def get_grouping(self, grouping):
"""
Create a temporally grouped variable using string group sequences.
:param grouping: The temporal grouping to use when creating the temporal group dimension.
>>> grouping = ['month']
:type grouping: `sequence` of :class:`str`
:rtype: :class:`~ocgis.variable.temporal.TemporalGroupVariable`
"""
# There is no need to go through the process of breaking out datetime parts when the grouping is 'all'.
if grouping == 'all':
new_bounds, date_parts, repr_dt, dgroups = self._get_grouping_all_()
# The process for getting "unique" seasons is also specialized.
elif 'unique' in grouping:
new_bounds, date_parts, repr_dt, dgroups = self._get_grouping_seasonal_unique_(grouping)
# For standard groups ("['month']") or seasons across entire time range.
else:
new_bounds, date_parts, repr_dt, dgroups = self._get_grouping_other_(grouping)
new_name = 'climatology_bounds'
time_dimension_name = self.dimensions[0].name
if self.has_bounds:
new_dimensions = [d.name for d in self.bounds.dimensions]
else:
new_dimensions = [time_dimension_name, 'bounds']
# Create the new time dimension as unlimited if the original time variable also has an unlimited dimension.
if self.dimensions[0].is_unlimited:
new_time_dimension = Dimension(name=time_dimension_name, size_current=len(repr_dt))
else:
new_time_dimension = time_dimension_name
new_dimensions[0] = new_time_dimension
new_bounds = TemporalVariable(value=new_bounds, name=new_name, dimensions=new_dimensions)
new_attrs = deepcopy(self.attrs)
# new_attrs['climatology'] = new_bounds.name
tgv = TemporalGroupVariable(grouping=grouping, date_parts=date_parts, bounds=new_bounds, dgroups=dgroups,
value=repr_dt, units=self.units, calendar=self.calendar, name=self.name,
attrs=new_attrs, dimensions=new_dimensions[0])
tgv.attrs.pop(TemporalVariable._bounds_attribute_name, None)
return tgv
def fixture_driver_scrip_netcdf_field(self):
xvalue = np.arange(10., 35., step=5)
yvalue = np.arange(45., 85., step=10)
grid_size = xvalue.shape[0] * yvalue.shape[0]
dim_grid_size = Dimension(name='grid_size', size=grid_size)
x = Variable(name='grid_center_lon', dimensions=dim_grid_size)
y = Variable(name='grid_center_lat', dimensions=dim_grid_size)
for idx, (xv, yv) in enumerate(itertools.product(xvalue, yvalue)):
x.get_value()[idx] = xv
y.get_value()[idx] = yv
gc = PointGC(x=x, y=y, crs=Spherical(), driver=DriverNetcdfSCRIP)
grid = GridUnstruct(geoms=[gc])
ret = Field(grid=grid, driver=DriverNetcdfSCRIP)
grid_dims = Variable(name='grid_dims',
value=[yvalue.shape[0], xvalue.shape[0]],
dimensions='grid_rank')
ret.add_variable(grid_dims)
return ret
def write_subsets(self, src_template, dst_template, wgt_template, index_path):
"""
Write grid subsets to netCDF files using the provided filename templates. The template must contain the full
file path with a single curly-bracer pair to insert the combination counter. ``wgt_template`` should not be a
full path. This name is used when generating weight files.
>>> template_example = '/path/to/data_{}.nc'
:param str src_template: The template for the source subset file.
:param str dst_template: The template for the destination subset file.
:param str wgt_template: The template for the weight filename.
>>> wgt_template = 'esmf_weights_{}.nc'
:param index_path: Path to the output indexing netCDF.
