Python Dataset.geospatial_vertical_min方法代码示例

# 需要导入模块: from netCDF4 import Dataset [as 别名]
# 或者: from netCDF4.Dataset import geospatial_vertical_min [as 别名]
def create_mhl_sst_ncfile(txtfile, site_code_short, data,
                          time, dtime, spatial_data):
    """
    create NetCDF file for MHL Wave data
    """
    site_code = site_list[site_code_short][0]
    netcdf_filename = create_netcdf_filename(site_code, data, dtime)
    netcdf_filepath = os.path.join(
        output_folder, "%s.nc") % netcdf_filename
    ncfile = Dataset(netcdf_filepath, "w", format="NETCDF4")


    # generate site and deployment specific attributes
    ncfile.title = ("IMOS - ANMN New South Wales(NSW) %s "
                    "Sea water temperature (%s) -"
                    "Deployment No. %s %s to %s") % (
            site_list[site_code_short][1], site_code,
            spatial_data[0], min(dtime).strftime("%d-%m-%Y"),
            max(dtime).strftime("%d-%m-%Y"))
    ncfile.institution = 'Manly Hydraulics Laboratory'
    ncfile.keywords = ('Oceans | Ocean temperature |'
                           'Sea Surface Temperature')
    ncfile.principal_investigator = 'Mark Kulmar'
    ncfile.cdm_data_type = 'Station'
    ncfile.platform_code = site_code

    abstract_default = ("The sea water temperature is measured by a thermistor mounted in the "
                        "buoy hull approximately 400 mm below the water "
                        "surface.  The thermistor has a resolution of 0.05 "
                        "Celsius and an accuracy of 0.2 Celsius.  The "
                        "measurements are transmitted to a shore station "
                        "where it is stored on a PC before routine transfer "
                        "to Manly Hydraulics Laboratory via email.")

    if site_code_short in ['COF', 'CRH', 'EDE', 'PTK']:

        abstract_specific = ("This dataset contains sea water temperature "
                             "data collected by a wave monitoring buoy moored off %s. ") % site_list[site_code_short][1]
    else:
        abstract_specific = ("This dataset contains sea water temperature "
                             "data collected by a wave monitoring buoy moored off %s "
                             "approximately %s kilometres from the coastline. ") % (

                          site_list[site_code_short][1], site_list[site_code_short][2])

    ncfile.abstract = abstract_specific + abstract_default
    ncfile.comment = ("The sea water temperature data (SST) is routinely quality controlled (usually twice per week) "
                      "using a quality control program developed by Manly Hydraulics Laboratory.  The SST data gathered "
                      "by the buoy is regularly compared to the latest available satellite derived sea SST images available "
                      "from the Bluelink ocean forecasting web pages to ensure the integrity of the dataset.  Erroneous SST "
                      "records are removed and good quality data is flagged as \'Quality Controlled\' in the "
                      "Manly Hydraulics Laboratory SST database.") 
    ncfile.sourceFilename = os.path.basename(txtfile)
    ncfile.date_created = datetime.utcnow().strftime("%Y-%m-%dT%H:%M:%SZ")
    ncfile.time_coverage_start = min(dtime).strftime("%Y-%m-%dT%H:%M:%SZ")
    ncfile.time_coverage_end = max(dtime).strftime("%Y-%m-%dT%H:%M:%SZ")
    ncfile.geospatial_lat_min = spatial_data[1]
    ncfile.geospatial_lat_max = spatial_data[1]
    ncfile.geospatial_lon_min = spatial_data[2]
    ncfile.geospatial_lon_max = spatial_data[2]
    ncfile.geospatial_vertical_max = 0.
    ncfile.geospatial_vertical_min = 0.
    ncfile.deployment_number = str(spatial_data[0])

    # add dimension and variables
    ncfile.createDimension('TIME', len(time))

    TIME = ncfile.createVariable('TIME', "d", 'TIME')
    TIMESERIES = ncfile.createVariable('TIMESERIES', "i")
    LATITUDE = ncfile.createVariable(
        'LATITUDE', "d", fill_value=99999.)
    LONGITUDE = ncfile.createVariable(
        'LONGITUDE', "d", fill_value=99999.)
    TEMP = ncfile.createVariable('TEMP', "f", 'TIME', fill_value=99999.)

