to be done here so that city label collision
# detection will work
fig.canvas.draw()
geoproj = mmap.geoproj
proj = mmap.proj
# project our population grid to the map projection
projstr = proj.proj4_init
popgrid_proj = popgrid.project(projstr)
popdata = popgrid_proj.getData()
newgd = popgrid_proj.getGeoDict()
# Use our GMT-inspired palette class to create population and MMI colormaps
popmap = ColorPalette.fromPreset('pop')
mmimap = ColorPalette.fromPreset('mmi')
# set the image extent to that of the data
img_extent = (newgd.xmin, newgd.xmax, newgd.ymin, newgd.ymax)
plt.imshow(popdata,
origin='upper',
extent=img_extent,
cmap=popmap.cmap,
vmin=popmap.vmin,
vmax=popmap.vmax,
zorder=POP_ZORDER,
interpolation='nearest')
# draw 10m res coastlines
ax.coastlines(resolution="10m", zorder=COAST_ZORDER)
states_provinces = cfeature.NaturalEarthFeature(
category='cultural',
name='admin_1_states_provinces_lines',
scale='50m',
facecolor='none')
ax.add_feature(states_provinces, edgecolor='black', zorder=COAST_ZORDER)
# draw country borders using natural earth data set
if borderfile is not None:
borders = ShapelyFeature(
Reader(borderfile).geometries(), ccrs.PlateCarree())
ax.add_feature(borders,
zorder=COAST_ZORDER,
edgecolor='black',
linewidth=2,
facecolor='none')
# clip the ocean data to the shakemap
bbox = (gd.xmin, gd.ymin, gd.xmax, gd.ymax)
oceanshapes = _clip_bounds(bbox, oceanfile)
ax.add_feature(ShapelyFeature(oceanshapes, crs=geoproj),
facecolor=WATERCOLOR,
zorder=OCEAN_ZORDER)
# So here we're going to project the MMI data to
# our mercator map, then smooth and contour that
# projected grid.
# smooth the MMI data for contouring, themn project
mmi = shakegrid.getLayer('mmi').getData()
smoothed_mmi = gaussian_filter(mmi, FILTER_SMOOTH)
newgd = shakegrid.getGeoDict().copy()
smooth_grid = Grid2D(data=smoothed_mmi, geodict=newgd)
smooth_grid_merc = smooth_grid.project(projstr)
newgd2 = smooth_grid_merc.getGeoDict()
# project the ocean grid
oceangrid_merc = oceangrid.project(projstr)
# create masked arrays using the ocean grid
data_xmin, data_xmax = newgd2.xmin, newgd2.xmax
data_ymin, data_ymax = newgd2.ymin, newgd2.ymax
smooth_data = smooth_grid_merc.getData()
landmask = np.ma.masked_where(oceangrid_merc._data == 0.0, smooth_data)
oceanmask = np.ma.masked_where(oceangrid_merc._data == 1.0, smooth_data)
# contour the data
contourx = np.linspace(data_xmin, data_xmax, newgd2.nx)
contoury = np.linspace(data_ymin, data_ymax, newgd2.ny)
ax.contour(
contourx,
contoury,
np.flipud(oceanmask),
linewidths=3.0,
linestyles='solid',
zorder=1000,
cmap=mmimap.cmap,
vmin=mmimap.vmin,
vmax=mmimap.vmax,
levels=np.arange(0.5, 10.5, 1.0),
)
ax.contour(
contourx,
contoury,
np.flipud(landmask),
linewidths=2.0,
linestyles='dashed',
zorder=OCEANC_ZORDER,
cmap=mmimap.cmap,
vmin=mmimap.vmin,
vmax=mmimap.vmax,
levels=np.arange(0.5, 10.5, 1.0),
)
# the idea here is to plot invisible MMI contours at integer levels
# and then label them. clabel method won't allow text to appear,
# which is this case is kind of ok, because it allows us an
# easy way to draw MMI labels as roman numerals.
cs_land = plt.contour(
contourx,
contoury,
np.flipud(oceanmask),
linewidths=0.0,
levels=np.arange(0, 11),
alpha=0.0,
zorder=CLABEL_ZORDER,
)
clabel_text = ax.clabel(cs_land,
cs_land.cvalues,
colors='k',
fmt='%.0f',
fontsize=40)
for clabel in clabel_text:
x, y = clabel.get_position()
label_str = clabel.get_text()
roman_label = MMI_LABELS[label_str]
th = plt.text(x,
y,
roman_label,
zorder=CLABEL_ZORDER,
ha='center',
va='center',
color='black',
weight='normal',
size=16)
th.set_path_effects([
path_effects.Stroke(linewidth=2.0, foreground='white'),
path_effects.Normal()
])
cs_ocean = plt.contour(
contourx,
contoury,
np.flipud(landmask),
linewidths=0.0,
levels=np.arange(0, 11),
zorder=CLABEL_ZORDER,
)
clabel_text = ax.clabel(cs_ocean,
cs_ocean.cvalues,
colors='k',
fmt='%.0f',
fontsize=40)
for clabel in clabel_text:
x, y = clabel.get_position()
label_str = clabel.get_text()
roman_label = MMI_LABELS[label_str]
th = plt.text(x,
y,
roman_label,
ha='center',
va='center',
color='black',
weight='normal',
size=16)
th.set_path_effects([
path_effects.Stroke(linewidth=2.0, foreground='white'),
path_effects.Normal()
])
# draw meridians and parallels using Cartopy's functions for that
gl = ax.gridlines(draw_labels=True,
linewidth=2,
color=(0.9, 0.9, 0.9),
alpha=0.5,
linestyle='-',
zorder=GRID_ZORDER)
gl.xlabels_top = False
gl.xlabels_bottom = False
gl.ylabels_left = False
gl.ylabels_right = False
gl.xlines = True
# let's floor/ceil the edges to nearest half a degree
gxmin = np.floor(xmin * 2) / 2
gxmax = np.ceil(xmax * 2) / 2
gymin = np.floor(ymin * 2) / 2
gymax = np.ceil(ymax * 2) / 2
xlocs = np.linspace(gxmin, gxmax + 0.5, num=5)
ylocs = np.linspace(gymin, gymax + 0.5, num=5)
gl.xlocator = mticker.FixedLocator(xlocs)
gl.ylocator = mticker.FixedLocator(ylocs)
gl.xformatter = LONGITUDE_FORMATTER
gl.yformatter = LATITUDE_FORMATTER
gl.xlabel_style = {'size': 15, 'color': 'black'}
gl.ylabel_style = {'size': 15, 'color': 'black'}
# TODO - figure out x/y axes data coordinates
# corresponding to 10% from left and 10% from top
# use geoproj and proj
dleft = 0.01
dtop = 0.97
proj_str = proj.proj4_init
merc_to_dd = pyproj.Proj(proj_str)
# use built-in transforms to get from axes units to data units
display_to_data = ax.transData.inverted()
axes_to_display = ax.transAxes
# these are x,y coordinates in projected space
yleft, t1 = display_to_data.transform(
axes_to_display.transform((dleft, 0.5)))
t2, xtop = display_to_data.transform(axes_to_display.transform(
(0.5, dtop)))
# these are coordinates in lon,lat space
yleft_dd, t1_dd = merc_to_dd(yleft, t1, inverse=True)
t2_dd, xtop_dd = merc_to_dd(t2, xtop, inverse=True)
