def run(self, args):
fmt, path = args[0].split(':')
log.info("Writing %s as %s" % (path, fmt))
g = stack[-1] # by default, do not pop from stack
if fmt in ['suntans_classic', 'suntans']:
g.write_suntans(path, overwrite=self.clobber)
elif fmt == 'suntans_hybrid':
g.write_suntans_hybrid(path, overwrite=self.clobber)
elif fmt == 'ugrid':
g.write_ugrid(path, overwrite=self.clobber)
elif fmt == 'untrim':
g.write_untrim08(path, overwrite=self.clobber)
elif fmt == 'cell_shp':
g.write_cells_shp(path, overwrite=self.clobber)
elif fmt == 'boundary_shp':
g.write_shore_shp(path, overwrite=self.clobber)
elif fmt == 'edge_shp':
g.write_edges_shp(path, overwrite=self.clobber)
elif fmt == 'node_shp':
g.write_node_shp(path, overwrite=self.clobber)
elif fmt == 'fishptm':
g.write_ptm_gridfile(path, overwrite=self.clobber)
elif fmt == 'dfm':
from stompy.model.delft import dfm_grid
if not path.endswith('_net.nc'):
log.warning(
"Writing DFM grid to filename not ending in '_net.nc'")
dfm_grid.write_dfm(g, path, overwrite=self.clobber)
else:
log.error("Did not understand format %s" % fmt)
log.error("Possible formats are: %s" % self.format_list())
sys.exit(1)
def run_all(run_base_dir,
storm_start_h,
storm_duration_h,
storm_flow,
sources=None,
force=False):
mdu = dio.MDUFile('template.mdu')
mdu['geometry', 'NetFile'] = 'stein_03_net.nc'
grid = dfm_grid.DFMGrid(mdu['geometry', 'NetFile'])
if os.path.exists(run_base_dir):
if force:
shutil.rmtree(run_base_dir) # Safer - blow it away
else:
log.warning("Will not run %s -- already exists" % run_base_dir)
return False
mdu.set_time_range(start=np.datetime64('2010-01-01'),
stop=np.datetime64('2010-01-05'))
os.path.exists(run_base_dir) or os.makedirs(run_base_dir)
mdu.set_filename(os.path.join(run_base_dir, 'flowfm.mdu'))
ext_fn = mdu.filepath(['external forcing', 'ExtForceFile'])
# Clear any pre-existing BC file:
os.path.exists(ext_fn) and os.unlink(ext_fn)
# Monkey patch the parameters:
Storm.storm_flow = storm_flow
Storm.storm_duration_h = storm_duration_h
Storm.storm_start_h = storm_start_h
bc_shp = 'forcing_with_q.shp'
bc_shp_data = wkb2shp.shp2geom(bc_shp)
for bc in bc_shp_data:
if sources is not None and bc['name'] not in sources:
print("Skipping %s" % bc['name'])
continue
for data_src in factory(bc):
data_src.write(mdu=mdu, feature=bc, grid=grid)
fixed_weir_out = "../derived"
if 1: # fixed weir file is just referenced as static input
shutil.copyfile(os.path.join(fixed_weir_out, 'fixed_weirs-v00.pli'),
os.path.join(run_base_dir, 'fixed_weirs-v00.pli'))
mdu['geometry', 'FixedWeirFile'] = 'fixed_weirs-v00.pli'
mdu.write()
dfm_grid.write_dfm(grid,
mdu.filepath(['geometry', 'NetFile']),
overwrite=True)
dflowfm(mdu.filename, ['-t', '1', '--autostartstop'])
grid=g,
dredge_depth=dredge_depth,
old_bc_fn=old_bc_fn,
all_flows_unit=False,
time_offset=np.datetime64('2016-01-01') -
np.datetime64('2017-01-01'))
# ---------- END SF FRESH, POTW, DELTA
##
if 1:
mdu['geometry',
'NetFile'] = os.path.basename(ugrid_file).replace('.nc', '_net.nc')
dfm_grid.write_dfm(g,
os.path.join(run_base_dir, mdu['geometry', 'NetFile']),
overwrite=True)
# This step is pretty slow the first time around.
if use_wind:
coamps.add_coamps_to_mdu(mdu, run_base_dir, g, use_existing=True)
##
# Setting a full 3D initial condition requires a partitioned
# run, so go ahead partition now:
dfm_output_count = 0
def dflowfm(mdu_fn, args=['--autostartstop']):
#!/usr/bin/env python
"""
Read a suntans grid in the current directory and write a DFM grid, output_net.nc
"""
from stompy.grid import unstructured_grid
from stompy.model.delft import dfm_grid
ug = unstructured_grid.SuntansGrid(".")
