def test_iter_array(self):
values = np.random.rand(2,2,4,4)
mask = np.random.random_integers(0,1,values.shape)
values = np.ma.array(values,mask=mask)
for idx in iter_array(values):
self.assertFalse(values.mask[idx])
self.assertEqual(len(list(iter_array(values,use_mask=True))),len(values.compressed()))
self.assertEqual(len(list(iter_array(values,use_mask=False))),len(values.data.flatten()))
def clip(coll,igeom):
'''Do an intersects + intersection and set weights based on geometry
areas.
coll :: OcgCollection
igeom :: Shapely Polygon or MultiPolygon
returns
OcgCollection'''
## logic for convenience. just return the provided collection if a NoneType
## is passed for the 'igeom' arugment
if igeom is not None:
## take advange of shapely speedups
prep_igeom = prepared.prep(igeom)
## the weight array
weights = np.empty(coll.gid.shape,dtype=float)
weights = np.ma.array(weights,mask=coll.gid.mask)
## do the spatial operation
for idx,geom in iter_array(coll.geom_masked,
return_value=True):
# import ipdb;ipdb.set_trace()
if keep(prep_igeom,igeom,geom):
# import ipdb;ipdb.set_trace()
new_geom = igeom.intersection(geom)
weights[idx] = new_geom.area
coll.geom[idx] = new_geom
## set maximum weight to one
coll.weights = weights/weights.max()
return(coll)
def _iter_consecutive_(self,values,threshold,operation):
## time index reference
ref = np.arange(0,values.shape[0])
## perform requested logical operation
if operation == 'gt':
arr = values > threshold
elif operation == 'lt':
arr = values < threshold
elif operation == 'gte':
arr = values >= threshold
elif operation == 'lte':
arr = values <= threshold
## find longest sequence for each geometry across time dimension
for zidx,rowidx,colidx in iter_array(values[0,:,:,:],use_mask=False):
vec = arr[:,zidx,rowidx,colidx]
## check first if there is a longer series than 1
if np.any(np.diff(ref[vec]) == 1):
## find locations where the values switch
diff_idx = np.diff(vec)
if diff_idx.shape != ref.shape:
diff_idx = np.append(diff_idx,[False])
split_idx = ref[diff_idx] + 1
splits = np.array_split(vec,split_idx)
fill = [a.sum() for a in splits if np.all(a)]
## case of only a singular occurrence
elif np.any(vec):
fill = [1]
## case for no occurrence
else:
fill = [0]
yield(fill)
def wrap_or_unwrap(self, action, target, force=False):
from ocgis.variable.geom import GeometryVariable
from ocgis.spatial.grid import Grid
if action not in (WrapAction.WRAP, WrapAction.UNWRAP):
raise ValueError('"action" not recognized: {}'.format(action))
if target.wrapped_state != action or force:
if action == WrapAction.WRAP:
attr = 'wrap'
else:
attr = 'unwrap'
if isinstance(target, GeometryVariable):
w = GeometryWrapper()
func = getattr(w, attr)
target_value = target.get_value()
for idx, target_geom in iter_array(target_value, use_mask=True, return_value=True,
mask=target.get_mask()):
target_value.__setitem__(idx, func(target_geom))
elif isinstance(target, Grid):
ca = CoordinateArrayWrapper()
func = getattr(ca, attr)
func(target.x.get_value())
target.remove_bounds()
if target.has_allocated_point:
getattr(target.get_point(), attr)()
if target.has_allocated_polygon:
getattr(target.get_polygon(), attr)()
else:
raise NotImplementedError(target)
def write(self,path):
geoms = []
uid = self.spatial.uid
for ii,geom in iter_array(self.spatial.geom,return_value=True):
geoms.append({'geom':geom,'ugid':uid[ii]})
sc = ShpCabinet()
sc.write(geoms,path,sr=self.spatial.projection.sr)
def write_RCM3(self):
rd = self.oblique_mercator
ds = nc.Dataset(rd.uri)
path = os.path.join(tempfile.mkdtemp(prefix='RCM3'),'RCM3.shp')
crs = fiona.crs.from_epsg(4326)
driver = 'ESRI Shapefile'
schema = {'geometry':'Point',
'properties':{}}
# path = os.path.join(tempfile.mkdtemp(prefix='RCM3'),'RCM3.shp')
# polygon = Polygon(coordinates)
# feature = {'id':feature_idx,'properties':{},'geometry':mapping(polygon)}
# f.write(feature)
# with fiona.open(out_path,'w',driver=driver,crs=crs,schema=schema) as f:
try:
lats = ds.variables['lat'][:]
lons = ds.variables['lon'][:] - 360
n = lons.shape[0]*lons.shape[1]
print n
with fiona.open(path,'w',driver=driver,crs=crs,schema=schema) as f:
for ctr,(ii,jj) in enumerate(iter_array(lats,use_mask=False)):
if ctr % 100 == 0:
print ctr,n
point = Point(lons[ii,jj],lats[ii,jj])
feature = {'properties':{},'geometry':mapping(point)}
f.write(feature)
import ipdb;ipdb.set_trace()
finally:
ds.close()
def write_RCM3(self):
rd = self.oblique_mercator
ds = nc.Dataset(rd.uri)
path = os.path.join(tempfile.mkdtemp(prefix='RCM3'), 'RCM3.shp')
crs = fiona.crs.from_epsg(4326)
driver = 'ESRI Shapefile'
schema = {'geometry': 'Point', 'properties': {}}
# path = os.path.join(tempfile.mkdtemp(prefix='RCM3'),'RCM3.shp')
# polygon = Polygon(coordinates)
# feature = {'id':feature_idx,'properties':{},'geometry':mapping(polygon)}
# f.write(feature)
# with fiona.open(out_path,'w',driver=driver,crs=crs,schema=schema) as f:
try:
lats = ds.variables['lat'][:]
lons = ds.variables['lon'][:] - 360
n = lons.shape[0] * lons.shape[1]
print n
with fiona.open(path, 'w', driver=driver, crs=crs,
schema=schema) as f:
for ctr, (ii, jj) in enumerate(iter_array(lats,
use_mask=False)):
if ctr % 100 == 0:
print ctr, n
point = Point(lons[ii, jj], lats[ii, jj])
feature = {'properties': {}, 'geometry': mapping(point)}
f.write(feature)
import ipdb
ipdb.set_trace()
finally:
ds.close()
def get_datetime(self,arr):
arr = np.atleast_1d(nc.num2date(arr,self.units,calendar=self.calendar))
dt = datetime.datetime
for idx,t in iter_array(arr,return_value=True):
arr[idx] = dt(t.year,t.month,t.day,
t.hour,t.minute,t.second)
return(arr)
def area(self):
r_value = self.value
fill = np.ones(r_value.shape,dtype=constants.np_float)
fill = np.ma.array(fill,mask=r_value.mask)
for (ii,jj),geom in iter_array(r_value,return_value=True):
fill[ii,jj] = geom.area
return(fill)
def update_crs(self,to_crs):
## if the crs values are the same, pass through
if to_crs != self.crs:
to_sr = to_crs.sr
from_sr = self.crs.sr
if self.geom.point is not None:
self.geom.point.update_crs(to_sr,from_sr)
try:
self.geom.polygon.update_crs(to_sr,from_sr)
except ImproperPolygonBoundsError:
pass
if self.grid is not None and self.geom.point is not None:
r_grid_value = self.grid.value.data
r_point_value = self.geom.point.value.data
for (idx_row,idx_col),geom in iter_array(r_point_value,return_value=True,use_mask=False):
x,y = geom.x,geom.y
r_grid_value[0,idx_row,idx_col] = y
r_grid_value[1,idx_row,idx_col] = x
## remove row and columns if they exist as this requires interpolation
## to make them vectors again.
self.grid.row = None
self.grid.col = None
## if there is not point dimension, then a grid representation is not
## possible. mask the grid values accordingly.
elif self.grid is not None and self.geom.point is None:
self.grid.value.mask = True
self.crs = to_crs
def get_datetime(self,arr):
arr = np.atleast_1d(nc.num2date(arr,self.units,calendar=self.calendar))
dt = datetime.datetime
for idx,t in iter_array(arr,return_value=True):
arr[idx] = dt(t.year,t.month,t.day,
t.hour,t.minute,t.second)
return(arr)
def wrap_or_unwrap(self, action, target):
from ocgis.variable.geom import GeometryVariable
from ocgis.spatial.grid import Grid
if action not in (WrapAction.WRAP, WrapAction.UNWRAP):
raise ValueError('"action" not recognized: {}'.format(action))
if action == WrapAction.WRAP:
attr = 'wrap'
else:
attr = 'unwrap'
if isinstance(target, GeometryVariable):
w = GeometryWrapper()
func = getattr(w, attr)
target_value = target.get_value()
for idx, target_geom in iter_array(target_value, use_mask=True, return_value=True,
mask=target.get_mask()):
target_value.__setitem__(idx, func(target_geom))
elif isinstance(target, Grid):
ca = CoordinateArrayWrapper()
func = getattr(ca, attr)
func(target.x.get_value())
target.remove_bounds()
if target.has_allocated_point:
getattr(target.get_point(), attr)()
if target.has_allocated_polygon:
getattr(target.get_polygon(), attr)()
else:
raise NotImplementedError(target)
def intersects(self, polygon):
## do the initial grid subset
grid = self.grid.subset(polygon=polygon)
## a prepared polygon
prep_polygon = prepared.prep(polygon)
## the fill arrays
geom = np.ones(grid.shape, dtype=object)
geom = np.ma.array(geom, mask=True)
geom_mask = geom.mask
try:
row = grid.row.value
col = grid.column.value
for ii, jj in product(range(row.shape[0]), range(col.shape[0])):
pt = Point(col[jj], row[ii])
geom[ii, jj] = pt
if prep_polygon.intersects(pt):
geom_mask[ii, jj] = False
else:
geom_mask[ii, jj] = True
## NcGridMatrixDimension correction
except AttributeError:
_row = grid.row
_col = grid.column
for ii, jj in iter_array(_row):
pt = Point(_col[ii, jj], _row[ii, jj])
geom[ii, jj] = pt
if prep_polygon.intersects(pt):
geom_mask[ii, jj] = False
else:
geom_mask[ii, jj] = True
ret = self.__class__(grid=grid, geom=geom, uid=grid.uid)
return (ret)
def unwrap(self, spatial):
"""
:type spatial: :class:`ocgis.interface.base.dimension.spatial.SpatialDimension`
"""
if self.get_wrapped_state(spatial) == self._flag_wrapped:
# unwrap the geometries
unwrap = Wrapper().unwrap
to_wrap = self._get_to_wrap_(spatial)
for tw in to_wrap:
if tw is not None:
geom = tw.value.data
for (ii, jj), to_wrap in iter_array(geom, return_value=True, use_mask=False):
geom[ii, jj] = unwrap(to_wrap)
if spatial._grid is not None:
ref = spatial.grid.value.data[1, :, :]
select = ref < 0
ref[select] += 360
if spatial.grid.col is not None:
ref = spatial.grid.col.value
select = ref < 0
ref[select] += 360
if spatial.grid.col.bounds is not None:
ref = spatial.grid.col.bounds
select = ref < 0
ref[select] += 360
# attempt to to unwrap the grid corners if they exist
if spatial.grid.corners is not None:
select = spatial.grid.corners[1] < 0
spatial.grid.corners[1][select] += 360
else:
raise SpatialWrappingError('Data does not need to be unwrapped.')