# drawing our own tick labels INSIDE the plot, as
# Cartopy doesn't seem to support this.
yrange = ymax - ymin
xrange = xmax - xmin
ddlabelsize = 12
for xloc in gl.xlocator.locs:
outside = xloc < xmin or xloc > xmax
# don't draw labels when we're too close to either edge
near_edge = (xloc - xmin) < (xrange * 0.1) or (xmax - xloc) < (xrange *
0.1)
if outside or near_edge:
continue
xtext = r'$%.1f^\circ$W' % (abs(xloc))
ax.text(xloc,
xtop_dd,
xtext,
fontsize=ddlabelsize,
zorder=GRID_ZORDER,
ha='center',
fontname=DEFAULT_FONT,
transform=ccrs.Geodetic())
for yloc in gl.ylocator.locs:
outside = yloc < gd.ymin or yloc > gd.ymax
# don't draw labels when we're too close to either edge
near_edge = (yloc - gd.ymin) < (yrange * 0.1) or (gd.ymax - yloc) < (
yrange * 0.1)
if outside or near_edge:
continue
if yloc < 0:
ytext = r'$%.1f^\circ$S' % (abs(yloc))
else:
ytext = r'$%.1f^\circ$N' % (abs(yloc))
ax.text(yleft_dd,
yloc,
ytext,
fontsize=ddlabelsize,
zorder=GRID_ZORDER,
va='center',
fontname=DEFAULT_FONT,
transform=ccrs.Geodetic())
# draw cities
mapcities = mmap.drawCities(shadow=True, zorder=CITIES_ZORDER)
# draw the figure border thickly
# TODO - figure out how to draw map border
# bwidth = 3
# ax.spines['top'].set_visible(True)
# ax.spines['left'].set_visible(True)
# ax.spines['bottom'].set_visible(True)
# ax.spines['right'].set_visible(True)
# ax.spines['top'].set_linewidth(bwidth)
# ax.spines['right'].set_linewidth(bwidth)
# ax.spines['bottom'].set_linewidth(bwidth)
# ax.spines['left'].set_linewidth(bwidth)
# Get the corner of the map with the lowest population
corner_rect, filled_corner = _get_open_corner(popgrid, ax)
clat2 = round_to_nearest(center_lat, 1.0)
clon2 = round_to_nearest(center_lon, 1.0)
# draw a little globe in the corner showing in small-scale
# where the earthquake is located.
proj = ccrs.Orthographic(central_latitude=clat2, central_longitude=clon2)
ax2 = fig.add_axes(corner_rect, projection=proj)
ax2.add_feature(cfeature.OCEAN,
zorder=0,
facecolor=WATERCOLOR,
edgecolor=WATERCOLOR)
ax2.add_feature(cfeature.LAND, zorder=0, edgecolor='black')
ax2.plot([clon2], [clat2],
'w*',
linewidth=1,
markersize=16,
markeredgecolor='k',
markerfacecolor='r')
ax2.gridlines()
ax2.set_global()
ax2.outline_patch.set_edgecolor('black')
ax2.outline_patch.set_linewidth(2)
# Draw the map scale in the unoccupied lower corner.
corner = 'lr'
if filled_corner == 'lr':
corner = 'll'
draw_scale(ax, corner, pady=0.05, padx=0.05)
# Draw the epicenter as a black star
plt.sca(ax)
plt.plot(center_lon,
center_lat,
'k*',
markersize=16,
zorder=EPICENTER_ZORDER,
transform=geoproj)
if is_scenario:
plt.text(center_lon,
center_lat,
'SCENARIO',
fontsize=64,
zorder=WATERMARK_ZORDER,
transform=geoproj,
alpha=0.2,
color='red',
horizontalalignment='center')
# create pdf and png output file names
pdf_file = basename + '.pdf'
png_file = basename + '.png'
# save to pdf
plt.savefig(pdf_file)
plt.savefig(png_file)
return (pdf_file, png_file, mapcities)
def draw_map(adict, override_scenario=False):
"""If adict['imtype'] is MMI, draw a map of intensity draped over
topography, otherwise Draw IMT contour lines over hill-shaded topography.
Args:
adict (dictionary): A dictionary containing the following keys:
'imtype' (str): The intensity measure type
'topogrid' (Grid2d): A topography grid
'allcities' (Cities): A list of global cities,
'states_provinces' (Cartopy Feature): States/province boundaries.
'countries' (Cartopy Feature): Country boundaries.
'oceans' (Cartopy Feature): Oceans.
'lakes' (Cartopy Feature): Lakes.
'roads' (Shapely Feature): Roads.
'faults' (Shapely Feature): Fault traces
'datadir' (str): The path into which to deposit products
'operator' (str): The producer of this shakemap
'filter_size' (int): The size of the filter used before contouring
'info' (dictionary): The shakemap info structure
'component' (str): The intensity measure component being plotted
'imtdict' (dictionary): Dict containing the IMT grids
'rupdict' (dictionary): Dict containing the rupture data
'stationdict' (dictionary): Dict of station data
'config' (dictionary): The configuration data for this shakemap
'tdict' (dictionary): The text strings to be printed on the map
in the user's choice of language.
'license_text' (str): License text to display at bottom of map
'license_logo' (str): Path to license logo image to display
next to license text
override_scenario (bool): Turn off scenario watermark.
Returns:
Tuple of (Matplotlib figure, Matplotlib figure): Objects containing
the map generated by this function, and the intensity legend,
respectively. If the imtype of this map is not 'MMI', the second
element of the tuple will be None.