    # add global attributes and variable attributes stored in config files
    config_file = os.path.join(os.getcwd(), 'global_att_sst.att')
    generate_netcdf_att(ncfile, config_file,
                        conf_file_point_of_truth=False)
    
    # replace nans with fillvalue in dataframe
    data = data.fillna(value=float(99999.))

    TIME[:] = time
    TIMESERIES[:] = 1
    LATITUDE[:] = spatial_data[1]
    LONGITUDE[:] = spatial_data[2]
    TEMP[:] = data['SEA_TEMP'].values
    ncfile.close()

# 需要导入模块: from netCDF4 import Dataset [as 别名]
# 或者: from netCDF4.Dataset import geospatial_vertical_min [as 别名]

#.........这里部分代码省略.........
    if fields[4] == "":
      sals[i, 0] = -9999
    else:
      sals[i, 0] = fields[4]

    if fields[5] == "":
      fco2s[i, 0] = -9999
    else:
      fco2s[i, 0] = fields[5]

    if len(fields[6]) == 0:
      fco2qcs[i, 0] = -128
    else:
      fco2qcs[i, 0] = makeqcvalue_(int(fields[6]))

  depthvar[:,:] = depths
  positionvar[:,:] = positions
  sstvar[:,:] = temps
  sssvar[:,:] = sals
  fco2var[:,:] = fco2s
  fco2qcvar[:,:] = fco2qcs
  depthdmvar[:,:] = dms
  sstdmvar[:,:] = dms
  sssdmvar[:,:] = dms
  fco2dmvar[:,:] = dms

  # Global attributes
  nc.id = filenameroot

  nc.data_type = "OceanSITES trajectory data"
  nc.netcdf_version = "netCDF-4 classic model"
  nc.format_version = "1.2"
  nc.Conventions = "CF-1.6 OceanSITES-Manual-1.2 Copernicus-InSituTAC-SRD-1.3 "\
    + "Copernicus-InSituTAC-ParametersList-3.1.0"

  nc.cdm_data_type = "Trajectory"
  nc.data_mode = "R"
  nc.area = "Global Ocean"

  nc.geospatial_lat_min = str(minlat)
  nc.geospatial_lat_max = str(maxlat)
  nc.geospatial_lon_min = str(minlon)
  nc.geospatial_lon_max = str(maxlon)
  nc.geospatial_vertical_min = "5.00"
  nc.geospatial_vertical_max = "5.00"

  nc.last_latitude_observation = lats[-1]
  nc.last_longitude_observation = lons[-1]
  nc.last_date_observation = endtime.strftime("%Y-%m-%dT%H:%M:%SZ")
  nc.time_coverage_start = starttime.strftime("%Y-%m-%dT%H:%M:%SZ")
  nc.time_coverage_end = endtime.strftime("%Y-%m-%dT%H:%M:%SZ")

  #datasetdate = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H:%M:%SZ")
  #nc.date_update = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H:%M:%SZ")
  #nc.history = datasetdate + " : Creation"

  nc.update_interval = "daily"

  nc.data_assembly_center = "BERGEN"
  nc.institution = "University of Bergen / Geophysical Institute"
  nc.institution_edmo_code = "4595"
  nc.institution_references = " "
  nc.contact = "[email protected]"
  nc.title = "Global Ocean - In Situ near-real time carbon observation"
  nc.author = "cmems-service"
  nc.naming_authority = "Copernicus"

  nc.platform_code = getplatformcallsign_(platform_code)
  nc.site_code = getplatformcallsign_(platform_code)

  # For buoys -> Mooring observation.
  platform_category_code = getplatformcategorycode_(platform_code)
  nc.platform_name = getplatformname_(platform_code)
  nc.source_platform_category_code = platform_category_code
  nc.source = PLATFORM_CODES[platform_category_code]

  nc.quality_control_indicator = "6" # "Not used"
  nc.quality_index = "0"

  nc.comment = " "
  nc.summary = " "
  nc.reference = "http://marine.copernicus.eu/, https://www.icos-cp.eu/"
  nc.citation = "These data were collected and made freely available by the " \
    + "Copernicus project and the programs that contribute to it."
  nc.distribution_statement = "These data follow Copernicus standards; they " \
    + "are public and free of charge. User assumes all risk for use of data. " \
    + "User must display citation in any publication or product using data. " \
    + "User must contact PI prior to any commercial use of data."

  # Write the netCDF
  nc.close()

  # Read the netCDF file into memory
  with open(ncpath, "rb") as ncfile:
    ncbytes = ncfile.read()

  # Delete the temp netCDF file
  os.remove(ncpath)

  return [filenameroot, ncbytes]

# 需要导入模块: from netCDF4 import Dataset [as 别名]
# 或者: from netCDF4.Dataset import geospatial_vertical_min [as 别名]
def create_pigment_tss_nc(metadata, data, output_folder):
    """ create a netcdf file for pigment or TSS data """
    netcdf_filepath   = os.path.join(output_folder, "%s.nc" % create_filename_output(metadata, data))
    output_netcdf_obj = Dataset(netcdf_filepath, "w", format="NETCDF4")

