Extra convenience methods for common responses

OPeNDAP

from erddapy import ERDDAP


e = ERDDAP(server="https://gliders.ioos.us/erddap")

from netCDF4 import Dataset


e.constraints = None
e.protocol = "tabledap"
e.dataset_id = "whoi_406-20160902T1700"

opendap_url = e.get_download_url(
    response="opendap",
)

print(opendap_url)
with Dataset(opendap_url) as nc:
    print(nc.summary)

https://gliders.ioos.us/erddap/tabledap/whoi_406-20160902T1700
Slocum glider dataset gathered as part of the TEMPESTS (The Experiment to Measure and Predict East coast STorm Strength), funded by NOAA through CINAR (Cooperative Institute for the North Atlantic Region).

netCDF Climate and Forecast

e.response = "nc"
e.variables = ["longitude", "latitude", "temperature", "salinity"]

nc = e.to_ncCF()

print(nc.Conventions)
print(nc["temperature"])

Unidata Dataset Discovery v1.0, COARDS, CF-1.6
<class 'netCDF4._netCDF4.Variable'>
float32 temperature(obs)
    _ChunkSizes: 106
    _FillValue: -999.0
    actual_range: [ 9.9473 22.6177]
    ancillary_variables: qartod_temperature_climatological_flag qartod_temperature_flat_line_flag qartod_temperature_gross_range_flag qartod_temperature_rate_of_change_flag qartod_temperature_spike_flag temperature_qc
    colorBarMaximum: 32.0
    colorBarMinimum: 0.0
    coordinates: time latitude longitude depth
    instrument: instrument_ctd
    ioos_category: Temperature
    long_name: Sea Water Temperature
    observation_type: measured
    platform: platform
    standard_name: sea_water_temperature
    units: Celsius
    valid_max: 40.0
    valid_min: -5.0
unlimited dimensions:
current shape = (54245,)
filling on

xarray

ds = e.to_xarray()

ds

<xarray.Dataset>
Dimensions:          (trajectory: 1, profile: 525, obs: 54245)
Coordinates:
  * trajectory       (trajectory) object 'whoi_406-20160902T1700'
    time             (profile) datetime64[ns] ...
    longitude        (profile) float64 ...
    latitude         (profile) float64 ...
    depth            (obs) float32 ...
Dimensions without coordinates: profile, obs
Data variables:
    profile_id       (profile) float64 ...
    trajectoryIndex  (profile) int32 ...
    rowSize          (profile) int32 ...
    temperature      (obs) float32 ...
    salinity         (obs) float32 ...
Attributes: (12/56)
    acknowledgment:                This deployment supported by NOAA through ...
    cdm_data_type:                 TrajectoryProfile
    cdm_profile_variables:         time_uv,lat_uv,lon_uv,u,v,profile_id,time,...
    cdm_trajectory_variables:      trajectory,wmo_id
    comment:                       Glider operatored by Woods Hole Oceanograp...
    contributor_name:              Robert Todd, Larry George, Patrick Deane, ...
    ...                            ...
    subsetVariables:               wmo_id,trajectory,profile_id,time,latitude...
    summary:                       Slocum glider dataset gathered as part of ...
    time_coverage_end:             2016-09-20T13:32:33Z
    time_coverage_start:           2016-09-02T17:05:38Z
    title:                         whoi_406-20160902T1700
    Westernmost_Easting:           -71.54982816987487

xarray.Dataset

• Dimensions:
  • trajectory: 1
  • profile: 525
  • obs: 54245
• Coordinates: (5)
  • trajectory
    (trajectory)
    object
    'whoi_406-20160902T1700'

    _ChunkSizes :

    22

    cf_role :

    trajectory_id

    comment :

    A trajectory is one deployment of a glider.

    ioos_category :

    Identifier

    long_name :

    Trajectory Name

    array(['whoi_406-20160902T1700'], dtype=object)

  • time
    (profile)
    datetime64[ns]
    ...

    _CoordinateAxisType :

    Time

    actual_range :

    [1.47283594e+09 1.47437835e+09]

    axis :

    T

    comment :

    Timestamp corresponding to the mid-point of the profile.

    ioos_category :

    Time

    long_name :

    Profile Time

    observation_type :

    calculated

    platform :

    platform

    standard_name :

    time

    time_origin :

    01-JAN-1970 00:00:00

    [525 values with dtype=datetime64[ns]]

  • longitude
    (profile)
    float64
    ...

