def append_Time_andDatetime_to_netcdf(fname_davitnc, fname_mossconc=None, time_var_name='time', dummy_values=False, log=True):
# --------------------------------------------------
# 3.1) fill netcdf with time variables (TIME and DATATIME)
# --------------------------------------------------
if dummy_values is False:
_nc = Dataset(fname_mossconc, mode='r')
time_var_units = _nc.variables[time_var_name].units
max_t = _nc.variables[time_var_name][:].max()
min_t = _nc.variables[time_var_name][:].min()
_nc.close()
else:
time_var_units = 'seconds since 2000-01-01 00:00:00'
max_t = 60*60*24
min_t = 0
var = process_cdl.cdlVariable()
var.set_name('nMesh2_time')
var.set_dtype('double')
var.set_dims(('nMesh2_time', ))
var.set_fillvalue(False)
var.set_attr('long_name', "time")
# because currently MOSSCO writes a time output as "hours since 2009-01-02 00:00:00",
# it is nessesary to modify it. Will be removed, after corrections in MOSSCO.
var.set_attr('units', time_var_units+' 01:00') # '01:00 is indicating timezone, see CF conventions for details'
var.set_attr('name_id', 1640)
var.set_attr('axis', "T")
var.set_attr('bounds', "nMesh2_time_bnd")
var.set_attr('calendar', "gregorian")
var.set_attr('standard_name', "time")
if dummy_values:
var.set_attr('comment', "warning: dummy values are used")
var_data = np.array([min_t])
append_VariableData_to_netcdf(fname_davitnc, var, var_data, fv=var.get_fillvalue(), log=log)
del var
var = process_cdl.cdlVariable()
var.set_name('nMesh2_time_bnd')
var.set_dtype('double')
var.set_dims(('nMesh2_time', 'two'))
var.set_fillvalue(False)
if dummy_values:
var.set_attr('comment', "warning: dummy values are used")
var_data = np.array([min_t, max_t])
append_VariableData_to_netcdf(fname_davitnc, var, var_data, fv=var.get_fillvalue(), log=log)
del var
if dummy_values is False:
var = process_cdl.cdlVariable()
var.set_name('nMesh2_data_time')
var.set_dtype('double')
var.set_dims(('nMesh2_data_time', ))
var.set_fillvalue(False)
var.set_attr('long_name', "time")
var.set_attr('units', time_var_units + ' 01:00')
var.set_attr('name_id', 1640)
var.set_attr('axis', "T")
var.set_attr('calendar', "gregorian")
var.set_attr('standard_name', "time")
var_data = process_mossco_netcdf.read_mossco_nc_1d(fname_mossconc, 'time')
append_VariableData_to_netcdf(fname_davitnc, var, var_data, fv=var.get_fillvalue(), log=log)
del var
def append_sigma_vertical_coord_vars(list_with_filenames, nLayers, nc_out_fname, add_eta=False, add_depth=False, mask=None, sigma_varname='level', log=False):
''' Appends variables that define vertical position of layers...
- nMesh2_layer_3d >>> 1d sigma coords of cell center
- Mesh2_face_z_face_3d >>> elevation cell center values
- Mesh2_face_z_face_3d_bnd >>> elevation cell border values
- (optionaly) Mesh2_face_Wasserstand_2d >>> water level
- (optionaly) Mesh2_face_depth_2d >>> bottom depth
... to passed `nc_out_fname` netcdf file
Args:
-----
list_with_filenames (list of str):
list with names of netcdf files. The var `sigma_varname` will be searched within this files
nLayers (int):
number of vertical layers
nc_out_fname (str):
filename of the output netcdf file
add_eta (bool):
flag to add variable "Mesh2_face_Wasserstand_2d" to file `nc_out_fname`.