    # read gatts from input, add them to output. Some gatts will be overwritten
    input_gatts = metadata['gatts']
    check_vessel_name(input_gatts['vessel_name'])  # this raises a warning only
    if input_gatts['vessel_name'].strip() == '':
        input_gatts['vessel_name'] = 'UNKNOWN VESSEL'

    gatt_to_dispose = ['geospatial_lat_min', 'geospatial_lat_max', 'geospatial_lon_min',
                       'geospatial_lon_max', 'geospatial_vertical_min', 'geospatial_vertical_max',
                       'conventions', 'local_time_zone']

    for gatt in input_gatts.keys():
        if gatt not in gatt_to_dispose:
            if input_gatts[gatt] != '':
                setattr(output_netcdf_obj, gatt, input_gatts[gatt])
    setattr(output_netcdf_obj, 'input_xls_filename', os.path.basename(metadata['filename_input']))

    if 'local_time_zone' in input_gatts.keys():
        if input_gatts['local_time_zone'] != '':
            setattr(output_netcdf_obj, 'local_time_zone', np.float(input_gatts['local_time_zone']))

    output_netcdf_obj.date_created            = datetime.now().strftime("%Y-%m-%dT%H:%M:%SZ")
    output_netcdf_obj.geospatial_vertical_min = data.Depth.min()
    output_netcdf_obj.geospatial_vertical_max = data.Depth.max()

    output_netcdf_obj.createDimension("obs", data.shape[0])
    output_netcdf_obj.createDimension("station", len(data.Station_Code.unique()))
    output_netcdf_obj.createDimension('name_strlen', 50)

    # a profile is defined by a time station combo. 2 profiles at the same time
    # but at a different location can exist. In order to find the unique
    # profiles, the unique values of a string array of 'time-station' is counted
    time_station_arr = ['%s_%s' % (a, b) for a, b in zip(data.index, data.Station_Code.values)]
    len_prof         = len(np.unique(time_station_arr))
    output_netcdf_obj.createDimension("profile", len_prof)

    var_time         = output_netcdf_obj.createVariable("TIME", "d", "profile", fill_value=get_imos_parameter_info('TIME', '_FillValue'))
    var_lat          = output_netcdf_obj.createVariable("LATITUDE", "f4", "station", fill_value=get_imos_parameter_info('LATITUDE', '_FillValue'))
    var_lon          = output_netcdf_obj.createVariable("LONGITUDE", "f4", "station", fill_value=get_imos_parameter_info('LONGITUDE', '_FillValue'))
    var_station_name = output_netcdf_obj.createVariable("station_name", "S1", (u'station', u'name_strlen'))
    var_station_idx  = output_netcdf_obj.createVariable("station_index", "i4", "profile")
    var_profile      = output_netcdf_obj.createVariable("profile", "i4", "profile")
    var_rowsize      = output_netcdf_obj.createVariable("row_size", "i4", "profile")
    var_depth        = output_netcdf_obj.createVariable("DEPTH", "f4", "obs", fill_value=get_imos_parameter_info('DEPTH', '_FillValue'))

    var = 'DEPTH'
    if metadata['varatts']['Depth']['Comments'] != '' or metadata['varatts']['Depth']['Comments'] != 'positive down':
        setattr(output_netcdf_obj[var], 'comments', metadata['varatts']['Depth']['Comments'].replace('positive down', ''))

    # creation of rest of variables
    var_to_dispose = ['Latitude', 'Longitude', 'Depth', 'Time', 'Station_Code']
    for var in data.columns:
        if var not in var_to_dispose:
            if metadata['varatts'][var]['Fill value'] == '':
                fillvalue = -999
            else:
                fillvalue = metadata['varatts'][var]['Fill value']

            output_netcdf_obj.createVariable(var, "d", "obs", fill_value=fillvalue)
            if metadata['varatts'][var]['IMOS long_name'] != '':
                setattr(output_netcdf_obj[var], 'long_name', metadata['varatts'][var]['IMOS long_name'])
            if metadata['varatts'][var]['Units'] != '':
                setattr(output_netcdf_obj[var], 'units', metadata['varatts'][var]['Units'])
            if metadata['varatts'][var]['Comments'] != '':
                setattr(output_netcdf_obj[var], 'comments', metadata['varatts'][var]['Comments'])

            # SPM is set wrongly as a standard_name is original xls files
            if 'SPM' not in var:
                if metadata['varatts'][var]['CF standard_name'] != '':
                    setattr(output_netcdf_obj[var], 'standard_name', metadata['varatts'][var]['CF standard_name'])

            if 'Sample_Number' in var:
                setattr(output_netcdf_obj[var], 'units', 1)

            if np.dtype(data[var]) == 'O':
                os.remove(netcdf_filepath)
                _error('Incorrect values for variable \"%s\"' % var)
            output_netcdf_obj[var][:] = np.array(data[var].values).astype(np.double)

    # Contigious ragged array representation of Stations netcdf 1.5
    # add gatts and variable attributes as stored in config files
    conf_file_generic = os.path.join(os.path.dirname(__file__), 'generate_nc_file_att')
    generate_netcdf_att(output_netcdf_obj, conf_file_generic, conf_file_point_of_truth=True)

    # lat lon depth
    _, idx_station_uniq = np.unique(data.Station_Code, return_index=True)
    idx_station_uniq.sort()
    var_lat[:]          = data.Latitude.values[idx_station_uniq].astype(np.float)
    var_lon[:]          = data.Longitude.values[idx_station_uniq].astype(np.float)
    if np.dtype(data.Depth) == 'O':
        try:
            var_depth[:] = data.Depth.values.astype(np.float)
        except ValueError:
            os.remove(netcdf_filepath)
            _error('Incorrect depth value')
    else:
#.........这里部分代码省略.........