"""
imtype = adict['imtype']
imtdict = adict['imtdict'] # mmidict
imtdata = np.nan_to_num(imtdict['mean'], nan=0.0) # mmidata
gd = GeoDict(imtdict['mean_metadata'])
imtgrid = Grid2D(imtdata, gd) # mmigrid
gd = imtgrid.getGeoDict()
# Retrieve the epicenter - this will get used on the map
rupture = rupture_from_dict(adict['ruptdict'])
origin = rupture.getOrigin()
center_lat = origin.lat
center_lon = origin.lon
# load the cities data, limit to cities within shakemap bounds
cities = adict['allcities'].limitByBounds((gd.xmin, gd.xmax,
gd.ymin, gd.ymax))
# get the map boundaries and figure size
bounds, figsize, aspect = _get_map_info(gd)
# Note: dimensions are: [left, bottom, width, height]
dim_left = 0.1
dim_bottom = 0.19
dim_width = 0.8
dim_height = dim_width/aspect
if dim_height > 0.8:
dim_height = 0.8
dim_width = 0.8 * aspect
dim_left = (1.0 - dim_width) / 2
# Create the MercatorMap object, which holds a separate but identical
# axes object used to determine collisions between city labels.
mmap = MercatorMap(
bounds, figsize, cities, padding=0.5,
dimensions=[dim_left, dim_bottom, dim_width, dim_height])
fig = mmap.figure
ax = mmap.axes
# this needs to be done here so that city label collision
# detection will work
fig.canvas.draw()
# get the geographic projection object
geoproj = mmap.geoproj
# get the mercator projection object
proj = mmap.proj
# get the proj4 string - used by Grid2D project() method
projstr = proj.proj4_init
# get the projected IMT and topo grids
pimtgrid, ptopogrid = _get_projected_grids(imtgrid, adict['topogrid'],
projstr)
# get the projected geodict
proj_gd = pimtgrid.getGeoDict()
pimtdata = pimtgrid.getData()
ptopo_data = ptopogrid.getData()
mmimap = ColorPalette.fromPreset('mmi')
if imtype == 'MMI':
draped_hsv = _get_draped(pimtdata, ptopo_data, mmimap)
else:
# get the draped topo data
topo_colormap = ColorPalette.fromPreset('shaketopo')
draped_hsv = _get_shaded(ptopo_data, topo_colormap)
# convert units
if imtype == 'PGV':
pimtdata = np.exp(pimtdata)
else:
pimtdata = np.exp(pimtdata) * 100
plt.sca(ax)
ax.set_xlim(proj_gd.xmin, proj_gd.xmax)
ax.set_ylim(proj_gd.ymin, proj_gd.ymax)
img_extent = (proj_gd.xmin, proj_gd.xmax, proj_gd.ymin, proj_gd.ymax)
plt.imshow(draped_hsv, origin='upper', extent=img_extent,
zorder=IMG_ZORDER, interpolation='none')
config = adict['config']
gmice = get_object_from_config('gmice', 'modeling', config)
gmice_imts = gmice.DEFINED_FOR_INTENSITY_MEASURE_TYPES
gmice_pers = gmice.DEFINED_FOR_SA_PERIODS
oqimt = imt.from_string(imtype)
if imtype != 'MMI' and (not isinstance(oqimt, tuple(gmice_imts)) or
(isinstance(oqimt, imt.SA) and
oqimt.period not in gmice_pers)):
my_gmice = None
else:
my_gmice = gmice
if imtype != 'MMI':
# call the contour module in plotting to get the vertices of the
# contour lines
contour_objects = contour(imtdict, imtype, adict['filter_size'],
my_gmice)
# get a color palette for the levels we have
# levels = [c['properties']['value'] for c in contour_objects]
# cartopy shapely feature has some weird behaviors, so I had to go
# rogue and draw contour lines/labels myself.
# To choose which contours to label, we will keep track of the lengths
# of contours, grouped by isovalue
contour_lens = defaultdict(lambda: [])
def arclen(path):
"""
Compute the arclength of *path*, which should be a list of pairs
of numbers.
"""
x0, y0 = [np.array(c) for c in zip(*path)]
x1, y1 = [np.roll(c, -1) for c in (x0, y0)] # offset by 1
# don't include first-last vertices as an edge:
x0, y0, x1, y1 = [c[:-1] for c in (x0, y0, x1, y1)]
return np.sum(np.sqrt((x0 - x1)**2 + (y0 - y1)**2))
# draw dashed contours first, the ones over land will be overridden by
# solid contours
for contour_object in contour_objects:
props = contour_object['properties']
multi_lines = sShape(contour_object['geometry'])
pmulti_lines = proj.project_geometry(multi_lines, src_crs=geoproj)
for multi_line in pmulti_lines:
pmulti_line = mapping(multi_line)['coordinates']
x, y = zip(*pmulti_line)
contour_lens[props['value']].append(arclen(pmulti_line))
# color = imt_cmap.getDataColor(props['value'])
ax.plot(x, y, color=props['color'], linestyle='dashed',
zorder=DASHED_CONTOUR_ZORDER)
white_box = dict(
boxstyle="round",
ec=(0, 0, 0),
fc=(1., 1, 1),
color='k'
)
# draw solid contours next - the ones over water will be covered by
# ocean polygon
for contour_object in contour_objects:
props = contour_object['properties']
multi_lines = sShape(contour_object['geometry'])
pmulti_lines = proj.project_geometry(multi_lines, src_crs=geoproj)
# only label long contours (relative to others with the same
# isovalue)
min_len = np.array(contour_lens[props['value']]).mean()
for multi_line in pmulti_lines:
pmulti_line = mapping(multi_line)['coordinates']
x, y = zip(*pmulti_line)
# color = imt_cmap.getDataColor(props['value'])
ax.plot(x, y, color=props['color'], linestyle='solid',
zorder=CONTOUR_ZORDER)
if arclen(pmulti_line) >= min_len:
# try to label each segment with black text in a white box
xc = x[int(len(x)/3)]
yc = y[int(len(y)/3)]
if _label_close_to_edge(
xc, yc, proj_gd.xmin, proj_gd.xmax,
proj_gd.ymin, proj_gd.ymax):
