Python Dataset.time_coverage_end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 time_coverage_end [as 别名]
    def test_time_extents(self):
        '''
        Test that the time extents are being checked
        '''
        result = self.acdd.check_time_extents(self.ds)
        self.assert_result_is_good(result)

        empty_ds = Dataset(os.devnull, 'w', diskless=True)
        self.addCleanup(empty_ds.close)

        # The dataset needs at least one variable to check that it's missing
        # all the required attributes.
        empty_ds.createDimension('time', 1)
        time_var = empty_ds.createVariable('time', 'float32', ('time',))
        time_var.units = 'seconds since 1970-01-01 00:00:00 UTC'
        time_var[:] = [1451692800]  # 20160102T000000Z in seconds since epoch
        empty_ds.time_coverage_start = '20160102T000000Z'
        empty_ds.time_coverage_end = '20160102T000000Z'
        result = self.acdd.check_time_extents(empty_ds)
        self.assert_result_is_good(result)
        # try the same thing with time offsets
        time_var.units = 'seconds since 1970-01-01 00:00:00-10:00'
        empty_ds.time_coverage_start = '20160102T000000-1000'
        empty_ds.time_coverage_end = '20160102T000000-1000'
        result = self.acdd.check_time_extents(empty_ds)
        self.assert_result_is_good(result)

# 需要导入模块: from netCDF4 import Dataset [as 别名]
# 或者: from netCDF4.Dataset import time_coverage_end [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 time_coverage_end [as 别名]
x_u = rootgrp.createVariable("x_u","f8",("eta_u", "xi_u",))
y_u = rootgrp.createVariable("y_u","f8",("eta_u", "xi_u",))
x_v = rootgrp.createVariable("x_v","f8",("eta_v", "xi_v",))
y_v = rootgrp.createVariable("y_v","f8",("eta_v", "xi_v",))
#angle = rootgrp.createVariable("angle","f8",("lat_rho","lon_rho",))
##lon_vert = rootgrp.createVariable("x_vert","f8",("lat","lon"))
##lat_vert = rootgrp.createVariable("y_vert","f8",("lat","lon"))
zp = rootgrp.createVariable("zp", "f8",("eta_rho","xi_rho"))
z = rootgrp.createVariable("z", "f8",("ocean_time","s_rho","eta_rho","xi_rho",),fill_value = 9.999999933815813e+36)

import time as t
# global
rootgrp.description = "Mikes Globcurrent subset + Grid Data"
rootgrp.history = "Created " + t.ctime(t.time())
rootgrp.time_coverage_start = "1-Jan-2008"
rootgrp.time_coverage_end = "31-Aug-2008"
rootgrp.spatialResolution = str(float(ds.spatial_resolution)) #RESOLUTION OF GLOBCURRENT!

# by variable
# longitudes
lon_v.units = "degrees_east"
lon_v.long_name = "longitude of V-points"
lon_v.standard_name = "longitude"
lon_v.field = "lon_v, scalar"
lon_u.units = "degrees_east"
lon_u.long_name = "longitude of U-points"
lon_u.standard_name = "longitude"
lon_u.field = "lon_u, scalar"
# latitudes
lat_v.units = "degrees_north"
lat_v.long_name = "latitude of V-points"

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

#.........这里部分代码省略.........
    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:
        var_depth[:]       = data.Depth.values.astype(np.float)
    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.index[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.astype(np.double)

    # station
    var_station_name[:] = stringtochar(np.array(data.Station_Code.values[idx_station_uniq], 'S50'))

    # compute number of observations per profile
    if len_prof == 1:
        var_rowsize[:] = data.shape[0]
    else:
        n_obs_per_prof = []
        for i in range(len_prof - 1):
            n_obs_per_prof.append(idx_time_station_uniq[i + 1] - idx_time_station_uniq[i])
        n_obs_per_prof.append(len(data.index.values) - idx_time_station_uniq[-1])

        var_rowsize[:] = n_obs_per_prof

    # compute association between profile number and station name
    # which station this profile is for
    aa = np.array(data.Station_Code)[idx_station_uniq].tolist()
    bb = np.array(data.Station_Code)[idx_time_station_uniq].tolist()
    var_station_idx[:] = [aa.index(b) + 1 for b in bb]