def clip(coll, igeom):
'''Do an intersects + intersection and set weights based on geometry
areas.
coll :: OcgCollection
igeom :: Shapely Polygon or MultiPolygon
returns
OcgCollection'''
## logic for convenience. just return the provided collection if a NoneType
## is passed for the 'igeom' arugment
if igeom is not None:
## take advange of shapely speedups
prep_igeom = prepared.prep(igeom)
## the weight array
weights = np.empty(coll.gid.shape, dtype=float)
weights = np.ma.array(weights, mask=coll.gid.mask)
## do the spatial operation
for idx, geom in iter_array(coll.geom_masked, return_value=True):
# import ipdb;ipdb.set_trace()
if keep(prep_igeom, igeom, geom):
# import ipdb;ipdb.set_trace()
new_geom = igeom.intersection(geom)
weights[idx] = new_geom.area
coll.geom[idx] = new_geom
## set maximum weight to one
coll.weights = weights / weights.max()
return (coll)
def get_buffer(self, *args, **kwargs):
"""
Return a shallow copy of the geometry variable with geometries buffered.
.. note:: Accepts all parameters to :meth:`shapely.geometry.base.BaseGeometry.buffer`.
An additional keyword argument is:
:keyword str geom_type: The geometry type for the new buffered geometry if known in advance.
:rtype: :class:`~ocgis.GeometryVariable`
:raises: :class:`~ocgis.exc.EmptyObjectError`
"""
raise_if_empty(self)
# New geometry type for the buffered object.
geom_type = kwargs.pop('geom_type', 'auto')
ret = self.copy()
new_value = np.empty_like(ret.get_value(), dtype=object)
to_buffer = self.get_value()
mask = self.get_mask()
for idx, mask_value in iter_array(mask, return_value=True):
if not mask_value:
new_value[idx] = to_buffer[idx].buffer(*args, **kwargs)
else:
new_value[idx] = None
ret.set_value(new_value)
ret._geom_type = geom_type
return ret
def write(self, path):
geoms = []
uid = self.spatial.uid
for ii, geom in iter_array(self.spatial.geom, return_value=True):
geoms.append({'geom': geom, 'ugid': uid[ii]})
sc = ShpCabinet()
sc.write(geoms, path, sr=self.spatial.projection.sr)
def get_datetime(self, arr):
"""
:param arr: An array of floats to convert ``datetime``-like objects.
:type arr: :class:`numpy.ndarray`
:returns: ``object`` array of the same shape as ``arr`` with float objects converted to ``datetime`` objects.
:rtype: :class:`numpy.ndarray`
"""
# If there are month units, call the special procedure to convert those to datetime objects.
if not self._has_months_units:
arr = np.atleast_1d(nc.num2date(arr, str(self.units), calendar=self.calendar))
dt = get_datetime_or_netcdftime
for idx, t in iter_array(arr, return_value=True):
# Attempt to convert times to datetime objects.
try:
arr[idx] = dt(t.year, t.month, t.day, t.hour, t.minute, t.second)
# This may fail for some calendars, in that case maintain the instance object returned from netcdftime.
# See: http://netcdf4-python.googlecode.com/svn/trunk/docs/netcdftime.netcdftime.datetime-class.html
except ValueError:
arr[idx] = arr[idx]
else:
arr = get_datetime_from_months_time_units(arr, str(self.units),
month_centroid=constants.CALC_MONTH_CENTROID)
return arr
def calc_weights(self,npd,geom):
weight = np.ma.array(np.zeros((npd.shape[2],npd.shape[3]),dtype=float),
mask=npd.mask[0,0,:,:])
for ii,jj in iter_array(weight):
weight[ii,jj] = geom[ii,jj].area
weight = weight/weight.max()
return(weight)
def get_datetime(self, arr):
"""
:param arr: An array of floats to convert ``datetime``-like objects.
:type arr: :class:`numpy.ndarray`
:returns: ``object`` array of the same shape as ``arr`` with float objects converted to ``datetime`` objects.
:rtype: :class:`numpy.ndarray`
"""
# If there are month units, call the special procedure to convert those to datetime objects.
if not self._has_months_units:
arr = np.atleast_1d(nc.num2date(arr, str(self.units), calendar=self.calendar))
dt = get_datetime_or_netcdftime
for idx, t in iter_array(arr, return_value=True):
# Attempt to convert times to datetime objects.
try:
arr[idx] = dt(t.year, t.month, t.day, t.hour, t.minute, t.second)