dfm_grid.write_dfm(ug, "output_net.nc")
def set_lsb_bathy(grid):
check_bathy()
# First, load in the original sfb_dfm grid to get bathymetry
log.info("Loading SFB DFM v2 grid")
sfb_dfm_grid=xr.open_dataset('sfb_dfm/sfei_v19_net.nc')
sfb_X=np.c_[ sfb_dfm_grid.NetNode_x.values,
sfb_dfm_grid.NetNode_y.values]
sfb_dfm_field=field.XYZField(X=sfb_X,
F=sfb_dfm_grid.NetNode_z.values)
lsb_X=grid.nodes['x']
# This will set all points within the convex hull of the original
# grid. These elevations are used in the output (a) outside the
# LSB merged_2m DEM, and (b) to prioritize which nodes to use when
# moving depths from edges to nodes.
# Could argue that it would be better to pull point elevations here
# from the DEM where they overlap. Probably makes very little difference
lsb_z=sfb_dfm_field(lsb_X) # still some nans at this point
#
log.info("Loading LSB dem from %s"%merged_2m_path)
dem=field.GdalGrid(merged_2m_path)
#
# Use the 2m DEM to find an effective minimum depth for each edge covered
# by the DEM.
edge_min_depths=depth_connectivity.edge_connection_depth(grid,dem,centers='lowest')
# move those edge depths to node depths
node_depths=depth_connectivity.greedy_edgemin_to_node(grid,lsb_z,edge_min_depths)
# Still have some nodes with nan depth, first try filling in with the DEM.
missing=np.isnan(node_depths)
node_depths[missing]=dem( lsb_X[missing,:] )
# And wrap it up with a more forgiving interpolation from the original sfb_dfm_v2
# grid (about 12 points on the convex hull)
still_missing=np.isnan(node_depths)
node_depths[still_missing]=sfb_dfm_field.interpolate( lsb_X[still_missing,:],
'nearest' )
assert np.isnan(node_depths).sum()==0
# Update the grid
grid.nodes['depth']=node_depths
if 0: # caller is going to deal with I/O
out_file='lsb_v99_bathy_net.nc'
os.path.exists(out_file) and os.unlink(out_file)
dfm_grid.write_dfm(grid,out_file)
if 0: # plot for development.
plt.figure(10).clf()
fig,ax=plt.subplots(num=10)
edge_mins=grid.nodes['depth'][grid.edges['nodes']].min(axis=1)
ecoll=grid.plot_edges(lw=1.5,values=edge_mins)
ncoll=grid.plot_nodes(values=grid.nodes['depth'])
plt.setp([ecoll,ncoll],clim=[-3,3])
plot_utils.cbar(ncoll,extras=[ecoll])
# Modified in place, but return just in case
return grid # QED.
##
if 1:
lines = [
"QUANTITY=frictioncoefficient",
"FILENAME=%s/friction12e.xyz" % rel_static_dir, "FILETYPE=7",
"METHOD=5", "OPERAND=O", ""
]
with open(old_bc_fn, 'at') as fp:
fp.write("\n".join(lines))
if 1: # Copy grid file into run directory and update mdu
mdu['geometry', 'NetFile'] = os.path.basename(net_file)
dest = os.path.join(run_base_dir, mdu['geometry', 'NetFile'])
# write out the modified grid
dfm_grid.write_dfm(grid, dest, overwrite=True)
sfb_dfm_utils.add_initial_salinity_dyn(run_base_dir, abs_static_dir, mdu,
run_start)
# WIND
ludwig_ok = sfb_dfm_utils.add_erddap_ludwig_wind(run_base_dir, run_start,
run_stop, old_bc_fn)
if not ludwig_ok:
const_ok = sfb_dfm_utils.add_constant_wind(run_base_dir, mdu, [0, 0],
run_start, run_stop)
assert const_ok
else:
assert ludwig_ok # or see lsb_dfm.py for constant field.