    # profile
    var_profile[:] = range(1, len_prof + 1)

    output_netcdf_obj.geospatial_vertical_min = output_netcdf_obj['DEPTH'][:].min()
    output_netcdf_obj.geospatial_vertical_max = output_netcdf_obj['DEPTH'][:].max()
    output_netcdf_obj.geospatial_lat_min      = output_netcdf_obj['LATITUDE'][:].min()
    output_netcdf_obj.geospatial_lat_max      = output_netcdf_obj['LATITUDE'][:].max()
    output_netcdf_obj.geospatial_lon_min      = output_netcdf_obj['LONGITUDE'][:].min()
    output_netcdf_obj.geospatial_lon_max      = output_netcdf_obj['LONGITUDE'][:].max()
    output_netcdf_obj.time_coverage_start     = min(time_values).strftime('%Y-%m-%dT%H:%M:%SZ')
    output_netcdf_obj.time_coverage_end       = max(time_values).strftime('%Y-%m-%dT%H:%M:%SZ')

    output_netcdf_obj.close()
    return netcdf_filepath

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

#.........这里部分代码省略.........
    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'])

    # stationss
    var_station_name[:] = stringtochar(np.array(data_dict['Station_Code'], 'S50')[np.sort(idx_station_uniq)])

    # compute number of observations per profile
    if len_prof == 1:
        var_rowsize[:] = data.shape[1]
    else:
        n_obs_per_prof = []
        for i in range(len_prof - 1):
            n_obs_per_prof.append(idx_time_station_uniq[i + 1] - idx_time_station_uniq[i])
        n_obs_per_prof.append(data_df.shape[1] - idx_time_station_uniq[-1])

        var_rowsize[:] = n_obs_per_prof

    # compute association between profile number and station name
    # which station this profile is for
    aa = np.array(data_dict['Station_Code'])[idx_station_uniq].tolist()
    bb = np.array(data_dict['Station_Code'])[idx_time_station_uniq].tolist()
    var_station_idx[:] = [aa.index(b) + 1 for b in bb]

    # profile
    var_profile[:] = range(1, len_prof + 1)

    output_netcdf_obj.geospatial_vertical_min = output_netcdf_obj['DEPTH'][:].min()
    output_netcdf_obj.geospatial_vertical_max = output_netcdf_obj['DEPTH'][:].max()
    output_netcdf_obj.geospatial_lat_min      = output_netcdf_obj['LATITUDE'][:].min()
    output_netcdf_obj.geospatial_lat_max      = output_netcdf_obj['LATITUDE'][:].max()
    output_netcdf_obj.geospatial_lon_min      = output_netcdf_obj['LONGITUDE'][:].min()
    output_netcdf_obj.geospatial_lon_max      = output_netcdf_obj['LONGITUDE'][:].max()
    output_netcdf_obj.time_coverage_start     = min(time_values).strftime('%Y-%m-%dT%H:%M:%SZ')
    output_netcdf_obj.time_coverage_end       = max(time_values).strftime('%Y-%m-%dT%H:%M:%SZ')

    output_netcdf_obj.close()
    return netcdf_filepath

# 需要导入模块: from netCDF4 import Dataset [as 别名]
# 或者: from netCDF4.Dataset import time_coverage_end [as 别名]
def modify_aims_netcdf(netcdf_file_path, channel_id_info):
    """ Modify the downloaded netCDF file so it passes both CF and IMOS checker
    input:
       netcdf_file_path(str)    : path of netcdf file to modify
       channel_id_index(dict) : information from xml for the channel
    """
    imos_env_path = os.path.join(os.environ.get('DATA_SERVICES_DIR'), 'lib', 'netcdf', 'imos_env')
    if not os.path.isfile(imos_env_path):
        logger = logging_aims()
        logger.error('%s is not accessible' % imos_env_path)
        close_logger(logger)
        sys.exit(1)

    dotenv.load_dotenv(imos_env_path)
    netcdf_file_obj = Dataset(netcdf_file_path, 'a', format='NETCDF4')
    netcdf_file_obj.naming_authority = 'IMOS'

    # add gatts to NetCDF
    netcdf_file_obj.aims_channel_id = int(channel_id_info['channel_id'])

    if not (channel_id_info['metadata_uuid'] == 'Not Available'):
        netcdf_file_obj.metadata_uuid = channel_id_info['metadata_uuid']

    if not netcdf_file_obj.instrument_serial_number:
        del(netcdf_file_obj.instrument_serial_number)

    # add CF gatts, values stored in lib/netcdf/imos_env
    netcdf_file_obj.Conventions            = os.environ.get('CONVENTIONS')
    netcdf_file_obj.data_centre_email      = os.environ.get('DATA_CENTRE_EMAIL')
    netcdf_file_obj.data_centre            = os.environ.get('DATA_CENTRE')
    netcdf_file_obj.project                = os.environ.get('PROJECT')
    netcdf_file_obj.acknowledgement        = os.environ.get('ACKNOWLEDGEMENT')
    netcdf_file_obj.distribution_statement = os.environ.get('DISTRIBUTION_STATEMENT')