This is useful because, most likely this var is already appended or will be
appended to file based on DICTIONARY4
add_depth (bool):
flag to add variable "Mesh2_face_depth_2d" to file `nc_out_fname`
This is useful because, most likely this var is already appended or will be
appended to file based on DICTIONARY4
mask (2D array of bool):
2d array of (y, x) dimensions with boolean mask (to treat NaN cells)
sigma_varname (str):
name of the varable to get sigma-layer info from
log (bool):
flag to print output
'''
_i = '\t'
_n = 'append_sigma_vertical_coord_vars()'
sprint(_n, 'Appending sigma_vertical coordinates ...', log=log, mode='bold')
# ----------------------------------------
# ----------------------------------------
# --------------- SIGMA ---------------
# ----------------------------------------
# ----------------------------------------
var = process_cdl.cdlVariable()
var.set_name('nMesh2_layer_3d')
var.set_dtype('double')
var.set_dims(('nMesh2_layer_3d', ))
var.set_fillvalue(False)
var.set_attr('standard_name', 'ocean_sigma_coordinate')
var.set_attr('long_name', "sigma at layer midpoints")
var.set_attr('positive', 'up')
var.set_attr('formula_terms', 'sigma: nMesh2_layer_3d eta: Mesh2_face_Wasserstand_2d depth: Mesh2_face_depth_2d')
sigma, sigma_type = process_mossco_netcdf.get_sigma_coordinates(list_with_filenames, nLayers, sigma_varname=sigma_varname, waterdepth_varname='water_depth_at_soil_surface', layerdepth_varname='getmGrid3D_getm_layer', indent=_i, log=log)
if sigma_type == 'center':
pass
elif sigma_type == 'border':
sigma = process_mixed_data.create_sigma_coords_of_layer_center(sigma)
append_VariableData_to_netcdf(nc_out_fname, var, sigma, fv=var.get_fillvalue(), log=log, indent=_i)
del var
bathymetry = None
for nc_file in list_with_filenames:
root_grp = Dataset(nc_file, mode='r')
if 'bathymetry' in root_grp.variables.keys() and bathymetry is None:
bathymetry = process_mossco_netcdf.read_mossco_nc_rawvar(nc_file, 'bathymetry')
root_grp.close()
del root_grp
# ----------------------------------------
# ----------------------------------------
# --------------- ETA -----------------
# ----------------------------------------
# ----------------------------------------
var_e = process_cdl.cdlVariable()
var_e.set_name('Mesh2_face_Wasserstand_2d')
var_e.set_dtype('float')
var_e.set_dims(('nMesh2_data_time', 'nMesh2_face'))
var_e.set_fillvalue(False)
var_e.set_attr('long_name', "Wasserstand, Face (Polygon)")
var_e.set_attr('standard_name', 'sea_surface_height')
var_e.set_attr('units', 'm')
var_e.set_attr('name_id', 3)
var_e.set_attr('cell_measures', 'area: Mesh2_face_wet_area')
var_e.set_attr('cell_measures', 'nMesh2_data_time: point area: mean')
var_e.set_attr('coordinates', 'Mesh2_face_x Mesh2_face_y Mesh2_face_lon Mesh2_face_lat')
var_e.set_attr('grid_mapping', 'Mesh2_crs')
var_e.set_attr('mesh', 'Mesh2')
var_e.set_attr('location', 'face')
sprint(_n, ' Get waterlevel ...', log=log, mode='bold')
water_level = process_mossco_netcdf.get_water_level(list_with_filenames, wl_vname='water_level',
water_depth_at_soil_surface_vname='water_depth_at_soil_surface', bathymetry_vname='bathymetry',
log=log, indent=_i)
# append var after
# ----------------------------------------
# ----------------------------------------
# -------------- DEPTH ----------------
# ----------------------------------------
# ----------------------------------------
var_d = process_cdl.cdlVariable()
var_d.set_name('Mesh2_face_depth_2d')
var_d.set_dtype('double')
var_d.set_dims(('nMesh2_time', 'nMesh2_face'))
var_d.set_fillvalue(False)
var_d.set_attr('long_name', "Topographie")
var_d.set_attr('standard_name', 'sea_floor_depth_below_geoid')
var_d.set_attr('units', 'm')
var_d.set_attr('name_id', 17)
var_d.set_attr('cell_measures', 'area: Mesh2_face_area')
var_d.set_attr('cell_measures', 'nMesh2_time: mean area: mean')
var_d.set_attr('coordinates', 'Mesh2_face_x Mesh2_face_y Mesh2_face_lon Mesh2_face_lat')
var_d.set_attr('grid_mapping', 'Mesh2_crs')
var_d.set_attr('mesh', 'Mesh2')
var_d.set_attr('location', 'face')