##
coll=g.plot_cells(mask=cells_to_dredge,ax=ax,color='orange',lw=3)
coll.set_edgecolors('orange')
##
Gdredge=dfm_grid.DFMGrid('sfei_v19_net.nc')
nodes_to_dredge=np.concatenate( [G.cell_to_nodes(c)
for c in cells_to_dredge] )
nodes_to_dredge=np.unique(nodes_to_dredge)
dredge_depth=-0.5
Gdredge.nodes['depth'][nodes_to_dredge] = np.minimum(Gdredge.nodes['depth'][nodes_to_dredge],
dredge_depth)
# No cell depth in this grid, so no need to dredge that
dfm_grid.write_dfm(Gdredge,'sfei_v19_dredge_net.nc')
##
# Plot nice version of that
plt.figure(4).clf()
fig,ax=plt.subplots(num=4)
Gdredge.contourf_node_values( Gdredge.nodes['depth'],
np.linspace(-2,3.5,12),
extend='both',
ax=ax)
ax.axis('equal')
ax.axis((587218.08074605372, 594548.22297297686, 4144516.3193028411, 4149286.1178460922))
if m:
edge_vals[j] = m['L_err']
plt.figure(22).clf()
fig, ax = plt.subplots(num=22)
g.plot_edges(ax=ax, color='k', lw=0.3, alpha=0.5)
ecoll = g.plot_edges(ax=ax, values=edge_vals, mask=np.isfinite(edge_vals))
#ecoll.set_clim([-2,2])
ecoll.set_clim([-100, 100])
ecoll.set_cmap('jet')
ecoll.set_lw(4)
ax.axis('equal')
plt.colorbar(ecoll)
##
g.add_node_field('depth', node_depths, on_exists='overwrite')
# bathy2 => with dredged out CSC region
dfm_grid.write_dfm(g,
'CacheSloughComplex_v100_bathy2_sparse_net.nc',
overwrite=True)
##
g.add_cell_field('depth',
g.interp_node_to_cell(node_depths),
on_exists='overwrite')
g.write_cells_shp('derived/grid-cells.shp', overwrite=True)
from sfb_dfm_utils import ca_roms
dem = ca_roms.coastal_dem()
sel_nodes = np.nonzero(g_complete.nodes['src'] == 3)[0]
sel_node_depth = dem(g_complete.nodes['x'][sel_nodes])
splice_bathy[sel_nodes] = sel_node_depth
##
g_complete.add_node_field('depth', splice_bathy)
##
g_complete.write_ugrid('spliced_grids_01_bathy.nc', overwrite=True)
dfm_grid.write_dfm(g_complete, 'spliced_grids_01_net.nc', overwrite=True)
##
plt.clf()
g_complete.contourf_node_values((-g_complete.nodes['depth']).clip(0,
np.inf)**0.2,
30,
cmap='jet',
extend='both')
g_complete.plot_edges(lw=0.5, color='k', alpha=0.3)
##
fig = plt.gcf()
ax = plt.gca()
##
if 1:
lines = [
"QUANTITY=frictioncoefficient",
"FILENAME=%s/friction12e.xyz" % rel_static_dir, "FILETYPE=7",
"METHOD=5", "OPERAND=O", ""
]
with open(str(old_bc_fn), 'at') as fp:
fp.write("\n".join(lines))
if 1: # Copy grid file into run directory and update mdu
mdu['geometry', 'NetFile'] = net_file.name
dest = run_base_dir / mdu['geometry', 'NetFile']
# write out the modified grid
dfm_grid.write_dfm(grid, str(dest), overwrite=True)
# update to work with rusty's changes to sfb_dfm_utils
#sfb_dfm_utils.add_initial_salinity_dyn(run_base_dir,
# abs_static_dir,
# mdu,
# run_start)
sfb_dfm_utils.add_initial_salinity(str(run_base_dir),
str(abs_static_dir),
str(old_bc_fn),
all_flows_unit=ALL_FLOWS_UNIT)
# WIND
#ludwig_ok=sfb_dfm_utils.add_erddap_ludwig_wind(run_base_dir,
# run_start,run_stop,
# old_bc_fn)
from bcs import *
def factory(feat):
code = '[' + feat['src'] + ']'
return eval(code)
bc_shp = 'forcing.shp'
bc_shp_data = wkb2shp.shp2geom(bc_shp)
for bc in bc_shp_data:
for data_src in factory(bc):
data_src.write(mdu=mdu, feature=bc, grid=grid)
###
fixed_weir_out = "../derived"
if 1: # fixed weir file is just referenced as static input
shutil.copyfile(os.path.join(fixed_weir_out, 'fixed_weirs-v00.pli'),
os.path.join(run_base_dir, 'fixed_weirs-v00.pli'))
mdu['geometry', 'FixedWeirFile'] = 'fixed_weirs-v00.pli'
##
mdu.write()
dfm_grid.write_dfm(grid, mdu.filepath(['geometry', 'NetFile']), overwrite=True)