# This may fail for some calendars, in that case maintain the instance object returned from netcdftime.
# See: http://netcdf4-python.googlecode.com/svn/trunk/docs/netcdftime.netcdftime.datetime-class.html
except ValueError:
arr[idx] = arr[idx]
else:
arr = get_datetime_from_months_time_units(arr, str(self.units),
month_centroid=constants.CALC_MONTH_CENTROID)
return arr
def _iter_consecutive_(self, values, threshold, operation):
## time index reference
ref = np.arange(0, values.shape[0])
## perform requested logical operation
if operation == 'gt':
arr = values > threshold
elif operation == 'lt':
arr = values < threshold
elif operation == 'gte':
arr = values >= threshold
elif operation == 'lte':
arr = values <= threshold
## find longest sequence for each geometry across time dimension
for zidx, rowidx, colidx in iter_array(values[0, :, :, :],
use_mask=False):
vec = arr[:, zidx, rowidx, colidx]
## check first if there is a longer series than 1
if np.any(np.diff(ref[vec]) == 1):
## find locations where the values switch
diff_idx = np.diff(vec)
if diff_idx.shape != ref.shape:
diff_idx = np.append(diff_idx, [False])
split_idx = ref[diff_idx] + 1
splits = np.array_split(vec, split_idx)
fill = [a.sum() for a in splits if np.all(a)]
## case of only a singular occurrence
elif np.any(vec):
fill = [1]
## case for no occurrence
else:
fill = [0]
yield (fill)
def intersects(self,polygon):
## do the initial grid subset
grid = self.grid.subset(polygon=polygon)
## a prepared polygon
prep_polygon = prepared.prep(polygon)
## the fill arrays
geom = np.ones(grid.shape,dtype=object)
geom = np.ma.array(geom,mask=True)
geom_mask = geom.mask
try:
row = grid.row.value
col = grid.column.value
for ii,jj in product(range(row.shape[0]),range(col.shape[0])):
pt = Point(col[jj],row[ii])
geom[ii,jj] = pt
if prep_polygon.intersects(pt):
geom_mask[ii,jj] = False
else:
geom_mask[ii,jj] = True
## NcGridMatrixDimension correction
except AttributeError:
_row = grid.row
_col = grid.column
for ii,jj in iter_array(_row):
pt = Point(_col[ii,jj],_row[ii,jj])
geom[ii,jj] = pt
if prep_polygon.intersects(pt):
geom_mask[ii,jj] = False
else:
geom_mask[ii,jj] = True
ret = self.__class__(grid=grid,geom=geom,uid=grid.uid)
return(ret)
def _calculate_(self,values,percentile=None,operation=None):
## first map the dates to dynamic percentiles index days
from ocgis import env
day_idx = self._get_day_index_(self.dataset.temporal.value[self._curr_group])
dy_day_idx = map(self._get_dynamic_index_,day_idx.flat)
gp = self._get_geometries_with_percentiles_(env.ops.dataset[0].variable,env.ops.geom.key,env.DIR_BIN,percentile)
## get threshold for each geometry
## special case for north carolina counties
if env.ops.geom.key == 'us_counties':
select_ugid = 39
else:
select_ugid = self.dataset.spatial._ugid
ugid_ref = gp[select_ugid]
compare = np.empty_like(values,dtype=float)
for ii,jj,kk,ll in iter_array(values):
## get the geometry id
gid = self.dataset.spatial.vector.uid[kk,ll]
gid_ref = ugid_ref[gid]
percentile_static = gid_ref[dy_day_idx[ii]]
compare[ii,jj,kk,ll] = percentile_static
## perform requested logical operation
if operation == 'gt':
idx = values > compare
elif operation == 'lt':
idx = values < compare
elif operation == 'gte':
idx = values >= compare
elif operation == 'lte':
idx = values <= compare
else:
raise(NotImplementedError('The operation "{0}" was not recognized.'.format(operation)))
ret = np.ma.sum(idx,axis=0)
return(ret)
def test_geom_polygon_bounds(self):
sdim = self.get_sdim(bounds=True)
poly = sdim.geom.polygon.value
fill = np.ma.array(np.zeros((2,3,4)),mask=False)
for idx_row,idx_col in iter_array(poly):
fill[0,idx_row,idx_col] = poly[idx_row,idx_col].centroid.y
fill[1,idx_row,idx_col] = poly[idx_row,idx_col].centroid.x
self.assertNumpyAll(fill,sdim.grid.value)
def get_iter(self):
geoms = self.vector.geom
name_id = self._name_id
uid = self.vector.uid
ret = {}
for ii,jj in iter_array(geoms):
ret[name_id] = uid[ii,jj]
yield(((ii,jj),geoms[ii,jj],ret))
def _get_all_geoms_(self):
geom = np.empty(self.col_pt.shape,dtype=object)
for ii,jj in iter_array(self.col_pt,use_mask=False):
geom[ii,jj] = Point(self.col_pt[ii,jj],self.row_pt[ii,jj])
row = self.real_row.reshape(-1)
col = self.real_col.reshape(-1)
return(geom,row,col)
def calculate(self, values, v=None, mode='same'):
"""
:param values: Array containing variable values.
:type values: :class:`numpy.ma.core.MaskedArray`
:param v: The one-dimensional array to convolve with ``values``.
:type v: :class:`numpy.core.multiarray.ndarray`
:param str mode: The convolution mode. See: http://docs.scipy.org/doc/numpy/reference/generated/numpy.convolve.html.
The output mode ``full`` is not supported.
