def step_3(topo_nc, list_with_synoptic_nc, dictionary_4, nc_out, create_davit_netcdf=True, log=False):
''' Procedure creates unstructured grid NetCDF file under `nc_out` fname.
Args:
-----
topo_nc (str):
path to netcdf file with x,y vectors and "bathymetry" variable for mask
list_with_synoptic_nc (list(str)):
paths to netcdf with synoptic data. At first position should be the main data-file
dictionary_1 (str):
path to txt file with dictionary to suggest standart mossco-baw variable name correlation
dictionary_2 (str):
path to txt file after scanning variables
dictionary_3 (str):
path to cdl file with standard variables
dictionary_4 (str):
path to cdl file to be created
Return:
-------
nc_out (str):
path to netcdf to be created
'''
sprint('{0}{0}{1}{0}{0}'.format(' '*20+'+'*30+'\n', ' '*20+'+'*10+' STEP 3 '+'+'*10+'\n'), log=log)
# --------------------------------------------------
# 1) Read, x any y vectors from the netcdf
# --------------------------------------------------
sprint('searching x, y, bathymetry ...', log=log)
#coords = process_mossco_netcdf.find_coordinate_vars(topo_nc, log=log)
structGrid = process_mixed_data.containerForGridGeneration(topo_nc, log=log)
coords = structGrid.get_data()
meta = structGrid.get_metadata()
# --------------------------------------------------
# 2) Create mask
# --------------------------------------------------
sprint('creating mask...', log=log)
#m = process_mossco_netcdf.make_mask_array_from_mossco_bathymetry(topo_nc, varname=coords['bName'], fillvalue=None, transpose=True, log=log)
m = structGrid.get_mask(transpose=False, log=log)
# --------------------------------------------------
# 3) Create grid, and unpack values
# --------------------------------------------------
start_index = 0
sprint('Generating uGrid... (be patient, this may take a while)')
dims, topo, nodes, edges, faces, bounds = make_grid.make_2d_qudratic_grid_or_curvilinear(coords['x'], coords['y'],
data_location=meta['x']['points_location'], mask=m, log=log, startingindex=start_index)
nMesh2_node = dims[0]
nMesh2_edge = dims[1]
nMesh2_face = dims[2]
nMaxMesh2_face_nodes = dims[3]
Mesh2_edge_nodes = topo[0]
Mesh2_edge_faces = topo[1]
Mesh2_face_nodes = topo[2]
Mesh2_face_edges = topo[3]
Mesh2_node_x = nodes[0]
Mesh2_node_y = nodes[1]
Mesh2_edge_x = edges[0]
Mesh2_edge_y = edges[1]
Mesh2_face_x = faces[0]
Mesh2_face_y = faces[1]
Mesh2_face_center_x = faces[2]
Mesh2_face_center_y = faces[3]
Mesh2_face_area = faces[4]
Mesh2_edge_x_bnd = bounds[0]
Mesh2_edge_y_bnd = bounds[1]
Mesh2_face_x_bnd = bounds[2]
Mesh2_face_y_bnd = bounds[3]
# --------------------------------------------------
# 4) Get bumber of vertical layers, dimensions from MOSSCO
# --------------------------------------------------
nLayers, layer_fname = process_mossco_netcdf.get_number_of_depth_layer_from_mossco(list_with_synoptic_nc, dimname='getmGrid3D_getm_3')
# --------------------------------------------------
# 5) Create netcdf
# --------------------------------------------------
if not create_davit_netcdf:
print "\nAbortig here...\nNetcdf has not been created, switch flag 'create_davit_netcdf' to True."
sys.exit(0)
process_davit_ncdf.create_uGrid_ncdf(nc_out,
nMesh2_node, nMesh2_edge, nMesh2_face, nMaxMesh2_face_nodes,
Mesh2_edge_nodes, Mesh2_edge_faces, Mesh2_face_nodes, Mesh2_face_edges,
Mesh2_node_x, Mesh2_node_y, Mesh2_edge_x, Mesh2_edge_y,
Mesh2_face_x, Mesh2_face_y, Mesh2_face_center_x, Mesh2_face_center_y,
Mesh2_face_area=Mesh2_face_area,
Mesh2_edge_x_bnd=Mesh2_edge_x_bnd, Mesh2_edge_y_bnd=Mesh2_edge_y_bnd,
Mesh2_face_x_bnd=Mesh2_face_x_bnd, Mesh2_face_y_bnd=Mesh2_face_y_bnd,
coord_type=meta['x']['coordinate_type'],
dim_nMesh2_layer2d=1, dim_nMesh2_layer3d=nLayers, dim_nMesh2_class_names_strlen=20, dim_nMesh2_suspension_classes=1,
start_index=start_index,
log=log)
if log: print 'grid created', '\n', '-'*100, '\n', 'Now adding data', '\n', '-'*100
# --------------------------------------------------
# 6) fill netcdf with time variables (TIME and DATATIME)
# --------------------------------------------------
if log: print '-'*100
time_added = False
for nc_file in list_with_synoptic_nc:
try:
process_davit_ncdf.append_Time_andDatetime_to_netcdf(nc_out, nc_file, time_var_name='time', log=log)
if log: print 'added "nMesh2_data_time" from file ', nc_file
time_added = True
break
except KeyError: # if var is not found in current file => skip to next file
pass
if not time_added:
print 'WARNING! added dummy "nMesh2_data_time"'
process_davit_ncdf.append_Time_andDatetime_to_netcdf(nc_out, dummy_values=True, log=log)
