def prepare_schism(args, use_logging=True):
if use_logging is True:
setup_logger()
logger = logging.getLogger('SCHISM')
else:
logger = logging.getLogger('')
logger.info("Start pre-processing SCHISM inputs...")
in_fname = args.main_inputfile
if not os.path.exists(in_fname):
logger.error("The main input file, %s, is not found", in_fname)
raise ValueError("Main input file not found")
with open(in_fname, 'r') as f:
inputs = schism_yaml.load(f)
keys_top_level = ["mesh", "gr3",
"prop", "hydraulics",
"sources_sinks", "flow_outputs"] \
+ schism_yaml.include_keywords
logger.info("Processing the top level...")
check_and_suggest(list(inputs.keys()), keys_top_level, logger)
out_fname = os.path.splitext(in_fname)[0] \
+ '_echo' + os.path.splitext(in_fname)[1]
with open(out_fname, 'w') as f:
f.write(schism_yaml.safe_dump(inputs))
# Mesh section
if item_exist(inputs, 'mesh'):
logger.info("Processing mesh section...")
mesh_items = inputs['mesh']
keys_mesh_section = ["mesh_inputfile", "dem_list",
"open_boundaries",
"depth_optimization",
"gr3_outputfile", "ll_outputfile"] \
+ schism_yaml.include_keywords
check_and_suggest(list(mesh_items.keys()), keys_mesh_section)
if item_exist(inputs['mesh'], 'mesh_inputfile'):
# Read the grid file to be processed
mesh_input_fpath = \
os.path.expanduser(mesh_items['mesh_inputfile'])
s = create_schism_setup(mesh_input_fpath, logger)
update_spatial_inputs(s, inputs, logger)
else:
raise ValueError("No mesh input file in the mesh section.")
else:
raise ValueError("No mesh section in the main input.")
logger.info("Done.")
def main():
parser = create_arg_parser()
args = parser.parse_args()
monterey_fpath = args.monterey
pt_reyes_fpath = args.pt_reyes
hgrid_fpath = args.hgrid
fpath_out = args.outfile
#todo: hardwire
nnode = 83
tbuf = days(16)
# convert start time string input to datetime
sdate = datetime(*map(int, re.split('[^\d]', args.stime)))
if args.etime:
# convert start time string input to datetime
edate = datetime(*map(int, re.split('[^\d]', args.etime)))
bufend = edate + tbuf
else:
edate = None
bufend = None
# UTM positions of Point Reyes, Monterey, SF
pos_pr = np.array([502195.03, 4205445.47])
pos_mt = np.array([599422.84, 4051630.37])
pos_sf = np.array([547094.79, 4184499.42])
var_subtidal = np.array([0.938, 0.905, 0.969]) # pr, mt, sf
var_semi = np.array([0.554, 0.493, 0.580])
# Assume 45 degree from north-west to south-east
tangent = np.array([1, -1])
tangent = tangent / np.linalg.norm(tangent) # Normalize
# Rotate 90 cw to get normal vec
normal = np.array([tangent[1], -tangent[0]])
print "tangent:", tangent
print "normal:", normal
mt_rel = pos_mt - pos_pr
x_mt = np.dot(tangent, mt_rel) # In pr-mt direction
y_mt = np.dot(normal, mt_rel) # Normal to x-direction to the
# Grid
#todo: what is the difference between this and m = read_grid()??
s = create_schism_setup(hgrid_fpath)
ocean_boundary = s.mesh.boundaries[0] # First one is ocean
# Data
print "Reading Point Reyes..."
pt_reyes = read_ts(pt_reyes_fpath, start=sdate - tbuf, end=bufend, force_regular=True)
pt_reyes = interpolate_ts_nan(pt_reyes)
if np.any(np.isnan(pt_reyes.data)):
print pt_reyes.times[np.isnan(pt_reyes.data)]
ts_pr_subtidal, ts_pr_diurnal, ts_pr_semi, noise = separate_species(
pt_reyes)
del noise
print "Reading Monterey..."