# 需要导入模块: from netCDF4 import Dataset [as 别名]
# 或者: from netCDF4.Dataset import geospatial_vertical_min [as 别名]
def create_absorption_nc(metadata, data, output_folder):
    """ create a netcdf file for absorption data """
    netcdf_filepath   = os.path.join(output_folder, "%s.nc" % create_filename_output(metadata, data))
    output_netcdf_obj = Dataset(netcdf_filepath, "w", format="NETCDF4")

    data_dict = data[1]
    data_df = data[0]

    # read gatts from input, add them to output. Some gatts will be overwritten
    input_gatts = metadata['gatts']
    check_vessel_name(input_gatts['vessel_name'])  # this raises a warning only
    if input_gatts['vessel_name'].strip() == '':
        input_gatts['vessel_name'] = 'UNKNOWN VESSEL'

    gatt_to_dispose = ['geospatial_lat_min', 'geospatial_lat_max', 'geospatial_lon_min',
                       'geospatial_lon_max', 'geospatial_vertical_min', 'geospatial_vertical_max',
                       'conventions', 'local_time_zone']

    for gatt in input_gatts.keys():
        if gatt not in gatt_to_dispose:
            if input_gatts[gatt] != '':
                setattr(output_netcdf_obj, gatt, input_gatts[gatt])
    setattr(output_netcdf_obj, 'input_xls_filename', os.path.basename(metadata['filename_input']))

    if 'local_time_zone' in input_gatts.keys():
        if input_gatts['local_time_zone'] != '':
            setattr(output_netcdf_obj, 'local_time_zone', np.float(input_gatts['local_time_zone']))

    output_netcdf_obj.date_created            = datetime.now().strftime("%Y-%m-%dT%H:%M:%SZ")
    output_netcdf_obj.geospatial_vertical_min = min(data_dict['Depth'])
    output_netcdf_obj.geospatial_vertical_max = max(data_dict['Depth'])

    output_netcdf_obj.createDimension("obs", data_df.shape[1])
    output_netcdf_obj.createDimension("station", len(np.unique(data_dict['Station_Code'])))
    output_netcdf_obj.createDimension('name_strlen', 50)
    output_netcdf_obj.createDimension('wavelength', data_df.shape[0])

    # a profile is defined by a time station combo. 2 profiles at the same time
    # but at a different location can exist. In order to find the unique
    # profiles, the unique values of a string array of 'time-station' is counted
    time_station_arr = ['%s_%s' % (a, b) for a, b in zip(data_dict['Dates'], data_dict['Station_Code'])]
    len_prof         = len(np.unique(time_station_arr))
    output_netcdf_obj.createDimension("profile", len_prof)

    var_time         = output_netcdf_obj.createVariable("TIME", "d", "profile", fill_value=get_imos_parameter_info('TIME', '_FillValue'))
    var_lat          = output_netcdf_obj.createVariable("LATITUDE", "f", "station", fill_value=get_imos_parameter_info('LATITUDE', '_FillValue'))
    var_lon          = output_netcdf_obj.createVariable("LONGITUDE", "f", "station", fill_value=get_imos_parameter_info('LONGITUDE', '_FillValue'))
    var_station_name = output_netcdf_obj.createVariable("station_name", "S1", (u'station', u'name_strlen'))
    var_station_idx  = output_netcdf_obj.createVariable("station_index", "i4", "profile")
    var_profile      = output_netcdf_obj.createVariable("profile", "i4", "profile")
    var_rowsize      = output_netcdf_obj.createVariable("row_size", "i4", "profile")
    var_depth        = output_netcdf_obj.createVariable("DEPTH", "f", "obs", fill_value=get_imos_parameter_info('DEPTH', '_FillValue'))
    var_wavelength   = output_netcdf_obj.createVariable("wavelength", "f", "wavelength")

    var = data_dict['main_var_name'][0]
    output_netcdf_obj.createVariable(var, "d", ("obs", "wavelength"), fill_value=metadata['varatts_col'][var]['Fill value'])
    if metadata['varatts_col'][var]['IMOS long_name'] != '':
        setattr(output_netcdf_obj[var], 'long_name', metadata['varatts_col'][var]['IMOS long_name'])
    if metadata['varatts_col'][var]['Units'] != '':
        setattr(output_netcdf_obj[var], 'units', metadata['varatts_col'][var]['Units'])
    if metadata['varatts_col'][var]['Comments'] != '':
        setattr(output_netcdf_obj[var], 'comments', metadata['varatts_col'][var]['Comments'])
    if metadata['varatts_col'][var]['CF standard_name'] != '':
        setattr(output_netcdf_obj[var], 'standard_name', metadata['varatts_col'][var]['CF standard_name'])

    data_val                  = data_df.transpose()
    output_netcdf_obj[var][:] = np.array(data_val.values)

