dfm-tools 0.10.55__py3-none-any.whl

dfm_tools/__init__.py

@@ -0,0 +1,26 @@
+"""
+.. include:: ../README.md
+"""
+
+__author__ = """Jelmer Veenstra"""
+__email__ = 'jelmer.veenstra@deltares.nl'
+__version__ = '0.10.55'
+
+from dfm_tools.deprecated import *
+from dfm_tools.errors import *
+from dfm_tools.download import *
+from dfm_tools.get_nc import *
+from dfm_tools.get_nc_helpers import *
+from dfm_tools.hydrolib_helpers import *
+from dfm_tools.meshkernel_helpers import *
+from dfm_tools.interpolate_grid2bnd import *
+from dfm_tools.linebuilder import *
+from dfm_tools.modplot import *
+from dfm_tools.regulargrid import *
+from dfm_tools.xarray_helpers import *
+from dfm_tools.energy_dissipation import *
+from dfm_tools.bathymetry import *
+#from dfm_tools.modelbuilder import * #commented since we do not want to expose these functions with hardcoded parameters
+
+import warnings
+warnings.filterwarnings('always',category=DeprecationWarning)

dfm_tools/bathymetry.py

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+# -*- coding: utf-8 -*-
+"""
+Created on Mon May 31 17:17:09 2021
+
+@author: veenstra
+"""
+
+import numpy as np
+
+
+def write_bathy_toasc(filename_asc,lon_sel_ext,lat_sel_ext,elev_sel_ext,asc_fmt='%9.2f',nodata_val=32767):
+
+    print('writing to asc file')
+    if elev_sel_ext.shape != (lat_sel_ext.shape[0], lon_sel_ext.shape[0]):
+        raise ValueError('resulting shape of elev_sel_ext %s is not consistent with lat_sel_ext/lon_sel_ext vars %s'%(elev_sel_ext.shape,(lat_sel_ext.shape[0], lon_sel_ext.shape[0])))
+    if isinstance(elev_sel_ext,np.ma.core.MaskedArray): #masked has to be filled in order for the nans to be visible
+        elev_sel_ext = elev_sel_ext.filled(np.nan)
+    if np.isnan(elev_sel_ext).sum()>0:
+        elev_sel_ext = elev_sel_ext.copy()
+        elev_sel_ext[np.isnan(elev_sel_ext)] = nodata_val
+        print('replaced nan values with %d'%(nodata_val))
+    resinv_lonlat = np.round(1/np.diff(lon_sel_ext[:2]),2)
+    resinv_lat = np.round(1/np.diff(lat_sel_ext[:2]),2)
+    if resinv_lonlat!=resinv_lat:
+        raise ValueError('inconsistent resolution over lat/lon')
+    
+    with open(filename_asc,'w') as file_asc:
+        file_asc.write('ncols         %d\n'%(elev_sel_ext.shape[1]))
+        file_asc.write('nrows         %d\n'%(elev_sel_ext.shape[0]))
+        file_asc.write('xllcenter     %13.8f\n'%(lon_sel_ext[0]))
+        file_asc.write('yllcenter     %13.8f\n'%(lat_sel_ext[0]))
+        file_asc.write('cellsize      %16.11f\n'%(1/resinv_lonlat))
+        #file_asc.write('NODATA_value  %d\n'%(nodata_val))
+        file_asc.write('NODATA_value  '+asc_fmt%(nodata_val)+'\n')
+    with open(filename_asc,'a') as file_asc:
+        np.savetxt(file_asc,np.flip(elev_sel_ext,axis=0),fmt=asc_fmt)
+    print('...finished')
+

dfm_tools/deprecated.py

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+# -*- coding: utf-8 -*-
+"""
+Created on Sun Apr 23 22:42:27 2023
+
+@author: veenstra
+"""
+
+
+def plot_background(ax=None, projection=None, google_style='satellite', resolution=1, features=None, nticks=6, latlon_format=False, gridlines=False, **kwargs):
+    raise DeprecationWarning('dfmt.plot_background() is deprecated, use contextily and cartopy instead like in https://github.com/Deltares/dfm_tools/blob/main/tests/examples_workinprogress/workinprogress_cartopy_satellite_coastlines.py')
+
+
+def get_ugrid_verts(data_xr_map):
+    """
+    getting ugrid verts from xugrid mapfile.