# append var after
# ----------------------------------------
# ----------------------------------------
# ------------ ELEVATION --------------
# ----------------------------------------
# ----------------------------------------
# FACE cell center values.....
# ----------------------------------------
var1 = process_cdl.cdlVariable()
var1.set_name('Mesh2_face_z_face_3d')
var1.set_dtype('float')
var1.set_dims(('nMesh2_data_time', 'nMesh2_layer_3d', 'nMesh2_face'))
var1.set_fillvalue(None)
var1.set_attr('long_name', 'z_face [ face ]')
var1.set_attr('units', 'm')
var1.set_attr('positive', 'up')
var1.set_attr('name_id', 1702)
var1.set_attr('bounds', 'Mesh2_face_z_face_bnd_3d')
var1.set_attr('standard_name', 'depth')
# ----------------------------------------
# FACE cell border values.....
# ----------------------------------------
var2 = process_cdl.cdlVariable()
var2.set_name('Mesh2_face_z_face_bnd_3d')
var2.set_dtype('float')
var2.set_dims(('nMesh2_data_time', 'nMesh2_layer_3d', 'nMesh2_face', 'two'))
var2.set_fillvalue(None)
var2.set_attr('long_name', 'elevations of lower and upper layer-boundaries')
var2.set_attr('units', 'm')
sprint(_n, ' Get elevation of cell centers and cell borders ...', log=log, mode='bold')
elev, elev_borders = process_mixed_data.create_layer_elevation_from_sigma_coords(water_level, sigma, bathymetry, log=log, indent=_i)
var_data1 = process_mixed_data.flatten_xy_data(elev, mask=mask)
var_data2 = process_mixed_data.flatten_xy_data(elev_borders, mask=mask)
append_VariableData_to_netcdf(nc_out_fname, var1, var_data1, fv=var1.get_fillvalue(), log=log, indent=_i)
append_VariableData_to_netcdf(nc_out_fname, var2, var_data2, fv=var2.get_fillvalue(), log=log, indent=_i)
del var1, var2
if add_depth:
var_data = process_mixed_data.flatten_xy_data(bathymetry, mask=mask)
append_VariableData_to_netcdf(nc_out_fname, var_d, var_data, fv=var_d.get_fillvalue(), log=log, indent=_i)
del var_d
if add_eta:
var_data = process_mixed_data.flatten_xy_data(water_level, mask=mask)
append_VariableData_to_netcdf(nc_out_fname, var_e, var_data, fv=var_e.get_fillvalue(), log=log, indent=_i)
del var_e
if log:
print '-'*25+'\n'
def append_test_Mesh2_face_z_3d_and_Mesh2_face_z_3d_bnd(fname_davit, nx=0, ny=0, mask=None, log=False):
'''
DUMMY VALUES!!!
Function appends to DAVIT netcdf following variables:
Mesh2_face_z_face_3d
Mesh2_face_z_face_bnd_3d
Mesh2_edge_z_edge_3d
Mesh2_edge_z_edge_bnd_3d
The data stored is artificial (!!!):
- layers are in down-positiv order (first layer is at surface)
- each layer is 1m thick
- layer-borders are (0,1), (1,2), (2,3), ..., (NLAYERS-1, NLAYERS) in meters
'''
'''
INPUT:
fname_davit, fname_mossco - strings, pathes to files
mask - an boolean mask 2D array. See function process_mossco_netcdf.make_mask_array_from_mossco_bathymetry()
log - boolean Flag to print output in console
CDL EXAMPLE:
float Mesh2_face_z_face_3d(nMesh2_data_time, nMesh2_layer_3d, nMesh2_face) ;
Mesh2_face_z_face_3d:long_name = "z_face [ face ]" ;
Mesh2_face_z_face_3d:units = "m" ;
Mesh2_face_z_face_3d:name_id = 1702 ;
Mesh2_face_z_face_3d:positive = "down" ;
Mesh2_face_z_face_3d:bounds = "Mesh2_face_z_face_bnd_3d" ;
Mesh2_face_z_face_3d:standard_name = "depth" ;
'''
if log: print 'running: append_test_Mesh2_face_z_3d_and_Mesh2_face_z_3d_bnd()'
# get dimensions....
# ----------------------------------------------------------------------------
_nc = Dataset(fname_davit, mode='r')
try:
nt = _nc.dimensions['nMesh2_data_time'].__len__()
except:
nt = _nc.dimensions['nMesh2_time'].__len__()
nz = _nc.dimensions['nMesh2_layer_3d'].__len__()
nFaces = _nc.dimensions['nMesh2_face'].__len__()
nEdges = _nc.dimensions['nMesh2_edge'].__len__()
_nc.close()
if log:
print 'nZ, nY, nX =', nz, ny, nx
print 'nTimesteps =', nt
print 'nFaces =', nFaces
print 'nEdges =', nEdges
# FACE middle values.....
# ----------------------------------------------------------------------------
var = process_cdl.cdlVariable()
var.set_name('Mesh2_face_z_face_3d')
var.set_dtype('float')
var.set_dims(('nMesh2_data_time', 'nMesh2_layer_3d', 'nMesh2_face'))
var.set_fillvalue(None)
var.set_attr('long_name', 'z_face [ face ]')
var.set_attr('units', 'm')
var.set_attr('positive', 'down')
var.set_attr('name_id', 1702)
var.set_attr('bounds', 'Mesh2_face_z_face_bnd_3d')
var.set_attr('standard_name', 'depth')
var.set_attr('comment', "warning: dummy values are used")
davit_dummy = np.zeros((nt, nz, nFaces))
for z in xrange(nz):
davit_dummy[:, z, :] = nz-z-0.5 # this equation will produce values like 0.5, 1.5, 2.5, ..., nz-1.0-0.5
var_data = davit_dummy
append_VariableData_to_netcdf(fname_davit, var, var_data, fv=var.get_fillvalue(), log=log)
del var
# FACE bounds values...
# ----------------------------------------------------------------------------
if log: print '{0}{1}\n{0}'.format('+'*50+'\n', 'Face Bounds')
var = process_cdl.cdlVariable()
var.set_name('Mesh2_face_z_face_bnd_3d')
var.set_dtype('float')
var.set_dims(('nMesh2_data_time', 'nMesh2_layer_3d', 'nMesh2_face', 'two'))
var.set_fillvalue(None)
var.set_attr('name_id', 1703)
#var.set_attr('units', 'm')
var.set_attr('comment', "warning: dummy values are used")
davit_dummy = np.zeros((nt, nz, nFaces, 2))
for z in xrange(nz):
davit_dummy[:, z, :, 0] = nz-z-1. # this equation will produce values like 0, 1, 2, ... nz-z
davit_dummy[:, z, :, 1] = nz-z+0. # this equation will produce values like 1, 2, 3, ... nz-z+1
var_data = davit_dummy
append_VariableData_to_netcdf(fname_davit, var, var_data, fv=var.get_fillvalue(), log=log)
del var
if log: print '{0}{1}\n{0}'.format('+'*50+'\n', 'EDGE')
# EDGE middle values.....
# ----------------------------------------------------------------------------
var = process_cdl.cdlVariable()
var.set_name('Mesh2_edge_z_edge_3d')
var.set_dtype('float')
var.set_dims(('nMesh2_data_time', 'nMesh2_layer_3d', 'nMesh2_edge'))
var.set_fillvalue(None)
var.set_attr('long_name', 'z_edge [ edge ]')
var.set_attr('units', 'm')
var.set_attr('positive', 'down')
var.set_attr('name_id', 1707)
var.set_attr('bounds', 'Mesh2_edge_z_edge_bnd_3d')
var.set_attr('standard_name', 'depth')
var.set_attr('comment', "warning: dummy values are used")
davit_dummy = np.zeros((nt, nz, nEdges))
for z in xrange(nz):
davit_dummy[:, z, :] = nz-z-0.5 # this equation will produce values like 0.5, 1.5, 2.5, ..., nz-1.0-0.5
var_data = davit_dummy
append_VariableData_to_netcdf(fname_davit, var, var_data, fv=var.get_fillvalue(), log=log)
del var
# EDGE bounds values...
# ----------------------------------------------------------------------------
if log: print '{0}{1}\n{0}'.format('+'*50+'\n', 'EDGE Bounds')
var = process_cdl.cdlVariable()
var.set_name('Mesh2_edge_z_edge_bnd_3d')
var.set_dtype('float')
var.set_dims(('nMesh2_data_time', 'nMesh2_layer_3d', 'nMesh2_edge', 'two'))
var.set_fillvalue(None)
var.set_attr('name_id', 1708)
#var.set_attr('units', 'm')
var.set_attr('comment', "warning: dummy values are used")
davit_dummy = np.zeros((nt, nz, nEdges, 2))
for z in xrange(nz):
davit_dummy[:, z, :, 0] = nz-z-1. # this equation will produce values like 0, 1, 2, ... nz-z
davit_dummy[:, z, :, 1] = nz-z+0. # this equation will produce values like 1, 2, 3, ... nz-z+1
var_data = davit_dummy
append_VariableData_to_netcdf(fname_davit, var, var_data, fv=var.get_fillvalue(), log=log)
del var
if log: print 'finished: append_test_Mesh2_face_z_3d_and_Mesh2_face_z_3d_bnd()'