continue
# TODO: figure out if box is going to go outside the map,
# if so choose a different point on the line.
# For small values, use scientific notation with 1 sig fig
# to avoid multiple contours labelled 0.0:
value = props['value']
fmt = '%.1g' if abs(value) < 0.1 else '%.1f'
ax.text(xc, yc, fmt % value, size=8,
ha="center", va="center",
bbox=white_box, zorder=AXES_ZORDER-1)
# make the border thicker
lw = 2.0
ax.outline_patch.set_zorder(BORDER_ZORDER)
ax.outline_patch.set_linewidth(lw)
ax.outline_patch.set_joinstyle('round')
ax.outline_patch.set_capstyle('round')
# Coastlines will get drawn when we draw the ocean edges
# ax.coastlines(resolution="10m", zorder=COAST_ZORDER, linewidth=3)
if adict['states_provinces']:
ax.add_feature(adict['states_provinces'], edgecolor='0.5',
zorder=COAST_ZORDER)
if adict['countries']:
ax.add_feature(adict['countries'], edgecolor='black',
zorder=BORDER_ZORDER)
if adict['oceans']:
ax.add_feature(adict['oceans'], edgecolor='black',
zorder=OCEAN_ZORDER)
if adict['lakes']:
ax.add_feature(adict['lakes'], edgecolor='black',
zorder=OCEAN_ZORDER)
if adict['faults'] is not None:
ax.add_feature(adict['faults'], edgecolor='firebrick',
zorder=ROAD_ZORDER)
if adict['roads'] is not None:
ax.add_feature(adict['roads'], edgecolor='dimgray',
zorder=ROAD_ZORDER)
# draw graticules, ticks, tick labels
_draw_graticules(ax, *bounds)
# is this event a scenario?
info = adict['info']
etype = info['input']['event_information']['event_type']
is_scenario = etype == 'SCENARIO'
if is_scenario and not override_scenario:
plt.text(
center_lon, center_lat,
adict['tdict']['title_parts']['scenario'],
fontsize=72,
zorder=SCENARIO_ZORDER, transform=geoproj,
alpha=WATERMARK_ALPHA, color=WATERMARK_COLOR,
horizontalalignment='center',
verticalalignment='center',
rotation=45,
path_effects=[
path_effects.Stroke(linewidth=1, foreground='black')]
)
# Draw the map scale in the unoccupied lower corner.
corner = 'll'
draw_scale(ax, corner, pady=0.05, padx=0.05, zorder=SCALE_ZORDER)
# draw cities
mmap.drawCities(shadow=True, zorder=CITIES_ZORDER, draw_dots=True)
# Draw the epicenter as a black star
plt.sca(ax)
plt.plot(center_lon, center_lat, 'k*', markersize=16,
zorder=EPICENTER_ZORDER, transform=geoproj)
# draw the rupture polygon(s) in black, if not point rupture
point_source = True
if not isinstance(rupture, PointRupture):
point_source = False
json_dict = rupture._geojson
for feature in json_dict['features']:
for coords in feature['geometry']['coordinates']:
for pcoords in coords:
poly2d = sLineString([xy[0:2] for xy in pcoords])
ppoly = proj.project_geometry(poly2d)
mppoly = mapping(ppoly)['coordinates']
for spoly in mppoly:
x, y = zip(*spoly)
ax.plot(x, y, 'k', lw=1, zorder=FAULT_ZORDER)
# draw the station data on the map
stations = adict['stationdict']
_draw_stations(ax, stations, imtype, mmimap, geoproj)
_draw_title(imtype, adict)
process_time = info['processing']['shakemap_versions']['process_time']
map_version = int(info['processing']['shakemap_versions']['map_version'])
if imtype == 'MMI':
_draw_mmi_legend(fig, mmimap, gmice, process_time,
map_version, point_source, adict['tdict'])
# make a separate MMI legend
fig2 = plt.figure(figsize=figsize)
_draw_mmi_legend(fig2, mmimap, gmice, process_time,
map_version, point_source, adict['tdict'])
else:
_draw_imt_legend(fig, mmimap, imtype, gmice, process_time, map_version,
point_source, adict['tdict'])
plt.draw()
fig2 = None
_draw_license(fig, adict)
return (fig, fig2)
def basic_test():
mmidata = np.array([[7, 8, 8, 8, 7], [8, 9, 9, 9, 8], [8, 9, 10, 9, 8],
[8, 9, 9, 8, 8], [7, 8, 8, 6, 5]],
dtype=np.float32)
popdata = np.ones_like(mmidata) * 1e7
isodata = np.array(
[[4, 4, 4, 4, 4], [4, 4, 4, 4, 4], [4, 4, 156, 156, 156],
[156, 156, 156, 156, 156], [156, 156, 156, 156, 156]],
dtype=np.int32)
shakefile = get_temp_file_name()
popfile = get_temp_file_name()
isofile = get_temp_file_name()
geodict = GeoDict({
'xmin': 0.5,
'xmax': 4.5,
'ymin': 0.5,
'ymax': 4.5,
'dx': 1.0,
'dy': 1.0,
'nx': 5,
'ny': 5
})
layers = OrderedDict([
('mmi', mmidata),
])
event_dict = {
'event_id': 'us12345678',
'magnitude': 7.8,
'depth': 10.0,
'lat': 34.123,
'lon': -118.123,
'event_timestamp': datetime.utcnow(),
'event_description': 'foo',
'event_network': 'us'
}
shake_dict = {
'event_id': 'us12345678',
'shakemap_id': 'us12345678',
'shakemap_version': 1,
'code_version': '4.5',
'process_timestamp': datetime.utcnow(),
'shakemap_originator': 'us',
'map_status': 'RELEASED',
'shakemap_event_type': 'ACTUAL'
}
unc_dict = {'mmi': (1, 1)}
shakegrid = ShakeGrid(layers, geodict, event_dict, shake_dict, unc_dict)
shakegrid.save(shakefile)
popgrid = Grid2D(popdata, geodict.copy())
isogrid = Grid2D(isodata, geodict.copy())
write(popgrid, popfile, 'netcdf')
write(isogrid, isofile, 'netcdf')
ratedict = {
4: {
'start': [2010, 2012, 2014, 2016],
'end': [2012, 2014, 2016, 2018],
'rate': [0.01, 0.02, 0.03, 0.04]
},
156: {
'start': [2010, 2012, 2014, 2016],
'end': [2012, 2014, 2016, 2018],
'rate': [0.02, 0.03, 0.04, 0.05]
}
}
popgrowth = PopulationGrowth(ratedict)
popyear = datetime.utcnow().year
exposure = Exposure(popfile, popyear, isofile, popgrowth=popgrowth)
expdict = exposure.calcExposure(shakefile)
modeldict = [
LognormalModel('AF', 11.613073, 0.180683, 1.0),
LognormalModel('CN', 10.328811, 0.100058, 1.0)
]
fatmodel = EmpiricalLoss(modeldict)
# for the purposes of this test, let's override the rates
# for Afghanistan and China with simpler numbers.
fatmodel.overrideModel(
'AF',
np.array([0, 0, 0, 0, 1e-6, 1e-5, 1e-4, 1e-3, 1e-2, 0],
dtype=np.float32))
fatmodel.overrideModel(
'CN',
np.array([0, 0, 0, 0, 1e-7, 1e-6, 1e-5, 1e-4, 1e-3, 0],
dtype=np.float32))
print('Testing very basic fatality calculation...')
fatdict = fatmodel.getLosses(expdict)
# strictly speaking, the afghanistant fatalities should be 462,000 but floating point precision dictates otherwise.
testdict = {'CN': 46111, 'AF': 461999, 'TotalFatalities': 508110}
for key, value in fatdict.items():
assert value == testdict[key]
print('Passed very basic fatality calculation...')
print('Testing grid fatality calculations...')
mmidata = exposure.getShakeGrid().getLayer('mmi').getData()
popdata = exposure.getPopulationGrid().getData()
isodata = exposure.getCountryGrid().getData()
fatgrid = fatmodel.getLossGrid(mmidata, popdata, isodata)
assert np.nansum(fatgrid) == 508111
print('Passed grid fatality calculations...')