+    """
+    raise DeprecationWarning('dfmt.get_ugrid_verts() is deprecated, use uds.grid.face_node_coordinates instead (https://github.com/Deltares/xugrid/issues/48)')
+
+
+def scatter_to_regulargrid(xcoords, ycoords, values, ncellx=None, ncelly=None, reg_x_vec=None, reg_y_vec=None, method='nearest', maskland_dist=None):
+    raise DeprecationWarning('dfm_tools.regulargrid.scatter_to_regulargrid() is deprecated, use ds = dfmt.rasterize_ugrid(uds) instead')
+
+
+def get_varnamefromattrs(data_xr, varname):
+    raise DeprecationWarning('dfmt.get_varnamefromattrs() will be deprecated in a future version of dfm_tools, ds=dfmt.rename_waqvars(ds) is a more convenient alternative')
+
+
+class Polygon:
+    def __init__(self, data, name, comments):
+        raise DeprecationWarning('the function dfm_tools.polygon.Polygon() is deprecated, please use the new hydrolib alternative.')
+        
+    def fromfile(self, file_pol, pd_output=False, tekmap_output=False):
+        raise DeprecationWarning('the function dfm_tools.polygon.Polygon.fromfile() is deprecated, please use the new hydrolib alternative. Example script: https://github.com/Deltares/dfm_tools/blob/main/tests/examples/preprocess_hydrolib_readwritepol.py')
+
+
+def write_bcfile(filename, datablocks, metadatas, refdate=None, tzone=0, float_format='%6.2f'):
+    raise DeprecationWarning('the function dfm_tools.io.bc.write_bcfile() is deprecated, please use the new hydrolib alternative. Example script: dfm_tools/tests/examples/CMEMS_interpolate_example.py')
+
+
+def read_bcfile(filename, converttime=False):
+    raise DeprecationWarning('the function dfm_tools.io.bc.read_bcfile() is deprecated, please use the new hydrolib alternative. Example script: dfm_tools/tests/examples/hydrolib_readbc.py')
+
+
+def write_timfile(filename, datablock, header, converttime=False, refdate=None, float_format='%6.2f'):
+    raise DeprecationWarning('the function dfm_tools.write_timfile() is deprecated, please use the new hydrolib alternative: https://github.com/Deltares/dfm_tools/blob/301-convert-timmodel-to-pandasdataframe/tests/examples/preprocess_hydrolib_readtim.py.')
+
+
+def read_timfile(filename, converttime=False, refdate=None):
+    raise DeprecationWarning('the function dfm_tools.read_timfile() is deprecated, please use the new hydrolib alternative: https://github.com/Deltares/dfm_tools/blob/301-convert-timmodel-to-pandasdataframe/tests/examples/preprocess_hydrolib_readtim.py.')
+

dfm_tools/download.py

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+# -*- coding: utf-8 -*-
+"""
+Created on Tue Oct 18 15:09:26 2022
+
+@author: veenstra
+"""
+
+import os
+import pandas as pd
+from pathlib import Path
+import xarray as xr
+from pydap.client import open_url
+from pydap.cas.get_cookies import setup_session
+import warnings
+from dfm_tools.errors import OutOfRangeError
+import cdsapi
+import cftime
+
+
+def download_ERA5(varkey,
+                  longitude_min, longitude_max, latitude_min, latitude_max, 
+                  date_min, date_max,
+                  dir_output='.', overwrite=False):
+    
+    #TODO: describe something about the .cdsapirc file
+    #TODO: make this function cdsapi generic, instead of ERA5 hardcoded (make flexible for product_type/name/name_output) (variables_dict is not used actively anymore, so this is possible)
+    
+    c = cdsapi.Client() # import cdsapi and create a Client instance # https://cds.climate.copernicus.eu/api-how-to
+    
+    #dictionary with ERA5 variables #this is not actively used
+    variables_dict = {'ssr':'surface_net_solar_radiation',
+                      'sst':'sea_surface_temperature',
+                      'strd':'surface_thermal_radiation_downwards',
+                      'slhf':'surface_latent_heat_flux',
+                      'sshf':'surface_sensible_heat_flux',
+                      'str':'surface_net_thermal_radiation',
+                      'chnk':'charnock',
+                      'd2m':'2m_dewpoint_temperature',
+                      't2m':'2m_temperature',
+                      'tcc':'total_cloud_cover',
+                      'msl':'mean_sea_level_pressure',
+                      'u10':'10m_u_component_of_wind',
+                      'u10n':'10m_u_component_of_neutral_wind',
+                      'v10':'10m_v_component_of_wind',
+                      'v10n':'10m_v_component_of_neutral_wind',
+                      'mer':'mean_evaporation_rate',
+                      'mtpr':'mean_total_precipitation_rate',
+                      }
+    if varkey not in variables_dict.keys(): #TODO: how to get list of available vars? mean_sea_level_pressure and msl both return a dataset with msl varkey, but standard_name air_pressure_at_mean_sea_level returns an error
+        raise KeyError(f'"{varkey}" not available, choose from: {list(variables_dict.keys())}')
+    
+    period_range = pd.period_range(date_min,date_max,freq='M')
+    print(f'retrieving data from {period_range[0]} to {period_range[-1]} (freq={period_range.freq})')
+    
+    for date in period_range:
+        name_output = f'era5_{varkey}_{date.strftime("%Y-%m")}.nc'
+        file_out = Path(dir_output,name_output)
+        if file_out.is_file() and not overwrite:
+            print(f'"{name_output}" found and overwrite=False, continuing.')