:rtype: :class:`numpy.ma.core.MaskedArray`
:raises: AssertionError
"""
# 'full' is not supported as this would add dates to the temporal dimension
assert (mode in ('same', 'valid'))
assert (len(values.shape) == 5)
# just to be safe, convert the second array to the same input data types as the values
v = v.astype(values.dtype)
# valid will have less values than the input as this checks if the two convolved arrays completely overlap
shape_fill = list(values.shape)
# if mode == 'valid':
# shape_fill[1] = max(values.shape[1], v.shape[0]) - min(values.shape[1], v.shape[0]) + 1
fill = np.zeros(shape_fill, dtype=self.dtype)
# perform the convolution on the time axis
itr = iter_array(values)
for ie, it, il, ir, ic in itr:
a = values[ie, :, il, ir, ic]
res_convolve = np.convolve(a, v, mode=mode)
if mode == 'valid':
time_slice = slice(
0,
max(values.shape[1], v.shape[0]) -
min(values.shape[1], v.shape[0]) + 1)
# fill[ie, :, il, ir, ic] = res_convolve
else:
time_slice = slice(None)
fill[ie, time_slice, il, ir, ic] = res_convolve
if mode == 'valid':
# generate the mask for the output data and convert the output to a masked array
mask = np.empty(fill.shape, dtype=bool)
mask[...] = values.mask[0, 0, 0, :, :]
fill = np.ma.array(fill, mask=mask)
# identify where the two arrays completely overlap and collect the indices to subset the field object
# attached to the calculation object
overlap_mask = np.ones(mask.shape, dtype=bool)
overlap_mask[:, slice(0, 0 - (v.shape[0] - 1)), :, :, :] = False
fill.mask[:] = np.logical_or(fill.mask, overlap_mask)
# self.field = self.field[:, slice(0, 0-(v.shape[0]-1)), :, :, :]
else:
# same does not modify the output array size
fill = np.ma.array(fill, mask=values.mask)
return fill
def get_approx_res_days(self):
diffs = np.array([],dtype=float)
for tidx,tval in iter_array(self.value,return_value=True):
try:
diffs = np.append(diffs,
np.abs((tval-self.value[tidx[0]+1]).days))
except IndexError:
break
return(diffs.mean())
def get_iter(self):
geoms = self.vector.geom
name_id = self._name_id
uid = self.vector.uid
ret = {}
for ii, jj in iter_array(geoms):
ret[name_id] = uid[ii, jj]
yield (((ii, jj), geoms[ii, jj], ret))
def iter_spatial_dimension(self,dim):
geoms = dim.vector.geom
name_id = dim._name_id
uid = dim.vector.uid
ret = {}
for (ii,jj),geom in iter_array(geoms,return_value=True):
ret[name_id] = uid[ii,jj]
yield(((ii,jj),geom,ret))
def iter_spatial_dimension(self, dim):
geoms = dim.vector.geom
name_id = dim._name_id
uid = dim.vector.uid
ret = {}
for (ii, jj), geom in iter_array(geoms, return_value=True):
ret[name_id] = uid[ii, jj]
yield (((ii, jj), geom, ret))
def __iter__(self):
_name_uid = self._name_uid
_name_value = self._name_value
uid = self.uid
_conv_to_multi_ = self._conv_to_multi_
for idx,geom in iter_array(self.value,return_value=True):
row = {_name_uid:uid[idx],
_name_value:_conv_to_multi_(geom)}
yield(idx,row)
def weights(self):
if self._weights is None:
geom = self.geom
weights = np.ones(geom.shape,dtype=float)
weights = np.ma.array(weights,mask=geom.mask)
for ii,jj in iter_array(geom):
weights[ii,jj] = geom[ii,jj].area
weights = weights/weights.max()
self._weights = weights
return(self._weights)
def resolution(self):
diffs = np.array([], dtype=float)
value = self.value
for tidx, tval in iter_array(value, return_value=True):
try:
diffs = np.append(diffs,
np.abs((tval - value[tidx[0] + 1]).days))
except IndexError:
break
return (diffs.mean())
def resolution(self):
diffs = np.array([],dtype=float)
value = self.value
for tidx,tval in iter_array(value,return_value=True):
try:
diffs = np.append(diffs,
np.abs((tval-value[tidx[0]+1]).days))
except IndexError:
break
return(diffs.mean())
def weights(self):
if self._weights is None:
geom = self.geom
weights = np.ones(geom.shape, dtype=float)
weights = np.ma.array(weights, mask=geom.mask)
for ii, jj in iter_array(geom):
weights[ii, jj] = geom[ii, jj].area
weights = weights / weights.max()
self._weights = weights
return (self._weights)
def test_geom_point(self):
sdim = self.get_sdim(bounds=True)
with self.assertRaises(AttributeError):
sdim.geom.value
pt = sdim.geom.point.value
fill = np.ma.array(np.zeros((2,3,4)),mask=False)
for idx_row,idx_col in iter_array(pt):
fill[0,idx_row,idx_col] = pt[idx_row,idx_col].y
fill[1,idx_row,idx_col] = pt[idx_row,idx_col].x
self.assertNumpyAll(fill,sdim.grid.value)
def write(self, path):
geoms = []
uid = self.spatial.uid
attrs = self.spatial.attrs
for ii, geom in iter_array(self.spatial.geom, return_value=True):
dct = {'geom': geom, 'UGID': uid[ii]}
for k, v in attrs.iteritems():
dct[k] = v[ii]
geoms.append(dct)
sc = ShpCabinet()
sc.write(geoms, path, sr=self.spatial.projection.sr)
def calculate(self, values, v=None, mode='same'):
"""
:param values: Array containing variable values.
:type values: :class:`numpy.ma.core.MaskedArray`
:param v: The one-dimensional array to convolve with ``values``.
:type v: :class:`numpy.core.multiarray.ndarray`
:param str mode: The convolution mode. See: http://docs.scipy.org/doc/numpy/reference/generated/numpy.convolve.html.
