def d3d(tmpdir,dic):
#initialize a model
rpath = str(tmpdir)+'/'
dic.update({'rpath':rpath}) # use tmpdir for running the model
b = pyposeidon.model(**dic)
try:
b.execute()
out = data.data(**dic)
a = pyposeidon.read_model(rpath+'d3d_model.json') # read model
a.execute()
out = data.data(**dic)
return True
except:
return False
def schism(tmpdir, dic):
#initialize a model
rpath = str(tmpdir) + '/'
dic.update({'rpath': rpath}) # use tmpdir for running the model
b = pyposeidon.model(**dic)
try:
b.execute()
b.results()
a = pyposeidon.read_model(rpath + 'test_model.json') # read model
a.execute()
a.results()
return True
except:
return False
def create_features(path="./", tag="schism"):
logger.info("create geojson file for elevation")
m = pyposeidon.read_model(path + tag + "_model.json")
m.get_data()
d = m.data.Dataset
vmin = d.elev.min().compute()
vmax = d.elev.max().compute()
x = d.SCHISM_hgrid_node_x.values
y = d.SCHISM_hgrid_node_y.values
tri = d.SCHISM_hgrid_face_nodes.values
nodes = pd.DataFrame({"lon": x, "lat": y})
tria = pd.DataFrame(tri, columns=["a", "b", "c"])
tria["ap"] = tria.apply(lambda x: nodes.loc[x.a, ["lon", "lat"]].values,
axis=1)
tria["bp"] = tria.apply(lambda x: nodes.loc[x.b, ["lon", "lat"]].values,
axis=1)
tria["cp"] = tria.apply(lambda x: nodes.loc[x.c, ["lon", "lat"]].values,
axis=1)
tria["geometry"] = tria.apply(
lambda x: shapely.geometry.Polygon([x.ap, x.bp, x.cp]), axis=1)
colormap = branca.colormap.LinearColormap(["green", "yellow", "red"],
vmin=vmin.values,
vmax=vmax.values)
colormap.caption = "Elevation"
# geopandas
gf_ = gp.GeoDataFrame(tria, crs={"init": "epsg:4326"})
gf_ = gf_.drop(["a", "b", "c", "ap", "bp", "cp"], axis=1)
## All frames
fs = []
for l in range(d.time.shape[0]):
fr = d.elev.isel(time=l)
a = fr.sel(nSCHISM_hgrid_node=tria.a.to_list()).values
b = fr.sel(nSCHISM_hgrid_node=tria.b.to_list()).values
c = fr.sel(nSCHISM_hgrid_node=tria.c.to_list()).values
tria["value"] = np.mean([a, b, c], axis=0)
tria["color"] = [colormap(x) for x in tria.value.to_list()]
fs.append(
create_geojson_features(
tria, d.time[l].values.astype(str).split(".")[0]))
tf = [j for i in fs for j in i]
if not os.path.exists(path + "server"):
os.makedirs(path + "server")
json.dump(tf, open(path + "server/anim.json", "w"))
gf_.to_file(path + "server/grid.geojson", driver="GeoJSON")
logger.info("... saved")
return
def create_features(path='./', tag='schism'):
logger.info('create geojson file for elevation')
m = pyposeidon.read_model(path + tag + '_model.json')
m.get_data()
d = m.data.Dataset
vmin = d.elev.min().compute()
vmax = d.elev.max().compute()
x = d.SCHISM_hgrid_node_x.values
y = d.SCHISM_hgrid_node_y.values
tri = d.SCHISM_hgrid_face_nodes.values
nodes = pd.DataFrame({'lon': x, 'lat': y})
tria = pd.DataFrame(tri, columns=['a', 'b', 'c'])
tria['ap'] = tria.apply(lambda x: nodes.loc[x.a, ['lon', 'lat']].values,
axis=1)
tria['bp'] = tria.apply(lambda x: nodes.loc[x.b, ['lon', 'lat']].values,
axis=1)
tria['cp'] = tria.apply(lambda x: nodes.loc[x.c, ['lon', 'lat']].values,
axis=1)
tria['geometry'] = tria.apply(
lambda x: shapely.geometry.Polygon([x.ap, x.bp, x.cp]), axis=1)
colormap = branca.colormap.LinearColormap(['green', 'yellow', 'red'],
vmin=vmin.values,
vmax=vmax.values)
colormap.caption = 'Elevation'
# geopandas
gf_ = gp.GeoDataFrame(tria, crs={'init': 'epsg:4326'})
gf_ = gf_.drop(['a', 'b', 'c', 'ap', 'bp', 'cp'], axis=1)
## All frames
fs = []
for l in range(d.time.shape[0]):