"""
src_filenames = []
dst_filenames = []
wgt_filenames = []
dst_slices = []
# nzeros = len(str(reduce(lambda x, y: x * y, self.nsplits_dst)))
for ctr, (sub_src, sub_dst, dst_slc) in enumerate(self.iter_src_grid_subsets(yield_dst=True), start=1):
# padded = create_zero_padded_integer(ctr, nzeros)
src_path = src_template.format(ctr)
dst_path = dst_template.format(ctr)
wgt_filename = wgt_template.format(ctr)
src_filenames.append(os.path.split(src_path)[1])
dst_filenames.append(os.path.split(dst_path)[1])
wgt_filenames.append(wgt_filename)
dst_slices.append(dst_slc)
for target, path in zip([sub_src, sub_dst], [src_path, dst_path]):
if target.is_empty:
is_empty = True
target = None
else:
is_empty = False
field = Field(grid=target, is_empty=is_empty)
ocgis_lh(msg='writing: {}'.format(path), level=logging.DEBUG)
with vm.scoped_by_emptyable('field.write', field):
if not vm.is_null:
field.write(path)
ocgis_lh(msg='finished writing: {}'.format(path), level=logging.DEBUG)
with vm.scoped('index write', [0]):
if not vm.is_null:
dim = Dimension('nfiles', len(src_filenames))
vname = ['source_filename', 'destination_filename', 'weights_filename']
values = [src_filenames, dst_filenames, wgt_filenames]
grid_splitter_destination = GridSplitterConstants.IndexFile.NAME_DESTINATION_VARIABLE
attrs = [{'esmf_role': 'grid_splitter_source'},
{'esmf_role': grid_splitter_destination},
{'esmf_role': 'grid_splitter_weights'}]
vc = VariableCollection()
grid_splitter_index = GridSplitterConstants.IndexFile.NAME_INDEX_VARIABLE
vidx = Variable(name=grid_splitter_index)
vidx.attrs['esmf_role'] = grid_splitter_index
vidx.attrs['grid_splitter_source'] = 'source_filename'
vidx.attrs[GridSplitterConstants.IndexFile.NAME_DESTINATION_VARIABLE] = 'destination_filename'
vidx.attrs['grid_splitter_weights'] = 'weights_filename'
x_bounds = GridSplitterConstants.IndexFile.NAME_X_BOUNDS_VARIABLE
vidx.attrs[x_bounds] = x_bounds
y_bounds = GridSplitterConstants.IndexFile.NAME_Y_BOUNDS_VARIABLE
vidx.attrs[y_bounds] = y_bounds
vc.add_variable(vidx)
for idx in range(len(vname)):
v = Variable(name=vname[idx], dimensions=dim, dtype=str, value=values[idx], attrs=attrs[idx])
vc.add_variable(v)
bounds_dimension = Dimension(name='bounds', size=2)
xb = Variable(name=x_bounds, dimensions=[dim, bounds_dimension], attrs={'esmf_role': 'x_split_bounds'},
dtype=int)
yb = Variable(name=y_bounds, dimensions=[dim, bounds_dimension], attrs={'esmf_role': 'y_split_bounds'},
dtype=int)
x_name = self.dst_grid.x.dimensions[0].name
y_name = self.dst_grid.y.dimensions[0].name
for idx, slc in enumerate(dst_slices):
xb.get_value()[idx, :] = slc[x_name].start, slc[x_name].stop
yb.get_value()[idx, :] = slc[y_name].start, slc[y_name].stop
vc.add_variable(xb)
vc.add_variable(yb)
vc.write(index_path)
vm.barrier()
def regrid_field(source,
destination,
regrid_method='auto',
value_mask=None,
split=True,
fill_value=None,
weights_in=None,
weights_out=None):
"""
Regrid ``source`` data to match the grid of ``destination``.
:param source: The source field.
:type source: :class:`ocgis.Field`
:param destination: The destination field.
:type destination: :class:`ocgis.Field`
:param regrid_method: See :func:`~ocgis.regrid.base.create_esmf_grid`.
:param value_mask: See :func:`~ocgis.regrid.base.iter_esmf_fields`.
:type value_mask: :class:`numpy.ndarray`
:param bool split: See :func:`~ocgis.regrid.base.iter_esmf_fields`.