    # Contigious ragged array representation of Stations netcdf 1.5
    # add gatts and variable attributes as stored in config files
    conf_file_generic = os.path.join(os.path.dirname(__file__), 'generate_nc_file_att')
    generate_netcdf_att(output_netcdf_obj, conf_file_generic, conf_file_point_of_truth=True)

    # lat lon depth
    _, idx_station_uniq = np.unique(data_dict['Station_Code'], return_index=True)
    idx_station_uniq.sort()
    var_lat[:]          = np.array(data_dict['Latitude'])[idx_station_uniq]
    var_lon[:]          = np.array(data_dict['Longitude'])[idx_station_uniq]
    var_depth[:]        = data_dict['Depth']
    var_depth.positive  = 'down'

    # time
    _, idx_time_station_uniq = np.unique(time_station_arr, return_index=True)
    idx_time_station_uniq.sort()
    time_values      = (data_dict['Dates'][idx_time_station_uniq]).to_pydatetime()
    time_val_dateobj = date2num(time_values, output_netcdf_obj['TIME'].units, output_netcdf_obj['TIME'].calendar)
    var_time[:]      = time_val_dateobj

    # wavelength
    var = 'Wavelength'
    var_wavelength[:] = data_dict['Wavelength']
    if metadata['varatts_col'][var]['IMOS long_name'] != '':
        setattr(var_wavelength, 'long_name', metadata['varatts_col'][var]['IMOS long_name'])
    if metadata['varatts_col'][var]['Units'] != '':
        setattr(var_wavelength, 'units', metadata['varatts_col'][var]['Units'])
    if metadata['varatts_col'][var]['Comments'] != '':
        setattr(var_wavelength, 'comments', metadata['varatts_col'][var]['Comments'])
    if metadata['varatts_col'][var]['CF standard_name'] != '':
        setattr(var_wavelength, 'standard_name', metadata['varatts_col'][var]['CF standard_name'])

#.........这里部分代码省略.........

# 需要导入模块: from netCDF4 import Dataset [as 别名]
# 或者: from netCDF4.Dataset import geospatial_vertical_min [as 别名]
def create_burst_average_netcdf(input_netcdf_file_path, output_dir):
    """
    generate the burst netcdf file for WQM product.
    see variable conf_file if editing of gatt and var att need to be done
    """
    input_file_rel_path = get_input_file_rel_path(input_netcdf_file_path)
    input_netcdf_obj    = Dataset(input_netcdf_file_path, 'r')

    global INSTRUMENT_SAMPLE_INTERVAL
    INSTRUMENT_SAMPLE_INTERVAL = getattr(input_netcdf_obj, 'instrument_sample_interval', 1)

    burst_vars          = create_burst_average_var(input_netcdf_obj)
    time_burst_vals     = burst_vars.values()[0]['time_mean']
    tmp_netcdf_dir      = tempfile.mkdtemp()

    output_netcdf_file_path = os.path.join(tmp_netcdf_dir, generate_netcdf_burst_filename(input_netcdf_file_path, burst_vars))
    output_netcdf_obj       = Dataset(output_netcdf_file_path, "w", format="NETCDF4")

    # read gatts from input, add them to output. Some gatts will be overwritten
    input_gatts     = input_netcdf_obj.__dict__.keys()
    gatt_to_dispose = ['author', 'file_version_quality_control', 'quality_control_set',
                       'compliance_checker_version', 'compliance_checker_last_updated',
                       'quality_control_log']

    for gatt in input_gatts:
        if gatt not in gatt_to_dispose:
            setattr(output_netcdf_obj, gatt, getattr(input_netcdf_obj, gatt))

    if 'WQM' in output_netcdf_obj.instrument:
        output_netcdf_obj.title = 'Burst-averaged biogeochemical measurements at %s' % (input_netcdf_obj.site_code)
    elif 'CTD' in output_netcdf_obj.instrument:
        output_netcdf_obj.title = 'Burst-averaged moored CTD measurements at %s' % (input_netcdf_obj.site_code)

    m = re.match('.*\.nc', input_file_rel_path)
    output_netcdf_obj.input_file   = m.group()
    output_netcdf_obj.date_created = DATE_UTC_NOW.strftime("%Y-%m-%dT%H:%M:%SZ")

    depth_burst_mean_val = burst_vars['DEPTH']['var_mean']
    if np.isnan(depth_burst_mean_val).all():
        output_netcdf_obj.geospatial_vertical_min = np.double(input_netcdf_obj['NOMINAL_DEPTH'][:])
        output_netcdf_obj.geospatial_vertical_max = np.double(input_netcdf_obj['NOMINAL_DEPTH'][:])
    else:
        output_netcdf_obj.geospatial_vertical_min = np.nanmin(depth_burst_mean_val)
        output_netcdf_obj.geospatial_vertical_max = np.nanmax(depth_burst_mean_val)