    _CoordinateAxisType :

    Lon

    actual_range :

    [-71.54982817 -70.67537292]

    axis :

    X

    colorBarMaximum :

    180.0

    colorBarMinimum :

    -180.0

    comment :

    Value is interpolated to provide an estimate of the longitude at the mid-point of the profile.

    ioos_category :

    Location

    long_name :

    Profile Longitude

    observation_type :

    calculated

    platform :

    platform

    standard_name :

    longitude

    units :

    degrees_east

    valid_max :

    180.0

    valid_min :

    -180.0

    [525 values with dtype=float64]

  • latitude
    (profile)
    float64
    ...

    _CoordinateAxisType :

    Lat

    actual_range :

    [40.25779415 41.1200183 ]

    axis :

    Y

    colorBarMaximum :

    90.0

    colorBarMinimum :

    -90.0

    comment :

    Value is interpolated to provide an estimate of the latitude at the mid-point of the profile.

    ioos_category :

    Location

    long_name :

    Profile Latitude

    observation_type :

    calculated

    platform :

    platform

    standard_name :

    latitude

    units :

    degrees_north

    valid_max :

    90.0

    valid_min :

    -90.0

    [525 values with dtype=float64]

  • depth
    (obs)
    float32
    ...

    _ChunkSizes :

    106

    _CoordinateAxisType :

    Height

    _CoordinateZisPositive :

    down

    actual_range :

    [ 2.49 98.05]

    ancillary_variables :

    depth_qc

    axis :

    Z

    colorBarMaximum :

    2000.0

    colorBarMinimum :

    0.0

    colorBarPalette :

    OceanDepth

    instrument :

    instrument_ctd

    ioos_category :

    Location

    long_name :

    Depth

    observation_type :

    calculated

    platform :

    platform

    positive :

    down

    reference_datum :

    sea-surface

    standard_name :

    depth

    units :

    m

    valid_max :

    2000.0

    valid_min :

    0.0

    [54245 values with dtype=float32]

• Data variables: (5)
  • profile_id
    (profile)
    float64
    ...

    actual_range :

    [ 1 545]

    cf_role :

    profile_id

    comment :

    Sequential profile number within the trajectory. This value is unique in each file that is part of a single trajectory/deployment.

    ioos_category :

    Identifier

    long_name :

    Profile ID

    valid_max :

    2147483647

    valid_min :

    1

    [525 values with dtype=float64]

  • trajectoryIndex
    (profile)
    int32
    ...

    instance_dimension :

    trajectory

    ioos_category :

    Identifier

    long_name :

    The trajectory to which this profile is associated.

    [525 values with dtype=int32]

  • rowSize
    (profile)
    int32
    ...

    ioos_category :

    Identifier

    long_name :

    Number of Observations for this Profile

    sample_dimension :

    obs

    [525 values with dtype=int32]

  • temperature
    (obs)
    float32
    ...

    _ChunkSizes :

    106

    actual_range :

    [ 9.9473 22.6177]

    ancillary_variables :

    qartod_temperature_climatological_flag qartod_temperature_flat_line_flag qartod_temperature_gross_range_flag qartod_temperature_rate_of_change_flag qartod_temperature_spike_flag temperature_qc

    colorBarMaximum :

    32.0

    colorBarMinimum :

    0.0

    instrument :

    instrument_ctd

    ioos_category :

    Temperature

    long_name :

    Sea Water Temperature

    observation_type :

    measured

    platform :

    platform

    standard_name :

    sea_water_temperature

    units :

    Celsius

    valid_max :

    40.0

    valid_min :

    -5.0

    [54245 values with dtype=float32]

  • salinity
    (obs)
    float32
    ...

    _ChunkSizes :

    106

    actual_range :

    [29.50964 36.43851]

    ancillary_variables :

    qartod_salinity_climatological_flag qartod_salinity_flat_line_flag qartod_salinity_rate_of_change_flag qartod_salinity_spike_flag salinity_qc

    colorBarMaximum :

    37.0

    colorBarMinimum :

    30.0

    instrument :

    instrument_ctd

    ioos_category :

    Salinity

    long_name :

    Sea Water Practical Salinity

    observation_type :

    calculated

    platform :

    platform

    standard_name :

    sea_water_practical_salinity

    units :

    1

    valid_max :

    40.0

    valid_min :

    0.0

    [54245 values with dtype=float32]

• Indexes: (1)
  • trajectory
    PandasIndex

    PandasIndex(Index(['whoi_406-20160902T1700'], dtype='object', name='trajectory'))

• Attributes: (56)

  acknowledgment :

  This deployment supported by NOAA through the Cooperative Institute for the North Atlantic Region

  cdm_data_type :