The output mode ``full`` is not supported.
:rtype: :class:`numpy.ma.core.MaskedArray`
:raises: AssertionError
"""
# 'full' is not supported as this would add dates to the temporal dimension
assert (mode in ('same', 'valid'))
assert (len(values.shape) == 5)
# just to be safe, convert the second array to the same input data types as the values
v = v.astype(values.dtype)
# valid will have less values than the input as this checks if the two convolved arrays completely overlap
shape_fill = list(values.shape)
# if mode == 'valid':
# shape_fill[1] = max(values.shape[1], v.shape[0]) - min(values.shape[1], v.shape[0]) + 1
fill = np.zeros(shape_fill, dtype=self.dtype)
# perform the convolution on the time axis
itr = iter_array(values)
for ie, it, il, ir, ic in itr:
a = values[ie, :, il, ir, ic]
res_convolve = np.convolve(a, v, mode=mode)
if mode == 'valid':
time_slice = slice(0, max(values.shape[1], v.shape[0]) - min(values.shape[1], v.shape[0]) + 1)
# fill[ie, :, il, ir, ic] = res_convolve
else:
time_slice = slice(None)
fill[ie, time_slice, il, ir, ic] = res_convolve
if mode == 'valid':
# generate the mask for the output data and convert the output to a masked array
mask = np.empty(fill.shape, dtype=bool)
mask[...] = values.mask[0, 0, 0, :, :]
fill = np.ma.array(fill, mask=mask)
# identify where the two arrays completely overlap and collect the indices to subset the field object
# attached to the calculation object
overlap_mask = np.ones(mask.shape, dtype=bool)
overlap_mask[:, slice(0, 0 - (v.shape[0] - 1)), :, :, :] = False
fill.mask[:] = np.logical_or(fill.mask, overlap_mask)
# self.field = self.field[:, slice(0, 0-(v.shape[0]-1)), :, :, :]
else:
# same does not modify the output array size
fill = np.ma.array(fill, mask=values.mask)
return fill
def write(self,path):
geoms = []
uid = self.spatial.uid
attrs = self.spatial.attrs
for ii,geom in iter_array(self.spatial.geom,return_value=True):
dct = {'geom':geom,'UGID':uid[ii]}
for k,v in attrs.iteritems():
dct[k] = v[ii]
geoms.append(dct)
sc = ShpCabinet()
sc.write(geoms,path,sr=self.spatial.projection.sr)
def wrap_var(var):
right_clip = make_poly((-90,90),(180,360))
left_clip = make_poly((-90,90),(-180,180))
def _shift_(geom):
try:
coords = np.array(geom.exterior.coords)
coords[:,0] = coords[:,0] - 360
ret = Polygon(coords)
except AttributeError:
polygons = np.empty(len(geom),dtype=object)
for ii,polygon in enumerate(geom):
coords = np.array(polygon.exterior.coords)
coords[:,0] = coords[:,0] - 360
polygons[ii] = Polygon(coords)
ret = MultiPolygon(polygons)
return(ret)
geoms = var.spatial._value
if not isinstance(geoms[0,0],Point):
for idx,geom in iter_array(geoms,return_value=True):
bounds = np.array(geom.bounds)
if np.all([bounds[0] > 180,bounds[2] > 180]):
geoms[idx] = _shift_(geom)
elif bounds[1] <= 180 and bounds[2] > 180:
left = [poly for poly in _get_iter_(geom.intersection(left_clip))]
right = [poly for poly in _get_iter_(_shift_(geom.intersection(right_clip)))]
try:
geoms[idx] = MultiPolygon(left+right)
except TypeError:
left = filter(lambda x: type(x) != LineString,left)
right = filter(lambda x: type(x) != LineString,right)
geoms[idx] = MultiPolygon(left+right)
else:
continue
else:
for idx,geom in iter_array(geoms,return_value=True):
if geom.x > 180:
geoms[idx] = Point(geom.x-360,geom.y)
def grid(self):
if self._grid is None and self._geom_to_grid:
## populate the grid using the point geometry representation
ref_pv = self.geom.point.value
shp = (2,ref_pv.shape[0],ref_pv.shape[1])
fill = np.empty(shp,dtype=constants.np_float)
for (idx_row,idx_col),geom in iter_array(ref_pv.data,return_value=True):
fill[:,idx_row,idx_col] = geom.y,geom.x
mask = np.empty_like(fill,dtype=bool)
mask[:,:,:] = ref_pv.mask
self._grid = SpatialGridDimension(value=np.ma.array(fill,mask=mask),
uid=self.geom.point.uid)
return(self._grid)
def _get_weights_(self):
value = self._value
value_mask = self._value_mask
if isinstance(value[0,0],Point) or env.OPTIMIZE_FOR_CALC:
weights = np.ones(value.shape,dtype=float)
weights_ma = np.ma.array(weights,mask=value_mask)
else:
weights = np.empty(value.shape,dtype=float)
for idx,geom in iter_array(value,return_value=True):
weights[idx] = geom.area
weights_ma = np.ma.array(weights/weights.max(),mask=value_mask)
return(weights_ma)
def _get_value_(self):
## we are interested in creating geometries for all the underly coordinates
## regardless if the data is masked
ref_grid = self.grid.value.data
fill = self._get_geometry_fill_()
r_data = fill.data
for idx_row,idx_col in iter_array(ref_grid[0],use_mask=False):
y = ref_grid[0,idx_row,idx_col]
x = ref_grid[1,idx_row,idx_col]
pt = Point(x,y)
r_data[idx_row,idx_col] = pt
return(fill)
def assertGridCorners(self, grid):
"""
:type grid: :class:`ocgis.new_interface.grid.Grid`
"""
assert grid.corners is not None
def _get_is_ascending_(arr):
"""
Return ``True`` if the array is ascending from index 0 to -1.