fr = d.elev.isel(time=l)
a = fr.sel(nSCHISM_hgrid_node=tria.a.to_list()).values
b = fr.sel(nSCHISM_hgrid_node=tria.b.to_list()).values
c = fr.sel(nSCHISM_hgrid_node=tria.c.to_list()).values
tria['value'] = np.mean([a, b, c], axis=0)
tria['color'] = [colormap(x) for x in tria.value.to_list()]
fs.append(
create_geojson_features(
tria, d.time[l].values.astype(str).split('.')[0]))
tf = [j for i in fs for j in i]
if not os.path.exists(path + 'server'):
os.makedirs(path + 'server')
json.dump(tf, open(path + 'server/anim.json', 'w'))
gf_.to_file(path + 'server/grid.geojson', driver='GeoJSON')
logger.info('... saved')
return
def run(self, **kwargs):
if isinstance(self.model, str):
self.model = pyposeidon.read_model(self.model)
for attr, value in self.model.__dict__.items():
if not hasattr(self, attr):
setattr(self, attr, value)
execute = get_value(self, kwargs, "execute", False)
pwd = os.getcwd()
files = [
self.tag + "_hydro.xml",
self.tag + ".enc",
self.tag + ".obs",
self.tag + ".bnd",
self.tag + ".bca",
"run_flow2d3d.sh",
]
files_sym = [self.tag + ".grd", self.tag + ".dep"]
self.origin = self.model.rpath
self.date0 = self.model.date
if not os.path.exists(self.origin):
sys.stdout.write("Initial folder not present {}\n".format(
self.origin))
sys.exit(1)
ppath = self.ppath
cf = [glob.glob(ppath + "/" + e) for e in files]
cfiles = [item.split("/")[-1] for sublist in cf for item in sublist]
# create the folder/run path
rpath = self.cpath
if not os.path.exists(rpath):
os.makedirs(rpath)
copy2(ppath + self.tag + "_model.json", rpath) # copy the info file
# load model
with open(rpath + self.tag + "_model.json", "rb") as f:
info = pd.read_json(f, lines=True).T
info[info.isnull().values] = None
info = info.to_dict()[0]
try:
args = set(kwargs.keys()).intersection(
info.keys()) # modify dic with kwargs
for attr in list(args):
info[attr] = kwargs[attr]
except:
pass
# update the properties
info["date"] = self.date
info["start_date"] = self.date
info["time_frame"] = self.time_frame
info["meteo_source"] = self.meteo
info["rpath"] = rpath
if self.restart_step:
info["restart_step"] = self.restart_step
m = pm.set(**info)
# copy/link necessary files
logger.debug("copy necessary files")
for filename in cfiles:
ipath = glob.glob(ppath + filename)
if ipath:
try:
copy2(ppath + filename, rpath + filename)
except:
dir_name, file_name = os.path.split(filename)
if not os.path.exists(rpath + dir_name):
os.makedirs(rpath + dir_name)
copy2(ppath + filename, rpath + filename)
logger.debug(".. done")
# symlink the big files
logger.debug("symlink model files")
for filename in files_sym:
ipath = glob.glob(self.origin + filename)
if ipath:
try:
os.symlink(
pathlib.Path(ipath[0]).resolve(strict=True),
rpath + filename)
except OSError as e:
if e.errno == errno.EEXIST:
logger.warning("Restart link present\n")
logger.warning("overwriting\n")
os.remove(rpath + filename)
os.symlink(
pathlib.Path(ipath[0]).resolve(strict=True),
rpath + filename,
)
logger.debug(".. done")
copy2(ppath + m.tag + ".mdf", rpath) # copy the mdf file
# copy restart file
inresfile = "tri-rst." + m.tag + "." + datetime.datetime.strftime(
self.date, "%Y%m%d.%H%M%M")
outresfile = "restart." + datetime.datetime.strftime(
self.date, "%Y%m%d.%H%M%M")
# copy2(ppath+inresfile,rpath+'tri-rst.'+outresfile)
try:
os.symlink(
pathlib.Path(ppath + "/" + inresfile).resolve(strict=True),
rpath + "tri-rst." + outresfile,
)
logger.debug("symlink {} to {}".format(