##
# is also modified to deepen areas near inflows, before being written
# out near the end of the script
# Bathy for LSB is evolving, so a few steps required to possibly update it here.
net_bathy_file=net_file.replace("_net.nc","_bathy_net.nc")
bathy_file="inputs-static/merged_2m.tif"
assert net_bathy_file!=net_file
if ( (not os.path.exists(net_bathy_file))
or (os.stat(net_file).st_mtime >= os.stat(net_bathy_file).st_mtime)
or (os.stat(bathy_file).st_mtime >= os.stat(net_bathy_file).st_mtime) ):
grid=dfm_grid.DFMGrid(net_file)
log.info("Will update bathymetry in grid - 2 minutes?")
set_bathy.set_lsb_bathy(grid)
log.info("Writing updated grid/bathy")
dfm_grid.write_dfm(grid,net_bathy_file,overwrite=True)
# Either way, read that back in
log.info("Reading grid with bathy")
grid=dfm_grid.DFMGrid(net_bathy_file)
##
# Write out a shapefile for the grid edges.
# Run this after changing the grid.
# Output written to "derived" subdirectory.
edges_shp="derived/grid-edges.shp"
if ( (not os.path.exists(edges_shp))
or (os.stat(net_file).st_mtime >= os.stat(edges_shp).st_mtime) ):
log.info("Writing new edge shapefile")
ncoll.set_clim([-1, 2])
ncoll.set_cmap('jet')
# ecoll=g.plot_edges(values=node_mean)
# ecoll.set_clim([-1,2])
# ecoll.set_cmap('jet')
ecoll = g.plot_edges(values=errors)
ecoll.set_clim([-1, 1])
ecoll.set_cmap('seismic')
# g.plot_edges(lw=0.4,color='k')
# plt.axis( (568259., 568614., 4150269., 4150641.) )
plt.axis((569564.3238793822, 569761.5851150813, 4151337.141236072,
4151543.8487844667))
##
g.add_node_field('depth', conn_depth, on_exists='overwrite')
# g.add_edge_field('depth_mean', g.nodes['depth'][g.edges['nodes']].mean(axis=1),on_exists='overwrite' )
##
grid_out_fn = 'dfm/stein_04_net.nc'
if os.path.exists(grid_out_fn):
os.unlink(grid_out_fn)
dfm_grid.write_dfm(g, grid_out_fn)
# Manually drawn polygon around Napa, and only muck with those nodes:
plt.figure(2).clf()
fig, ax = plt.subplots(num=2)
g.contourf_node_values(g.nodes['depth'],
np.linspace(-10, 2, 20),
extend='both',
cmap='jet')
ax.axis('equal')
pnts = plot_utils.draw_polyline(ax=ax)
else:
pnts = np.array([[565555.92717692, 4214418.23511226],
[566275.67385296, 4213788.45677072],
[567295.31497736, 4214388.24566743],
[563996.47604549, 4226863.85471885],
[559707.98543407, 4227793.52750873],
[559108.19653736, 4226264.06582214],
[563456.66603846, 4216757.4118094],
[565136.07494923, 4215167.97123314]])
##
poly = geometry.Polygon(pnts)
sel_nodes = g.select_nodes_intersecting(poly)
g.nodes['depth'][sel_nodes] = dem(g.nodes['x'][sel_nodes])
##
dfm_grid.write_dfm(g, 'sfei_v20_net.nc')