  TrajectoryProfile

  cdm_profile_variables :

  time_uv,lat_uv,lon_uv,u,v,profile_id,time,latitude,longitude

  cdm_trajectory_variables :

  trajectory,wmo_id

  comment :

  Glider operatored by Woods Hole Oceanographic Institution

  contributor_name :

  Robert Todd, Larry George, Patrick Deane, Sean Whalen, John Kerfoot

  contributor_role :

  Principal Investigator, pilot and technician, technician, technician, data management

  Conventions :

  Unidata Dataset Discovery v1.0, COARDS, CF-1.6

  creator_email :

  rtodd@whoi.edu

  creator_name :

  Robert Todd

  creator_url :

  gliders.whoi.edu

  date_created :

  2016-09-09T22:06:05Z

  date_issued :

  2016-09-09T22:06:05Z

  Easternmost_Easting :

  -70.67537291773046

  featureType :

  TrajectoryProfile

  format_version :

  /tmp/IOOS_Glider_NetCDF_v2.0-qartod.nc

  geospatial_lat_max :

  41.120018298037856

  geospatial_lat_min :

  40.257794149155615

  geospatial_lat_units :

  degrees_north

  geospatial_lon_max :

  -70.67537291773046

  geospatial_lon_min :

  -71.54982816987487

  geospatial_lon_units :

  degrees_east

  geospatial_vertical_max :

  98.05

  geospatial_vertical_min :

  2.49

  geospatial_vertical_positive :

  down

  geospatial_vertical_units :

  m

  gts_ingest :

  true

  history :

  2016-09-09T22:06:05Z /home/kerfoot/slocum/matlab/spt/export/nc/IOOS/DAC/writeQartodGliderFlatNc.m%standard names for qartod flags have changed on 2022-07-04 2023-08-09T14:30:00Z (local files) 2023-08-09T14:30:00Z https://gliders.ioos.us/erddap/tabledap/whoi_406-20160902T1700.ncCF?trajectory,profile_id,time,depth,longitude,latitude,temperature,salinity

  id :

  whoi_406-20160905T0304

  infoUrl :

  https://gliders.ioos.us/erddap/

  institution :

  Woods Hole Oceanographic Institution

  ioos_dac_checksum :

  6e67c5e2c364def562bb32242dec8fd5

  ioos_dac_completed :

  True

  keywords :

  AUVS > Autonomous Underwater Vehicles, Earth Science > Oceans > Ocean Pressure > Water Pressure, Earth Science > Oceans > Ocean Temperature > Water Temperature, Earth Science > Oceans > Salinity/Density > Conductivity, Earth Science > Oceans > Salinity/Density > Density, Earth Science > Oceans > Salinity/Density > Salinity, glider, In Situ Ocean-based platforms > Seaglider, Slocum, Spray, trajectory, underwater glider, water, wmo

  keywords_vocabulary :

  GCMD Science Keywords

  license :

  This data may be redistributed and used without restriction. Data provided as is with no expressed or implied assurance of quality assurance or quality control

  Metadata_Conventions :

  Unidata Dataset Discovery v1.0, COARDS, CF-1.6

  naming_authority :

  edu.rutgers.marine

  Northernmost_Northing :

  41.120018298037856

  platform_type :

  Slocum Glider

  project :

  TEMPESTS

  publisher_email :

  kerfoot@marine.rutgers.edu

  publisher_name :

  John Kerfoot

  publisher_url :

  https://rucool/marine.rutgers.edu

  references :

  https://ioos.noaa.gov/wp-content/uploads/2015/10/Manual-for-QC-of-Glider-Data_05_09_16.pdf

  sea_name :

  Mid-Atlantic Bight

  source :

  Observational data from a profiling glider

  sourceUrl :

  (local files)

  Southernmost_Northing :

  40.257794149155615

  standard_name_vocabulary :

  CF-v25

  subsetVariables :

  wmo_id,trajectory,profile_id,time,latitude,longitude

  summary :

  Slocum glider dataset gathered as part of the TEMPESTS (The Experiment to Measure and Predict East coast STorm Strength), funded by NOAA through CINAR (Cooperative Institute for the North Atlantic Region).

  time_coverage_end :

  2016-09-20T13:32:33Z

  time_coverage_start :

  2016-09-02T17:05:38Z

  title :

  whoi_406-20160902T1700

  Westernmost_Easting :

  -71.54982816987487

iris

import warnings

# Iris warnings are quire verbose!
with warnings.catch_warnings():
    warnings.simplefilter("ignore")
    cubes = e.to_iris()

print(cubes)