ppath + "/" + inresfile, rpath + "tri-rst." + outresfile))
except OSError as e:
if e.errno == errno.EEXIST:
logger.warning("Restart symlink present\n")
logger.warning("overwriting\n")
os.remove(rpath + "tri-rst." + outresfile)
os.symlink(
pathlib.Path(ppath + "/" + inresfile).resolve(strict=True),
rpath + "tri-rst." + outresfile,
)
else:
raise e
# get new meteo
logger.info("process meteo\n")
flag = get_value(self, kwargs, "update", ["meteo"])
check = [
os.path.exists(rpath + f) for f in ["u.amu", "v.amv", "p.amp"]
]
if (np.any(check) == False) or ("meteo" in flag):
m.force()
m.to_force(m.meteo.Dataset,
vars=["msl", "u10", "v10"],
rpath=rpath) # write u,v,p files
else:
logger.info("meteo files present\n")
# modify mdf file
m.config(
config_file=ppath + m.tag + ".mdf",
config={"Restid": outresfile},
output=True,
)
m.config_file = rpath + m.tag + ".mdf"
os.chdir(rpath)
m.save()
if execute:
m.run()
# cleanup
os.remove(rpath + "tri-rst." + outresfile)
logger.info("done for date :" +
datetime.datetime.strftime(self.date, "%Y%m%d.%H"))
os.chdir(pwd)
def run(self, **kwargs):
if isinstance(self.model, str):
self.model = pyposeidon.read_model(self.model)
for attr, value in self.model.__dict__.items():
if not hasattr(self, attr):
setattr(self, attr, value)
execute = get_value(self, kwargs, "execute", True)
pwd = os.getcwd()
files = [
"bctides.in",
"launchSchism.sh",
"/sflux/sflux_inputs.txt",
"/outputs/flux.out",
]
files_sym = [
"hgrid.gr3",
"hgrid.ll",
"manning.gr3",
"vgrid.in",
"drag.gr3",
"rough.gr3",
"station.in",
"windrot_geo2proj.gr3",
]
station_files = [
"/outputs/staout_1",
"/outputs/staout_2",
"/outputs/staout_3",
"/outputs/staout_4",
"/outputs/staout_5",
"/outputs/staout_6",
"/outputs/staout_7",
"/outputs/staout_8",
"/outputs/staout_9",
]
self.origin = self.model.rpath
self.date0 = self.model.date
if not os.path.exists(self.origin):
sys.stdout.write("Initial folder not present {}\n".format(
self.origin))
sys.exit(1)
ppath = self.ppath
# create the new folder/run path
rpath = self.cpath
if not os.path.exists(rpath):
os.makedirs(rpath)
tag = kwargs.get("tag", "schism")
copy2(ppath + self.tag + "_model.json", rpath) # copy the info file
# load model
with open(rpath + self.tag + "_model.json", "rb") as f:
info = pd.read_json(f, lines=True).T
info[info.isnull().values] = None
info = info.to_dict()[0]
try:
args = set(kwargs.keys()).intersection(
info.keys()) # modify dic with kwargs
for attr in list(args):
info[attr] = kwargs[attr]
except:
pass
info["config_file"] = ppath + "param.nml"
# update the properties
info["date"] = self.date0
info["start_date"] = self.sdate
info["time_frame"] = self.time_frame
info["end_date"] = self.sdate + pd.to_timedelta(self.time_frame)
info["meteo_source"] = self.meteo
info["rpath"] = rpath
m = pm.set(**info)
# Mesh
gfile = glob.glob(ppath + "hgrid.gr3")
if gfile:
info["mesh_file"] = gfile[0]
self.mesh_file = gfile[0]
info["mesh_generator"] = None
self.mesh_generator = None
m.mesh = pmesh.set(type="tri2d", **info)
# get lat/lon from file
if hasattr(self, "mesh_file"):
info.update(
{"lon_min": m.mesh.Dataset.SCHISM_hgrid_node_x.values.min()})
info.update(
{"lon_max": m.mesh.Dataset.SCHISM_hgrid_node_x.values.max()})
info.update(
{"lat_min": m.mesh.Dataset.SCHISM_hgrid_node_y.values.min()})
info.update(
{"lat_max": m.mesh.Dataset.SCHISM_hgrid_node_y.values.max()})
# copy/link necessary files
logger.debug("copy necessary files")
for filename in files:
ipath = glob.glob(ppath + filename)