    # set up dimensions and variables
    output_netcdf_obj.createDimension("TIME", len(time_burst_vals))
    var_time = output_netcdf_obj.createVariable("TIME", input_netcdf_obj["TIME"].dtype,
                                                ("TIME",))

    dimensionless_var = list_dimensionless_var(input_netcdf_obj)
    # No FillValue for dimensions as for IMOS conventions
    for var in dimensionless_var:
        output_netcdf_obj.createVariable(var, input_netcdf_obj[var].dtype)
        output_netcdf_obj[var][:] = input_netcdf_obj[var][:]

    for var in burst_vars.keys():
        var_dtype = input_netcdf_obj[var].dtype
        fillvalue = getattr(input_netcdf_obj[var], '_FillValue', None)

        output_var_mean    = output_netcdf_obj.createVariable(var, var_dtype, ("TIME",), fill_value=fillvalue)
        output_var_min     = output_netcdf_obj.createVariable('%s_burst_min' % var, var_dtype, ("TIME",), fill_value=fillvalue)
        output_var_max     = output_netcdf_obj.createVariable('%s_burst_max' % var, var_dtype, ("TIME",), fill_value=fillvalue)
        output_var_sd      = output_netcdf_obj.createVariable('%s_burst_sd' % var, var_dtype, ("TIME",), fill_value=fillvalue)
        output_var_num_obs = output_netcdf_obj.createVariable('%s_num_obs' % var, "i4", ("TIME",))

        # set up 'bonus' var att from original FV01 file into FV02
        input_var_object   = input_netcdf_obj[var]
        input_var_list_att = input_var_object.__dict__.keys()
        var_att_disposable = ['name', 'long_name', \
                              '_FillValue', 'ancillary_variables', \
                              'ChunkSize', 'coordinates']
        for var_att in [att for att in input_var_list_att if att not in var_att_disposable]:
            setattr(output_netcdf_obj[var], var_att, getattr(input_netcdf_obj[var], var_att))
            if var_att != 'comment':
                setattr(output_var_min, var_att, getattr(input_netcdf_obj[var], var_att))
                setattr(output_var_max, var_att, getattr(input_netcdf_obj[var], var_att))
                setattr(output_var_sd, var_att, getattr(input_netcdf_obj[var], var_att))

        # make sur standard_deviation variable doesnt have a standard_name attr
        if hasattr(output_var_sd, 'standard_name'):
            delattr(output_var_sd, 'standard_name')


        setattr(output_var_mean, 'coordinates', getattr(input_netcdf_obj[var], 'coordinates', ''))
        setattr(output_var_mean, 'ancillary_variables', ('%s_num_obs %s_burst_sd %s_burst_min %s_burst_max' % (var, var, var, var)))

        setattr(output_var_mean, 'cell_methods', 'TIME: mean')
        setattr(output_var_min, 'cell_methods', 'TIME: minimum')
        setattr(output_var_max, 'cell_methods', 'TIME: maximum')
        setattr(output_var_sd, 'cell_methods', 'TIME: standard_deviation')

        setattr(output_var_sd, 'long_name', 'Standard deviation of values in burst, after rejection of flagged data')
        setattr(output_var_num_obs, 'long_name', 'Number of observations included in the averaging process')
        setattr(output_var_min, 'long_name', 'Minimum data value in burst, after rejection of flagged data')
        setattr(output_var_max, 'long_name', 'Maximum data value in burst, after rejection of flagged data')
        setattr(output_var_mean, 'long_name', 'Mean of %s values in burst, after rejection of flagged data' % (getattr(input_netcdf_obj[var], 'standard_name',
                                                                                                                       getattr(input_netcdf_obj[var], 'long_name', ''))))

        output_var_num_obs.units = "1"
#.........这里部分代码省略.........

# 需要导入模块: from netCDF4 import Dataset [as 别名]
# 或者: from netCDF4.Dataset import geospatial_vertical_min [as 别名]
def create_mhl_wave_ncfile(txtfile, site_code_short, data,
                           time, dtime, spatial_data):
    """
    create NetCDF file for MHL Wave data
    """
    site_code = site_list[site_code_short][0]
    netcdf_filename = create_netcdf_filename(site_code, data, dtime)
    netcdf_filepath = os.path.join(
        output_folder, "%s.nc") % netcdf_filename
    ncfile = Dataset(netcdf_filepath, "w", format="NETCDF4")