monterey = read_ts(monterey_fpath, start=sdate - tbuf, end=bufend, force_regular=True)
monterey = interpolate_ts_nan(monterey)
if pt_reyes.interval != monterey.interval:
raise ValueError(
"Point Reyes and Monterey time step must be the same in gen_elev2D.py")
ts_mt_subtidal, ts_mt_diurnal, ts_mt_semi, noise = separate_species(
monterey)
del noise
dt = monterey.interval.seconds
print "Done Reading"
print "Interpolating Point Reyes"
# interpolate_ts(ts_pr_subtidal.window(sdate,edate),step)
ts_pr_subtidal = ts_pr_subtidal.window(sdate, edate)
ts_pr_diurnal = ts_pr_diurnal.window(sdate, edate) # interpolate_ts(,step)
# interpolate_ts(ts_pr_semi.window(sdate,edate),step)
ts_pr_semi = ts_pr_semi.window(sdate, edate)
print "Interpolating Monterey"
# interpolate_ts(ts_mt_subtidal.window(sdate,edate),step)
ts_mt_subtidal = ts_mt_subtidal.window(sdate, edate)
# interpolate_ts(ts_mt_diurnal.window(sdate,edate),step)
ts_mt_diurnal = ts_mt_diurnal.window(sdate, edate)
# interpolate_ts(ts_mt_semi.window(sdate,edate),step)
ts_mt_semi = ts_mt_semi.window(sdate, edate)
print "Creating writer" # requires dt be known for netcdf
if fpath_out.endswith("th"):
thwriter = BinaryTHWriter(fpath_out,nnode,None)
elif fpath_out.endswith("nc"):
thwriter = NetCDFTHWriter(fpath_out,nnode,sdate,dt)
else:
raise ValueError("File extension for output not recognized in file: {}".format(fpath_out))
# Grid
boundaries = s.mesh.nodes[ocean_boundary.nodes]
pos_rel = boundaries[:, :2] - pos_pr
# x, y in a new principal axes
x = np.dot(pos_rel, tangent.reshape((2, -1)))
y = np.dot(pos_rel, normal.reshape((2, -1)))
theta_x = x / x_mt
theta_x_comp = 1. - theta_x
theta_y = y / y_mt
theta_y_comp = 1. - theta_y
var_y = (theta_y_comp * var_semi[0] + theta_y * var_semi[1])
# adj_subtidal_mt = 0.08 # Adjustment in Monterey subtidal signal
# scaling_diurnal_mt = 0.95 # Scaling of Monterey diurnal signal (for K1/Q1)
# Used this up to v75
adj_subtidal_mt = 0. # Adjustment in Monterey subtidal signal
scaling_diurnal_mt = 1. # Scaling of Monterey diurnal signal (for K1/Q1)
# New trial for LSC2 with v75
adj_subtidal_mt = -0.07 # Adjustment in Monterey subtidal signal
scaling_diurnal_mt = 0.95 # Scaling of Monterey diurnal signal (for K1/Q1)
scaling_semidiurnal_mt = 1.03
adj_subtidal_mt = -0.14 # Adjustment in Monterey subtidal signal
scaling_diurnal_mt = 0.90 # Scaling of Monterey diurnal signal (for K1/Q1)
scaling_semidiurnal_mt = 1.07
adj_subtidal_mt = 0.10 # Adjustment in Monterey subtidal signal
scaling_diurnal_mt = 0.90 # Scaling of Monterey diurnal signal (for K1/Q1)
scaling_semidiurnal_mt = 1.03
adj_subtidal_mt = 0.10 # Adjustment in Monterey subtidal signal
scaling_diurnal_mt = 0.97 # Scaling of Monterey diurnal signal (for K1/Q1)
# Scaling of Point Reyes diurnal signal (for K1/Q1)
scaling_diurnal_pr = 0.97
scaling_semidiurnal_mt = 1.025 # Scaling at Monterey semi-diurnal signal
adj_subtidal_mt = 0.09 # Adjustment in Monterey subtidal signal
scaling_diurnal_mt = 0.94 # Scaling of Monterey diurnal signal (for K1/Q1)
# Scaling of Point Reyes diurnal signal (for K1/Q1)
scaling_diurnal_pr = 0.94
scaling_semidiurnal_mt = 1.0 # Scaling at Monterey semi-diurnal signal
slr = 0.0 # Sea level rise
if np.any(np.isnan(ts_pr_semi.data)):
print ts_pr_semi.times[np.isnan(ts_pr_semi.data)]
raise ValueError('')
# temp=np.zeros((len(ts_pr_semi),nnode))
# times[:]=[dt*i for i in xrange(len(ts_pr_semi))]
for i in xrange(len(ts_pr_semi)):
t = float(dt * i)
# semi-diurnal
# Scaling
pr = ts_pr_semi[i].value
mt = ts_mt_semi[i].value * scaling_semidiurnal_mt
if np.isnan(pr) or np.isnan(mt):
print pr
print mt
raise ValueError("One of values is numpy.nan.")
eta_pr_side = var_y / var_semi[0] * pr
eta_mt_side = var_y / var_semi[1] * mt
eta = eta_pr_side * theta_x_comp + eta_mt_side * theta_x
# diurnal
# Interpolate in x-direction only to get a better phase
pr = ts_pr_diurnal[i].value * scaling_diurnal_pr
mt = ts_mt_diurnal[i].value * scaling_diurnal_mt
if np.isnan(pr) or np.isnan(mt):
raise ValueError("One of values is numpy.nan.")
eta += pr * theta_x_comp + mt * theta_x
# Subtidal
# No phase change in x-direction. Simply interpolate in
# y-direction.
pr = ts_pr_subtidal[i].value + slr
mt = ts_mt_subtidal[i].value + adj_subtidal_mt + slr
if np.isnan(pr) or np.isnan(mt):
raise ValueError("One of values is numpy.nan.")
eta += pr * theta_y_comp + mt * theta_y
# write data to netCDF file
thwriter.write_step(i,t,eta)
# Delete class
del thwriter