:type arr: :class:`numpy.ndarray`
:rtype: bool
"""
assert arr.ndim == 1
if arr[0] < arr[-1]:
ret = True
else:
ret = False
return ret
# Assert polygon constructed from grid corners contains the associated centroid value.
for ii, jj in itertools.product(list(range(grid.shape[0])),
list(range(grid.shape[1]))):
pt = Point(grid.get_value().data[1, ii, jj],
grid.get_value().data[0, ii, jj])
poly_corners = grid.corners.data[:, ii, jj]
rtup = (poly_corners[0, :].min(), poly_corners[0, :].max())
ctup = (poly_corners[1, :].min(), poly_corners[1, :].max())
poly = make_poly(rtup, ctup)
self.assertTrue(poly.contains(pt))
# Assert masks are equivalent between value and corners.
for (ii, jj), m in iter_array(grid.get_value().mask[0, :, :],
return_value=True):
if m:
self.assertTrue(grid.corners.mask[:, ii, jj].all())
else:
self.assertFalse(grid.corners.mask[:, ii, jj].any())
grid_y = grid._y
grid_x = grid._x
if grid_y is not None or grid_x is not None:
self.assertEqual(
_get_is_ascending_(grid_y.get_value()),
_get_is_ascending_(grid.corners.data[0, :, 0][:, 0]))
self.assertEqual(
_get_is_ascending_(grid_x.get_value()),
_get_is_ascending_(grid.corners.data[1, 0, :][:, 0]))
def _get_all_geoms_(self):
geom = np.empty(self.shape,dtype=object)
min_col,max_col,min_row,max_row = self.min_col,self.max_col,self.min_row,self.max_row
for ii,jj in iter_array(geom,use_mask=False):
geom[ii,jj] = Polygon(((min_col[ii,jj],min_row[ii,jj]),
(max_col[ii,jj],min_row[ii,jj]),
(max_col[ii,jj],max_row[ii,jj]),
(min_col[ii,jj],max_row[ii,jj])))
row = self.real_row.reshape(-1)
col = self.real_col.reshape(-1)
return(geom,row,col)
def update_crs(self,to_sr,from_sr):
## we are modifying the original source data and need to copy the new
## values.
new_value = self.value.copy()
## be sure and project masked geometries to maintain underlying geometries
## for masked values.
r_value = new_value.data
r_loads = wkb.loads
for (idx_row,idx_col),geom in iter_array(r_value,return_value=True,use_mask=False):
ogr_geom = CreateGeometryFromWkb(geom.wkb)
ogr_geom.AssignSpatialReference(from_sr)
ogr_geom.TransformTo(to_sr)
r_value[idx_row,idx_col] = r_loads(ogr_geom.ExportToWkb())
self._value = new_value
def _iter_value_(self, var):
## TODO: optimize
if len(var.calc_value) > 0:
for k, v in var.calc_value.iteritems():
for gidx0, gidx1 in iter_array(var.spatial.value):
for tidx, lidx in itertools.product(
range(v.shape[0]), range(v.shape[1])):
value = v[tidx, lidx, gidx0, gidx1]
tgid = var.temporal_group.uid[tidx]
yield (tidx, lidx, gidx0, gidx1, value, k, tgid)
# for (tidx,lidx,gidx0,gidx1),value in iter_array(v,return_value=True):
# to_get = np.empty((1,var.temporal_group.value.shape[1]+2),dtype=object)
# to_get[:,0:-2] = var.temporal_group.value[tidx,:]
# to_get[:,-2:] = var.temporal_group.bounds[tidx,:]
# tgid = self.tgid.get(to_get)
# yield(tidx,lidx,gidx0,gidx1,value,k,tgid)
elif type(var) == OcgMultivariateCalculationVariable:
for gidx0, gidx1 in iter_array(var.spatial.value):
for tidx, lidx in itertools.product(range(var.value.shape[0]),
range(var.value.shape[1])):
value = var.value[tidx, lidx, gidx0, gidx1]
if var.temporal_group is None:
tgid = None
else:
tgid = var.temporal_group.uid[tidx]
yield (tidx, lidx, gidx0, gidx1, value, var.name, tgid)
elif self.mode == 'raw':
for gidx0, gidx1 in iter_array(var.spatial.value):
for tidx, lidx in itertools.product(range(var.value.shape[0]),
range(var.value.shape[1])):
value = var.value[tidx, lidx, gidx0, gidx1]
yield (tidx, lidx, gidx0, gidx1, value, None, None)
else:
if self.mode == 'calc' and type(var) == OcgVariable:
pass
else:
raise (NotImplementedError)
def _select_(self,polygon):
geom = np.empty(self.shape,dtype=object)
row = np.array([],dtype=int)
col = np.array([],dtype=int)
# append = append
prep_polygon = prepared.prep(polygon)
for ii,jj in iter_array(self.col_pt,use_mask=False):
pt = Point(self.col_pt[ii,jj],self.row_pt[ii,jj])
geom[ii,jj] = pt
if prep_polygon.intersects(pt):
append(row,self.real_row[ii,jj])
append(col,self.real_col[ii,jj])
return(geom,row,col)
def _select_(self,polygon):
# prep_polygon = prepared.prep(polygon)
emin_col,emin_row,emax_col,emax_row = polygon.envelope.bounds
smin_col = contains(self.min_col,
emin_col,emax_col,
self.resolution)
smax_col = contains(self.max_col,
emin_col,emax_col,
self.resolution)
smin_row = contains(self.min_row,
emin_row,emax_row,
self.resolution)
smax_row = contains(self.max_row,
emin_row,emax_row,
self.resolution)