# Testing modifying rates and stuffing them back in...
chile = LognormalModel('CL', 19.786773, 0.259531, 0.0)
rates = chile.getLossRates(np.arange(5, 10))
modrates = rates * 2 # does this make event twice as deadly?
# roughly the exposures from 2015-9-16 CL event
expo_pop = np.array(
[0, 0, 0, 1047000, 7314000, 1789000, 699000, 158000, 0, 0])
mmirange = np.arange(5, 10)
chile_deaths = chile.getLosses(expo_pop[4:9], mmirange)
chile_double_deaths = chile.getLosses(expo_pop[4:9],
mmirange,
rates=modrates)
print('Chile model fatalities: %f' % chile_deaths)
print('Chile model x2 fatalities: %f' % chile_double_deaths)
def execute(self):
"""
Raises:
NotADirectoryError: When the event data directory does not exist.
FileNotFoundError: When the the shake_result HDF file does not
exist.
"""
install_path, data_path = get_config_paths()
datadir = os.path.join(data_path, self._eventid, 'current', 'products')
if not os.path.isdir(datadir):
raise NotADirectoryError('%s is not a valid directory.' % datadir)
datafile = os.path.join(datadir, 'shake_result.hdf')
if not os.path.isfile(datafile):
raise FileNotFoundError('%s does not exist.' % datafile)
# Open the ShakeMapOutputContainer and extract the data
container = ShakeMapOutputContainer.load(datafile)
if container.getDataType() != 'grid':
raise NotImplementedError('mapping module can only operate on '
'gridded data, not sets of points')
# get the path to the products.conf file, load the config
config_file = os.path.join(install_path, 'config', 'products.conf')
spec_file = get_configspec('products')
validator = get_custom_validator()
config = ConfigObj(config_file, configspec=spec_file)
results = config.validate(validator)
check_extra_values(config, self.logger)
if not isinstance(results, bool) or not results:
config_error(config, results)
# create contour files
self.logger.debug('Mapping...')
# get the filter size from the products.conf
filter_size = config['products']['contour']['filter_size']
# get the operator setting from config
operator = config['products']['mapping']['operator']
# get all of the pieces needed for the mapping functions
layers = config['products']['mapping']['layers']
if 'topography' in layers and layers['topography'] != '':
topofile = layers['topography']
else:
topofile = None
if 'roads' in layers and layers['roads'] != '':
roadfile = layers['roads']
else:
roadfile = None
if 'faults' in layers and layers['faults'] != '':
faultfile = layers['faults']
else:
faultfile = None
# Get the number of parallel workers
max_workers = config['products']['mapping']['max_workers']
# Reading HDF5 files currently takes a long time, due to poor
# programming in MapIO. To save us some time until that issue is
# resolved, we'll coarsely subset the topo grid once here and pass
# it into both mapping functions
# get the bounds of the map
info = container.getMetadata()
xmin = info['output']['map_information']['min']['longitude']
xmax = info['output']['map_information']['max']['longitude']
ymin = info['output']['map_information']['min']['latitude']
ymax = info['output']['map_information']['max']['latitude']
dy = float(
info['output']['map_information']['grid_spacing']['latitude'])
dx = float(
info['output']['map_information']['grid_spacing']['longitude'])
padx = 5 * dx
pady = 5 * dy
sxmin = float(xmin) - padx
sxmax = float(xmax) + padx
symin = float(ymin) - pady
symax = float(ymax) + pady
sampledict = GeoDict.createDictFromBox(sxmin, sxmax, symin, symax, dx,
dy)
if topofile:
topogrid = read(topofile, samplegeodict=sampledict, resample=False)
else:
tdata = np.full([sampledict.ny, sampledict.nx], 0.0)
topogrid = Grid2D(data=tdata, geodict=sampledict)
model_config = container.getConfig()
imtlist = container.getIMTs()
textfile = os.path.join(
get_data_path(), 'mapping',
'map_strings.' + config['products']['mapping']['language'])
text_dict = get_text_strings(textfile)
if config['products']['mapping']['fontfamily'] != '':
matplotlib.rcParams['font.family'] = \
config['products']['mapping']['fontfamily']
matplotlib.rcParams['axes.unicode_minus'] = False
allcities = Cities.fromDefault()
states_provs = None
countries = None
oceans = None
lakes = None
extent = (float(xmin), float(ymin), float(xmax), float(ymax))
if 'CALLED_FROM_PYTEST' not in os.environ:
states_provs = cfeature.NaturalEarthFeature(
category='cultural',
name='admin_1_states_provinces_lines',
scale='10m',
facecolor='none')
states_provs = list(states_provs.intersecting_geometries(extent))
if len(states_provs) > 300:
states_provs = None
else:
states_provs = cfeature.NaturalEarthFeature(
category='cultural',
name='admin_1_states_provinces_lines',
scale='10m',
facecolor='none')
countries = cfeature.NaturalEarthFeature(category='cultural',
name='admin_0_countries',
scale='10m',
facecolor='none')
oceans = cfeature.NaturalEarthFeature(category='physical',
name='ocean',
scale='10m',
facecolor=WATERCOLOR)
lakes = cfeature.NaturalEarthFeature(category='physical',
name='lakes',
scale='10m',
facecolor=WATERCOLOR)
if faultfile is not None:
faults = ShapelyFeature(Reader(faultfile).geometries(),
ccrs.PlateCarree(),
facecolor='none')
else:
faults = None
if roadfile is not None:
roads = ShapelyFeature(Reader(roadfile).geometries(),
ccrs.PlateCarree(),
facecolor='none')
if len(list(roads.intersecting_geometries(extent))) > 200:
roads = None
else:
roads = ShapelyFeature(Reader(roadfile).geometries(),
ccrs.PlateCarree(),
facecolor='none')
else:
roads = None
alist = []
for imtype in imtlist:
component, imtype = imtype.split('/')