    # add IMOS1.4 global attributes and variable attributes stored in config
    # files
    config_file = os.path.join(os.getcwd(),'mhl_wave_library', 'global_att_wave.att')
    generate_netcdf_att(ncfile, config_file,
                        conf_file_point_of_truth=False)
    # Additional attribute either retrieved from original necdtf file
    # (if exists) or defined below
    original_netcdf_file_path = os.path.join(
        input_folder, "%s.nc") % netcdf_filename

    if os.path.exists(original_netcdf_file_path):
        # get glob attributes from original netcdf files.
        parse_nc_attribute(original_netcdf_file_path, ncfile)
    else:
        # generate site and deployment specific attributes
        ncfile.title = ("IMOS - ANMN New South Wales(NSW) %s"
                        "Offshore Wave Data (% s) -"
                        "Deployment No. %s %s to %s") % (
            site_list[site_code_short][1], site_code,
            spatial_data[0], min(dtime).strftime("%d-%m-%Y"),
            max(dtime).strftime("%d-%m-%Y"))
        ncfile.institution = 'Manly Hydraulics Laboratory'
        ncfile.keywords = ('Oceans | Ocean Waves |'
                           'Significant Wave Height, Oceans | Ocean Waves'
                           '| Wave Period, Oceans | Ocean Waves |'
                           'Wave Spectra, Oceans | Ocean Waves |'
                           'Wave Speed / direction')
        ncfile.principal_investigator = 'Mark Kulmar'
        ncfile.cdm_data_type = 'Station'
        ncfile.platform_code = site_code
        ncfile.site_name = site_list[site_code_short][1]
        if site_code in ['WAVEPOK', 'WAVECOH', 'WAVECRH', 'WAVEEDN']:
            config_file = os.path.join(
                os.getcwd(), 'common', 'abstract_WAVE_default.att')
        elif site_code == 'WAVEBAB':
            config_file = os.path.join(os.getcwd(),'common', 'abstract_WAVEBAB.att')
        elif site_code == 'WAVEBYB':
            config_file = os.path.join(os.getcwd(), 'common', 'abstract_WAVEBYB.att')
        else:  # WAVESYD
            config_file = os.path.join(os.getcwd(), 'common', 'abstract_WAVESYD.att')

        generate_netcdf_att(ncfile, config_file,
                            conf_file_point_of_truth=False)

    ncfile.sourceFilename = os.path.basename(txtfile)
    ncfile.date_created = datetime.utcnow().strftime("%Y-%m-%dT%H:%M:%SZ")
    ncfile.time_coverage_start = min(dtime).strftime("%Y-%m-%dT%H:%M:%SZ")
    ncfile.time_coverage_end = max(dtime).strftime("%Y-%m-%dT%H:%M:%SZ")
    ncfile.geospatial_lat_min = spatial_data[1]
    ncfile.geospatial_lat_max = spatial_data[1]
    ncfile.geospatial_lon_min = spatial_data[2]
    ncfile.geospatial_lon_max = spatial_data[2]
    ncfile.geospatial_vertical_max = 0.
    ncfile.geospatial_vertical_min = 0.
    ncfile.deployment_number = str(spatial_data[0])

    # add dimension and variables
    ncfile.createDimension('TIME', len(time))

    TIME = ncfile.createVariable('TIME', "d", 'TIME')
    TIMESERIES = ncfile.createVariable('TIMESERIES', "i")
    LATITUDE = ncfile.createVariable(
        'LATITUDE', "d", fill_value=99999.)
    LONGITUDE = ncfile.createVariable(
        'LONGITUDE', "d", fill_value=99999.)
    WHTH = ncfile.createVariable('WHTH', "f", 'TIME', fill_value=99999.)
    WMSH = ncfile.createVariable('WMSH', "f", 'TIME', fill_value=99999.)
    HRMS = ncfile.createVariable('HRMS', "f", 'TIME', fill_value=99999.)
    WHTE = ncfile.createVariable('WHTE', "f", 'TIME', fill_value=99999.)
    WMXH = ncfile.createVariable('WMXH', "f", 'TIME', fill_value=99999.)
    TCREST = ncfile.createVariable('TCREST', "f", 'TIME', fill_value=99999.)
    WPMH = ncfile.createVariable('WPMH', "f", 'TIME', fill_value=99999.)
    WPTH = ncfile.createVariable('WPTH', "f", 'TIME', fill_value=99999.)
    YRMS = ncfile.createVariable('YRMS', "f", 'TIME', fill_value=99999.)
    WPPE = ncfile.createVariable('WPPE', "f", 'TIME', fill_value=99999.)
    TP2 = ncfile.createVariable('TP2', "f", 'TIME', fill_value=99999.)
    M0 = ncfile.createVariable('M0', "f", 'TIME', fill_value=99999.)
    WPDI = ncfile.createVariable('WPDI', "f", 'TIME', fill_value=99999.)

    # add global attributes and variable attributes stored in config files
    config_file = os.path.join(os.getcwd(),'mhl_wave_library', 'global_att_wave.att')
    generate_netcdf_att(ncfile, config_file,
                        conf_file_point_of_truth=True)

    for nc_var in [WPTH, WPPE, WPMH, WPDI, WMXH,WMSH, WHTH, WHTE, TP2, TCREST]:
        nc_var.valid_max = np.float32(nc_var.valid_max)
        nc_var.valid_min = np.float32(nc_var.valid_min)

    # replace nans with fillvalue in dataframe
#.........这里部分代码省略.........

# 需要导入模块: from netCDF4 import Dataset [as 别名]
# 或者: from netCDF4.Dataset import geospatial_vertical_min [as 别名]
def initialize_output(filename, id_dim_name, time_len,
                      id_len, time_step_seconds):
    """Creates netCDF file with CF dimensions and variables, but no data.