include = np.any((smin_col,smax_col),axis=0)*\
np.any((smin_row,smax_row),axis=0)
from ocgis.util.spatial import index as si
grid = si.build_index_grid(30.0,polygon)
index = si.build_index(polygon,grid)
index_intersects = si.index_intersects
## construct the reference matrices
geom = np.empty(self.shape,dtype=object)
row = np.array([],dtype=int)
col = np.array([],dtype=int)
real_row = self.real_row
real_col = self.real_col
min_row = self.min_row
min_col = self.min_col
max_row = self.max_row
max_col = self.max_col
# append = append
for ii,jj in iter_array(include,use_mask=False):
if include[ii,jj]:
test_geom = Polygon(((min_col[ii,jj],min_row[ii,jj]),
(max_col[ii,jj],min_row[ii,jj]),
(max_col[ii,jj],max_row[ii,jj]),
(min_col[ii,jj],max_row[ii,jj])))
geom[ii,jj] = test_geom
if index_intersects(test_geom,index):
append(row,real_row[ii,jj])
append(col,real_col[ii,jj])
return(geom,row,col)
def get_intersection(self, *args, **kwargs):
"""
.. note:: Accepts all parameters to :meth:`~ocgis.new_interface.geom.GeometryVariable.get_intersects`. Same
return types.
Additional arguments and/or keyword arguments are:
:keyword bool inplace: (``=False``) If ``False`` (the default), deep copy the geometry array on the output
before executing an intersection. If ``True``, modify the geometries in-place.
:keyword bool intersects_check: (``=True``) If ``True`` (the default), first perform an intersects operation to
limit the geometries tests for intersection. If ``False``, perform the intersection as is.
"""
inplace = kwargs.pop(KeywordArgument.INPLACE, False)
intersects_check = kwargs.pop(KeywordArgument.INTERSECTS_CHECK, True)
return_slice = kwargs.get(KeywordArgument.RETURN_SLICE, False)
subset_geometry = args[0]
if intersects_check:
ret = self.get_intersects(*args, **kwargs)
else:
if inplace:
ret = self
else:
ret = self.copy()
if intersects_check:
# If indices are being returned, this will be a tuple.
if return_slice:
obj = ret[0]
else:
obj = ret
else:
if return_slice:
global_slice = [(slice(d.bounds_global[0], d.bounds_global[1])
for d in self.dimensions)]
ret = (ret, global_slice)
obj = ret
else:
obj = ret
if not obj.is_empty:
if not inplace:
obj.set_value(deepcopy(obj.get_value()))
obj_value = obj.get_masked_value()
for idx, geom in iter_array(obj_value, return_value=True):
obj_value.data[idx] = geom.intersection(subset_geometry)
return ret
def clip(self, polygon):
## perform an intersects operation first
vd = self.intersects(polygon)
## prepare the geometry for intersection
prep_igeom = prepared.prep(polygon)
## loop for the intersection
geom = vd._geom
for ii, jj in iter_array(geom):
ref = geom[ii, jj]
if not prep_igeom.contains(ref):
new_geom = polygon.intersection(ref)
geom[ii, jj] = new_geom
ret = self.__class__(grid=vd.grid, geom=geom, uid=vd.uid)
return (ret)
def _get_all_geoms_(self):
## the fill arrays
geom = np.ones(self.grid.shape, dtype=object)
geom = np.ma.array(geom, mask=False)
## loop performing the spatial operation
try:
row = self.grid.row.value
col = self.grid.column.value
for ii, jj in product(range(row.shape[0]), range(col.shape[0])):
geom[ii, jj] = Point(col[jj], row[ii])
## NcGridMatrixDimension correction
except AttributeError:
_row = self.grid.row
_col = self.grid.column
for ii, jj in iter_array(_row):
geom[ii, jj] = Point(_col[ii, jj], _row[ii, jj])
return (geom)
def clip(self,igeom):
## logic for convenience. just return the provided collection if a NoneType
## is passed for the 'igeom' arugment
if igeom is not None:
## take advange of shapely speedups
prep_igeom = prepared.prep(igeom)
## the weight array
weights = np.zeros(self.spatial.shape,dtype=float)
weights = np.ma.array(weights,mask=self.spatial._value_mask)
## do the spatial operation
for idx,geom in iter_array(self.spatial.value,return_value=True):
if not prep_igeom.contains(geom):
# if keep(prep_igeom,igeom,geom):
new_geom = igeom.intersection(geom)
weights[idx] = new_geom.area
self.spatial._value[idx] = new_geom
## set maximum weight to one
self.spatial.weights = weights/np.ma.max(weights)
def area(self):
"""
:return: geometry areas as a float masked array
:rtype: :class:`numpy.ma.MaskedArray`
"""
if self.is_empty:
fill = None
else:
r_value = self.get_masked_value()
fill = np.ones(r_value.shape, dtype=env.NP_FLOAT)
mask = self.get_mask()
if mask is not None:
mask = mask.copy()
fill = np.ma.array(fill, mask=mask)
for slc, geom in iter_array(r_value, return_value=True):
fill.data[slc] = geom.area
return fill