comp = container.getComponents(imtype)[0]
d = {
'imtype': imtype,
'topogrid': topogrid,
'allcities': allcities,
'states_provinces': states_provs,
'countries': countries,
'oceans': oceans,
'lakes': lakes,
'roads': roads,
'faults': faults,
'datadir': datadir,
'operator': operator,
'filter_size': filter_size,
'info': info,
'component': comp,
'imtdict': container.getIMTGrids(imtype, comp),
'ruptdict': copy.deepcopy(container.getRuptureDict()),
'stationdict': container.getStationDict(),
'config': model_config,
'tdict': text_dict
}
alist.append(d)
if imtype == 'MMI':
g = copy.deepcopy(d)
g['imtype'] = 'thumbnail'
alist.append(g)
h = copy.deepcopy(d)
h['imtype'] = 'overlay'
alist.append(h)
self.contents.addFile('intensityMap', 'Intensity Map',
'Map of macroseismic intensity.',
'intensity.jpg', 'image/jpeg')
self.contents.addFile('intensityMap', 'Intensity Map',
'Map of macroseismic intensity.',
'intensity.pdf', 'application/pdf')
self.contents.addFile('intensityThumbnail',
'Intensity Thumbnail',
'Thumbnail of intensity map.',
'pin-thumbnail.png', 'image/png')
self.contents.addFile(
'intensityOverlay', 'Intensity Overlay and World File',
'Macroseismic intensity rendered as a '
'PNG overlay and associated world file',
'intensity_overlay.png', 'image/png')
self.contents.addFile(
'intensityOverlay', 'Intensity Overlay and World File',
'Macroseismic intensity rendered as a '
'PNG overlay and associated world file',
'intensity_overlay.pngw', 'text/plain')
else:
fileimt = oq_to_file(imtype)
self.contents.addFile(fileimt + 'Map',
fileimt.upper() + ' Map',
'Map of ' + imtype + '.',
fileimt + '.jpg', 'image/jpeg')
self.contents.addFile(fileimt + 'Map',
fileimt.upper() + ' Map',
'Map of ' + imtype + '.',
fileimt + '.pdf', 'application/pdf')
if max_workers > 0:
with cf.ProcessPoolExecutor(max_workers=max_workers) as ex:
results = ex.map(make_map, alist)
list(results)
else:
for adict in alist:
make_map(adict)
container.close()
def _get_grids(config, simfile):
"""Create a dictionary of Grid2D objects for each IMT in input CSV file.
Args:
config (ConfigObj): Dictionary containing fields:
- simulation: (dict)
- order = (required) "rows" or "cols"
- projection = (optional) Proj4 string
defining input X/Y data projection.
- nx Number of columns in input grid.
- ny Number of rows in input grid.
- dx Resolution of columns (if XY, whatever
those units are, otherwise decimal degrees).
- dy Resolution of rows (if XY, whatever those
units are, otherwise decimal degrees).
simfile (str): Path to a CSV file with columns:
- LAT Latitudes for each cell. If irregular, X/Y data
will be used.
- LON Longitudes for each cell. If irregular, X/Y data
will be used.
- X Regularized X coordinates for each cell.
- Y Regularized Y coordinates for each cell.
- H1_<IMT> First horizontal channel for given IMT.
Supported IMTs are: PGA, PGV, SA(period).
- H2_<IMT> Second horizontal channel for given IMT.
Supported IMTs are: PGA, PGV, SA(period).
Returns:
dict: Dictionary of IMTs (PGA, PGV, SA(1.0), etc.) and Grid2D
objects. If XY data was used, these grids are the result of a
projection/resampling of that XY data back to a regular lat/lon grid.
"""
row_order = 'C'
if config['simulation']['order'] != 'rows':
row_order = 'F'
dataframe = pd.read_csv(simfile)
# construct a geodict
geodict = _get_geodict(dataframe, config)
# figure out which IMTs we have...
column_list = []
for column in dataframe.columns:
for imtmatch in IMT_MATCHES:
if re.search(imtmatch, column):
column_list.append(column)
# gather up all "channels" for each IMT
imtdict = {} # dictionary of imts and a list of columns
for col in column_list:
channel, imt = col.split('_')
if imt in imtdict:
imtdict[imt].append(col)
else:
imtdict[imt] = [col]
# make a dictionary of Grid2D objects containing max of two "channels"
# for each IMT
nrows = geodict.ny
ncols = geodict.nx
imtgrids = {}
for imt, imtcols in imtdict.items():
icount = len(imtcols)
if icount != 2:
raise IndexError(
'Incorrect number of channels for IMT %s.' % imt)
channel1, channel2 = imtcols
maximt = dataframe[[channel1, channel2]].max(axis=1).values
data = np.reshape(maximt, (nrows, ncols), order=row_order)
grid = Grid2D(data, geodict)
# if we need to project data back to geographic, do that here
if geodict.projection != GEO_PROJ_STR:
grid = grid.project(GEO_PROJ_STR)
imtgrids[imt] = grid
return imtgrids
def test_subdivide():
print('Testing subdivide method - aligned grids...')
data = np.arange(0, 4).reshape((2, 2))
geodict = GeoDict({'xmin': 0.0, 'xmax': 1.0,
'ymin': 0.0, 'ymax': 1.0,
'dx': 1.0, 'dy': 1.0,
'ny': 2, 'nx': 2})
hostgrid = Grid2D(data, geodict)
finedict = GeoDict({'xmin': 0.0-(1.0/3.0), 'xmax': 1.0+(1.0/3.0),
'ymin': 0.0-(1.0/3.0), 'ymax': 1.0+(1.0/3.0),
'dx': 1.0/3.0, 'dy': 1.0/3.0,
'ny': 6, 'nx': 6})
finegrid = hostgrid.subdivide(finedict)
output = np.array([[0., 0., 0., 1., 1., 1.],
[0., 0., 0., 1., 1., 1.],
[0., 0., 0., 1., 1., 1.],
[2., 2., 2., 3., 3., 3.],
[2., 2., 2., 3., 3., 3.],
[2., 2., 2., 3., 3., 3.]])
np.testing.assert_almost_equal(finegrid.getData(), output)
print('Passed subdivide method test - aligned grids.')
print('Testing subdivide method - non-aligned grids...')
data = np.arange(0, 9).reshape((3, 3))
geodict = GeoDict({'xmin': 0.0, 'xmax': 10.0,
'ymin': 0.0, 'ymax': 10.0,
'dx': 5.0, 'dy': 5.0,
'ny': 3, 'nx': 3})
hostgrid = Grid2D(data, geodict)
finedict = GeoDict({'xmin': -2.5, 'xmax': 11.5,
'ymin': -1.5, 'ymax': 10.5,
'dx': 2.0, 'dy': 2.0,
'nx': 8, 'ny': 7})
N = np.nan
print('Testing subdivide with min parameter...')