:param fill_value: Destination fill value used to fill the destination field before regridding. If ``None``, then
the default fill value for the destination field data type will be used.
:type fill_value: int | float
:rtype: :class:`ocgis.Field`
:param weights_in: Optional path to an input weights file. The route handle will be created from weights in this
file. Assumes a SCRIP-like structure for the input weight file.
:type weights_in: str
:param weights_out: Optional path to an output weight file. Does NOT do any regridding - just writes the weights.
:type weights_out: str
"""
# This function runs a series of asserts to make sure the sources and destination are compatible.
check_fields_for_regridding(source,
destination,
regrid_method=regrid_method)
dst_grid = destination.grid # Reference the destination grid
# Spatial coordinate dimensions for the destination grid
dst_spatial_coordinate_dimensions = OrderedDict([
(dim.name, dim) for dim in dst_grid.dimensions
])
# Spatial coordinate dimensions for the source grid
src_spatial_coordinate_dimensions = OrderedDict([
(dim.name, dim) for dim in source.grid.dimensions
])
try:
archetype = source.data_variables[
0] # Reference an archetype data variable.
except IndexError:
# There may be no data variables. Use the grid as reference instead.
archetype = source.grid
# Extra dimensions (like time or level) to iterate over or use for ndbounds depending on the split protocol
extra_dimensions = OrderedDict([
(dim.name, dim) for dim in archetype.dimensions
if dim.name not in dst_spatial_coordinate_dimensions
and dim.name not in src_spatial_coordinate_dimensions
])
# If there are no extra dimensions, then there is no need to split fields.
if len(extra_dimensions) == 0:
split = False
if split:
# There are no extra, ungridded dimensions for ESMF to use.
ndbounds = None
else:
# These are the extra, ungridded dimensions for ESMF to use (ndbounds).
ndbounds = [len(dim) for dim in extra_dimensions.values()]
ndbounds.reverse() # Fortran order is used by ESMF
# Regrid each source.
ocgis_lh(logger='iter_regridded_fields',
msg='starting source regrid loop',
level=logging.DEBUG)
build = True # Flag for first loop
fills = {} # Holds destination field fill variables.
# TODO: OPTIMIZE: The source and destination field objects should be reused and refilled when split=False
# Main field iterator for use in the regridding loop
for variable_name, src_efield, current_slice in iter_esmf_fields(
source,
regrid_method=regrid_method,
value_mask=value_mask,
split=split):
# We need to generate new variables given the change in shape
if variable_name not in fills:
# Create the destination data variable dimensions. These are a combination of the extra dimensions and
# spatial coordinate dimensions.
if len(extra_dimensions) > 0:
new_dimensions = list(extra_dimensions.values())
else:
new_dimensions = []
new_dimensions += list(dst_grid.dimensions)
# Reverse the dimensions for the creation as we are working in Fortran ordering with ESMF.
new_dimensions.reverse()
# Create the destination fill variable and cache it
source_variable = source[variable_name]
new_variable = Variable(name=variable_name,
dimensions=new_dimensions,
dtype=source_variable.dtype,
fill_value=source_variable.fill_value,
attrs=source_variable.attrs)
fills[variable_name] = new_variable
# Only build the ESMF/OCGIS destination grids and fields once.
if build:
# Build the destination grid once.
ocgis_lh(logger='iter_regridded_fields',
msg='before create_esmf_grid',
level=logging.DEBUG)
esmf_destination_grid = create_esmf_grid(
destination.grid,
regrid_method=regrid_method,
value_mask=value_mask)
# Check for corners on the destination grid. If they exist, conservative regridding is possible.
if regrid_method == 'auto':
if esmf_grid_has_corners(
esmf_destination_grid) and esmf_grid_has_corners(
src_efield.grid):
regrid_method = ESMF.RegridMethod.CONSERVE
else:
regrid_method = None
# Prepare the regridded sourced field. This amounts to exchanging the grids between the objects.
regridded_source = source.copy()
regridded_source.grid.extract(clean_break=True)
regridded_source.set_grid(destination.grid.extract())
# Destination ESMF field
dst_efield = ESMF.Field(esmf_destination_grid,
name='destination',
ndbounds=ndbounds)
fill_variable = fills[
variable_name] # Reference the destination data variable object
if fill_value is None:
fv = fill_variable.fill_value # The fill value used for the variable data type
else:
fv = fill_value
dst_efield.data.fill(
fv
) # Fill the ESMF destination field with that fill value to help track masks
# Construct the regrid object. Weight generation actually occurs in this call.
ocgis_lh(logger='iter_regridded_fields',
msg='before ESMF.Regrid',
level=logging.DEBUG)
if build: # Only create the regrid object once. It may be reused if split=True.
if weights_in is None:
if weights_out is None:
create_rh = False
else:
create_rh = True
# Create the weights and ESMF route handle from the grids
regrid = ESMF.Regrid(
src_efield,
dst_efield,
unmapped_action=ESMF.UnmappedAction.IGNORE,
regrid_method=regrid_method,
src_mask_values=[0],
dst_mask_values=[0],
filename=weights_out,
create_rh=create_rh)
else:
# Create ESMF route handle with weights read from file
regrid = ESMF.RegridFromFile(src_efield, dst_efield,
weights_in)
build = False
ocgis_lh(logger='iter_regridded_fields',
msg='after ESMF.Regrid',
level=logging.DEBUG)
# If we are just writing the weights file, bail out after it is written.
if weights_out is not None:
destroy_esmf_objects(
[regrid, src_efield, dst_efield, esmf_destination_grid])
return
# Perform the regrid operation. "zero_region" only fills values involved with regridding.
ocgis_lh(logger='iter_regridded_fields',
msg='before regrid',
level=logging.DEBUG)
regridded_esmf_field = regrid(src_efield,
dst_efield,
zero_region=ESMF.Region.SELECT)
e_data = regridded_esmf_field.data # Regridded data values
# These are the unmapped values coming out of the ESMF regrid operation.
unmapped_mask = e_data[:] == fv
# If all data is masked, raise an exception.
if unmapped_mask.all():
# Destroy ESMF objects.
destroy_esmf_objects([regrid, dst_efield, esmf_destination_grid])
msg = 'All regridded elements are masked. Do the input spatial extents overlap?'
raise RegriddingError(msg)
if current_slice is not None:
# Create an OCGIS variable to use for setting on the destination. We want to use label-based slicing since
# arbitrary dimensions are possible with the extra dimensions. First, set defaults for the spatial
# coordinate slices.
for k in dst_spatial_coordinate_dimensions.keys():
current_slice[k] = slice(None)
# The spatial coordinate dimension names for ESMF in Fortran order
e_data_dimensions = deepcopy(
list(dst_spatial_coordinate_dimensions.keys()))
e_data_dimensions.reverse()
# The extra dimension names for ESMF in Fortran order
e_data_dimensions_extra = deepcopy(list(extra_dimensions.keys()))
e_data_dimensions_extra.reverse()
# Wrap the ESMF data in an OCGIS variable
e_data_var = Variable(name='e_data',
value=e_data,
dimensions=e_data_dimensions,
mask=unmapped_mask)
# Expand the new variable's dimension to account for the extra dimensions
reshape_dims = list(e_data_var.dimensions) + [
Dimension(name=n, size=1) for n in e_data_dimensions_extra
]
e_data_var.reshape(reshape_dims)
# Set the destination fill variable with the ESMF regridded data
fill_variable[current_slice] = e_data_var
else:
# ESMF and OCGIS dimensions align at this point, so just insert the data
fill_variable.v()[:] = e_data
# Create a new variable collection and add the variables to the output field.
for v in list(fills.values()):
regridded_source.add_variable(v, is_data=True, force=True)
# Destroy ESMF objects.
if weights_out is None:
destroy_esmf_objects(
[regrid, dst_efield, src_efield, esmf_destination_grid])
else:
destroy_esmf_objects([dst_efield, src_efield, esmf_destination_grid])
# Broadcast ESMF (Fortran) ordering to Python (C) ordering.
dst_names = [dim.name for dim in new_dimensions]
dst_names.reverse()
for data_variable in regridded_source.data_variables:
broadcast_variable(data_variable, dst_names)
return regridded_source
def fixture_element_dimension(self):
return Dimension('elements', size=6)
def write_subsets(self):
"""
Write grid subsets to netCDF files using the provided filename templates.