    netcdf_file_obj.date_created           = strftime("%Y-%m-%dT%H:%M:%SZ", gmtime())
    netcdf_file_obj.quality_control_set    = 1
    imos_qc_convention                     = 'IMOS standard set using the IODE flags'
    netcdf_file_obj.author                 = 'laurent besnard'
    netcdf_file_obj.author_email           = '[email protected]'

    rename_netcdf_attribute(netcdf_file_obj, 'geospatial_LAT_max', 'geospatial_lat_max')
    rename_netcdf_attribute(netcdf_file_obj, 'geospatial_LAT_min', 'geospatial_lat_min')
    rename_netcdf_attribute(netcdf_file_obj, 'geospatial_LON_max', 'geospatial_lon_max')
    rename_netcdf_attribute(netcdf_file_obj, 'geospatial_LON_min', 'geospatial_lon_min')

    # variables modifications
    time           = netcdf_file_obj.variables['time']
    time.calendar  = 'gregorian'
    time.axis      = 'T'
    time.valid_min = 0.0
    time.valid_max = 9999999999.0
    netcdf_file_obj.renameDimension('time', 'TIME')
    netcdf_file_obj.renameVariable('time', 'TIME')

    netcdf_file_obj.time_coverage_start = num2date(time[:], time.units, time.calendar).min().strftime('%Y-%m-%dT%H:%M:%SZ')
    netcdf_file_obj.time_coverage_end   = num2date(time[:], time.units, time.calendar).max().strftime('%Y-%m-%dT%H:%M:%SZ')

    # latitude longitude
    latitude                  = netcdf_file_obj.variables['LATITUDE']
    latitude.axis             = 'Y'
    latitude.valid_min        = -90.0
    latitude.valid_max        = 90.0
    latitude.reference_datum  = 'geographical coordinates, WGS84 projection'
    latitude.standard_name    = 'latitude'
    latitude.long_name        = 'latitude'

    longitude                 = netcdf_file_obj.variables['LONGITUDE']
    longitude.axis            = 'X'
    longitude.valid_min       = -180.0
    longitude.valid_max       = 180.0
    longitude.reference_datum = 'geographical coordinates, WGS84 projection'
    longitude.standard_name   = 'longitude'
    longitude.long_name       = 'longitude'

    # handle masked arrays
    lon_array = longitude[:]
    lat_array = latitude[:]
    if type(lon_array) != numpy.ma.core.MaskedArray or len(lon_array) == 1:
        netcdf_file_obj.geospatial_lon_min = min(lon_array)
        netcdf_file_obj.geospatial_lon_max = max(lon_array)
    else:
        netcdf_file_obj.geospatial_lon_min = numpy.ma.MaskedArray.min(lon_array)
        netcdf_file_obj.geospatial_lon_max = numpy.ma.MaskedArray.max(lon_array)

    if type(lat_array) != numpy.ma.core.MaskedArray or len(lat_array) == 1:
        netcdf_file_obj.geospatial_lat_min = min(lat_array)
        netcdf_file_obj.geospatial_lat_max = max(lat_array)
    else:
        numpy.ma.MaskedArray.min(lat_array)
        netcdf_file_obj.geospatial_lat_min = numpy.ma.MaskedArray.min(lat_array)
        netcdf_file_obj.geospatial_lat_max = numpy.ma.MaskedArray.max(lat_array)

    # Change variable name, standard name, longname, untis ....
    if 'Seawater_Intake_Temperature' in netcdf_file_obj.variables.keys():
        var                     = netcdf_file_obj.variables['Seawater_Intake_Temperature']
        var.units               = 'Celsius'
        netcdf_file_obj.renameVariable('Seawater_Intake_Temperature', 'TEMP')
        netcdf_file_obj.renameVariable('Seawater_Intake_Temperature_quality_control', 'TEMP_quality_control')
        var.ancillary_variables = 'TEMP_quality_control'

#.........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 time_coverage_end [as 别名]

#.........这里部分代码省略.........
        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"
        var_units = getattr(input_netcdf_obj[var], 'units')
        if var_units:
            output_var_mean.units = var_units
            output_var_min.units  = var_units
            output_var_max.units  = var_units
            output_var_sd.units   = var_units

        var_stdname = getattr(input_netcdf_obj[var], 'standard_name', '')
        if var_stdname != '':
            output_var_num_obs.standard_name = "%s number_of_observations" % var_stdname

        # set up var values
        output_var_mean[:]    = np.ma.masked_invalid(burst_vars[var]['var_mean'])
        output_var_min[:]     = np.ma.masked_invalid(burst_vars[var]['var_min'])
        output_var_max[:]     = np.ma.masked_invalid(burst_vars[var]['var_max'])
        output_var_sd[:]      = np.ma.masked_invalid(burst_vars[var]['var_sd'])
        output_var_num_obs[:] = np.ma.masked_invalid(burst_vars[var]['var_num_obs'])