    Arguments:
        filename -- full path and filename for output netCDF file
        id_dim_name -- name of Id dimension and variable, e.g., COMID
        time_len -- (integer) length of time dimension (number of time steps)
        id_len -- (integer) length of Id dimension (number of time series)
        time_step_seconds -- (integer) number of seconds per time step
    """

    cf_nc = Dataset(filename, 'w', format='NETCDF3_CLASSIC')

    # Create global attributes
    log('    globals', 'DEBUG')
    cf_nc.featureType = 'timeSeries'
    cf_nc.Metadata_Conventions = 'Unidata Dataset Discovery v1.0'
    cf_nc.Conventions = 'CF-1.6'
    cf_nc.cdm_data_type = 'Station'
    cf_nc.nodc_template_version = (
        'NODC_NetCDF_TimeSeries_Orthogonal_Template_v1.1')
    cf_nc.standard_name_vocabulary = ('NetCDF Climate and Forecast (CF) ' +
                                      'Metadata Convention Standard Name ' +
                                      'Table v28')
    cf_nc.title = 'RAPID Result'
    cf_nc.summary = ("Results of RAPID river routing simulation. Each river " +
                     "reach (i.e., feature) is represented by a point " +
                     "feature at its midpoint, and is identified by the " +
                     "reach's unique NHDPlus COMID identifier.")
    cf_nc.time_coverage_resolution = 'point'
    cf_nc.geospatial_lat_min = 0.0
    cf_nc.geospatial_lat_max = 0.0
    cf_nc.geospatial_lat_units = 'degrees_north'
    cf_nc.geospatial_lat_resolution = 'midpoint of stream feature'
    cf_nc.geospatial_lon_min = 0.0
    cf_nc.geospatial_lon_max = 0.0
    cf_nc.geospatial_lon_units = 'degrees_east'
    cf_nc.geospatial_lon_resolution = 'midpoint of stream feature'
    cf_nc.geospatial_vertical_min = 0.0
    cf_nc.geospatial_vertical_max = 0.0
    cf_nc.geospatial_vertical_units = 'm'
    cf_nc.geospatial_vertical_resolution = 'midpoint of stream feature'
    cf_nc.geospatial_vertical_positive = 'up'
    cf_nc.project = 'National Flood Interoperability Experiment'
    cf_nc.processing_level = 'Raw simulation result'
    cf_nc.keywords_vocabulary = ('NASA/Global Change Master Directory ' +
                                 '(GCMD) Earth Science Keywords. Version ' +
                                 '8.0.0.0.0')
    cf_nc.keywords = 'DISCHARGE/FLOW'
    cf_nc.comment = 'Result time step (seconds): ' + str(time_step_seconds)

    timestamp = datetime.utcnow().isoformat() + 'Z'
    cf_nc.date_created = timestamp
    cf_nc.history = (timestamp + '; added time, lat, lon, z, crs variables; ' +
                     'added metadata to conform to NODC_NetCDF_TimeSeries_' +
                     'Orthogonal_Template_v1.1')

    # Create dimensions
    log('    dimming', 'DEBUG')
    cf_nc.createDimension('time', time_len)
    cf_nc.createDimension(id_dim_name, id_len)

    # Create variables
    log('    timeSeries_var', 'DEBUG')
    timeSeries_var = cf_nc.createVariable(id_dim_name, 'i4', (id_dim_name,))
    timeSeries_var.long_name = (
        'Unique NHDPlus COMID identifier for each river reach feature')
    timeSeries_var.cf_role = 'timeseries_id'

    log('    time_var', 'DEBUG')
    time_var = cf_nc.createVariable('time', 'i4', ('time',))
    time_var.long_name = 'time'
    time_var.standard_name = 'time'
    time_var.units = 'seconds since 1970-01-01 00:00:00 0:00'
    time_var.axis = 'T'

    log('    lat_var', 'DEBUG')
    lat_var = cf_nc.createVariable('lat', 'f8', (id_dim_name,),
                                   fill_value=-9999.0)
    lat_var.long_name = 'latitude'
    lat_var.standard_name = 'latitude'
    lat_var.units = 'degrees_north'
    lat_var.axis = 'Y'

    log('    lon_var', 'DEBUG')
    lon_var = cf_nc.createVariable('lon', 'f8', (id_dim_name,),
                                   fill_value=-9999.0)
    lon_var.long_name = 'longitude'
    lon_var.standard_name = 'longitude'
    lon_var.units = 'degrees_east'
    lon_var.axis = 'X'

    log('    z_var', 'DEBUG')
    z_var = cf_nc.createVariable('z', 'f8', (id_dim_name,),
                                 fill_value=-9999.0)
    z_var.long_name = ('Elevation referenced to the North American ' +
                       'Vertical Datum of 1988 (NAVD88)')
    z_var.standard_name = 'surface_altitude'
    z_var.units = 'm'
#.........这里部分代码省略.........