finegrid = hostgrid.subdivide(finedict, cellFill='min')
output = np.array([[N, 0., 0., 1., 1., 1., 2., 2.],
[N, 0., 0., 1., 1., 1., 2., 2.],
[N, 3., 3., 4., 4., 4., 5., 5.],
[N, 3., 3., 4., 4., 4., 5., 5.],
[N, 3., 3., 4., 4., 4., 5., 5.],
[N, 6., 6., 7., 7., 7., 8., 8.],
[N, 6., 6., 7., 7., 7., 8., 8.]])
np.testing.assert_almost_equal(finegrid.getData(), output)
print('Passed subdivide with min parameter...')
print('Testing subdivide with max parameter...')
finegrid = hostgrid.subdivide(finedict, cellFill='max')
output = np.array([[N, 0., 0., 1., 1., 2., 2., 2.],
[N, 0., 0., 1., 1., 2., 2., 2.],
[N, 3., 3., 4., 4., 5., 5., 5.],
[N, 3., 3., 4., 4., 5., 5., 5.],
[N, 6., 6., 7., 7., 8., 8., 8.],
[N, 6., 6., 7., 7., 8., 8., 8.],
[N, 6., 6., 7., 7., 8., 8., 8.]])
np.testing.assert_almost_equal(finegrid.getData(), output)
print('Passed subdivide with max parameter...')
print('Testing subdivide with mean parameter...')
finegrid = hostgrid.subdivide(finedict, cellFill='mean')
output = np.array([[N, 0., 0., 1., 1., 1.5, 2., 2.],
[N, 0., 0., 1., 1., 1.5, 2., 2.],
[N, 3., 3., 4., 4., 4.5, 5., 5.],
[N, 3., 3., 4., 4., 4.5, 5., 5.],
[N, 4.5, 4.5, 5.5, 5.5, 6.0, 6.5, 6.5],
[N, 6., 6., 7., 7., 7.5, 8., 8.],
[N, 6., 6., 7., 7., 7.5, 8., 8.]])
np.testing.assert_almost_equal(finegrid.getData(), output)
print('Passed subdivide with mean parameter...')
print('Passed subdivide method test - non-aligned grids.')
def calculate(self, cleanup=True, rowmax=300, colmax=None):
"""
Calculate the model.
Args:
cleanup (bool): If True, delete temporary hdf5 files
rowmax (int): Number of rows to compute at once; If None, all rows
will be computed at once.
colmax (int): Number of columns to compute at once; If None, all
columns will be computed at once.
Returns:
dict: Dictionary containing the model results (and model inputs if
saveinputs was set to True). See
`the description <https://github.com/usgs/groundfailure#api-for-model-output>`_
of the structure.
"""
tk = list(self.shakemap.keys())[0]
# Figure out what slices to do
rowstarts, rowends, colstarts, colends = \
self.shakemap[tk].getSliceDiv(rowmax, colmax)
# Make empty matrix to fill
X = np.empty([self.geodict.ny, self.geodict.nx])
# Loop through slices, appending output each time
for rowstart, rowend, colstart, colend in \
zip(rowstarts, rowends, colstarts, colends):
X[rowstart:rowend, colstart:colend] = eval(self.equation)
P = 1 / (1 + np.exp(-X))
if 'vs30max' in self.config[self.model].keys():
vs30 = self.layerdict['vs30'].getSlice(None,
None,
None,
None,
name='vs30')
P[vs30 > float(self.config[self.model]['vs30max'])] = 0.0
if 'minpgv' in self.config[self.model].keys():
pgv = self.shakemap['pgv'].getSlice(None,
None,
None,
None,
name='pgv')
P[pgv < float(self.config[self.model]['minpgv'])] = 0.0
if 'minpga' in self.config[self.model].keys():
pga = self.shakemap['pga'].getSlice(None,
None,
None,
None,
name='pga')
P[pga < float(self.config[self.model]['minpga'])] = 0.0
if self.uncert is not None: # hard code for now
if 'Zhu and others (2017)' in self.modelrefs['shortref']:
if 'stddev' in self.layerdict.keys():
stdX = self.layerdict['stddev'].getSlice()
else:
stdX = float(self.config[self.model]['default_stddev'])
varX = stdX**2. + \
(self.coeffs['b1']**2. *
self.uncert['stdpgv'].getSlice()**2.)
varP = (np.exp(-X) / (np.exp(-X) + 1)**2.)**2. * varX
if 'coverage' in self.config[self.model].keys():
a = 0.4915
b = 42.4
c = 9.165
# ((2*a*b*c*np.exp(2*c*P))/(b+np.exp(c*P))**3.)**2.*varP
varL = ((2 * a * b * c * np.exp(-c * P)) /
((1 + b * np.exp(-c * P))**3.))**2. * varP
std1 = np.sqrt(varL)
else:
std1 = np.sqrt(varP)
elif 'Jessee' in self.modelrefs['shortref']:
if 'stddev' in self.layerdict.keys():
stdX = self.layerdict['stddev'].getSlice()
else:
stdX = float(self.config[self.model]['default_stddev'])
varX = stdX**2. + (
(self.coeffs['b1'] + self.coeffs['b6'] *
(np.arctan(self.layerdict['slope'].getSlice()) * 180 /
np.pi))**2. * self.uncert['stdpgv'].getSlice()**2.)
varP = (np.exp(-X) / (np.exp(-X) + 1)**2.)**2. * varX
if 'coverage' in self.config[self.model].keys():
a = -7.592
b = 5.237
c = -3.042
d = 4.035
varL = (np.exp(a + b * P + c * P**2. + d * P**3.) *
(b + 2. * P * c + 3. * d * P**2.))**2. * varP
std1 = np.sqrt(varL)
else:
std1 = np.sqrt(varP)
else:
print(
'cannot do uncertainty for %s model currently, skipping' %
self.modelrefs['shortref'])
self.uncert = None
std1 = None
else:
std1 = None
# P needs to be converted to areal coverage after dealing with uncertainty
if 'coverage' in self.config[self.model].keys():
eqn = self.config[self.model]['coverage']['eqn']
P = eval(eqn)
if self.slopefile is not None and self.nonzero is not None:
# Apply slope min/max limits
print('applying slope thresholds')
P = P * self.nonzero
if std1 is not None:
# No uncert for masked values
std1[P == 0] = 0.