"""
src_filenames = []
dst_filenames = []
wgt_filenames = []
dst_slices = []
src_slices = []
index_path = self.create_full_path_from_template('index_file')
# nzeros = len(str(reduce(lambda x, y: x * y, self.nsplits_dst)))
ctr = 1
for sub_src, src_slc, sub_dst, dst_slc in self.iter_src_grid_subsets(yield_dst=True):
# if vm.rank == 0:
# vm.rank_print('write_subset iterator count :: {}'.format(ctr))
# tstart = time.time()
# padded = create_zero_padded_integer(ctr, nzeros)
src_path = self.create_full_path_from_template('src_template', index=ctr)
dst_path = self.create_full_path_from_template('dst_template', index=ctr)
wgt_path = self.create_full_path_from_template('wgt_template', index=ctr)
src_filenames.append(os.path.split(src_path)[1])
dst_filenames.append(os.path.split(dst_path)[1])
wgt_filenames.append(wgt_path)
dst_slices.append(dst_slc)
src_slices.append(src_slc)
# Only write destinations if an iterator is not provided.
if self.iter_dst is None:
zip_args = [[sub_src, sub_dst], [src_path, dst_path]]
else:
zip_args = [[sub_src], [src_path]]
for target, path in zip(*zip_args):
with vm.scoped_by_emptyable('field.write', target):
if not vm.is_null:
ocgis_lh(msg='writing: {}'.format(path), level=logging.DEBUG)
field = Field(grid=target)
field.write(path)
ocgis_lh(msg='finished writing: {}'.format(path), level=logging.DEBUG)
# Increment the counter outside of the loop to avoid counting empty subsets.
ctr += 1
# if vm.rank == 0:
# tstop = time.time()
# vm.rank_print('timing::write_subset iteration::{}'.format(tstop - tstart))
# Global shapes require a VM global scope to collect.
src_global_shape = global_grid_shape(self.src_grid)
dst_global_shape = global_grid_shape(self.dst_grid)
# Gather and collapse source slices as some may be empty and we write on rank 0.
gathered_src_grid_slice = vm.gather(src_slices)
if vm.rank == 0:
len_src_slices = len(src_slices)
new_src_grid_slice = [None] * len_src_slices
for idx in range(len_src_slices):
for rank_src_grid_slice in gathered_src_grid_slice:
if rank_src_grid_slice[idx] is not None:
new_src_grid_slice[idx] = rank_src_grid_slice[idx]
break
src_slices = new_src_grid_slice
with vm.scoped('index write', [0]):
if not vm.is_null:
dim = Dimension('nfiles', len(src_filenames))
vname = ['source_filename', 'destination_filename', 'weights_filename']
values = [src_filenames, dst_filenames, wgt_filenames]
grid_splitter_destination = GridSplitterConstants.IndexFile.NAME_DESTINATION_VARIABLE
attrs = [{'esmf_role': 'grid_splitter_source'},
{'esmf_role': grid_splitter_destination},
{'esmf_role': 'grid_splitter_weights'}]
vc = VariableCollection()
grid_splitter_index = GridSplitterConstants.IndexFile.NAME_INDEX_VARIABLE
vidx = Variable(name=grid_splitter_index)
vidx.attrs['esmf_role'] = grid_splitter_index
vidx.attrs['grid_splitter_source'] = 'source_filename'
vidx.attrs[GridSplitterConstants.IndexFile.NAME_DESTINATION_VARIABLE] = 'destination_filename'
vidx.attrs['grid_splitter_weights'] = 'weights_filename'
vidx.attrs[GridSplitterConstants.IndexFile.NAME_SRC_GRID_SHAPE] = src_global_shape
vidx.attrs[GridSplitterConstants.IndexFile.NAME_DST_GRID_SHAPE] = dst_global_shape
vc.add_variable(vidx)
for idx in range(len(vname)):
v = Variable(name=vname[idx], dimensions=dim, dtype=str, value=values[idx], attrs=attrs[idx])
vc.add_variable(v)
bounds_dimension = Dimension(name='bounds', size=2)