if ipath:
try:
copy2(ppath + filename, rpath + filename)
except:
dir_name, file_name = os.path.split(filename)
if not os.path.exists(rpath + dir_name):
os.makedirs(rpath + dir_name)
copy2(ppath + filename, rpath + filename)
logger.debug(".. done")
# copy the station files
logger.debug("copy station files")
for filename in station_files:
ipath = glob.glob(ppath + filename)
if ipath:
try:
copy2(ppath + filename, rpath + filename)
except:
dir_name, file_name = os.path.split(filename)
if not os.path.exists(rpath + dir_name):
os.makedirs(rpath + dir_name)
copy2(ppath + filename, rpath + filename)
logger.debug(".. done")
# symlink the big files
logger.debug("symlink model files")
for filename in files_sym:
ipath = glob.glob(self.origin + filename)
if ipath:
try:
os.symlink(
pathlib.Path(ipath[0]).resolve(strict=True),
rpath + filename)
except OSError as e:
if e.errno == errno.EEXIST:
logger.warning("Restart link present\n")
logger.warning("overwriting\n")
os.remove(rpath + filename)
os.symlink(
pathlib.Path(ipath[0]).resolve(strict=True),
rpath + filename,
)
logger.debug(".. done")
# create restart file
logger.debug("create restart file")
# check for combine hotstart
hotout = int((self.sdate - self.date0).total_seconds() /
info["params"]["core"]["dt"])
logger.debug("hotout_it = {}".format(hotout))
resfile = glob.glob(ppath +
"/outputs/hotstart_it={}.nc".format(hotout))
if not resfile:
# load model model from ppath
with open(ppath + self.tag + "_model.json", "rb") as f:
ph = pd.read_json(f, lines=True).T
ph[ph.isnull().values] = None
ph = ph.to_dict()[0]
p = pm.set(**ph)
p.hotstart(it=hotout)
# link restart file
inresfile = "/outputs/hotstart_it={}.nc".format(hotout)
outresfile = "/hotstart.nc"
logger.info("set restart\n")
try:
os.symlink(
pathlib.Path(ppath + inresfile).resolve(strict=True),
rpath + outresfile)
except OSError as e:
if e.errno == errno.EEXIST:
logger.warning("Restart link present\n")
logger.warning("overwriting\n")
os.remove(rpath + outresfile)
os.symlink(
pathlib.Path(ppath + inresfile).resolve(strict=True),
rpath + outresfile,
)
else:
raise e
# get new meteo
logger.info("process meteo\n")
flag = get_value(self, kwargs, "update", [])
check = [
os.path.exists(rpath + "sflux/" + f)
for f in ["sflux_air_1.0001.nc"]
]
if (np.any(check) == False) or ("meteo" in flag):
m.force(**info)
if hasattr(self, "meteo_split_by"):
times, datasets = zip(*m.meteo.Dataset.groupby(
"time.{}".format(self.meteo_split_by)))
mpaths = [
"sflux/sflux_air_1.{:04d}.nc".format(t + 1)
for t in np.arange(len(times))
]
for das, mpath in list(zip(datasets, mpaths)):
m.to_force(
das,
vars=["msl", "u10", "v10"],
rpath=rpath,
filename=mpath,
date=self.date0,
)
else:
m.to_force(
m.meteo.Dataset,
vars=["msl", "u10", "v10"],
rpath=rpath,
date=self.date0,
)
else:
logger.warning("meteo files present\n")
# modify param file
rnday_new = (self.sdate - self.date0).total_seconds() / (
3600 * 24.0) + pd.to_timedelta(
self.time_frame).total_seconds() / (3600 * 24.0)
hotout_write = int(rnday_new * 24 * 3600 /
info["params"]["core"]["dt"])
info["parameters"].update({
"ihot": 2,
"rnday": rnday_new,
"start_hour": self.date0.hour,
"start_day": self.date0.day,
"start_month": self.date0.month,
"start_year": self.date0.year,
})
m.config(output=True, **info) # save param.nml
m.config_file = rpath + "param.nml"
m.save()
if execute:
m.run()
logger.info("done for date :" + self.sdate.strftime("%Y%m%d.%H"))
os.chdir(pwd)