# Stuff into Grid2D object
if 'Jessee' in self.modelrefs['shortref']:
if 'coverage' not in self.config[self.model].keys():
units5 = 'Relative Hazard'
else:
units5 = 'Proportion of area affected'
elif 'Zhu' in self.modelrefs['shortref']:
if 'coverage' not in self.config[self.model].keys(
) and '2017' in self.modelrefs['shortref']:
units5 = 'Relative Hazard'
else:
units5 = 'Proportion of area affected'
else:
units5 = 'Probability of any occurrence'
shakedetail = ('%s_ver%s' % (self.shakedict['shakemap_id'],
self.shakedict['shakemap_version']))
description = {
'name': self.modelrefs['shortref'],
'longref': self.modelrefs['longref'],
'units': units5,
'shakemap': shakedetail,
'event_id': self.eventdict['event_id'],
'parameters': {
'slopemin': self.slopemin,
'slopemax': self.slopemax,
'modeltype': self.modeltype,
'notes': self.notes
}
}
if 'vs30max' in self.config[self.model].keys():
description['vs30max'] = float(self.config[self.model]['vs30max'])
if 'minpgv' in self.config[self.model].keys():
description['minpgv'] = float(self.config[self.model]['minpgv'])
Pgrid = Grid2D(P, self.geodict)
if self.trimfile is not None:
# Turn all offshore cells to nan
Pgrid = trim_ocean(Pgrid, self.trimfile, nodata=float('nan'))
rdict = collections.OrderedDict()
rdict['model'] = {
'grid':
Pgrid,
'label': ('%s estimate - %s') %
(self.modeltype.capitalize(), units5.title()),
'type':
'output',
'description':
description
}
if self.uncert is not None:
Stdgrid = Grid2D(std1, self.geodict)
if self.trimfile is not None:
Stdgrid = trim_ocean(Stdgrid,
self.trimfile,
nodata=float('nan'))
rdict['std'] = {
'grid':
Stdgrid,
'label': ('%s estimate - %s (std)' %
(self.modeltype.capitalize(), units5.title())),
'type':
'output',
'description':
description
}
# This step might swamp memory for higher resolution runs
if self.saveinputs is True:
for layername, layergrid in list(self.layerdict.items()):
units = self.units[layername]
if units is None:
units = ''
rdict[layername] = {
'grid':
Grid2D(
layergrid.getSlice(None,
None,
None,
None,
name=layername), self.geodict),
'label':
'%s (%s)' % (layername, units),
'type':
'input',
'description': {
'units': units,
'name': self.shortrefs[layername],
'longref': self.longrefs[layername]
}
}
for gmused in self.gmused:
if 'pga' in gmused:
units = '%g'
getkey = 'pga'
elif 'pgv' in gmused:
units = 'cm/s'
getkey = 'pgv'
elif 'mmi' in gmused:
units = 'intensity'
getkey = 'mmi'
else:
continue
# Layer is derived from several input layers, skip
# outputting this layer
if getkey in rdict:
continue
layer = self.shakemap[getkey].getSlice(None,
None,
None,
None,
name=getkey)
rdict[getkey] = {
'grid': Grid2D(layer, self.geodict),
'label': '%s (%s)' % (getkey.upper(), units),
'type': 'input',
'description': {
'units': units,
'shakemap': shakedetail
}
}
if cleanup:
shutil.rmtree(self.tempdir)
return rdict
def get_exposures(grid,
pop_file,
shakefile=None,
shakethreshtype=None,
shakethresh=None,
probthresh=None):
"""
Get exposure-based statistics.
Args:
grid: Model grid.
pop_file (str): Path to the landscan population grid.
shakefile (str): Optional, path to shakemap file to use for ground
motion threshold.
shakethreshtype(str): Optional, Type of ground motion to use for
shakethresh, 'pga', 'pgv', or 'mmi'.
shakethresh: Optional, Float or list of shaking thresholds in %g for
pga, cm/s for pgv, float for mmi.
probthresh: Optional, None or float, exclude any cells with probabilities
less than or equal to this value
Returns:
dict: Dictionary with keys named exp_pop_# where # is the shakethresh
"""
# If probthresh defined, zero out any areas less than or equal to probthresh
# before proceeding
if probthresh is not None:
origdata = grid.getData()
moddat = origdata.copy()
moddat[moddat <= probthresh] = 0.0
moddat[np.isnan(origdata)] = float('nan')
else:
moddat = grid.getData()
mdict = grid.getGeoDict()
# Cut out area from population file
popcut = quickcut(pop_file,
mdict,
precise=False,
extrasamp=2.,
method='nearest')
popdat = popcut.getData()
pdict = popcut.getGeoDict()
# Pad grid with nans to beyond extent of pdict
pad_dict = {}
pad_dict['padleft'] = int(
np.abs(np.ceil((mdict.xmin - pdict.xmin) / mdict.dx)))
pad_dict['padright'] = int(
np.abs(np.ceil((pdict.xmax - mdict.xmax) / mdict.dx)))
pad_dict['padbottom'] = int(
np.abs(np.ceil((mdict.ymin - pdict.ymin) / mdict.dy)))
pad_dict['padtop'] = int(
np.abs(np.ceil((pdict.ymax - mdict.ymax) / mdict.dy)))
padgrid, mdict2 = Grid2D.padGrid(moddat, mdict, pad_dict) # padds with inf
padgrid[np.isinf(padgrid)] = float('nan') # change to pad with nan
padgrid = Grid2D(data=padgrid, geodict=mdict2) # Turn into grid2d object
# Resample model grid so as to be the nearest integer multiple of popdict
factor = np.round(pdict.dx / mdict2.dx)
# Create geodictionary that is a factor of X higher res but otherwise
# identical
ndict = GeoDict.createDictFromBox(pdict.xmin, pdict.xmax, pdict.ymin,
pdict.ymax, pdict.dx / factor,
pdict.dy / factor)
# Resample
grid2 = padgrid.interpolate2(ndict, method='linear')
# Get proportion of each cell that has values (to account properly
# for any nans)
prop = block_reduce(~np.isnan(grid2.getData().copy()),
block_size=(int(factor), int(factor)),
cval=float('nan'),
func=np.sum) / (factor**2.)
# Now block reduce to same geodict as popfile
modresamp = block_reduce(grid2.getData().copy(),
block_size=(int(factor), int(factor)),
cval=float('nan'),
func=np.nanmean)
exp_pop = {}
if shakefile is not None:
# Resample shakefile to population grid
# , doPadding=True, padValue=0.)
shakemap = ShakeGrid.load(shakefile, resample=False)
shakemap = shakemap.getLayer(shakethreshtype)
shakemap = shakemap.interpolate2(pdict)
shkdat = shakemap.getData()
for shaket in shakethresh:
threshmult = shkdat > shaket
threshmult = threshmult.astype(float)
exp_pop['exp_pop_%1.2fg' % (shaket / 100., )] = np.nansum(
popdat * prop * modresamp * threshmult)
else:
exp_pop['exp_pop_0.00g'] = np.nansum(popdat * prop * modresamp)
return exp_pop