+            continue
+        print (f'retrieving ERA5 data for variable "{varkey}" and month {date.strftime("%Y-%m")} (YYYY-MM)')
+
+        request_dict = {'product_type':'reanalysis',
+                        'variable':variables_dict[varkey],
+                        'year':date.strftime('%Y'),
+                        'month':date.strftime('%m'),
+                        #'month':[f'{x:02d}' for x in range(1,12+1)], #all months, but instead retrieving per month
+                        'day':[f'{x:02d}' for x in range(1,31+1)], #all days
+                        'time':[f'{x:02d}:00' for x in range(0,23+1)], #all times/hours
+                        'area':[latitude_max,longitude_min,latitude_min,longitude_max], # north, west, south, east. default: global - option not available through the Climate Data Store (CDS) web interface (for cmip data)
+                        #'grid': [1.0, 1.0], # latitude/longitude grid: east-west (longitude) and north-south resolution (latitude). default: 0.25 x 0.25 - option not available through the Climate Data Store (CDS) web interface
+                        'format':'netcdf'}
+        
+        c.retrieve(name='reanalysis-era5-single-levels', request=request_dict, target=file_out)
+
+
+def download_CMEMS(varkey,
+                   longitude_min, longitude_max, latitude_min, latitude_max, 
+                   date_min, date_max, freq='D',
+                   dir_output='.', file_prefix='', overwrite=False,
+                   credentials=None):
+
+    date_min = pd.Timestamp(date_min)-pd.Timedelta(days=1) #CMEMS has daily noon values (not midnight), so subtract one day from date_min to cover desired time extent
+    
+    if 'my_datemax' not in globals(): #set multiyear date_max (my_datemax) as global variable, so it only has to be retreived once per download run (otherwise once per variable)
+        print('retrieving enddate of multiyear CMEMS dataset')
+        dataset_url = 'https://my.cmems-du.eu/thredds/dodsC/cmems_mod_glo_phy_my_0.083_P1D-m' #assuming here that physchem and bio reanalyisus/multiyear datasets have the same enddate, this seems safe
+        ds = open_OPeNDAP_xr(dataset_url=dataset_url, credentials=credentials)
+        my_times = ds.time.to_series()
+        global my_datemax
+        my_datemax = my_times.iloc[-1]
+
+    if pd.Timestamp(date_max) <= my_datemax:
+        product = 'reanalysis'
+    elif pd.Timestamp(date_min) > my_datemax:
+        product = 'analysisforecast'
+    else:
+        raise ValueError(f'Requested timerange is {date_min} to {date_max}. Currently, it is only possible to query periods before OR after the multiyear/reanalysis enddate ({my_datemax}).')