0: The trajectory to which this profile is associated. / (unknown) (-- : 525)
1: sea_water_temperature / (Celsius)   (-- : 54245)
2: Profile ID / (unknown)              (-- : 525)
3: sea_water_practical_salinity / (1)  (-- : 54245)
4: Number of Observations for this Profile / (unknown) (-- : 525)
5: Trajectory Name / (unknown)         (-- : 1)
6: latitude / (degrees)                (-- : 525)
7: time / (seconds since 1970-01-01T00:00:00Z) (-- : 525)
8: longitude / (degrees)               (-- : 525)

cubes.extract_cube("sea_water_temperature")

Sea Water Temperature (Celsius)	--
Shape	54245
Auxiliary coordinates
depth	x
Attributes
Conventions	'Unidata Dataset Discovery v1.0, COARDS, CF-1.6'
Easternmost_Easting	-70.67537291773046
Metadata_Conventions	'Unidata Dataset Discovery v1.0, COARDS, CF-1.6'
Northernmost_Northing	41.120018298037856
Southernmost_Northing	40.257794149155615
Westernmost_Easting	-71.54982816987487
_ChunkSizes	106
acknowledgment	'This deployment supported by NOAA through the Cooperative Institute for ...'
actual_range	array([ 9.9473, 22.6177], dtype=float32)
cdm_data_type	'TrajectoryProfile'
cdm_profile_variables	'time_uv,lat_uv,lon_uv,u,v,profile_id,time,latitude,longitude'
cdm_trajectory_variables	'trajectory,wmo_id'
colorBarMaximum	32.0
colorBarMinimum	0.0
comment	'Glider operatored by Woods Hole Oceanographic Institution'
contributor_name	'Robert Todd, Larry George, Patrick Deane, Sean Whalen, John Kerfoot'
contributor_role	'Principal Investigator, pilot and technician, technician, technician, data ...'
creator_email	'rtodd@whoi.edu'
creator_name	'Robert Todd'
creator_url	'gliders.whoi.edu'
date_created	'2016-09-09T22:06:05Z'
date_issued	'2016-09-09T22:06:05Z'
featureType	'TrajectoryProfile'
format_version	'/tmp/IOOS_Glider_NetCDF_v2.0-qartod.nc'
geospatial_lat_max	41.120018298037856
geospatial_lat_min	40.257794149155615
geospatial_lat_units	'degrees_north'
geospatial_lon_max	-70.67537291773046
geospatial_lon_min	-71.54982816987487
geospatial_lon_units	'degrees_east'
geospatial_vertical_max	98.05
geospatial_vertical_min	2.49
geospatial_vertical_positive	#x27;down'
geospatial_vertical_units	'm'
gts_ingest	'true'
history	'2016-09-09T22:06:05Z /home/kerfoot/slocum/matlab/spt/export/nc/IOOS/DAC/writeQartodGliderFlatNc.m%standard ...'
id	'whoi_406-20160905T0304'
infoUrl	'https://gliders.ioos.us/erddap/'
institution	'Woods Hole Oceanographic Institution'
instrument	'instrument_ctd'
ioos_category	'Temperature'
ioos_dac_checksum	'6e67c5e2c364def562bb32242dec8fd5'
ioos_dac_completed	'True'
keywords	'AUVS > Autonomous Underwater Vehicles, Earth Science > Oceans > Ocean Pressure ...'
keywords_vocabulary	'GCMD Science Keywords'
license	'This data may be redistributed and used without restriction. Data provided ...'
naming_authority	'edu.rutgers.marine'
observation_type	'measured'
platform	'platform'
platform_type	'Slocum Glider'
project	'TEMPESTS'
publisher_email	'kerfoot@marine.rutgers.edu'
publisher_name	'John Kerfoot'
publisher_url	'https://rucool/marine.rutgers.edu'
references	'https://ioos.noaa.gov/wp-content/uploads/2015/10/Manual-for-QC-of-Glid ...'
sea_name	'Mid-Atlantic Bight'
source	'Observational data from a profiling glider'
sourceUrl	'(local files)'
standard_name_vocabulary	'CF-v25'
subsetVariables	'wmo_id,trajectory,profile_id,time,latitude,longitude'
summary	'Slocum glider dataset gathered as part of the TEMPESTS (The Experiment ...'
time_coverage_end	'2016-09-20T13:32:33Z'
time_coverage_start	'2016-09-02T17:05:38Z'
title	'whoi_406-20160902T1700'
valid_max	40.0
valid_min	-5.0