if log: print '-'*100
# ---------------------------------------------------------------------------
# 7) Layer thicness
# ---------------------------------------------------------------------------
# now moved to the very bottom, since we want to use dictionary VARS
# that is generated by processing Dict4
# --------------------------------------------------
# 8) fill netcdf with SYNOPTIC data!!!
# --------------------------------------------------
if log: print '-'*100+'\n+Now adding data based on Dictionary 4.\n'+'-'*100
# --------------------------------------------------
# -- 8.1) fill netcdf with SYNOPTIC data!!!
# --------------------------------------------------
VARS = process_cdl.read_file_with_only_variables(process_cdl.read_file_delete_comments(dictionary_4, comments='//'))
# -----------------------------------------------------------------------------------------------
# -- 8.2) cycle through found variables
# -----------------------------------------------------------------------------------------------
for var_name, var in VARS.iteritems():
sprint('Variable read from Dictionary 4:', var.get_name(), log=log)
varExt = process_mixed_data.cdlVariableExt(var) #var is an instance of type <cdlVariable>
source = varExt.get_source_metadata()
# -----------------------------------------------------------------------------------------------
# 8.2.4) add data
# -----------------------------------------------------------------------------------------------
if source['nNonOneDims'] not in [0, 1, 2, 3, 4]:
ui.promt('WARNING! Skipping variable: <{0}> with dimensions <{1}> of shape <{2}>. It has <{3}> non-one dimensions. Currently <=4 is supported. Press ENTER to continue'.format(
source['name'], source['dims'], source['shape']), source['nNonOneDims'], color='yellow', pause=True)
break
raw_data = process_mossco_netcdf.read_mossco_nc_rawvar(source['fname'], source['name'])
var_data = process_mixed_data.flatten_xy_data(raw_data, mask=m)
# -----------------------------------------------------------------------------------------------
# 8.2.6) append data variable to nc_out...
# -----------------------------------------------------------------------------------------------
process_davit_ncdf.append_VariableData_to_netcdf(nc_out, var, var_data, fv=source['fillvalue'], log=log)
sprint('\n', log=log)
del varExt
# -----------------------------------------------------------------------------------------------
# 9) Layer thickness
# -----------------------------------------------------------------------------------------------
sprint('-'*100, log=log)
sprint('Now adding vertical layer information', log=log)
sprint('-'*100, log=log)
vertical_coord_mode = 'sigma'
if nLayers > 1: #if a real 3d is here
LAYERS_ADDED = False
if vertical_coord_mode == 'sigma':
add_eta = 'Mesh2_face_Wasserstand_2d' in VARS.keys()
add_depth = 'Mesh2_face_depth_2d' in VARS.keys()
try:
process_davit_ncdf.append_sigma_vertical_coord_vars(list_with_synoptic_nc, nLayers, nc_out, add_eta=add_eta, add_depth=add_depth, mask=m, log=log)
LAYERS_ADDED = True
except Exception as exp:
sprint(exp, mode='fail')
traceback.print_exc(file=sys.stderr)
else:
raise NotImplementedError()
if not LAYERS_ADDED:
ui.promt('Now i will try to add dummy vertical data. Press ENTER to see info about these values', pause=True)
sprint(process_davit_ncdf.append_test_Mesh2_face_z_3d_and_Mesh2_face_z_3d_bnd.__doc__)
if ui.promtYesNo('Do you want to proceed?', quitonno=True):
try:
process_davit_ncdf.append_test_Mesh2_face_z_3d_and_Mesh2_face_z_3d_bnd(nc_out, nx=meta['b']['shape'][-1],
ny=meta['b']['shape'][-2], mask=m, log=log)
except Exception as exp:
sprint(exp, mode='fail')
traceback.print_exc(file=sys.stderr)
ui.promt('Failed to find any vertical-layer information. Will proceed without any. Press ENTER', color='yellow', pause=True)
if log: print '-'*100
if create_davit_netcdf:
print 'File created:', os.path.abspath(nc_out)
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'