+    
+    Path(dir_output).mkdir(parents=True, exist_ok=True)
+    if varkey in ['bottomT','tob','mlotst','siconc','sithick','so','thetao','uo','vo','usi','vsi','zos']: #for physchem
+        if product == 'analysisforecast': #forecast: https://data.marine.copernicus.eu/product/GLOBAL_ANALYSISFORECAST_PHY_001_024/description
+            if varkey=='bottomT': #rename old to new anfc varname (still called bottomT in reanalysis)
+                varkey = 'tob'
+            if varkey in ['uo','vo']:
+                varkey_name = 'phy-cur'
+            elif varkey in ['so','thetao']:
+                varkey_name = 'phy-'+varkey
+            else:
+                varkey_name = 'phy'
+            dataset_url = f'https://nrt.cmems-du.eu/thredds/dodsC/cmems_mod_glo_{varkey_name}_anfc_0.083deg_P1D-m'#.html' #TODO: also PT6H-i timeresolution available but not for all variables and not for reanalysis
+        else: #reanalysis: https://data.marine.copernicus.eu/product/GLOBAL_MULTIYEAR_PHY_001_030/description
+            dataset_url = 'https://my.cmems-du.eu/thredds/dodsC/cmems_mod_glo_phy_my_0.083_P1D-m'
+    else: #for bio
+        if product == 'analysisforecast': #forecast: https://data.marine.copernicus.eu/product/GLOBAL_ANALYSISFORECAST_PHY_001_024/description
+            dataset_url = 'https://nrt.cmems-du.eu/thredds/dodsC/global-analysis-forecast-bio-001-028-daily' #contains ['chl','fe','no3','nppv','o2','ph','phyc','po4','si','spco2']
+        else: #https://data.marine.copernicus.eu/product/GLOBAL_MULTIYEAR_BGC_001_029/description
+            dataset_url = 'https://my.cmems-du.eu/thredds/dodsC/cmems_mod_glo_bgc_my_0.25_P1D-m' #contains ['chl','no3','nppv','o2','po4','si']
+    
+    download_OPeNDAP(dataset_url=dataset_url,
+                     credentials=credentials, #credentials=['username','password'], or create "%USERPROFILE%/CMEMS_credentials.txt" with username on line 1 and password on line 2. Register at: https://resources.marine.copernicus.eu/registration-form'
+                     varkey=varkey,
+                     longitude_min=longitude_min, longitude_max=longitude_max, latitude_min=latitude_min, latitude_max=latitude_max,
+                     date_min=date_min, date_max=date_max,
+                     dir_output=dir_output, file_prefix=file_prefix, overwrite=overwrite)
+
+
+def open_OPeNDAP_xr(dataset_url, credentials=None):
+    """
+    How to get the opendap dataset_url (CMEMS example):
+        - https://data.marine.copernicus.eu/products
+        - go to the data access tab of a product, e.g.: https://data.marine.copernicus.eu/product/GLOBAL_MULTIYEAR_PHY_001_030/services
+        - click the opendap link of the dataset of your choice
+        - copy the dataset_url from the adress bar (excl .html), e.g.: https://my.cmems-du.eu/thredds/dodsC/cmems_mod_glo_phy_my_0.083_P1D-m
+        
+        Example multiyear phys/chem:
+            https://data.marine.copernicus.eu/product/GLOBAL_MULTIYEAR_PHY_001_030/services
+            https://my.cmems-du.eu/thredds/dodsC/cmems_mod_glo_phy_my_0.083_P1D-m
+            ['bottomT','mlotst','siconc','sithick','so','thetao','uo','usi','vo','vsi','zos']
+        Example multiyear bio:
+            https://data.marine.copernicus.eu/product/GLOBAL_MULTIYEAR_BGC_001_029/services
+            https://my.cmems-du.eu/thredds/dodsC/cmems_mod_glo_bgc_my_0.25_P1D-m
+            ['chl','no3','nppv','o2','po4','si']
+        Example forecast phys/chem:
+            https://data.marine.copernicus.eu/product/GLOBAL_ANALYSIS_FORECAST_PHY_001_024/services
+            https://nrt.cmems-du.eu/thredds/dodsC/global-analysis-forecast-phy-001-024
+            ['bottomT','mlotst','siconc','sithick','so','thetao','uo','usi','vo','vsi','zos']
+        Example forecast bio:
+            https://data.marine.copernicus.eu/product/GLOBAL_ANALYSIS_FORECAST_BIO_001_028/services
+            https://nrt.cmems-du.eu/thredds/dodsC/global-analysis-forecast-bio-001-028-daily
+            ['chl','fe','no3','nppv','o2','ph','phyc','po4','si','spco2']
+    
+    How to get the opendap dataset_url (HYCOM example):
+        - https://www.hycom.org/dataserver
+        - Select a product and search for THREDDS, e.g.: https://www.hycom.org/dataserver/gofs-3pt1/analysis
+        - find an opendap dataset_url, it depends per product/run where to find it.