# TODO: This needs to work with four dimensions.
# Source -----------------------------------------------------------------------------------------------
self.src_grid._gs_create_index_bounds_(RegriddingRole.SOURCE, vidx, vc, src_slices, dim,
bounds_dimension)
# Destination ------------------------------------------------------------------------------------------
self.dst_grid._gs_create_index_bounds_(RegriddingRole.DESTINATION, vidx, vc, dst_slices, dim,
bounds_dimension)
vc.write(index_path)
vm.barrier()
def create_merged_weight_file(self, merged_weight_filename, strict=False):
"""
Merge weight file chunks to a single, global weight file.
:param str merged_weight_filename: Path to the merged weight file.
:param bool strict: If ``False``, allow "missing" files where the iterator index cannot create a found file.
It is best to leave these ``False`` as not all source and destinations are mapped. If ``True``, raise an
"""
if vm.size > 1:
raise ValueError("'create_merged_weight_file' does not work in parallel")
index_filename = self.create_full_path_from_template('index_file')
ifile = RequestDataset(uri=index_filename).get()
ifile.load()
ifc = GridSplitterConstants.IndexFile
gidx = ifile[ifc.NAME_INDEX_VARIABLE].attrs
src_global_shape = gidx[ifc.NAME_SRC_GRID_SHAPE]
dst_global_shape = gidx[ifc.NAME_DST_GRID_SHAPE]
# Get the global weight dimension size.
n_s_size = 0
weight_filename = ifile[gidx[ifc.NAME_WEIGHTS_VARIABLE]]
wv = weight_filename.join_string_value()
split_weight_file_directory = self.paths['wd']
for wfn in map(lambda x: os.path.join(split_weight_file_directory, x), wv):
if not os.path.exists(wfn):
if strict:
raise IOError(wfn)
else:
continue
n_s_size += RequestDataset(wfn).get().dimensions['n_s'].size
# Create output weight file.
wf_varnames = ['row', 'col', 'S']
wf_dtypes = [np.int32, np.int32, np.float64]
vc = VariableCollection()
dim = Dimension('n_s', n_s_size)
for w, wd in zip(wf_varnames, wf_dtypes):
var = Variable(name=w, dimensions=dim, dtype=wd)
vc.add_variable(var)
vc.write(merged_weight_filename)
# Transfer weights to the merged file.
sidx = 0
src_indices = self.src_grid._gs_create_global_indices_(src_global_shape)
dst_indices = self.dst_grid._gs_create_global_indices_(dst_global_shape)
out_wds = nc.Dataset(merged_weight_filename, 'a')
for ii, wfn in enumerate(map(lambda x: os.path.join(split_weight_file_directory, x), wv)):
if not os.path.exists(wfn):
if strict:
raise IOError(wfn)
else:
continue
wdata = RequestDataset(wfn).get()
for wvn in wf_varnames:
odata = wdata[wvn].get_value()
try:
split_grids_directory = self.paths['wd']
odata = self._gs_remap_weight_variable_(ii, wvn, odata, src_indices, dst_indices, ifile, gidx,
split_grids_directory=split_grids_directory)
except IndexError as e:
msg = "Weight filename: '{}'; Weight Variable Name: '{}'. {}".format(wfn, wvn, e.message)
raise IndexError(msg)
out_wds[wvn][sidx:sidx + odata.size] = odata
out_wds.sync()
sidx += odata.size
out_wds.close()