    # 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)

    # set up original varatts for the following dim, var
    varnames = dimensionless_var
    varnames.append('TIME')
    for varname in varnames:
        for varatt in input_netcdf_obj[varname].__dict__.keys():
            output_netcdf_obj.variables[varname].setncattr(varatt, getattr(input_netcdf_obj[varname], varatt))
    time_comment = '%s. Time stamp corresponds to the middle of the burst measurement.' % getattr(input_netcdf_obj['TIME'], 'comment', '')
    output_netcdf_obj.variables['TIME'].comment = time_comment.lstrip('. ')

    time_burst_val_dateobj = num2date(time_burst_vals, input_netcdf_obj['TIME'].units, input_netcdf_obj['TIME'].calendar)
    output_netcdf_obj.time_coverage_start = time_burst_val_dateobj.min().strftime('%Y-%m-%dT%H:%M:%SZ')
    output_netcdf_obj.time_coverage_end   = time_burst_val_dateobj.max().strftime('%Y-%m-%dT%H:%M:%SZ')

    # append original gatt to burst average gatt
    gatt = 'comment'
    if hasattr(input_netcdf_obj, gatt):
        setattr(output_netcdf_obj, gatt, getattr(input_netcdf_obj, gatt))

    gatt = 'history'
    setattr(output_netcdf_obj, gatt, ('%s. %s' % (getattr(input_netcdf_obj, gatt, ''), 'Created %s' % time.ctime(time.time()))).lstrip('. '))

    gatt = 'abstract'
    setattr(output_netcdf_obj, gatt, ('%s. %s' % (getattr(output_netcdf_obj, gatt, ''), \
                                                 'Data from the bursts have been cleaned and averaged to create data products. This file is one such product.')).lstrip('. '))

    # add burst keywords
    gatt           = 'keywords'
    keywords_burst = 'AVERAGED, BINNED'
    setattr(output_netcdf_obj, gatt, ('%s, %s' % (getattr(input_netcdf_obj, gatt, ''), keywords_burst)).lstrip(', '))

    # add values to variables
    output_netcdf_obj['TIME'][:] = np.ma.masked_invalid(time_burst_vals)

    github_comment = 'Product created with %s' % get_git_revision_script_url(os.path.realpath(__file__))
    output_netcdf_obj.lineage = ('%s. %s' % (getattr(output_netcdf_obj, 'lineage', ''), github_comment)).lstrip('. ')

    output_netcdf_obj.close()
    input_netcdf_obj.close()

    shutil.move(output_netcdf_file_path, output_dir)
    shutil.rmtree(tmp_netcdf_dir)
    return os.path.join(output_dir, os.path.basename(output_netcdf_file_path))

# 需要导入模块: from netCDF4 import Dataset [as 别名]
# 或者: from netCDF4.Dataset import time_coverage_end [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 time_coverage_end [as 别名]
rootgrp.data_type = 'EGO glider time-series data'
rootgrp.format_version = '1.0'
rootgrp.platform_code = '99999'
rootgrp.date_update = change_dataformat(rootgrp.date_modified)  # should be converted from rootgrp.date_modified
rootgrp.data_mode = data_mode_dic[rootgrp.data_mode]
rootgrp.naming_authority = 'EGO'
rootgrp.id = outputfile.split('.')[0]  # taken from file name... maybe something better to do
rootgrp.source = "Glider observation"
rootgrp.Conventions = "CF-1.4 EGO-1.0"
rootgrp.geospatial_lat_min = str(rootgrp.geospatial_lat_min)
rootgrp.geospatial_lat_max = str(rootgrp.geospatial_lat_max)
rootgrp.geospatial_lon_min = str(rootgrp.geospatial_lon_min)
rootgrp.geospatial_lon_max = str(rootgrp.geospatial_lon_max)

rootgrp.time_coverage_start = change_dataformat(rootgrp.time_coverage_start)
rootgrp.time_coverage_end = change_dataformat(rootgrp.time_coverage_end)

rootgrp.renameVariable('depth', 'DEPTH')

# Rename TIME variable and add attributes
rootgrp.renameVariable('time', 'TIME')
TIME = rootgrp.variables['TIME']
TIME.long_name = "Epoch time"
TIME.units = "seconds since 1970-01-01T00:00:00Z"
TIME.valid_min = "0."  # problem to be mentionned
TIME.valid_max = "9000000000"  # problem to be mentionned
TIME.QC_procedure, = "1"
TIME.comment, = " "
TIME.ancillary_variable = "TIME_QC"
TIME.sdn_parameter_urn = "SDN:P01::ELTMEP01"
TIME.sdn_uom_urn = "SDN:P061::UTBB"