+        Some examples:
+            https://tds.hycom.org/thredds/dodsC/GLBu0.08/expt_19.1/2010
+            https://tds.hycom.org/thredds/dodsC/GLBy0.08/expt_93.0
+
+    """
+    
+    def copernicusmarine_datastore(dataset_url, username, password):
+        #https://help.marine.copernicus.eu/en/articles/5182598-how-to-consume-the-opendap-api-and-cas-sso-using-python
+        cas_url = 'https://cmems-cas.cls.fr/cas/login'
+        session = setup_session(cas_url, username, password)
+        cookies_dict = session.cookies.get_dict()
+        if 'CASTGC' not in cookies_dict.keys():
+            raise KeyError('CASTGC key missing from session cookies_dict, probably authentication failure')
+        session.cookies.set("CASTGC", cookies_dict['CASTGC'])
+        #TODO: add check for wrong dataset_id (now always "AttributeError: You cannot set the charset when no content-type is defined")
+        DAP_dataset = open_url(dataset_url, session=session)#, user_charset='utf-8') # TODO: user_charset needs PyDAP >= v3.3.0 see https://github.com/pydap/pydap/pull/223/commits 
+        data_store = xr.backends.PydapDataStore(DAP_dataset)
+        return data_store
+    
+    if isinstance(dataset_url,list):
+        dataset_url_one = dataset_url[0]
+    else:
+        dataset_url_one = dataset_url
+    
+    if 'cmems-du.eu' in dataset_url_one:
+        if isinstance(dataset_url,list):
+            raise TypeError('list not supported by opendap method used for cmems')
+        
+        #parse credentials to username/password #TODO: now CMEMS specific, make more generic
+        if credentials is None:
+            file_credentials = f'{os.path.expanduser("~")}/CMEMS_credentials.txt'
+            if not os.path.exists(file_credentials):
+                raise FileNotFoundError(f'credentials argument not supplied and file_credentials not available ({file_credentials})')
+            with open(file_credentials) as fc:
+                username = fc.readline().strip()
+                password = fc.readline().strip()
+        else:
+            username,password = credentials
+
+        print(f'opening pydap connection to opendap dataset: {dataset_url}.html')
+        data_store = copernicusmarine_datastore(dataset_url=dataset_url, username=username, password=password)
+        print('xarray opening opendap dataset')
+        data_xr = xr.open_dataset(data_store)
+    elif 'hycom.org' in dataset_url_one:
+        if isinstance(dataset_url,list):
+            print(f'xarray opening opendap dataset like: {dataset_url[0]}.html ({len(dataset_url)} urls/years)')
+            data_xr = xr.open_mfdataset(dataset_url,decode_times=False) #TODO: for some reason decode_times does not work: "ValueError: unable to decode time units 'hours since analysis' with 'the default calendar'."
+        else:
+            print(f'xarray opening opendap dataset: {dataset_url}.html')
+            data_xr = xr.open_dataset(dataset_url,decode_times=False) #TODO: for some reason decode_times does not work: "ValueError: unable to decode time units 'hours since analysis' with 'the default calendar
+        data_xr['time'] = cftime.num2date(data_xr.time,units=data_xr.time.units,calendar=data_xr.time.calendar)
+        data_xr = data_xr.rename({'lon':'longitude','lat':'latitude'})
+    else:
+        print(f'unspecified dataset_url, might fail: {dataset_url}')
+        if isinstance(dataset_url,list):
+            print(f'xarray opening opendap dataset like: {dataset_url[0]}.html ({len(dataset_url)} urls/years)')
+            data_xr = xr.open_mfdataset(dataset_url)
+        else:
+            print(f'xarray opening opendap dataset: {dataset_url}.html')
+            data_xr = xr.open_dataset(dataset_url)
+        if 'lon' in data_xr.dims:
+            data_xr = data_xr.rename({'lon':'longitude','lat':'latitude'})
+        
+    return data_xr
+
+
+def download_OpenDAP_gettimes(dataset_url,credentials=None):
+    ds = open_OPeNDAP_xr(dataset_url=dataset_url, credentials=credentials)
+    ds_time = ds.time.to_series()
+    return ds_time
+
+
+def download_OPeNDAP(dataset_url,
+                     varkey,
+                     longitude_min, longitude_max, latitude_min, latitude_max, 
+                     date_min, date_max, freq='D',
+                     dir_output='.', file_prefix='', overwrite=False,
+                     credentials=None):
+    """
+    
+
+    Parameters
+    ----------
+    dataset_url : TYPE
+        DESCRIPTION.
+    varkey : TYPE
+        DESCRIPTION.
+    longitude_min : TYPE
+        DESCRIPTION.
+    longitude_max : TYPE
+        DESCRIPTION.
+    latitude_min : TYPE
+        DESCRIPTION.
+    latitude_max : TYPE
+        DESCRIPTION.
+    date_min : TYPE
+        DESCRIPTION.
+    date_max : TYPE
+        DESCRIPTION.
+    freq : TYPE, optional
+        DESCRIPTION. The default is 'D'.
+    dir_output : TYPE, optional
+        DESCRIPTION. The default is '.'.
+    file_prefix : TYPE, optional
+        DESCRIPTION. The default is ''.
+    overwrite : TYPE, optional
+        DESCRIPTION. The default is False.
+    credentials : TYPE, optional
+        for CMEMS: credentials=['username','password'], or create "%USERPROFILE%/CMEMS_credentials.txt" with username on line 1 and password on line 2. Register at: https://resources.marine.copernicus.eu/registration-form'. The default is None.
+
+    Raises
+    ------
+    KeyError
+        DESCRIPTION.
+    OutOfRangeError
+        DESCRIPTION.
+
+    Returns
+    -------
+    None.
+
+    """
+    
+    data_xr = open_OPeNDAP_xr(dataset_url=dataset_url, credentials=credentials)
+    
+    print(f'xarray subsetting data (variable \'{varkey}\' and lon/lat extents)')
+    if varkey not in data_xr.data_vars:
+        raise KeyError(f'"{varkey}" not found in dataset, available are: {list(data_xr.data_vars)}')
+    data_xr_var = data_xr[[varkey]]
+    data_xr_var = data_xr_var.sel(longitude=slice(longitude_min,longitude_max), #TODO: add depth selection?
+                                  latitude=slice(latitude_min,latitude_max))
+    data_xr_times = data_xr_var.time.to_series()
+    print(f'available time range in dataset from {data_xr_times.index[0]} to {data_xr_times.index[-1]}')
+    period_range = pd.period_range(date_min,date_max,freq=freq)
+    
+    #check if date_min/date_max are available in dataset
+    if not (data_xr_times.index[0] <= period_range[0].to_timestamp() <= data_xr_times.index[-1]):
+        raise OutOfRangeError(f'date_min ({period_range[0]}) is outside available time range in dataset: {data_xr_times.index[0]} to {data_xr_times.index[-1]}')
+    if not (data_xr_times.index[0] <= period_range[-1].to_timestamp() <= data_xr_times.index[-1]):
+        raise OutOfRangeError(f'date_max ({period_range[-1]}) is outside available time range in dataset: {data_xr_times.index[0]} to {data_xr_times.index[-1]}')
+    
+    for date in period_range:
+        date_str = str(date)
+        name_output = f'{file_prefix}{varkey}_{date_str}.nc'
+        file_out = Path(dir_output,name_output)
+        if file_out.is_file() and not overwrite:
+            print(f'"{name_output}" found and overwrite=False, continuing.')
+            continue
+        
+        print(f'xarray subsetting data per {period_range.freq}: {date_str}')
+        data_xr_var_seltime = data_xr_var.sel(time=slice(date_str,date_str)) #+' 12:00:00', 
+        
+        print(f'xarray writing netcdf file: {name_output}')
+        data_xr_var_seltime.to_netcdf(os.path.join(dir_output,name_output)) #TODO: add chunks={'time':1} or only possible with opening?
+        data_xr_var_seltime.close()

dfm_tools/energy_dissipation.py

@@ -0,0 +1,73 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Thu Dec  8 22:07:22 2022
+
+@author: veenstra
+"""
+import datetime as dt
+from dask.diagnostics import ProgressBar
+
+
+def compute_energy_dissipation(data_xr_map,file_ED_computed):
+    """
+    Example:
+        data_xr_map = dfmt.open_partitioned_dataset(file_nc_map,chunks={'time':100}) #TODO: important to have time>1, otherwise time-mean floods memory (100-200 seems optimal for GTSM 1month, but memory still floods so 1 year would probably be impossible).
+        data_xr_map = data_xr_map.sel(time=slice('2014-01-01','2014-02-01'))
+        dfmt.compute_energy_dissipation(data_xr_map,file_ED_computed)
+
+    
+    TODO: clean up these comments
+    
+    Stel de bodemwrijving is (tau_x,tau_y) dan is het verlies aan energie in W/m^2
+    E_loss = tau_x*u_x + tau_y*u_y
+    
+    Voor Chezy geldt (zo uit mijn hoofd):
+    tau_x = - (rho*g)/(C^2) u_x * sqrt(u_x^2+u_y^2)
+    tau_y = - (rho*g)/(C^2) u_y * sqrt(u_x^2+u_y^2)
+    
+    En gecombineerd
+    E_loss = - (rho*g)/(C^2) * (u_x^2+u_y^2)^(3/2)
+    
+    Approximation: using velocities in cell centers, this is averaged but easiest
+    
+    E_loss(area) = sum_cells [ - (rho*g)/(C^2) * (sqrt(u_x^2+u_y^2))^3 ] * cell_area
+    
+    Dit is dan voor een tijdstip. Ik zou middelen over een iets langere periode zodat het de variatie over het getij verdwijnt, want de waarde is bij springtij waarschijnlijk groter.
+
+    """
+    rho = 1020 #kg/m3
+    g = 9.81 #m/s2
+    
+    attrs_ED = {'long_name':'energy dissipation','units':'W'}    
+    attrs_ED_pm2 = {'long_name':'energy dissipation','units':'W/m^2'}    
+    attrs_ED_areasum = {'long_name':'area-sum energy dissipation', 'units':'W'}
+    attrs_ED_timemean = {'long_name':'springneaptide-mean energy dissipation', 'units': 'W'}
+    attrs_ED_pm2_timemean = {'long_name':'springneaptide-mean energy dissipation', 'units':'Wm^2'}
+    
+    print('>> compute energyloss from C/u/area: ',end='')
+    dtstart = dt.datetime.now()
+    data_ucmag = data_xr_map.mesh2d_ucmag #m/s
+    data_czs = data_xr_map.mesh2d_czs #m0.5s-1
+    data_czs = data_czs.where(data_czs!=0) #0 will result in inf energyloss, so replace by nan
+    data_ba = data_xr_map.mesh2d_flowelem_ba #m2
+    data_xr_map['ED'] = ((rho*g)/(data_czs**2) * data_ucmag**3 * data_ba).assign_attrs(attrs_ED) #equation: (kg/m3)*(m/s2)/(m/s2)*(m3/s3)*m2 = kg/s3*m2 = W = J/s
+    data_xr_map['ED_pm2'] = (data_xr_map['ED'] / data_ba).assign_attrs(attrs_ED_pm2) #TODO: maybe include ba instead of supplying _pm2 separately?
+    
+    #TODO: check da.sum(split_every=4): https://github.com/dask/dask/issues/883. Does not seem to work: "TypeError: nansum() got an unexpected keyword argument 'split_every'"
+    #TODO: chunking: float32 = 32 bits = 4 bytes >> use this to calculate chunking sizes (100-200MB per chunk is optimal)
+    data_xr_map['ED_areasum'] = data_xr_map.ED.sum(dim='mesh2d_nFaces').assign_attrs(attrs_ED_areasum)
+    data_xr_map['ED_timemean'] = data_xr_map.ED.mean(dim='time').assign_attrs(attrs_ED_timemean)
+    data_xr_map['ED_pm2_timemean'] = data_xr_map.ED_pm2.mean(dim='time').assign_attrs(attrs_ED_pm2_timemean)
+    
+    
+    print(f'{(dt.datetime.now()-dtstart).total_seconds():.2f} sec')
+    
+    data_xr_map_computed = data_xr_map[['mesh2d_flowelem_ba','ED_areasum','ED_timemean','ED_pm2_timemean']] #has to contain some var with cells (not only ED_areasum), otherwise ugrid accessor is not valid
+    #data_xr_map_computed.ED_timemean.data.visualize() #does not yet work >> visualizes tasks of dask array
+    
+    print('>> compute and save data_xr_map_computed to netcdf: ')
+    with ProgressBar():
+        data_xr_map_computed.ugrid.to_netcdf(file_ED_computed)
+    
+    data_xr_map_computed.close()
+    

dfm_tools/errors.py

@@ -0,0 +1,9 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Apr  3 14:38:20 2023
+
+@author: veenstra
+"""
+
+class OutOfRangeError(Exception):
+    pass